diff --git a/CODE_STYLE.md b/CODE_STYLE.md new file mode 100644 index 00000000000..1e0225e8ecb --- /dev/null +++ b/CODE_STYLE.md @@ -0,0 +1,392 @@ +## Introduction + +This document defines the coding standards for source files in the cBioPortal (Backend). + +The structure of this document is based on the [Google Java Style](https://google.github.io/styleguide/javaguide.html) reference and is a _work in progress_. + +## Source File Basics + +### File encoding: UTF-8 + +Source files must be encoded using `UTF-8`. + +### Indentation + +* Indentation uses _spaces_ (not tabs) +* Unix (LF), not DOS (CRLF) line endings +* Eliminate all trailing whitespace + * On Linux, Mac, etc.: `find . -type f -name "*.java" -exec perl -p -i -e "s/[ \t]$//g" {} \;` + +## Source file structure + +A source file consists of the following, in this exact order: + +* License +* Package statement +* Import statements +* Exactly one top-level class + +Exactly one blank line separates each of the above sections. + +### License (Need Help With License) + +Each source file must specify the following license at the very top of the file: + +```java +/* + * Copyright 2002-2023 the original author or authors. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * https://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +``` + +Always check the date range in the license header. For example, if you've modified a file in 2022 whose header still reads: + +``` +* Copyright 2002-2018 the original author or authors. +``` + +Then be sure to update it to 2023 accordingly: + +``` +* Copyright 2002-2023 the original author or authors. +``` + +### Import statements + +The import statements are structured as follow: + +* import `org.cbioportal.*` +* import `org.springframework.*` +* import all other imports +* blank line +* import `java.*` +* blank line +* blank line +* import static all other imports + +Static imports should not be used in production code, but they should be used in test code, especially for things like `import static org.assertj.core.api.Assertions.assertThat;`. + +Although static imports are generally forbidden in production code, the following are use cases for which static imports are permissible. + +* constants (including enum constants): such as those in `java.nio.charset.StandardCharsets` or `org.springframework.core.annotation.MergedAnnotations.SearchStrategy` +* static factory methods for third-party DSLs: such as the methods in `org.junit.platform.engine.discovery.DiscoverySelectors` when used with the JUnit Platform `Launcher` API + +Wildcard imports such as `import java.util.*` or `import static org.assertj.core.api.Assertions.*` are forbidden, even in test code. + +### Java source file organization + +The following governs how the elements of a source file are organized: + +1. static fields +1. normal fields +1. constructors +1. (private) methods called from constructors +1. static factory methods +1. JavaBean properties (i.e., getters and setters) +1. method implementations coming from interfaces +1. private or protected templates that get called from method implementations coming from interfaces +1. other methods +1. `equals`, `hashCode`, and `toString` + +Note that private or protected methods called from method implementations should be placed immediately below the methods where they're used. In other words if there 3 interface method implementations with 3 private methods (one used from each), then the order of methods should include 1 interface and 1 private method in sequence, not 3 interface and then 3 private methods at the bottom. + +Above all, the organization of the code should feel _natural_. + +## Formatting + +### Braces + +#### Block-like constructs: K&R style + +Braces mostly follow the _Kernighan and Ritchie style_ (a.k.a., "Egyptian brackets") for nonempty blocks and block-like constructs: + +* No line break before the opening brace but prefixed by a single space +* Line break after the opening brace +* Line break before the closing brace +* Line break after the closing brace if that brace terminates a statement or the body of a method, constructor, or named class +* Line break before else, catch and finally statements + +Example: + +```java +return new MyClass() { + @Override + public void method() { + if (condition()) { + something(); + } + else { + try { + alternative(); + } + catch (ProblemException ex) { + recover(); + } + } + } +}; +``` + +### Line wrapping + +90 characters is the _preferred_ line length we aim for. In some cases the preferred length can be achieved by refactoring code slightly. In other cases it's just not possible. + +90 is not a hard limit. Lines between 90-105 are perfectly acceptable in many cases where it aids readability and where wrapping has the opposite effect of reducing readability. This is a judgement call and it's also important to seek consistency. Many times you can learn by looking how specific situations are handled in other parts of the code. + +Lines between 105-120 are allowed but discouraged and should be few. + +No lines should exceed 120 characters. + +The one big exception to the above line wrapping rules is Javadoc where we aim to wrap around 80 characters for maximum readability in all kinds of contexts -- for example, reading on Github, on your phone, etc. + +When wrapping a lengthy expression, 90 characters is the length at which we aim to wrap. Place separator symbols at the end of the current line rather than at the beginning of the next line. In this context, the following are considered separator symbols: `,`, `+`, `?`, `:`, `&&`, `||`. For example: + +```java +if (thisLengthyMethodCall(param1, param2) && anotherCheck() && + yetAnotherCheck()) { + + // .... +} +``` + +### Blank Lines + +Add two blank lines before the following elements: + +* `static {}` block +* Fields +* Constructors +* Inner classes + +Add one blank line after a method signature that is multiline, i.e. + +```java +@Override +protected Object invoke(FooBarOperationContext context, + AnotherSuperLongName name) { + + // code here +} +``` + +For inner-classes, extra blank lines around fields and constructors are typically not +added as the inner class is already separated by 2 lines, unless the inner class is +more substantial in which case the 2 extra lines could still help with readability. + +## Class declaration + +Try as much as possible to put the `implements`, `extends` section of a class declaration on the same line as the class itself. + +Order the classes so that the most important comes first. + +## Naming + +### Constant names + +Constant names use `CONSTANT_CASE`: all uppercase letters, with words separated by underscores. + +Every constant is a `static final` field, but not all `static final` fields are constants. Constant case should therefore be chosen only if the field **is really** a constant. + +Example: + +```java +// Constants +private static final Object NULL_HOLDER = new NullHolder(); +public static final int DEFAULT_PORT = -1; + +// Not constants +private static final ThreadLocal executorHolder = new ThreadLocal(); +private static final Set internalAnnotationAttributes = new HashSet(); +``` + +### Variable names + +Avoid using single characters as variable names. For instance prefer `Method method` to `Method m`. + +## Programming Practices + +### File history + +* A file should look like it was crafted by a single author, not like a history of changes. +* Don't artificially spread things out that belong together. + +### Organization of setter methods + +Choose wisely where to add a new setter method; it should not be simply added at the end of the list. Perhaps the setter is related to another setter or relates to a group. In that case it should be placed near related methods. + +* Setter order should reflect order of importance, not historical order. +* Ordering of _fields_ and _setters_ should be **consistent**. + +### Ternary Operator + +Wrap the ternary operator within parentheses -- for example, `return (foo != null ? foo : "default");`. + +Also make sure that the _not null_ condition comes first. + +### Null Checks + +Use the `org.springframework.util.Assert.notNull` static method to check that a method argument is not `null` and throw an `IllegalArgumentException` otherwise. Format the exception message so that the name of the parameter comes first with its first character capitalized, followed by "_must not be null_". For instance: + +```java +public void handle(Event event) { + Assert.notNull(event, "Event must not be null"); + //... +} +``` + +For other use cases, use the `org.springframework.util.Assert.state` static method to ensure a variable is not `null` and throw an `IllegalStateException` otherwise. Format the exception message so that the identifier related to the variable (name, type or description) comes first with its first character capitalized, followed by "_must not be null_". For instance: + +```java +//... +Event event = ... +Assert.state(event != null, "Event must not be null"); +//... +``` + +### Null Safety of APIs and fields + + +Nullable fields, return values and parameters are expected to be specified explicitly using `@Nullable`: + +```java +import org.springframework.lang.Nullable; + +public class MyClass { + + @Nullable + private Class nullableType; + + public void setNullableType(@Nullable Class nullableType) { + this.nullableType = nullableType; + } + + @Nullable + public Class getNullableType() { + return this.nullableType; + } +} +``` + +[`org.springframework.lang.Contract` annotation](https://docs.spring.io/spring-framework/docs/6.2.0-SNAPSHOT/javadoc-api/org/springframework/lang/Contract.html) can be used to specify some aspects of the method behavior depending on the arguments that are then [taken in account by NullAway](https://github.com/uber/NullAway/wiki/Supported-Annotations#contracts). See for example how `@Contract` is used in Spring Framework codebase in the `Assert` class: + +`Related guidelines: + +* When overriding a method, null-safety annotations of the super method need to be specified on the overridden method unless you want to override null-safety. +* Use `@SuppressWarnings("NullAway")` when NullAway triggers irrelevant errors, which can happen due to [NullAway bugs or missing features](https://github.com/uber/NullAway/issues) or when the analysis is not able to prove null-safety (can happen with lambdas). + +### Use of @Override + +Always add `@Override` on methods overriding or implementing a method declared in a super type. + +### Utility classes + +A class that is only a collection of static utility methods must be named with a `Utils` suffix, must have a `private` default constructor, and must be `abstract`. Making the class `abstract` and providing a `private` _default_ constructor prevent anyone from instantiating it. For example: + +```java +public abstract MyUtils { + + private MyUtils() { + /* prevent instantiation */ + } + + // static utility methods +} +``` + +### Field and method references + +A field of a class should _always_ be referenced using `this`. A method of a class, however, should never be referenced using `this`. + +### Local variable type inference + +The use of `var` for variable declarations (_local variable type inference_) is only allowed where it can improve +readability. Instead, declare variables using the concrete type or interface (where applicable). + +## Javadoc + +### Javadoc formatting + +The following template summarizes typical Javadoc usage for a method. + +```java +/** + * Parse the specified {@link Element} and register the resulting + * {@link BeanDefinition BeanDefinition(s)}. + *

Implementations must return the primary {@link BeanDefinition} that results + * from the parsing if they will ever be used in a nested fashion (for example as + * an inner tag in a {@code } tag). Implementations may return + * {@code null} if they will not be used in a nested fashion. + * @param element the element that is to be parsed into one or more {@link BeanDefinition BeanDefinitions} + * @param parserContext the object encapsulating the current state of the parsing process; + * provides access to a {@link org.springframework.beans.factory.support.BeanDefinitionRegistry} + * @return the primary {@link BeanDefinition} + */ +BeanDefinition parse(Element element, ParserContext parserContext); +``` + +In particular, please note: + +* Use an imperative style (i.e. _Return_ and not _Returns_) for the first sentence. +* No blank lines between the description and the parameter descriptions. +* If the description is defined with multiple paragraphs, start each of them with `

`. +* If a parameter description needs to be wrapped, do not indent subsequent lines (see `parserContext`). + +The Javadoc of a class has some extra rules that are illustrated by the sample below: + +```java +/* + * Interface used by the {@link DefaultBeanDefinitionDocumentReader} to handle custom, + * top-level (directly under {@code }) tags. + * + *

Implementations are free to turn the metadata in the custom tag into as many + * {@link BeanDefinition BeanDefinitions} as required. + * + *

The parser locates a {@link BeanDefinitionParser} from the associated + * {@link NamespaceHandler} for the namespace in which the custom tag resides. + * + * @author Rob Harrop + * @since 2.0 + * @see NamespaceHandler + * @see AbstractBeanDefinitionParser + */ +``` + +* The order of tags for type-level Javadoc is: `@author`, `@param`, `@see`, `@deprecated`. +* The order of tags for constructor-level, method-level, and field-level Javadoc is: `@param`, `@return`, `@throws`, `@see`, `@deprecated`. +* In contrast to constructor-level, method-level, and field-level Javadoc, the paragraphs of a class description _are_ separated by blank lines. + +The following are additional general rules to apply when writing Javadoc: + +* Use `{@code}` to wrap code statements or values such as `null`. +* If a type is only referenced by a `{@link}` element, use the fully qualified name in order to avoid an unnecessary `import` declaration. + +## Tests + +### Testing cBioPortal + +Tests must be written using JUnit 4 + +Stretch Goal Upgrade tests to JUnit 5!! + +### Naming + +Each test class name must end with a `Tests` suffix. + +### Assertions + +Use AssertJ for assertions. + +### Mocking + +Use the BDD Mockito support. diff --git a/docker/web-and-data/Dockerfile b/docker/web-and-data/Dockerfile index c8658f23fac..dcabf787a54 100644 --- a/docker/web-and-data/Dockerfile +++ b/docker/web-and-data/Dockerfile @@ -73,4 +73,4 @@ COPY --from=build ${DEPENDENCY}/BOOT-INF/classes $PORTAL_WEB_HOME/ # add entrypoint COPY --from=build /cbioportal/docker/web-and-data/docker-entrypoint.sh /usr/local/bin/ ENTRYPOINT ["docker-entrypoint.sh"] -CMD ["sh", "-c", "java $(echo $JAVA_OPTS) -cp /cbioportal-webapp:/cbioportal-webapp/lib/* org.cbioportal.PortalApplication $(echo $WEBAPP_OPTS)"] +CMD ["sh", "-c", "java $(echo $JAVA_OPTS) -cp /cbioportal-webapp:/cbioportal-webapp/lib/* org.cbioportal.application.PortalApplication $(echo $WEBAPP_OPTS)"] diff --git a/pom.xml b/pom.xml index 9e8555525b2..e68469d013b 100644 --- a/pom.xml +++ b/pom.xml @@ -17,7 +17,8 @@ cBioPortal for Cancer Genomics - 21 + jdt_apt + 21 21 21 @@ -100,6 +101,7 @@ 7.1.0 1.19.7 1.78 + 1.6.3 @@ -385,6 +387,19 @@ spring-boot-testcontainers test + + org.mapstruct + mapstruct + ${mapstruct.version} + + + + + org.osgi + org.osgi.service.component.annotations + 1.5.1 + provided + @@ -470,6 +485,21 @@ + + org.apache.maven.plugins + maven-compiler-plugin + 3.13.0 + + 21 + + + org.mapstruct + mapstruct-processor + ${mapstruct.version} + + + + org.springframework.boot spring-boot-maven-plugin @@ -483,7 +513,7 @@ - + io.github.git-commit-id git-commit-id-maven-plugin diff --git a/src/main/java/org/cbioportal/AsyncConfig.java b/src/main/java/org/cbioportal/application/AsyncConfig.java similarity index 84% rename from src/main/java/org/cbioportal/AsyncConfig.java rename to src/main/java/org/cbioportal/application/AsyncConfig.java index a1e5b3041a4..7a9d543ab91 100644 --- a/src/main/java/org/cbioportal/AsyncConfig.java +++ b/src/main/java/org/cbioportal/application/AsyncConfig.java @@ -1,14 +1,11 @@ -package org.cbioportal; +package org.cbioportal.application; import org.springframework.beans.factory.annotation.Value; -import org.springframework.core.env.Environment; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.annotation.Configuration; import org.springframework.scheduling.annotation.EnableAsync; import org.springframework.scheduling.annotation.AsyncConfigurer; import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor; -import java.lang.Runtime; import java.util.concurrent.Executor; @Configuration diff --git a/src/main/java/org/cbioportal/WebAppConfig.java b/src/main/java/org/cbioportal/application/WebAppConfig.java similarity index 94% rename from src/main/java/org/cbioportal/WebAppConfig.java rename to src/main/java/org/cbioportal/application/WebAppConfig.java index 2f951690c33..dd04ee7c5e0 100644 --- a/src/main/java/org/cbioportal/WebAppConfig.java +++ b/src/main/java/org/cbioportal/application/WebAppConfig.java @@ -1,9 +1,9 @@ -package org.cbioportal; +package org.cbioportal.application; import java.util.List; -import org.cbioportal.web.ExecuterTimeInterceptor; -import org.cbioportal.web.util.InvolvedCancerStudyExtractorInterceptor; +import org.cbioportal.legacy.web.ExecuterTimeInterceptor; +import org.cbioportal.legacy.web.util.InvolvedCancerStudyExtractorInterceptor; import org.springframework.beans.factory.annotation.Value; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; diff --git a/src/main/java/org/cbioportal/documentation/ExternalPageController.java b/src/main/java/org/cbioportal/application/documentation/ExternalPageController.java similarity index 97% rename from src/main/java/org/cbioportal/documentation/ExternalPageController.java rename to src/main/java/org/cbioportal/application/documentation/ExternalPageController.java index c8a246d38ed..a6a2d1f21f1 100644 --- a/src/main/java/org/cbioportal/documentation/ExternalPageController.java +++ b/src/main/java/org/cbioportal/application/documentation/ExternalPageController.java @@ -1,4 +1,4 @@ -package org.cbioportal.documentation; +package org.cbioportal.application.documentation; import org.springframework.stereotype.Controller; import org.springframework.transaction.annotation.Transactional; diff --git a/src/main/java/org/cbioportal/proxy/LegacyProxyController.java b/src/main/java/org/cbioportal/application/proxy/LegacyProxyController.java similarity index 99% rename from src/main/java/org/cbioportal/proxy/LegacyProxyController.java rename to src/main/java/org/cbioportal/application/proxy/LegacyProxyController.java index a2403f22f86..636a205df2f 100644 --- a/src/main/java/org/cbioportal/proxy/LegacyProxyController.java +++ b/src/main/java/org/cbioportal/application/proxy/LegacyProxyController.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.proxy; +package org.cbioportal.application.proxy; import java.io.IOException; import java.net.URI; diff --git a/src/main/java/org/cbioportal/proxy/Monkifier.java b/src/main/java/org/cbioportal/application/proxy/Monkifier.java similarity index 97% rename from src/main/java/org/cbioportal/proxy/Monkifier.java rename to src/main/java/org/cbioportal/application/proxy/Monkifier.java index b50d6da4dfb..ac368ab3f9c 100644 --- a/src/main/java/org/cbioportal/proxy/Monkifier.java +++ b/src/main/java/org/cbioportal/application/proxy/Monkifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.proxy; +package org.cbioportal.application.proxy; import jakarta.servlet.http.HttpServletRequest; import org.apache.commons.codec.binary.Base64; diff --git a/src/main/java/org/cbioportal/proxy/ProxyController.java b/src/main/java/org/cbioportal/application/proxy/ProxyController.java similarity index 98% rename from src/main/java/org/cbioportal/proxy/ProxyController.java rename to src/main/java/org/cbioportal/application/proxy/ProxyController.java index 0296aec3390..1158e427adc 100644 --- a/src/main/java/org/cbioportal/proxy/ProxyController.java +++ b/src/main/java/org/cbioportal/application/proxy/ProxyController.java @@ -1,8 +1,8 @@ -package org.cbioportal.proxy; +package org.cbioportal.application.proxy; import jakarta.servlet.http.HttpServletRequest; import org.apache.commons.lang3.StringUtils; -import org.cbioportal.proxy.util.CheckDarwinAccessUtil; +import org.cbioportal.application.proxy.util.CheckDarwinAccessUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpEntity; diff --git a/src/main/java/org/cbioportal/proxy/util/CheckDarwinAccessUtil.java b/src/main/java/org/cbioportal/application/proxy/util/CheckDarwinAccessUtil.java similarity index 99% rename from src/main/java/org/cbioportal/proxy/util/CheckDarwinAccessUtil.java rename to src/main/java/org/cbioportal/application/proxy/util/CheckDarwinAccessUtil.java index be9dc2b1152..39e6ba1e7bf 100644 --- a/src/main/java/org/cbioportal/proxy/util/CheckDarwinAccessUtil.java +++ b/src/main/java/org/cbioportal/application/proxy/util/CheckDarwinAccessUtil.java @@ -1,4 +1,4 @@ -package org.cbioportal.proxy.util; +package org.cbioportal.application.proxy.util; import com.fasterxml.jackson.annotation.JsonAnyGetter; import com.fasterxml.jackson.annotation.JsonAnySetter; diff --git a/src/main/java/org/cbioportal/application/rest/mapper/CancerStudyMetadataMapper.java b/src/main/java/org/cbioportal/application/rest/mapper/CancerStudyMetadataMapper.java new file mode 100644 index 00000000000..cbf1467d815 --- /dev/null +++ b/src/main/java/org/cbioportal/application/rest/mapper/CancerStudyMetadataMapper.java @@ -0,0 +1,20 @@ +package org.cbioportal.application.rest.mapper; + +import org.cbioportal.application.rest.response.CancerStudyMetadataDTO; +import org.cbioportal.cancerstudy.CancerStudyMetadata; +import org.mapstruct.Mapper; +import org.mapstruct.Mapping; +import org.mapstruct.factory.Mappers; + +import java.util.List; + +@Mapper +public interface CancerStudyMetadataMapper { + CancerStudyMetadataMapper INSTANCE = Mappers.getMapper(CancerStudyMetadataMapper.class); + + @Mapping(target = "importDate", source = "importDate", dateFormat = "yyyy-MM-dd HH:mm:ss") + CancerStudyMetadataDTO toDto(CancerStudyMetadata cancerStudyMetadata); + + @Mapping(target = "importDate", source = "importDate", dateFormat = "yyyy-MM-dd HH:mm:ss") + List toDtos(List cancerStudyMetadataList); +} diff --git a/src/main/java/org/cbioportal/application/rest/response/CancerStudyMetadataDTO.java b/src/main/java/org/cbioportal/application/rest/response/CancerStudyMetadataDTO.java new file mode 100644 index 00000000000..448de69ca28 --- /dev/null +++ b/src/main/java/org/cbioportal/application/rest/response/CancerStudyMetadataDTO.java @@ -0,0 +1,16 @@ +package org.cbioportal.application.rest.response; + +import io.swagger.v3.oas.annotations.media.Schema; +import org.cbioportal.cancerstudy.TypeOfCancer; + +@Schema(name = "CancerStudyMetadata", description = "Represents a cancer study") +public record CancerStudyMetadataDTO(String cancerStudyIdentifier, String typeOfCancerId, + String name, String description, Boolean publicStudy, String pmid, String citation, + String groups, Integer status, String importDate, Integer allSampleCount, + Integer sequencedSampleCount, Integer cnaSampleCount, Integer mrnaRnaSeqSampleCount, + Integer mrnaRnaSeqV2SampleCount, Integer mrnaMicroarraySampleCount, + Integer miRnaSampleCount, Integer methylationHm27SampleCount, Integer rppaSampleCount, + Integer massSpectrometrySampleCount, Integer completeSampleCount, + String referenceGenome, Integer treatmentCount, Integer structuralVariantCount, + TypeOfCancer typeOfCancer) { +} diff --git a/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java b/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java new file mode 100644 index 00000000000..c8bcb5c28b6 --- /dev/null +++ b/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java @@ -0,0 +1,94 @@ +package org.cbioportal.application.rest.vcolumnstore; + +import io.swagger.v3.oas.annotations.Hidden; +import io.swagger.v3.oas.annotations.Parameter; +import org.cbioportal.application.rest.mapper.CancerStudyMetadataMapper; +import org.cbioportal.application.rest.response.CancerStudyMetadataDTO; +import org.cbioportal.cancerstudy.usecase.GetCancerStudyMetadataUseCase; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.sort.StudySortBy; +import org.cbioportal.shared.SortAndSearchCriteria; +import org.cbioportal.shared.enums.ProjectionType; +import org.springframework.context.annotation.Profile; +import org.springframework.http.HttpStatus; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.GetMapping; +import org.springframework.web.bind.annotation.RequestMapping; +import org.springframework.web.bind.annotation.RequestParam; +import org.springframework.web.bind.annotation.RestController; + +import java.util.List; + +/** + * REST controller for managing and retrieving cancer study metadata from a column-store data source. + *

+ * This controller provides an endpoint to fetch cancer study metadata with support for filtering, + * sorting, and controlling the level of detail in the response. It is designed to work with a + * column-store database, which is optimized for querying large datasets efficiently. + *

+ * + * @see GetCancerStudyMetadataUseCase + * @see CancerStudyMetadataDTO + * @see ProjectionType + * @see StudySortBy + * @see Direction + */ +@RestController +@RequestMapping("/api/column-store") +@Profile("clickhouse") +public class ColumnStoreStudyController { + + private final GetCancerStudyMetadataUseCase getCancerStudyMetadataUseCase; + + /** + * Constructs a new {@link ColumnStoreStudyController} with the specified use case. + * + * @param getCancerStudyMetadataUseCase the use case responsible for retrieving cancer study metadata. + */ + public ColumnStoreStudyController(GetCancerStudyMetadataUseCase getCancerStudyMetadataUseCase) { + this.getCancerStudyMetadataUseCase = getCancerStudyMetadataUseCase; + } + + + /** + * Retrieves a list of cancer study metadata based on the specified criteria. + *

+ * This endpoint supports filtering by keyword, controlling the level of detail in the response + * through the projection parameter, and sorting the results by a specified property and direction. + *

+ *

+ * Note: This endpoint is marked as {@link Hidden} and will not be exposed in the API documentation. + *

+ * + * @param keyword the search keyword that applies to the name and cancer type of the studies. + * This parameter is optional. + * @param projection the level of detail of the response. Defaults to {@link ProjectionType#SUMMARY}. + * @param sortBy the name of the property that the result list is sorted by. This parameter is optional. + * @param direction the direction of the sort. Defaults to {@link Direction#ASC}. + * @return a {@link ResponseEntity} containing a list of {@link CancerStudyMetadataDTO} objects + * and an HTTP status code {@link HttpStatus#OK}. + * + * @see ProjectionType + * @see StudySortBy + * @see Direction + */ + @Hidden + @GetMapping(value = "/studies", produces = MediaType.APPLICATION_JSON_VALUE) + public ResponseEntity> getAllStudies( + @Parameter(description = "Search keyword that applies to name and cancer type of the studies") + @RequestParam(required = false) String keyword, + @Parameter(description = "Level of detail of the response") + @RequestParam(defaultValue = "SUMMARY") ProjectionType projection, + @Parameter(description = "Name of the property that the result list is sorted by") + @RequestParam(required = false) StudySortBy sortBy, + @Parameter(description = "Direction of the sort") + @RequestParam(defaultValue = "ASC") Direction direction) { + + + var sortAndSearchCriteria = new SortAndSearchCriteria(keyword, (sortBy != null ? sortBy.getOriginalValue(): ""), + direction.toString()); + return ResponseEntity.ok(CancerStudyMetadataMapper.INSTANCE.toDtos(getCancerStudyMetadataUseCase.execute(projection, sortAndSearchCriteria))); + } + +} diff --git a/src/main/java/org/cbioportal/security/CancerStudyPermissionEvaluator.java b/src/main/java/org/cbioportal/application/security/CancerStudyPermissionEvaluator.java similarity index 98% rename from src/main/java/org/cbioportal/security/CancerStudyPermissionEvaluator.java rename to src/main/java/org/cbioportal/application/security/CancerStudyPermissionEvaluator.java index 3cd7c732b7c..d92ecd70a5d 100644 --- a/src/main/java/org/cbioportal/security/CancerStudyPermissionEvaluator.java +++ b/src/main/java/org/cbioportal/application/security/CancerStudyPermissionEvaluator.java @@ -30,18 +30,18 @@ * along with this program. If not, see . */ -package org.cbioportal.security; +package org.cbioportal.application.security; import java.io.Serializable; import java.util.*; import java.util.stream.Collectors; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Patient; -import org.cbioportal.model.SampleList; -import org.cbioportal.persistence.cachemaputil.CacheMapUtil; -import org.cbioportal.utils.security.AccessLevel; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.persistence.cachemaputil.CacheMapUtil; +import org.cbioportal.legacy.utils.security.AccessLevel; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.security.access.PermissionEvaluator; diff --git a/src/main/java/org/cbioportal/security/basic/BasicRestfulAuthenticationSuccessHandler.java b/src/main/java/org/cbioportal/application/security/basic/BasicRestfulAuthenticationSuccessHandler.java similarity index 97% rename from src/main/java/org/cbioportal/security/basic/BasicRestfulAuthenticationSuccessHandler.java rename to src/main/java/org/cbioportal/application/security/basic/BasicRestfulAuthenticationSuccessHandler.java index 9291f27abcd..e0620f0f6f6 100644 --- a/src/main/java/org/cbioportal/security/basic/BasicRestfulAuthenticationSuccessHandler.java +++ b/src/main/java/org/cbioportal/application/security/basic/BasicRestfulAuthenticationSuccessHandler.java @@ -1,4 +1,4 @@ -package org.cbioportal.security.basic; +package org.cbioportal.application.security.basic; import jakarta.servlet.http.HttpServletRequest; import jakarta.servlet.http.HttpServletResponse; diff --git a/src/main/java/org/cbioportal/security/config/ApiSecurityConfig.java b/src/main/java/org/cbioportal/application/security/config/ApiSecurityConfig.java similarity index 91% rename from src/main/java/org/cbioportal/security/config/ApiSecurityConfig.java rename to src/main/java/org/cbioportal/application/security/config/ApiSecurityConfig.java index b83524d0869..902af9a9440 100644 --- a/src/main/java/org/cbioportal/security/config/ApiSecurityConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/ApiSecurityConfig.java @@ -1,10 +1,10 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; -import org.cbioportal.security.token.RestAuthenticationEntryPoint; -import org.cbioportal.security.token.TokenAuthenticationFilter; -import org.cbioportal.security.token.TokenAuthenticationSuccessHandler; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.application.security.token.RestAuthenticationEntryPoint; +import org.cbioportal.application.security.token.TokenAuthenticationFilter; +import org.cbioportal.application.security.token.TokenAuthenticationSuccessHandler; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; diff --git a/src/main/java/org/cbioportal/security/config/AutoconfigureExcludeConfig.java b/src/main/java/org/cbioportal/application/security/config/AutoconfigureExcludeConfig.java similarity index 92% rename from src/main/java/org/cbioportal/security/config/AutoconfigureExcludeConfig.java rename to src/main/java/org/cbioportal/application/security/config/AutoconfigureExcludeConfig.java index 5c14beb51e6..5c4c8ee61bc 100644 --- a/src/main/java/org/cbioportal/security/config/AutoconfigureExcludeConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/AutoconfigureExcludeConfig.java @@ -1,6 +1,6 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.boot.autoconfigure.EnableAutoConfiguration; import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; import org.springframework.boot.autoconfigure.data.redis.RedisAutoConfiguration; diff --git a/src/main/java/org/cbioportal/security/config/CorsConfig.java b/src/main/java/org/cbioportal/application/security/config/CorsConfig.java similarity index 96% rename from src/main/java/org/cbioportal/security/config/CorsConfig.java rename to src/main/java/org/cbioportal/application/security/config/CorsConfig.java index d96050013cc..830e52c18b6 100644 --- a/src/main/java/org/cbioportal/security/config/CorsConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/CorsConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; import org.springframework.beans.factory.annotation.Value; import org.springframework.context.annotation.Bean; diff --git a/src/main/java/org/cbioportal/security/config/CustomOAuth2AuthorizationConfig.java b/src/main/java/org/cbioportal/application/security/config/CustomOAuth2AuthorizationConfig.java similarity index 94% rename from src/main/java/org/cbioportal/security/config/CustomOAuth2AuthorizationConfig.java rename to src/main/java/org/cbioportal/application/security/config/CustomOAuth2AuthorizationConfig.java index 7929fdce39f..4561c996079 100644 --- a/src/main/java/org/cbioportal/security/config/CustomOAuth2AuthorizationConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/CustomOAuth2AuthorizationConfig.java @@ -1,8 +1,8 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; -import org.cbioportal.model.User; -import org.cbioportal.model.UserAuthorities; -import org.cbioportal.persistence.SecurityRepository; +import org.cbioportal.legacy.model.User; +import org.cbioportal.legacy.model.UserAuthorities; +import org.cbioportal.legacy.persistence.SecurityRepository; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/cbioportal/security/config/MethodSecurityConfig.java b/src/main/java/org/cbioportal/application/security/config/MethodSecurityConfig.java similarity index 90% rename from src/main/java/org/cbioportal/security/config/MethodSecurityConfig.java rename to src/main/java/org/cbioportal/application/security/config/MethodSecurityConfig.java index c6bd8d04645..c48c8532ed6 100644 --- a/src/main/java/org/cbioportal/security/config/MethodSecurityConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/MethodSecurityConfig.java @@ -1,7 +1,7 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; -import org.cbioportal.persistence.cachemaputil.CacheMapUtil; -import org.cbioportal.security.CancerStudyPermissionEvaluator; +import org.cbioportal.legacy.persistence.cachemaputil.CacheMapUtil; +import org.cbioportal.application.security.CancerStudyPermissionEvaluator; import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; import org.springframework.context.annotation.Bean; diff --git a/src/main/java/org/cbioportal/security/config/NoSecurityConfig.java b/src/main/java/org/cbioportal/application/security/config/NoSecurityConfig.java similarity index 95% rename from src/main/java/org/cbioportal/security/config/NoSecurityConfig.java rename to src/main/java/org/cbioportal/application/security/config/NoSecurityConfig.java index 42f49c96cd3..9c8d7e068e8 100644 --- a/src/main/java/org/cbioportal/security/config/NoSecurityConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/NoSecurityConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; import org.springframework.context.annotation.Bean; diff --git a/src/main/java/org/cbioportal/security/config/OAuth2SecurityConfig.java b/src/main/java/org/cbioportal/application/security/config/OAuth2SecurityConfig.java similarity index 96% rename from src/main/java/org/cbioportal/security/config/OAuth2SecurityConfig.java rename to src/main/java/org/cbioportal/application/security/config/OAuth2SecurityConfig.java index fd3b8b48b3f..ee82bc1adba 100644 --- a/src/main/java/org/cbioportal/security/config/OAuth2SecurityConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/OAuth2SecurityConfig.java @@ -1,7 +1,7 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; -import org.cbioportal.security.util.ClaimRoleExtractorUtil; -import org.cbioportal.security.util.GrantedAuthorityUtil; +import org.cbioportal.application.security.util.ClaimRoleExtractorUtil; +import org.cbioportal.application.security.util.GrantedAuthorityUtil; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Value; diff --git a/src/main/java/org/cbioportal/security/config/OptionalOAuth2SecurityConfig.java b/src/main/java/org/cbioportal/application/security/config/OptionalOAuth2SecurityConfig.java similarity index 96% rename from src/main/java/org/cbioportal/security/config/OptionalOAuth2SecurityConfig.java rename to src/main/java/org/cbioportal/application/security/config/OptionalOAuth2SecurityConfig.java index 248921b2235..8d8649b4b9d 100644 --- a/src/main/java/org/cbioportal/security/config/OptionalOAuth2SecurityConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/OptionalOAuth2SecurityConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; import org.springframework.boot.autoconfigure.security.SecurityProperties; diff --git a/src/main/java/org/cbioportal/security/config/Saml2AndBasicConfig.java b/src/main/java/org/cbioportal/application/security/config/Saml2AndBasicConfig.java similarity index 97% rename from src/main/java/org/cbioportal/security/config/Saml2AndBasicConfig.java rename to src/main/java/org/cbioportal/application/security/config/Saml2AndBasicConfig.java index 691979c0072..e4117b8ba2a 100644 --- a/src/main/java/org/cbioportal/security/config/Saml2AndBasicConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/Saml2AndBasicConfig.java @@ -1,6 +1,6 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; -import org.cbioportal.security.basic.BasicRestfulAuthenticationSuccessHandler; +import org.cbioportal.application.security.basic.BasicRestfulAuthenticationSuccessHandler; import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; import org.springframework.context.annotation.Bean; diff --git a/src/main/java/org/cbioportal/security/config/Saml2SecurityConfig.java b/src/main/java/org/cbioportal/application/security/config/Saml2SecurityConfig.java similarity index 97% rename from src/main/java/org/cbioportal/security/config/Saml2SecurityConfig.java rename to src/main/java/org/cbioportal/application/security/config/Saml2SecurityConfig.java index 527df01140b..5e71912965e 100644 --- a/src/main/java/org/cbioportal/security/config/Saml2SecurityConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/Saml2SecurityConfig.java @@ -1,6 +1,6 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; -import org.cbioportal.security.util.GrantedAuthorityUtil; +import org.cbioportal.application.security.util.GrantedAuthorityUtil; import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; diff --git a/src/main/java/org/cbioportal/security/token/RestAuthenticationEntryPoint.java b/src/main/java/org/cbioportal/application/security/token/RestAuthenticationEntryPoint.java similarity index 97% rename from src/main/java/org/cbioportal/security/token/RestAuthenticationEntryPoint.java rename to src/main/java/org/cbioportal/application/security/token/RestAuthenticationEntryPoint.java index 8b5136520b2..3f91aec7a19 100644 --- a/src/main/java/org/cbioportal/security/token/RestAuthenticationEntryPoint.java +++ b/src/main/java/org/cbioportal/application/security/token/RestAuthenticationEntryPoint.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token; +package org.cbioportal.application.security.token; import java.io.IOException; diff --git a/src/main/java/org/cbioportal/security/token/TokenAuthenticationFilter.java b/src/main/java/org/cbioportal/application/security/token/TokenAuthenticationFilter.java similarity index 97% rename from src/main/java/org/cbioportal/security/token/TokenAuthenticationFilter.java rename to src/main/java/org/cbioportal/application/security/token/TokenAuthenticationFilter.java index 42988160137..e1cef698518 100644 --- a/src/main/java/org/cbioportal/security/token/TokenAuthenticationFilter.java +++ b/src/main/java/org/cbioportal/application/security/token/TokenAuthenticationFilter.java @@ -30,12 +30,12 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token; +package org.cbioportal.application.security.token; import jakarta.servlet.ServletException; import jakarta.servlet.http.HttpServletRequest; import jakarta.servlet.http.HttpServletResponse; -import org.cbioportal.service.DataAccessTokenService; +import org.cbioportal.legacy.service.DataAccessTokenService; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.security.authentication.AuthenticationManager; diff --git a/src/main/java/org/cbioportal/security/token/TokenAuthenticationSuccessHandler.java b/src/main/java/org/cbioportal/application/security/token/TokenAuthenticationSuccessHandler.java similarity index 97% rename from src/main/java/org/cbioportal/security/token/TokenAuthenticationSuccessHandler.java rename to src/main/java/org/cbioportal/application/security/token/TokenAuthenticationSuccessHandler.java index b2db8dddabf..9eefe2a66cc 100644 --- a/src/main/java/org/cbioportal/security/token/TokenAuthenticationSuccessHandler.java +++ b/src/main/java/org/cbioportal/application/security/token/TokenAuthenticationSuccessHandler.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token; +package org.cbioportal.application.security.token; import jakarta.servlet.ServletException; import jakarta.servlet.http.HttpServletRequest; diff --git a/src/main/java/org/cbioportal/security/token/config/DataAccessTokenConfig.java b/src/main/java/org/cbioportal/application/security/token/config/DataAccessTokenConfig.java similarity index 69% rename from src/main/java/org/cbioportal/security/token/config/DataAccessTokenConfig.java rename to src/main/java/org/cbioportal/application/security/token/config/DataAccessTokenConfig.java index a800772cfa7..58126b1143f 100644 --- a/src/main/java/org/cbioportal/security/token/config/DataAccessTokenConfig.java +++ b/src/main/java/org/cbioportal/application/security/token/config/DataAccessTokenConfig.java @@ -1,13 +1,13 @@ -package org.cbioportal.security.token.config; +package org.cbioportal.application.security.token.config; -import org.cbioportal.persistence.SecurityRepository; -import org.cbioportal.security.token.oauth2.JwtTokenVerifierBuilder; -import org.cbioportal.security.token.oauth2.OAuth2DataAccessTokenServiceImpl; -import org.cbioportal.security.token.oauth2.OAuth2TokenAuthenticationProvider; -import org.cbioportal.security.token.oauth2.OAuth2TokenRefreshRestTemplate; -import org.cbioportal.security.token.uuid.UuidTokenAuthenticationProvider; -import org.cbioportal.service.impl.UnauthDataAccessTokenServiceImpl; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.persistence.SecurityRepository; +import org.cbioportal.application.security.token.oauth2.JwtTokenVerifierBuilder; +import org.cbioportal.application.security.token.oauth2.OAuth2DataAccessTokenServiceImpl; +import org.cbioportal.application.security.token.oauth2.OAuth2TokenAuthenticationProvider; +import org.cbioportal.application.security.token.oauth2.OAuth2TokenRefreshRestTemplate; +import org.cbioportal.application.security.token.uuid.UuidTokenAuthenticationProvider; +import org.cbioportal.legacy.service.impl.UnauthDataAccessTokenServiceImpl; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; import org.springframework.web.client.RestTemplate; diff --git a/src/main/java/org/cbioportal/security/token/oauth2/JwtTokenVerifierBuilder.java b/src/main/java/org/cbioportal/application/security/token/oauth2/JwtTokenVerifierBuilder.java similarity index 97% rename from src/main/java/org/cbioportal/security/token/oauth2/JwtTokenVerifierBuilder.java rename to src/main/java/org/cbioportal/application/security/token/oauth2/JwtTokenVerifierBuilder.java index a14fba88b1e..5f82071f317 100644 --- a/src/main/java/org/cbioportal/security/token/oauth2/JwtTokenVerifierBuilder.java +++ b/src/main/java/org/cbioportal/application/security/token/oauth2/JwtTokenVerifierBuilder.java @@ -29,7 +29,7 @@ * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see . */ -package org.cbioportal.security.token.oauth2; +package org.cbioportal.application.security.token.oauth2; import java.net.MalformedURLException; import java.net.URL; diff --git a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2BearerAuthenticationToken.java b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2BearerAuthenticationToken.java similarity index 97% rename from src/main/java/org/cbioportal/security/token/oauth2/OAuth2BearerAuthenticationToken.java rename to src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2BearerAuthenticationToken.java index 1e60681df90..833488780d7 100644 --- a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2BearerAuthenticationToken.java +++ b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2BearerAuthenticationToken.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token.oauth2; +package org.cbioportal.application.security.token.oauth2; import java.util.Collection; import java.util.HashSet; diff --git a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2DataAccessTokenServiceImpl.java b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2DataAccessTokenServiceImpl.java similarity index 97% rename from src/main/java/org/cbioportal/security/token/oauth2/OAuth2DataAccessTokenServiceImpl.java rename to src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2DataAccessTokenServiceImpl.java index 9e546ce10bf..d2e5a548f78 100644 --- a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2DataAccessTokenServiceImpl.java +++ b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2DataAccessTokenServiceImpl.java @@ -30,12 +30,12 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token.oauth2; +package org.cbioportal.application.security.token.oauth2; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.DataAccessTokenService; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.service.DataAccessTokenService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpEntity; diff --git a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenAuthenticationProvider.java b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenAuthenticationProvider.java similarity index 95% rename from src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenAuthenticationProvider.java rename to src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenAuthenticationProvider.java index d8dfafa7b66..903f069df23 100644 --- a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenAuthenticationProvider.java +++ b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenAuthenticationProvider.java @@ -30,12 +30,12 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token.oauth2; +package org.cbioportal.application.security.token.oauth2; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.security.util.ClaimRoleExtractorUtil; -import org.cbioportal.security.util.GrantedAuthorityUtil; +import org.cbioportal.application.security.util.ClaimRoleExtractorUtil; +import org.cbioportal.application.security.util.GrantedAuthorityUtil; import org.springframework.beans.factory.annotation.Value; import org.springframework.security.authentication.AuthenticationProvider; import org.springframework.security.authentication.BadCredentialsException; diff --git a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenDataAccessConfiguration.java b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenDataAccessConfiguration.java similarity index 97% rename from src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenDataAccessConfiguration.java rename to src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenDataAccessConfiguration.java index f9dc65c0889..c3453f8a89e 100644 --- a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenDataAccessConfiguration.java +++ b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenDataAccessConfiguration.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token.oauth2; +package org.cbioportal.application.security.token.oauth2; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; diff --git a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenRefreshRestTemplate.java b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenRefreshRestTemplate.java similarity index 98% rename from src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenRefreshRestTemplate.java rename to src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenRefreshRestTemplate.java index fefe7ccb2d8..47b81bf7b3c 100644 --- a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenRefreshRestTemplate.java +++ b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenRefreshRestTemplate.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token.oauth2; +package org.cbioportal.application.security.token.oauth2; import com.fasterxml.jackson.databind.ObjectMapper; import org.slf4j.Logger; diff --git a/src/main/java/org/cbioportal/security/token/uuid/UuidTokenAuthenticationProvider.java b/src/main/java/org/cbioportal/application/security/token/uuid/UuidTokenAuthenticationProvider.java similarity index 91% rename from src/main/java/org/cbioportal/security/token/uuid/UuidTokenAuthenticationProvider.java rename to src/main/java/org/cbioportal/application/security/token/uuid/UuidTokenAuthenticationProvider.java index 85268a3df22..9dcebe548f6 100644 --- a/src/main/java/org/cbioportal/security/token/uuid/UuidTokenAuthenticationProvider.java +++ b/src/main/java/org/cbioportal/application/security/token/uuid/UuidTokenAuthenticationProvider.java @@ -1,7 +1,7 @@ -package org.cbioportal.security.token.uuid; +package org.cbioportal.application.security.token.uuid; -import org.cbioportal.model.UserAuthorities; -import org.cbioportal.persistence.SecurityRepository; +import org.cbioportal.legacy.model.UserAuthorities; +import org.cbioportal.legacy.persistence.SecurityRepository; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.security.authentication.AuthenticationProvider; diff --git a/src/main/java/org/cbioportal/security/util/ClaimRoleExtractorUtil.java b/src/main/java/org/cbioportal/application/security/util/ClaimRoleExtractorUtil.java similarity index 98% rename from src/main/java/org/cbioportal/security/util/ClaimRoleExtractorUtil.java rename to src/main/java/org/cbioportal/application/security/util/ClaimRoleExtractorUtil.java index 1f3e094529a..5f36f077cb3 100644 --- a/src/main/java/org/cbioportal/security/util/ClaimRoleExtractorUtil.java +++ b/src/main/java/org/cbioportal/application/security/util/ClaimRoleExtractorUtil.java @@ -1,4 +1,4 @@ -package org.cbioportal.security.util; +package org.cbioportal.application.security.util; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; diff --git a/src/main/java/org/cbioportal/security/util/GrantedAuthorityUtil.java b/src/main/java/org/cbioportal/application/security/util/GrantedAuthorityUtil.java similarity index 91% rename from src/main/java/org/cbioportal/security/util/GrantedAuthorityUtil.java rename to src/main/java/org/cbioportal/application/security/util/GrantedAuthorityUtil.java index 68645faf456..456b03385b4 100644 --- a/src/main/java/org/cbioportal/security/util/GrantedAuthorityUtil.java +++ b/src/main/java/org/cbioportal/application/security/util/GrantedAuthorityUtil.java @@ -1,4 +1,4 @@ -package org.cbioportal.security.util; +package org.cbioportal.application.security.util; import org.springframework.security.core.GrantedAuthority; import org.springframework.security.core.authority.SimpleGrantedAuthority; diff --git a/src/main/java/org/cbioportal/cancerstudy/CancerStudyMetadata.java b/src/main/java/org/cbioportal/cancerstudy/CancerStudyMetadata.java new file mode 100644 index 00000000000..4631e559084 --- /dev/null +++ b/src/main/java/org/cbioportal/cancerstudy/CancerStudyMetadata.java @@ -0,0 +1,24 @@ +package org.cbioportal.cancerstudy; + +import java.util.Date; + +public record CancerStudyMetadata(Integer cancerStudyId, String cancerStudyIdentifier, String typeOfCancerId, + String name, String description, Boolean publicStudy, String pmid, String citation, + String groups, Integer status, Date importDate, Integer allSampleCount, + Integer sequencedSampleCount, Integer cnaSampleCount, Integer mrnaRnaSeqSampleCount, + Integer mrnaRnaSeqV2SampleCount, Integer mrnaMicroarraySampleCount, + Integer miRnaSampleCount, Integer methylationHm27SampleCount, Integer rppaSampleCount, + Integer massSpectrometrySampleCount, Integer completeSampleCount, + String referenceGenome, Integer treatmentCount, Integer structuralVariantCount, + TypeOfCancer typeOfCancer) { + + public CancerStudyMetadata(Integer cancerStudyId, String cancerStudyIdentifier, String typeOfCancerId, + String name, String description, Boolean publicStudy, String pmid, String citation, + String groups, Integer status, Date importDate, String referenceGenome, TypeOfCancer typeOfCancer){ + this(cancerStudyId, cancerStudyIdentifier, typeOfCancerId, name, description, publicStudy, pmid,citation, groups, + status, importDate, null, null, null, null, null, + null, null, null, null, null, + null, referenceGenome, null, null, typeOfCancer); + } + +} diff --git a/src/main/java/org/cbioportal/cancerstudy/TypeOfCancer.java b/src/main/java/org/cbioportal/cancerstudy/TypeOfCancer.java new file mode 100644 index 00000000000..a1265421641 --- /dev/null +++ b/src/main/java/org/cbioportal/cancerstudy/TypeOfCancer.java @@ -0,0 +1,4 @@ +package org.cbioportal.cancerstudy; + +public record TypeOfCancer(String id, String name, String dedicatedColor, String shortName, String parent) { +} diff --git a/src/main/java/org/cbioportal/cancerstudy/repository/CancerStudyRepository.java b/src/main/java/org/cbioportal/cancerstudy/repository/CancerStudyRepository.java new file mode 100644 index 00000000000..fe9856e7c9c --- /dev/null +++ b/src/main/java/org/cbioportal/cancerstudy/repository/CancerStudyRepository.java @@ -0,0 +1,77 @@ +package org.cbioportal.cancerstudy.repository; + +import org.cbioportal.cancerstudy.CancerStudyMetadata; +import org.cbioportal.shared.SortAndSearchCriteria; + +import java.util.List; + +/** + * Repository interface for accessing and managing cancer study data. + *

+ * This repository provides methods to retrieve metadata and summary information + * about cancer studies. It serves as an abstraction layer between the domain + * logic and the data source, allowing for flexible and maintainable data access. + *

+ *

+ * Usage Example: + * 

+ * {@code
+ * // Inject the repository into a service
+ * private final CancerStudyRepository cancerStudyRepository;
+ *
+ * public CancerStudyService(CancerStudyRepository cancerStudyRepository) {
+ *     this.cancerStudyRepository = cancerStudyRepository;
+ * }
+ *
+ * // Retrieve metadata for all cancer studies
+ * List metadata = cancerStudyRepository.getCancerStudiesMetadata();
+ *
+ * // Retrieve summary metadata for cancer studies
+ * List summaryMetadata = cancerStudyRepository.getCancerStudiesMetadataSummary();
+ * }
+ *
+ *

+ * + * @see CancerStudyMetadata + */ +public interface CancerStudyRepository { + + /** + * Retrieves a list of metadata for all cancer studies. + *

+ * This method returns detailed metadata for all available cancer studies, + * including information such as study identifiers, descriptions, and + * associated data sources. The metadata can be used for comprehensive + * analysis or display purposes. + *

+ *

+ * Note: The returned list may be large, depending on the number of + * cancer studies in the database. Consider using pagination or filtering + * if performance is a concern. + *

+ * + * @return a list of {@link CancerStudyMetadata} objects containing detailed + * metadata for all cancer studies. The list may be empty if no + * studies are found. + */ + List getCancerStudiesMetadata(SortAndSearchCriteria sortAndSearchCriteria); + + /** + * Retrieves a list of summary metadata for cancer studies. + *

+ * This method returns a lightweight representation of cancer study metadata, + * containing only the most essential fields. It is suitable for scenarios + * where a high-level overview of the studies is sufficient, such as displaying + * a list of studies in a UI or performing quick lookups. + *

+ *

+ * Note: The summary metadata typically excludes detailed information + * to reduce the size of the response and improve performance. + *

+ * + * @return a list of {@link CancerStudyMetadata} objects containing summary + * metadata for cancer studies. The list may be empty if no studies + * are found. + */ + List getCancerStudiesMetadataSummary(SortAndSearchCriteria sortAndSearchCriteria); +} diff --git a/src/main/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCase.java b/src/main/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCase.java new file mode 100644 index 00000000000..47241038b1e --- /dev/null +++ b/src/main/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCase.java @@ -0,0 +1,88 @@ +package org.cbioportal.cancerstudy.usecase; + +import org.cbioportal.cancerstudy.CancerStudyMetadata; +import org.cbioportal.cancerstudy.repository.CancerStudyRepository; +import org.cbioportal.shared.SortAndSearchCriteria; +import org.cbioportal.shared.enums.ProjectionType; +import org.springframework.context.annotation.Profile; +import org.springframework.stereotype.Service; + +import java.util.Collections; +import java.util.List; + +/** + * Service class responsible for retrieving cancer study metadata based on the specified projection type. + *

+ * This use case encapsulates the logic for fetching cancer study metadata from the repository + * and returning the appropriate data based on the requested level of detail (projection). + * It acts as an intermediary between the controller and the repository, ensuring that the + * domain logic is decoupled from the data access layer. + *

+ *

+ * Usage Example: + * 

+ * {@code
+ * // Inject the use case into a controller or service
+ * private final GetCancerStudyMetadataUseCase getCancerStudyMetadataUseCase;
+ *
+ * public CancerStudyController(GetCancerStudyMetadataUseCase getCancerStudyMetadataUseCase) {
+ *     this.getCancerStudyMetadataUseCase = getCancerStudyMetadataUseCase;
+ * }
+ *
+ * // Retrieve detailed metadata for cancer studies
+ * List detailedMetadata = getCancerStudyMetadataUseCase.execute(ProjectionType.DETAILED);
+ *
+ * // Retrieve summary metadata for cancer studies
+ * List summaryMetadata = getCancerStudyMetadataUseCase.execute(ProjectionType.SUMMARY);
+ * }
+ *
+ *

+ * + * @see CancerStudyRepository + * @see ProjectionType + * @see CancerStudyMetadata + */ +@Service +@Profile("clickhouse") +public final class GetCancerStudyMetadataUseCase { + + private final CancerStudyRepository studyRepository; + + + /** + * Constructs a new {@link GetCancerStudyMetadataUseCase} with the specified repository. + * + * @param studyRepository the repository used to access cancer study metadata. + */ + public GetCancerStudyMetadataUseCase(CancerStudyRepository studyRepository) { + this.studyRepository = studyRepository; + } + + /** + * Executes the use case to retrieve cancer study metadata based on the specified projection type. + *

+ * This method determines the level of detail to fetch from the repository based on the + * provided {@link ProjectionType}. It supports the following projections: + *

    + *
  • {@link ProjectionType#DETAILED}: Fetches all available metadata for cancer studies.
    • + *
  • {@link ProjectionType#SUMMARY}: Fetches a summarized version of the metadata.
    • + *
  • Other projection types: Returns an empty list.
    • + *
+ *

+ * + * @param projectionType the level of detail to fetch. Determines which repository method is called. + * @param sortAndSearchCriteria enables sorting and searching feature within persistence layer. {@link SortAndSearchCriteria} + * @return a list of {@link CancerStudyMetadata} objects based on the specified projection type. + * Returns an empty list if the projection type is not supported. + * + * @see ProjectionType + * @see CancerStudyMetadata + */ + public List execute(ProjectionType projectionType, SortAndSearchCriteria sortAndSearchCriteria) { + return switch (projectionType) { + case DETAILED -> studyRepository.getCancerStudiesMetadata(sortAndSearchCriteria); + case SUMMARY -> studyRepository.getCancerStudiesMetadataSummary(sortAndSearchCriteria); + default -> Collections.emptyList(); + }; + } +} diff --git a/src/main/java/org/cbioportal/infrastructure/config/ClickhouseMyBatisConfig.java b/src/main/java/org/cbioportal/infrastructure/config/ClickhouseMyBatisConfig.java new file mode 100644 index 00000000000..a60a7365661 --- /dev/null +++ b/src/main/java/org/cbioportal/infrastructure/config/ClickhouseMyBatisConfig.java @@ -0,0 +1,18 @@ +package org.cbioportal.infrastructure.config; + +import org.mybatis.spring.SqlSessionFactoryBean; +import org.springframework.beans.factory.annotation.Qualifier; +import org.springframework.context.ApplicationContext; +import org.springframework.context.annotation.Configuration; + +import java.io.IOException; + +@Configuration +public class ClickhouseMyBatisConfig { + + public void addClickhouseMybatisConfig( @Qualifier("sqlColumnarSessionFactory") SqlSessionFactoryBean sqlSessionFactoryBean, + ApplicationContext applicationContext) throws IOException { + sqlSessionFactoryBean.addMapperLocations( + applicationContext.getResources("classpath:mappers/clickhouse/**/*.xml")); + } +} diff --git a/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyMapper.java b/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyMapper.java new file mode 100644 index 00000000000..68ae7968782 --- /dev/null +++ b/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyMapper.java @@ -0,0 +1,46 @@ +package org.cbioportal.infrastructure.repository.clickhouse.cancerstudy; + +import org.cbioportal.cancerstudy.CancerStudyMetadata; +import org.cbioportal.shared.SortAndSearchCriteria; + +import java.util.List; + +/** + * Provides methods for retrieving cancer study metadata from a ClickHouse database. + * This interface defines the contract for fetching detailed and summarized metadata + * for cancer studies based on specified criteria. + */ +public interface ClickhouseCancerStudyMapper { + /** + * Retrieves detailed metadata for cancer studies based on the provided sorting, + * search criteria, and a list of study IDs. This method is intended to return + * comprehensive information about each study. + * + * @param sortAndSearchCriteria the criteria used for sorting and searching the + * cancer study metadata. This includes parameters + * such as sort direction, sort by field, and search keywords. + * @param studyIds a list of study IDs to filter the results. If empty, all studies + * matching the criteria should be returned. + * @return a list of {@link CancerStudyMetadata} containing detailed metadata + * for each study that matches the provided criteria and study IDs. + * The list may be empty if no studies match the criteria. + */ + List getCancerStudiesMetadata(SortAndSearchCriteria sortAndSearchCriteria, List studyIds); + + + /** + * Retrieves a summarized version of cancer study metadata based on the provided + * sorting, search criteria, and a list of study IDs. This method is intended to + * return a concise overview of each study. + * + * @param sortAndSearchCriteria the criteria used for sorting and searching the + * cancer study metadata. This includes parameters + * such as sort direction, sort by field, and search keywords. + * @param studyIds a list of study IDs to filter the results. If empty, all studies + * matching the criteria should be returned. + * @return a list of {@link CancerStudyMetadata} containing summarized metadata + * for each study that matches the provided criteria and study IDs. + * The list may be empty if no studies match the criteria. + */ + List getCancerStudiesMetadataSummary(SortAndSearchCriteria sortAndSearchCriteria, List studyIds); +} diff --git a/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyRepository.java b/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyRepository.java new file mode 100644 index 00000000000..a523ee1f5f4 --- /dev/null +++ b/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyRepository.java @@ -0,0 +1,53 @@ +package org.cbioportal.infrastructure.repository.clickhouse.cancerstudy; + +import org.cbioportal.cancerstudy.CancerStudyMetadata; +import org.cbioportal.cancerstudy.repository.CancerStudyRepository; +import org.cbioportal.shared.SortAndSearchCriteria; +import org.springframework.context.annotation.Profile; +import org.springframework.stereotype.Repository; + +import java.util.List; + +/** + * Repository implementation for accessing cancer study metadata from ClickHouse. + * This class delegates database queries to {@link ClickhouseCancerStudyMapper}. + */ +@Repository +@Profile("clickhouse") +public class ClickhouseCancerStudyRepository implements CancerStudyRepository { + + private final ClickhouseCancerStudyMapper cancerStudyMapper; + + /** + * Constructs a new {@code ClickhouseCancerStudyRepository} with the required mapper. + * + * @param cancerStudyMapper the mapper responsible for executing ClickHouse queries + */ + public ClickhouseCancerStudyRepository(ClickhouseCancerStudyMapper cancerStudyMapper) { + this.cancerStudyMapper = cancerStudyMapper; + } + + /** + * Retrieves detailed metadata for all cancer studies. + * @param sortAndSearchCriteria the criteria used for sorting and searching the cancer study metadata. + * This includes parameters such as sort direction, sort by field, and search keywords. + * + * @return a list of {@link CancerStudyMetadata} containing detailed metadata for each study + */ + @Override + public List getCancerStudiesMetadata(SortAndSearchCriteria sortAndSearchCriteria) { + return cancerStudyMapper.getCancerStudiesMetadata(sortAndSearchCriteria, List.of()); + } + + /** + * Retrieves a summarized version of cancer study metadata. + * + * @param sortAndSearchCriteria the criteria used for sorting and searching the cancer study metadata. + * This includes parameters such as sort direction, sort by field, and search keywords. + * @return a list of {@link CancerStudyMetadata} containing summarized metadata for each study + */ + @Override + public List getCancerStudiesMetadataSummary(SortAndSearchCriteria sortAndSearchCriteria) { + return cancerStudyMapper.getCancerStudiesMetadataSummary(sortAndSearchCriteria, List.of()); + } +} diff --git a/src/main/java/org/cbioportal/model/AlleleSpecificCopyNumber.java b/src/main/java/org/cbioportal/legacy/model/AlleleSpecificCopyNumber.java similarity index 98% rename from src/main/java/org/cbioportal/model/AlleleSpecificCopyNumber.java rename to src/main/java/org/cbioportal/legacy/model/AlleleSpecificCopyNumber.java index 4ac94988d19..81f1bac9086 100644 --- a/src/main/java/org/cbioportal/model/AlleleSpecificCopyNumber.java +++ b/src/main/java/org/cbioportal/legacy/model/AlleleSpecificCopyNumber.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/Alteration.java b/src/main/java/org/cbioportal/legacy/model/Alteration.java similarity index 98% rename from src/main/java/org/cbioportal/model/Alteration.java rename to src/main/java/org/cbioportal/legacy/model/Alteration.java index 1e7e6e96cde..3df1a3992a0 100644 --- a/src/main/java/org/cbioportal/model/Alteration.java +++ b/src/main/java/org/cbioportal/legacy/model/Alteration.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/AlterationCountBase.java b/src/main/java/org/cbioportal/legacy/model/AlterationCountBase.java similarity index 97% rename from src/main/java/org/cbioportal/model/AlterationCountBase.java rename to src/main/java/org/cbioportal/legacy/model/AlterationCountBase.java index cbe79790563..a57c487e6a9 100644 --- a/src/main/java/org/cbioportal/model/AlterationCountBase.java +++ b/src/main/java/org/cbioportal/legacy/model/AlterationCountBase.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Set; diff --git a/src/main/java/org/cbioportal/model/AlterationCountByGene.java b/src/main/java/org/cbioportal/legacy/model/AlterationCountByGene.java similarity index 97% rename from src/main/java/org/cbioportal/model/AlterationCountByGene.java rename to src/main/java/org/cbioportal/legacy/model/AlterationCountByGene.java index 0c09a79351f..92e0558e3e0 100644 --- a/src/main/java/org/cbioportal/model/AlterationCountByGene.java +++ b/src/main/java/org/cbioportal/legacy/model/AlterationCountByGene.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/model/AlterationCountByStructuralVariant.java b/src/main/java/org/cbioportal/legacy/model/AlterationCountByStructuralVariant.java similarity index 97% rename from src/main/java/org/cbioportal/model/AlterationCountByStructuralVariant.java rename to src/main/java/org/cbioportal/legacy/model/AlterationCountByStructuralVariant.java index 88800d1f84f..1e629c61b40 100644 --- a/src/main/java/org/cbioportal/model/AlterationCountByStructuralVariant.java +++ b/src/main/java/org/cbioportal/legacy/model/AlterationCountByStructuralVariant.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public class AlterationCountByStructuralVariant extends AlterationCountBase { diff --git a/src/main/java/org/cbioportal/model/AlterationDriverAnnotation.java b/src/main/java/org/cbioportal/legacy/model/AlterationDriverAnnotation.java similarity index 98% rename from src/main/java/org/cbioportal/model/AlterationDriverAnnotation.java rename to src/main/java/org/cbioportal/legacy/model/AlterationDriverAnnotation.java index 02f0f909db9..4297e967b1e 100644 --- a/src/main/java/org/cbioportal/model/AlterationDriverAnnotation.java +++ b/src/main/java/org/cbioportal/legacy/model/AlterationDriverAnnotation.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/AlterationEnrichment.java b/src/main/java/org/cbioportal/legacy/model/AlterationEnrichment.java similarity index 97% rename from src/main/java/org/cbioportal/model/AlterationEnrichment.java rename to src/main/java/org/cbioportal/legacy/model/AlterationEnrichment.java index d1fdbc4ba34..95fe0f5e25f 100644 --- a/src/main/java/org/cbioportal/model/AlterationEnrichment.java +++ b/src/main/java/org/cbioportal/legacy/model/AlterationEnrichment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/AlterationFilter.java b/src/main/java/org/cbioportal/legacy/model/AlterationFilter.java similarity index 98% rename from src/main/java/org/cbioportal/model/AlterationFilter.java rename to src/main/java/org/cbioportal/legacy/model/AlterationFilter.java index c10f8d697e7..d59bd52fa18 100644 --- a/src/main/java/org/cbioportal/model/AlterationFilter.java +++ b/src/main/java/org/cbioportal/legacy/model/AlterationFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Arrays; @@ -10,7 +10,7 @@ import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.annotation.JsonInclude; -import org.cbioportal.model.util.Select; +import org.cbioportal.legacy.model.util.Select; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/src/main/java/org/cbioportal/model/AlterationType.java b/src/main/java/org/cbioportal/legacy/model/AlterationType.java similarity index 77% rename from src/main/java/org/cbioportal/model/AlterationType.java rename to src/main/java/org/cbioportal/legacy/model/AlterationType.java index b20a642669d..c143b182b73 100644 --- a/src/main/java/org/cbioportal/model/AlterationType.java +++ b/src/main/java/org/cbioportal/legacy/model/AlterationType.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum AlterationType { MUTATION_EXTENDED, diff --git a/src/main/java/org/cbioportal/model/BaseAlterationFilter.java b/src/main/java/org/cbioportal/legacy/model/BaseAlterationFilter.java similarity index 98% rename from src/main/java/org/cbioportal/model/BaseAlterationFilter.java rename to src/main/java/org/cbioportal/legacy/model/BaseAlterationFilter.java index df2d2f72a63..e4957b8339f 100644 --- a/src/main/java/org/cbioportal/model/BaseAlterationFilter.java +++ b/src/main/java/org/cbioportal/legacy/model/BaseAlterationFilter.java @@ -1,10 +1,10 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.annotation.JsonInclude.Include; -import org.cbioportal.model.util.Select; +import org.cbioportal.legacy.model.util.Select; import java.io.Serializable; import java.util.HashMap; diff --git a/src/main/java/org/cbioportal/model/Binnable.java b/src/main/java/org/cbioportal/legacy/model/Binnable.java similarity index 87% rename from src/main/java/org/cbioportal/model/Binnable.java rename to src/main/java/org/cbioportal/legacy/model/Binnable.java index 358cafc1685..ee2d3aff1be 100644 --- a/src/main/java/org/cbioportal/model/Binnable.java +++ b/src/main/java/org/cbioportal/legacy/model/Binnable.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; /** * Data that can be binned, clinical or custom diff --git a/src/main/java/org/cbioportal/model/CNA.java b/src/main/java/org/cbioportal/legacy/model/CNA.java similarity index 95% rename from src/main/java/org/cbioportal/model/CNA.java rename to src/main/java/org/cbioportal/legacy/model/CNA.java index 1840eb7e6f5..3513cec79c5 100644 --- a/src/main/java/org/cbioportal/model/CNA.java +++ b/src/main/java/org/cbioportal/legacy/model/CNA.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.util.HashMap; import java.util.Map; diff --git a/src/main/java/org/cbioportal/model/CancerStudy.java b/src/main/java/org/cbioportal/legacy/model/CancerStudy.java similarity index 99% rename from src/main/java/org/cbioportal/model/CancerStudy.java rename to src/main/java/org/cbioportal/legacy/model/CancerStudy.java index 8504a8bd55a..8d12850c09f 100644 --- a/src/main/java/org/cbioportal/model/CancerStudy.java +++ b/src/main/java/org/cbioportal/legacy/model/CancerStudy.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Date; diff --git a/src/main/java/org/cbioportal/model/CancerStudyTags.java b/src/main/java/org/cbioportal/legacy/model/CancerStudyTags.java similarity index 94% rename from src/main/java/org/cbioportal/model/CancerStudyTags.java rename to src/main/java/org/cbioportal/legacy/model/CancerStudyTags.java index 48f987036c0..ffe0354c932 100644 --- a/src/main/java/org/cbioportal/model/CancerStudyTags.java +++ b/src/main/java/org/cbioportal/legacy/model/CancerStudyTags.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/CaseListDataCount.java b/src/main/java/org/cbioportal/legacy/model/CaseListDataCount.java similarity index 94% rename from src/main/java/org/cbioportal/model/CaseListDataCount.java rename to src/main/java/org/cbioportal/legacy/model/CaseListDataCount.java index 218a83ffd3c..68842379d4c 100644 --- a/src/main/java/org/cbioportal/model/CaseListDataCount.java +++ b/src/main/java/org/cbioportal/legacy/model/CaseListDataCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalAttribute.java b/src/main/java/org/cbioportal/legacy/model/ClinicalAttribute.java similarity index 98% rename from src/main/java/org/cbioportal/model/ClinicalAttribute.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalAttribute.java index ef1d10e9026..db97f3dca48 100644 --- a/src/main/java/org/cbioportal/model/ClinicalAttribute.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalAttribute.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/ClinicalAttributeCount.java b/src/main/java/org/cbioportal/legacy/model/ClinicalAttributeCount.java similarity index 91% rename from src/main/java/org/cbioportal/model/ClinicalAttributeCount.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalAttributeCount.java index 440654eb68f..8828273a0de 100644 --- a/src/main/java/org/cbioportal/model/ClinicalAttributeCount.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalAttributeCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalData.java b/src/main/java/org/cbioportal/legacy/model/ClinicalData.java similarity index 97% rename from src/main/java/org/cbioportal/model/ClinicalData.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalData.java index 3943de6044f..1a2be4a7e68 100644 --- a/src/main/java/org/cbioportal/model/ClinicalData.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/ClinicalDataBin.java b/src/main/java/org/cbioportal/legacy/model/ClinicalDataBin.java similarity index 89% rename from src/main/java/org/cbioportal/model/ClinicalDataBin.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalDataBin.java index 86be0ae127c..7ed24fff9df 100644 --- a/src/main/java/org/cbioportal/model/ClinicalDataBin.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalDataBin.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalDataCount.java b/src/main/java/org/cbioportal/legacy/model/ClinicalDataCount.java similarity index 93% rename from src/main/java/org/cbioportal/model/ClinicalDataCount.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalDataCount.java index c16e98ba08c..594b59a6fbd 100644 --- a/src/main/java/org/cbioportal/model/ClinicalDataCount.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalDataCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalDataCountItem.java b/src/main/java/org/cbioportal/legacy/model/ClinicalDataCountItem.java similarity index 93% rename from src/main/java/org/cbioportal/model/ClinicalDataCountItem.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalDataCountItem.java index aaf56ec10ba..cfb068b976d 100644 --- a/src/main/java/org/cbioportal/model/ClinicalDataCountItem.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalDataCountItem.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/ClinicalDataEnrichment.java b/src/main/java/org/cbioportal/legacy/model/ClinicalDataEnrichment.java similarity index 96% rename from src/main/java/org/cbioportal/model/ClinicalDataEnrichment.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalDataEnrichment.java index 10c13ac2242..9cd83c65e9b 100644 --- a/src/main/java/org/cbioportal/model/ClinicalDataEnrichment.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalDataEnrichment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/ClinicalEvent.java b/src/main/java/org/cbioportal/legacy/model/ClinicalEvent.java similarity index 98% rename from src/main/java/org/cbioportal/model/ClinicalEvent.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalEvent.java index c98a7ea95f0..91ec86ff4c4 100644 --- a/src/main/java/org/cbioportal/model/ClinicalEvent.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalEvent.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/ClinicalEventData.java b/src/main/java/org/cbioportal/legacy/model/ClinicalEventData.java similarity index 95% rename from src/main/java/org/cbioportal/model/ClinicalEventData.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalEventData.java index 6430954af39..01408270785 100644 --- a/src/main/java/org/cbioportal/model/ClinicalEventData.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalEventData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/ClinicalEventKeyCode.java b/src/main/java/org/cbioportal/legacy/model/ClinicalEventKeyCode.java similarity index 95% rename from src/main/java/org/cbioportal/model/ClinicalEventKeyCode.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalEventKeyCode.java index 3808f8aed10..bc57dc416ce 100644 --- a/src/main/java/org/cbioportal/model/ClinicalEventKeyCode.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalEventKeyCode.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; /** * Clinical event data objects are key value pairs. diff --git a/src/main/java/org/cbioportal/model/ClinicalEventSample.java b/src/main/java/org/cbioportal/legacy/model/ClinicalEventSample.java similarity index 97% rename from src/main/java/org/cbioportal/model/ClinicalEventSample.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalEventSample.java index 75d53fc84f7..10e62881b07 100644 --- a/src/main/java/org/cbioportal/model/ClinicalEventSample.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalEventSample.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.util.Objects; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalEventTypeCount.java b/src/main/java/org/cbioportal/legacy/model/ClinicalEventTypeCount.java similarity index 94% rename from src/main/java/org/cbioportal/model/ClinicalEventTypeCount.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalEventTypeCount.java index 95d1e129fb5..00eba0a728b 100644 --- a/src/main/java/org/cbioportal/model/ClinicalEventTypeCount.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalEventTypeCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotBoxData.java b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotBoxData.java similarity index 97% rename from src/main/java/org/cbioportal/model/ClinicalViolinPlotBoxData.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotBoxData.java index c2e24d4d4e2..dabe4eeec5a 100644 --- a/src/main/java/org/cbioportal/model/ClinicalViolinPlotBoxData.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotBoxData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotData.java b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotData.java similarity index 96% rename from src/main/java/org/cbioportal/model/ClinicalViolinPlotData.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotData.java index 452cabf0bcd..21371353f2d 100644 --- a/src/main/java/org/cbioportal/model/ClinicalViolinPlotData.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotIndividualPoint.java b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotIndividualPoint.java similarity index 95% rename from src/main/java/org/cbioportal/model/ClinicalViolinPlotIndividualPoint.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotIndividualPoint.java index 7cff49930b0..3bfd0dd91ff 100644 --- a/src/main/java/org/cbioportal/model/ClinicalViolinPlotIndividualPoint.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotIndividualPoint.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotRowData.java b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotRowData.java similarity index 97% rename from src/main/java/org/cbioportal/model/ClinicalViolinPlotRowData.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotRowData.java index 3a2ef647e35..5675e10d598 100644 --- a/src/main/java/org/cbioportal/model/ClinicalViolinPlotRowData.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotRowData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/CoExpression.java b/src/main/java/org/cbioportal/legacy/model/CoExpression.java similarity index 97% rename from src/main/java/org/cbioportal/model/CoExpression.java rename to src/main/java/org/cbioportal/legacy/model/CoExpression.java index 22fdec80784..88ab187e1f8 100644 --- a/src/main/java/org/cbioportal/model/CoExpression.java +++ b/src/main/java/org/cbioportal/legacy/model/CoExpression.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/CopyNumberCount.java b/src/main/java/org/cbioportal/legacy/model/CopyNumberCount.java similarity index 97% rename from src/main/java/org/cbioportal/model/CopyNumberCount.java rename to src/main/java/org/cbioportal/legacy/model/CopyNumberCount.java index 3748da9228c..2d2f8a89159 100644 --- a/src/main/java/org/cbioportal/model/CopyNumberCount.java +++ b/src/main/java/org/cbioportal/legacy/model/CopyNumberCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/CopyNumberCountByGene.java b/src/main/java/org/cbioportal/legacy/model/CopyNumberCountByGene.java similarity index 94% rename from src/main/java/org/cbioportal/model/CopyNumberCountByGene.java rename to src/main/java/org/cbioportal/legacy/model/CopyNumberCountByGene.java index ef1143066e7..f60447d6740 100644 --- a/src/main/java/org/cbioportal/model/CopyNumberCountByGene.java +++ b/src/main/java/org/cbioportal/legacy/model/CopyNumberCountByGene.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/CopyNumberSeg.java b/src/main/java/org/cbioportal/legacy/model/CopyNumberSeg.java similarity index 98% rename from src/main/java/org/cbioportal/model/CopyNumberSeg.java rename to src/main/java/org/cbioportal/legacy/model/CopyNumberSeg.java index ea304052666..aca3ff34415 100644 --- a/src/main/java/org/cbioportal/model/CopyNumberSeg.java +++ b/src/main/java/org/cbioportal/legacy/model/CopyNumberSeg.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.math.BigDecimal; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/CosmicMutation.java b/src/main/java/org/cbioportal/legacy/model/CosmicMutation.java similarity index 96% rename from src/main/java/org/cbioportal/model/CosmicMutation.java rename to src/main/java/org/cbioportal/legacy/model/CosmicMutation.java index 2656205c146..4ba6bafd089 100644 --- a/src/main/java/org/cbioportal/model/CosmicMutation.java +++ b/src/main/java/org/cbioportal/legacy/model/CosmicMutation.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/CountSummary.java b/src/main/java/org/cbioportal/legacy/model/CountSummary.java similarity index 95% rename from src/main/java/org/cbioportal/model/CountSummary.java rename to src/main/java/org/cbioportal/legacy/model/CountSummary.java index 3466117a2ba..119d36694c0 100644 --- a/src/main/java/org/cbioportal/model/CountSummary.java +++ b/src/main/java/org/cbioportal/legacy/model/CountSummary.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/CustomDriverAnnotationReport.java b/src/main/java/org/cbioportal/legacy/model/CustomDriverAnnotationReport.java similarity index 93% rename from src/main/java/org/cbioportal/model/CustomDriverAnnotationReport.java rename to src/main/java/org/cbioportal/legacy/model/CustomDriverAnnotationReport.java index e86668f82e3..507a19ba410 100644 --- a/src/main/java/org/cbioportal/model/CustomDriverAnnotationReport.java +++ b/src/main/java/org/cbioportal/legacy/model/CustomDriverAnnotationReport.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Set; diff --git a/src/main/java/org/cbioportal/model/DataAccessToken.java b/src/main/java/org/cbioportal/legacy/model/DataAccessToken.java similarity index 98% rename from src/main/java/org/cbioportal/model/DataAccessToken.java rename to src/main/java/org/cbioportal/legacy/model/DataAccessToken.java index 0895475428d..e0223d4a573 100644 --- a/src/main/java/org/cbioportal/model/DataAccessToken.java +++ b/src/main/java/org/cbioportal/legacy/model/DataAccessToken.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Date; diff --git a/src/main/java/org/cbioportal/model/DataBin.java b/src/main/java/org/cbioportal/legacy/model/DataBin.java similarity index 95% rename from src/main/java/org/cbioportal/model/DataBin.java rename to src/main/java/org/cbioportal/legacy/model/DataBin.java index f39c57704da..7158d4d6079 100644 --- a/src/main/java/org/cbioportal/model/DataBin.java +++ b/src/main/java/org/cbioportal/legacy/model/DataBin.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/DensityPlotBin.java b/src/main/java/org/cbioportal/legacy/model/DensityPlotBin.java similarity index 97% rename from src/main/java/org/cbioportal/model/DensityPlotBin.java rename to src/main/java/org/cbioportal/legacy/model/DensityPlotBin.java index 6bff6384fbe..4cfebeefd43 100644 --- a/src/main/java/org/cbioportal/model/DensityPlotBin.java +++ b/src/main/java/org/cbioportal/legacy/model/DensityPlotBin.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/DensityPlotData.java b/src/main/java/org/cbioportal/legacy/model/DensityPlotData.java similarity index 95% rename from src/main/java/org/cbioportal/model/DensityPlotData.java rename to src/main/java/org/cbioportal/legacy/model/DensityPlotData.java index 06adc10bca5..ba24806ce15 100644 --- a/src/main/java/org/cbioportal/model/DensityPlotData.java +++ b/src/main/java/org/cbioportal/legacy/model/DensityPlotData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/DiscreteCopyNumberData.java b/src/main/java/org/cbioportal/legacy/model/DiscreteCopyNumberData.java similarity index 95% rename from src/main/java/org/cbioportal/model/DiscreteCopyNumberData.java rename to src/main/java/org/cbioportal/legacy/model/DiscreteCopyNumberData.java index 11c20fe6068..419a59cd4c8 100644 --- a/src/main/java/org/cbioportal/model/DiscreteCopyNumberData.java +++ b/src/main/java/org/cbioportal/legacy/model/DiscreteCopyNumberData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import com.fasterxml.jackson.annotation.JsonRawValue; diff --git a/src/main/java/org/cbioportal/model/EnrichmentType.java b/src/main/java/org/cbioportal/legacy/model/EnrichmentType.java similarity index 60% rename from src/main/java/org/cbioportal/model/EnrichmentType.java rename to src/main/java/org/cbioportal/legacy/model/EnrichmentType.java index af13ab2020e..833d881c30b 100644 --- a/src/main/java/org/cbioportal/model/EnrichmentType.java +++ b/src/main/java/org/cbioportal/legacy/model/EnrichmentType.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum EnrichmentType { SAMPLE, diff --git a/src/main/java/org/cbioportal/model/EntityType.java b/src/main/java/org/cbioportal/legacy/model/EntityType.java similarity index 70% rename from src/main/java/org/cbioportal/model/EntityType.java rename to src/main/java/org/cbioportal/legacy/model/EntityType.java index 507b9b6d090..94070bfe1ba 100644 --- a/src/main/java/org/cbioportal/model/EntityType.java +++ b/src/main/java/org/cbioportal/legacy/model/EntityType.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum EntityType { GENE, diff --git a/src/main/java/org/cbioportal/model/ExpressionEnrichment.java b/src/main/java/org/cbioportal/legacy/model/ExpressionEnrichment.java similarity index 95% rename from src/main/java/org/cbioportal/model/ExpressionEnrichment.java rename to src/main/java/org/cbioportal/legacy/model/ExpressionEnrichment.java index c6c562c4b64..fd1b5e35162 100644 --- a/src/main/java/org/cbioportal/model/ExpressionEnrichment.java +++ b/src/main/java/org/cbioportal/legacy/model/ExpressionEnrichment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/FractionGenomeAltered.java b/src/main/java/org/cbioportal/legacy/model/FractionGenomeAltered.java similarity index 96% rename from src/main/java/org/cbioportal/model/FractionGenomeAltered.java rename to src/main/java/org/cbioportal/legacy/model/FractionGenomeAltered.java index f9e3d67fcdb..2020536cfd8 100644 --- a/src/main/java/org/cbioportal/model/FractionGenomeAltered.java +++ b/src/main/java/org/cbioportal/legacy/model/FractionGenomeAltered.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.math.BigDecimal; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/Gene.java b/src/main/java/org/cbioportal/legacy/model/Gene.java similarity index 96% rename from src/main/java/org/cbioportal/model/Gene.java rename to src/main/java/org/cbioportal/legacy/model/Gene.java index a2325da6856..ef58277d17b 100644 --- a/src/main/java/org/cbioportal/model/Gene.java +++ b/src/main/java/org/cbioportal/legacy/model/Gene.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/GeneAlias.java b/src/main/java/org/cbioportal/legacy/model/GeneAlias.java similarity index 92% rename from src/main/java/org/cbioportal/model/GeneAlias.java rename to src/main/java/org/cbioportal/legacy/model/GeneAlias.java index 664a73cb831..15f7e00ef43 100644 --- a/src/main/java/org/cbioportal/model/GeneAlias.java +++ b/src/main/java/org/cbioportal/legacy/model/GeneAlias.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GeneFilter.java b/src/main/java/org/cbioportal/legacy/model/GeneFilter.java similarity index 94% rename from src/main/java/org/cbioportal/model/GeneFilter.java rename to src/main/java/org/cbioportal/legacy/model/GeneFilter.java index ae6f62890dc..9f1d2105440 100644 --- a/src/main/java/org/cbioportal/model/GeneFilter.java +++ b/src/main/java/org/cbioportal/legacy/model/GeneFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/GeneFilterQuery.java b/src/main/java/org/cbioportal/legacy/model/GeneFilterQuery.java similarity index 95% rename from src/main/java/org/cbioportal/model/GeneFilterQuery.java rename to src/main/java/org/cbioportal/legacy/model/GeneFilterQuery.java index e8280b4ce27..1035c91cbca 100644 --- a/src/main/java/org/cbioportal/model/GeneFilterQuery.java +++ b/src/main/java/org/cbioportal/legacy/model/GeneFilterQuery.java @@ -1,6 +1,6 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; -import org.cbioportal.model.util.Select; +import org.cbioportal.legacy.model.util.Select; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/GeneMolecularAlteration.java b/src/main/java/org/cbioportal/legacy/model/GeneMolecularAlteration.java similarity index 95% rename from src/main/java/org/cbioportal/model/GeneMolecularAlteration.java rename to src/main/java/org/cbioportal/legacy/model/GeneMolecularAlteration.java index 05938ed539c..427f382ffce 100644 --- a/src/main/java/org/cbioportal/model/GeneMolecularAlteration.java +++ b/src/main/java/org/cbioportal/legacy/model/GeneMolecularAlteration.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GeneMolecularData.java b/src/main/java/org/cbioportal/legacy/model/GeneMolecularData.java similarity index 94% rename from src/main/java/org/cbioportal/model/GeneMolecularData.java rename to src/main/java/org/cbioportal/legacy/model/GeneMolecularData.java index 6ce9e1cef68..a634b7aa69c 100644 --- a/src/main/java/org/cbioportal/model/GeneMolecularData.java +++ b/src/main/java/org/cbioportal/legacy/model/GeneMolecularData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/GenePanel.java b/src/main/java/org/cbioportal/legacy/model/GenePanel.java similarity index 96% rename from src/main/java/org/cbioportal/model/GenePanel.java rename to src/main/java/org/cbioportal/legacy/model/GenePanel.java index 6c47f89016d..ec8e62d93e5 100644 --- a/src/main/java/org/cbioportal/model/GenePanel.java +++ b/src/main/java/org/cbioportal/legacy/model/GenePanel.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/GenePanelData.java b/src/main/java/org/cbioportal/legacy/model/GenePanelData.java similarity index 97% rename from src/main/java/org/cbioportal/model/GenePanelData.java rename to src/main/java/org/cbioportal/legacy/model/GenePanelData.java index ac1bfbf78b4..30892b83e79 100644 --- a/src/main/java/org/cbioportal/model/GenePanelData.java +++ b/src/main/java/org/cbioportal/legacy/model/GenePanelData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/GenePanelToGene.java b/src/main/java/org/cbioportal/legacy/model/GenePanelToGene.java similarity index 95% rename from src/main/java/org/cbioportal/model/GenePanelToGene.java rename to src/main/java/org/cbioportal/legacy/model/GenePanelToGene.java index b09698966f3..b4a787f8931 100644 --- a/src/main/java/org/cbioportal/model/GenePanelToGene.java +++ b/src/main/java/org/cbioportal/legacy/model/GenePanelToGene.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/GenericAssayAdditionalProperty.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayAdditionalProperty.java similarity index 95% rename from src/main/java/org/cbioportal/model/GenericAssayAdditionalProperty.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayAdditionalProperty.java index 8fab77071aa..ab4e6277c8b 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayAdditionalProperty.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayAdditionalProperty.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenericAssayBinaryEnrichment.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayBinaryEnrichment.java similarity index 92% rename from src/main/java/org/cbioportal/model/GenericAssayBinaryEnrichment.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayBinaryEnrichment.java index 24e84145227..9bf443593cf 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayBinaryEnrichment.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayBinaryEnrichment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/GenericAssayCategoricalEnrichment.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayCategoricalEnrichment.java similarity index 92% rename from src/main/java/org/cbioportal/model/GenericAssayCategoricalEnrichment.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayCategoricalEnrichment.java index afc72993136..0159bed7927 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayCategoricalEnrichment.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayCategoricalEnrichment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import com.fasterxml.jackson.annotation.JsonProperty; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/GenericAssayCountSummary.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayCountSummary.java similarity index 95% rename from src/main/java/org/cbioportal/model/GenericAssayCountSummary.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayCountSummary.java index 49edb224e4a..2356b38cd6a 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayCountSummary.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayCountSummary.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenericAssayData.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayData.java similarity index 94% rename from src/main/java/org/cbioportal/model/GenericAssayData.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayData.java index 3fd08f55e77..150e1d00644 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayData.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/GenericAssayDataBin.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayDataBin.java similarity index 93% rename from src/main/java/org/cbioportal/model/GenericAssayDataBin.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayDataBin.java index 62b44070388..22fc03d4717 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayDataBin.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayDataBin.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenericAssayDataCount.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayDataCount.java similarity index 94% rename from src/main/java/org/cbioportal/model/GenericAssayDataCount.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayDataCount.java index 62c14562fca..fb3d15640ce 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayDataCount.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayDataCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenericAssayDataCountItem.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayDataCountItem.java similarity index 95% rename from src/main/java/org/cbioportal/model/GenericAssayDataCountItem.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayDataCountItem.java index c272b617f87..da6c4a2260b 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayDataCountItem.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayDataCountItem.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/GenericAssayEnrichment.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayEnrichment.java similarity index 97% rename from src/main/java/org/cbioportal/model/GenericAssayEnrichment.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayEnrichment.java index 9116783494a..79256bde774 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayEnrichment.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayEnrichment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/GenericAssayMolecularAlteration.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayMolecularAlteration.java similarity index 96% rename from src/main/java/org/cbioportal/model/GenericAssayMolecularAlteration.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayMolecularAlteration.java index 24ddbcd09bb..1c06f7961ff 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayMolecularAlteration.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayMolecularAlteration.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenericEntityProperty.java b/src/main/java/org/cbioportal/legacy/model/GenericEntityProperty.java similarity index 95% rename from src/main/java/org/cbioportal/model/GenericEntityProperty.java rename to src/main/java/org/cbioportal/legacy/model/GenericEntityProperty.java index da2fbac1631..3d10afa784d 100644 --- a/src/main/java/org/cbioportal/model/GenericEntityProperty.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericEntityProperty.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/Geneset.java b/src/main/java/org/cbioportal/legacy/model/Geneset.java similarity index 97% rename from src/main/java/org/cbioportal/model/Geneset.java rename to src/main/java/org/cbioportal/legacy/model/Geneset.java index 5fc022ae804..1a564ba88a0 100644 --- a/src/main/java/org/cbioportal/model/Geneset.java +++ b/src/main/java/org/cbioportal/legacy/model/Geneset.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenesetCorrelation.java b/src/main/java/org/cbioportal/legacy/model/GenesetCorrelation.java similarity index 97% rename from src/main/java/org/cbioportal/model/GenesetCorrelation.java rename to src/main/java/org/cbioportal/legacy/model/GenesetCorrelation.java index 6bfe13ba346..8bb672d7ed7 100644 --- a/src/main/java/org/cbioportal/model/GenesetCorrelation.java +++ b/src/main/java/org/cbioportal/legacy/model/GenesetCorrelation.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenesetHierarchyInfo.java b/src/main/java/org/cbioportal/legacy/model/GenesetHierarchyInfo.java similarity index 96% rename from src/main/java/org/cbioportal/model/GenesetHierarchyInfo.java rename to src/main/java/org/cbioportal/legacy/model/GenesetHierarchyInfo.java index dac02f3d454..1567d55378a 100644 --- a/src/main/java/org/cbioportal/model/GenesetHierarchyInfo.java +++ b/src/main/java/org/cbioportal/legacy/model/GenesetHierarchyInfo.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/GenesetMolecularAlteration.java b/src/main/java/org/cbioportal/legacy/model/GenesetMolecularAlteration.java similarity index 94% rename from src/main/java/org/cbioportal/model/GenesetMolecularAlteration.java rename to src/main/java/org/cbioportal/legacy/model/GenesetMolecularAlteration.java index e4720949596..938f84dfd6f 100644 --- a/src/main/java/org/cbioportal/model/GenesetMolecularAlteration.java +++ b/src/main/java/org/cbioportal/legacy/model/GenesetMolecularAlteration.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenesetMolecularData.java b/src/main/java/org/cbioportal/legacy/model/GenesetMolecularData.java similarity index 93% rename from src/main/java/org/cbioportal/model/GenesetMolecularData.java rename to src/main/java/org/cbioportal/legacy/model/GenesetMolecularData.java index 16fb8b7161a..25e28a3dd87 100644 --- a/src/main/java/org/cbioportal/model/GenesetMolecularData.java +++ b/src/main/java/org/cbioportal/legacy/model/GenesetMolecularData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GeneticEntity.java b/src/main/java/org/cbioportal/legacy/model/GeneticEntity.java similarity index 97% rename from src/main/java/org/cbioportal/model/GeneticEntity.java rename to src/main/java/org/cbioportal/legacy/model/GeneticEntity.java index f6bf9335db7..97c25b8d990 100644 --- a/src/main/java/org/cbioportal/model/GeneticEntity.java +++ b/src/main/java/org/cbioportal/legacy/model/GeneticEntity.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenomicDataBin.java b/src/main/java/org/cbioportal/legacy/model/GenomicDataBin.java similarity index 93% rename from src/main/java/org/cbioportal/model/GenomicDataBin.java rename to src/main/java/org/cbioportal/legacy/model/GenomicDataBin.java index f177bd8c35c..6df471cc2f9 100644 --- a/src/main/java/org/cbioportal/model/GenomicDataBin.java +++ b/src/main/java/org/cbioportal/legacy/model/GenomicDataBin.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenomicDataCount.java b/src/main/java/org/cbioportal/legacy/model/GenomicDataCount.java similarity index 97% rename from src/main/java/org/cbioportal/model/GenomicDataCount.java rename to src/main/java/org/cbioportal/legacy/model/GenomicDataCount.java index f86fda5bc8f..b8f10bb056c 100644 --- a/src/main/java/org/cbioportal/model/GenomicDataCount.java +++ b/src/main/java/org/cbioportal/legacy/model/GenomicDataCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Objects; diff --git a/src/main/java/org/cbioportal/model/GenomicDataCountItem.java b/src/main/java/org/cbioportal/legacy/model/GenomicDataCountItem.java similarity index 96% rename from src/main/java/org/cbioportal/model/GenomicDataCountItem.java rename to src/main/java/org/cbioportal/legacy/model/GenomicDataCountItem.java index a2123a9386c..dd546a6f7b4 100644 --- a/src/main/java/org/cbioportal/model/GenomicDataCountItem.java +++ b/src/main/java/org/cbioportal/legacy/model/GenomicDataCountItem.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/GenomicEnrichment.java b/src/main/java/org/cbioportal/legacy/model/GenomicEnrichment.java similarity index 95% rename from src/main/java/org/cbioportal/model/GenomicEnrichment.java rename to src/main/java/org/cbioportal/legacy/model/GenomicEnrichment.java index a4442cf1cf1..a7c8f999b60 100644 --- a/src/main/java/org/cbioportal/model/GenomicEnrichment.java +++ b/src/main/java/org/cbioportal/legacy/model/GenomicEnrichment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/Gistic.java b/src/main/java/org/cbioportal/legacy/model/Gistic.java similarity index 98% rename from src/main/java/org/cbioportal/model/Gistic.java rename to src/main/java/org/cbioportal/legacy/model/Gistic.java index 66a8646e2d3..0acc1368137 100644 --- a/src/main/java/org/cbioportal/model/Gistic.java +++ b/src/main/java/org/cbioportal/legacy/model/Gistic.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/GisticToGene.java b/src/main/java/org/cbioportal/legacy/model/GisticToGene.java similarity index 95% rename from src/main/java/org/cbioportal/model/GisticToGene.java rename to src/main/java/org/cbioportal/legacy/model/GisticToGene.java index 49593eedaf9..2ade673dd21 100644 --- a/src/main/java/org/cbioportal/model/GisticToGene.java +++ b/src/main/java/org/cbioportal/legacy/model/GisticToGene.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/GroupStatistics.java b/src/main/java/org/cbioportal/legacy/model/GroupStatistics.java similarity index 95% rename from src/main/java/org/cbioportal/model/GroupStatistics.java rename to src/main/java/org/cbioportal/legacy/model/GroupStatistics.java index df0950caf02..98b862d3dba 100644 --- a/src/main/java/org/cbioportal/model/GroupStatistics.java +++ b/src/main/java/org/cbioportal/legacy/model/GroupStatistics.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/Info.java b/src/main/java/org/cbioportal/legacy/model/Info.java similarity index 98% rename from src/main/java/org/cbioportal/model/Info.java rename to src/main/java/org/cbioportal/legacy/model/Info.java index beee09b26d7..443ead4e5db 100644 --- a/src/main/java/org/cbioportal/model/Info.java +++ b/src/main/java/org/cbioportal/legacy/model/Info.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/MolecularAlteration.java b/src/main/java/org/cbioportal/legacy/model/MolecularAlteration.java similarity index 96% rename from src/main/java/org/cbioportal/model/MolecularAlteration.java rename to src/main/java/org/cbioportal/legacy/model/MolecularAlteration.java index 0728d8aebbf..a8096d96639 100644 --- a/src/main/java/org/cbioportal/model/MolecularAlteration.java +++ b/src/main/java/org/cbioportal/legacy/model/MolecularAlteration.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/MolecularData.java b/src/main/java/org/cbioportal/legacy/model/MolecularData.java similarity index 96% rename from src/main/java/org/cbioportal/model/MolecularData.java rename to src/main/java/org/cbioportal/legacy/model/MolecularData.java index 260f20d9e34..c9906b84983 100644 --- a/src/main/java/org/cbioportal/model/MolecularData.java +++ b/src/main/java/org/cbioportal/legacy/model/MolecularData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/MolecularProfile.java b/src/main/java/org/cbioportal/legacy/model/MolecularProfile.java similarity index 99% rename from src/main/java/org/cbioportal/model/MolecularProfile.java rename to src/main/java/org/cbioportal/legacy/model/MolecularProfile.java index da172984a56..ace865909d9 100644 --- a/src/main/java/org/cbioportal/model/MolecularProfile.java +++ b/src/main/java/org/cbioportal/legacy/model/MolecularProfile.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/MolecularProfileCaseIdentifier.java b/src/main/java/org/cbioportal/legacy/model/MolecularProfileCaseIdentifier.java similarity index 98% rename from src/main/java/org/cbioportal/model/MolecularProfileCaseIdentifier.java rename to src/main/java/org/cbioportal/legacy/model/MolecularProfileCaseIdentifier.java index 743fee3cb0d..ebced8cc65d 100644 --- a/src/main/java/org/cbioportal/model/MolecularProfileCaseIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/model/MolecularProfileCaseIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/MolecularProfileSamples.java b/src/main/java/org/cbioportal/legacy/model/MolecularProfileSamples.java similarity index 97% rename from src/main/java/org/cbioportal/model/MolecularProfileSamples.java rename to src/main/java/org/cbioportal/legacy/model/MolecularProfileSamples.java index ee3b23b5c3c..1c020eb0d0f 100644 --- a/src/main/java/org/cbioportal/model/MolecularProfileSamples.java +++ b/src/main/java/org/cbioportal/legacy/model/MolecularProfileSamples.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/MrnaPercentile.java b/src/main/java/org/cbioportal/legacy/model/MrnaPercentile.java similarity index 97% rename from src/main/java/org/cbioportal/model/MrnaPercentile.java rename to src/main/java/org/cbioportal/legacy/model/MrnaPercentile.java index 278e65eb61b..9b100b308e2 100644 --- a/src/main/java/org/cbioportal/model/MrnaPercentile.java +++ b/src/main/java/org/cbioportal/legacy/model/MrnaPercentile.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/MutSig.java b/src/main/java/org/cbioportal/legacy/model/MutSig.java similarity index 98% rename from src/main/java/org/cbioportal/model/MutSig.java rename to src/main/java/org/cbioportal/legacy/model/MutSig.java index 1d60c06e801..cd52a34aaa1 100644 --- a/src/main/java/org/cbioportal/model/MutSig.java +++ b/src/main/java/org/cbioportal/legacy/model/MutSig.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/Mutation.java b/src/main/java/org/cbioportal/legacy/model/Mutation.java similarity index 99% rename from src/main/java/org/cbioportal/model/Mutation.java rename to src/main/java/org/cbioportal/legacy/model/Mutation.java index 3ddae915587..c0026638504 100644 --- a/src/main/java/org/cbioportal/model/Mutation.java +++ b/src/main/java/org/cbioportal/legacy/model/Mutation.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import com.fasterxml.jackson.annotation.JsonRawValue; import io.swagger.v3.oas.annotations.media.Schema; diff --git a/src/main/java/org/cbioportal/model/MutationCountByGene.java b/src/main/java/org/cbioportal/legacy/model/MutationCountByGene.java similarity index 77% rename from src/main/java/org/cbioportal/model/MutationCountByGene.java rename to src/main/java/org/cbioportal/legacy/model/MutationCountByGene.java index 0f949838fc1..d9ae4ee30e1 100644 --- a/src/main/java/org/cbioportal/model/MutationCountByGene.java +++ b/src/main/java/org/cbioportal/legacy/model/MutationCountByGene.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/MutationCountByPosition.java b/src/main/java/org/cbioportal/legacy/model/MutationCountByPosition.java similarity index 96% rename from src/main/java/org/cbioportal/model/MutationCountByPosition.java rename to src/main/java/org/cbioportal/legacy/model/MutationCountByPosition.java index f92b2fb1d17..dae52601468 100644 --- a/src/main/java/org/cbioportal/model/MutationCountByPosition.java +++ b/src/main/java/org/cbioportal/legacy/model/MutationCountByPosition.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/MutationEventType.java b/src/main/java/org/cbioportal/legacy/model/MutationEventType.java similarity index 98% rename from src/main/java/org/cbioportal/model/MutationEventType.java rename to src/main/java/org/cbioportal/legacy/model/MutationEventType.java index e1957f20e71..507d2bba2ba 100644 --- a/src/main/java/org/cbioportal/model/MutationEventType.java +++ b/src/main/java/org/cbioportal/legacy/model/MutationEventType.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum MutationEventType { diff --git a/src/main/java/org/cbioportal/model/MutationFilterOption.java b/src/main/java/org/cbioportal/legacy/model/MutationFilterOption.java similarity index 92% rename from src/main/java/org/cbioportal/model/MutationFilterOption.java rename to src/main/java/org/cbioportal/legacy/model/MutationFilterOption.java index fd83da4f051..c846da87fd8 100644 --- a/src/main/java/org/cbioportal/model/MutationFilterOption.java +++ b/src/main/java/org/cbioportal/legacy/model/MutationFilterOption.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum MutationFilterOption { MUTATED("Mutated"), // Samples that have mutations diff --git a/src/main/java/org/cbioportal/model/MutationSpectrum.java b/src/main/java/org/cbioportal/legacy/model/MutationSpectrum.java similarity index 98% rename from src/main/java/org/cbioportal/model/MutationSpectrum.java rename to src/main/java/org/cbioportal/legacy/model/MutationSpectrum.java index f130728b86d..277f9c61e9f 100644 --- a/src/main/java/org/cbioportal/model/MutationSpectrum.java +++ b/src/main/java/org/cbioportal/legacy/model/MutationSpectrum.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/NumericGeneMolecularData.java b/src/main/java/org/cbioportal/legacy/model/NumericGeneMolecularData.java similarity index 97% rename from src/main/java/org/cbioportal/model/NumericGeneMolecularData.java rename to src/main/java/org/cbioportal/legacy/model/NumericGeneMolecularData.java index 3e519807477..71e08c4a6a6 100644 --- a/src/main/java/org/cbioportal/model/NumericGeneMolecularData.java +++ b/src/main/java/org/cbioportal/legacy/model/NumericGeneMolecularData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/Patient.java b/src/main/java/org/cbioportal/legacy/model/Patient.java similarity index 97% rename from src/main/java/org/cbioportal/model/Patient.java rename to src/main/java/org/cbioportal/legacy/model/Patient.java index 4d2a2f1d9a6..18f906fd275 100644 --- a/src/main/java/org/cbioportal/model/Patient.java +++ b/src/main/java/org/cbioportal/legacy/model/Patient.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/PatientTreatment.java b/src/main/java/org/cbioportal/legacy/model/PatientTreatment.java similarity index 77% rename from src/main/java/org/cbioportal/model/PatientTreatment.java rename to src/main/java/org/cbioportal/legacy/model/PatientTreatment.java index c838d23777e..73393494319 100644 --- a/src/main/java/org/cbioportal/model/PatientTreatment.java +++ b/src/main/java/org/cbioportal/legacy/model/PatientTreatment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/PatientTreatmentReport.java b/src/main/java/org/cbioportal/legacy/model/PatientTreatmentReport.java similarity index 91% rename from src/main/java/org/cbioportal/model/PatientTreatmentReport.java rename to src/main/java/org/cbioportal/legacy/model/PatientTreatmentReport.java index d09a2276f06..240f0b44189 100644 --- a/src/main/java/org/cbioportal/model/PatientTreatmentReport.java +++ b/src/main/java/org/cbioportal/legacy/model/PatientTreatmentReport.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Collections; diff --git a/src/main/java/org/cbioportal/model/PatientTreatmentRow.java b/src/main/java/org/cbioportal/legacy/model/PatientTreatmentRow.java similarity index 97% rename from src/main/java/org/cbioportal/model/PatientTreatmentRow.java rename to src/main/java/org/cbioportal/legacy/model/PatientTreatmentRow.java index 6fc5f75395e..0e0f28dd8ea 100644 --- a/src/main/java/org/cbioportal/model/PatientTreatmentRow.java +++ b/src/main/java/org/cbioportal/legacy/model/PatientTreatmentRow.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Objects; diff --git a/src/main/java/org/cbioportal/model/QueryElement.java b/src/main/java/org/cbioportal/legacy/model/QueryElement.java similarity index 91% rename from src/main/java/org/cbioportal/model/QueryElement.java rename to src/main/java/org/cbioportal/legacy/model/QueryElement.java index 0112edbdc44..7132d8db007 100644 --- a/src/main/java/org/cbioportal/model/QueryElement.java +++ b/src/main/java/org/cbioportal/legacy/model/QueryElement.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; /* QueryElement represents three types of behavior for a SQL statement in MyBatis mappers diff --git a/src/main/java/org/cbioportal/model/ReadPermission.java b/src/main/java/org/cbioportal/legacy/model/ReadPermission.java similarity index 78% rename from src/main/java/org/cbioportal/model/ReadPermission.java rename to src/main/java/org/cbioportal/legacy/model/ReadPermission.java index c215b4aa648..9721a17245d 100644 --- a/src/main/java/org/cbioportal/model/ReadPermission.java +++ b/src/main/java/org/cbioportal/legacy/model/ReadPermission.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public interface ReadPermission { public void setReadPermission(Boolean permission); diff --git a/src/main/java/org/cbioportal/model/ReferenceGenome.java b/src/main/java/org/cbioportal/legacy/model/ReferenceGenome.java similarity index 99% rename from src/main/java/org/cbioportal/model/ReferenceGenome.java rename to src/main/java/org/cbioportal/legacy/model/ReferenceGenome.java index 287b17272ef..95f640228a1 100644 --- a/src/main/java/org/cbioportal/model/ReferenceGenome.java +++ b/src/main/java/org/cbioportal/legacy/model/ReferenceGenome.java @@ -15,7 +15,7 @@ * along with this program. If not, see . */ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.util.Date; diff --git a/src/main/java/org/cbioportal/model/ReferenceGenomeGene.java b/src/main/java/org/cbioportal/legacy/model/ReferenceGenomeGene.java similarity index 98% rename from src/main/java/org/cbioportal/model/ReferenceGenomeGene.java rename to src/main/java/org/cbioportal/legacy/model/ReferenceGenomeGene.java index 34ff3d82c9f..f76cb6fb26b 100644 --- a/src/main/java/org/cbioportal/model/ReferenceGenomeGene.java +++ b/src/main/java/org/cbioportal/legacy/model/ReferenceGenomeGene.java @@ -15,7 +15,7 @@ * along with this program. If not, see . */ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.net.Inet4Address; diff --git a/src/main/java/org/cbioportal/model/ResourceData.java b/src/main/java/org/cbioportal/legacy/model/ResourceData.java similarity index 97% rename from src/main/java/org/cbioportal/model/ResourceData.java rename to src/main/java/org/cbioportal/legacy/model/ResourceData.java index 243b86af47c..fdfb09812b7 100644 --- a/src/main/java/org/cbioportal/model/ResourceData.java +++ b/src/main/java/org/cbioportal/legacy/model/ResourceData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ResourceDefinition.java b/src/main/java/org/cbioportal/legacy/model/ResourceDefinition.java similarity index 97% rename from src/main/java/org/cbioportal/model/ResourceDefinition.java rename to src/main/java/org/cbioportal/legacy/model/ResourceDefinition.java index 73eacd6f287..1bffe659837 100644 --- a/src/main/java/org/cbioportal/model/ResourceDefinition.java +++ b/src/main/java/org/cbioportal/legacy/model/ResourceDefinition.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/ResourceType.java b/src/main/java/org/cbioportal/legacy/model/ResourceType.java similarity index 63% rename from src/main/java/org/cbioportal/model/ResourceType.java rename to src/main/java/org/cbioportal/legacy/model/ResourceType.java index 17a9a09df40..a2eb1d649e4 100644 --- a/src/main/java/org/cbioportal/model/ResourceType.java +++ b/src/main/java/org/cbioportal/legacy/model/ResourceType.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum ResourceType { STUDY, diff --git a/src/main/java/org/cbioportal/model/Sample.java b/src/main/java/org/cbioportal/legacy/model/Sample.java similarity index 98% rename from src/main/java/org/cbioportal/model/Sample.java rename to src/main/java/org/cbioportal/legacy/model/Sample.java index a3d72e955ce..ac8e2ba79d5 100644 --- a/src/main/java/org/cbioportal/model/Sample.java +++ b/src/main/java/org/cbioportal/legacy/model/Sample.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; import java.util.Objects; diff --git a/src/main/java/org/cbioportal/model/SampleClinicalDataCollection.java b/src/main/java/org/cbioportal/legacy/model/SampleClinicalDataCollection.java similarity index 96% rename from src/main/java/org/cbioportal/model/SampleClinicalDataCollection.java rename to src/main/java/org/cbioportal/legacy/model/SampleClinicalDataCollection.java index c67d5277e8b..00b1c4e4df9 100644 --- a/src/main/java/org/cbioportal/model/SampleClinicalDataCollection.java +++ b/src/main/java/org/cbioportal/legacy/model/SampleClinicalDataCollection.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.util.Collections; import java.util.HashMap; diff --git a/src/main/java/org/cbioportal/model/SampleList.java b/src/main/java/org/cbioportal/legacy/model/SampleList.java similarity index 98% rename from src/main/java/org/cbioportal/model/SampleList.java rename to src/main/java/org/cbioportal/legacy/model/SampleList.java index bda4d2fc681..a9de3585687 100644 --- a/src/main/java/org/cbioportal/model/SampleList.java +++ b/src/main/java/org/cbioportal/legacy/model/SampleList.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/SampleListToSampleId.java b/src/main/java/org/cbioportal/legacy/model/SampleListToSampleId.java similarity index 93% rename from src/main/java/org/cbioportal/model/SampleListToSampleId.java rename to src/main/java/org/cbioportal/legacy/model/SampleListToSampleId.java index bfbdb9f548b..a4110199bcd 100644 --- a/src/main/java/org/cbioportal/model/SampleListToSampleId.java +++ b/src/main/java/org/cbioportal/legacy/model/SampleListToSampleId.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/SampleTreatment.java b/src/main/java/org/cbioportal/legacy/model/SampleTreatment.java similarity index 71% rename from src/main/java/org/cbioportal/model/SampleTreatment.java rename to src/main/java/org/cbioportal/legacy/model/SampleTreatment.java index edf9ef7541a..5dfacd6075f 100644 --- a/src/main/java/org/cbioportal/model/SampleTreatment.java +++ b/src/main/java/org/cbioportal/legacy/model/SampleTreatment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public record SampleTreatment(String treatment, int preSampleCount, int postSampleCount) { } diff --git a/src/main/java/org/cbioportal/model/SampleTreatmentReport.java b/src/main/java/org/cbioportal/legacy/model/SampleTreatmentReport.java similarity index 78% rename from src/main/java/org/cbioportal/model/SampleTreatmentReport.java rename to src/main/java/org/cbioportal/legacy/model/SampleTreatmentReport.java index 12cf93f4fa6..60ac34247d3 100644 --- a/src/main/java/org/cbioportal/model/SampleTreatmentReport.java +++ b/src/main/java/org/cbioportal/legacy/model/SampleTreatmentReport.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.util.Collection; diff --git a/src/main/java/org/cbioportal/model/SampleTreatmentRow.java b/src/main/java/org/cbioportal/legacy/model/SampleTreatmentRow.java similarity index 98% rename from src/main/java/org/cbioportal/model/SampleTreatmentRow.java rename to src/main/java/org/cbioportal/legacy/model/SampleTreatmentRow.java index ff3c56693c9..0feef887361 100644 --- a/src/main/java/org/cbioportal/model/SampleTreatmentRow.java +++ b/src/main/java/org/cbioportal/legacy/model/SampleTreatmentRow.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Objects; diff --git a/src/main/java/org/cbioportal/model/StructuralVariant.java b/src/main/java/org/cbioportal/legacy/model/StructuralVariant.java similarity index 99% rename from src/main/java/org/cbioportal/model/StructuralVariant.java rename to src/main/java/org/cbioportal/legacy/model/StructuralVariant.java index 3c803a1b337..9c8a4151ffc 100644 --- a/src/main/java/org/cbioportal/model/StructuralVariant.java +++ b/src/main/java/org/cbioportal/legacy/model/StructuralVariant.java @@ -21,11 +21,11 @@ * along with this program. If not, see . */ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import com.fasterxml.jackson.annotation.*; import io.swagger.v3.oas.annotations.media.Schema; -import org.cbioportal.model.UniqueKeyBase; +import org.cbioportal.legacy.model.UniqueKeyBase; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/StructuralVariantFilterQuery.java b/src/main/java/org/cbioportal/legacy/model/StructuralVariantFilterQuery.java similarity index 95% rename from src/main/java/org/cbioportal/model/StructuralVariantFilterQuery.java rename to src/main/java/org/cbioportal/legacy/model/StructuralVariantFilterQuery.java index 0b857f2367a..cddf930357f 100644 --- a/src/main/java/org/cbioportal/model/StructuralVariantFilterQuery.java +++ b/src/main/java/org/cbioportal/legacy/model/StructuralVariantFilterQuery.java @@ -1,6 +1,6 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; -import org.cbioportal.model.util.Select; +import org.cbioportal.legacy.model.util.Select; import org.springframework.lang.Nullable; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/StructuralVariantGeneSubQuery.java b/src/main/java/org/cbioportal/legacy/model/StructuralVariantGeneSubQuery.java similarity index 98% rename from src/main/java/org/cbioportal/model/StructuralVariantGeneSubQuery.java rename to src/main/java/org/cbioportal/legacy/model/StructuralVariantGeneSubQuery.java index 224ba6bec2a..a0454de9033 100644 --- a/src/main/java/org/cbioportal/model/StructuralVariantGeneSubQuery.java +++ b/src/main/java/org/cbioportal/legacy/model/StructuralVariantGeneSubQuery.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import com.fasterxml.jackson.annotation.JsonIgnore; import org.springframework.lang.Nullable; diff --git a/src/main/java/org/cbioportal/model/StructuralVariantQuery.java b/src/main/java/org/cbioportal/legacy/model/StructuralVariantQuery.java similarity index 96% rename from src/main/java/org/cbioportal/model/StructuralVariantQuery.java rename to src/main/java/org/cbioportal/legacy/model/StructuralVariantQuery.java index 6dc8856869e..fe34e3dd0ef 100644 --- a/src/main/java/org/cbioportal/model/StructuralVariantQuery.java +++ b/src/main/java/org/cbioportal/legacy/model/StructuralVariantQuery.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.Valid; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/StructuralVariantSpecialValue.java b/src/main/java/org/cbioportal/legacy/model/StructuralVariantSpecialValue.java similarity index 80% rename from src/main/java/org/cbioportal/model/StructuralVariantSpecialValue.java rename to src/main/java/org/cbioportal/legacy/model/StructuralVariantSpecialValue.java index 8af29b9fd75..8a165e03928 100644 --- a/src/main/java/org/cbioportal/model/StructuralVariantSpecialValue.java +++ b/src/main/java/org/cbioportal/legacy/model/StructuralVariantSpecialValue.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum StructuralVariantSpecialValue { diff --git a/src/main/java/org/cbioportal/model/StudyViewFilterContext.java b/src/main/java/org/cbioportal/legacy/model/StudyViewFilterContext.java similarity index 55% rename from src/main/java/org/cbioportal/model/StudyViewFilterContext.java rename to src/main/java/org/cbioportal/legacy/model/StudyViewFilterContext.java index e23e5f7d9d4..22406ecd128 100644 --- a/src/main/java/org/cbioportal/model/StudyViewFilterContext.java +++ b/src/main/java/org/cbioportal/legacy/model/StudyViewFilterContext.java @@ -1,7 +1,7 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; -import org.cbioportal.web.parameter.CustomSampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.CustomSampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/StudyViewStructuralVariantFilter.java b/src/main/java/org/cbioportal/legacy/model/StudyViewStructuralVariantFilter.java similarity index 98% rename from src/main/java/org/cbioportal/model/StudyViewStructuralVariantFilter.java rename to src/main/java/org/cbioportal/legacy/model/StudyViewStructuralVariantFilter.java index d4ae0879873..41300c91961 100644 --- a/src/main/java/org/cbioportal/model/StudyViewStructuralVariantFilter.java +++ b/src/main/java/org/cbioportal/legacy/model/StudyViewStructuralVariantFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.AssertTrue; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/TableTimestampPair.java b/src/main/java/org/cbioportal/legacy/model/TableTimestampPair.java similarity index 93% rename from src/main/java/org/cbioportal/model/TableTimestampPair.java rename to src/main/java/org/cbioportal/legacy/model/TableTimestampPair.java index 1587bfc8e85..6bc8e3c1c5e 100644 --- a/src/main/java/org/cbioportal/model/TableTimestampPair.java +++ b/src/main/java/org/cbioportal/legacy/model/TableTimestampPair.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/TemporalRelation.java b/src/main/java/org/cbioportal/legacy/model/TemporalRelation.java similarity index 58% rename from src/main/java/org/cbioportal/model/TemporalRelation.java rename to src/main/java/org/cbioportal/legacy/model/TemporalRelation.java index 8c204c46208..66448ed3ab0 100644 --- a/src/main/java/org/cbioportal/model/TemporalRelation.java +++ b/src/main/java/org/cbioportal/legacy/model/TemporalRelation.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum TemporalRelation { Pre, diff --git a/src/main/java/org/cbioportal/model/Treatment.java b/src/main/java/org/cbioportal/legacy/model/Treatment.java similarity index 97% rename from src/main/java/org/cbioportal/model/Treatment.java rename to src/main/java/org/cbioportal/legacy/model/Treatment.java index 746d88dcebe..c40c8377efb 100644 --- a/src/main/java/org/cbioportal/model/Treatment.java +++ b/src/main/java/org/cbioportal/legacy/model/Treatment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Objects; diff --git a/src/main/java/org/cbioportal/model/TreatmentRow.java b/src/main/java/org/cbioportal/legacy/model/TreatmentRow.java similarity index 74% rename from src/main/java/org/cbioportal/model/TreatmentRow.java rename to src/main/java/org/cbioportal/legacy/model/TreatmentRow.java index 32662b7222c..f19152585ac 100644 --- a/src/main/java/org/cbioportal/model/TreatmentRow.java +++ b/src/main/java/org/cbioportal/legacy/model/TreatmentRow.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.util.Set; diff --git a/src/main/java/org/cbioportal/model/TypeOfCancer.java b/src/main/java/org/cbioportal/legacy/model/TypeOfCancer.java similarity index 96% rename from src/main/java/org/cbioportal/model/TypeOfCancer.java rename to src/main/java/org/cbioportal/legacy/model/TypeOfCancer.java index 6c564c3e37a..3f706f5e367 100644 --- a/src/main/java/org/cbioportal/model/TypeOfCancer.java +++ b/src/main/java/org/cbioportal/legacy/model/TypeOfCancer.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/UniqueKeyBase.java b/src/main/java/org/cbioportal/legacy/model/UniqueKeyBase.java similarity index 93% rename from src/main/java/org/cbioportal/model/UniqueKeyBase.java rename to src/main/java/org/cbioportal/legacy/model/UniqueKeyBase.java index 33198b81f3b..7b079b4f3db 100644 --- a/src/main/java/org/cbioportal/model/UniqueKeyBase.java +++ b/src/main/java/org/cbioportal/legacy/model/UniqueKeyBase.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/User.java b/src/main/java/org/cbioportal/legacy/model/User.java similarity index 98% rename from src/main/java/org/cbioportal/model/User.java rename to src/main/java/org/cbioportal/legacy/model/User.java index 646e8cac647..481b41cd851 100644 --- a/src/main/java/org/cbioportal/model/User.java +++ b/src/main/java/org/cbioportal/legacy/model/User.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/UserAuthorities.java b/src/main/java/org/cbioportal/legacy/model/UserAuthorities.java similarity index 98% rename from src/main/java/org/cbioportal/model/UserAuthorities.java rename to src/main/java/org/cbioportal/legacy/model/UserAuthorities.java index d8d4e641f6c..2bc42b84c88 100644 --- a/src/main/java/org/cbioportal/model/UserAuthorities.java +++ b/src/main/java/org/cbioportal/legacy/model/UserAuthorities.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.model; +package org.cbioportal.legacy.model; // imports import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/VariantCount.java b/src/main/java/org/cbioportal/legacy/model/VariantCount.java similarity index 97% rename from src/main/java/org/cbioportal/model/VariantCount.java rename to src/main/java/org/cbioportal/legacy/model/VariantCount.java index fdc43b721cb..f6e8b5dcbe0 100644 --- a/src/main/java/org/cbioportal/model/VariantCount.java +++ b/src/main/java/org/cbioportal/legacy/model/VariantCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/meta/BaseMeta.java b/src/main/java/org/cbioportal/legacy/model/meta/BaseMeta.java similarity index 87% rename from src/main/java/org/cbioportal/model/meta/BaseMeta.java rename to src/main/java/org/cbioportal/legacy/model/meta/BaseMeta.java index dac0a7caba4..81102101bc4 100644 --- a/src/main/java/org/cbioportal/model/meta/BaseMeta.java +++ b/src/main/java/org/cbioportal/legacy/model/meta/BaseMeta.java @@ -1,4 +1,4 @@ -package org.cbioportal.model.meta; +package org.cbioportal.legacy.model.meta; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/meta/GenericAssayMeta.java b/src/main/java/org/cbioportal/legacy/model/meta/GenericAssayMeta.java similarity index 98% rename from src/main/java/org/cbioportal/model/meta/GenericAssayMeta.java rename to src/main/java/org/cbioportal/legacy/model/meta/GenericAssayMeta.java index 2f22fd9b5e0..2a94c66498b 100644 --- a/src/main/java/org/cbioportal/model/meta/GenericAssayMeta.java +++ b/src/main/java/org/cbioportal/legacy/model/meta/GenericAssayMeta.java @@ -1,4 +1,4 @@ -package org.cbioportal.model.meta; +package org.cbioportal.legacy.model.meta; import java.io.Serializable; import java.util.HashMap; diff --git a/src/main/java/org/cbioportal/model/meta/MutationMeta.java b/src/main/java/org/cbioportal/legacy/model/meta/MutationMeta.java similarity index 86% rename from src/main/java/org/cbioportal/model/meta/MutationMeta.java rename to src/main/java/org/cbioportal/legacy/model/meta/MutationMeta.java index bb9f82a83a0..49a5226f950 100644 --- a/src/main/java/org/cbioportal/model/meta/MutationMeta.java +++ b/src/main/java/org/cbioportal/legacy/model/meta/MutationMeta.java @@ -1,4 +1,4 @@ -package org.cbioportal.model.meta; +package org.cbioportal.legacy.model.meta; public class MutationMeta extends BaseMeta { diff --git a/src/main/java/org/cbioportal/model/util/QueryElement.java b/src/main/java/org/cbioportal/legacy/model/util/QueryElement.java similarity index 57% rename from src/main/java/org/cbioportal/model/util/QueryElement.java rename to src/main/java/org/cbioportal/legacy/model/util/QueryElement.java index d7b78a96de2..2948f6b81e1 100644 --- a/src/main/java/org/cbioportal/model/util/QueryElement.java +++ b/src/main/java/org/cbioportal/legacy/model/util/QueryElement.java @@ -1,4 +1,4 @@ -package org.cbioportal.model.util; +package org.cbioportal.legacy.model.util; public enum QueryElement { INACTIVE, ACTIVE, PASS diff --git a/src/main/java/org/cbioportal/model/util/Select.java b/src/main/java/org/cbioportal/legacy/model/util/Select.java similarity index 98% rename from src/main/java/org/cbioportal/model/util/Select.java rename to src/main/java/org/cbioportal/legacy/model/util/Select.java index e10f2c0ebda..bc0e320afd2 100644 --- a/src/main/java/org/cbioportal/model/util/Select.java +++ b/src/main/java/org/cbioportal/legacy/model/util/Select.java @@ -1,4 +1,4 @@ -package org.cbioportal.model.util; +package org.cbioportal.legacy.model.util; import java.util.*; import java.util.function.Function; diff --git a/src/main/java/org/cbioportal/persistence/AlterationDriverAnnotationRepository.java b/src/main/java/org/cbioportal/legacy/persistence/AlterationDriverAnnotationRepository.java similarity index 77% rename from src/main/java/org/cbioportal/persistence/AlterationDriverAnnotationRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/AlterationDriverAnnotationRepository.java index d89b33ed9b6..2a2d55c8f0e 100644 --- a/src/main/java/org/cbioportal/persistence/AlterationDriverAnnotationRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/AlterationDriverAnnotationRepository.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.AlterationDriverAnnotation; +import org.cbioportal.legacy.model.AlterationDriverAnnotation; import org.springframework.cache.annotation.Cacheable; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/AlterationRepository.java b/src/main/java/org/cbioportal/legacy/persistence/AlterationRepository.java similarity index 82% rename from src/main/java/org/cbioportal/persistence/AlterationRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/AlterationRepository.java index b8f436eea09..00e83d942d4 100644 --- a/src/main/java/org/cbioportal/persistence/AlterationRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/AlterationRepository.java @@ -1,7 +1,11 @@ -package org.cbioportal.persistence; - -import org.cbioportal.model.*; -import org.cbioportal.model.util.Select; +package org.cbioportal.legacy.persistence; + +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.util.Select; import org.springframework.cache.annotation.Cacheable; import java.util.List; @@ -31,7 +35,7 @@ List getPatientCnaGeneCounts(Set getSampleStructuralVariantCounts(Set molecularProfileCaseIdentifiers, - AlterationFilter alterationFilter); + AlterationFilter alterationFilter); @Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()") List getPatientStructuralVariantCounts(Set molecularProfileCaseIdentifiers, diff --git a/src/main/java/org/cbioportal/persistence/CacheEnabledConfig.java b/src/main/java/org/cbioportal/legacy/persistence/CacheEnabledConfig.java similarity index 97% rename from src/main/java/org/cbioportal/persistence/CacheEnabledConfig.java rename to src/main/java/org/cbioportal/legacy/persistence/CacheEnabledConfig.java index 45b22f5bbf4..056810fb731 100644 --- a/src/main/java/org/cbioportal/persistence/CacheEnabledConfig.java +++ b/src/main/java/org/cbioportal/legacy/persistence/CacheEnabledConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import jakarta.annotation.PostConstruct; import org.slf4j.Logger; diff --git a/src/main/java/org/cbioportal/persistence/CancerTypeRepository.java b/src/main/java/org/cbioportal/legacy/persistence/CancerTypeRepository.java similarity index 83% rename from src/main/java/org/cbioportal/persistence/CancerTypeRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/CancerTypeRepository.java index a670d074007..667bdd9beaa 100644 --- a/src/main/java/org/cbioportal/persistence/CancerTypeRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/CancerTypeRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/ClinicalAttributeRepository.java b/src/main/java/org/cbioportal/legacy/persistence/ClinicalAttributeRepository.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/ClinicalAttributeRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/ClinicalAttributeRepository.java index aa7c8ede12f..4828ad541e7 100644 --- a/src/main/java/org/cbioportal/persistence/ClinicalAttributeRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/ClinicalAttributeRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/ClinicalDataRepository.java b/src/main/java/org/cbioportal/legacy/persistence/ClinicalDataRepository.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/ClinicalDataRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/ClinicalDataRepository.java index ed320908d2e..305455aec13 100644 --- a/src/main/java/org/cbioportal/persistence/ClinicalDataRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/ClinicalDataRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/ClinicalEventRepository.java b/src/main/java/org/cbioportal/legacy/persistence/ClinicalEventRepository.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/ClinicalEventRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/ClinicalEventRepository.java index bf6d31470c9..bbdd597a142 100644 --- a/src/main/java/org/cbioportal/persistence/ClinicalEventRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/ClinicalEventRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/CopyNumberSegmentRepository.java b/src/main/java/org/cbioportal/legacy/persistence/CopyNumberSegmentRepository.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/CopyNumberSegmentRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/CopyNumberSegmentRepository.java index 3618de022df..03a92ef60f4 100644 --- a/src/main/java/org/cbioportal/persistence/CopyNumberSegmentRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/CopyNumberSegmentRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/CosmicCountRepository.java b/src/main/java/org/cbioportal/legacy/persistence/CosmicCountRepository.java similarity index 76% rename from src/main/java/org/cbioportal/persistence/CosmicCountRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/CosmicCountRepository.java index c45133c25e8..4f3a7ec7e30 100644 --- a/src/main/java/org/cbioportal/persistence/CosmicCountRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/CosmicCountRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; -import org.cbioportal.model.CosmicMutation; +import org.cbioportal.legacy.model.CosmicMutation; import org.springframework.cache.annotation.Cacheable; public interface CosmicCountRepository { diff --git a/src/main/java/org/cbioportal/persistence/DataAccessTokenRepository.java b/src/main/java/org/cbioportal/legacy/persistence/DataAccessTokenRepository.java similarity index 79% rename from src/main/java/org/cbioportal/persistence/DataAccessTokenRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/DataAccessTokenRepository.java index ddd46236a9e..47d4dd92a06 100644 --- a/src/main/java/org/cbioportal/persistence/DataAccessTokenRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/DataAccessTokenRepository.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.DataAccessToken; +import org.cbioportal.legacy.model.DataAccessToken; import java.util.List; public interface DataAccessTokenRepository { diff --git a/src/main/java/org/cbioportal/persistence/DiscreteCopyNumberRepository.java b/src/main/java/org/cbioportal/legacy/persistence/DiscreteCopyNumberRepository.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/DiscreteCopyNumberRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/DiscreteCopyNumberRepository.java index ae07f0e3f2f..c2ef1a85434 100644 --- a/src/main/java/org/cbioportal/persistence/DiscreteCopyNumberRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/DiscreteCopyNumberRepository.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/GenePanelRepository.java b/src/main/java/org/cbioportal/legacy/persistence/GenePanelRepository.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/GenePanelRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/GenePanelRepository.java index 49817ff86be..d8fdd05d52a 100644 --- a/src/main/java/org/cbioportal/persistence/GenePanelRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/GenePanelRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/GeneRepository.java b/src/main/java/org/cbioportal/legacy/persistence/GeneRepository.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/GeneRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/GeneRepository.java index a0bdd4b5715..4a5a14cc62f 100644 --- a/src/main/java/org/cbioportal/persistence/GeneRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/GeneRepository.java @@ -29,11 +29,11 @@ * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see . */ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneAlias; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneAlias; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/GenericAssayRepository.java b/src/main/java/org/cbioportal/legacy/persistence/GenericAssayRepository.java similarity index 81% rename from src/main/java/org/cbioportal/persistence/GenericAssayRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/GenericAssayRepository.java index 27f8f1f8964..3c8c10e724a 100644 --- a/src/main/java/org/cbioportal/persistence/GenericAssayRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/GenericAssayRepository.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.model.GenericAssayAdditionalProperty; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.model.GenericAssayAdditionalProperty; import org.springframework.cache.annotation.Cacheable; public interface GenericAssayRepository { diff --git a/src/main/java/org/cbioportal/persistence/GenesetHierarchyRepository.java b/src/main/java/org/cbioportal/legacy/persistence/GenesetHierarchyRepository.java similarity index 82% rename from src/main/java/org/cbioportal/persistence/GenesetHierarchyRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/GenesetHierarchyRepository.java index 5db19320acf..c8157388660 100644 --- a/src/main/java/org/cbioportal/persistence/GenesetHierarchyRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/GenesetHierarchyRepository.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/GenesetRepository.java b/src/main/java/org/cbioportal/legacy/persistence/GenesetRepository.java similarity index 86% rename from src/main/java/org/cbioportal/persistence/GenesetRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/GenesetRepository.java index dcd73779403..6de723c09cb 100644 --- a/src/main/java/org/cbioportal/persistence/GenesetRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/GenesetRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/MolecularDataRepository.java b/src/main/java/org/cbioportal/legacy/persistence/MolecularDataRepository.java similarity index 90% rename from src/main/java/org/cbioportal/persistence/MolecularDataRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/MolecularDataRepository.java index 5c2f8a9600a..28bdc404e44 100644 --- a/src/main/java/org/cbioportal/persistence/MolecularDataRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/MolecularDataRepository.java @@ -1,14 +1,14 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; import java.util.Map; import java.util.Set; -import org.cbioportal.model.GeneMolecularAlteration; -import org.cbioportal.model.GenericAssayMolecularAlteration; -import org.cbioportal.model.GenesetMolecularAlteration; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.GenesetMolecularAlteration; import org.springframework.cache.annotation.Cacheable; -import org.cbioportal.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.MolecularProfileSamples; public interface MolecularDataRepository { diff --git a/src/main/java/org/cbioportal/persistence/MolecularProfileRepository.java b/src/main/java/org/cbioportal/legacy/persistence/MolecularProfileRepository.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/MolecularProfileRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/MolecularProfileRepository.java index 41cb01bc8ec..bffe6f952d7 100644 --- a/src/main/java/org/cbioportal/persistence/MolecularProfileRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/MolecularProfileRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/MutationRepository.java b/src/main/java/org/cbioportal/legacy/persistence/MutationRepository.java similarity index 93% rename from src/main/java/org/cbioportal/persistence/MutationRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/MutationRepository.java index ffcef1b6f0c..78867ccfefc 100644 --- a/src/main/java/org/cbioportal/persistence/MutationRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/MutationRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.meta.MutationMeta; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.meta.MutationMeta; import org.springframework.cache.annotation.Cacheable; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/PatientRepository.java b/src/main/java/org/cbioportal/legacy/persistence/PatientRepository.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/PatientRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/PatientRepository.java index 54c92024b79..5a881416792 100644 --- a/src/main/java/org/cbioportal/persistence/PatientRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/PatientRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/PersistenceConstants.java b/src/main/java/org/cbioportal/legacy/persistence/PersistenceConstants.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/PersistenceConstants.java rename to src/main/java/org/cbioportal/legacy/persistence/PersistenceConstants.java index c5b3124a7ef..c141621346f 100644 --- a/src/main/java/org/cbioportal/persistence/PersistenceConstants.java +++ b/src/main/java/org/cbioportal/legacy/persistence/PersistenceConstants.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; public class PersistenceConstants { diff --git a/src/main/java/org/cbioportal/persistence/ReferenceGenomeGeneRepository.java b/src/main/java/org/cbioportal/legacy/persistence/ReferenceGenomeGeneRepository.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/ReferenceGenomeGeneRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/ReferenceGenomeGeneRepository.java index 7b906fed60a..a4aa1d7e66b 100644 --- a/src/main/java/org/cbioportal/persistence/ReferenceGenomeGeneRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/ReferenceGenomeGeneRepository.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.ReferenceGenomeGene; +import org.cbioportal.legacy.model.ReferenceGenomeGene; import java.util.List; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/ResourceDataRepository.java b/src/main/java/org/cbioportal/legacy/persistence/ResourceDataRepository.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/ResourceDataRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/ResourceDataRepository.java index c93898dd2ce..29b84fe7eca 100644 --- a/src/main/java/org/cbioportal/persistence/ResourceDataRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/ResourceDataRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; -import org.cbioportal.model.ResourceData; +import org.cbioportal.legacy.model.ResourceData; import org.springframework.cache.annotation.Cacheable; public interface ResourceDataRepository { diff --git a/src/main/java/org/cbioportal/persistence/ResourceDefinitionRepository.java b/src/main/java/org/cbioportal/legacy/persistence/ResourceDefinitionRepository.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/ResourceDefinitionRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/ResourceDefinitionRepository.java index 1f248d5775c..248689c8a25 100644 --- a/src/main/java/org/cbioportal/persistence/ResourceDefinitionRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/ResourceDefinitionRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; -import org.cbioportal.model.ResourceDefinition; +import org.cbioportal.legacy.model.ResourceDefinition; import org.springframework.cache.annotation.Cacheable; public interface ResourceDefinitionRepository { diff --git a/src/main/java/org/cbioportal/persistence/SampleListRepository.java b/src/main/java/org/cbioportal/legacy/persistence/SampleListRepository.java similarity index 90% rename from src/main/java/org/cbioportal/persistence/SampleListRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/SampleListRepository.java index 0c0e7745d8a..5faae73b52d 100644 --- a/src/main/java/org/cbioportal/persistence/SampleListRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/SampleListRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.SampleListToSampleId; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.SampleListToSampleId; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/SampleRepository.java b/src/main/java/org/cbioportal/legacy/persistence/SampleRepository.java similarity index 96% rename from src/main/java/org/cbioportal/persistence/SampleRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/SampleRepository.java index 8ce831fe951..97834540aa2 100644 --- a/src/main/java/org/cbioportal/persistence/SampleRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/SampleRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/SecurityRepository.java b/src/main/java/org/cbioportal/legacy/persistence/SecurityRepository.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/SecurityRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/SecurityRepository.java index 68ff9f1a3a5..111cadd2fe4 100644 --- a/src/main/java/org/cbioportal/persistence/SecurityRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/SecurityRepository.java @@ -30,13 +30,13 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; // imports import java.util.Set; -import org.cbioportal.model.User; -import org.cbioportal.model.UserAuthorities; +import org.cbioportal.legacy.model.User; +import org.cbioportal.legacy.model.UserAuthorities; /** * Interface to use to retrieve diff --git a/src/main/java/org/cbioportal/persistence/SignificantCopyNumberRegionRepository.java b/src/main/java/org/cbioportal/legacy/persistence/SignificantCopyNumberRegionRepository.java similarity index 81% rename from src/main/java/org/cbioportal/persistence/SignificantCopyNumberRegionRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/SignificantCopyNumberRegionRepository.java index 4e5fa225ce0..92c753b1487 100644 --- a/src/main/java/org/cbioportal/persistence/SignificantCopyNumberRegionRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/SignificantCopyNumberRegionRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/SignificantlyMutatedGeneRepository.java b/src/main/java/org/cbioportal/legacy/persistence/SignificantlyMutatedGeneRepository.java similarity index 82% rename from src/main/java/org/cbioportal/persistence/SignificantlyMutatedGeneRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/SignificantlyMutatedGeneRepository.java index 4c20a80e31d..c220b92f9b8 100644 --- a/src/main/java/org/cbioportal/persistence/SignificantlyMutatedGeneRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/SignificantlyMutatedGeneRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/StaticDataTimeStampRepository.java b/src/main/java/org/cbioportal/legacy/persistence/StaticDataTimeStampRepository.java similarity index 62% rename from src/main/java/org/cbioportal/persistence/StaticDataTimeStampRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/StaticDataTimeStampRepository.java index 616d5e158d5..aae13dd31e9 100644 --- a/src/main/java/org/cbioportal/persistence/StaticDataTimeStampRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/StaticDataTimeStampRepository.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.TableTimestampPair; +import org.cbioportal.legacy.model.TableTimestampPair; import java.util.Date; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/StructuralVariantRepository.java b/src/main/java/org/cbioportal/legacy/persistence/StructuralVariantRepository.java similarity index 83% rename from src/main/java/org/cbioportal/persistence/StructuralVariantRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/StructuralVariantRepository.java index 8818779e193..f3ac9db08dc 100644 --- a/src/main/java/org/cbioportal/persistence/StructuralVariantRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/StructuralVariantRepository.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantQuery; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantQuery; import org.springframework.cache.annotation.Cacheable; public interface StructuralVariantRepository { diff --git a/src/main/java/org/cbioportal/persistence/StudyRepository.java b/src/main/java/org/cbioportal/legacy/persistence/StudyRepository.java similarity index 88% rename from src/main/java/org/cbioportal/persistence/StudyRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/StudyRepository.java index 875250b5b23..4efa5d6a8eb 100644 --- a/src/main/java/org/cbioportal/persistence/StudyRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/StudyRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/legacy/persistence/StudyViewRepository.java similarity index 74% rename from src/main/java/org/cbioportal/persistence/StudyViewRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/StudyViewRepository.java index c39158ad433..dbda846e43e 100644 --- a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/StudyViewRepository.java @@ -1,26 +1,26 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.PatientTreatment; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleTreatment; -import org.cbioportal.model.StudyViewFilterContext; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.GenericAssayDataBinFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.PatientTreatment; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleTreatment; +import org.cbioportal.legacy.model.StudyViewFilterContext; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; import java.util.List; import java.util.Map; diff --git a/src/main/java/org/cbioportal/persistence/TreatmentRepository.java b/src/main/java/org/cbioportal/legacy/persistence/TreatmentRepository.java similarity index 88% rename from src/main/java/org/cbioportal/persistence/TreatmentRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/TreatmentRepository.java index bc2e0705b16..60e1257a447 100644 --- a/src/main/java/org/cbioportal/persistence/TreatmentRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/TreatmentRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.model.ClinicalEventSample; -import org.cbioportal.model.Treatment; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.Treatment; import org.springframework.cache.annotation.Cacheable; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/VariantCountRepository.java b/src/main/java/org/cbioportal/legacy/persistence/VariantCountRepository.java similarity index 81% rename from src/main/java/org/cbioportal/persistence/VariantCountRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/VariantCountRepository.java index b3f6e078cbd..bd8b953a4a5 100644 --- a/src/main/java/org/cbioportal/persistence/VariantCountRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/VariantCountRepository.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.VariantCount; +import org.cbioportal.legacy.model.VariantCount; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/cachemaputil/CacheMapBuilder.java b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/CacheMapBuilder.java similarity index 83% rename from src/main/java/org/cbioportal/persistence/cachemaputil/CacheMapBuilder.java rename to src/main/java/org/cbioportal/legacy/persistence/cachemaputil/CacheMapBuilder.java index ed189f01c7d..e1ea290ede9 100644 --- a/src/main/java/org/cbioportal/persistence/cachemaputil/CacheMapBuilder.java +++ b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/CacheMapBuilder.java @@ -1,15 +1,15 @@ -package org.cbioportal.persistence.cachemaputil; +package org.cbioportal.legacy.persistence.cachemaputil; import java.util.function.Function; import java.util.stream.Collectors; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.EntityType; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.SampleList; -import org.cbioportal.persistence.GenericAssayRepository; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.persistence.StudyRepository; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.EntityType; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.persistence.GenericAssayRepository; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.persistence.StudyRepository; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/cbioportal/persistence/cachemaputil/CacheMapUtil.java b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/CacheMapUtil.java similarity index 55% rename from src/main/java/org/cbioportal/persistence/cachemaputil/CacheMapUtil.java rename to src/main/java/org/cbioportal/legacy/persistence/cachemaputil/CacheMapUtil.java index f476c301186..89237b721e9 100644 --- a/src/main/java/org/cbioportal/persistence/cachemaputil/CacheMapUtil.java +++ b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/CacheMapUtil.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.cachemaputil; +package org.cbioportal.legacy.persistence.cachemaputil; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.SampleList; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.SampleList; import java.util.Map; diff --git a/src/main/java/org/cbioportal/persistence/cachemaputil/InactiveCacheMapUtil.java b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/InactiveCacheMapUtil.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/cachemaputil/InactiveCacheMapUtil.java rename to src/main/java/org/cbioportal/legacy/persistence/cachemaputil/InactiveCacheMapUtil.java index 8213ede2aaf..b7b57c6c717 100644 --- a/src/main/java/org/cbioportal/persistence/cachemaputil/InactiveCacheMapUtil.java +++ b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/InactiveCacheMapUtil.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.cachemaputil; +package org.cbioportal.legacy.persistence.cachemaputil; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.SampleList; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.SampleList; import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/persistence/cachemaputil/SpringManagedCacheMapUtil.java b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/SpringManagedCacheMapUtil.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/cachemaputil/SpringManagedCacheMapUtil.java rename to src/main/java/org/cbioportal/legacy/persistence/cachemaputil/SpringManagedCacheMapUtil.java index c492b2400b0..0325dd78f74 100644 --- a/src/main/java/org/cbioportal/persistence/cachemaputil/SpringManagedCacheMapUtil.java +++ b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/SpringManagedCacheMapUtil.java @@ -30,12 +30,12 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.cachemaputil; +package org.cbioportal.legacy.persistence.cachemaputil; import jakarta.annotation.PostConstruct; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.SampleList; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.SampleList; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/cbioportal/persistence/cachemaputil/StaticRefCacheMapUtil.java b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/StaticRefCacheMapUtil.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/cachemaputil/StaticRefCacheMapUtil.java rename to src/main/java/org/cbioportal/legacy/persistence/cachemaputil/StaticRefCacheMapUtil.java index 48d07e0bff1..c9af82f0b31 100644 --- a/src/main/java/org/cbioportal/persistence/cachemaputil/StaticRefCacheMapUtil.java +++ b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/StaticRefCacheMapUtil.java @@ -30,12 +30,12 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.cachemaputil; +package org.cbioportal.legacy.persistence.cachemaputil; import jakarta.annotation.PostConstruct; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.SampleList; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.SampleList; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/cbioportal/persistence/config/EhCacheConfig.java b/src/main/java/org/cbioportal/legacy/persistence/config/EhCacheConfig.java similarity index 84% rename from src/main/java/org/cbioportal/persistence/config/EhCacheConfig.java rename to src/main/java/org/cbioportal/legacy/persistence/config/EhCacheConfig.java index 15c7d10f76b..2b64da7e2ca 100644 --- a/src/main/java/org/cbioportal/persistence/config/EhCacheConfig.java +++ b/src/main/java/org/cbioportal/legacy/persistence/config/EhCacheConfig.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.config; +package org.cbioportal.legacy.persistence.config; -import org.cbioportal.persistence.util.CustomEhcachingProvider; -import org.cbioportal.persistence.util.CustomKeyGenerator; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.persistence.util.CustomEhcachingProvider; +import org.cbioportal.legacy.persistence.util.CustomKeyGenerator; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.cache.CacheManager; import org.springframework.cache.annotation.CachingConfigurerSupport; import org.springframework.cache.annotation.EnableCaching; diff --git a/src/main/java/org/cbioportal/persistence/config/RedisConfig.java b/src/main/java/org/cbioportal/legacy/persistence/config/RedisConfig.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/config/RedisConfig.java rename to src/main/java/org/cbioportal/legacy/persistence/config/RedisConfig.java index 99c225a33bd..4333b8661d5 100644 --- a/src/main/java/org/cbioportal/persistence/config/RedisConfig.java +++ b/src/main/java/org/cbioportal/legacy/persistence/config/RedisConfig.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.config; +package org.cbioportal.legacy.persistence.config; -import org.cbioportal.persistence.util.CustomKeyGenerator; -import org.cbioportal.persistence.util.CustomRedisCachingProvider; -import org.cbioportal.persistence.util.LoggingCacheErrorHandler; +import org.cbioportal.legacy.persistence.util.CustomKeyGenerator; +import org.cbioportal.legacy.persistence.util.CustomRedisCachingProvider; +import org.cbioportal.legacy.persistence.util.LoggingCacheErrorHandler; import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; import org.springframework.cache.CacheManager; diff --git a/src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataType.java b/src/main/java/org/cbioportal/legacy/persistence/enums/ClinicalAttributeDataType.java similarity index 85% rename from src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataType.java rename to src/main/java/org/cbioportal/legacy/persistence/enums/ClinicalAttributeDataType.java index 591f67e117d..f91798a828a 100644 --- a/src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataType.java +++ b/src/main/java/org/cbioportal/legacy/persistence/enums/ClinicalAttributeDataType.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.enums; +package org.cbioportal.legacy.persistence.enums; public enum ClinicalAttributeDataType { CATEGORICAL("CATEGORICAL"), diff --git a/src/main/java/org/cbioportal/persistence/enums/DataSource.java b/src/main/java/org/cbioportal/legacy/persistence/enums/DataSource.java similarity index 83% rename from src/main/java/org/cbioportal/persistence/enums/DataSource.java rename to src/main/java/org/cbioportal/legacy/persistence/enums/DataSource.java index 09b81b79edb..4a9eecb1fdd 100644 --- a/src/main/java/org/cbioportal/persistence/enums/DataSource.java +++ b/src/main/java/org/cbioportal/legacy/persistence/enums/DataSource.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.enums; +package org.cbioportal.legacy.persistence.enums; public enum DataSource { PATIENT("PATIENT"),SAMPLE("SAMPLE"); diff --git a/src/main/java/org/cbioportal/persistence/helper/AlterationFilterHelper.java b/src/main/java/org/cbioportal/legacy/persistence/helper/AlterationFilterHelper.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/helper/AlterationFilterHelper.java rename to src/main/java/org/cbioportal/legacy/persistence/helper/AlterationFilterHelper.java index 1d8f63a55f2..420bf4de630 100644 --- a/src/main/java/org/cbioportal/persistence/helper/AlterationFilterHelper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/helper/AlterationFilterHelper.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.helper; +package org.cbioportal.legacy.persistence.helper; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.model.util.Select; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.model.util.Select; import org.springframework.lang.NonNull; import org.springframework.lang.Nullable; diff --git a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java b/src/main/java/org/cbioportal/legacy/persistence/helper/StudyViewFilterHelper.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java rename to src/main/java/org/cbioportal/legacy/persistence/helper/StudyViewFilterHelper.java index d88956864af..cd9c75ba4e4 100644 --- a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/helper/StudyViewFilterHelper.java @@ -1,15 +1,15 @@ -package org.cbioportal.persistence.helper; +package org.cbioportal.legacy.persistence.helper; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.persistence.enums.DataSource; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.CategorizedGenericAssayDataCountFilter; -import org.cbioportal.web.parameter.CustomSampleIdentifier; -import org.cbioportal.web.parameter.DataFilter; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.persistence.enums.DataSource; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.CategorizedGenericAssayDataCountFilter; +import org.cbioportal.legacy.web.parameter.CustomSampleIdentifier; +import org.cbioportal.legacy.web.parameter.DataFilter; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.springframework.lang.NonNull; import org.springframework.lang.Nullable; diff --git a/src/main/java/org/cbioportal/persistence/model/SampleAcquisitionEventRecord.java b/src/main/java/org/cbioportal/legacy/persistence/model/SampleAcquisitionEventRecord.java similarity index 72% rename from src/main/java/org/cbioportal/persistence/model/SampleAcquisitionEventRecord.java rename to src/main/java/org/cbioportal/legacy/persistence/model/SampleAcquisitionEventRecord.java index b02c24c7100..a0eddeb4eb9 100644 --- a/src/main/java/org/cbioportal/persistence/model/SampleAcquisitionEventRecord.java +++ b/src/main/java/org/cbioportal/legacy/persistence/model/SampleAcquisitionEventRecord.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.model; +package org.cbioportal.legacy.persistence.model; public record SampleAcquisitionEventRecord(String sampleId, String patientUniqueId, String cancerStudyId, int timeTaken) { } diff --git a/src/main/java/org/cbioportal/persistence/model/TreatmentRecord.java b/src/main/java/org/cbioportal/legacy/persistence/model/TreatmentRecord.java similarity index 68% rename from src/main/java/org/cbioportal/persistence/model/TreatmentRecord.java rename to src/main/java/org/cbioportal/legacy/persistence/model/TreatmentRecord.java index aeeac35723b..54bad64fe84 100644 --- a/src/main/java/org/cbioportal/persistence/model/TreatmentRecord.java +++ b/src/main/java/org/cbioportal/legacy/persistence/model/TreatmentRecord.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.model; +package org.cbioportal.legacy.persistence.model; public record TreatmentRecord(String patientUniqueId, String treatment, int startTime, int stopTime) { } diff --git a/src/main/java/org/cbioportal/persistence/mybatis/AlterationCountsMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationCountsMapper.java similarity index 96% rename from src/main/java/org/cbioportal/persistence/mybatis/AlterationCountsMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationCountsMapper.java index 4b1461cdbb8..585efd73e58 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/AlterationCountsMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationCountsMapper.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.util.Select; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.util.Select; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMapper.java similarity index 69% rename from src/main/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMapper.java index 34b5a02eb05..8bfd91c9615 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import org.apache.ibatis.annotations.Param; -import org.cbioportal.model.AlterationDriverAnnotation; +import org.cbioportal.legacy.model.AlterationDriverAnnotation; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMyBatisRepository.java similarity index 79% rename from src/main/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMyBatisRepository.java index 222336aac14..ffb087d8228 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMyBatisRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.*; -import org.cbioportal.persistence.AlterationDriverAnnotationRepository; +import org.cbioportal.legacy.model.AlterationDriverAnnotation; +import org.cbioportal.legacy.persistence.AlterationDriverAnnotationRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepository.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepository.java index a48b6476b59..4344b8da3ca 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepository.java @@ -1,17 +1,17 @@ -package org.cbioportal.persistence.mybatis; - -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.model.MolecularProfile.MolecularAlterationType; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.AlterationRepository; -import org.cbioportal.persistence.MolecularProfileRepository; +package org.cbioportal.legacy.persistence.mybatis; + +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.model.MolecularProfile.MolecularAlterationType; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.AlterationRepository; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/CancerTypeMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMapper.java similarity index 69% rename from src/main/java/org/cbioportal/persistence/mybatis/CancerTypeMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMapper.java index 4fbe328f514..7957f368b6f 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/CancerTypeMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/CancerTypeMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMyBatisRepository.java similarity index 73% rename from src/main/java/org/cbioportal/persistence/mybatis/CancerTypeMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMyBatisRepository.java index 64cc83d3af3..70d62797edd 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/CancerTypeMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CancerTypeRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CancerTypeRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMapper.java similarity index 78% rename from src/main/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMapper.java index cfee6ac5933..4cdaf28d418 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMyBatisRepository.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMyBatisRepository.java index 58fbbba59a2..31d55612d22 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMyBatisRepository.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; - -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalAttributeRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +package org.cbioportal.legacy.persistence.mybatis; + +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalAttributeRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMapper.java similarity index 93% rename from src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMapper.java index 50bb0c4e197..2e95cfa2409 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMyBatisRepository.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMyBatisRepository.java index 19cdde259fa..40be60a5a8c 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMyBatisRepository.java @@ -1,15 +1,15 @@ -package org.cbioportal.persistence.mybatis; - -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalDataRepository; -import org.cbioportal.persistence.ClinicalAttributeRepository; -import org.cbioportal.persistence.PatientRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +package org.cbioportal.legacy.persistence.mybatis; + +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalDataRepository; +import org.cbioportal.legacy.persistence.ClinicalAttributeRepository; +import org.cbioportal.legacy.persistence.PatientRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; import org.springframework.util.Assert; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalEventMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMapper.java similarity index 85% rename from src/main/java/org/cbioportal/persistence/mybatis/ClinicalEventMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMapper.java index d87b0e8467d..c983210b3fa 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalEventMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalEventMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMyBatisRepository.java similarity index 90% rename from src/main/java/org/cbioportal/persistence/mybatis/ClinicalEventMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMyBatisRepository.java index ef65f4fa879..0f09e58c567 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalEventMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalEventRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalEventRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMapper.java similarity index 82% rename from src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMapper.java index 1a0878bd654..24d2df192c0 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java similarity index 90% rename from src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java index 4e586ddb8c6..85da2187e46 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CopyNumberSegmentRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CopyNumberSegmentRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/CosmicCountMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMapper.java similarity index 57% rename from src/main/java/org/cbioportal/persistence/mybatis/CosmicCountMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMapper.java index bfa7dec8af9..e9c8787eb4e 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/CosmicCountMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMapper.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.CosmicMutation; +import org.cbioportal.legacy.model.CosmicMutation; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/CosmicCountMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMyBatisRepository.java similarity index 73% rename from src/main/java/org/cbioportal/persistence/mybatis/CosmicCountMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMyBatisRepository.java index 9c2612f6576..417ccbf0c8b 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/CosmicCountMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMyBatisRepository.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; import java.util.List; -import org.cbioportal.model.CosmicMutation; -import org.cbioportal.persistence.CosmicCountRepository; +import org.cbioportal.legacy.model.CosmicMutation; +import org.cbioportal.legacy.persistence.CosmicCountRepository; @Repository public class CosmicCountMyBatisRepository implements CosmicCountRepository { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/DataAccessTokenMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMapper.java similarity index 78% rename from src/main/java/org/cbioportal/persistence/mybatis/DataAccessTokenMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMapper.java index bdadadf7e83..9c7dd88f201 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/DataAccessTokenMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMapper.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.DataAccessToken; +import org.cbioportal.legacy.model.DataAccessToken; import java.util.List; public interface DataAccessTokenMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/DataAccessTokenMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMyBatisRepository.java similarity index 86% rename from src/main/java/org/cbioportal/persistence/mybatis/DataAccessTokenMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMyBatisRepository.java index e0e15bcd751..8689df346e6 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/DataAccessTokenMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMyBatisRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.persistence.DataAccessTokenRepository; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.persistence.DataAccessTokenRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMapper.java similarity index 90% rename from src/main/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMapper.java index ab2934e6496..e5ba6252215 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMapper.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMyBatisRepository.java similarity index 93% rename from src/main/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMyBatisRepository.java index fdde1d8d0c6..43e76412dff 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.DiscreteCopyNumberRepository; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.DiscreteCopyNumberRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GeneMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GeneMapper.java similarity index 84% rename from src/main/java/org/cbioportal/persistence/mybatis/GeneMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GeneMapper.java index 79cc63318df..15330c13435 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GeneMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GeneMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneAlias; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneAlias; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GeneMyBatisRepository.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GeneMyBatisRepository.java index abf41874294..e9fc0275e5e 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GeneMyBatisRepository.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; - -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneAlias; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GeneRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +package org.cbioportal.legacy.persistence.mybatis; + +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneAlias; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GeneRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenePanelMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMapper.java similarity index 77% rename from src/main/java/org/cbioportal/persistence/mybatis/GenePanelMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMapper.java index 5d5d8371754..741fafa3b45 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenePanelMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMapper.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; import java.util.Set; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenePanelMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMyBatisRepository.java similarity index 84% rename from src/main/java/org/cbioportal/persistence/mybatis/GenePanelMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMyBatisRepository.java index cd984b312f1..0c7c7002f9d 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenePanelMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMyBatisRepository.java @@ -1,13 +1,13 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GenePanelRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GenePanelRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenericAssayMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMapper.java similarity index 76% rename from src/main/java/org/cbioportal/persistence/mybatis/GenericAssayMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMapper.java index 08a2f175fdd..9321118fbee 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenericAssayMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMapper.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.HashMap; import java.util.List; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.model.GenericAssayAdditionalProperty; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.model.GenericAssayAdditionalProperty; public interface GenericAssayMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenericAssayMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMyBatisRepository.java similarity index 90% rename from src/main/java/org/cbioportal/persistence/mybatis/GenericAssayMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMyBatisRepository.java index 4ee5a68de22..aeb9a3e2084 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenericAssayMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMyBatisRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.model.GenericAssayAdditionalProperty; -import org.cbioportal.persistence.GenericAssayRepository; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.model.GenericAssayAdditionalProperty; +import org.cbioportal.legacy.persistence.GenericAssayRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMapper.java similarity index 71% rename from src/main/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMapper.java index aa612490fe0..eb5088ce6f4 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMapper.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; import org.apache.ibatis.annotations.Param; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; public interface GenesetHierarchyMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMyBatisRepository.java similarity index 78% rename from src/main/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMyBatisRepository.java index a5ab47711a7..001d8d2daff 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetHierarchyInfo; -import org.cbioportal.persistence.GenesetHierarchyRepository; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.persistence.GenesetHierarchyRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenesetMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetMapper.java similarity index 80% rename from src/main/java/org/cbioportal/persistence/mybatis/GenesetMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetMapper.java index b6484cb55ff..07cd96d5f82 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenesetMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetMapper.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.meta.BaseMeta; public interface GenesetMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenesetMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetMyBatisRepository.java similarity index 75% rename from src/main/java/org/cbioportal/persistence/mybatis/GenesetMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetMyBatisRepository.java index 0cba9bef284..cf0658621d9 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenesetMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetMyBatisRepository.java @@ -1,13 +1,13 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GenesetRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GenesetRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMapper.java similarity index 85% rename from src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMapper.java index 9191f75494c..89dd3911c4c 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMapper.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.GeneMolecularAlteration; -import org.cbioportal.model.GenericAssayMolecularAlteration; -import org.cbioportal.model.GenesetMolecularAlteration; -import org.cbioportal.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.GenesetMolecularAlteration; +import org.cbioportal.legacy.model.MolecularProfileSamples; import java.util.List; import java.util.Set; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMyBatisRepository.java similarity index 89% rename from src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMyBatisRepository.java index b724350c86f..b93f08e519b 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMyBatisRepository.java @@ -1,7 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.*; -import org.cbioportal.persistence.MolecularDataRepository; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.GenesetMolecularAlteration; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.persistence.MolecularDataRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; @@ -34,7 +37,7 @@ public Map commaSeparatedSampleIdsOfMolecularPr } @Override - public List getGeneMolecularAlterations(String molecularProfileId, + public List getGeneMolecularAlterations(String molecularProfileId, List entrezGeneIds, String projection) { return molecularDataMapper.getGeneMolecularAlterations(molecularProfileId, entrezGeneIds, projection); @@ -66,7 +69,7 @@ public List getGeneMolecularAlterationsInMultipleMolecu } @Override - public List getGenesetMolecularAlterations(String molecularProfileId, + public List getGenesetMolecularAlterations(String molecularProfileId, List genesetIds, String projection) { return molecularDataMapper.getGenesetMolecularAlterations(molecularProfileId, genesetIds, projection); diff --git a/src/main/java/org/cbioportal/persistence/mybatis/MolecularProfileMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMapper.java similarity index 84% rename from src/main/java/org/cbioportal/persistence/mybatis/MolecularProfileMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMapper.java index 64bf0a5936d..ea972aca916 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/MolecularProfileMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; import java.util.Set; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/MolecularProfileMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMyBatisRepository.java similarity index 89% rename from src/main/java/org/cbioportal/persistence/mybatis/MolecularProfileMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMyBatisRepository.java index bf0e656f401..fdae0ff7eba 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/MolecularProfileMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; import java.util.Arrays; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/MutationMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MutationMapper.java similarity index 89% rename from src/main/java/org/cbioportal/persistence/mybatis/MutationMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/MutationMapper.java index 26a26ddfad9..aa854e74422 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/MutationMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MutationMapper.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.meta.MutationMeta; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.meta.MutationMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MutationMyBatisRepository.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/MutationMyBatisRepository.java index d5e5ae0d3f6..24325692773 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MutationMyBatisRepository.java @@ -1,13 +1,13 @@ -package org.cbioportal.persistence.mybatis; - -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.persistence.MutationRepository; -import org.cbioportal.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +package org.cbioportal.legacy.persistence.mybatis; + +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.persistence.MutationRepository; +import org.cbioportal.legacy.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/PatientMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/PatientMapper.java similarity index 77% rename from src/main/java/org/cbioportal/persistence/mybatis/PatientMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/PatientMapper.java index 70864aa54ec..0a9ec0f173e 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/PatientMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/PatientMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/PatientMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/PatientMyBatisRepository.java similarity index 86% rename from src/main/java/org/cbioportal/persistence/mybatis/PatientMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/PatientMyBatisRepository.java index af4f1593030..2f8415fa730 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/PatientMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/PatientMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.PatientRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.PatientRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMapper.java similarity index 85% rename from src/main/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMapper.java index 39e7bdb5d50..0bf6f0250c6 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMapper.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ReferenceGenomeGene; +import org.cbioportal.legacy.model.ReferenceGenomeGene; import java.util.List; public interface ReferenceGenomeGeneMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMyBatisRepository.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMyBatisRepository.java index dc4091a2ec7..882f8e66806 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.persistence.ReferenceGenomeGeneRepository; -import org.cbioportal.persistence.PersistenceConstants; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.persistence.ReferenceGenomeGeneRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMapper.java similarity index 91% rename from src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMapper.java index ec3ea25ab9d..9e76d96b45a 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.ResourceData; +import org.cbioportal.legacy.model.ResourceData; public interface ResourceDataMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMyBatisRepository.java similarity index 91% rename from src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMyBatisRepository.java index 79a66956f5c..252ec7da68a 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.ResourceData; -import org.cbioportal.persistence.ResourceDataRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.ResourceData; +import org.cbioportal.legacy.persistence.ResourceDataRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMapper.java similarity index 76% rename from src/main/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMapper.java index e15c5218bb0..e41c5c09dcf 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.ResourceDefinition; +import org.cbioportal.legacy.model.ResourceDefinition; public interface ResourceDefinitionMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMyBatisRepository.java similarity index 75% rename from src/main/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMyBatisRepository.java index 4a07420fb73..54e4f8a62f6 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMyBatisRepository.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.ResourceDefinitionRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.ResourceDefinitionRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SampleListMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.java similarity index 75% rename from src/main/java/org/cbioportal/persistence/mybatis/SampleListMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.java index af777db0597..8130882d0f2 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SampleListMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.SampleListToSampleId; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.SampleListToSampleId; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SampleListMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleListMyBatisRepository.java similarity index 84% rename from src/main/java/org/cbioportal/persistence/mybatis/SampleListMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleListMyBatisRepository.java index f7141eef555..a27b268a33c 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SampleListMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleListMyBatisRepository.java @@ -1,13 +1,13 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.SampleListToSampleId; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.SampleListToSampleId; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SampleMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleMapper.java similarity index 86% rename from src/main/java/org/cbioportal/persistence/mybatis/SampleMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleMapper.java index 8d77020b1fc..6d67151dd04 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SampleMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SampleMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleMyBatisRepository.java similarity index 93% rename from src/main/java/org/cbioportal/persistence/mybatis/SampleMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleMyBatisRepository.java index 0fc72b39234..29e9347938c 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SampleMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SampleRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SampleRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SecurityMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SecurityMapper.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/mybatis/SecurityMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SecurityMapper.java index 3f47af78354..c37ce170225 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SecurityMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SecurityMapper.java @@ -30,13 +30,13 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; // imports import org.apache.ibatis.annotations.Param; -import org.cbioportal.model.User; -import org.cbioportal.model.UserAuthorities; +import org.cbioportal.legacy.model.User; +import org.cbioportal.legacy.model.UserAuthorities; /** * Interface to use to retrieve diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SecurityMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SecurityMyBatisRepository.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/mybatis/SecurityMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SecurityMyBatisRepository.java index 3172948d2a5..edc29b31f6c 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SecurityMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SecurityMyBatisRepository.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; // imports import java.util.Arrays; @@ -41,9 +41,9 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import org.cbioportal.model.User; -import org.cbioportal.model.UserAuthorities; -import org.cbioportal.persistence.SecurityRepository; +import org.cbioportal.legacy.model.User; +import org.cbioportal.legacy.model.UserAuthorities; +import org.cbioportal.legacy.persistence.SecurityRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMapper.java similarity index 68% rename from src/main/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMapper.java index dbcc1f2b852..61ea2bb38a7 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepository.java similarity index 77% rename from src/main/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepository.java index 7cadd7e8cd1..29a273c297e 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SignificantCopyNumberRegionRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SignificantCopyNumberRegionRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMapper.java similarity index 69% rename from src/main/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMapper.java index 0cb1eccefe6..61a86f9ff06 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepository.java similarity index 76% rename from src/main/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepository.java index 69225317885..b31f209ad2d 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepository.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SignificantlyMutatedGeneRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SignificantlyMutatedGeneRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/StaticDataTimeStampMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StaticDataTimeStampMyBatisRepository.java similarity index 77% rename from src/main/java/org/cbioportal/persistence/mybatis/StaticDataTimeStampMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/StaticDataTimeStampMyBatisRepository.java index bdcf5eb308a..66bdd7fd252 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/StaticDataTimeStampMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StaticDataTimeStampMyBatisRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.TableTimestampPair; -import org.cbioportal.persistence.StaticDataTimeStampRepository; +import org.cbioportal.legacy.model.TableTimestampPair; +import org.cbioportal.legacy.persistence.StaticDataTimeStampRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/StaticDataTimestampMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StaticDataTimestampMapper.java similarity index 59% rename from src/main/java/org/cbioportal/persistence/mybatis/StaticDataTimestampMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/StaticDataTimestampMapper.java index 573d0d8be6c..667f659d4f0 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/StaticDataTimestampMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StaticDataTimestampMapper.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.TableTimestampPair; +import org.cbioportal.legacy.model.TableTimestampPair; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/StructuralVariantMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMapper.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/mybatis/StructuralVariantMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMapper.java index 2a24f753b0d..27c88835e1e 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/StructuralVariantMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMapper.java @@ -21,14 +21,14 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantQuery; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantQuery; public interface StructuralVariantMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/StructuralVariantMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMyBatisRepository.java similarity index 89% rename from src/main/java/org/cbioportal/persistence/mybatis/StructuralVariantMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMyBatisRepository.java index f03d42130da..0affdf9fada 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/StructuralVariantMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMyBatisRepository.java @@ -21,14 +21,14 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantQuery; -import org.cbioportal.persistence.StructuralVariantRepository; -import org.cbioportal.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantQuery; +import org.cbioportal.legacy.persistence.StructuralVariantRepository; +import org.cbioportal.legacy.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/StudyMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StudyMapper.java similarity index 70% rename from src/main/java/org/cbioportal/persistence/mybatis/StudyMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/StudyMapper.java index 04290b77c80..2394f2128ff 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/StudyMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StudyMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/StudyMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StudyMyBatisRepository.java similarity index 83% rename from src/main/java/org/cbioportal/persistence/mybatis/StudyMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/StudyMyBatisRepository.java index 813c6ff5ab6..22f59350cd0 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/StudyMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StudyMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.StudyRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.StudyRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/TreatmentMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMapper.java similarity index 78% rename from src/main/java/org/cbioportal/persistence/mybatis/TreatmentMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMapper.java index 44e4f856079..344cdb0b9b8 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/TreatmentMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ClinicalEventSample; -import org.cbioportal.model.Treatment; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.Treatment; import java.util.List; import java.util.Set; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/TreatmentMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMyBatisRepository.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/mybatis/TreatmentMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMyBatisRepository.java index d44bdfc808a..cc4ec1c42f3 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/TreatmentMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMyBatisRepository.java @@ -1,7 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.*; -import org.cbioportal.persistence.TreatmentRepository; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.Treatment; +import org.cbioportal.legacy.persistence.TreatmentRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/VariantCountMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMapper.java similarity index 70% rename from src/main/java/org/cbioportal/persistence/mybatis/VariantCountMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMapper.java index 2d67d112897..3ec11587d6a 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/VariantCountMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMapper.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.VariantCount; +import org.cbioportal.legacy.model.VariantCount; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/VariantCountMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMyBatisRepository.java similarity index 78% rename from src/main/java/org/cbioportal/persistence/mybatis/VariantCountMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMyBatisRepository.java index 723c2bafa30..6b726f882a1 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/VariantCountMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMyBatisRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.VariantCount; -import org.cbioportal.persistence.VariantCountRepository; +import org.cbioportal.legacy.model.VariantCount; +import org.cbioportal.legacy.persistence.VariantCountRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/config/PersistenceConfig.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/config/PersistenceConfig.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/mybatis/config/PersistenceConfig.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/config/PersistenceConfig.java index b8dba141ae4..0e93dbbbfa3 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/config/PersistenceConfig.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/config/PersistenceConfig.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis.config; +package org.cbioportal.legacy.persistence.mybatis.config; -import org.cbioportal.model.Sample; -import org.cbioportal.persistence.mybatis.typehandler.SampleTypeTypeHandler; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.persistence.mybatis.typehandler.SampleTypeTypeHandler; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.mybatis.spring.SqlSessionFactoryBean; import org.mybatis.spring.annotation.MapperScan; import org.mybatis.spring.boot.autoconfigure.ConfigurationCustomizer; @@ -17,7 +17,8 @@ @Configuration -@MapperScan(value="org.cbioportal.persistence.mybatis", sqlSessionFactoryRef="sqlSessionFactory") +@MapperScan(value="org.cbioportal.legacy.persistence.mybatis", sqlSessionFactoryRef= + "sqlSessionFactory") public class PersistenceConfig { // This is the only way I was able to register the SampleType TypeHandler to MyBatis. @@ -50,7 +51,7 @@ private SqlSessionFactoryBean sqlSessionFactory(DataSource dataSource, Applicati SqlSessionFactoryBean sessionFactory = new SqlSessionFactoryBean(); sessionFactory.setDataSource(dataSource); sessionFactory.setMapperLocations( - applicationContext.getResources("classpath:org/cbioportal/persistence/mybatis/*.xml") + applicationContext.getResources("classpath:org/cbioportal/legacy/persistence/mybatis/*.xml") ); sessionFactory.setTypeHandlers(new SampleTypeTypeHandler()); return sessionFactory; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/typehandler/SampleTypeTypeHandler.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/typehandler/SampleTypeTypeHandler.java similarity index 91% rename from src/main/java/org/cbioportal/persistence/mybatis/typehandler/SampleTypeTypeHandler.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/typehandler/SampleTypeTypeHandler.java index 1b3d7b9986b..676ae17f8fb 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/typehandler/SampleTypeTypeHandler.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/typehandler/SampleTypeTypeHandler.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis.typehandler; +package org.cbioportal.legacy.persistence.mybatis.typehandler; import org.apache.ibatis.type.JdbcType; import org.apache.ibatis.type.MappedTypes; import org.apache.ibatis.type.TypeHandler; -import org.cbioportal.model.Sample; +import org.cbioportal.legacy.model.Sample; import java.sql.CallableStatement; import java.sql.PreparedStatement; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/util/CustomMyBatisObjectFactory.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/CustomMyBatisObjectFactory.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/mybatis/util/CustomMyBatisObjectFactory.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/util/CustomMyBatisObjectFactory.java index 4899efbed12..43000f0e6db 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/util/CustomMyBatisObjectFactory.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/CustomMyBatisObjectFactory.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.mybatis.util; +package org.cbioportal.legacy.persistence.mybatis.util; import org.apache.ibatis.reflection.factory.DefaultObjectFactory; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/util/LimitedPermissionArrayList.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/LimitedPermissionArrayList.java similarity index 97% rename from src/main/java/org/cbioportal/persistence/mybatis/util/LimitedPermissionArrayList.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/util/LimitedPermissionArrayList.java index 3c864c42d72..fb194add891 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/util/LimitedPermissionArrayList.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/LimitedPermissionArrayList.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.mybatis.util; +package org.cbioportal.legacy.persistence.mybatis.util; import java.util.*; import java.util.function.*; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/util/MolecularProfileCaseIdentifierUtil.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/MolecularProfileCaseIdentifierUtil.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/mybatis/util/MolecularProfileCaseIdentifierUtil.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/util/MolecularProfileCaseIdentifierUtil.java index 699f3f239b5..1c2785e1732 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/util/MolecularProfileCaseIdentifierUtil.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/MolecularProfileCaseIdentifierUtil.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.mybatis.util; +package org.cbioportal.legacy.persistence.mybatis.util; import org.apache.commons.math3.util.Pair; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/util/PaginationCalculator.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/PaginationCalculator.java similarity index 93% rename from src/main/java/org/cbioportal/persistence/mybatis/util/PaginationCalculator.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/util/PaginationCalculator.java index ab2b4588052..d2f123ce39c 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/util/PaginationCalculator.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/PaginationCalculator.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.mybatis.util; +package org.cbioportal.legacy.persistence.mybatis.util; public class PaginationCalculator { diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMapper.java similarity index 75% rename from src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMapper.java index dca5ad64125..3a2eea2f9b2 100644 --- a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMapper.java @@ -1,28 +1,28 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; import org.apache.ibatis.annotations.Param; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.PatientTreatment; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleTreatment; -import org.cbioportal.persistence.helper.AlterationFilterHelper; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.web.parameter.GenericAssayDataBinFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.PatientTreatment; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleTreatment; +import org.cbioportal.legacy.persistence.helper.AlterationFilterHelper; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; import java.util.List; import java.util.Map; diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java similarity index 86% rename from src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java index d3f594d61be..ef76a7926ca 100644 --- a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java @@ -1,32 +1,32 @@ -package org.cbioportal.persistence.mybatisclickhouse; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.PatientTreatment; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleTreatment; -import org.cbioportal.model.StudyViewFilterContext; -import org.cbioportal.persistence.StudyViewRepository; -import org.cbioportal.persistence.enums.DataSource; -import org.cbioportal.persistence.helper.AlterationFilterHelper; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.service.util.StudyViewColumnarServiceUtil; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.GenericAssayDataBinFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; +package org.cbioportal.legacy.persistence.mybatisclickhouse; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.PatientTreatment; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleTreatment; +import org.cbioportal.legacy.model.StudyViewFilterContext; +import org.cbioportal.legacy.persistence.StudyViewRepository; +import org.cbioportal.legacy.persistence.enums.DataSource; +import org.cbioportal.legacy.persistence.helper.AlterationFilterHelper; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.service.util.StudyViewColumnarServiceUtil; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java b/src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java similarity index 64% rename from src/main/java/org/cbioportal/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java index 7acea62ecec..b9f09e41284 100644 --- a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatisclickhouse.config; +package org.cbioportal.legacy.persistence.mybatisclickhouse.config; -import org.cbioportal.persistence.mybatis.typehandler.SampleTypeTypeHandler; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.persistence.mybatis.typehandler.SampleTypeTypeHandler; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.mybatis.spring.SqlSessionFactoryBean; import org.mybatis.spring.annotation.MapperScan; import org.springframework.beans.factory.annotation.Qualifier; @@ -15,7 +15,10 @@ @Configuration @ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true") -@MapperScan(value= "org.cbioportal.persistence.mybatisclickhouse", sqlSessionFactoryRef ="sqlColumnarSessionFactory") +@MapperScan(value= "org.cbioportal.legacy.persistence.mybatisclickhouse", + sqlSessionFactoryRef ="sqlColumnarSessionFactory") +@MapperScan(value= "org.cbioportal.infrastructure.repository.clickhouse", + sqlSessionFactoryRef = "sqlColumnarSessionFactory") public class PersistenceColumnarConfig { @Bean("sqlColumnarSessionFactory") @@ -25,6 +28,9 @@ public SqlSessionFactoryBean sqlColumnarSessionFactory(@Qualifier("clickhouseDat sessionFactory.setMapperLocations( applicationContext.getResources("classpath:org/cbioportal/persistence/mybatisclickhouse/*.xml") ); + sessionFactory.addMapperLocations( + applicationContext.getResources("classpath:mappers/clickhouse/**/*.xml")); + sessionFactory.setTypeHandlers(new SampleTypeTypeHandler()); return sessionFactory; } diff --git a/src/main/java/org/cbioportal/persistence/util/CacheEventLogger.java b/src/main/java/org/cbioportal/legacy/persistence/util/CacheEventLogger.java similarity index 98% rename from src/main/java/org/cbioportal/persistence/util/CacheEventLogger.java rename to src/main/java/org/cbioportal/legacy/persistence/util/CacheEventLogger.java index d7dd14d1374..f3c6a813086 100644 --- a/src/main/java/org/cbioportal/persistence/util/CacheEventLogger.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/CacheEventLogger.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import org.ehcache.event.*; import org.slf4j.Logger; diff --git a/src/main/java/org/cbioportal/persistence/util/CacheUtils.java b/src/main/java/org/cbioportal/legacy/persistence/util/CacheUtils.java similarity index 76% rename from src/main/java/org/cbioportal/persistence/util/CacheUtils.java rename to src/main/java/org/cbioportal/legacy/persistence/util/CacheUtils.java index 46b33334ab7..b6ebdc6411b 100644 --- a/src/main/java/org/cbioportal/persistence/util/CacheUtils.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/CacheUtils.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/util/CustomEhcachingProvider.java b/src/main/java/org/cbioportal/legacy/persistence/util/CustomEhcachingProvider.java similarity index 99% rename from src/main/java/org/cbioportal/persistence/util/CustomEhcachingProvider.java rename to src/main/java/org/cbioportal/legacy/persistence/util/CustomEhcachingProvider.java index b4591cc3600..10cf9b5631f 100644 --- a/src/main/java/org/cbioportal/persistence/util/CustomEhcachingProvider.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/CustomEhcachingProvider.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import java.io.*; import java.net.URL; @@ -49,7 +49,7 @@ import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.ehcache.impl.config.persistence.DefaultPersistenceConfiguration; -import org.cbioportal.persistence.CacheEnabledConfig; +import org.cbioportal.legacy.persistence.CacheEnabledConfig; public class CustomEhcachingProvider extends EhcacheCachingProvider { diff --git a/src/main/java/org/cbioportal/persistence/util/CustomKeyGenerator.java b/src/main/java/org/cbioportal/legacy/persistence/util/CustomKeyGenerator.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/util/CustomKeyGenerator.java rename to src/main/java/org/cbioportal/legacy/persistence/util/CustomKeyGenerator.java index 948d5d344c5..91146f40e4e 100644 --- a/src/main/java/org/cbioportal/persistence/util/CustomKeyGenerator.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/CustomKeyGenerator.java @@ -30,14 +30,14 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.CacheEnabledConfig; -import org.cbioportal.persistence.StudyRepository; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.CacheEnabledConfig; +import org.cbioportal.legacy.persistence.StudyRepository; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/cbioportal/persistence/util/CustomRedisCache.java b/src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCache.java similarity index 99% rename from src/main/java/org/cbioportal/persistence/util/CustomRedisCache.java rename to src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCache.java index 5036bdd6e9a..a05f201cc89 100644 --- a/src/main/java/org/cbioportal/persistence/util/CustomRedisCache.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCache.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import org.redisson.api.RedissonClient; import org.slf4j.Logger; diff --git a/src/main/java/org/cbioportal/persistence/util/CustomRedisCacheManager.java b/src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheManager.java similarity index 97% rename from src/main/java/org/cbioportal/persistence/util/CustomRedisCacheManager.java rename to src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheManager.java index 0c5cdb93dcd..4f7a941fb9b 100644 --- a/src/main/java/org/cbioportal/persistence/util/CustomRedisCacheManager.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheManager.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import jakarta.validation.constraints.NotNull; import org.redisson.api.RedissonClient; diff --git a/src/main/java/org/cbioportal/persistence/util/CustomRedisCachingProvider.java b/src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCachingProvider.java similarity index 98% rename from src/main/java/org/cbioportal/persistence/util/CustomRedisCachingProvider.java rename to src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCachingProvider.java index 88b6aaa79c3..d2449d5509d 100644 --- a/src/main/java/org/cbioportal/persistence/util/CustomRedisCachingProvider.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCachingProvider.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import org.redisson.Redisson; import org.redisson.api.RedissonClient; diff --git a/src/main/java/org/cbioportal/persistence/util/EhCacheUtils.java b/src/main/java/org/cbioportal/legacy/persistence/util/EhCacheUtils.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/util/EhCacheUtils.java rename to src/main/java/org/cbioportal/legacy/persistence/util/EhCacheUtils.java index b8226ec0f80..7c219f7824d 100644 --- a/src/main/java/org/cbioportal/persistence/util/EhCacheUtils.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/EhCacheUtils.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import jakarta.annotation.PostConstruct; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/persistence/util/EhcacheStatistics.java b/src/main/java/org/cbioportal/legacy/persistence/util/EhcacheStatistics.java similarity index 98% rename from src/main/java/org/cbioportal/persistence/util/EhcacheStatistics.java rename to src/main/java/org/cbioportal/legacy/persistence/util/EhcacheStatistics.java index bbf5d273ed9..ae6244bb2cc 100644 --- a/src/main/java/org/cbioportal/persistence/util/EhcacheStatistics.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/EhcacheStatistics.java @@ -30,10 +30,10 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import jakarta.annotation.PostConstruct; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.ehcache.core.statistics.*; import org.ehcache.config.ResourceType; import org.ehcache.impl.internal.statistics.DefaultStatisticsService; diff --git a/src/main/java/org/cbioportal/persistence/util/LoggingCacheErrorHandler.java b/src/main/java/org/cbioportal/legacy/persistence/util/LoggingCacheErrorHandler.java similarity index 97% rename from src/main/java/org/cbioportal/persistence/util/LoggingCacheErrorHandler.java rename to src/main/java/org/cbioportal/legacy/persistence/util/LoggingCacheErrorHandler.java index a682c568dca..74893052276 100644 --- a/src/main/java/org/cbioportal/persistence/util/LoggingCacheErrorHandler.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/LoggingCacheErrorHandler.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/src/main/java/org/cbioportal/persistence/util/RedisCacheUtils.java b/src/main/java/org/cbioportal/legacy/persistence/util/RedisCacheUtils.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/util/RedisCacheUtils.java rename to src/main/java/org/cbioportal/legacy/persistence/util/RedisCacheUtils.java index ec5579c544d..121339bb96b 100644 --- a/src/main/java/org/cbioportal/persistence/util/RedisCacheUtils.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/RedisCacheUtils.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; -import static org.cbioportal.persistence.util.CustomRedisCache.DELIMITER; +import static org.cbioportal.legacy.persistence.util.CustomRedisCache.DELIMITER; import org.redisson.api.RedissonClient; diff --git a/src/main/java/org/cbioportal/properties/CustomDataSourceConfiguration.java b/src/main/java/org/cbioportal/legacy/properties/CustomDataSourceConfiguration.java similarity index 90% rename from src/main/java/org/cbioportal/properties/CustomDataSourceConfiguration.java rename to src/main/java/org/cbioportal/legacy/properties/CustomDataSourceConfiguration.java index f71d07b1393..d2b78d4e4e9 100644 --- a/src/main/java/org/cbioportal/properties/CustomDataSourceConfiguration.java +++ b/src/main/java/org/cbioportal/legacy/properties/CustomDataSourceConfiguration.java @@ -1,6 +1,6 @@ -package org.cbioportal.properties; +package org.cbioportal.legacy.properties; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.boot.autoconfigure.jdbc.DataSourceProperties; import org.springframework.boot.context.properties.ConfigurationProperties; import org.springframework.context.annotation.Bean; diff --git a/src/main/java/org/cbioportal/properties/PortalProperties.java b/src/main/java/org/cbioportal/legacy/properties/PortalProperties.java similarity index 85% rename from src/main/java/org/cbioportal/properties/PortalProperties.java rename to src/main/java/org/cbioportal/legacy/properties/PortalProperties.java index 298c343a7be..5d315c9c960 100644 --- a/src/main/java/org/cbioportal/properties/PortalProperties.java +++ b/src/main/java/org/cbioportal/legacy/properties/PortalProperties.java @@ -1,6 +1,6 @@ -package org.cbioportal.properties; +package org.cbioportal.legacy.properties; -import org.cbioportal.utils.validation.AllowedValues; +import org.cbioportal.legacy.utils.validation.AllowedValues; import org.springframework.boot.context.properties.ConfigurationProperties; import org.springframework.context.annotation.Configuration; import org.springframework.validation.annotation.Validated; diff --git a/src/main/java/org/cbioportal/service/AlterationCountService.java b/src/main/java/org/cbioportal/legacy/service/AlterationCountService.java similarity index 94% rename from src/main/java/org/cbioportal/service/AlterationCountService.java rename to src/main/java/org/cbioportal/legacy/service/AlterationCountService.java index 639c1daab7d..5210c59e9d6 100644 --- a/src/main/java/org/cbioportal/service/AlterationCountService.java +++ b/src/main/java/org/cbioportal/legacy/service/AlterationCountService.java @@ -1,13 +1,12 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.*; -import org.cbioportal.model.util.Select; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter; -import org.cbioportal.web.parameter.CustomSampleIdentifier; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.util.Select; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/AlterationDriverAnnotationService.java b/src/main/java/org/cbioportal/legacy/service/AlterationDriverAnnotationService.java similarity index 63% rename from src/main/java/org/cbioportal/service/AlterationDriverAnnotationService.java rename to src/main/java/org/cbioportal/legacy/service/AlterationDriverAnnotationService.java index 6f13a93f0f0..0cc2dda4fca 100644 --- a/src/main/java/org/cbioportal/service/AlterationDriverAnnotationService.java +++ b/src/main/java/org/cbioportal/legacy/service/AlterationDriverAnnotationService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.CustomDriverAnnotationReport; +import org.cbioportal.legacy.model.CustomDriverAnnotationReport; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/AlterationEnrichmentService.java b/src/main/java/org/cbioportal/legacy/service/AlterationEnrichmentService.java similarity index 51% rename from src/main/java/org/cbioportal/service/AlterationEnrichmentService.java rename to src/main/java/org/cbioportal/legacy/service/AlterationEnrichmentService.java index 98d01347e38..fe094702477 100644 --- a/src/main/java/org/cbioportal/service/AlterationEnrichmentService.java +++ b/src/main/java/org/cbioportal/legacy/service/AlterationEnrichmentService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.AlterationEnrichment; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.AlterationEnrichment; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import java.util.List; import java.util.Map; diff --git a/src/main/java/org/cbioportal/service/AttributeByStudyService.java b/src/main/java/org/cbioportal/legacy/service/AttributeByStudyService.java similarity index 67% rename from src/main/java/org/cbioportal/service/AttributeByStudyService.java rename to src/main/java/org/cbioportal/legacy/service/AttributeByStudyService.java index a1f198d1e15..1dd37130aaa 100644 --- a/src/main/java/org/cbioportal/service/AttributeByStudyService.java +++ b/src/main/java/org/cbioportal/legacy/service/AttributeByStudyService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttribute; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/CacheService.java b/src/main/java/org/cbioportal/legacy/service/CacheService.java similarity index 68% rename from src/main/java/org/cbioportal/service/CacheService.java rename to src/main/java/org/cbioportal/legacy/service/CacheService.java index ca0831f361e..75e8cecceac 100644 --- a/src/main/java/org/cbioportal/service/CacheService.java +++ b/src/main/java/org/cbioportal/legacy/service/CacheService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.service.exception.CacheOperationException; +import org.cbioportal.legacy.service.exception.CacheOperationException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/CacheStatisticsService.java b/src/main/java/org/cbioportal/legacy/service/CacheStatisticsService.java similarity index 71% rename from src/main/java/org/cbioportal/service/CacheStatisticsService.java rename to src/main/java/org/cbioportal/legacy/service/CacheStatisticsService.java index 94453f84c6f..6fe7d878920 100644 --- a/src/main/java/org/cbioportal/service/CacheStatisticsService.java +++ b/src/main/java/org/cbioportal/legacy/service/CacheStatisticsService.java @@ -1,7 +1,7 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.*; -import org.cbioportal.service.exception.CacheNotFoundException; +import org.cbioportal.legacy.service.exception.CacheNotFoundException; public interface CacheStatisticsService { diff --git a/src/main/java/org/cbioportal/service/CancerTypeService.java b/src/main/java/org/cbioportal/legacy/service/CancerTypeService.java similarity index 67% rename from src/main/java/org/cbioportal/service/CancerTypeService.java rename to src/main/java/org/cbioportal/legacy/service/CancerTypeService.java index fad6e41b1d3..97919472a89 100644 --- a/src/main/java/org/cbioportal/service/CancerTypeService.java +++ b/src/main/java/org/cbioportal/legacy/service/CancerTypeService.java @@ -1,8 +1,8 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.CancerTypeNotFoundException; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException; import java.util.List; import java.util.Map; diff --git a/src/main/java/org/cbioportal/service/ClinicalAttributeService.java b/src/main/java/org/cbioportal/legacy/service/ClinicalAttributeService.java similarity index 77% rename from src/main/java/org/cbioportal/service/ClinicalAttributeService.java rename to src/main/java/org/cbioportal/legacy/service/ClinicalAttributeService.java index 3b648824419..6d7a3120744 100644 --- a/src/main/java/org/cbioportal/service/ClinicalAttributeService.java +++ b/src/main/java/org/cbioportal/legacy/service/ClinicalAttributeService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.ClinicalAttributeNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.ClinicalAttributeNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/ClinicalDataDensityPlotService.java b/src/main/java/org/cbioportal/legacy/service/ClinicalDataDensityPlotService.java similarity index 50% rename from src/main/java/org/cbioportal/service/ClinicalDataDensityPlotService.java rename to src/main/java/org/cbioportal/legacy/service/ClinicalDataDensityPlotService.java index 211963e11b8..280b7a991d1 100644 --- a/src/main/java/org/cbioportal/service/ClinicalDataDensityPlotService.java +++ b/src/main/java/org/cbioportal/legacy/service/ClinicalDataDensityPlotService.java @@ -1,9 +1,9 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.DensityPlotData; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.DensityPlotParameters; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.DensityPlotData; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.DensityPlotParameters; import java.math.BigDecimal; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/ClinicalDataService.java b/src/main/java/org/cbioportal/legacy/service/ClinicalDataService.java similarity index 86% rename from src/main/java/org/cbioportal/service/ClinicalDataService.java rename to src/main/java/org/cbioportal/legacy/service/ClinicalDataService.java index b57474d1c4f..1b96099ee97 100644 --- a/src/main/java/org/cbioportal/service/ClinicalDataService.java +++ b/src/main/java/org/cbioportal/legacy/service/ClinicalDataService.java @@ -1,13 +1,13 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import org.apache.commons.lang3.tuple.ImmutablePair; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.SampleClinicalDataCollection; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.SampleClinicalDataCollection; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; public interface ClinicalDataService { diff --git a/src/main/java/org/cbioportal/service/ClinicalEventService.java b/src/main/java/org/cbioportal/legacy/service/ClinicalEventService.java similarity index 77% rename from src/main/java/org/cbioportal/service/ClinicalEventService.java rename to src/main/java/org/cbioportal/legacy/service/ClinicalEventService.java index ad0009ac0b6..8610e0af939 100644 --- a/src/main/java/org/cbioportal/service/ClinicalEventService.java +++ b/src/main/java/org/cbioportal/legacy/service/ClinicalEventService.java @@ -1,12 +1,12 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.parameter.SurvivalRequest; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.parameter.SurvivalRequest; import java.util.List; import java.util.Map; diff --git a/src/main/java/org/cbioportal/service/CoExpressionService.java b/src/main/java/org/cbioportal/legacy/service/CoExpressionService.java similarity index 77% rename from src/main/java/org/cbioportal/service/CoExpressionService.java rename to src/main/java/org/cbioportal/legacy/service/CoExpressionService.java index fe9137f806f..1068413d3ab 100644 --- a/src/main/java/org/cbioportal/service/CoExpressionService.java +++ b/src/main/java/org/cbioportal/legacy/service/CoExpressionService.java @@ -1,11 +1,11 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.CoExpression; -import org.cbioportal.model.EntityType; -import org.cbioportal.service.exception.GeneNotFoundException; -import org.cbioportal.service.exception.GenesetNotFoundException; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.CoExpression; +import org.cbioportal.legacy.model.EntityType; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/CopyNumberSegmentService.java b/src/main/java/org/cbioportal/legacy/service/CopyNumberSegmentService.java similarity index 78% rename from src/main/java/org/cbioportal/service/CopyNumberSegmentService.java rename to src/main/java/org/cbioportal/legacy/service/CopyNumberSegmentService.java index f251e710474..6656a397262 100644 --- a/src/main/java/org/cbioportal/service/CopyNumberSegmentService.java +++ b/src/main/java/org/cbioportal/legacy/service/CopyNumberSegmentService.java @@ -1,9 +1,9 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/CosmicCountService.java b/src/main/java/org/cbioportal/legacy/service/CosmicCountService.java similarity index 61% rename from src/main/java/org/cbioportal/service/CosmicCountService.java rename to src/main/java/org/cbioportal/legacy/service/CosmicCountService.java index 4ba451f6008..b9614760fdd 100644 --- a/src/main/java/org/cbioportal/service/CosmicCountService.java +++ b/src/main/java/org/cbioportal/legacy/service/CosmicCountService.java @@ -1,8 +1,8 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.CosmicMutation; +import org.cbioportal.legacy.model.CosmicMutation; public interface CosmicCountService { diff --git a/src/main/java/org/cbioportal/service/CustomDataService.java b/src/main/java/org/cbioportal/legacy/service/CustomDataService.java similarity index 62% rename from src/main/java/org/cbioportal/service/CustomDataService.java rename to src/main/java/org/cbioportal/legacy/service/CustomDataService.java index 6f1b96f8c65..9cadacb327c 100644 --- a/src/main/java/org/cbioportal/service/CustomDataService.java +++ b/src/main/java/org/cbioportal/legacy/service/CustomDataService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.service.util.CustomDataSession; +import org.cbioportal.legacy.service.util.CustomDataSession; import java.util.List; import java.util.Map; diff --git a/src/main/java/org/cbioportal/service/DataAccessTokenService.java b/src/main/java/org/cbioportal/legacy/service/DataAccessTokenService.java similarity index 96% rename from src/main/java/org/cbioportal/service/DataAccessTokenService.java rename to src/main/java/org/cbioportal/legacy/service/DataAccessTokenService.java index 77447dab63e..2679b8b0f64 100644 --- a/src/main/java/org/cbioportal/service/DataAccessTokenService.java +++ b/src/main/java/org/cbioportal/legacy/service/DataAccessTokenService.java @@ -30,12 +30,12 @@ * along with this program. If not, see . */ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.Date; import java.util.List; -import org.cbioportal.model.DataAccessToken; +import org.cbioportal.legacy.model.DataAccessToken; import org.springframework.security.core.Authentication; public interface DataAccessTokenService { diff --git a/src/main/java/org/cbioportal/service/DiscreteCopyNumberService.java b/src/main/java/org/cbioportal/legacy/service/DiscreteCopyNumberService.java similarity index 90% rename from src/main/java/org/cbioportal/service/DiscreteCopyNumberService.java rename to src/main/java/org/cbioportal/legacy/service/DiscreteCopyNumberService.java index 7dbd1e8a5a9..a6de88b9752 100644 --- a/src/main/java/org/cbioportal/service/DiscreteCopyNumberService.java +++ b/src/main/java/org/cbioportal/legacy/service/DiscreteCopyNumberService.java @@ -1,8 +1,11 @@ -package org.cbioportal.service; - -import org.cbioportal.model.*; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service; + +import org.cbioportal.legacy.model.CopyNumberCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/ExpressionEnrichmentService.java b/src/main/java/org/cbioportal/legacy/service/ExpressionEnrichmentService.java similarity index 73% rename from src/main/java/org/cbioportal/service/ExpressionEnrichmentService.java rename to src/main/java/org/cbioportal/legacy/service/ExpressionEnrichmentService.java index d3c2a444bd8..03bd46668fa 100644 --- a/src/main/java/org/cbioportal/service/ExpressionEnrichmentService.java +++ b/src/main/java/org/cbioportal/legacy/service/ExpressionEnrichmentService.java @@ -1,15 +1,15 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; import java.util.Map; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.GenericAssayEnrichment; -import org.cbioportal.model.GenomicEnrichment; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.GenericAssayBinaryEnrichment; -import org.cbioportal.model.GenericAssayCategoricalEnrichment; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.GenericAssayEnrichment; +import org.cbioportal.legacy.model.GenomicEnrichment; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.GenericAssayBinaryEnrichment; +import org.cbioportal.legacy.model.GenericAssayCategoricalEnrichment; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; public interface ExpressionEnrichmentService { diff --git a/src/main/java/org/cbioportal/service/FrontendPropertiesService.java b/src/main/java/org/cbioportal/legacy/service/FrontendPropertiesService.java similarity index 84% rename from src/main/java/org/cbioportal/service/FrontendPropertiesService.java rename to src/main/java/org/cbioportal/legacy/service/FrontendPropertiesService.java index a965eaf40d1..647cdce704e 100644 --- a/src/main/java/org/cbioportal/service/FrontendPropertiesService.java +++ b/src/main/java/org/cbioportal/legacy/service/FrontendPropertiesService.java @@ -1,4 +1,4 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.Map; diff --git a/src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/FrontendPropertiesServiceImpl.java similarity index 99% rename from src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/FrontendPropertiesServiceImpl.java index abe7f299226..e760e3fd985 100644 --- a/src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/FrontendPropertiesServiceImpl.java @@ -1,4 +1,4 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import jakarta.annotation.PostConstruct; import org.slf4j.Logger; diff --git a/src/main/java/org/cbioportal/service/GeneMemoizerService.java b/src/main/java/org/cbioportal/legacy/service/GeneMemoizerService.java similarity index 68% rename from src/main/java/org/cbioportal/service/GeneMemoizerService.java rename to src/main/java/org/cbioportal/legacy/service/GeneMemoizerService.java index 995afc60a27..67dc7bfcba5 100644 --- a/src/main/java/org/cbioportal/service/GeneMemoizerService.java +++ b/src/main/java/org/cbioportal/legacy/service/GeneMemoizerService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ReferenceGenomeGene; +import org.cbioportal.legacy.model.ReferenceGenomeGene; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/GenePanelService.java b/src/main/java/org/cbioportal/legacy/service/GenePanelService.java similarity index 79% rename from src/main/java/org/cbioportal/service/GenePanelService.java rename to src/main/java/org/cbioportal/legacy/service/GenePanelService.java index 9c0b2c6c8e6..d6205b28544 100644 --- a/src/main/java/org/cbioportal/service/GenePanelService.java +++ b/src/main/java/org/cbioportal/legacy/service/GenePanelService.java @@ -1,11 +1,11 @@ -package org.cbioportal.service; - -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.GenePanelNotFoundException; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service; + +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.GenePanelNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.cache.annotation.Cacheable; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/GeneService.java b/src/main/java/org/cbioportal/legacy/service/GeneService.java similarity index 72% rename from src/main/java/org/cbioportal/service/GeneService.java rename to src/main/java/org/cbioportal/legacy/service/GeneService.java index ce60d3a4c79..6544f52485a 100644 --- a/src/main/java/org/cbioportal/service/GeneService.java +++ b/src/main/java/org/cbioportal/legacy/service/GeneService.java @@ -1,9 +1,9 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.Gene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.GeneNotFoundException; -import org.cbioportal.service.exception.GeneWithMultipleEntrezIdsException; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.service.exception.GeneWithMultipleEntrezIdsException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/GenericAssayService.java b/src/main/java/org/cbioportal/legacy/service/GenericAssayService.java similarity index 80% rename from src/main/java/org/cbioportal/service/GenericAssayService.java rename to src/main/java/org/cbioportal/legacy/service/GenericAssayService.java index 8f85a4fd179..3051d564ba8 100644 --- a/src/main/java/org/cbioportal/service/GenericAssayService.java +++ b/src/main/java/org/cbioportal/legacy/service/GenericAssayService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.GenericAssayData; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.GenericAssayData; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; public interface GenericAssayService { diff --git a/src/main/java/org/cbioportal/service/GenesetCorrelationService.java b/src/main/java/org/cbioportal/legacy/service/GenesetCorrelationService.java similarity index 69% rename from src/main/java/org/cbioportal/service/GenesetCorrelationService.java rename to src/main/java/org/cbioportal/legacy/service/GenesetCorrelationService.java index 8136290b344..f27e8b18dfb 100644 --- a/src/main/java/org/cbioportal/service/GenesetCorrelationService.java +++ b/src/main/java/org/cbioportal/legacy/service/GenesetCorrelationService.java @@ -1,11 +1,11 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.GenesetCorrelation; -import org.cbioportal.service.exception.GenesetNotFoundException; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.GenesetCorrelation; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; public interface GenesetCorrelationService { diff --git a/src/main/java/org/cbioportal/service/GenesetDataService.java b/src/main/java/org/cbioportal/legacy/service/GenesetDataService.java similarity index 64% rename from src/main/java/org/cbioportal/service/GenesetDataService.java rename to src/main/java/org/cbioportal/legacy/service/GenesetDataService.java index 9ad80bf9f08..87936bccdf7 100644 --- a/src/main/java/org/cbioportal/service/GenesetDataService.java +++ b/src/main/java/org/cbioportal/legacy/service/GenesetDataService.java @@ -1,11 +1,11 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.GenesetMolecularAlteration; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.GenesetMolecularAlteration; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; public interface GenesetDataService { diff --git a/src/main/java/org/cbioportal/service/GenesetHierarchyService.java b/src/main/java/org/cbioportal/legacy/service/GenesetHierarchyService.java similarity index 73% rename from src/main/java/org/cbioportal/service/GenesetHierarchyService.java rename to src/main/java/org/cbioportal/legacy/service/GenesetHierarchyService.java index 4aea20dab8e..84b82a74e97 100644 --- a/src/main/java/org/cbioportal/service/GenesetHierarchyService.java +++ b/src/main/java/org/cbioportal/legacy/service/GenesetHierarchyService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.GenesetHierarchyInfo; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; public interface GenesetHierarchyService { diff --git a/src/main/java/org/cbioportal/service/GenesetService.java b/src/main/java/org/cbioportal/legacy/service/GenesetService.java similarity index 64% rename from src/main/java/org/cbioportal/service/GenesetService.java rename to src/main/java/org/cbioportal/legacy/service/GenesetService.java index 29a3630f5c3..92a511d5872 100644 --- a/src/main/java/org/cbioportal/service/GenesetService.java +++ b/src/main/java/org/cbioportal/legacy/service/GenesetService.java @@ -1,11 +1,11 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; public interface GenesetService { diff --git a/src/main/java/org/cbioportal/service/MolecularDataService.java b/src/main/java/org/cbioportal/legacy/service/MolecularDataService.java similarity index 86% rename from src/main/java/org/cbioportal/service/MolecularDataService.java rename to src/main/java/org/cbioportal/legacy/service/MolecularDataService.java index b1ac3fa3eaa..9e2da76bec4 100644 --- a/src/main/java/org/cbioportal/service/MolecularDataService.java +++ b/src/main/java/org/cbioportal/legacy/service/MolecularDataService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GeneMolecularAlteration; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/MolecularProfileService.java b/src/main/java/org/cbioportal/legacy/service/MolecularProfileService.java similarity index 85% rename from src/main/java/org/cbioportal/service/MolecularProfileService.java rename to src/main/java/org/cbioportal/legacy/service/MolecularProfileService.java index e3724261798..47e0f31351d 100644 --- a/src/main/java/org/cbioportal/service/MolecularProfileService.java +++ b/src/main/java/org/cbioportal/legacy/service/MolecularProfileService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; import java.util.Set; diff --git a/src/main/java/org/cbioportal/service/MrnaPercentileService.java b/src/main/java/org/cbioportal/legacy/service/MrnaPercentileService.java similarity index 58% rename from src/main/java/org/cbioportal/service/MrnaPercentileService.java rename to src/main/java/org/cbioportal/legacy/service/MrnaPercentileService.java index 98e0ed5a0f5..b9c276a5ac2 100644 --- a/src/main/java/org/cbioportal/service/MrnaPercentileService.java +++ b/src/main/java/org/cbioportal/legacy/service/MrnaPercentileService.java @@ -1,7 +1,7 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.MrnaPercentile; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.MrnaPercentile; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/MutationService.java b/src/main/java/org/cbioportal/legacy/service/MutationService.java similarity index 88% rename from src/main/java/org/cbioportal/service/MutationService.java rename to src/main/java/org/cbioportal/legacy/service/MutationService.java index c51153d1111..662664a83a0 100644 --- a/src/main/java/org/cbioportal/service/MutationService.java +++ b/src/main/java/org/cbioportal/legacy/service/MutationService.java @@ -1,11 +1,11 @@ -package org.cbioportal.service; - -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service; + +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/MutationSpectrumService.java b/src/main/java/org/cbioportal/legacy/service/MutationSpectrumService.java similarity index 68% rename from src/main/java/org/cbioportal/service/MutationSpectrumService.java rename to src/main/java/org/cbioportal/legacy/service/MutationSpectrumService.java index 63c0a050991..4002bc200d5 100644 --- a/src/main/java/org/cbioportal/service/MutationSpectrumService.java +++ b/src/main/java/org/cbioportal/legacy/service/MutationSpectrumService.java @@ -1,7 +1,7 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.MutationSpectrum; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.MutationSpectrum; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/PatientService.java b/src/main/java/org/cbioportal/legacy/service/PatientService.java similarity index 77% rename from src/main/java/org/cbioportal/service/PatientService.java rename to src/main/java/org/cbioportal/legacy/service/PatientService.java index 7ee3b93db76..04e62f18f3f 100644 --- a/src/main/java/org/cbioportal/service/PatientService.java +++ b/src/main/java/org/cbioportal/legacy/service/PatientService.java @@ -1,9 +1,9 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/ReadPermissionService.java b/src/main/java/org/cbioportal/legacy/service/ReadPermissionService.java similarity index 73% rename from src/main/java/org/cbioportal/service/ReadPermissionService.java rename to src/main/java/org/cbioportal/legacy/service/ReadPermissionService.java index 7c3bc23c8d4..fdd9c3cab64 100644 --- a/src/main/java/org/cbioportal/service/ReadPermissionService.java +++ b/src/main/java/org/cbioportal/legacy/service/ReadPermissionService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ReadPermission; +import org.cbioportal.legacy.model.ReadPermission; import org.springframework.security.core.Authentication; import java.util.Collection; diff --git a/src/main/java/org/cbioportal/service/ReferenceGenomeGeneService.java b/src/main/java/org/cbioportal/legacy/service/ReferenceGenomeGeneService.java similarity index 85% rename from src/main/java/org/cbioportal/service/ReferenceGenomeGeneService.java rename to src/main/java/org/cbioportal/legacy/service/ReferenceGenomeGeneService.java index 1fb09b586c9..604207db053 100644 --- a/src/main/java/org/cbioportal/service/ReferenceGenomeGeneService.java +++ b/src/main/java/org/cbioportal/legacy/service/ReferenceGenomeGeneService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ReferenceGenomeGene; +import org.cbioportal.legacy.model.ReferenceGenomeGene; import java.util.List; public interface ReferenceGenomeGeneService { diff --git a/src/main/java/org/cbioportal/service/ResourceDataService.java b/src/main/java/org/cbioportal/legacy/service/ResourceDataService.java similarity index 78% rename from src/main/java/org/cbioportal/service/ResourceDataService.java rename to src/main/java/org/cbioportal/legacy/service/ResourceDataService.java index 5727906394c..d04336283cc 100644 --- a/src/main/java/org/cbioportal/service/ResourceDataService.java +++ b/src/main/java/org/cbioportal/legacy/service/ResourceDataService.java @@ -1,11 +1,11 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.ResourceData; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.ResourceData; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; public interface ResourceDataService { diff --git a/src/main/java/org/cbioportal/service/ResourceDefinitionService.java b/src/main/java/org/cbioportal/legacy/service/ResourceDefinitionService.java similarity index 69% rename from src/main/java/org/cbioportal/service/ResourceDefinitionService.java rename to src/main/java/org/cbioportal/legacy/service/ResourceDefinitionService.java index 9c413cf64b5..4c4754678a3 100644 --- a/src/main/java/org/cbioportal/service/ResourceDefinitionService.java +++ b/src/main/java/org/cbioportal/legacy/service/ResourceDefinitionService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.service.exception.ResourceDefinitionNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.service.exception.ResourceDefinitionNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; public interface ResourceDefinitionService { diff --git a/src/main/java/org/cbioportal/service/SampleListService.java b/src/main/java/org/cbioportal/legacy/service/SampleListService.java similarity index 75% rename from src/main/java/org/cbioportal/service/SampleListService.java rename to src/main/java/org/cbioportal/legacy/service/SampleListService.java index bae2e8205e5..0a921258022 100644 --- a/src/main/java/org/cbioportal/service/SampleListService.java +++ b/src/main/java/org/cbioportal/legacy/service/SampleListService.java @@ -1,9 +1,9 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/SampleService.java b/src/main/java/org/cbioportal/legacy/service/SampleService.java similarity index 85% rename from src/main/java/org/cbioportal/service/SampleService.java rename to src/main/java/org/cbioportal/legacy/service/SampleService.java index 4d1c6d9c9e1..7ee43f334e9 100644 --- a/src/main/java/org/cbioportal/service/SampleService.java +++ b/src/main/java/org/cbioportal/legacy/service/SampleService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/legacy/service/ServerStatusService.java b/src/main/java/org/cbioportal/legacy/service/ServerStatusService.java new file mode 100644 index 00000000000..5bde6e3ed55 --- /dev/null +++ b/src/main/java/org/cbioportal/legacy/service/ServerStatusService.java @@ -0,0 +1,7 @@ +package org.cbioportal.legacy.service; + +import org.cbioportal.legacy.service.impl.ServerStatusServiceImpl.ServerStatusMessage; + +public interface ServerStatusService { + ServerStatusMessage getServerStatus(); +} diff --git a/src/main/java/org/cbioportal/service/SignificantCopyNumberRegionService.java b/src/main/java/org/cbioportal/legacy/service/SignificantCopyNumberRegionService.java similarity index 67% rename from src/main/java/org/cbioportal/service/SignificantCopyNumberRegionService.java rename to src/main/java/org/cbioportal/legacy/service/SignificantCopyNumberRegionService.java index 712e980a99b..7b10c8ee5f3 100644 --- a/src/main/java/org/cbioportal/service/SignificantCopyNumberRegionService.java +++ b/src/main/java/org/cbioportal/legacy/service/SignificantCopyNumberRegionService.java @@ -1,8 +1,8 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/SignificantlyMutatedGeneService.java b/src/main/java/org/cbioportal/legacy/service/SignificantlyMutatedGeneService.java similarity index 66% rename from src/main/java/org/cbioportal/service/SignificantlyMutatedGeneService.java rename to src/main/java/org/cbioportal/legacy/service/SignificantlyMutatedGeneService.java index dc60a5b485b..820cf8d8936 100644 --- a/src/main/java/org/cbioportal/service/SignificantlyMutatedGeneService.java +++ b/src/main/java/org/cbioportal/legacy/service/SignificantlyMutatedGeneService.java @@ -1,8 +1,8 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/StaticDataTimestampService.java b/src/main/java/org/cbioportal/legacy/service/StaticDataTimestampService.java similarity index 72% rename from src/main/java/org/cbioportal/service/StaticDataTimestampService.java rename to src/main/java/org/cbioportal/legacy/service/StaticDataTimestampService.java index 07c6abb0221..6831ec0a400 100644 --- a/src/main/java/org/cbioportal/service/StaticDataTimestampService.java +++ b/src/main/java/org/cbioportal/legacy/service/StaticDataTimestampService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.TableTimestampPair; +import org.cbioportal.legacy.model.TableTimestampPair; import java.util.Date; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/StructuralVariantService.java b/src/main/java/org/cbioportal/legacy/service/StructuralVariantService.java similarity index 86% rename from src/main/java/org/cbioportal/service/StructuralVariantService.java rename to src/main/java/org/cbioportal/legacy/service/StructuralVariantService.java index 6fe7dc5d34d..ca7228411a8 100644 --- a/src/main/java/org/cbioportal/service/StructuralVariantService.java +++ b/src/main/java/org/cbioportal/legacy/service/StructuralVariantService.java @@ -21,14 +21,14 @@ * along with this program. If not, see . */ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantQuery; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantQuery; public interface StructuralVariantService { diff --git a/src/main/java/org/cbioportal/service/StudyService.java b/src/main/java/org/cbioportal/legacy/service/StudyService.java similarity index 70% rename from src/main/java/org/cbioportal/service/StudyService.java rename to src/main/java/org/cbioportal/legacy/service/StudyService.java index 4d80c394d65..96082714a3d 100644 --- a/src/main/java/org/cbioportal/service/StudyService.java +++ b/src/main/java/org/cbioportal/legacy/service/StudyService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.utils.security.AccessLevel; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.utils.security.AccessLevel; import org.springframework.security.core.Authentication; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java b/src/main/java/org/cbioportal/legacy/service/StudyViewColumnarService.java similarity index 67% rename from src/main/java/org/cbioportal/service/StudyViewColumnarService.java rename to src/main/java/org/cbioportal/legacy/service/StudyViewColumnarService.java index 67ee1f9efe4..5643abc01b7 100644 --- a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java +++ b/src/main/java/org/cbioportal/legacy/service/StudyViewColumnarService.java @@ -1,24 +1,24 @@ -package org.cbioportal.service; - -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.PatientTreatmentReport; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleTreatmentReport; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.GenericAssayDataBinFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.StudyViewFilter; +package org.cbioportal.legacy.service; + +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.PatientTreatmentReport; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleTreatmentReport; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import java.util.List; import java.util.Map; diff --git a/src/main/java/org/cbioportal/service/StudyViewService.java b/src/main/java/org/cbioportal/legacy/service/StudyViewService.java similarity index 75% rename from src/main/java/org/cbioportal/service/StudyViewService.java rename to src/main/java/org/cbioportal/legacy/service/StudyViewService.java index c4cb00151e5..d1f2604476d 100644 --- a/src/main/java/org/cbioportal/service/StudyViewService.java +++ b/src/main/java/org/cbioportal/legacy/service/StudyViewService.java @@ -1,14 +1,14 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/TreatmentService.java b/src/main/java/org/cbioportal/legacy/service/TreatmentService.java similarity index 71% rename from src/main/java/org/cbioportal/service/TreatmentService.java rename to src/main/java/org/cbioportal/legacy/service/TreatmentService.java index 0c7ff536b49..b518eac149b 100644 --- a/src/main/java/org/cbioportal/service/TreatmentService.java +++ b/src/main/java/org/cbioportal/legacy/service/TreatmentService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.PatientTreatmentRow; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; public interface TreatmentService { public List getAllSampleTreatmentRows(List samples, List studies, ClinicalEventKeyCode key); diff --git a/src/main/java/org/cbioportal/service/VariantCountService.java b/src/main/java/org/cbioportal/legacy/service/VariantCountService.java similarity index 58% rename from src/main/java/org/cbioportal/service/VariantCountService.java rename to src/main/java/org/cbioportal/legacy/service/VariantCountService.java index 74dc9758461..e5631b272b0 100644 --- a/src/main/java/org/cbioportal/service/VariantCountService.java +++ b/src/main/java/org/cbioportal/legacy/service/VariantCountService.java @@ -1,7 +1,7 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.VariantCount; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.VariantCount; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/ViolinPlotService.java b/src/main/java/org/cbioportal/legacy/service/ViolinPlotService.java similarity index 64% rename from src/main/java/org/cbioportal/service/ViolinPlotService.java rename to src/main/java/org/cbioportal/legacy/service/ViolinPlotService.java index 37eade2f739..e3177b33b72 100644 --- a/src/main/java/org/cbioportal/service/ViolinPlotService.java +++ b/src/main/java/org/cbioportal/legacy/service/ViolinPlotService.java @@ -1,9 +1,9 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalViolinPlotData; -import org.cbioportal.model.Sample; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalViolinPlotData; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import java.math.BigDecimal; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/alteration/AlterationCountByGeneService.java b/src/main/java/org/cbioportal/legacy/service/alteration/AlterationCountByGeneService.java similarity index 60% rename from src/main/java/org/cbioportal/service/alteration/AlterationCountByGeneService.java rename to src/main/java/org/cbioportal/legacy/service/alteration/AlterationCountByGeneService.java index 79d29dc8ff3..bd43d19924b 100644 --- a/src/main/java/org/cbioportal/service/alteration/AlterationCountByGeneService.java +++ b/src/main/java/org/cbioportal/legacy/service/alteration/AlterationCountByGeneService.java @@ -1,9 +1,9 @@ -package org.cbioportal.service.alteration; +package org.cbioportal.legacy.service.alteration; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.StudyViewFilterContext; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.StudyViewFilterContext; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/alteration/AlterationCountByGeneServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/alteration/AlterationCountByGeneServiceImpl.java similarity index 92% rename from src/main/java/org/cbioportal/service/alteration/AlterationCountByGeneServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/alteration/AlterationCountByGeneServiceImpl.java index 9aea4ade562..18cdc722dff 100644 --- a/src/main/java/org/cbioportal/service/alteration/AlterationCountByGeneServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/alteration/AlterationCountByGeneServiceImpl.java @@ -1,20 +1,20 @@ -package org.cbioportal.service.alteration; +package org.cbioportal.legacy.service.alteration; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationType; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.StudyViewFilterContext; -import org.cbioportal.persistence.StudyViewRepository; -import org.cbioportal.service.SignificantCopyNumberRegionService; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.service.util.AlterationCountServiceUtil; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.parameter.Projection; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationType; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.StudyViewFilterContext; +import org.cbioportal.legacy.persistence.StudyViewRepository; +import org.cbioportal.legacy.service.SignificantCopyNumberRegionService; +import org.cbioportal.legacy.service.SignificantlyMutatedGeneService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.util.AlterationCountServiceUtil; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.lang.NonNull; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/exception/AccessForbiddenException.java b/src/main/java/org/cbioportal/legacy/service/exception/AccessForbiddenException.java similarity index 75% rename from src/main/java/org/cbioportal/service/exception/AccessForbiddenException.java rename to src/main/java/org/cbioportal/legacy/service/exception/AccessForbiddenException.java index d9dd8b64bd5..200830035ef 100644 --- a/src/main/java/org/cbioportal/service/exception/AccessForbiddenException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/AccessForbiddenException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class AccessForbiddenException extends RuntimeException { public AccessForbiddenException(String message) { diff --git a/src/main/java/org/cbioportal/service/exception/CacheNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/CacheNotFoundException.java similarity index 89% rename from src/main/java/org/cbioportal/service/exception/CacheNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/CacheNotFoundException.java index 457db60daa2..7585d074973 100644 --- a/src/main/java/org/cbioportal/service/exception/CacheNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/CacheNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class CacheNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/CacheOperationException.java b/src/main/java/org/cbioportal/legacy/service/exception/CacheOperationException.java similarity index 77% rename from src/main/java/org/cbioportal/service/exception/CacheOperationException.java rename to src/main/java/org/cbioportal/legacy/service/exception/CacheOperationException.java index 1580a77c476..5a7b45a5d18 100644 --- a/src/main/java/org/cbioportal/service/exception/CacheOperationException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/CacheOperationException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class CacheOperationException extends Exception { public CacheOperationException(String message, Throwable cause) { diff --git a/src/main/java/org/cbioportal/service/exception/CancerTypeNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/CancerTypeNotFoundException.java similarity index 89% rename from src/main/java/org/cbioportal/service/exception/CancerTypeNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/CancerTypeNotFoundException.java index e8f0ef923d6..3dbb4e7784d 100644 --- a/src/main/java/org/cbioportal/service/exception/CancerTypeNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/CancerTypeNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class CancerTypeNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/ClinicalAttributeNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/ClinicalAttributeNotFoundException.java similarity index 93% rename from src/main/java/org/cbioportal/service/exception/ClinicalAttributeNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/ClinicalAttributeNotFoundException.java index beca71b82e9..12c41d224fa 100644 --- a/src/main/java/org/cbioportal/service/exception/ClinicalAttributeNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/ClinicalAttributeNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class ClinicalAttributeNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/DataAccessTokenNoUserIdentityException.java b/src/main/java/org/cbioportal/legacy/service/exception/DataAccessTokenNoUserIdentityException.java similarity index 97% rename from src/main/java/org/cbioportal/service/exception/DataAccessTokenNoUserIdentityException.java rename to src/main/java/org/cbioportal/legacy/service/exception/DataAccessTokenNoUserIdentityException.java index e698c562792..83b09e3e33c 100644 --- a/src/main/java/org/cbioportal/service/exception/DataAccessTokenNoUserIdentityException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/DataAccessTokenNoUserIdentityException.java @@ -46,7 +46,7 @@ * along with this program. If not, see . */ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class DataAccessTokenNoUserIdentityException extends RuntimeException { diff --git a/src/main/java/org/cbioportal/service/exception/DataAccessTokenProhibitedUserException.java b/src/main/java/org/cbioportal/legacy/service/exception/DataAccessTokenProhibitedUserException.java similarity index 97% rename from src/main/java/org/cbioportal/service/exception/DataAccessTokenProhibitedUserException.java rename to src/main/java/org/cbioportal/legacy/service/exception/DataAccessTokenProhibitedUserException.java index 6ed9a7ac6dc..c6277dda5c5 100644 --- a/src/main/java/org/cbioportal/service/exception/DataAccessTokenProhibitedUserException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/DataAccessTokenProhibitedUserException.java @@ -46,7 +46,7 @@ * along with this program. If not, see . */ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class DataAccessTokenProhibitedUserException extends RuntimeException { diff --git a/src/main/java/org/cbioportal/service/exception/GeneNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/GeneNotFoundException.java similarity index 87% rename from src/main/java/org/cbioportal/service/exception/GeneNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/GeneNotFoundException.java index 4f69921765e..d4b814d4332 100644 --- a/src/main/java/org/cbioportal/service/exception/GeneNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/GeneNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class GeneNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/GenePanelNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/GenePanelNotFoundException.java similarity index 88% rename from src/main/java/org/cbioportal/service/exception/GenePanelNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/GenePanelNotFoundException.java index 0511561f851..424543e925a 100644 --- a/src/main/java/org/cbioportal/service/exception/GenePanelNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/GenePanelNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class GenePanelNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/GeneWithMultipleEntrezIdsException.java b/src/main/java/org/cbioportal/legacy/service/exception/GeneWithMultipleEntrezIdsException.java similarity index 89% rename from src/main/java/org/cbioportal/service/exception/GeneWithMultipleEntrezIdsException.java rename to src/main/java/org/cbioportal/legacy/service/exception/GeneWithMultipleEntrezIdsException.java index e475eb07546..fdeecf15f46 100644 --- a/src/main/java/org/cbioportal/service/exception/GeneWithMultipleEntrezIdsException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/GeneWithMultipleEntrezIdsException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; //TODO: this class should be removed once the issue is resolved database public class GeneWithMultipleEntrezIdsException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/GenericAssayNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/GenericAssayNotFoundException.java similarity index 90% rename from src/main/java/org/cbioportal/service/exception/GenericAssayNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/GenericAssayNotFoundException.java index ec19640c509..1761e39d3a4 100644 --- a/src/main/java/org/cbioportal/service/exception/GenericAssayNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/GenericAssayNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class GenericAssayNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/GenesetNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/GenesetNotFoundException.java similarity index 88% rename from src/main/java/org/cbioportal/service/exception/GenesetNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/GenesetNotFoundException.java index 6019759bf58..eaae23c36db 100644 --- a/src/main/java/org/cbioportal/service/exception/GenesetNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/GenesetNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class GenesetNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/InvalidDataAccessTokenException.java b/src/main/java/org/cbioportal/legacy/service/exception/InvalidDataAccessTokenException.java similarity index 98% rename from src/main/java/org/cbioportal/service/exception/InvalidDataAccessTokenException.java rename to src/main/java/org/cbioportal/legacy/service/exception/InvalidDataAccessTokenException.java index d158d258a7c..7fda71ec58f 100644 --- a/src/main/java/org/cbioportal/service/exception/InvalidDataAccessTokenException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/InvalidDataAccessTokenException.java @@ -47,7 +47,7 @@ */ // TODO move back package org.cbioportal.security.exception; -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class InvalidDataAccessTokenException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/MolecularProfileNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/MolecularProfileNotFoundException.java similarity index 90% rename from src/main/java/org/cbioportal/service/exception/MolecularProfileNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/MolecularProfileNotFoundException.java index 574356a8e18..83ec3bb9fcd 100644 --- a/src/main/java/org/cbioportal/service/exception/MolecularProfileNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/MolecularProfileNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class MolecularProfileNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/PatientNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/PatientNotFoundException.java similarity index 92% rename from src/main/java/org/cbioportal/service/exception/PatientNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/PatientNotFoundException.java index 7f19e4d9e0c..007eb7fecc1 100644 --- a/src/main/java/org/cbioportal/service/exception/PatientNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/PatientNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class PatientNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/ResourceDefinitionNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/ResourceDefinitionNotFoundException.java similarity index 92% rename from src/main/java/org/cbioportal/service/exception/ResourceDefinitionNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/ResourceDefinitionNotFoundException.java index 45451464f5e..e6aa86889e2 100644 --- a/src/main/java/org/cbioportal/service/exception/ResourceDefinitionNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/ResourceDefinitionNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class ResourceDefinitionNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/SampleListNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/SampleListNotFoundException.java similarity index 89% rename from src/main/java/org/cbioportal/service/exception/SampleListNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/SampleListNotFoundException.java index fcda0ca5ba0..6f67343565a 100644 --- a/src/main/java/org/cbioportal/service/exception/SampleListNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/SampleListNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class SampleListNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/SampleNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/SampleNotFoundException.java similarity index 92% rename from src/main/java/org/cbioportal/service/exception/SampleNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/SampleNotFoundException.java index d95f89d0712..76db484c137 100644 --- a/src/main/java/org/cbioportal/service/exception/SampleNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/SampleNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class SampleNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/StudyNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/StudyNotFoundException.java similarity index 87% rename from src/main/java/org/cbioportal/service/exception/StudyNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/StudyNotFoundException.java index 119acd4a898..70f79a70c0b 100644 --- a/src/main/java/org/cbioportal/service/exception/StudyNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/StudyNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class StudyNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/TokenNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/TokenNotFoundException.java similarity index 97% rename from src/main/java/org/cbioportal/service/exception/TokenNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/TokenNotFoundException.java index 7a964e7aa98..2150e39af8c 100644 --- a/src/main/java/org/cbioportal/service/exception/TokenNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/TokenNotFoundException.java @@ -48,7 +48,7 @@ */ // TODO move back package org.cbioportal.security.exception; -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class TokenNotFoundException extends RuntimeException { diff --git a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/AlterationCountServiceImpl.java similarity index 93% rename from src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/AlterationCountServiceImpl.java index 8c5ebc5c1fa..9bf3db30278 100644 --- a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/AlterationCountServiceImpl.java @@ -1,22 +1,22 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountBase; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.AlterationRepository; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.persistence.StudyViewRepository; -import org.cbioportal.service.AlterationCountService; -import org.cbioportal.service.SignificantCopyNumberRegionService; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.service.util.AlterationCountServiceUtil; -import org.cbioportal.service.util.AlterationEnrichmentUtil; +import org.cbioportal.legacy.model.AlterationCountBase; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.AlterationRepository; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.persistence.StudyViewRepository; +import org.cbioportal.legacy.service.AlterationCountService; +import org.cbioportal.legacy.service.SignificantCopyNumberRegionService; +import org.cbioportal.legacy.service.SignificantlyMutatedGeneService; +import org.cbioportal.legacy.service.util.AlterationCountServiceUtil; +import org.cbioportal.legacy.service.util.AlterationEnrichmentUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/AlterationDriverAnnotationServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/AlterationDriverAnnotationServiceImpl.java similarity index 79% rename from src/main/java/org/cbioportal/service/impl/AlterationDriverAnnotationServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/AlterationDriverAnnotationServiceImpl.java index d5846ca02c1..0010c723bdb 100644 --- a/src/main/java/org/cbioportal/service/impl/AlterationDriverAnnotationServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/AlterationDriverAnnotationServiceImpl.java @@ -1,9 +1,9 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.AlterationDriverAnnotation; -import org.cbioportal.model.CustomDriverAnnotationReport; -import org.cbioportal.persistence.AlterationDriverAnnotationRepository; -import org.cbioportal.service.AlterationDriverAnnotationService; +import org.cbioportal.legacy.model.AlterationDriverAnnotation; +import org.cbioportal.legacy.model.CustomDriverAnnotationReport; +import org.cbioportal.legacy.persistence.AlterationDriverAnnotationRepository; +import org.cbioportal.legacy.service.AlterationDriverAnnotationService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/AlterationEnrichmentServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/AlterationEnrichmentServiceImpl.java similarity index 81% rename from src/main/java/org/cbioportal/service/impl/AlterationEnrichmentServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/AlterationEnrichmentServiceImpl.java index cbe49e76429..9cb2d091760 100644 --- a/src/main/java/org/cbioportal/service/impl/AlterationEnrichmentServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/AlterationEnrichmentServiceImpl.java @@ -1,11 +1,15 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.*; -import org.cbioportal.model.util.Select; -import org.cbioportal.service.AlterationEnrichmentService; -import org.cbioportal.service.AlterationCountService; -import org.cbioportal.service.util.AlterationEnrichmentUtil; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationEnrichment; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.service.AlterationEnrichmentService; +import org.cbioportal.legacy.service.AlterationCountService; +import org.cbioportal.legacy.service.util.AlterationEnrichmentUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/CacheServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/CacheServiceImpl.java similarity index 90% rename from src/main/java/org/cbioportal/service/impl/CacheServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/CacheServiceImpl.java index 41896b98d9b..4c7364adb69 100644 --- a/src/main/java/org/cbioportal/service/impl/CacheServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/CacheServiceImpl.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.cbioportal.persistence.StudyRepository; -import org.cbioportal.persistence.cachemaputil.CacheMapUtil; -import org.cbioportal.persistence.cachemaputil.StaticRefCacheMapUtil; -import org.cbioportal.persistence.util.CacheUtils; -import org.cbioportal.service.CacheService; -import org.cbioportal.service.exception.CacheOperationException; +import org.cbioportal.legacy.persistence.StudyRepository; +import org.cbioportal.legacy.persistence.cachemaputil.CacheMapUtil; +import org.cbioportal.legacy.persistence.cachemaputil.StaticRefCacheMapUtil; +import org.cbioportal.legacy.persistence.util.CacheUtils; +import org.cbioportal.legacy.service.CacheService; +import org.cbioportal.legacy.service.exception.CacheOperationException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.CacheManager; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/service/impl/CacheStatisticsServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/CacheStatisticsServiceImpl.java similarity index 91% rename from src/main/java/org/cbioportal/service/impl/CacheStatisticsServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/CacheStatisticsServiceImpl.java index f5f74f15e23..8404198ee73 100644 --- a/src/main/java/org/cbioportal/service/impl/CacheStatisticsServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/CacheStatisticsServiceImpl.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import jakarta.annotation.PostConstruct; -import org.cbioportal.persistence.util.CustomEhcachingProvider; -import org.cbioportal.service.CacheStatisticsService; -import org.cbioportal.service.exception.CacheNotFoundException; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.persistence.util.CustomEhcachingProvider; +import org.cbioportal.legacy.service.CacheStatisticsService; +import org.cbioportal.legacy.service.exception.CacheNotFoundException; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/CancerTypeServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/CancerTypeServiceImpl.java similarity index 87% rename from src/main/java/org/cbioportal/service/impl/CancerTypeServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/CancerTypeServiceImpl.java index e039b58eaab..515421eccb6 100644 --- a/src/main/java/org/cbioportal/service/impl/CancerTypeServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/CancerTypeServiceImpl.java @@ -1,11 +1,11 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import jakarta.annotation.PostConstruct; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CancerTypeRepository; -import org.cbioportal.service.CancerTypeService; -import org.cbioportal.service.exception.CancerTypeNotFoundException; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CancerTypeRepository; +import org.cbioportal.legacy.service.CancerTypeService; +import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/ClinicalAttributeServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalAttributeServiceImpl.java similarity index 86% rename from src/main/java/org/cbioportal/service/impl/ClinicalAttributeServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ClinicalAttributeServiceImpl.java index bb245846cc9..423faf0d256 100644 --- a/src/main/java/org/cbioportal/service/impl/ClinicalAttributeServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalAttributeServiceImpl.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalAttributeRepository; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.ClinicalAttributeNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalAttributeRepository; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.ClinicalAttributeNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.security.access.prepost.PostFilter; @@ -27,7 +27,7 @@ public class ClinicalAttributeServiceImpl implements ClinicalAttributeService { private String AUTHENTICATE; @Override - @PostFilter("hasPermission(filterObject.cancerStudyIdentifier, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PostFilter("hasPermission(filterObject.cancerStudyIdentifier, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") public List getAllClinicalAttributes(String projection, Integer pageSize, Integer pageNumber, String sortBy, String direction) { diff --git a/src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalDataDensityPlotServiceImpl.java similarity index 94% rename from src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ClinicalDataDensityPlotServiceImpl.java index cb4d8d780e9..f153b2ef134 100644 --- a/src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalDataDensityPlotServiceImpl.java @@ -1,15 +1,15 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.math3.stat.correlation.PearsonsCorrelation; import org.apache.commons.math3.stat.correlation.SpearmansCorrelation; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.DensityPlotBin; -import org.cbioportal.model.DensityPlotData; -import org.cbioportal.service.ClinicalDataDensityPlotService; -import org.cbioportal.web.columnar.StudyViewColumnStoreController; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.DensityPlotParameters; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.DensityPlotBin; +import org.cbioportal.legacy.model.DensityPlotData; +import org.cbioportal.legacy.service.ClinicalDataDensityPlotService; +import org.cbioportal.legacy.web.columnar.StudyViewColumnStoreController; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.DensityPlotParameters; import org.springframework.cache.annotation.Cacheable; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/ClinicalDataServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalDataServiceImpl.java similarity index 90% rename from src/main/java/org/cbioportal/service/impl/ClinicalDataServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ClinicalDataServiceImpl.java index 7258f8e313e..beb3e8af12f 100644 --- a/src/main/java/org/cbioportal/service/impl/ClinicalDataServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalDataServiceImpl.java @@ -1,13 +1,24 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.lang3.tuple.ImmutablePair; -import org.cbioportal.model.*; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalDataRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; -import org.cbioportal.service.*; -import org.cbioportal.service.exception.*; -import org.cbioportal.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.SampleClinicalDataCollection; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalDataRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; @@ -16,7 +27,7 @@ import java.util.stream.Collectors; import java.util.stream.Stream; -import static org.cbioportal.utils.Encoder.calculateBase64; +import static org.cbioportal.legacy.utils.Encoder.calculateBase64; @Service public class ClinicalDataServiceImpl implements ClinicalDataService { @@ -35,7 +46,7 @@ public class ClinicalDataServiceImpl implements ClinicalDataService { private ClinicalAttributeUtil clinicalAttributeUtil; @Override - public List getAllClinicalDataOfSampleInStudy(String studyId, String sampleId, String attributeId, + public List getAllClinicalDataOfSampleInStudy(String studyId, String sampleId, String attributeId, String projection, Integer pageSize, Integer pageNumber, String sortBy, String direction) throws SampleNotFoundException, StudyNotFoundException { @@ -134,7 +145,7 @@ public BaseMeta fetchMetaClinicalData(List studyIds, List ids, L @Override public List fetchClinicalDataCounts(List studyIds, List sampleIds, - List attributeIds) { + List attributeIds) { if (attributeIds.isEmpty()) { return new ArrayList<>(); diff --git a/src/main/java/org/cbioportal/service/impl/ClinicalEventServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalEventServiceImpl.java similarity index 93% rename from src/main/java/org/cbioportal/service/impl/ClinicalEventServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ClinicalEventServiceImpl.java index 187bec33ef1..dfb89a38bc8 100644 --- a/src/main/java/org/cbioportal/service/impl/ClinicalEventServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalEventServiceImpl.java @@ -1,20 +1,20 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.collections4.CollectionUtils; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalEventRepository; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.parameter.ClinicalEventRequestIdentifier; -import org.cbioportal.web.parameter.OccurrencePosition; -import org.cbioportal.web.parameter.SurvivalRequest; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalEventRepository; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.parameter.ClinicalEventRequestIdentifier; +import org.cbioportal.legacy.web.parameter.OccurrencePosition; +import org.cbioportal.legacy.web.parameter.SurvivalRequest; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/CoExpressionServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/CoExpressionServiceImpl.java similarity index 91% rename from src/main/java/org/cbioportal/service/impl/CoExpressionServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/CoExpressionServiceImpl.java index ced09b17dc5..256a897555d 100644 --- a/src/main/java/org/cbioportal/service/impl/CoExpressionServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/CoExpressionServiceImpl.java @@ -1,11 +1,24 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.*; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.service.*; -import org.cbioportal.service.exception.*; -import org.cbioportal.service.util.CoExpressionAsyncMethods; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.CoExpression; +import org.cbioportal.legacy.model.EntityType; +import org.cbioportal.legacy.model.MolecularAlteration; +import org.cbioportal.legacy.model.MolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.CoExpressionService; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.service.util.CoExpressionAsyncMethods; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.transaction.annotation.Transactional; import org.springframework.stereotype.Service; @@ -38,7 +51,7 @@ public class CoExpressionServiceImpl implements CoExpressionService { // transaction needs to be setup here in order to return Iterable from molecularDataService in fetchCoExpressions @Transactional(readOnly=true) public List getCoExpressions(String geneticEntityId, EntityType geneticEntityType, - String sampleListId, String molecularProfileIdA, String molecularProfileIdB, Double threshold) + String sampleListId, String molecularProfileIdA, String molecularProfileIdB, Double threshold) throws MolecularProfileNotFoundException, SampleListNotFoundException, GenesetNotFoundException, GeneNotFoundException { diff --git a/src/main/java/org/cbioportal/service/impl/CopyNumberSegmentServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/CopyNumberSegmentServiceImpl.java similarity index 85% rename from src/main/java/org/cbioportal/service/impl/CopyNumberSegmentServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/CopyNumberSegmentServiceImpl.java index efa3a34c482..1665f3ba54f 100644 --- a/src/main/java/org/cbioportal/service/impl/CopyNumberSegmentServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/CopyNumberSegmentServiceImpl.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CopyNumberSegmentRepository; -import org.cbioportal.service.CopyNumberSegmentService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CopyNumberSegmentRepository; +import org.cbioportal.legacy.service.CopyNumberSegmentService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/CosmicCountServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/CosmicCountServiceImpl.java similarity index 68% rename from src/main/java/org/cbioportal/service/impl/CosmicCountServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/CosmicCountServiceImpl.java index 218201c21db..cef62e6b65b 100644 --- a/src/main/java/org/cbioportal/service/impl/CosmicCountServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/CosmicCountServiceImpl.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; import java.util.List; -import org.cbioportal.model.CosmicMutation; -import org.cbioportal.service.CosmicCountService; -import org.cbioportal.persistence.CosmicCountRepository; +import org.cbioportal.legacy.model.CosmicMutation; +import org.cbioportal.legacy.service.CosmicCountService; +import org.cbioportal.legacy.persistence.CosmicCountRepository; @Service public class CosmicCountServiceImpl implements CosmicCountService { diff --git a/src/main/java/org/cbioportal/service/impl/CustomDataServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/CustomDataServiceImpl.java similarity index 88% rename from src/main/java/org/cbioportal/service/impl/CustomDataServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/CustomDataServiceImpl.java index 3d339efb176..58178eebb31 100644 --- a/src/main/java/org/cbioportal/service/impl/CustomDataServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/CustomDataServiceImpl.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.service.CustomDataService; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.service.util.SessionServiceRequestHandler; -import org.cbioportal.utils.removeme.Session; +import org.cbioportal.legacy.service.CustomDataService; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.service.util.SessionServiceRequestHandler; +import org.cbioportal.legacy.utils.removeme.Session; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/DiscreteCopyNumberServiceImpl.java similarity index 93% rename from src/main/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/DiscreteCopyNumberServiceImpl.java index c862e7924ce..9975b249462 100644 --- a/src/main/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/DiscreteCopyNumberServiceImpl.java @@ -1,18 +1,18 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.CNA; -import org.cbioportal.model.CopyNumberCount; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.DiscreteCopyNumberRepository; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CopyNumberCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.DiscreteCopyNumberRepository; +import org.cbioportal.legacy.service.DiscreteCopyNumberService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/EhcacheStatisticsServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/EhcacheStatisticsServiceImpl.java similarity index 79% rename from src/main/java/org/cbioportal/service/impl/EhcacheStatisticsServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/EhcacheStatisticsServiceImpl.java index dfa1019e51f..76f5ed21fa4 100644 --- a/src/main/java/org/cbioportal/service/impl/EhcacheStatisticsServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/EhcacheStatisticsServiceImpl.java @@ -1,7 +1,7 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.persistence.util.EhcacheStatistics; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.persistence.util.EhcacheStatistics; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.annotation.Primary; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/ExpressionEnrichmentServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ExpressionEnrichmentServiceImpl.java similarity index 92% rename from src/main/java/org/cbioportal/service/impl/ExpressionEnrichmentServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ExpressionEnrichmentServiceImpl.java index 849983cbd3c..967fe1f9064 100644 --- a/src/main/java/org/cbioportal/service/impl/ExpressionEnrichmentServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ExpressionEnrichmentServiceImpl.java @@ -1,32 +1,32 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.math.BigDecimal; import java.util.*; import java.util.function.Function; import java.util.stream.Collectors; import org.apache.commons.lang3.BooleanUtils; -import org.cbioportal.model.MolecularProfile.MolecularAlterationType; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.GenericAssayBinaryEnrichment; -import org.cbioportal.model.GenericAssayCategoricalEnrichment; -import org.cbioportal.model.GenericAssayMolecularAlteration; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Sample; -import org.cbioportal.model.GenericAssayEnrichment; -import org.cbioportal.model.GenomicEnrichment; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneMolecularAlteration; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.service.ExpressionEnrichmentService; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.util.ExpressionEnrichmentUtil; -import org.cbioportal.service.util.FisherExactTestCalculator; +import org.cbioportal.legacy.model.MolecularProfile.MolecularAlterationType; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.GenericAssayBinaryEnrichment; +import org.cbioportal.legacy.model.GenericAssayCategoricalEnrichment; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.GenericAssayEnrichment; +import org.cbioportal.legacy.model.GenomicEnrichment; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.service.ExpressionEnrichmentService; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.util.ExpressionEnrichmentUtil; +import org.cbioportal.legacy.service.util.FisherExactTestCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; import org.springframework.transaction.annotation.Transactional; diff --git a/src/main/java/org/cbioportal/service/impl/GeneMemoizerServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GeneMemoizerServiceImpl.java similarity index 87% rename from src/main/java/org/cbioportal/service/impl/GeneMemoizerServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GeneMemoizerServiceImpl.java index 2c0a097f16a..f6bf7752ab9 100644 --- a/src/main/java/org/cbioportal/service/impl/GeneMemoizerServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GeneMemoizerServiceImpl.java @@ -1,8 +1,8 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.service.GeneMemoizerService; -import org.cbioportal.service.StaticDataTimestampService; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.service.GeneMemoizerService; +import org.cbioportal.legacy.service.StaticDataTimestampService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/GenePanelServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GenePanelServiceImpl.java similarity index 89% rename from src/main/java/org/cbioportal/service/impl/GenePanelServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GenePanelServiceImpl.java index cde04fc14d6..94d2840a340 100644 --- a/src/main/java/org/cbioportal/service/impl/GenePanelServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GenePanelServiceImpl.java @@ -1,16 +1,21 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.collections4.CollectionUtils; -import org.cbioportal.model.*; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GenePanelRepository; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.exception.GenePanelNotFoundException; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GenePanelRepository; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.exception.GenePanelNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; @@ -37,7 +42,7 @@ public class GenePanelServiceImpl implements GenePanelService { private final Function PATIENT_IDENTIFIER_GENERATOR = d -> d.getMolecularProfileId() + d.getPatientId(); @Override - public List getAllGenePanels(String projection, Integer pageSize, Integer pageNumber, String sortBy, + public List getAllGenePanels(String projection, Integer pageSize, Integer pageNumber, String sortBy, String direction) { List genePanels = genePanelRepository.getAllGenePanels(projection, pageSize, pageNumber, sortBy, diff --git a/src/main/java/org/cbioportal/service/impl/GeneServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GeneServiceImpl.java similarity index 93% rename from src/main/java/org/cbioportal/service/impl/GeneServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GeneServiceImpl.java index a8ae132a090..4f8156dc231 100644 --- a/src/main/java/org/cbioportal/service/impl/GeneServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GeneServiceImpl.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import jakarta.annotation.PostConstruct; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneAlias; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GeneRepository; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.exception.GeneNotFoundException; -import org.cbioportal.service.exception.GeneWithMultipleEntrezIdsException; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneAlias; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GeneRepository; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.service.exception.GeneWithMultipleEntrezIdsException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/GenericAssayServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GenericAssayServiceImpl.java similarity index 91% rename from src/main/java/org/cbioportal/service/impl/GenericAssayServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GenericAssayServiceImpl.java index 9b8ddd1ba9b..2d3f214d666 100644 --- a/src/main/java/org/cbioportal/service/impl/GenericAssayServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GenericAssayServiceImpl.java @@ -1,24 +1,24 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.*; import java.util.function.Function; import java.util.stream.Collectors; -import org.cbioportal.model.GenericAssayAdditionalProperty; -import org.cbioportal.model.GenericAssayData; -import org.cbioportal.model.GenericAssayMolecularAlteration; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfile.MolecularAlterationType; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.persistence.GenericAssayRepository; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.GenericAssayAdditionalProperty; +import org.cbioportal.legacy.model.GenericAssayData; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfile.MolecularAlterationType; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.persistence.GenericAssayRepository; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/GenesetCorrelationServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GenesetCorrelationServiceImpl.java similarity index 91% rename from src/main/java/org/cbioportal/service/impl/GenesetCorrelationServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GenesetCorrelationServiceImpl.java index ccf39027515..24d61d2aac6 100644 --- a/src/main/java/org/cbioportal/service/impl/GenesetCorrelationServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GenesetCorrelationServiceImpl.java @@ -21,7 +21,7 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.Arrays; @@ -32,23 +32,23 @@ import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.math3.stat.correlation.SpearmansCorrelation; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GenesetCorrelation; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Sample; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.GenesetService; -import org.cbioportal.service.GenesetCorrelationService; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.GenesetNotFoundException; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GenesetCorrelation; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.GenesetService; +import org.cbioportal.legacy.service.GenesetCorrelationService; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/GenesetDataServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GenesetDataServiceImpl.java similarity index 85% rename from src/main/java/org/cbioportal/service/impl/GenesetDataServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GenesetDataServiceImpl.java index 0b0a762fd61..6b8646bff14 100644 --- a/src/main/java/org/cbioportal/service/impl/GenesetDataServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GenesetDataServiceImpl.java @@ -21,25 +21,25 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; -import org.cbioportal.model.GenesetMolecularAlteration; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.model.Sample; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.GenesetMolecularAlteration; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/GenesetHierarchyServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GenesetHierarchyServiceImpl.java similarity index 94% rename from src/main/java/org/cbioportal/service/impl/GenesetHierarchyServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GenesetHierarchyServiceImpl.java index 0c831bf19e3..85826f072d4 100644 --- a/src/main/java/org/cbioportal/service/impl/GenesetHierarchyServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GenesetHierarchyServiceImpl.java @@ -20,7 +20,7 @@ * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.Arrays; @@ -31,20 +31,20 @@ import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.lang3.tuple.ImmutablePair; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.GenesetHierarchyInfo; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Sample; -import org.cbioportal.persistence.GenesetHierarchyRepository; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.service.GenesetHierarchyService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.persistence.GenesetHierarchyRepository; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.GenesetHierarchyService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/GenesetServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GenesetServiceImpl.java similarity index 80% rename from src/main/java/org/cbioportal/service/impl/GenesetServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GenesetServiceImpl.java index d0184582870..e2c58f7c653 100644 --- a/src/main/java/org/cbioportal/service/impl/GenesetServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GenesetServiceImpl.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GenesetRepository; -import org.cbioportal.service.GenesetService; -import org.cbioportal.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GenesetRepository; +import org.cbioportal.legacy.service.GenesetService; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/JwtDataAccessTokenServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/JwtDataAccessTokenServiceImpl.java similarity index 93% rename from src/main/java/org/cbioportal/service/impl/JwtDataAccessTokenServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/JwtDataAccessTokenServiceImpl.java index f3fbbe3b21f..f67a20132c5 100644 --- a/src/main/java/org/cbioportal/service/impl/JwtDataAccessTokenServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/JwtDataAccessTokenServiceImpl.java @@ -30,15 +30,15 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.service.exception.InvalidDataAccessTokenException; -import org.cbioportal.service.util.JwtUtils; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.service.exception.InvalidDataAccessTokenException; +import org.cbioportal.legacy.service.util.JwtUtils; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.security.authentication.BadCredentialsException; import org.springframework.security.authentication.UsernamePasswordAuthenticationToken; diff --git a/src/main/java/org/cbioportal/service/impl/MolecularDataServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/MolecularDataServiceImpl.java similarity index 93% rename from src/main/java/org/cbioportal/service/impl/MolecularDataServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/MolecularDataServiceImpl.java index 40f60c0dbff..def0c45cdd9 100644 --- a/src/main/java/org/cbioportal/service/impl/MolecularDataServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/MolecularDataServiceImpl.java @@ -1,16 +1,21 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.*; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.MolecularProfile.MolecularAlterationType; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.DiscreteCopyNumberRepository; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.MolecularProfile.MolecularAlterationType; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.DiscreteCopyNumberRepository; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.security.access.prepost.PreAuthorize; import org.springframework.stereotype.Service; @@ -261,7 +266,7 @@ public List getMolecularDataInMultipleMolecularProfilesByGene } @Override - @PreAuthorize("hasPermission(#molecularProfileIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") public BaseMeta getMetaMolecularDataInMultipleMolecularProfiles(List molecularProfileIds, List sampleIds, List entrezGeneIds) { diff --git a/src/main/java/org/cbioportal/service/impl/MolecularProfileServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/MolecularProfileServiceImpl.java similarity index 89% rename from src/main/java/org/cbioportal/service/impl/MolecularProfileServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/MolecularProfileServiceImpl.java index 3a4d6c8a1d7..3c91568e123 100644 --- a/src/main/java/org/cbioportal/service/impl/MolecularProfileServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/MolecularProfileServiceImpl.java @@ -1,15 +1,15 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.service.util.MolecularProfileUtil; -import org.cbioportal.web.parameter.Projection; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.security.access.prepost.PostFilter; @@ -34,7 +34,7 @@ public class MolecularProfileServiceImpl implements MolecularProfileService { private String AUTHENTICATE; @Override - @PostFilter("hasPermission(filterObject, T(org.cbioportal.utils.security.AccessLevel).READ)") + @PostFilter("hasPermission(filterObject, T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") public List getAllMolecularProfiles(String projection, Integer pageSize, Integer pageNumber, String sortBy, String direction) { diff --git a/src/main/java/org/cbioportal/service/impl/MrnaPercentileServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/MrnaPercentileServiceImpl.java similarity index 88% rename from src/main/java/org/cbioportal/service/impl/MrnaPercentileServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/MrnaPercentileServiceImpl.java index af97c101c09..102073de20e 100644 --- a/src/main/java/org/cbioportal/service/impl/MrnaPercentileServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/MrnaPercentileServiceImpl.java @@ -1,16 +1,16 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.math3.stat.ranking.NaNStrategy; import org.apache.commons.math3.stat.ranking.NaturalRanking; import org.apache.commons.math3.stat.ranking.TiesStrategy; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MrnaPercentile; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.MrnaPercentileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MrnaPercentile; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.MrnaPercentileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/MutationServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/MutationServiceImpl.java similarity index 91% rename from src/main/java/org/cbioportal/service/impl/MutationServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/MutationServiceImpl.java index 44602217b68..01df4b19132 100644 --- a/src/main/java/org/cbioportal/service/impl/MutationServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/MutationServiceImpl.java @@ -1,15 +1,15 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.persistence.MutationRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.persistence.MutationRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/MutationSpectrumServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/MutationSpectrumServiceImpl.java similarity index 91% rename from src/main/java/org/cbioportal/service/impl/MutationSpectrumServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/MutationSpectrumServiceImpl.java index 36c685b14f4..ac4b62f060b 100644 --- a/src/main/java/org/cbioportal/service/impl/MutationSpectrumServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/MutationSpectrumServiceImpl.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationSpectrum; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.MutationSpectrumService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationSpectrum; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.MutationSpectrumService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/PatientServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/PatientServiceImpl.java similarity index 84% rename from src/main/java/org/cbioportal/service/impl/PatientServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/PatientServiceImpl.java index a317dce672f..26dba601205 100644 --- a/src/main/java/org/cbioportal/service/impl/PatientServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/PatientServiceImpl.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.PatientRepository; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.PatientRepository; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.security.access.prepost.PostFilter; @@ -26,7 +26,7 @@ public class PatientServiceImpl implements PatientService { private String AUTHENTICATE; @Override - @PostFilter("hasPermission(filterObject, T(org.cbioportal.utils.security.AccessLevel).READ)") + @PostFilter("hasPermission(filterObject, T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") public List getAllPatients(String keyword, String projection, Integer pageSize, Integer pageNumber, String sortBy, String direction) { diff --git a/src/main/java/org/cbioportal/service/impl/ReadPermissionServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ReadPermissionServiceImpl.java similarity index 79% rename from src/main/java/org/cbioportal/service/impl/ReadPermissionServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ReadPermissionServiceImpl.java index 0662008422b..d48cdc3f7e3 100644 --- a/src/main/java/org/cbioportal/service/impl/ReadPermissionServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ReadPermissionServiceImpl.java @@ -1,9 +1,9 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.service.ReadPermissionService; -import org.cbioportal.model.ReadPermission; -import org.cbioportal.security.CancerStudyPermissionEvaluator; -import org.cbioportal.utils.security.AccessLevel; +import org.cbioportal.legacy.service.ReadPermissionService; +import org.cbioportal.legacy.model.ReadPermission; +import org.cbioportal.application.security.CancerStudyPermissionEvaluator; +import org.cbioportal.legacy.utils.security.AccessLevel; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.security.core.Authentication; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/RedisCacheStatisticsServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/RedisCacheStatisticsServiceImpl.java similarity index 90% rename from src/main/java/org/cbioportal/service/impl/RedisCacheStatisticsServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/RedisCacheStatisticsServiceImpl.java index ef8e447355a..1114e92dece 100644 --- a/src/main/java/org/cbioportal/service/impl/RedisCacheStatisticsServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/RedisCacheStatisticsServiceImpl.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.persistence.util.CustomKeyGenerator; -import org.cbioportal.persistence.util.CustomRedisCache; -import org.cbioportal.service.CacheStatisticsService; -import org.cbioportal.service.exception.CacheNotFoundException; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.persistence.util.CustomKeyGenerator; +import org.cbioportal.legacy.persistence.util.CustomRedisCache; +import org.cbioportal.legacy.service.CacheStatisticsService; +import org.cbioportal.legacy.service.exception.CacheNotFoundException; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; diff --git a/src/main/java/org/cbioportal/service/impl/ReferenceGenomeGeneServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ReferenceGenomeGeneServiceImpl.java similarity index 85% rename from src/main/java/org/cbioportal/service/impl/ReferenceGenomeGeneServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ReferenceGenomeGeneServiceImpl.java index d371743f716..287ac235530 100644 --- a/src/main/java/org/cbioportal/service/impl/ReferenceGenomeGeneServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ReferenceGenomeGeneServiceImpl.java @@ -1,9 +1,9 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.persistence.ReferenceGenomeGeneRepository; -import org.cbioportal.service.ReferenceGenomeGeneService; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.persistence.ReferenceGenomeGeneRepository; +import org.cbioportal.legacy.service.ReferenceGenomeGeneService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/ResourceDataServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ResourceDataServiceImpl.java similarity index 83% rename from src/main/java/org/cbioportal/service/impl/ResourceDataServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ResourceDataServiceImpl.java index 6e1d94ebe77..b57b21b4655 100644 --- a/src/main/java/org/cbioportal/service/impl/ResourceDataServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ResourceDataServiceImpl.java @@ -1,17 +1,17 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.List; import java.util.ArrayList; -import org.cbioportal.model.ResourceData; -import org.cbioportal.persistence.ResourceDataRepository; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.ResourceDataService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.ResourceData; +import org.cbioportal.legacy.persistence.ResourceDataRepository; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.ResourceDataService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/ResourceDefinitionServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ResourceDefinitionServiceImpl.java similarity index 78% rename from src/main/java/org/cbioportal/service/impl/ResourceDefinitionServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ResourceDefinitionServiceImpl.java index 4fa493d1294..11b1d13e304 100644 --- a/src/main/java/org/cbioportal/service/impl/ResourceDefinitionServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ResourceDefinitionServiceImpl.java @@ -1,14 +1,14 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.Collections; import java.util.List; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.persistence.ResourceDefinitionRepository; -import org.cbioportal.service.ResourceDefinitionService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.ResourceDefinitionNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.persistence.ResourceDefinitionRepository; +import org.cbioportal.legacy.service.ResourceDefinitionService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.ResourceDefinitionNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/SampleListServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/SampleListServiceImpl.java similarity index 88% rename from src/main/java/org/cbioportal/service/impl/SampleListServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/SampleListServiceImpl.java index 583a4a29fb9..6dd175ce6a7 100644 --- a/src/main/java/org/cbioportal/service/impl/SampleListServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/SampleListServiceImpl.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.SampleList; -import org.cbioportal.model.SampleListToSampleId; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.SampleListToSampleId; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.security.access.prepost.PostFilter; @@ -29,7 +29,7 @@ public class SampleListServiceImpl implements SampleListService { private String AUTHENTICATE; @Override - @PostFilter("hasPermission(filterObject, T(org.cbioportal.utils.security.AccessLevel).READ)") + @PostFilter("hasPermission(filterObject, T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") public List getAllSampleLists(String projection, Integer pageSize, Integer pageNumber, String sortBy, String direction) { diff --git a/src/main/java/org/cbioportal/service/impl/SampleServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/SampleServiceImpl.java similarity index 90% rename from src/main/java/org/cbioportal/service/impl/SampleServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/SampleServiceImpl.java index 5d3bd389517..bf308a59481 100644 --- a/src/main/java/org/cbioportal/service/impl/SampleServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/SampleServiceImpl.java @@ -1,17 +1,17 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CopyNumberSegmentRepository; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.persistence.SampleRepository; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CopyNumberSegmentRepository; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.persistence.SampleRepository; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/ServerStatusServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ServerStatusServiceImpl.java similarity index 85% rename from src/main/java/org/cbioportal/service/impl/ServerStatusServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ServerStatusServiceImpl.java index 4a60a65ea58..8ae8d850d35 100644 --- a/src/main/java/org/cbioportal/service/impl/ServerStatusServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ServerStatusServiceImpl.java @@ -1,11 +1,11 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.io.Serializable; import java.util.List; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.persistence.CancerTypeRepository; -import org.cbioportal.service.ServerStatusService; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.persistence.CancerTypeRepository; +import org.cbioportal.legacy.service.ServerStatusService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/SignificantCopyNumberRegionServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/SignificantCopyNumberRegionServiceImpl.java similarity index 79% rename from src/main/java/org/cbioportal/service/impl/SignificantCopyNumberRegionServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/SignificantCopyNumberRegionServiceImpl.java index c1616ac8473..64e81dfa85c 100644 --- a/src/main/java/org/cbioportal/service/impl/SignificantCopyNumberRegionServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/SignificantCopyNumberRegionServiceImpl.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SignificantCopyNumberRegionRepository; -import org.cbioportal.service.SignificantCopyNumberRegionService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SignificantCopyNumberRegionRepository; +import org.cbioportal.legacy.service.SignificantCopyNumberRegionService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/SignificantlyMutatedGeneServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/SignificantlyMutatedGeneServiceImpl.java similarity index 73% rename from src/main/java/org/cbioportal/service/impl/SignificantlyMutatedGeneServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/SignificantlyMutatedGeneServiceImpl.java index e48c8c259fe..294027699db 100644 --- a/src/main/java/org/cbioportal/service/impl/SignificantlyMutatedGeneServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/SignificantlyMutatedGeneServiceImpl.java @@ -1,11 +1,11 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SignificantlyMutatedGeneRepository; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SignificantlyMutatedGeneRepository; +import org.cbioportal.legacy.service.SignificantlyMutatedGeneService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/StaticDataTimestampServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/StaticDataTimestampServiceImpl.java similarity index 86% rename from src/main/java/org/cbioportal/service/impl/StaticDataTimestampServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/StaticDataTimestampServiceImpl.java index 47ad5e78220..40674d934f5 100644 --- a/src/main/java/org/cbioportal/service/impl/StaticDataTimestampServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/StaticDataTimestampServiceImpl.java @@ -1,8 +1,8 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.TableTimestampPair; -import org.cbioportal.service.StaticDataTimestampService; -import org.cbioportal.persistence.StaticDataTimeStampRepository; +import org.cbioportal.legacy.model.TableTimestampPair; +import org.cbioportal.legacy.service.StaticDataTimestampService; +import org.cbioportal.legacy.persistence.StaticDataTimeStampRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/StructuralVariantServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/StructuralVariantServiceImpl.java similarity index 83% rename from src/main/java/org/cbioportal/service/impl/StructuralVariantServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/StructuralVariantServiceImpl.java index 07222ad3ee6..0d80f405fa6 100644 --- a/src/main/java/org/cbioportal/service/impl/StructuralVariantServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/StructuralVariantServiceImpl.java @@ -21,22 +21,22 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantQuery; -import org.cbioportal.persistence.StructuralVariantRepository; -import org.cbioportal.service.StructuralVariantService; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantQuery; +import org.cbioportal.legacy.persistence.StructuralVariantRepository; +import org.cbioportal.legacy.service.StructuralVariantService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; import java.util.List; import java.util.*; import java.util.stream.Collectors; import java.util.stream.Stream; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; import org.springframework.util.CollectionUtils; @Service diff --git a/src/main/java/org/cbioportal/service/impl/StudyServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/StudyServiceImpl.java similarity index 89% rename from src/main/java/org/cbioportal/service/impl/StudyServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/StudyServiceImpl.java index a2209fe38d9..cd0e79b429f 100644 --- a/src/main/java/org/cbioportal/service/impl/StudyServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/StudyServiceImpl.java @@ -1,15 +1,15 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.StudyRepository; -import org.cbioportal.service.CancerTypeService; -import org.cbioportal.service.ReadPermissionService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.utils.security.AccessLevel; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.StudyRepository; +import org.cbioportal.legacy.service.CancerTypeService; +import org.cbioportal.legacy.service.ReadPermissionService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.utils.security.AccessLevel; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.security.access.prepost.PostFilter; import org.springframework.security.access.prepost.PreAuthorize; diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/StudyViewColumnarServiceImpl.java similarity index 87% rename from src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/StudyViewColumnarServiceImpl.java index f827a33411f..4e24dcf881d 100644 --- a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/StudyViewColumnarServiceImpl.java @@ -1,40 +1,40 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.PatientTreatmentReport; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleTreatmentReport; -import org.cbioportal.model.StudyViewFilterContext; -import org.cbioportal.persistence.StudyViewRepository; -import org.cbioportal.service.StudyViewColumnarService; -import org.cbioportal.service.alteration.AlterationCountByGeneService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.service.treatment.TreatmentCountReportService; -import org.cbioportal.service.util.StudyViewColumnarServiceUtil; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.CustomSampleIdentifier; -import org.cbioportal.web.parameter.GenericAssayDataBinFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.columnar.util.CustomDataFilterUtil; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.PatientTreatmentReport; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleTreatmentReport; +import org.cbioportal.legacy.model.StudyViewFilterContext; +import org.cbioportal.legacy.persistence.StudyViewRepository; +import org.cbioportal.legacy.service.StudyViewColumnarService; +import org.cbioportal.legacy.service.alteration.AlterationCountByGeneService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.treatment.TreatmentCountReportService; +import org.cbioportal.legacy.service.util.StudyViewColumnarServiceUtil; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.CustomSampleIdentifier; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.columnar.util.CustomDataFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.stereotype.Service; -import static org.cbioportal.web.columnar.util.ClinicalDataXyPlotUtil.combineClinicalDataForXyPlot; +import static org.cbioportal.legacy.web.columnar.util.ClinicalDataXyPlotUtil.combineClinicalDataForXyPlot; import java.util.ArrayList; import java.util.Collections; diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/StudyViewServiceImpl.java similarity index 92% rename from src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/StudyViewServiceImpl.java index 67276a42b38..98dee029793 100644 --- a/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/StudyViewServiceImpl.java @@ -1,42 +1,42 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.collections4.map.MultiKeyMap; import org.apache.commons.lang3.StringUtils; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenericAssayData; -import org.cbioportal.model.GenericAssayDataCount; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.MutationFilterOption; -import org.cbioportal.model.util.Select; -import org.cbioportal.service.AlterationCountService; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.SignificantCopyNumberRegionService; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.service.StudyViewService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.service.util.MolecularProfileUtil; -import org.cbioportal.web.parameter.GeneIdType; -import org.cbioportal.web.parameter.Projection; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenericAssayData; +import org.cbioportal.legacy.model.GenericAssayDataCount; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.MutationFilterOption; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.service.AlterationCountService; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.SignificantCopyNumberRegionService; +import org.cbioportal.legacy.service.SignificantlyMutatedGeneService; +import org.cbioportal.legacy.service.StudyViewService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.web.parameter.GeneIdType; +import org.cbioportal.legacy.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/TreatmentServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/TreatmentServiceImpl.java similarity index 94% rename from src/main/java/org/cbioportal/service/impl/TreatmentServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/TreatmentServiceImpl.java index 75784a01c15..380ad8897d0 100644 --- a/src/main/java/org/cbioportal/service/impl/TreatmentServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/TreatmentServiceImpl.java @@ -1,10 +1,15 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.lang3.tuple.ImmutablePair; import org.apache.commons.lang3.tuple.Pair; -import org.cbioportal.model.*; -import org.cbioportal.persistence.TreatmentRepository; -import org.cbioportal.service.TreatmentService; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.model.TemporalRelation; +import org.cbioportal.legacy.model.Treatment; +import org.cbioportal.legacy.persistence.TreatmentRepository; +import org.cbioportal.legacy.service.TreatmentService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/UnauthDataAccessTokenServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/UnauthDataAccessTokenServiceImpl.java similarity index 94% rename from src/main/java/org/cbioportal/service/impl/UnauthDataAccessTokenServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/UnauthDataAccessTokenServiceImpl.java index 11cb8749223..fbca7235531 100644 --- a/src/main/java/org/cbioportal/service/impl/UnauthDataAccessTokenServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/UnauthDataAccessTokenServiceImpl.java @@ -30,11 +30,11 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.security.access.AccessDeniedException; import org.springframework.security.core.Authentication; diff --git a/src/main/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImpl.java similarity index 95% rename from src/main/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImpl.java index b1c977edb75..9020ddaf6ad 100644 --- a/src/main/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImpl.java @@ -30,15 +30,15 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.persistence.DataAccessTokenRepository; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.service.exception.TokenNotFoundException; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.persistence.DataAccessTokenRepository; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.service.exception.TokenNotFoundException; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.security.authentication.BadCredentialsException; diff --git a/src/main/java/org/cbioportal/service/impl/VariantCountServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/VariantCountServiceImpl.java similarity index 80% rename from src/main/java/org/cbioportal/service/impl/VariantCountServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/VariantCountServiceImpl.java index 0c1bdfd2fbe..d41be62a5d8 100644 --- a/src/main/java/org/cbioportal/service/impl/VariantCountServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/VariantCountServiceImpl.java @@ -1,14 +1,14 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.VariantCount; -import org.cbioportal.persistence.VariantCountRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.VariantCountService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.VariantCount; +import org.cbioportal.legacy.persistence.VariantCountRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.VariantCountService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/ViolinPlotServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ViolinPlotServiceImpl.java similarity index 95% rename from src/main/java/org/cbioportal/service/impl/ViolinPlotServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ViolinPlotServiceImpl.java index 92c0ef233a9..545edd70595 100644 --- a/src/main/java/org/cbioportal/service/impl/ViolinPlotServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ViolinPlotServiceImpl.java @@ -1,11 +1,16 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.math3.analysis.function.Gaussian; import org.apache.commons.math3.stat.descriptive.rank.Percentile; -import org.cbioportal.model.*; -import org.cbioportal.service.ViolinPlotService; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalViolinPlotBoxData; +import org.cbioportal.legacy.model.ClinicalViolinPlotData; +import org.cbioportal.legacy.model.ClinicalViolinPlotIndividualPoint; +import org.cbioportal.legacy.model.ClinicalViolinPlotRowData; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.ViolinPlotService; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.springframework.cache.annotation.Cacheable; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/legacy/service/treatment/TreatmentCountReportService.java b/src/main/java/org/cbioportal/legacy/service/treatment/TreatmentCountReportService.java new file mode 100644 index 00000000000..82ca2829d96 --- /dev/null +++ b/src/main/java/org/cbioportal/legacy/service/treatment/TreatmentCountReportService.java @@ -0,0 +1,14 @@ +package org.cbioportal.legacy.service.treatment; + +import org.cbioportal.legacy.model.PatientTreatmentReport; +import org.cbioportal.legacy.model.SampleTreatmentReport; +import org.cbioportal.legacy.model.StudyViewFilterContext; +import org.cbioportal.legacy.web.parameter.CustomSampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; + +import java.util.List; + +public interface TreatmentCountReportService { + PatientTreatmentReport getPatientTreatmentReport(StudyViewFilterContext studyViewFilterContext); + SampleTreatmentReport getSampleTreatmentReport(StudyViewFilterContext studyViewFilterContext); +} diff --git a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/treatment/TreatmentCountReportServiceImpl.java similarity index 80% rename from src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/treatment/TreatmentCountReportServiceImpl.java index 4a96bcdaf85..1cbdc366a29 100644 --- a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/treatment/TreatmentCountReportServiceImpl.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.treatment; +package org.cbioportal.legacy.service.treatment; -import org.cbioportal.model.PatientTreatmentReport; -import org.cbioportal.model.SampleTreatmentReport; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.model.StudyViewFilterContext; -import org.cbioportal.model.TemporalRelation; -import org.cbioportal.persistence.StudyViewRepository; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.model.PatientTreatmentReport; +import org.cbioportal.legacy.model.SampleTreatmentReport; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.model.StudyViewFilterContext; +import org.cbioportal.legacy.model.TemporalRelation; +import org.cbioportal.legacy.persistence.StudyViewRepository; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/util/AlterationCountServiceUtil.java b/src/main/java/org/cbioportal/legacy/service/util/AlterationCountServiceUtil.java similarity index 95% rename from src/main/java/org/cbioportal/service/util/AlterationCountServiceUtil.java rename to src/main/java/org/cbioportal/legacy/service/util/AlterationCountServiceUtil.java index 9f565e216fc..926cb03ff73 100644 --- a/src/main/java/org/cbioportal/service/util/AlterationCountServiceUtil.java +++ b/src/main/java/org/cbioportal/legacy/service/util/AlterationCountServiceUtil.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountBase; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MutSig; +import org.cbioportal.legacy.model.AlterationCountBase; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MutSig; import org.springframework.lang.NonNull; import java.util.HashMap; diff --git a/src/main/java/org/cbioportal/service/util/AlterationEnrichmentUtil.java b/src/main/java/org/cbioportal/legacy/service/util/AlterationEnrichmentUtil.java similarity index 93% rename from src/main/java/org/cbioportal/service/util/AlterationEnrichmentUtil.java rename to src/main/java/org/cbioportal/legacy/service/util/AlterationEnrichmentUtil.java index 8113cc63f73..a234f7928fd 100644 --- a/src/main/java/org/cbioportal/service/util/AlterationEnrichmentUtil.java +++ b/src/main/java/org/cbioportal/legacy/service/util/AlterationEnrichmentUtil.java @@ -1,20 +1,20 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import org.apache.commons.math3.stat.inference.ChiSquareTest; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountBase; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationEnrichment; -import org.cbioportal.model.CountSummary; -import org.cbioportal.model.Gene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfile.MolecularAlterationType; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.AlterationCountBase; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationEnrichment; +import org.cbioportal.legacy.model.CountSummary; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfile.MolecularAlterationType; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/service/util/BinnableCustomDataValue.java b/src/main/java/org/cbioportal/legacy/service/util/BinnableCustomDataValue.java similarity index 92% rename from src/main/java/org/cbioportal/service/util/BinnableCustomDataValue.java rename to src/main/java/org/cbioportal/legacy/service/util/BinnableCustomDataValue.java index a8b07f0dd4a..c88c14f5cb2 100644 --- a/src/main/java/org/cbioportal/service/util/BinnableCustomDataValue.java +++ b/src/main/java/org/cbioportal/legacy/service/util/BinnableCustomDataValue.java @@ -1,7 +1,7 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; -import org.cbioportal.model.Binnable; +import org.cbioportal.legacy.model.Binnable; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/service/util/ChromosomeCalculator.java b/src/main/java/org/cbioportal/legacy/service/util/ChromosomeCalculator.java similarity index 93% rename from src/main/java/org/cbioportal/service/util/ChromosomeCalculator.java rename to src/main/java/org/cbioportal/legacy/service/util/ChromosomeCalculator.java index 21b81cdd73f..f5e26b904fc 100644 --- a/src/main/java/org/cbioportal/service/util/ChromosomeCalculator.java +++ b/src/main/java/org/cbioportal/legacy/service/util/ChromosomeCalculator.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/service/util/ClinicalAttributeUtil.java b/src/main/java/org/cbioportal/legacy/service/util/ClinicalAttributeUtil.java similarity index 95% rename from src/main/java/org/cbioportal/service/util/ClinicalAttributeUtil.java rename to src/main/java/org/cbioportal/legacy/service/util/ClinicalAttributeUtil.java index fc64d5b8d58..aaca33921a3 100644 --- a/src/main/java/org/cbioportal/service/util/ClinicalAttributeUtil.java +++ b/src/main/java/org/cbioportal/legacy/service/util/ClinicalAttributeUtil.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.util.HashSet; import java.util.List; @@ -6,7 +6,7 @@ import java.util.Set; import java.util.stream.Collectors; -import org.cbioportal.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttribute; import org.springframework.stereotype.Component; @Component diff --git a/src/main/java/org/cbioportal/service/util/CoExpressionAsyncMethods.java b/src/main/java/org/cbioportal/legacy/service/util/CoExpressionAsyncMethods.java similarity index 96% rename from src/main/java/org/cbioportal/service/util/CoExpressionAsyncMethods.java rename to src/main/java/org/cbioportal/legacy/service/util/CoExpressionAsyncMethods.java index 6e07ab2c1a9..88d172e20ae 100644 --- a/src/main/java/org/cbioportal/service/util/CoExpressionAsyncMethods.java +++ b/src/main/java/org/cbioportal/legacy/service/util/CoExpressionAsyncMethods.java @@ -1,8 +1,8 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import org.springframework.stereotype.Component; import org.springframework.scheduling.annotation.Async; -import org.cbioportal.model.CoExpression; +import org.cbioportal.legacy.model.CoExpression; import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.math3.linear.Array2DRowRealMatrix; import org.apache.commons.math3.linear.RealMatrix; diff --git a/src/main/java/org/cbioportal/service/util/CustomAttributeWithData.java b/src/main/java/org/cbioportal/legacy/service/util/CustomAttributeWithData.java similarity index 98% rename from src/main/java/org/cbioportal/service/util/CustomAttributeWithData.java rename to src/main/java/org/cbioportal/legacy/service/util/CustomAttributeWithData.java index ce7e5bcd159..fd4f766d30c 100644 --- a/src/main/java/org/cbioportal/service/util/CustomAttributeWithData.java +++ b/src/main/java/org/cbioportal/legacy/service/util/CustomAttributeWithData.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.io.Serializable; import java.util.Arrays; diff --git a/src/main/java/org/cbioportal/service/util/CustomDataSession.java b/src/main/java/org/cbioportal/legacy/service/util/CustomDataSession.java similarity index 91% rename from src/main/java/org/cbioportal/service/util/CustomDataSession.java rename to src/main/java/org/cbioportal/legacy/service/util/CustomDataSession.java index 151af9b4227..0061488acc2 100644 --- a/src/main/java/org/cbioportal/service/util/CustomDataSession.java +++ b/src/main/java/org/cbioportal/legacy/service/util/CustomDataSession.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.io.IOException; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import org.cbioportal.utils.removeme.Session; +import org.cbioportal.legacy.utils.removeme.Session; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.databind.ObjectMapper; diff --git a/src/main/java/org/cbioportal/service/util/CustomDataValue.java b/src/main/java/org/cbioportal/legacy/service/util/CustomDataValue.java similarity index 95% rename from src/main/java/org/cbioportal/service/util/CustomDataValue.java rename to src/main/java/org/cbioportal/legacy/service/util/CustomDataValue.java index 9e9343a7e2a..96ccb8bda4a 100644 --- a/src/main/java/org/cbioportal/service/util/CustomDataValue.java +++ b/src/main/java/org/cbioportal/legacy/service/util/CustomDataValue.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/service/util/ExpressionEnrichmentUtil.java b/src/main/java/org/cbioportal/legacy/service/util/ExpressionEnrichmentUtil.java similarity index 95% rename from src/main/java/org/cbioportal/service/util/ExpressionEnrichmentUtil.java rename to src/main/java/org/cbioportal/legacy/service/util/ExpressionEnrichmentUtil.java index 2fedb6eb5dd..1706bbca0cd 100644 --- a/src/main/java/org/cbioportal/service/util/ExpressionEnrichmentUtil.java +++ b/src/main/java/org/cbioportal/legacy/service/util/ExpressionEnrichmentUtil.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.math.BigDecimal; import java.util.ArrayList; @@ -12,20 +12,20 @@ import java.util.stream.Collectors; import java.util.stream.IntStream; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.ExpressionEnrichment; -import org.cbioportal.model.GenericAssayEnrichment; -import org.cbioportal.model.GenericAssayBinaryEnrichment; -import org.cbioportal.model.GenericAssayCategoricalEnrichment; -import org.cbioportal.model.GenericAssayMolecularAlteration; -import org.cbioportal.model.GenomicEnrichment; -import org.cbioportal.model.GroupStatistics; -import org.cbioportal.model.GenericAssayCountSummary; -import org.cbioportal.model.MolecularAlteration; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.model.Sample; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.ExpressionEnrichment; +import org.cbioportal.legacy.model.GenericAssayEnrichment; +import org.cbioportal.legacy.model.GenericAssayBinaryEnrichment; +import org.cbioportal.legacy.model.GenericAssayCategoricalEnrichment; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.GenomicEnrichment; +import org.cbioportal.legacy.model.GroupStatistics; +import org.cbioportal.legacy.model.GenericAssayCountSummary; +import org.cbioportal.legacy.model.MolecularAlteration; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.math3.stat.StatUtils; @@ -33,8 +33,8 @@ import org.apache.commons.math3.stat.inference.ChiSquareTest; import org.apache.commons.math3.stat.inference.OneWayAnova; import org.apache.commons.math3.stat.inference.TestUtils; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.service.SampleService; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.service.SampleService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/service/util/FisherExactTestCalculator.java b/src/main/java/org/cbioportal/legacy/service/util/FisherExactTestCalculator.java similarity index 98% rename from src/main/java/org/cbioportal/service/util/FisherExactTestCalculator.java rename to src/main/java/org/cbioportal/legacy/service/util/FisherExactTestCalculator.java index 150fb370178..e0ebbf1c173 100644 --- a/src/main/java/org/cbioportal/service/util/FisherExactTestCalculator.java +++ b/src/main/java/org/cbioportal/legacy/service/util/FisherExactTestCalculator.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/service/util/JwtUtils.java b/src/main/java/org/cbioportal/legacy/service/util/JwtUtils.java similarity index 97% rename from src/main/java/org/cbioportal/service/util/JwtUtils.java rename to src/main/java/org/cbioportal/legacy/service/util/JwtUtils.java index e7022de31a7..8b67b1f8af2 100644 --- a/src/main/java/org/cbioportal/service/util/JwtUtils.java +++ b/src/main/java/org/cbioportal/legacy/service/util/JwtUtils.java @@ -46,10 +46,10 @@ * along with this program. If not, see . */ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.exception.InvalidDataAccessTokenException; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.service.exception.InvalidDataAccessTokenException; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/src/main/java/org/cbioportal/service/util/MolecularProfileUtil.java b/src/main/java/org/cbioportal/legacy/service/util/MolecularProfileUtil.java similarity index 96% rename from src/main/java/org/cbioportal/service/util/MolecularProfileUtil.java rename to src/main/java/org/cbioportal/legacy/service/util/MolecularProfileUtil.java index a9cbfa3839e..d9b62752a0b 100644 --- a/src/main/java/org/cbioportal/service/util/MolecularProfileUtil.java +++ b/src/main/java/org/cbioportal/legacy/service/util/MolecularProfileUtil.java @@ -1,7 +1,7 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; import org.springframework.stereotype.Component; import java.util.ArrayList; diff --git a/src/main/java/org/cbioportal/service/util/MskWholeSlideViewerTokenGenerator.java b/src/main/java/org/cbioportal/legacy/service/util/MskWholeSlideViewerTokenGenerator.java similarity index 96% rename from src/main/java/org/cbioportal/service/util/MskWholeSlideViewerTokenGenerator.java rename to src/main/java/org/cbioportal/legacy/service/util/MskWholeSlideViewerTokenGenerator.java index 22ac7e776ae..be192127af0 100644 --- a/src/main/java/org/cbioportal/service/util/MskWholeSlideViewerTokenGenerator.java +++ b/src/main/java/org/cbioportal/legacy/service/util/MskWholeSlideViewerTokenGenerator.java @@ -1,5 +1,5 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.util.Base64; import javax.crypto.Mac; diff --git a/src/main/java/org/cbioportal/service/util/ProfiledCasesCounter.java b/src/main/java/org/cbioportal/legacy/service/util/ProfiledCasesCounter.java similarity index 96% rename from src/main/java/org/cbioportal/service/util/ProfiledCasesCounter.java rename to src/main/java/org/cbioportal/legacy/service/util/ProfiledCasesCounter.java index 874a2cd0652..a9b1b8d272e 100644 --- a/src/main/java/org/cbioportal/service/util/ProfiledCasesCounter.java +++ b/src/main/java/org/cbioportal/legacy/service/util/ProfiledCasesCounter.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountBase; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.service.GenePanelService; +import org.cbioportal.legacy.model.AlterationCountBase; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.service.GenePanelService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/service/util/SessionServiceConfig.java b/src/main/java/org/cbioportal/legacy/service/util/SessionServiceConfig.java similarity index 91% rename from src/main/java/org/cbioportal/service/util/SessionServiceConfig.java rename to src/main/java/org/cbioportal/legacy/service/util/SessionServiceConfig.java index ff0adc546ef..d19ef4a7025 100644 --- a/src/main/java/org/cbioportal/service/util/SessionServiceConfig.java +++ b/src/main/java/org/cbioportal/legacy/service/util/SessionServiceConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; diff --git a/src/main/java/org/cbioportal/service/util/SessionServiceRequestHandler.java b/src/main/java/org/cbioportal/legacy/service/util/SessionServiceRequestHandler.java similarity index 96% rename from src/main/java/org/cbioportal/service/util/SessionServiceRequestHandler.java rename to src/main/java/org/cbioportal/legacy/service/util/SessionServiceRequestHandler.java index af9749ee052..f02dc93bb52 100644 --- a/src/main/java/org/cbioportal/service/util/SessionServiceRequestHandler.java +++ b/src/main/java/org/cbioportal/legacy/service/util/SessionServiceRequestHandler.java @@ -1,6 +1,6 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; -import static org.cbioportal.utils.removeme.Session.*; +import static org.cbioportal.legacy.utils.removeme.Session.*; import java.nio.charset.Charset; @@ -10,8 +10,8 @@ import com.mongodb.BasicDBObject; import org.apache.commons.codec.binary.Base64; import org.apache.commons.lang3.StringUtils; -import org.cbioportal.web.parameter.VirtualStudy; -import org.cbioportal.web.parameter.VirtualStudyData; +import org.cbioportal.legacy.web.parameter.VirtualStudy; +import org.cbioportal.legacy.web.parameter.VirtualStudyData; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Value; diff --git a/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java b/src/main/java/org/cbioportal/legacy/service/util/StudyViewColumnarServiceUtil.java similarity index 94% rename from src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java rename to src/main/java/org/cbioportal/legacy/service/util/StudyViewColumnarServiceUtil.java index 981dbb80cf2..7af71652243 100644 --- a/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java +++ b/src/main/java/org/cbioportal/legacy/service/util/StudyViewColumnarServiceUtil.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.util; - -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.web.parameter.GenomicDataFilter; +package org.cbioportal.legacy.service.util; + +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; import java.util.ArrayList; import java.util.Collection; diff --git a/src/main/java/org/cbioportal/url_shortener/URLShortenerController.java b/src/main/java/org/cbioportal/legacy/url_shortener/URLShortenerController.java similarity index 97% rename from src/main/java/org/cbioportal/url_shortener/URLShortenerController.java rename to src/main/java/org/cbioportal/legacy/url_shortener/URLShortenerController.java index 00804ca9769..5816d264812 100644 --- a/src/main/java/org/cbioportal/url_shortener/URLShortenerController.java +++ b/src/main/java/org/cbioportal/legacy/url_shortener/URLShortenerController.java @@ -1,4 +1,4 @@ -package org.cbioportal.url_shortener; +package org.cbioportal.legacy.url_shortener; import fr.plaisance.bitly.Bit; import fr.plaisance.bitly.Bitly; diff --git a/src/main/java/org/cbioportal/url_shortener/URLShortenerResponse.java b/src/main/java/org/cbioportal/legacy/url_shortener/URLShortenerResponse.java similarity index 92% rename from src/main/java/org/cbioportal/url_shortener/URLShortenerResponse.java rename to src/main/java/org/cbioportal/legacy/url_shortener/URLShortenerResponse.java index bf822857b05..a023fdb2c83 100644 --- a/src/main/java/org/cbioportal/url_shortener/URLShortenerResponse.java +++ b/src/main/java/org/cbioportal/legacy/url_shortener/URLShortenerResponse.java @@ -1,4 +1,4 @@ -package org.cbioportal.url_shortener; +package org.cbioportal.legacy.url_shortener; public class URLShortenerResponse { diff --git a/src/main/java/org/cbioportal/utils/Encoder.java b/src/main/java/org/cbioportal/legacy/utils/Encoder.java similarity index 94% rename from src/main/java/org/cbioportal/utils/Encoder.java rename to src/main/java/org/cbioportal/legacy/utils/Encoder.java index 4cbe5f3f8dc..d9cd7207541 100644 --- a/src/main/java/org/cbioportal/utils/Encoder.java +++ b/src/main/java/org/cbioportal/legacy/utils/Encoder.java @@ -1,4 +1,4 @@ -package org.cbioportal.utils; +package org.cbioportal.legacy.utils; import java.util.Base64; diff --git a/src/main/java/org/cbioportal/utils/config/PropertyCondition.java b/src/main/java/org/cbioportal/legacy/utils/config/PropertyCondition.java similarity index 96% rename from src/main/java/org/cbioportal/utils/config/PropertyCondition.java rename to src/main/java/org/cbioportal/legacy/utils/config/PropertyCondition.java index 42a61f22f9b..04b35373619 100644 --- a/src/main/java/org/cbioportal/utils/config/PropertyCondition.java +++ b/src/main/java/org/cbioportal/legacy/utils/config/PropertyCondition.java @@ -29,9 +29,9 @@ * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see . */ -package org.cbioportal.utils.config; +package org.cbioportal.legacy.utils.config; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.context.annotation.Condition; import org.springframework.context.annotation.ConditionContext; import org.springframework.context.annotation.PropertySource; diff --git a/src/main/java/org/cbioportal/utils/config/annotation/ConditionalOnProperty.java b/src/main/java/org/cbioportal/legacy/utils/config/annotation/ConditionalOnProperty.java similarity index 94% rename from src/main/java/org/cbioportal/utils/config/annotation/ConditionalOnProperty.java rename to src/main/java/org/cbioportal/legacy/utils/config/annotation/ConditionalOnProperty.java index 57257cb4908..764db0c06e8 100644 --- a/src/main/java/org/cbioportal/utils/config/annotation/ConditionalOnProperty.java +++ b/src/main/java/org/cbioportal/legacy/utils/config/annotation/ConditionalOnProperty.java @@ -1,6 +1,6 @@ -package org.cbioportal.utils.config.annotation; +package org.cbioportal.legacy.utils.config.annotation; -import org.cbioportal.utils.config.PropertyCondition; +import org.cbioportal.legacy.utils.config.PropertyCondition; import org.springframework.context.annotation.Conditional; import java.lang.annotation.ElementType; diff --git a/src/main/java/org/cbioportal/utils/removeme/Session.java b/src/main/java/org/cbioportal/legacy/utils/removeme/Session.java similarity index 95% rename from src/main/java/org/cbioportal/utils/removeme/Session.java rename to src/main/java/org/cbioportal/legacy/utils/removeme/Session.java index 6d12df58d79..ceeaab8d960 100644 --- a/src/main/java/org/cbioportal/utils/removeme/Session.java +++ b/src/main/java/org/cbioportal/legacy/utils/removeme/Session.java @@ -1,4 +1,4 @@ -package org.cbioportal.utils.removeme; +package org.cbioportal.legacy.utils.removeme; import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.annotation.JsonView; @@ -66,7 +66,7 @@ public void setType(SessionType type) { this.type = type; } - @JsonView(org.cbioportal.utils.removeme.Session.Views.Full.class) + @JsonView(Session.Views.Full.class) public SessionType getType() { return type; } diff --git a/src/main/java/org/cbioportal/legacy/utils/security/AccessLevel.java b/src/main/java/org/cbioportal/legacy/utils/security/AccessLevel.java new file mode 100644 index 00000000000..c98448c1407 --- /dev/null +++ b/src/main/java/org/cbioportal/legacy/utils/security/AccessLevel.java @@ -0,0 +1,5 @@ +package org.cbioportal.legacy.utils.security; + +public enum AccessLevel { + READ, LIST +} diff --git a/src/main/java/org/cbioportal/utils/security/PortalSecurityConfig.java b/src/main/java/org/cbioportal/legacy/utils/security/PortalSecurityConfig.java similarity index 89% rename from src/main/java/org/cbioportal/utils/security/PortalSecurityConfig.java rename to src/main/java/org/cbioportal/legacy/utils/security/PortalSecurityConfig.java index 068a1641d68..383ea699093 100644 --- a/src/main/java/org/cbioportal/utils/security/PortalSecurityConfig.java +++ b/src/main/java/org/cbioportal/legacy/utils/security/PortalSecurityConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.utils.security; +package org.cbioportal.legacy.utils.security; public class PortalSecurityConfig { diff --git a/src/main/java/org/cbioportal/utils/validation/AllowedValues.java b/src/main/java/org/cbioportal/legacy/utils/validation/AllowedValues.java similarity index 94% rename from src/main/java/org/cbioportal/utils/validation/AllowedValues.java rename to src/main/java/org/cbioportal/legacy/utils/validation/AllowedValues.java index b42d3b0679b..a4ea42cd2a6 100644 --- a/src/main/java/org/cbioportal/utils/validation/AllowedValues.java +++ b/src/main/java/org/cbioportal/legacy/utils/validation/AllowedValues.java @@ -1,4 +1,4 @@ -package org.cbioportal.utils.validation; +package org.cbioportal.legacy.utils.validation; import jakarta.validation.Constraint; import jakarta.validation.Payload; diff --git a/src/main/java/org/cbioportal/utils/validation/AllowedValuesValidatorImpl.java b/src/main/java/org/cbioportal/legacy/utils/validation/AllowedValuesValidatorImpl.java similarity index 95% rename from src/main/java/org/cbioportal/utils/validation/AllowedValuesValidatorImpl.java rename to src/main/java/org/cbioportal/legacy/utils/validation/AllowedValuesValidatorImpl.java index 08eb9800b5c..b018f09df33 100644 --- a/src/main/java/org/cbioportal/utils/validation/AllowedValuesValidatorImpl.java +++ b/src/main/java/org/cbioportal/legacy/utils/validation/AllowedValuesValidatorImpl.java @@ -1,4 +1,4 @@ -package org.cbioportal.utils.validation; +package org.cbioportal.legacy.utils.validation; import jakarta.validation.ConstraintValidator; import jakarta.validation.ConstraintValidatorContext; diff --git a/src/main/java/org/cbioportal/web/AlterationDriverAnnotationController.java b/src/main/java/org/cbioportal/legacy/web/AlterationDriverAnnotationController.java similarity index 87% rename from src/main/java/org/cbioportal/web/AlterationDriverAnnotationController.java rename to src/main/java/org/cbioportal/legacy/web/AlterationDriverAnnotationController.java index 35880303b77..4c730566343 100644 --- a/src/main/java/org/cbioportal/web/AlterationDriverAnnotationController.java +++ b/src/main/java/org/cbioportal/legacy/web/AlterationDriverAnnotationController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -6,9 +6,9 @@ import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; -import org.cbioportal.model.CustomDriverAnnotationReport; -import org.cbioportal.service.AlterationDriverAnnotationService; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.model.CustomDriverAnnotationReport; +import org.cbioportal.legacy.service.AlterationDriverAnnotationService; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -33,7 +33,7 @@ public class AlterationDriverAnnotationController { @Autowired private AlterationDriverAnnotationService alterationDriverAnnotationService; - @PreAuthorize("hasPermission(#molecularProfileIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/custom-driver-annotation-report/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(summary = "Return availability of custom driver annotations for molecular profiles") diff --git a/src/main/java/org/cbioportal/web/AlterationEnrichmentController.java b/src/main/java/org/cbioportal/legacy/web/AlterationEnrichmentController.java similarity index 84% rename from src/main/java/org/cbioportal/web/AlterationEnrichmentController.java rename to src/main/java/org/cbioportal/legacy/web/AlterationEnrichmentController.java index 2d635e1e3e9..6c752b67780 100644 --- a/src/main/java/org/cbioportal/web/AlterationEnrichmentController.java +++ b/src/main/java/org/cbioportal/legacy/web/AlterationEnrichmentController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,15 +8,15 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.AlterationEnrichment; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.service.AlterationEnrichmentService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupAndAlterationTypeFilter; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupFilter; +import org.cbioportal.legacy.model.AlterationEnrichment; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.AlterationEnrichmentService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupAndAlterationTypeFilter; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -46,7 +46,7 @@ public class AlterationEnrichmentController { @Autowired private AlterationEnrichmentService alterationEnrichmentService; - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/alteration-enrichments/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(summary ="Fetch alteration enrichments in molecular profiles") diff --git a/src/main/java/org/cbioportal/web/CacheController.java b/src/main/java/org/cbioportal/legacy/web/CacheController.java similarity index 94% rename from src/main/java/org/cbioportal/web/CacheController.java rename to src/main/java/org/cbioportal/legacy/web/CacheController.java index c86982c2b6f..694cef77c96 100644 --- a/src/main/java/org/cbioportal/web/CacheController.java +++ b/src/main/java/org/cbioportal/legacy/web/CacheController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -6,9 +6,9 @@ import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; -import org.cbioportal.service.CacheService; -import org.cbioportal.service.exception.CacheOperationException; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.service.CacheService; +import org.cbioportal.legacy.service.exception.CacheOperationException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpStatus; diff --git a/src/main/java/org/cbioportal/web/CacheStatsController.java b/src/main/java/org/cbioportal/legacy/web/CacheStatsController.java similarity index 92% rename from src/main/java/org/cbioportal/web/CacheStatsController.java rename to src/main/java/org/cbioportal/legacy/web/CacheStatsController.java index abcdff97a9d..1363cc406e3 100644 --- a/src/main/java/org/cbioportal/web/CacheStatsController.java +++ b/src/main/java/org/cbioportal/legacy/web/CacheStatsController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Hidden; import io.swagger.v3.oas.annotations.Operation; @@ -8,9 +8,9 @@ import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; -import org.cbioportal.service.CacheStatisticsService; -import org.cbioportal.service.exception.CacheNotFoundException; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.service.CacheStatisticsService; +import org.cbioportal.legacy.service.exception.CacheNotFoundException; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/CancerTypeController.java b/src/main/java/org/cbioportal/legacy/web/CancerTypeController.java similarity index 85% rename from src/main/java/org/cbioportal/web/CancerTypeController.java rename to src/main/java/org/cbioportal/legacy/web/CancerTypeController.java index 3ea034f775a..29aed4ad834 100644 --- a/src/main/java/org/cbioportal/web/CancerTypeController.java +++ b/src/main/java/org/cbioportal/legacy/web/CancerTypeController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -9,16 +9,16 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.service.CancerTypeService; -import org.cbioportal.service.exception.CancerTypeNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.CancerTypeSortBy; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.service.CancerTypeService; +import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.CancerTypeSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; diff --git a/src/main/java/org/cbioportal/web/ClinicalAttributeController.java b/src/main/java/org/cbioportal/legacy/web/ClinicalAttributeController.java similarity index 90% rename from src/main/java/org/cbioportal/web/ClinicalAttributeController.java rename to src/main/java/org/cbioportal/legacy/web/ClinicalAttributeController.java index 730b8925810..b65e7debef7 100644 --- a/src/main/java/org/cbioportal/web/ClinicalAttributeController.java +++ b/src/main/java/org/cbioportal/legacy/web/ClinicalAttributeController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,17 +10,17 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.exception.ClinicalAttributeNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.ClinicalAttributeSortBy; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.exception.ClinicalAttributeNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.ClinicalAttributeSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -79,7 +79,7 @@ public ResponseEntity> getAllClinicalAttributes( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/clinical-attributes", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all clinical attributes in the specified study") @@ -115,7 +115,7 @@ public ResponseEntity> getAllClinicalAttributesInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/clinical-attributes/{clinicalAttributeId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get specified clinical attribute") @@ -132,7 +132,7 @@ public ResponseEntity getClinicalAttributeInStudy( HttpStatus.OK); } - @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-attributes/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical attributes") diff --git a/src/main/java/org/cbioportal/web/ClinicalAttributeCountController.java b/src/main/java/org/cbioportal/legacy/web/ClinicalAttributeCountController.java similarity index 88% rename from src/main/java/org/cbioportal/web/ClinicalAttributeCountController.java rename to src/main/java/org/cbioportal/legacy/web/ClinicalAttributeCountController.java index 7bf96005675..8456ca07850 100644 --- a/src/main/java/org/cbioportal/web/ClinicalAttributeCountController.java +++ b/src/main/java/org/cbioportal/legacy/web/ClinicalAttributeCountController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,12 +8,12 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.ClinicalAttributeCountFilter; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.ClinicalAttributeCountFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -40,7 +40,7 @@ public class ClinicalAttributeCountController { @Autowired private ClinicalAttributeService clinicalAttributeService; - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-attributes/counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get counts for clinical attributes according to their data availability for selected samples/patients") diff --git a/src/main/java/org/cbioportal/web/ClinicalDataController.java b/src/main/java/org/cbioportal/legacy/web/ClinicalDataController.java similarity index 90% rename from src/main/java/org/cbioportal/web/ClinicalDataController.java rename to src/main/java/org/cbioportal/legacy/web/ClinicalDataController.java index 1831c3b5689..f7df97657dd 100644 --- a/src/main/java/org/cbioportal/web/ClinicalDataController.java +++ b/src/main/java/org/cbioportal/legacy/web/ClinicalDataController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,23 +10,23 @@ import jakarta.validation.Valid; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.ClinicalDataIdentifier; -import org.cbioportal.web.parameter.ClinicalDataMultiStudyFilter; -import org.cbioportal.web.parameter.ClinicalDataSingleStudyFilter; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.ClinicalDataSortBy; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.ClinicalDataIdentifier; +import org.cbioportal.legacy.web.parameter.ClinicalDataMultiStudyFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataSingleStudyFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.ClinicalDataSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -59,7 +59,7 @@ public class ClinicalDataController { @Autowired private ClinicalDataService clinicalDataService; - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/samples/{sampleId}/clinical-data", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all clinical data of a sample in a study") @@ -100,7 +100,7 @@ public ResponseEntity> getAllClinicalDataOfSampleInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/patients/{patientId}/clinical-data", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all clinical data of a patient in a study") @@ -141,7 +141,7 @@ public ResponseEntity> getAllClinicalDataOfPatientInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/clinical-data", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all clinical data in a study") @@ -181,7 +181,7 @@ public ResponseEntity> getAllClinicalDataInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/clinical-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical data by patient IDs or sample IDs (specific study)") @@ -211,7 +211,7 @@ public ResponseEntity> fetchAllClinicalDataInStudy( } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical data by patient IDs or sample IDs (all studies)") diff --git a/src/main/java/org/cbioportal/web/ClinicalDataEnrichmentController.java b/src/main/java/org/cbioportal/legacy/web/ClinicalDataEnrichmentController.java similarity index 89% rename from src/main/java/org/cbioportal/web/ClinicalDataEnrichmentController.java rename to src/main/java/org/cbioportal/legacy/web/ClinicalDataEnrichmentController.java index 7e880875916..2e5f488ceed 100644 --- a/src/main/java/org/cbioportal/web/ClinicalDataEnrichmentController.java +++ b/src/main/java/org/cbioportal/legacy/web/ClinicalDataEnrichmentController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -9,16 +9,16 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalDataEnrichment; -import org.cbioportal.model.Sample; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.SampleService; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.GroupFilter; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.util.ClinicalDataEnrichmentUtil; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalDataEnrichment; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.GroupFilter; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.util.ClinicalDataEnrichmentUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -54,7 +54,7 @@ public class ClinicalDataEnrichmentController { @Autowired private SampleService sampleService; - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-data-enrichments/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical data enrichments for the sample groups") @ApiResponse(responseCode = "200", description = "OK", diff --git a/src/main/java/org/cbioportal/web/ClinicalEventController.java b/src/main/java/org/cbioportal/legacy/web/ClinicalEventController.java similarity index 89% rename from src/main/java/org/cbioportal/web/ClinicalEventController.java rename to src/main/java/org/cbioportal/legacy/web/ClinicalEventController.java index 487adbd479d..cfbd8f1db42 100644 --- a/src/main/java/org/cbioportal/web/ClinicalEventController.java +++ b/src/main/java/org/cbioportal/legacy/web/ClinicalEventController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,14 +10,19 @@ import jakarta.validation.Valid; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.*; -import org.cbioportal.web.parameter.sort.ClinicalEventSortBy; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.ClinicalEventAttributeRequest; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.PatientIdentifier; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.ClinicalEventSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.http.HttpHeaders; @@ -48,7 +53,7 @@ public class ClinicalEventController { @Autowired private ClinicalEventService clinicalEventService; - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/patients/{patientId}/clinical-events", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all clinical events of a patient in a study") @@ -87,7 +92,7 @@ public ResponseEntity> getAllClinicalEventsOfPatientInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/clinical-events", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all clinical events in a study") @@ -124,7 +129,7 @@ public ResponseEntity> getAllClinicalEventsInStudy( } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-events-meta/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, diff --git a/src/main/java/org/cbioportal/web/CoExpressionController.java b/src/main/java/org/cbioportal/legacy/web/CoExpressionController.java similarity index 88% rename from src/main/java/org/cbioportal/web/CoExpressionController.java rename to src/main/java/org/cbioportal/legacy/web/CoExpressionController.java index fd71a7fabc7..7b6b20f0f42 100644 --- a/src/main/java/org/cbioportal/web/CoExpressionController.java +++ b/src/main/java/org/cbioportal/legacy/web/CoExpressionController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,11 +8,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.CoExpression; -import org.cbioportal.model.EntityType; -import org.cbioportal.service.CoExpressionService; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.CoExpressionFilter; +import org.cbioportal.legacy.model.CoExpression; +import org.cbioportal.legacy.model.EntityType; +import org.cbioportal.legacy.service.CoExpressionService; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.CoExpressionFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -38,7 +38,7 @@ public class CoExpressionController { private CoExpressionService coExpressionService; // requires permission to access both molecularProfileIdA and molecularProfileIdB because service layer does not enforce requirement that both profiles are in the same study - @PreAuthorize("hasPermission(#molecularProfileIdA, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ) and hasPermission(#molecularProfileIdB, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileIdA, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ) and hasPermission(#molecularProfileIdB, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/co-expressions/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/CopyNumberSegmentController.java b/src/main/java/org/cbioportal/legacy/web/CopyNumberSegmentController.java similarity index 88% rename from src/main/java/org/cbioportal/web/CopyNumberSegmentController.java rename to src/main/java/org/cbioportal/legacy/web/CopyNumberSegmentController.java index c16406066f1..93cc5cdb919 100644 --- a/src/main/java/org/cbioportal/web/CopyNumberSegmentController.java +++ b/src/main/java/org/cbioportal/legacy/web/CopyNumberSegmentController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,18 +10,18 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.service.CopyNumberSegmentService; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.sort.CopyNumberSegmentSortBy; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.service.CopyNumberSegmentService; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.sort.CopyNumberSegmentSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -54,7 +54,7 @@ public class CopyNumberSegmentController { @Autowired private CopyNumberSegmentService copyNumberSegmentService; - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/samples/{sampleId}/copy-number-segments", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get copy number segments in a sample in a study") @@ -95,7 +95,7 @@ public ResponseEntity> getCopyNumberSegmentsInSampleInStudy( } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/copy-number-segments/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch copy number segments by sample ID") diff --git a/src/main/java/org/cbioportal/web/CosmicCountController.java b/src/main/java/org/cbioportal/legacy/web/CosmicCountController.java similarity index 90% rename from src/main/java/org/cbioportal/web/CosmicCountController.java rename to src/main/java/org/cbioportal/legacy/web/CosmicCountController.java index b696179554a..dae701ddd79 100644 --- a/src/main/java/org/cbioportal/web/CosmicCountController.java +++ b/src/main/java/org/cbioportal/legacy/web/CosmicCountController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,9 +8,9 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Size; -import org.cbioportal.model.CosmicMutation; -import org.cbioportal.service.CosmicCountService; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.model.CosmicMutation; +import org.cbioportal.legacy.service.CosmicCountService; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/DataAccessTokenController.java b/src/main/java/org/cbioportal/legacy/web/DataAccessTokenController.java similarity index 94% rename from src/main/java/org/cbioportal/web/DataAccessTokenController.java rename to src/main/java/org/cbioportal/legacy/web/DataAccessTokenController.java index ca3681d1aec..61e7b798940 100644 --- a/src/main/java/org/cbioportal/web/DataAccessTokenController.java +++ b/src/main/java/org/cbioportal/legacy/web/DataAccessTokenController.java @@ -15,7 +15,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -27,12 +27,12 @@ import jakarta.servlet.http.HttpServletRequest; import jakarta.servlet.http.HttpServletResponse; import org.apache.commons.lang3.StringUtils; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.service.exception.DataAccessTokenNoUserIdentityException; -import org.cbioportal.service.exception.DataAccessTokenProhibitedUserException; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.service.exception.DataAccessTokenNoUserIdentityException; +import org.cbioportal.legacy.service.exception.DataAccessTokenProhibitedUserException; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpStatus; diff --git a/src/main/java/org/cbioportal/web/DiscreteCopyNumberController.java b/src/main/java/org/cbioportal/legacy/web/DiscreteCopyNumberController.java similarity index 89% rename from src/main/java/org/cbioportal/web/DiscreteCopyNumberController.java rename to src/main/java/org/cbioportal/legacy/web/DiscreteCopyNumberController.java index 5a865c054a0..604474d218b 100644 --- a/src/main/java/org/cbioportal/web/DiscreteCopyNumberController.java +++ b/src/main/java/org/cbioportal/legacy/web/DiscreteCopyNumberController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,16 +8,16 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.DiscreteCopyNumberEventType; -import org.cbioportal.web.parameter.DiscreteCopyNumberFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.Projection; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.DiscreteCopyNumberService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.DiscreteCopyNumberEventType; +import org.cbioportal.legacy.web.parameter.DiscreteCopyNumberFilter; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -44,7 +44,7 @@ public class DiscreteCopyNumberController { @Autowired private DiscreteCopyNumberService discreteCopyNumberService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/discrete-copy-number", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get discrete copy number alterations in a molecular profile") @@ -74,7 +74,7 @@ public ResponseEntity> getDiscreteCopyNumbersInMole } } - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/discrete-copy-number/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/DiscreteCopyNumberCountController.java b/src/main/java/org/cbioportal/legacy/web/DiscreteCopyNumberCountController.java similarity index 86% rename from src/main/java/org/cbioportal/web/DiscreteCopyNumberCountController.java rename to src/main/java/org/cbioportal/legacy/web/DiscreteCopyNumberCountController.java index da8952d57ee..5ef9e5237b3 100644 --- a/src/main/java/org/cbioportal/web/DiscreteCopyNumberCountController.java +++ b/src/main/java/org/cbioportal/legacy/web/DiscreteCopyNumberCountController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,12 +8,12 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Size; -import org.cbioportal.model.CopyNumberCount; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.CopyNumberCountIdentifier; +import org.cbioportal.legacy.model.CopyNumberCount; +import org.cbioportal.legacy.service.DiscreteCopyNumberService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.CopyNumberCountIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -41,7 +41,7 @@ public class DiscreteCopyNumberCountController { @Autowired private DiscreteCopyNumberService discreteCopyNumberService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/discrete-copy-number-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/DocRedirectController.java b/src/main/java/org/cbioportal/legacy/web/DocRedirectController.java similarity index 98% rename from src/main/java/org/cbioportal/web/DocRedirectController.java rename to src/main/java/org/cbioportal/legacy/web/DocRedirectController.java index e04443556f0..d4cb77317fc 100644 --- a/src/main/java/org/cbioportal/web/DocRedirectController.java +++ b/src/main/java/org/cbioportal/legacy/web/DocRedirectController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import jakarta.servlet.http.HttpServletRequest; import org.springframework.web.bind.annotation.GetMapping; diff --git a/src/main/java/org/cbioportal/web/ExecuterTimeInterceptor.java b/src/main/java/org/cbioportal/legacy/web/ExecuterTimeInterceptor.java similarity index 95% rename from src/main/java/org/cbioportal/web/ExecuterTimeInterceptor.java rename to src/main/java/org/cbioportal/legacy/web/ExecuterTimeInterceptor.java index cd53de8c347..d4a6e8548a0 100644 --- a/src/main/java/org/cbioportal/web/ExecuterTimeInterceptor.java +++ b/src/main/java/org/cbioportal/legacy/web/ExecuterTimeInterceptor.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import org.springframework.ui.ModelMap; import org.springframework.web.context.request.WebRequest; diff --git a/src/main/java/org/cbioportal/web/ExpressionEnrichmentController.java b/src/main/java/org/cbioportal/legacy/web/ExpressionEnrichmentController.java similarity index 88% rename from src/main/java/org/cbioportal/web/ExpressionEnrichmentController.java rename to src/main/java/org/cbioportal/legacy/web/ExpressionEnrichmentController.java index a32ffd37a1d..11cb7be6fad 100644 --- a/src/main/java/org/cbioportal/web/ExpressionEnrichmentController.java +++ b/src/main/java/org/cbioportal/legacy/web/ExpressionEnrichmentController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,16 +8,16 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.ExpressionEnrichment; -import org.cbioportal.model.GenericAssayEnrichment; -import org.cbioportal.model.GenomicEnrichment; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.service.ExpressionEnrichmentService; -import org.cbioportal.service.exception.GenericAssayNotFoundException; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupFilter; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.ExpressionEnrichment; +import org.cbioportal.legacy.model.GenericAssayEnrichment; +import org.cbioportal.legacy.model.GenomicEnrichment; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.ExpressionEnrichmentService; +import org.cbioportal.legacy.service.exception.GenericAssayNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -46,7 +46,7 @@ public class ExpressionEnrichmentController { @Autowired private ExpressionEnrichmentService expressionEnrichmentService; - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/expression-enrichments/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -68,7 +68,7 @@ public ResponseEntity> fetchGenomicEnrichments( HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/generic-assay-enrichments/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/GeneController.java b/src/main/java/org/cbioportal/legacy/web/GeneController.java similarity index 89% rename from src/main/java/org/cbioportal/web/GeneController.java rename to src/main/java/org/cbioportal/legacy/web/GeneController.java index 51774d20bfa..f3d25ad4689 100644 --- a/src/main/java/org/cbioportal/web/GeneController.java +++ b/src/main/java/org/cbioportal/legacy/web/GeneController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,18 +10,18 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.Gene; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.exception.GeneNotFoundException; -import org.cbioportal.service.exception.GeneWithMultipleEntrezIdsException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.GeneIdType; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.GeneSortBy; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.service.exception.GeneWithMultipleEntrezIdsException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.GeneIdType; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.GeneSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; diff --git a/src/main/java/org/cbioportal/web/GenePanelController.java b/src/main/java/org/cbioportal/legacy/web/GenePanelController.java similarity index 90% rename from src/main/java/org/cbioportal/web/GenePanelController.java rename to src/main/java/org/cbioportal/legacy/web/GenePanelController.java index 9bd73ff27bd..8949849d41b 100644 --- a/src/main/java/org/cbioportal/web/GenePanelController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenePanelController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Hidden; import io.swagger.v3.oas.annotations.Operation; @@ -13,16 +13,16 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.GenePanel; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.exception.GenePanelNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.GenePanelSortBy; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.exception.GenePanelNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.GenePanelSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; diff --git a/src/main/java/org/cbioportal/web/GenePanelDataController.java b/src/main/java/org/cbioportal/legacy/web/GenePanelDataController.java similarity index 88% rename from src/main/java/org/cbioportal/web/GenePanelDataController.java rename to src/main/java/org/cbioportal/legacy/web/GenePanelDataController.java index 6864a6c5db3..9b9741fdc30 100644 --- a/src/main/java/org/cbioportal/web/GenePanelDataController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenePanelDataController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,14 +8,14 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.GenePanelDataFilter; -import org.cbioportal.web.parameter.GenePanelDataMultipleStudyFilter; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.GenePanelDataFilter; +import org.cbioportal.legacy.web.parameter.GenePanelDataMultipleStudyFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -45,7 +45,7 @@ public class GenePanelDataController { @Autowired private GenePanelService genePanelService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/gene-panel-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get gene panel data") @@ -69,7 +69,7 @@ public ResponseEntity> getGenePanelData( return new ResponseEntity<>(genePanelDataList, HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/gene-panel-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch gene panel data") diff --git a/src/main/java/org/cbioportal/web/GeneralControllerAdvice.java b/src/main/java/org/cbioportal/legacy/web/GeneralControllerAdvice.java similarity index 97% rename from src/main/java/org/cbioportal/web/GeneralControllerAdvice.java rename to src/main/java/org/cbioportal/legacy/web/GeneralControllerAdvice.java index dbf2fc9d867..d916b0aeedd 100644 --- a/src/main/java/org/cbioportal/web/GeneralControllerAdvice.java +++ b/src/main/java/org/cbioportal/legacy/web/GeneralControllerAdvice.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import org.springframework.core.MethodParameter; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/GenericAssayController.java b/src/main/java/org/cbioportal/legacy/web/GenericAssayController.java similarity index 91% rename from src/main/java/org/cbioportal/web/GenericAssayController.java rename to src/main/java/org/cbioportal/legacy/web/GenericAssayController.java index ae10b64c88b..9bbafc1f703 100644 --- a/src/main/java/org/cbioportal/web/GenericAssayController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenericAssayController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,13 +8,13 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.exception.GenericAssayNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.GenericAssayMetaFilter; -import org.cbioportal.web.parameter.Projection; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.exception.GenericAssayNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.GenericAssayMetaFilter; +import org.cbioportal.legacy.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/GenericAssayDataController.java b/src/main/java/org/cbioportal/legacy/web/GenericAssayDataController.java similarity index 90% rename from src/main/java/org/cbioportal/web/GenericAssayDataController.java rename to src/main/java/org/cbioportal/legacy/web/GenericAssayDataController.java index 8cfc55bdb7a..9ecc0709fe7 100644 --- a/src/main/java/org/cbioportal/web/GenericAssayDataController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenericAssayDataController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -9,16 +9,16 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; import org.apache.commons.lang3.StringUtils; -import org.cbioportal.model.GenericAssayData; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.GenericAssayDataMultipleStudyFilter; -import org.cbioportal.web.parameter.GenericAssayFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.model.GenericAssayData; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.GenericAssayDataMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayFilter; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -50,7 +50,7 @@ public class GenericAssayDataController { @Autowired private GenericAssayService genericAssayService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/generic-assay-data/{molecularProfileId}/generic-assay/{genericAssayStableId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get generic_assay_data in a molecular profile") @@ -77,7 +77,7 @@ public ResponseEntity> getGenericAssayDataInMolecularProf } } - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/generic_assay_data/{molecularProfileId}/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -110,7 +110,7 @@ public ResponseEntity> fetchGenericAssayDataInMolecularPr } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/generic_assay_data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch generic_assay_data") diff --git a/src/main/java/org/cbioportal/web/GenericAssayEnrichmentController.java b/src/main/java/org/cbioportal/legacy/web/GenericAssayEnrichmentController.java similarity index 90% rename from src/main/java/org/cbioportal/web/GenericAssayEnrichmentController.java rename to src/main/java/org/cbioportal/legacy/web/GenericAssayEnrichmentController.java index 8959681e09b..f37bbacb7b0 100644 --- a/src/main/java/org/cbioportal/web/GenericAssayEnrichmentController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenericAssayEnrichmentController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,14 +8,14 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.GenericAssayBinaryEnrichment; -import org.cbioportal.model.GenericAssayCategoricalEnrichment; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.service.ExpressionEnrichmentService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupFilter; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.GenericAssayBinaryEnrichment; +import org.cbioportal.legacy.model.GenericAssayCategoricalEnrichment; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.ExpressionEnrichmentService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -43,7 +43,7 @@ public class GenericAssayEnrichmentController { @Autowired private ExpressionEnrichmentService expressionEnrichmentService; - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/api/generic-assay-categorical-enrichments/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -65,7 +65,7 @@ public ResponseEntity> fetchGenericAssay HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/api/generic-assay-binary-enrichments/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/GenesetController.java b/src/main/java/org/cbioportal/legacy/web/GenesetController.java similarity index 91% rename from src/main/java/org/cbioportal/web/GenesetController.java rename to src/main/java/org/cbioportal/legacy/web/GenesetController.java index 0e4eeb56bcc..4761de8af9d 100644 --- a/src/main/java/org/cbioportal/web/GenesetController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenesetController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,13 +10,13 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.Geneset; -import org.cbioportal.service.GenesetService; -import org.cbioportal.service.exception.GenesetNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.service.GenesetService; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; diff --git a/src/main/java/org/cbioportal/web/GenesetCorrelationController.java b/src/main/java/org/cbioportal/legacy/web/GenesetCorrelationController.java similarity index 90% rename from src/main/java/org/cbioportal/web/GenesetCorrelationController.java rename to src/main/java/org/cbioportal/legacy/web/GenesetCorrelationController.java index 1859079bbbe..09b9c7b7086 100644 --- a/src/main/java/org/cbioportal/web/GenesetCorrelationController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenesetCorrelationController.java @@ -21,7 +21,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -32,12 +32,12 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.GenesetCorrelation; -import org.cbioportal.service.GenesetCorrelationService; -import org.cbioportal.service.exception.GenesetNotFoundException; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.model.GenesetCorrelation; +import org.cbioportal.legacy.service.GenesetCorrelationService; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -63,7 +63,7 @@ public class GenesetCorrelationController { @Autowired private GenesetCorrelationService genesetCorrelationService; - @PreAuthorize("hasPermission(#geneticProfileId, 'GeneticProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#geneticProfileId, 'GeneticProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/genesets/{genesetId}/expression-correlation/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get the genes in a gene set that have expression correlated to the gene set scores (calculated using Spearman's correlation)") diff --git a/src/main/java/org/cbioportal/web/GenesetDataController.java b/src/main/java/org/cbioportal/legacy/web/GenesetDataController.java similarity index 87% rename from src/main/java/org/cbioportal/web/GenesetDataController.java rename to src/main/java/org/cbioportal/legacy/web/GenesetDataController.java index 9c911d8d18e..f95e4309a7b 100644 --- a/src/main/java/org/cbioportal/web/GenesetDataController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenesetDataController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -7,12 +7,12 @@ import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.GenesetDataFilterCriteria; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.GenesetDataFilterCriteria; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -38,7 +38,7 @@ public class GenesetDataController { @Autowired private GenesetDataService genesetDataService; - @PreAuthorize("hasPermission(#geneticProfileId, 'GeneticProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#geneticProfileId, 'GeneticProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/genetic-profiles/{geneticProfileId}/geneset-genetic-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch gene set \"genetic data\" items (gene set scores) by profile Id, gene set ids and sample ids") diff --git a/src/main/java/org/cbioportal/web/GenesetHierarchyController.java b/src/main/java/org/cbioportal/legacy/web/GenesetHierarchyController.java similarity index 92% rename from src/main/java/org/cbioportal/web/GenesetHierarchyController.java rename to src/main/java/org/cbioportal/legacy/web/GenesetHierarchyController.java index 1efd7019138..85dd248ed34 100644 --- a/src/main/java/org/cbioportal/web/GenesetHierarchyController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenesetHierarchyController.java @@ -21,7 +21,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -32,11 +32,11 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.GenesetHierarchyInfo; -import org.cbioportal.service.GenesetHierarchyService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.service.GenesetHierarchyService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -61,7 +61,7 @@ public class GenesetHierarchyController { @Autowired private GenesetHierarchyService genesetHierarchyService; - @PreAuthorize("hasPermission(#geneticProfileId, 'GeneticProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#geneticProfileId, 'GeneticProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/geneset-hierarchy/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get gene set hierarchical organization information. I.e. how different gene sets relate to other gene sets, in a hierarchy") diff --git a/src/main/java/org/cbioportal/web/IndexPageController.java b/src/main/java/org/cbioportal/legacy/web/IndexPageController.java similarity index 94% rename from src/main/java/org/cbioportal/web/IndexPageController.java rename to src/main/java/org/cbioportal/legacy/web/IndexPageController.java index 2bd3b95b66f..a00cec65b04 100644 --- a/src/main/java/org/cbioportal/web/IndexPageController.java +++ b/src/main/java/org/cbioportal/legacy/web/IndexPageController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.core.JsonGenerator; import com.fasterxml.jackson.core.JsonProcessingException; @@ -7,9 +7,9 @@ import com.fasterxml.jackson.databind.SerializerProvider; import com.fasterxml.jackson.databind.module.SimpleModule; import jakarta.servlet.http.HttpServletRequest; -import org.cbioportal.service.FrontendPropertiesService; -import org.cbioportal.service.util.MskWholeSlideViewerTokenGenerator; -import org.cbioportal.web.util.HttpRequestUtils; +import org.cbioportal.legacy.service.FrontendPropertiesService; +import org.cbioportal.legacy.service.util.MskWholeSlideViewerTokenGenerator; +import org.cbioportal.legacy.web.util.HttpRequestUtils; import org.json.simple.JSONObject; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -26,7 +26,7 @@ import java.util.HashMap; import java.util.Map; -import static org.cbioportal.service.FrontendPropertiesServiceImpl.FrontendProperty; +import static org.cbioportal.legacy.service.FrontendPropertiesServiceImpl.FrontendProperty; @Controller public class IndexPageController { diff --git a/src/main/java/org/cbioportal/web/InfoController.java b/src/main/java/org/cbioportal/legacy/web/InfoController.java similarity index 93% rename from src/main/java/org/cbioportal/web/InfoController.java rename to src/main/java/org/cbioportal/legacy/web/InfoController.java index 59e9352ca5b..2f899d2712a 100644 --- a/src/main/java/org/cbioportal/web/InfoController.java +++ b/src/main/java/org/cbioportal/legacy/web/InfoController.java @@ -1,13 +1,13 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.media.Content; import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; -import org.cbioportal.model.Info; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; +import org.cbioportal.legacy.model.Info; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/LegacyApiController.java b/src/main/java/org/cbioportal/legacy/web/LegacyApiController.java similarity index 98% rename from src/main/java/org/cbioportal/web/LegacyApiController.java rename to src/main/java/org/cbioportal/legacy/web/LegacyApiController.java index 6e696460b59..14055451944 100644 --- a/src/main/java/org/cbioportal/web/LegacyApiController.java +++ b/src/main/java/org/cbioportal/legacy/web/LegacyApiController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.JsonNode; diff --git a/src/main/java/org/cbioportal/web/LoginPageController.java b/src/main/java/org/cbioportal/legacy/web/LoginPageController.java similarity index 96% rename from src/main/java/org/cbioportal/web/LoginPageController.java rename to src/main/java/org/cbioportal/legacy/web/LoginPageController.java index cadcdb10838..ee31b83ed79 100644 --- a/src/main/java/org/cbioportal/web/LoginPageController.java +++ b/src/main/java/org/cbioportal/legacy/web/LoginPageController.java @@ -1,8 +1,8 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import jakarta.servlet.http.HttpServletRequest; -import org.cbioportal.service.FrontendPropertiesService; -import org.cbioportal.service.FrontendPropertiesServiceImpl; +import org.cbioportal.legacy.service.FrontendPropertiesService; +import org.cbioportal.legacy.service.FrontendPropertiesServiceImpl; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/cbioportal/web/MatchMinerController.java b/src/main/java/org/cbioportal/legacy/web/MatchMinerController.java similarity index 99% rename from src/main/java/org/cbioportal/web/MatchMinerController.java rename to src/main/java/org/cbioportal/legacy/web/MatchMinerController.java index 3b1ad15f694..7a870f5df3a 100644 --- a/src/main/java/org/cbioportal/web/MatchMinerController.java +++ b/src/main/java/org/cbioportal/legacy/web/MatchMinerController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.media.Content; import io.swagger.v3.oas.annotations.media.Schema; diff --git a/src/main/java/org/cbioportal/web/MolecularDataController.java b/src/main/java/org/cbioportal/legacy/web/MolecularDataController.java similarity index 91% rename from src/main/java/org/cbioportal/web/MolecularDataController.java rename to src/main/java/org/cbioportal/legacy/web/MolecularDataController.java index 69ed27f83bf..ac8c03494e9 100644 --- a/src/main/java/org/cbioportal/web/MolecularDataController.java +++ b/src/main/java/org/cbioportal/legacy/web/MolecularDataController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -9,17 +9,17 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; import org.apache.commons.lang3.math.NumberUtils; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.NumericGeneMolecularData; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.MolecularDataFilter; -import org.cbioportal.web.parameter.MolecularDataMultipleStudyFilter; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.NumericGeneMolecularData; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.MolecularDataFilter; +import org.cbioportal.legacy.web.parameter.MolecularDataMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -51,7 +51,7 @@ public class MolecularDataController { @Autowired private MolecularDataService molecularDataService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/molecular-data", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all molecular data in a molecular profile") @@ -79,7 +79,7 @@ public ResponseEntity> getAllMolecularDataInMolec } } - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/molecular-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -112,7 +112,7 @@ public ResponseEntity> fetchAllMolecularDataInMol } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch molecular data") diff --git a/src/main/java/org/cbioportal/web/MolecularProfileController.java b/src/main/java/org/cbioportal/legacy/web/MolecularProfileController.java similarity index 89% rename from src/main/java/org/cbioportal/web/MolecularProfileController.java rename to src/main/java/org/cbioportal/legacy/web/MolecularProfileController.java index ee887e13eff..3a342f59bc6 100644 --- a/src/main/java/org/cbioportal/web/MolecularProfileController.java +++ b/src/main/java/org/cbioportal/legacy/web/MolecularProfileController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,19 +10,19 @@ import jakarta.validation.Valid; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.MolecularProfileFilter; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.MolecularProfileSortBy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.MolecularProfileFilter; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.MolecularProfileSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -83,7 +83,7 @@ public ResponseEntity> getAllMolecularProfiles( } } - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get molecular profile") @@ -96,7 +96,7 @@ public ResponseEntity getMolecularProfile( return new ResponseEntity<>(molecularProfileService.getMolecularProfile(molecularProfileId), HttpStatus.OK); } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/molecular-profiles", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all molecular profiles in a study") @@ -131,7 +131,7 @@ public ResponseEntity> getAllMolecularProfilesInStudy( } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch molecular profiles") diff --git a/src/main/java/org/cbioportal/web/MrnaPercentileController.java b/src/main/java/org/cbioportal/legacy/web/MrnaPercentileController.java similarity index 86% rename from src/main/java/org/cbioportal/web/MrnaPercentileController.java rename to src/main/java/org/cbioportal/legacy/web/MrnaPercentileController.java index 816da438e08..c5624aaf905 100644 --- a/src/main/java/org/cbioportal/web/MrnaPercentileController.java +++ b/src/main/java/org/cbioportal/legacy/web/MrnaPercentileController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,11 +8,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Size; -import org.cbioportal.model.MrnaPercentile; -import org.cbioportal.service.MrnaPercentileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.PagingConstants; +import org.cbioportal.legacy.model.MrnaPercentile; +import org.cbioportal.legacy.service.MrnaPercentileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.PagingConstants; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -38,7 +38,7 @@ public class MrnaPercentileController { @Autowired private MrnaPercentileService mrnaPercentileService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/mrna-percentile/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/MskEntityTranslationController.java b/src/main/java/org/cbioportal/legacy/web/MskEntityTranslationController.java similarity index 96% rename from src/main/java/org/cbioportal/web/MskEntityTranslationController.java rename to src/main/java/org/cbioportal/legacy/web/MskEntityTranslationController.java index a9152a02716..42fff4851aa 100644 --- a/src/main/java/org/cbioportal/web/MskEntityTranslationController.java +++ b/src/main/java/org/cbioportal/legacy/web/MskEntityTranslationController.java @@ -30,14 +30,14 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.context.annotation.PropertySource; diff --git a/src/main/java/org/cbioportal/web/MutationController.java b/src/main/java/org/cbioportal/legacy/web/MutationController.java similarity index 92% rename from src/main/java/org/cbioportal/web/MutationController.java rename to src/main/java/org/cbioportal/legacy/web/MutationController.java index 7c72d36db41..a98e793ab36 100644 --- a/src/main/java/org/cbioportal/web/MutationController.java +++ b/src/main/java/org/cbioportal/legacy/web/MutationController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,20 +10,20 @@ import jakarta.validation.Valid; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.MutationFilter; -import org.cbioportal.web.parameter.MutationMultipleStudyFilter; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; -import org.cbioportal.web.parameter.sort.MutationSortBy; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.MutationFilter; +import org.cbioportal.legacy.web.parameter.MutationMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.web.parameter.sort.MutationSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -54,7 +54,7 @@ public class MutationController { @Autowired private MutationService mutationService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/mutations", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get mutations in a molecular profile by Sample List ID") @@ -96,7 +96,7 @@ public ResponseEntity> getMutationsInMolecularProfileBySampleList } } - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/mutations/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch mutations in a molecular profile") @@ -151,7 +151,7 @@ public ResponseEntity> fetchMutationsInMolecularProfile( } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/mutations/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch mutations in multiple molecular profiles by sample IDs") diff --git a/src/main/java/org/cbioportal/web/MutationCountController.java b/src/main/java/org/cbioportal/legacy/web/MutationCountController.java similarity index 88% rename from src/main/java/org/cbioportal/web/MutationCountController.java rename to src/main/java/org/cbioportal/legacy/web/MutationCountController.java index 7450c7fe131..d89f2701025 100644 --- a/src/main/java/org/cbioportal/web/MutationCountController.java +++ b/src/main/java/org/cbioportal/legacy/web/MutationCountController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,11 +8,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Size; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.service.MutationService; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.MutationPositionIdentifier; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.MutationPositionIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/MutationSpectrumController.java b/src/main/java/org/cbioportal/legacy/web/MutationSpectrumController.java similarity index 86% rename from src/main/java/org/cbioportal/web/MutationSpectrumController.java rename to src/main/java/org/cbioportal/legacy/web/MutationSpectrumController.java index c6c8a28b718..ecb8bb168a0 100644 --- a/src/main/java/org/cbioportal/web/MutationSpectrumController.java +++ b/src/main/java/org/cbioportal/legacy/web/MutationSpectrumController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,11 +8,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.MutationSpectrum; -import org.cbioportal.service.MutationSpectrumService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.MutationSpectrumFilter; +import org.cbioportal.legacy.model.MutationSpectrum; +import org.cbioportal.legacy.service.MutationSpectrumService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.MutationSpectrumFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -37,7 +37,7 @@ public class MutationSpectrumController { @Autowired private MutationSpectrumService mutationSpectrumService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/mutation-spectrums/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/OAuth2DataAccessTokenController.java b/src/main/java/org/cbioportal/legacy/web/OAuth2DataAccessTokenController.java similarity index 95% rename from src/main/java/org/cbioportal/web/OAuth2DataAccessTokenController.java rename to src/main/java/org/cbioportal/legacy/web/OAuth2DataAccessTokenController.java index 94df3e2f7da..be563f0462c 100644 --- a/src/main/java/org/cbioportal/web/OAuth2DataAccessTokenController.java +++ b/src/main/java/org/cbioportal/legacy/web/OAuth2DataAccessTokenController.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -43,12 +43,12 @@ import jakarta.servlet.http.HttpServletRequest; import jakarta.servlet.http.HttpServletResponse; import org.apache.commons.lang3.StringUtils; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.service.exception.DataAccessTokenNoUserIdentityException; -import org.cbioportal.service.exception.DataAccessTokenProhibitedUserException; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.service.exception.DataAccessTokenNoUserIdentityException; +import org.cbioportal.legacy.service.exception.DataAccessTokenProhibitedUserException; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpHeaders; diff --git a/src/main/java/org/cbioportal/web/PatientController.java b/src/main/java/org/cbioportal/legacy/web/PatientController.java similarity index 90% rename from src/main/java/org/cbioportal/web/PatientController.java rename to src/main/java/org/cbioportal/legacy/web/PatientController.java index 7c082509bc9..1623b6ab028 100644 --- a/src/main/java/org/cbioportal/web/PatientController.java +++ b/src/main/java/org/cbioportal/legacy/web/PatientController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,20 +10,20 @@ import jakarta.validation.Valid; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.Patient; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.PatientFilter; -import org.cbioportal.web.parameter.PatientIdentifier; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.PatientSortBy; -import org.cbioportal.web.util.UniqueKeyExtractor; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.PatientFilter; +import org.cbioportal.legacy.web.parameter.PatientIdentifier; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.PatientSortBy; +import org.cbioportal.legacy.web.util.UniqueKeyExtractor; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -87,7 +87,7 @@ public ResponseEntity> getAllPatients( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/patients", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all patients in a study") @@ -122,7 +122,7 @@ public ResponseEntity> getAllPatientsInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/patients/{patientId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get a patient in a study") @@ -137,7 +137,7 @@ public ResponseEntity getPatientInStudy( return new ResponseEntity<>(patientService.getPatientInStudy(studyId, patientId), HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/patients/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @ApiResponse(responseCode = "200", description = "OK", diff --git a/src/main/java/org/cbioportal/web/PublicVirtualStudiesController.java b/src/main/java/org/cbioportal/legacy/web/PublicVirtualStudiesController.java similarity index 93% rename from src/main/java/org/cbioportal/web/PublicVirtualStudiesController.java rename to src/main/java/org/cbioportal/legacy/web/PublicVirtualStudiesController.java index c48ac446041..30f615f001b 100644 --- a/src/main/java/org/cbioportal/web/PublicVirtualStudiesController.java +++ b/src/main/java/org/cbioportal/legacy/web/PublicVirtualStudiesController.java @@ -1,14 +1,14 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.media.Content; import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; -import org.cbioportal.service.CancerTypeService; -import org.cbioportal.service.exception.AccessForbiddenException; -import org.cbioportal.service.exception.CancerTypeNotFoundException; -import org.cbioportal.service.util.SessionServiceRequestHandler; -import org.cbioportal.web.parameter.VirtualStudy; -import org.cbioportal.web.parameter.VirtualStudyData; +import org.cbioportal.legacy.service.CancerTypeService; +import org.cbioportal.legacy.service.exception.AccessForbiddenException; +import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException; +import org.cbioportal.legacy.service.util.SessionServiceRequestHandler; +import org.cbioportal.legacy.web.parameter.VirtualStudy; +import org.cbioportal.legacy.web.parameter.VirtualStudyData; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Value; diff --git a/src/main/java/org/cbioportal/web/ReferenceGenomeGeneController.java b/src/main/java/org/cbioportal/legacy/web/ReferenceGenomeGeneController.java similarity index 92% rename from src/main/java/org/cbioportal/web/ReferenceGenomeGeneController.java rename to src/main/java/org/cbioportal/legacy/web/ReferenceGenomeGeneController.java index 5273ba1a165..8558b9f81c8 100644 --- a/src/main/java/org/cbioportal/web/ReferenceGenomeGeneController.java +++ b/src/main/java/org/cbioportal/legacy/web/ReferenceGenomeGeneController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,12 +8,12 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Size; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.service.GeneMemoizerService; -import org.cbioportal.service.ReferenceGenomeGeneService; -import org.cbioportal.service.exception.GeneNotFoundException; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.service.GeneMemoizerService; +import org.cbioportal.legacy.service.ReferenceGenomeGeneService; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/ResourceDataController.java b/src/main/java/org/cbioportal/legacy/web/ResourceDataController.java similarity index 92% rename from src/main/java/org/cbioportal/web/ResourceDataController.java rename to src/main/java/org/cbioportal/legacy/web/ResourceDataController.java index 4920791285a..012d307df39 100644 --- a/src/main/java/org/cbioportal/web/ResourceDataController.java +++ b/src/main/java/org/cbioportal/legacy/web/ResourceDataController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,17 +10,17 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.ResourceData; -import org.cbioportal.service.ResourceDataService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.ResourceDataSortBy; +import org.cbioportal.legacy.model.ResourceData; +import org.cbioportal.legacy.service.ResourceDataService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.ResourceDataSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.ApplicationContext; import org.springframework.cache.annotation.Cacheable; @@ -62,7 +62,7 @@ private ResourceDataController getInstance() { return instance; } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/samples/{sampleId}/resource-data", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all resource data of a sample in a study") @@ -100,7 +100,7 @@ public ResponseEntity> getAllResourceDataOfSampleInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/patients/{patientId}/resource-data", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all resource data of a patient in a study") @@ -138,7 +138,7 @@ public ResponseEntity> getAllResourceDataOfPatientInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/resource-data", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all resource data for a study") @@ -172,7 +172,7 @@ public ResponseEntity> getAllStudyResourceDataInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/resource-data-all", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all resource data for for all patients and all samples within a study") diff --git a/src/main/java/org/cbioportal/web/ResourceDefinitionController.java b/src/main/java/org/cbioportal/legacy/web/ResourceDefinitionController.java similarity index 86% rename from src/main/java/org/cbioportal/web/ResourceDefinitionController.java rename to src/main/java/org/cbioportal/legacy/web/ResourceDefinitionController.java index 4f4658166c8..13d1737dd14 100644 --- a/src/main/java/org/cbioportal/web/ResourceDefinitionController.java +++ b/src/main/java/org/cbioportal/legacy/web/ResourceDefinitionController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,16 +10,16 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.service.ResourceDefinitionService; -import org.cbioportal.service.exception.ResourceDefinitionNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.ResourceDefinitionSortBy; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.service.ResourceDefinitionService; +import org.cbioportal.legacy.service.exception.ResourceDefinitionNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.ResourceDefinitionSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -45,7 +45,7 @@ public class ResourceDefinitionController { @Autowired private ResourceDefinitionService resourceDefinitionService; - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/resource-definitions", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all resource definitions in the specified study") @@ -78,7 +78,7 @@ public ResponseEntity> getAllResourceDefinitionsInStudy } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/resource-definitions/{resourceId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get specified resource definition") @@ -95,7 +95,7 @@ public ResponseEntity getResourceDefinitionInStudy( HttpStatus.OK); } - @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/resource-definitions/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all resource definitions for specified studies") diff --git a/src/main/java/org/cbioportal/web/SamlAndBasicLoginController.java b/src/main/java/org/cbioportal/legacy/web/SamlAndBasicLoginController.java similarity index 87% rename from src/main/java/org/cbioportal/web/SamlAndBasicLoginController.java rename to src/main/java/org/cbioportal/legacy/web/SamlAndBasicLoginController.java index 0364e0d981f..6e0b60969df 100644 --- a/src/main/java/org/cbioportal/web/SamlAndBasicLoginController.java +++ b/src/main/java/org/cbioportal/legacy/web/SamlAndBasicLoginController.java @@ -1,8 +1,8 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import jakarta.servlet.http.HttpServletRequest; -import org.cbioportal.service.FrontendPropertiesService; -import org.cbioportal.service.FrontendPropertiesServiceImpl; +import org.cbioportal.legacy.service.FrontendPropertiesService; +import org.cbioportal.legacy.service.FrontendPropertiesServiceImpl; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/SampleController.java b/src/main/java/org/cbioportal/legacy/web/SampleController.java similarity index 90% rename from src/main/java/org/cbioportal/web/SampleController.java rename to src/main/java/org/cbioportal/legacy/web/SampleController.java index 83cd4df45b5..d9a3dd69106 100644 --- a/src/main/java/org/cbioportal/web/SampleController.java +++ b/src/main/java/org/cbioportal/legacy/web/SampleController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,28 +10,28 @@ import jakarta.validation.Valid; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.utils.security.AccessLevel; -import org.cbioportal.utils.security.PortalSecurityConfig; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleFilter; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.sort.SampleSortBy; -import org.cbioportal.web.util.UniqueKeyExtractor; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.utils.security.AccessLevel; +import org.cbioportal.legacy.utils.security.PortalSecurityConfig; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.sort.SampleSortBy; +import org.cbioportal.legacy.web.util.UniqueKeyExtractor; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpHeaders; @@ -145,7 +145,7 @@ public ResponseEntity> getSamplesByKeyword( ); } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/samples", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all samples in a study") @@ -180,7 +180,7 @@ public ResponseEntity> getAllSamplesInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/samples/{sampleId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get a sample in a study") @@ -195,7 +195,7 @@ public ResponseEntity getSampleInStudy( return new ResponseEntity<>(sampleService.getSampleInStudy(studyId, sampleId), HttpStatus.OK); } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/patients/{patientId}/samples", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all samples of a patient in a study") @@ -233,7 +233,7 @@ public ResponseEntity> getAllSamplesOfPatientInStudy( } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/samples/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch samples by ID") diff --git a/src/main/java/org/cbioportal/web/SampleListController.java b/src/main/java/org/cbioportal/legacy/web/SampleListController.java similarity index 89% rename from src/main/java/org/cbioportal/web/SampleListController.java rename to src/main/java/org/cbioportal/legacy/web/SampleListController.java index ce1e82eff1c..2ef821925dc 100644 --- a/src/main/java/org/cbioportal/web/SampleListController.java +++ b/src/main/java/org/cbioportal/legacy/web/SampleListController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,17 +10,17 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.SampleList; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.SampleListSortBy; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.SampleListSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -79,7 +79,7 @@ public ResponseEntity> getAllSampleLists( } } - @PreAuthorize("hasPermission(#sampleListId, 'SampleListId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#sampleListId, 'SampleListId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/sample-lists/{sampleListId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get sample list") @@ -92,7 +92,7 @@ public ResponseEntity getSampleList( return new ResponseEntity<>(sampleListService.getSampleList(sampleListId), HttpStatus.OK); } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/sample-lists", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all sample lists in a study") @@ -127,7 +127,7 @@ public ResponseEntity> getAllSampleListsInStudy( } } - @PreAuthorize("hasPermission(#sampleListId, 'SampleListId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#sampleListId, 'SampleListId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/sample-lists/{sampleListId}/sample-ids", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all sample IDs in a sample list") @@ -140,7 +140,7 @@ public ResponseEntity> getAllSampleIdsInSampleList( return new ResponseEntity<>(sampleListService.getAllSampleIdsInSampleList(sampleListId), HttpStatus.OK); } - @PreAuthorize("hasPermission(#sampleListIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#sampleListIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/sample-lists/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch sample lists by ID") diff --git a/src/main/java/org/cbioportal/web/ServerStatusController.java b/src/main/java/org/cbioportal/legacy/web/ServerStatusController.java similarity index 85% rename from src/main/java/org/cbioportal/web/ServerStatusController.java rename to src/main/java/org/cbioportal/legacy/web/ServerStatusController.java index 4aa7963a63b..62dbb170e97 100644 --- a/src/main/java/org/cbioportal/web/ServerStatusController.java +++ b/src/main/java/org/cbioportal/legacy/web/ServerStatusController.java @@ -1,13 +1,13 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.media.Content; import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; -import org.cbioportal.service.ServerStatusService; -import org.cbioportal.service.impl.ServerStatusServiceImpl.ServerStatusMessage; -import org.cbioportal.web.config.annotation.PublicApi; +import org.cbioportal.legacy.service.ServerStatusService; +import org.cbioportal.legacy.service.impl.ServerStatusServiceImpl.ServerStatusMessage; +import org.cbioportal.legacy.web.config.annotation.PublicApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/SessionServiceController.java b/src/main/java/org/cbioportal/legacy/web/SessionServiceController.java similarity index 96% rename from src/main/java/org/cbioportal/web/SessionServiceController.java rename to src/main/java/org/cbioportal/legacy/web/SessionServiceController.java index d2ad7499c1f..d23f3528d80 100644 --- a/src/main/java/org/cbioportal/web/SessionServiceController.java +++ b/src/main/java/org/cbioportal/legacy/web/SessionServiceController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.annotation.JsonInclude.Include; import com.fasterxml.jackson.core.JsonProcessingException; @@ -12,24 +12,24 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import jakarta.servlet.http.HttpServletResponse; import jakarta.validation.constraints.Size; -import org.cbioportal.service.util.CustomAttributeWithData; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.service.util.SessionServiceRequestHandler; -import org.cbioportal.utils.removeme.Session; -import org.cbioportal.web.parameter.CustomGeneList; -import org.cbioportal.web.parameter.CustomGeneListData; -import org.cbioportal.web.parameter.PageSettings; -import org.cbioportal.web.parameter.PageSettingsData; -import org.cbioportal.web.parameter.PageSettingsIdentifier; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.ResultsPageSettings; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.SessionPage; -import org.cbioportal.web.parameter.StudyPageSettings; -import org.cbioportal.web.parameter.VirtualStudy; -import org.cbioportal.web.parameter.VirtualStudyData; -import org.cbioportal.web.parameter.VirtualStudySamples; -import org.cbioportal.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.service.util.CustomAttributeWithData; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.service.util.SessionServiceRequestHandler; +import org.cbioportal.legacy.utils.removeme.Session; +import org.cbioportal.legacy.web.parameter.CustomGeneList; +import org.cbioportal.legacy.web.parameter.CustomGeneListData; +import org.cbioportal.legacy.web.parameter.PageSettings; +import org.cbioportal.legacy.web.parameter.PageSettingsData; +import org.cbioportal.legacy.web.parameter.PageSettingsIdentifier; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.ResultsPageSettings; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.SessionPage; +import org.cbioportal.legacy.web.parameter.StudyPageSettings; +import org.cbioportal.legacy.web.parameter.VirtualStudy; +import org.cbioportal.legacy.web.parameter.VirtualStudyData; +import org.cbioportal.legacy.web.parameter.VirtualStudySamples; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; import org.json.simple.JSONObject; import org.json.simple.parser.JSONParser; import org.json.simple.parser.ParseException; @@ -61,7 +61,7 @@ import java.util.regex.Pattern; import java.util.stream.Collectors; -import static org.cbioportal.web.PublicVirtualStudiesController.ALL_USERS; +import static org.cbioportal.legacy.web.PublicVirtualStudiesController.ALL_USERS; @Controller @RequestMapping("/api/session") diff --git a/src/main/java/org/cbioportal/web/SignificantCopyNumberRegionController.java b/src/main/java/org/cbioportal/legacy/web/SignificantCopyNumberRegionController.java similarity index 84% rename from src/main/java/org/cbioportal/web/SignificantCopyNumberRegionController.java rename to src/main/java/org/cbioportal/legacy/web/SignificantCopyNumberRegionController.java index 48c4919003a..86b0efa4594 100644 --- a/src/main/java/org/cbioportal/web/SignificantCopyNumberRegionController.java +++ b/src/main/java/org/cbioportal/legacy/web/SignificantCopyNumberRegionController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -9,15 +9,15 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.Gistic; -import org.cbioportal.service.SignificantCopyNumberRegionService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.SignificantCopyNumberRegionSortBy; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.service.SignificantCopyNumberRegionService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.SignificantCopyNumberRegionSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -43,7 +43,7 @@ public class SignificantCopyNumberRegionController { @Autowired private SignificantCopyNumberRegionService significantCopyNumberRegionService; - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/significant-copy-number-regions", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get significant copy number alteration regions in a study") diff --git a/src/main/java/org/cbioportal/web/SignificantlyMutatedGenesController.java b/src/main/java/org/cbioportal/legacy/web/SignificantlyMutatedGenesController.java similarity index 84% rename from src/main/java/org/cbioportal/web/SignificantlyMutatedGenesController.java rename to src/main/java/org/cbioportal/legacy/web/SignificantlyMutatedGenesController.java index 3a661feeae2..056408daf43 100644 --- a/src/main/java/org/cbioportal/web/SignificantlyMutatedGenesController.java +++ b/src/main/java/org/cbioportal/legacy/web/SignificantlyMutatedGenesController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -9,15 +9,15 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.MutSig; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.SignificantlyMutatedGeneSortBy; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.service.SignificantlyMutatedGeneService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.SignificantlyMutatedGeneSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -43,7 +43,7 @@ public class SignificantlyMutatedGenesController { @Autowired private SignificantlyMutatedGeneService significantlyMutatedGeneService; - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/significantly-mutated-genes", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get significantly mutated genes in a study") diff --git a/src/main/java/org/cbioportal/web/StaticDataTimestampController.java b/src/main/java/org/cbioportal/legacy/web/StaticDataTimestampController.java similarity index 90% rename from src/main/java/org/cbioportal/web/StaticDataTimestampController.java rename to src/main/java/org/cbioportal/legacy/web/StaticDataTimestampController.java index 39f3d5da978..b440f36dc18 100644 --- a/src/main/java/org/cbioportal/web/StaticDataTimestampController.java +++ b/src/main/java/org/cbioportal/legacy/web/StaticDataTimestampController.java @@ -1,12 +1,12 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.media.Content; import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; -import org.cbioportal.service.StaticDataTimestampService; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.service.StaticDataTimestampService; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/StructuralVariantController.java b/src/main/java/org/cbioportal/legacy/web/StructuralVariantController.java similarity index 91% rename from src/main/java/org/cbioportal/web/StructuralVariantController.java rename to src/main/java/org/cbioportal/legacy/web/StructuralVariantController.java index 69e03bf3303..3701f6e3979 100644 --- a/src/main/java/org/cbioportal/web/StructuralVariantController.java +++ b/src/main/java/org/cbioportal/legacy/web/StructuralVariantController.java @@ -21,7 +21,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -31,11 +31,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.service.StructuralVariantService; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.StructuralVariantFilter; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.service.StructuralVariantService; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.StructuralVariantFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -61,7 +61,7 @@ public class StructuralVariantController { @Autowired private StructuralVariantService structuralVariantService; - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/structural-variant/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch structural variants for entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers") diff --git a/src/main/java/org/cbioportal/web/StudyController.java b/src/main/java/org/cbioportal/legacy/web/StudyController.java similarity index 90% rename from src/main/java/org/cbioportal/web/StudyController.java rename to src/main/java/org/cbioportal/legacy/web/StudyController.java index 253b591719d..b795153518b 100644 --- a/src/main/java/org/cbioportal/web/StudyController.java +++ b/src/main/java/org/cbioportal/legacy/web/StudyController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.core.JsonParseException; import com.fasterxml.jackson.databind.JsonMappingException; @@ -14,19 +14,19 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.utils.security.AccessLevel; -import org.cbioportal.utils.security.PortalSecurityConfig; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.StudySortBy; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.utils.security.AccessLevel; +import org.cbioportal.legacy.utils.security.PortalSecurityConfig; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.StudySortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpHeaders; @@ -136,7 +136,7 @@ public ResponseEntity> getAllStudies( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get a study") @@ -149,7 +149,7 @@ public ResponseEntity getStudy( return new ResponseEntity<>(studyService.getStudy(studyId), HttpStatus.OK); } - @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch studies by IDs") @@ -194,8 +194,8 @@ public ResponseEntity getTags( return new ResponseEntity<>(map, HttpStatus.OK); } - @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") - @PreFilter("hasPermission(#studyIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") + @PreFilter("hasPermission(#studyIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/tags/fetch", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get the study tags by IDs") diff --git a/src/main/java/org/cbioportal/web/StudyViewController.java b/src/main/java/org/cbioportal/legacy/web/StudyViewController.java similarity index 93% rename from src/main/java/org/cbioportal/web/StudyViewController.java rename to src/main/java/org/cbioportal/legacy/web/StudyViewController.java index 90e53af20b7..2db202c5db9 100644 --- a/src/main/java/org/cbioportal/web/StudyViewController.java +++ b/src/main/java/org/cbioportal/legacy/web/StudyViewController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -16,61 +16,61 @@ import org.apache.commons.math3.stat.correlation.PearsonsCorrelation; import org.apache.commons.math3.stat.correlation.SpearmansCorrelation; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataBin; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.ClinicalViolinPlotData; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.DensityPlotBin; -import org.cbioportal.model.DensityPlotData; -import org.cbioportal.model.GenericAssayDataBin; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataBin; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Patient; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleClinicalDataCollection; -import org.cbioportal.model.SampleList; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.StudyViewService; -import org.cbioportal.service.ViolinPlotService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.service.util.ClinicalAttributeUtil; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; -import org.cbioportal.web.parameter.ClinicalDataBinFilter; -import org.cbioportal.web.parameter.ClinicalDataCountFilter; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.DataBinMethod; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.GenericAssayDataBinCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinCountFilter; -import org.cbioportal.web.parameter.GenomicDataCountFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.MutationOption; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.ClinicalDataBinUtil; -import org.cbioportal.web.util.ClinicalDataFetcher; -import org.cbioportal.web.util.StudyViewFilterApplier; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataBin; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.ClinicalViolinPlotData; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DensityPlotBin; +import org.cbioportal.legacy.model.DensityPlotData; +import org.cbioportal.legacy.model.GenericAssayDataBin; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataBin; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleClinicalDataCollection; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyViewService; +import org.cbioportal.legacy.service.ViolinPlotService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.DataBinMethod; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.MutationOption; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.ClinicalDataBinUtil; +import org.cbioportal.legacy.web.util.ClinicalDataFetcher; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.context.ApplicationContext; @@ -144,7 +144,7 @@ private StudyViewController getInstance() { } return instance; } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical data counts by study view filter") @@ -198,7 +198,7 @@ public List cachedClinicalDataCounts(ClinicalDataCountFil return result; } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-data-bin-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical data bin counts by study view filter") @@ -240,7 +240,7 @@ public List cachableFetchClinicalDataBinCounts(DataBinMethod da ); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/custom-data-bin-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch custom data bin counts by study view filter") @@ -273,7 +273,7 @@ public ResponseEntity> fetchCustomDataBinCounts( return new ResponseEntity<>(clinicalDataBins, HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection',T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection',T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/mutated-genes/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch mutated genes by study view filter") @@ -312,7 +312,7 @@ public List cachedFetchMutatedGenes(StudyViewFilter inter return alterationCountByGenes; } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/structuralvariant-genes/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch structural variant genes by study view filter") @@ -353,7 +353,7 @@ public List cacheableFetchStructuralVariantGenes(StudyVie return alterationCountByGenes; } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/structuralvariant-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch structural variant genes by study view filter") @@ -392,7 +392,7 @@ public List cacheableFetchStructuralVariantC return new ArrayList<>(); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/cna-genes/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch CNA genes by study view filter") @@ -431,7 +431,7 @@ public List cacheableFetchCNAGenes(StudyViewFilter interc return copyNumberCountByGenes; } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/filtered-samples/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch sample IDs by study view filter") @@ -460,7 +460,7 @@ public ResponseEntity> fetchFilteredSamples( return new ResponseEntity<>(result, HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profile-sample-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch sample counts by study view filter") @@ -514,7 +514,7 @@ private static double parseValueLinear(ClinicalData c) { return Double.parseDouble(c.getAttrValue()); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-data-density-plot/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical data density plot bins by study view filter") @@ -735,7 +735,7 @@ public ResponseEntity fetchClinicalDataDensityPlot( return new ResponseEntity<>(result, HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-data-violin-plots/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch violin plot curves per categorical clinical data value, filtered by study view filter") @@ -871,7 +871,7 @@ public ResponseEntity fetchClinicalDataViolinPlots( return new ResponseEntity<>(result, HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/sample-lists-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch case list sample counts by study view filter") @@ -929,7 +929,7 @@ public List fetchCaseListCounts( } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/genomic-data-bin-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch genomic data bin counts by study view filter") @ApiResponse(responseCode = "200", description = "OK", @@ -946,7 +946,7 @@ public ResponseEntity> fetchGenomicDataBinCounts( return new ResponseEntity<>(studyViewFilterApplier.getDataBins(dataBinMethod, interceptedGenomicDataBinCountFilter), HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/genomic-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch genomic data counts by GenomicDataCountFilter") @@ -988,7 +988,7 @@ public ResponseEntity> fetchGenomicDataCounts( return new ResponseEntity<>(result, HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/generic-assay-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch generic assay data counts by study view filter") @ApiResponse(responseCode = "200", description = "OK", @@ -1028,7 +1028,7 @@ public ResponseEntity> fetchGenericAssayDataCoun return new ResponseEntity<>(result, HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/generic-assay-data-bin-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch generic assay data bin counts by study view filter") @ApiResponse(responseCode = "200", description = "OK", @@ -1045,7 +1045,7 @@ public ResponseEntity> fetchGenericAssayDataBinCounts( return new ResponseEntity<>(studyViewFilterApplier.getDataBins(dataBinMethod, interceptedGenericAssayDataBinCountFilter), HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-data-table/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical data for the Clinical Tab of Study View") @@ -1126,7 +1126,7 @@ public ImmutablePair cachedClinicalDataTa ); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-event-type-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get Counts of Clinical Event Types by Study View Filter") @@ -1167,7 +1167,7 @@ public List cachedClinicalEventTypeCounts(StudyViewFilte return clinicalEventService.getClinicalEventTypeCounts(studyIds, sampleIds); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/mutation-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch mutation data counts by GenomicDataCountFilter") diff --git a/src/main/java/org/cbioportal/web/SurvivalController.java b/src/main/java/org/cbioportal/legacy/web/SurvivalController.java similarity index 90% rename from src/main/java/org/cbioportal/web/SurvivalController.java rename to src/main/java/org/cbioportal/legacy/web/SurvivalController.java index 06e5e68b74d..8c4ab8c07d3 100644 --- a/src/main/java/org/cbioportal/web/SurvivalController.java +++ b/src/main/java/org/cbioportal/legacy/web/SurvivalController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,11 +8,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.PatientIdentifier; -import org.cbioportal.web.parameter.SurvivalRequest; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.PatientIdentifier; +import org.cbioportal.legacy.web.parameter.SurvivalRequest; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.http.HttpStatus; @@ -43,7 +43,7 @@ public SurvivalController(ClinicalEventService clinicalEventService) { this.clinicalEventService = clinicalEventService; } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/survival-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, diff --git a/src/main/java/org/cbioportal/web/TestController.java b/src/main/java/org/cbioportal/legacy/web/TestController.java similarity index 89% rename from src/main/java/org/cbioportal/web/TestController.java rename to src/main/java/org/cbioportal/legacy/web/TestController.java index 3c227e7a97b..19c08642d6e 100644 --- a/src/main/java/org/cbioportal/web/TestController.java +++ b/src/main/java/org/cbioportal/legacy/web/TestController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import org.springframework.web.bind.annotation.GetMapping; import org.springframework.web.bind.annotation.RestController; diff --git a/src/main/java/org/cbioportal/web/TreatmentController.java b/src/main/java/org/cbioportal/legacy/web/TreatmentController.java similarity index 91% rename from src/main/java/org/cbioportal/web/TreatmentController.java rename to src/main/java/org/cbioportal/legacy/web/TreatmentController.java index 370b7e9e99a..f4eba59e3e2 100644 --- a/src/main/java/org/cbioportal/web/TreatmentController.java +++ b/src/main/java/org/cbioportal/legacy/web/TreatmentController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -9,16 +9,16 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; import jakarta.validation.constraints.Size; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.model.PatientTreatmentRow; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.service.TreatmentService; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.StudyViewFilterApplier; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.service.TreatmentService; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.context.ApplicationContext; @@ -68,7 +68,7 @@ private TreatmentController getInstance() { } return instance; } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/treatments/patient", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all patient level treatments") @ApiResponse(responseCode = "200", description = "OK", @@ -114,7 +114,7 @@ public List cachableGetAllPatientTreatments( } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/treatments/sample", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all sample level treatments") @ApiResponse(responseCode = "200", description = "OK", @@ -160,7 +160,7 @@ public List cacheableGetAllSampleTreatments( return treatmentService.getAllSampleTreatmentRows(sampleIds, studyIds, tier); } - @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/treatments/display-patient", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Should patient level treatments be displayed") @ApiResponse(responseCode = "200", description = "OK", @@ -186,7 +186,7 @@ public Boolean cacheableGetContainsTreatmentData(Set studyIds, ClinicalE return treatmentService.containsTreatmentData(new ArrayList<>(studyIds), tier); } - @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/treatments/display-sample", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Should sample level treatments be displayed") @ApiResponse(responseCode = "200", description = "OK", diff --git a/src/main/java/org/cbioportal/web/VariantCountController.java b/src/main/java/org/cbioportal/legacy/web/VariantCountController.java similarity index 87% rename from src/main/java/org/cbioportal/web/VariantCountController.java rename to src/main/java/org/cbioportal/legacy/web/VariantCountController.java index cff905808e4..ac6e7607cf8 100644 --- a/src/main/java/org/cbioportal/web/VariantCountController.java +++ b/src/main/java/org/cbioportal/legacy/web/VariantCountController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,11 +8,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Size; -import org.cbioportal.model.VariantCount; -import org.cbioportal.service.VariantCountService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.VariantCountIdentifier; +import org.cbioportal.legacy.model.VariantCount; +import org.cbioportal.legacy.service.VariantCountService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.VariantCountIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -40,7 +40,7 @@ public class VariantCountController { @Autowired private VariantCountService variantCountService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/variant-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java b/src/main/java/org/cbioportal/legacy/web/columnar/BasicDataBinner.java similarity index 91% rename from src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java rename to src/main/java/org/cbioportal/legacy/web/columnar/BasicDataBinner.java index 1efaa2b01b9..5f9755830b6 100644 --- a/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java +++ b/src/main/java/org/cbioportal/legacy/web/columnar/BasicDataBinner.java @@ -1,15 +1,33 @@ -package org.cbioportal.web.columnar; +package org.cbioportal.legacy.web.columnar; -import org.cbioportal.model.*; -import org.cbioportal.service.CustomDataService; -import org.cbioportal.service.StudyViewColumnarService; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.columnar.util.CustomDataFilterUtil; -import org.cbioportal.web.columnar.util.NewClinicalDataBinUtil; -import org.cbioportal.web.parameter.*; -import org.cbioportal.web.util.DataBinner; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataBin; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.DataBin; +import org.cbioportal.legacy.model.GenericAssayDataBin; +import org.cbioportal.legacy.model.GenomicDataBin; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.DataBinCountFilter; +import org.cbioportal.legacy.web.parameter.DataBinFilter; +import org.cbioportal.legacy.web.parameter.DataBinMethod; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.service.CustomDataService; +import org.cbioportal.legacy.service.StudyViewColumnarService; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.columnar.util.CustomDataFilterUtil; +import org.cbioportal.legacy.web.columnar.util.NewClinicalDataBinUtil; +import org.cbioportal.legacy.web.util.DataBinner; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java b/src/main/java/org/cbioportal/legacy/web/columnar/ClinicalDataBinner.java similarity index 86% rename from src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java rename to src/main/java/org/cbioportal/legacy/web/columnar/ClinicalDataBinner.java index b14d6726dbc..2e8b9375b93 100644 --- a/src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java +++ b/src/main/java/org/cbioportal/legacy/web/columnar/ClinicalDataBinner.java @@ -1,19 +1,19 @@ -package org.cbioportal.web.columnar; - -import org.cbioportal.model.Binnable; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataBin; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.service.StudyViewColumnarService; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.columnar.util.NewClinicalDataBinUtil; -import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; -import org.cbioportal.web.parameter.ClinicalDataBinFilter; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.DataBinMethod; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.DataBinner; +package org.cbioportal.legacy.web.columnar; + +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataBin; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.service.StudyViewColumnarService; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.columnar.util.NewClinicalDataBinUtil; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.DataBinMethod; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.DataBinner; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java b/src/main/java/org/cbioportal/legacy/web/columnar/StudyViewColumnStoreController.java similarity index 90% rename from src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java rename to src/main/java/org/cbioportal/legacy/web/columnar/StudyViewColumnStoreController.java index 39fc7001b8b..3686d3ad7f6 100644 --- a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java +++ b/src/main/java/org/cbioportal/legacy/web/columnar/StudyViewColumnStoreController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.columnar; +package org.cbioportal.legacy.web.columnar; import io.swagger.v3.oas.annotations.Hidden; import io.swagger.v3.oas.annotations.Operation; @@ -8,51 +8,51 @@ import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import jakarta.validation.Valid; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataBin; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.ClinicalViolinPlotData; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.DensityPlotData; -import org.cbioportal.model.GenericAssayDataBin; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataBin; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.PatientTreatmentReport; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleTreatmentReport; -import org.cbioportal.service.ClinicalDataDensityPlotService; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.service.CustomDataService; -import org.cbioportal.service.StudyViewColumnarService; -import org.cbioportal.service.ViolinPlotService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.columnar.util.CustomDataFilterUtil; -import org.cbioportal.web.columnar.util.NewStudyViewFilterUtil; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; -import org.cbioportal.web.parameter.ClinicalDataCountFilter; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.DataBinMethod; -import org.cbioportal.web.parameter.GenericAssayDataBinCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinCountFilter; -import org.cbioportal.web.parameter.GenomicDataCountFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.MutationOption; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.DensityPlotParameters; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataBin; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.ClinicalViolinPlotData; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DensityPlotData; +import org.cbioportal.legacy.model.GenericAssayDataBin; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataBin; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.PatientTreatmentReport; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleTreatmentReport; +import org.cbioportal.legacy.service.ClinicalDataDensityPlotService; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.service.CustomDataService; +import org.cbioportal.legacy.service.StudyViewColumnarService; +import org.cbioportal.legacy.service.ViolinPlotService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.columnar.util.CustomDataFilterUtil; +import org.cbioportal.legacy.web.columnar.util.NewStudyViewFilterUtil; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.DataBinMethod; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.MutationOption; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.DensityPlotParameters; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -112,7 +112,7 @@ public StudyViewColumnStoreController(StudyViewColumnarService studyViewColumnar @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/filtered-samples/fetch", consumes = MediaType.APPLICATION_JSON_VALUE, method=RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) public ResponseEntity> fetchFilteredSamples( @@ -127,7 +127,7 @@ public ResponseEntity> fetchFilteredSamples( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/mutated-genes/fetch", consumes = MediaType.APPLICATION_JSON_VALUE, method=RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) public ResponseEntity> fetchMutatedGenes( @@ -143,7 +143,7 @@ public ResponseEntity> fetchMutatedGenes( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/molecular-profile-sample-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch sample counts by study view filter") @@ -195,7 +195,7 @@ public ResponseEntity> fetchStructuralVariantGenes( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/clinical-data-counts/fetch", method=RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -218,7 +218,7 @@ public ResponseEntity> fetchClinicalDataCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/sample-lists-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch case list sample counts by study view filter") @@ -235,7 +235,7 @@ public List fetchCaseListCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/clinical-data-bin-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) public ResponseEntity> fetchClinicalDataBinCounts( @@ -253,7 +253,7 @@ public ResponseEntity> fetchClinicalDataBinCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/clinical-data-density-plot/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, @@ -321,7 +321,7 @@ public ResponseEntity fetchClinicalDataDensityPlot( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/clinical-data-violin-plots/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -390,7 +390,7 @@ public ResponseEntity fetchClinicalDataViolinPlots( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/genomic-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -423,7 +423,7 @@ public ResponseEntity> fetchGenomicDataCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/generic-assay-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -452,7 +452,7 @@ public ResponseEntity> fetchGenericAssayDataCoun } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/mutation-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -488,7 +488,7 @@ public ResponseEntity> fetchMutationDataCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/clinical-event-type-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, @@ -514,7 +514,7 @@ public ResponseEntity> getClinicalEventTypeCounts( return new ResponseEntity<>(studyViewColumnarService.getClinicalEventTypeCounts(interceptedStudyViewFilter), HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/treatments/patient-counts/fetch", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @@ -544,7 +544,7 @@ public ResponseEntity fetchPatientTreatmentCounts( HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/treatments/sample-counts/fetch", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @@ -574,7 +574,7 @@ public ResponseEntity fetchSampleTreatmentCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/custom-data-counts/fetch", method=RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -612,7 +612,7 @@ public ResponseEntity> fetchCustomDataCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/custom-data-bin-counts/fetch", consumes = MediaType.APPLICATION_JSON_VALUE, method= RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch custom data bin counts by study view filter") @@ -638,7 +638,7 @@ public ResponseEntity> fetchCustomDataBinCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/genomic-data-bin-counts/fetch", consumes = MediaType.APPLICATION_JSON_VALUE, method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @ApiResponse(responseCode = "200", description = "OK", @@ -658,7 +658,7 @@ public ResponseEntity> fetchGenomicDataBinCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/generic-assay-data-bin-counts/fetch", consumes = MediaType.APPLICATION_JSON_VALUE, method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @ApiResponse(responseCode = "200", description = "OK", diff --git a/src/main/java/org/cbioportal/web/columnar/util/ClinicalDataXyPlotUtil.java b/src/main/java/org/cbioportal/legacy/web/columnar/util/ClinicalDataXyPlotUtil.java similarity index 95% rename from src/main/java/org/cbioportal/web/columnar/util/ClinicalDataXyPlotUtil.java rename to src/main/java/org/cbioportal/legacy/web/columnar/util/ClinicalDataXyPlotUtil.java index 58b2d1e9c4e..5c75cf806a6 100644 --- a/src/main/java/org/cbioportal/web/columnar/util/ClinicalDataXyPlotUtil.java +++ b/src/main/java/org/cbioportal/legacy/web/columnar/util/ClinicalDataXyPlotUtil.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.columnar.util; +package org.cbioportal.legacy.web.columnar.util; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.Sample; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.Sample; import java.util.ArrayList; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/columnar/util/CustomDataFilterUtil.java b/src/main/java/org/cbioportal/legacy/web/columnar/util/CustomDataFilterUtil.java similarity index 95% rename from src/main/java/org/cbioportal/web/columnar/util/CustomDataFilterUtil.java rename to src/main/java/org/cbioportal/legacy/web/columnar/util/CustomDataFilterUtil.java index 9987bf510c1..786c695e5f3 100644 --- a/src/main/java/org/cbioportal/web/columnar/util/CustomDataFilterUtil.java +++ b/src/main/java/org/cbioportal/legacy/web/columnar/util/CustomDataFilterUtil.java @@ -1,17 +1,21 @@ -package org.cbioportal.web.columnar.util; +package org.cbioportal.legacy.web.columnar.util; import com.google.common.collect.Range; import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.Patient; -import org.cbioportal.service.CustomDataService; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.web.parameter.*; -import org.cbioportal.web.util.CustomDatatype; -import org.cbioportal.web.util.DataBinHelper; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.service.CustomDataService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.CustomSampleIdentifier; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.CustomDatatype; +import org.cbioportal.legacy.web.util.DataBinHelper; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/columnar/util/NewClinicalDataBinUtil.java b/src/main/java/org/cbioportal/legacy/web/columnar/util/NewClinicalDataBinUtil.java similarity index 90% rename from src/main/java/org/cbioportal/web/columnar/util/NewClinicalDataBinUtil.java rename to src/main/java/org/cbioportal/legacy/web/columnar/util/NewClinicalDataBinUtil.java index df1b9524c6e..8ea39ca19da 100644 --- a/src/main/java/org/cbioportal/web/columnar/util/NewClinicalDataBinUtil.java +++ b/src/main/java/org/cbioportal/legacy/web/columnar/util/NewClinicalDataBinUtil.java @@ -1,16 +1,16 @@ -package org.cbioportal.web.columnar.util; - -import org.cbioportal.model.Binnable; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataBin; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.DataBin; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; -import org.cbioportal.web.parameter.ClinicalDataBinFilter; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.DataBinner; +package org.cbioportal.legacy.web.columnar.util; + +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataBin; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.DataBin; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.DataBinner; import java.util.ArrayList; import java.util.HashMap; diff --git a/src/main/java/org/cbioportal/web/columnar/util/NewStudyViewFilterUtil.java b/src/main/java/org/cbioportal/legacy/web/columnar/util/NewStudyViewFilterUtil.java similarity index 73% rename from src/main/java/org/cbioportal/web/columnar/util/NewStudyViewFilterUtil.java rename to src/main/java/org/cbioportal/legacy/web/columnar/util/NewStudyViewFilterUtil.java index 5363802afe2..d42bb7e8786 100644 --- a/src/main/java/org/cbioportal/web/columnar/util/NewStudyViewFilterUtil.java +++ b/src/main/java/org/cbioportal/legacy/web/columnar/util/NewStudyViewFilterUtil.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.columnar.util; +package org.cbioportal.legacy.web.columnar.util; -import org.cbioportal.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/config/CustomObjectMapper.java b/src/main/java/org/cbioportal/legacy/web/config/CustomObjectMapper.java similarity index 56% rename from src/main/java/org/cbioportal/web/config/CustomObjectMapper.java rename to src/main/java/org/cbioportal/legacy/web/config/CustomObjectMapper.java index d5853d58218..8b72a455616 100644 --- a/src/main/java/org/cbioportal/web/config/CustomObjectMapper.java +++ b/src/main/java/org/cbioportal/legacy/web/config/CustomObjectMapper.java @@ -30,77 +30,77 @@ * along with this program. If not, see . */ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.SerializationFeature; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetCorrelation; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationSpectrum; -import org.cbioportal.model.Patient; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.service.util.CustomAttributeWithData; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.utils.removeme.Session; -import org.cbioportal.web.mixin.CancerStudyMixin; -import org.cbioportal.web.mixin.ClinicalAttributeCountMixin; -import org.cbioportal.web.mixin.ClinicalAttributeMixin; -import org.cbioportal.web.mixin.ClinicalDataCountMixin; -import org.cbioportal.web.mixin.ClinicalDataMixin; -import org.cbioportal.web.mixin.ClinicalEventDataMixin; -import org.cbioportal.web.mixin.ClinicalEventMixin; -import org.cbioportal.web.mixin.CopyNumberSegMixin; -import org.cbioportal.web.mixin.DataAccessTokenMixin; -import org.cbioportal.web.mixin.DiscreteCopyNumberDataMixin; -import org.cbioportal.web.mixin.GeneMixin; -import org.cbioportal.web.mixin.GenePanelMixin; -import org.cbioportal.web.mixin.GenePanelToGeneMixin; -import org.cbioportal.web.mixin.GenesetCorrelationMixin; -import org.cbioportal.web.mixin.GenesetMixin; -import org.cbioportal.web.mixin.GenesetMolecularDataMixin; -import org.cbioportal.web.mixin.GisticMixin; -import org.cbioportal.web.mixin.GisticToGeneMixin; -import org.cbioportal.web.mixin.MolecularProfileMixin; -import org.cbioportal.web.mixin.MutSigMixin; -import org.cbioportal.web.mixin.MutationMixin; -import org.cbioportal.web.mixin.MutationSpectrumMixin; -import org.cbioportal.web.mixin.PatientMixin; -import org.cbioportal.web.mixin.ResourceDefinitionMixin; -import org.cbioportal.web.mixin.SampleListMixin; -import org.cbioportal.web.mixin.SampleMixin; -import org.cbioportal.web.mixin.SessionDataMixin; -import org.cbioportal.web.mixin.SessionMixin; -import org.cbioportal.web.mixin.StructuralVariantMixin; -import org.cbioportal.web.mixin.TypeOfCancerMixin; -import org.cbioportal.web.parameter.PageSettings; -import org.cbioportal.web.parameter.PageSettingsData; -import org.cbioportal.web.parameter.StudyPageSettings; -import org.cbioportal.web.parameter.VirtualStudy; -import org.cbioportal.web.parameter.VirtualStudyData; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetCorrelation; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationSpectrum; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.service.util.CustomAttributeWithData; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.utils.removeme.Session; +import org.cbioportal.legacy.web.mixin.CancerStudyMixin; +import org.cbioportal.legacy.web.mixin.ClinicalAttributeCountMixin; +import org.cbioportal.legacy.web.mixin.ClinicalAttributeMixin; +import org.cbioportal.legacy.web.mixin.ClinicalDataCountMixin; +import org.cbioportal.legacy.web.mixin.ClinicalDataMixin; +import org.cbioportal.legacy.web.mixin.ClinicalEventDataMixin; +import org.cbioportal.legacy.web.mixin.ClinicalEventMixin; +import org.cbioportal.legacy.web.mixin.CopyNumberSegMixin; +import org.cbioportal.legacy.web.mixin.DataAccessTokenMixin; +import org.cbioportal.legacy.web.mixin.DiscreteCopyNumberDataMixin; +import org.cbioportal.legacy.web.mixin.GeneMixin; +import org.cbioportal.legacy.web.mixin.GenePanelMixin; +import org.cbioportal.legacy.web.mixin.GenePanelToGeneMixin; +import org.cbioportal.legacy.web.mixin.GenesetCorrelationMixin; +import org.cbioportal.legacy.web.mixin.GenesetMixin; +import org.cbioportal.legacy.web.mixin.GenesetMolecularDataMixin; +import org.cbioportal.legacy.web.mixin.GisticMixin; +import org.cbioportal.legacy.web.mixin.GisticToGeneMixin; +import org.cbioportal.legacy.web.mixin.MolecularProfileMixin; +import org.cbioportal.legacy.web.mixin.MutSigMixin; +import org.cbioportal.legacy.web.mixin.MutationMixin; +import org.cbioportal.legacy.web.mixin.MutationSpectrumMixin; +import org.cbioportal.legacy.web.mixin.PatientMixin; +import org.cbioportal.legacy.web.mixin.ResourceDefinitionMixin; +import org.cbioportal.legacy.web.mixin.SampleListMixin; +import org.cbioportal.legacy.web.mixin.SampleMixin; +import org.cbioportal.legacy.web.mixin.SessionDataMixin; +import org.cbioportal.legacy.web.mixin.SessionMixin; +import org.cbioportal.legacy.web.mixin.StructuralVariantMixin; +import org.cbioportal.legacy.web.mixin.TypeOfCancerMixin; +import org.cbioportal.legacy.web.parameter.PageSettings; +import org.cbioportal.legacy.web.parameter.PageSettingsData; +import org.cbioportal.legacy.web.parameter.StudyPageSettings; +import org.cbioportal.legacy.web.parameter.VirtualStudy; +import org.cbioportal.legacy.web.parameter.VirtualStudyData; import java.util.HashMap; import java.util.Map; diff --git a/src/main/java/org/cbioportal/web/config/DataAccessTokenConfig.java b/src/main/java/org/cbioportal/legacy/web/config/DataAccessTokenConfig.java similarity index 100% rename from src/main/java/org/cbioportal/web/config/DataAccessTokenConfig.java rename to src/main/java/org/cbioportal/legacy/web/config/DataAccessTokenConfig.java diff --git a/src/main/java/org/cbioportal/web/config/InternalApiTags.java b/src/main/java/org/cbioportal/legacy/web/config/InternalApiTags.java similarity index 94% rename from src/main/java/org/cbioportal/web/config/InternalApiTags.java rename to src/main/java/org/cbioportal/legacy/web/config/InternalApiTags.java index 810cbb21939..be1ee85a2db 100644 --- a/src/main/java/org/cbioportal/web/config/InternalApiTags.java +++ b/src/main/java/org/cbioportal/legacy/web/config/InternalApiTags.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; public class InternalApiTags { public static final String CLINICAL_EVENTS = "Clinical Events"; diff --git a/src/main/java/org/cbioportal/web/config/JacksonConfig.java b/src/main/java/org/cbioportal/legacy/web/config/JacksonConfig.java similarity index 90% rename from src/main/java/org/cbioportal/web/config/JacksonConfig.java rename to src/main/java/org/cbioportal/legacy/web/config/JacksonConfig.java index 6e0c7a00247..06ead7110e7 100644 --- a/src/main/java/org/cbioportal/web/config/JacksonConfig.java +++ b/src/main/java/org/cbioportal/legacy/web/config/JacksonConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import com.fasterxml.jackson.databind.ObjectMapper; import org.springframework.context.annotation.Bean; diff --git a/src/main/java/org/cbioportal/web/config/MethodValidationConfig.java b/src/main/java/org/cbioportal/legacy/web/config/MethodValidationConfig.java similarity index 94% rename from src/main/java/org/cbioportal/web/config/MethodValidationConfig.java rename to src/main/java/org/cbioportal/legacy/web/config/MethodValidationConfig.java index 52ec3c80cfb..14e447aa3f3 100644 --- a/src/main/java/org/cbioportal/web/config/MethodValidationConfig.java +++ b/src/main/java/org/cbioportal/legacy/web/config/MethodValidationConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; diff --git a/src/main/java/org/cbioportal/web/config/PublicApiTags.java b/src/main/java/org/cbioportal/legacy/web/config/PublicApiTags.java similarity index 96% rename from src/main/java/org/cbioportal/web/config/PublicApiTags.java rename to src/main/java/org/cbioportal/legacy/web/config/PublicApiTags.java index 55952192cfa..3b8eeda1e89 100644 --- a/src/main/java/org/cbioportal/web/config/PublicApiTags.java +++ b/src/main/java/org/cbioportal/legacy/web/config/PublicApiTags.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; public class PublicApiTags { public static final String CANCER_TYPES = "Cancer Types"; diff --git a/src/main/java/org/cbioportal/web/config/SwaggerConfig.java b/src/main/java/org/cbioportal/legacy/web/config/SwaggerConfig.java similarity index 95% rename from src/main/java/org/cbioportal/web/config/SwaggerConfig.java rename to src/main/java/org/cbioportal/legacy/web/config/SwaggerConfig.java index 1c3b485865a..1468f14575d 100644 --- a/src/main/java/org/cbioportal/web/config/SwaggerConfig.java +++ b/src/main/java/org/cbioportal/legacy/web/config/SwaggerConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import com.fasterxml.jackson.databind.ObjectMapper; import io.swagger.v3.core.converter.ModelConverters; @@ -8,8 +8,8 @@ import io.swagger.v3.oas.models.info.Contact; import io.swagger.v3.oas.models.info.Info; import io.swagger.v3.oas.models.info.License; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.config.annotation.PublicApi; import org.springdoc.core.customizers.OperationCustomizer; import org.springdoc.core.models.GroupedOpenApi; import org.springframework.context.annotation.Bean; diff --git a/src/main/java/org/cbioportal/web/config/WebServletContextListener.java b/src/main/java/org/cbioportal/legacy/web/config/WebServletContextListener.java similarity index 98% rename from src/main/java/org/cbioportal/web/config/WebServletContextListener.java rename to src/main/java/org/cbioportal/legacy/web/config/WebServletContextListener.java index 8311df288df..f770db7f400 100644 --- a/src/main/java/org/cbioportal/web/config/WebServletContextListener.java +++ b/src/main/java/org/cbioportal/legacy/web/config/WebServletContextListener.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import jakarta.servlet.ServletContextEvent; import jakarta.servlet.ServletContextListener; diff --git a/src/main/java/org/cbioportal/web/config/annotation/InternalApi.java b/src/main/java/org/cbioportal/legacy/web/config/annotation/InternalApi.java similarity index 74% rename from src/main/java/org/cbioportal/web/config/annotation/InternalApi.java rename to src/main/java/org/cbioportal/legacy/web/config/annotation/InternalApi.java index f9717fb0610..6e5ff9e37f8 100644 --- a/src/main/java/org/cbioportal/web/config/annotation/InternalApi.java +++ b/src/main/java/org/cbioportal/legacy/web/config/annotation/InternalApi.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config.annotation; +package org.cbioportal.legacy.web.config.annotation; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; diff --git a/src/main/java/org/cbioportal/web/config/annotation/PublicApi.java b/src/main/java/org/cbioportal/legacy/web/config/annotation/PublicApi.java similarity index 74% rename from src/main/java/org/cbioportal/web/config/annotation/PublicApi.java rename to src/main/java/org/cbioportal/legacy/web/config/annotation/PublicApi.java index 76dc021ee72..6fdfbbff2dd 100644 --- a/src/main/java/org/cbioportal/web/config/annotation/PublicApi.java +++ b/src/main/java/org/cbioportal/legacy/web/config/annotation/PublicApi.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config.annotation; +package org.cbioportal.legacy.web.config.annotation; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; diff --git a/src/main/java/org/cbioportal/web/error/ErrorResponse.java b/src/main/java/org/cbioportal/legacy/web/error/ErrorResponse.java similarity index 87% rename from src/main/java/org/cbioportal/web/error/ErrorResponse.java rename to src/main/java/org/cbioportal/legacy/web/error/ErrorResponse.java index cf37cafb850..4e9d7463fcd 100644 --- a/src/main/java/org/cbioportal/web/error/ErrorResponse.java +++ b/src/main/java/org/cbioportal/legacy/web/error/ErrorResponse.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.error; +package org.cbioportal.legacy.web.error; public class ErrorResponse { diff --git a/src/main/java/org/cbioportal/web/error/GlobalExceptionHandler.java b/src/main/java/org/cbioportal/legacy/web/error/GlobalExceptionHandler.java similarity index 87% rename from src/main/java/org/cbioportal/web/error/GlobalExceptionHandler.java rename to src/main/java/org/cbioportal/legacy/web/error/GlobalExceptionHandler.java index 1c24d60c431..b2c00e8579b 100644 --- a/src/main/java/org/cbioportal/web/error/GlobalExceptionHandler.java +++ b/src/main/java/org/cbioportal/legacy/web/error/GlobalExceptionHandler.java @@ -1,10 +1,28 @@ -package org.cbioportal.web.error; +package org.cbioportal.legacy.web.error; import jakarta.validation.ConstraintViolation; import jakarta.validation.ConstraintViolationException; import jakarta.validation.ElementKind; import jakarta.validation.Path; -import org.cbioportal.service.exception.*; +import org.cbioportal.legacy.service.exception.AccessForbiddenException; +import org.cbioportal.legacy.service.exception.CacheNotFoundException; +import org.cbioportal.legacy.service.exception.CacheOperationException; +import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException; +import org.cbioportal.legacy.service.exception.ClinicalAttributeNotFoundException; +import org.cbioportal.legacy.service.exception.DataAccessTokenNoUserIdentityException; +import org.cbioportal.legacy.service.exception.DataAccessTokenProhibitedUserException; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.service.exception.GenePanelNotFoundException; +import org.cbioportal.legacy.service.exception.GeneWithMultipleEntrezIdsException; +import org.cbioportal.legacy.service.exception.GenericAssayNotFoundException; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.ResourceDefinitionNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.exception.TokenNotFoundException; import org.springframework.beans.TypeMismatchException; import org.springframework.http.HttpStatus; import org.springframework.http.ResponseEntity; @@ -24,7 +42,7 @@ // TODO // - consider extending extends ResponseEntityExceptionHandler // - check controllers for not catching exceptions themselves -@ControllerAdvice("org.cbioportal.web") +@ControllerAdvice("org.cbioportal.legacy.web") public class GlobalExceptionHandler { @ExceptionHandler(UnsupportedOperationException.class) diff --git a/src/main/java/org/cbioportal/web/interceptor/UniqueKeyInterceptor.java b/src/main/java/org/cbioportal/legacy/web/interceptor/UniqueKeyInterceptor.java similarity index 88% rename from src/main/java/org/cbioportal/web/interceptor/UniqueKeyInterceptor.java rename to src/main/java/org/cbioportal/legacy/web/interceptor/UniqueKeyInterceptor.java index baba716ecef..a216e24558b 100644 --- a/src/main/java/org/cbioportal/web/interceptor/UniqueKeyInterceptor.java +++ b/src/main/java/org/cbioportal/legacy/web/interceptor/UniqueKeyInterceptor.java @@ -1,18 +1,18 @@ -package org.cbioportal.web.interceptor; +package org.cbioportal.legacy.web.interceptor; -import org.cbioportal.model.Alteration; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.MolecularData; -import org.cbioportal.model.MrnaPercentile; -import org.cbioportal.model.MutationSpectrum; -import org.cbioportal.model.NumericGeneMolecularData; -import org.cbioportal.model.Patient; -import org.cbioportal.model.ResourceData; -import org.cbioportal.model.Sample; -import org.cbioportal.model.StructuralVariant; +import org.cbioportal.legacy.model.Alteration; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.MolecularData; +import org.cbioportal.legacy.model.MrnaPercentile; +import org.cbioportal.legacy.model.MutationSpectrum; +import org.cbioportal.legacy.model.NumericGeneMolecularData; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.ResourceData; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.StructuralVariant; import org.springframework.core.MethodParameter; import org.springframework.http.MediaType; import org.springframework.http.converter.json.MappingJacksonValue; @@ -23,9 +23,9 @@ import java.util.List; -import static org.cbioportal.utils.Encoder.calculateBase64; +import static org.cbioportal.legacy.utils.Encoder.calculateBase64; -@ControllerAdvice("org.cbioportal.web") +@ControllerAdvice("org.cbioportal.legacy.web") public class UniqueKeyInterceptor extends AbstractMappingJacksonResponseBodyAdvice { @Override diff --git a/src/main/java/org/cbioportal/web/mixin/CancerStudyMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/CancerStudyMixin.java similarity index 88% rename from src/main/java/org/cbioportal/web/mixin/CancerStudyMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/CancerStudyMixin.java index f8fc1045e66..631bdb7ab47 100644 --- a/src/main/java/org/cbioportal/web/mixin/CancerStudyMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/CancerStudyMixin.java @@ -1,9 +1,9 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonFormat; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; -import org.cbioportal.model.TypeOfCancer; +import org.cbioportal.legacy.model.TypeOfCancer; import java.util.Date; diff --git a/src/main/java/org/cbioportal/web/mixin/ClinicalAttributeCountMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalAttributeCountMixin.java similarity index 80% rename from src/main/java/org/cbioportal/web/mixin/ClinicalAttributeCountMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ClinicalAttributeCountMixin.java index 4510c009639..de011b02113 100644 --- a/src/main/java/org/cbioportal/web/mixin/ClinicalAttributeCountMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalAttributeCountMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/ClinicalAttributeMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalAttributeMixin.java similarity index 89% rename from src/main/java/org/cbioportal/web/mixin/ClinicalAttributeMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ClinicalAttributeMixin.java index e5b23cbc539..de07b86d37b 100644 --- a/src/main/java/org/cbioportal/web/mixin/ClinicalAttributeMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalAttributeMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/ClinicalDataCountMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalDataCountMixin.java similarity index 77% rename from src/main/java/org/cbioportal/web/mixin/ClinicalDataCountMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ClinicalDataCountMixin.java index 92c5c657ccb..93ae2bdf58f 100644 --- a/src/main/java/org/cbioportal/web/mixin/ClinicalDataCountMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalDataCountMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/src/main/java/org/cbioportal/web/mixin/ClinicalDataMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalDataMixin.java similarity index 88% rename from src/main/java/org/cbioportal/web/mixin/ClinicalDataMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ClinicalDataMixin.java index 7f5e481fc4d..8cf37cb6378 100644 --- a/src/main/java/org/cbioportal/web/mixin/ClinicalDataMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalDataMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/ClinicalEventDataMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalEventDataMixin.java similarity index 78% rename from src/main/java/org/cbioportal/web/mixin/ClinicalEventDataMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ClinicalEventDataMixin.java index c889e865a55..d15b7c840ba 100644 --- a/src/main/java/org/cbioportal/web/mixin/ClinicalEventDataMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalEventDataMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/src/main/java/org/cbioportal/web/mixin/ClinicalEventMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalEventMixin.java similarity index 89% rename from src/main/java/org/cbioportal/web/mixin/ClinicalEventMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ClinicalEventMixin.java index 1b6c4fc4822..111649b73a8 100644 --- a/src/main/java/org/cbioportal/web/mixin/ClinicalEventMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalEventMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/CopyNumberSegMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/CopyNumberSegMixin.java similarity index 92% rename from src/main/java/org/cbioportal/web/mixin/CopyNumberSegMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/CopyNumberSegMixin.java index 896c371400e..9176a060b90 100644 --- a/src/main/java/org/cbioportal/web/mixin/CopyNumberSegMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/CopyNumberSegMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/DataAccessTokenMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/DataAccessTokenMixin.java similarity index 89% rename from src/main/java/org/cbioportal/web/mixin/DataAccessTokenMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/DataAccessTokenMixin.java index 119cae61c5a..72aa3a9dc40 100644 --- a/src/main/java/org/cbioportal/web/mixin/DataAccessTokenMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/DataAccessTokenMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonFormat; diff --git a/src/main/java/org/cbioportal/web/mixin/DiscreteCopyNumberDataMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/DiscreteCopyNumberDataMixin.java similarity index 80% rename from src/main/java/org/cbioportal/web/mixin/DiscreteCopyNumberDataMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/DiscreteCopyNumberDataMixin.java index ef9a17f3871..d10468dbde8 100644 --- a/src/main/java/org/cbioportal/web/mixin/DiscreteCopyNumberDataMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/DiscreteCopyNumberDataMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/legacy/web/mixin/GeneMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GeneMixin.java new file mode 100644 index 00000000000..608583da0a7 --- /dev/null +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GeneMixin.java @@ -0,0 +1,5 @@ +package org.cbioportal.legacy.web.mixin; + +public class GeneMixin { + +} diff --git a/src/main/java/org/cbioportal/web/mixin/GenePanelMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GenePanelMixin.java similarity index 85% rename from src/main/java/org/cbioportal/web/mixin/GenePanelMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/GenePanelMixin.java index 1ccbc6af9bd..fc440b14c66 100644 --- a/src/main/java/org/cbioportal/web/mixin/GenePanelMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GenePanelMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/GenePanelToGeneMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GenePanelToGeneMixin.java similarity index 77% rename from src/main/java/org/cbioportal/web/mixin/GenePanelToGeneMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/GenePanelToGeneMixin.java index aacf2d62ba2..b851c55a543 100644 --- a/src/main/java/org/cbioportal/web/mixin/GenePanelToGeneMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GenePanelToGeneMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/src/main/java/org/cbioportal/web/mixin/GenesetCorrelationMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GenesetCorrelationMixin.java similarity index 87% rename from src/main/java/org/cbioportal/web/mixin/GenesetCorrelationMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/GenesetCorrelationMixin.java index fa42833f5fe..9dbf25d51e4 100644 --- a/src/main/java/org/cbioportal/web/mixin/GenesetCorrelationMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GenesetCorrelationMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/GenesetMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GenesetMixin.java similarity index 76% rename from src/main/java/org/cbioportal/web/mixin/GenesetMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/GenesetMixin.java index a1a2adecc67..f3b63b38f62 100644 --- a/src/main/java/org/cbioportal/web/mixin/GenesetMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GenesetMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/src/main/java/org/cbioportal/web/mixin/GenesetMolecularDataMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GenesetMolecularDataMixin.java similarity index 81% rename from src/main/java/org/cbioportal/web/mixin/GenesetMolecularDataMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/GenesetMolecularDataMixin.java index ae836c19de1..c95d3e396fb 100644 --- a/src/main/java/org/cbioportal/web/mixin/GenesetMolecularDataMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GenesetMolecularDataMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/GisticMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GisticMixin.java similarity index 87% rename from src/main/java/org/cbioportal/web/mixin/GisticMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/GisticMixin.java index 5913c07dbb5..e7e9d986198 100644 --- a/src/main/java/org/cbioportal/web/mixin/GisticMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GisticMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/GisticToGeneMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GisticToGeneMixin.java similarity index 76% rename from src/main/java/org/cbioportal/web/mixin/GisticToGeneMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/GisticToGeneMixin.java index b43b1cebd75..3c7d4a19c7b 100644 --- a/src/main/java/org/cbioportal/web/mixin/GisticToGeneMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GisticToGeneMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/src/main/java/org/cbioportal/web/mixin/MolecularProfileMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/MolecularProfileMixin.java similarity index 83% rename from src/main/java/org/cbioportal/web/mixin/MolecularProfileMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/MolecularProfileMixin.java index 78f58c76163..d16c96987f3 100644 --- a/src/main/java/org/cbioportal/web/mixin/MolecularProfileMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/MolecularProfileMixin.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; -import org.cbioportal.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudy; public class MolecularProfileMixin { diff --git a/src/main/java/org/cbioportal/web/mixin/MutSigMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/MutSigMixin.java similarity index 91% rename from src/main/java/org/cbioportal/web/mixin/MutSigMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/MutSigMixin.java index f837ef99240..89a830e1e45 100644 --- a/src/main/java/org/cbioportal/web/mixin/MutSigMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/MutSigMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/MutationMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/MutationMixin.java similarity index 93% rename from src/main/java/org/cbioportal/web/mixin/MutationMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/MutationMixin.java index 36e59eaba4e..37ce10a26d2 100644 --- a/src/main/java/org/cbioportal/web/mixin/MutationMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/MutationMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; import com.fasterxml.jackson.annotation.JsonRawValue; diff --git a/src/main/java/org/cbioportal/web/mixin/MutationSpectrumMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/MutationSpectrumMixin.java similarity index 90% rename from src/main/java/org/cbioportal/web/mixin/MutationSpectrumMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/MutationSpectrumMixin.java index b4ef6b1dbe6..1dedaf5eadf 100644 --- a/src/main/java/org/cbioportal/web/mixin/MutationSpectrumMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/MutationSpectrumMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/PatientMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/PatientMixin.java similarity index 90% rename from src/main/java/org/cbioportal/web/mixin/PatientMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/PatientMixin.java index 3e555424e4e..ac743b7b0e2 100644 --- a/src/main/java/org/cbioportal/web/mixin/PatientMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/PatientMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/ReferenceGenomeGeneMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ReferenceGenomeGeneMixin.java similarity index 83% rename from src/main/java/org/cbioportal/web/mixin/ReferenceGenomeGeneMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ReferenceGenomeGeneMixin.java index 0a333d11eb0..efa7ed39a2e 100644 --- a/src/main/java/org/cbioportal/web/mixin/ReferenceGenomeGeneMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ReferenceGenomeGeneMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/ResourceDefinitionMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ResourceDefinitionMixin.java similarity index 80% rename from src/main/java/org/cbioportal/web/mixin/ResourceDefinitionMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ResourceDefinitionMixin.java index b1c60d06509..5b4a3f2ffa2 100644 --- a/src/main/java/org/cbioportal/web/mixin/ResourceDefinitionMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ResourceDefinitionMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/SampleListMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/SampleListMixin.java similarity index 82% rename from src/main/java/org/cbioportal/web/mixin/SampleListMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/SampleListMixin.java index d6919ae56aa..f57b40f92c2 100644 --- a/src/main/java/org/cbioportal/web/mixin/SampleListMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/SampleListMixin.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; -import org.cbioportal.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudy; public class SampleListMixin { diff --git a/src/main/java/org/cbioportal/web/mixin/SampleMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/SampleMixin.java similarity index 84% rename from src/main/java/org/cbioportal/web/mixin/SampleMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/SampleMixin.java index 4242a9f5d10..215d205072b 100644 --- a/src/main/java/org/cbioportal/web/mixin/SampleMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/SampleMixin.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; -import org.cbioportal.model.Patient; +import org.cbioportal.legacy.model.Patient; public class SampleMixin { diff --git a/src/main/java/org/cbioportal/web/mixin/SessionDataMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/SessionDataMixin.java similarity index 88% rename from src/main/java/org/cbioportal/web/mixin/SessionDataMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/SessionDataMixin.java index 60b4351eb2a..c65cdc76d2e 100644 --- a/src/main/java/org/cbioportal/web/mixin/SessionDataMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/SessionDataMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import java.util.Set; diff --git a/src/main/java/org/cbioportal/web/mixin/SessionMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/SessionMixin.java similarity index 83% rename from src/main/java/org/cbioportal/web/mixin/SessionMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/SessionMixin.java index 0d7e0a89d45..e76a61f0903 100644 --- a/src/main/java/org/cbioportal/web/mixin/SessionMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/SessionMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/src/main/java/org/cbioportal/web/mixin/StructuralVariantMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/StructuralVariantMixin.java similarity index 79% rename from src/main/java/org/cbioportal/web/mixin/StructuralVariantMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/StructuralVariantMixin.java index a0d840ed5ff..9fe36ab21be 100644 --- a/src/main/java/org/cbioportal/web/mixin/StructuralVariantMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/StructuralVariantMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.*; diff --git a/src/main/java/org/cbioportal/web/mixin/TypeOfCancerMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/TypeOfCancerMixin.java similarity index 79% rename from src/main/java/org/cbioportal/web/mixin/TypeOfCancerMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/TypeOfCancerMixin.java index 73f4d8a1520..48268be7a08 100644 --- a/src/main/java/org/cbioportal/web/mixin/TypeOfCancerMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/TypeOfCancerMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/parameter/BinsGeneratorConfig.java b/src/main/java/org/cbioportal/legacy/web/parameter/BinsGeneratorConfig.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/BinsGeneratorConfig.java rename to src/main/java/org/cbioportal/legacy/web/parameter/BinsGeneratorConfig.java index 78b0de399e4..de6f54136b0 100644 --- a/src/main/java/org/cbioportal/web/parameter/BinsGeneratorConfig.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/BinsGeneratorConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/parameter/CategorizedClinicalDataCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/CategorizedClinicalDataCountFilter.java similarity index 98% rename from src/main/java/org/cbioportal/web/parameter/CategorizedClinicalDataCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/CategorizedClinicalDataCountFilter.java index 22ce588453e..92dc23f6bbf 100644 --- a/src/main/java/org/cbioportal/web/parameter/CategorizedClinicalDataCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/CategorizedClinicalDataCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/CategorizedGenericAssayDataCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/CategorizedGenericAssayDataCountFilter.java similarity index 98% rename from src/main/java/org/cbioportal/web/parameter/CategorizedGenericAssayDataCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/CategorizedGenericAssayDataCountFilter.java index 3d9face92c8..f46ff86da14 100644 --- a/src/main/java/org/cbioportal/web/parameter/CategorizedGenericAssayDataCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/CategorizedGenericAssayDataCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalAttributeCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalAttributeCountFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/ClinicalAttributeCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalAttributeCountFilter.java index 63e59aa5944..0e32556a484 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalAttributeCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalAttributeCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataBinCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataBinCountFilter.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataBinCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataBinCountFilter.java index 565b7286556..9e63e7fcdbb 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataBinCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataBinCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataBinFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataBinFilter.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataBinFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataBinFilter.java index 4df9e8add07..854726c53eb 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataBinFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataBinFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataCountFilter.java similarity index 93% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataCountFilter.java index 66679896da5..d49a9a8f210 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataFilter.java index 1b406b31532..2a59867b519 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import io.swagger.v3.oas.annotations.Hidden; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataIdentifier.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataIdentifier.java index 9b015f866b7..b7ada176860 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataMultiStudyFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataMultiStudyFilter.java similarity index 81% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataMultiStudyFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataMultiStudyFilter.java index 784331533e7..0bf1ec9726f 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataMultiStudyFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataMultiStudyFilter.java @@ -1,12 +1,12 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; -import org.cbioportal.web.ClinicalDataController; +import org.cbioportal.legacy.web.ClinicalDataController; import jakarta.validation.constraints.Size; import java.util.List; import java.io.Serializable; -import static org.cbioportal.web.parameter.PagingConstants.MAX_PAGE_SIZE; +import static org.cbioportal.legacy.web.parameter.PagingConstants.MAX_PAGE_SIZE; public class ClinicalDataMultiStudyFilter implements Serializable { diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataSingleStudyFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataSingleStudyFilter.java similarity index 77% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataSingleStudyFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataSingleStudyFilter.java index f76f9daf0b7..76bab723b2c 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataSingleStudyFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataSingleStudyFilter.java @@ -1,11 +1,11 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.Size; -import org.cbioportal.web.ClinicalDataController; +import org.cbioportal.legacy.web.ClinicalDataController; import java.util.List; -import static org.cbioportal.web.parameter.PagingConstants.MAX_PAGE_SIZE; +import static org.cbioportal.legacy.web.parameter.PagingConstants.MAX_PAGE_SIZE; public class ClinicalDataSingleStudyFilter { diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataType.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataType.java similarity index 56% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataType.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataType.java index 6f7121c8fb2..5431a41dc26 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataType.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataType.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public enum ClinicalDataType { SAMPLE, diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalEventAttributeRequest.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventAttributeRequest.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/ClinicalEventAttributeRequest.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventAttributeRequest.java index 4cc2d6f254e..c6e22dbc817 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalEventAttributeRequest.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventAttributeRequest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalEventRequest.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventRequest.java similarity index 86% rename from src/main/java/org/cbioportal/web/parameter/ClinicalEventRequest.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventRequest.java index 1397e0dcb85..29db8c56ee4 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalEventRequest.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventRequest.java @@ -1,6 +1,6 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; -import org.cbioportal.model.ClinicalEventData; +import org.cbioportal.legacy.model.ClinicalEventData; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalEventRequestIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventRequestIdentifier.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/ClinicalEventRequestIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventRequestIdentifier.java index 2d38a85e91c..17162d9965b 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalEventRequestIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventRequestIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalTrackConfig.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalTrackConfig.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/ClinicalTrackConfig.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalTrackConfig.java index 9683a4b2fbe..6b33604d3f8 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalTrackConfig.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalTrackConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import com.fasterxml.jackson.annotation.JsonInclude; diff --git a/src/main/java/org/cbioportal/web/parameter/CoExpressionFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/CoExpressionFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/CoExpressionFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/CoExpressionFilter.java index 0bc03751278..5a97d8e8c69 100644 --- a/src/main/java/org/cbioportal/web/parameter/CoExpressionFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/CoExpressionFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/CopyNumberCountIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/CopyNumberCountIdentifier.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/CopyNumberCountIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/CopyNumberCountIdentifier.java index 20d14894d2e..8b23b101278 100644 --- a/src/main/java/org/cbioportal/web/parameter/CopyNumberCountIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/CopyNumberCountIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public class CopyNumberCountIdentifier { diff --git a/src/main/java/org/cbioportal/web/parameter/CustomGeneList.java b/src/main/java/org/cbioportal/legacy/web/parameter/CustomGeneList.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/CustomGeneList.java rename to src/main/java/org/cbioportal/legacy/web/parameter/CustomGeneList.java index ae762277a51..4738ac4a60a 100644 --- a/src/main/java/org/cbioportal/web/parameter/CustomGeneList.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/CustomGeneList.java @@ -1,9 +1,9 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.utils.removeme.Session; +import org.cbioportal.legacy.utils.removeme.Session; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/src/main/java/org/cbioportal/web/parameter/CustomGeneListData.java b/src/main/java/org/cbioportal/legacy/web/parameter/CustomGeneListData.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/CustomGeneListData.java rename to src/main/java/org/cbioportal/legacy/web/parameter/CustomGeneListData.java index 6e9f1c5d194..dbf66fe8546 100644 --- a/src/main/java/org/cbioportal/web/parameter/CustomGeneListData.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/CustomGeneListData.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; diff --git a/src/main/java/org/cbioportal/web/parameter/CustomSampleIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/CustomSampleIdentifier.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/CustomSampleIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/CustomSampleIdentifier.java index 51692168fcb..f8dbfda42ef 100644 --- a/src/main/java/org/cbioportal/web/parameter/CustomSampleIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/CustomSampleIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/DataBinCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/DataBinCountFilter.java similarity index 88% rename from src/main/java/org/cbioportal/web/parameter/DataBinCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/DataBinCountFilter.java index 4ed75c840d7..149059e0693 100644 --- a/src/main/java/org/cbioportal/web/parameter/DataBinCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/DataBinCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/DataBinFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/DataBinFilter.java similarity index 98% rename from src/main/java/org/cbioportal/web/parameter/DataBinFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/DataBinFilter.java index 4011b5547a4..de27ecdb7f3 100644 --- a/src/main/java/org/cbioportal/web/parameter/DataBinFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/DataBinFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/parameter/DataBinMethod.java b/src/main/java/org/cbioportal/legacy/web/parameter/DataBinMethod.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/DataBinMethod.java rename to src/main/java/org/cbioportal/legacy/web/parameter/DataBinMethod.java index c63dda3c48c..e336647ae0c 100644 --- a/src/main/java/org/cbioportal/web/parameter/DataBinMethod.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/DataBinMethod.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; /** * STATIC and DYNAMIC binning relate to the way bin boundaries are derived from numerical data of a sample cohort diff --git a/src/main/java/org/cbioportal/web/parameter/DataFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/DataFilter.java similarity index 87% rename from src/main/java/org/cbioportal/web/parameter/DataFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/DataFilter.java index 05d9c52c8b7..8a26dcf7b31 100644 --- a/src/main/java/org/cbioportal/web/parameter/DataFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/DataFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/DataFilterValue.java b/src/main/java/org/cbioportal/legacy/web/parameter/DataFilterValue.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/DataFilterValue.java rename to src/main/java/org/cbioportal/legacy/web/parameter/DataFilterValue.java index 47fdb0937e9..53e39525114 100644 --- a/src/main/java/org/cbioportal/web/parameter/DataFilterValue.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/DataFilterValue.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/parameter/Direction.java b/src/main/java/org/cbioportal/legacy/web/parameter/Direction.java similarity index 50% rename from src/main/java/org/cbioportal/web/parameter/Direction.java rename to src/main/java/org/cbioportal/legacy/web/parameter/Direction.java index 1453d856420..f8044124309 100644 --- a/src/main/java/org/cbioportal/web/parameter/Direction.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/Direction.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public enum Direction { diff --git a/src/main/java/org/cbioportal/web/parameter/DiscreteCopyNumberEventType.java b/src/main/java/org/cbioportal/legacy/web/parameter/DiscreteCopyNumberEventType.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/DiscreteCopyNumberEventType.java rename to src/main/java/org/cbioportal/legacy/web/parameter/DiscreteCopyNumberEventType.java index 520c58f98bb..d37d2c63917 100644 --- a/src/main/java/org/cbioportal/web/parameter/DiscreteCopyNumberEventType.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/DiscreteCopyNumberEventType.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.util.Arrays; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/DiscreteCopyNumberFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/DiscreteCopyNumberFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/DiscreteCopyNumberFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/DiscreteCopyNumberFilter.java index 859575119c4..ae11c289b94 100644 --- a/src/main/java/org/cbioportal/web/parameter/DiscreteCopyNumberFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/DiscreteCopyNumberFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/EnrichmentFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/EnrichmentFilter.java similarity index 93% rename from src/main/java/org/cbioportal/web/parameter/EnrichmentFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/EnrichmentFilter.java index 571f086a951..13a05367216 100644 --- a/src/main/java/org/cbioportal/web/parameter/EnrichmentFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/EnrichmentFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.NotNull; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/GeneFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GeneFilter.java similarity index 97% rename from src/main/java/org/cbioportal/web/parameter/GeneFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GeneFilter.java index a956f5a63c7..6936beb1b72 100644 --- a/src/main/java/org/cbioportal/web/parameter/GeneFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GeneFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.*; @@ -8,7 +8,7 @@ import jakarta.validation.constraints.AssertTrue; import org.apache.commons.collections4.CollectionUtils; -import org.cbioportal.model.CNA; +import org.cbioportal.legacy.model.CNA; import com.fasterxml.jackson.annotation.JsonIgnore; public class GeneFilter implements Serializable { diff --git a/src/main/java/org/cbioportal/web/parameter/GeneIdType.java b/src/main/java/org/cbioportal/legacy/web/parameter/GeneIdType.java similarity index 60% rename from src/main/java/org/cbioportal/web/parameter/GeneIdType.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GeneIdType.java index a46435d1cdb..fe1f7a2da39 100644 --- a/src/main/java/org/cbioportal/web/parameter/GeneIdType.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GeneIdType.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public enum GeneIdType { diff --git a/src/main/java/org/cbioportal/web/parameter/GenePanelDataFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenePanelDataFilter.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/GenePanelDataFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenePanelDataFilter.java index 9b28bf8c510..783a5debace 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenePanelDataFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenePanelDataFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/GenePanelDataMultipleStudyFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenePanelDataMultipleStudyFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/GenePanelDataMultipleStudyFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenePanelDataMultipleStudyFilter.java index f4e70978c6b..d3132930fbd 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenePanelDataMultipleStudyFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenePanelDataMultipleStudyFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataBinCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataBinCountFilter.java similarity index 92% rename from src/main/java/org/cbioportal/web/parameter/GenericAssayDataBinCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataBinCountFilter.java index eb088eb6faa..078e80b9949 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataBinCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataBinCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataBinFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataBinFilter.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/GenericAssayDataBinFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataBinFilter.java index 0d30f34b7c0..d7f6dd89139 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataBinFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataBinFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataCountFilter.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/GenericAssayDataCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataCountFilter.java index b4e60373894..c03153055ad 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataFilter.java similarity index 93% rename from src/main/java/org/cbioportal/web/parameter/GenericAssayDataFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataFilter.java index 14dfbf0a46d..a10b1966c5b 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataMultipleStudyFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataMultipleStudyFilter.java similarity index 97% rename from src/main/java/org/cbioportal/web/parameter/GenericAssayDataMultipleStudyFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataMultipleStudyFilter.java index 35a1afb390f..60f3d9989c4 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataMultipleStudyFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataMultipleStudyFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/GenericAssayFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayFilter.java index c0f4a75998c..ba5443d7461 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayMetaFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayMetaFilter.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/GenericAssayMetaFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayMetaFilter.java index f877912b2a2..7e9f2b9f285 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayMetaFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayMetaFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.Size; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/GenesetDataFilterCriteria.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenesetDataFilterCriteria.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/GenesetDataFilterCriteria.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenesetDataFilterCriteria.java index f0c9c3397f9..9ec3cfea761 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenesetDataFilterCriteria.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenesetDataFilterCriteria.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/GenomicDataBinCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataBinCountFilter.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/GenomicDataBinCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataBinCountFilter.java index b2e9ad1734a..a8d0e031c2c 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenomicDataBinCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataBinCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/GenomicDataBinFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataBinFilter.java similarity index 92% rename from src/main/java/org/cbioportal/web/parameter/GenomicDataBinFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataBinFilter.java index 5629c027ec8..e58b06bcee0 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenomicDataBinFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataBinFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/GenomicDataCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataCountFilter.java similarity index 93% rename from src/main/java/org/cbioportal/web/parameter/GenomicDataCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataCountFilter.java index c01ec7696c1..c805d346c57 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenomicDataCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataFilter.java index 34aca9c0894..3a1ed36f62d 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/Group.java b/src/main/java/org/cbioportal/legacy/web/parameter/Group.java similarity index 93% rename from src/main/java/org/cbioportal/web/parameter/Group.java rename to src/main/java/org/cbioportal/legacy/web/parameter/Group.java index ae9e8c184e9..970f4592740 100644 --- a/src/main/java/org/cbioportal/web/parameter/Group.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/Group.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/GroupFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GroupFilter.java similarity index 89% rename from src/main/java/org/cbioportal/web/parameter/GroupFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GroupFilter.java index 8cfcba4859b..9cf85d87d4c 100644 --- a/src/main/java/org/cbioportal/web/parameter/GroupFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GroupFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.Valid; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/HeaderKeyConstants.java b/src/main/java/org/cbioportal/legacy/web/parameter/HeaderKeyConstants.java similarity index 85% rename from src/main/java/org/cbioportal/web/parameter/HeaderKeyConstants.java rename to src/main/java/org/cbioportal/legacy/web/parameter/HeaderKeyConstants.java index 89a51ea7e13..1fe54913a15 100644 --- a/src/main/java/org/cbioportal/web/parameter/HeaderKeyConstants.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/HeaderKeyConstants.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; /* When changing these edit them in portal/src/main/webapp/WEB-INF/web.xml as * well to expose the CORS headers */ diff --git a/src/main/java/org/cbioportal/web/parameter/MolecularDataFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularDataFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/MolecularDataFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MolecularDataFilter.java index d8765076905..821bd314977 100644 --- a/src/main/java/org/cbioportal/web/parameter/MolecularDataFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularDataFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/MolecularDataMultipleStudyFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularDataMultipleStudyFilter.java similarity index 97% rename from src/main/java/org/cbioportal/web/parameter/MolecularDataMultipleStudyFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MolecularDataMultipleStudyFilter.java index 3527ca674c1..a065f4d804a 100644 --- a/src/main/java/org/cbioportal/web/parameter/MolecularDataMultipleStudyFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularDataMultipleStudyFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/MolecularProfileCasesGroupAndAlterationTypeFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileCasesGroupAndAlterationTypeFilter.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/MolecularProfileCasesGroupAndAlterationTypeFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileCasesGroupAndAlterationTypeFilter.java index a8d991ca95e..fbb4d340e09 100644 --- a/src/main/java/org/cbioportal/web/parameter/MolecularProfileCasesGroupAndAlterationTypeFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileCasesGroupAndAlterationTypeFilter.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import io.swagger.v3.oas.annotations.media.Schema; -import org.cbioportal.model.AlterationFilter; +import org.cbioportal.legacy.model.AlterationFilter; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/MolecularProfileCasesGroupFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileCasesGroupFilter.java similarity index 88% rename from src/main/java/org/cbioportal/web/parameter/MolecularProfileCasesGroupFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileCasesGroupFilter.java index decdc4748e5..87d975c7fcf 100644 --- a/src/main/java/org/cbioportal/web/parameter/MolecularProfileCasesGroupFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileCasesGroupFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.util.ArrayList; import java.util.HashSet; @@ -6,7 +6,7 @@ import jakarta.validation.constraints.Size; -import org.cbioportal.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; public class MolecularProfileCasesGroupFilter { diff --git a/src/main/java/org/cbioportal/web/parameter/MolecularProfileFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/MolecularProfileFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileFilter.java index bc5a460dc9b..7c015b3bb19 100644 --- a/src/main/java/org/cbioportal/web/parameter/MolecularProfileFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/MutationDataFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MutationDataFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/MutationDataFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MutationDataFilter.java index cb5401aaac6..6b5770bcfb6 100644 --- a/src/main/java/org/cbioportal/web/parameter/MutationDataFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MutationDataFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.annotation.JsonInclude; diff --git a/src/main/java/org/cbioportal/web/parameter/MutationFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MutationFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/MutationFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MutationFilter.java index f9d10a3fccd..48fccdfeb2f 100644 --- a/src/main/java/org/cbioportal/web/parameter/MutationFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MutationFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/MutationMultipleStudyFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MutationMultipleStudyFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/MutationMultipleStudyFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MutationMultipleStudyFilter.java index c487cf754fa..0305859ca9a 100644 --- a/src/main/java/org/cbioportal/web/parameter/MutationMultipleStudyFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MutationMultipleStudyFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/MutationOption.java b/src/main/java/org/cbioportal/legacy/web/parameter/MutationOption.java similarity index 81% rename from src/main/java/org/cbioportal/web/parameter/MutationOption.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MutationOption.java index 32d98555dce..f91e6a5cc5e 100644 --- a/src/main/java/org/cbioportal/web/parameter/MutationOption.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MutationOption.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public enum MutationOption { MUTATED, // fetch mutation data with MUTATED, NOT_MUTATED, NOT_PROFILED in MutationFilterOption diff --git a/src/main/java/org/cbioportal/web/parameter/MutationPositionIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/MutationPositionIdentifier.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/MutationPositionIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MutationPositionIdentifier.java index a54854ecec9..ed8a5063c3f 100644 --- a/src/main/java/org/cbioportal/web/parameter/MutationPositionIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MutationPositionIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public class MutationPositionIdentifier { diff --git a/src/main/java/org/cbioportal/web/parameter/MutationSpectrumFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MutationSpectrumFilter.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/MutationSpectrumFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MutationSpectrumFilter.java index 8d97f0b85f8..9e401b08908 100644 --- a/src/main/java/org/cbioportal/web/parameter/MutationSpectrumFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MutationSpectrumFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/OccurrencePosition.java b/src/main/java/org/cbioportal/legacy/web/parameter/OccurrencePosition.java similarity index 55% rename from src/main/java/org/cbioportal/web/parameter/OccurrencePosition.java rename to src/main/java/org/cbioportal/legacy/web/parameter/OccurrencePosition.java index b9a5dbc9aad..28f9378b0e3 100644 --- a/src/main/java/org/cbioportal/web/parameter/OccurrencePosition.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/OccurrencePosition.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public enum OccurrencePosition { FIRST, diff --git a/src/main/java/org/cbioportal/web/parameter/PageSettings.java b/src/main/java/org/cbioportal/legacy/web/parameter/PageSettings.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/PageSettings.java rename to src/main/java/org/cbioportal/legacy/web/parameter/PageSettings.java index 0d9c32dfe00..dcbb78024af 100644 --- a/src/main/java/org/cbioportal/web/parameter/PageSettings.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/PageSettings.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.IOException; -import org.cbioportal.utils.removeme.Session; +import org.cbioportal.legacy.utils.removeme.Session; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/src/main/java/org/cbioportal/web/parameter/PageSettingsData.java b/src/main/java/org/cbioportal/legacy/web/parameter/PageSettingsData.java similarity index 97% rename from src/main/java/org/cbioportal/web/parameter/PageSettingsData.java rename to src/main/java/org/cbioportal/legacy/web/parameter/PageSettingsData.java index 2a22e333bf8..33e25bc49fb 100644 --- a/src/main/java/org/cbioportal/web/parameter/PageSettingsData.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/PageSettingsData.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.Set; diff --git a/src/main/java/org/cbioportal/web/parameter/PageSettingsIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/PageSettingsIdentifier.java similarity index 93% rename from src/main/java/org/cbioportal/web/parameter/PageSettingsIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/PageSettingsIdentifier.java index 6dbd479e2ad..a3b78b24d81 100644 --- a/src/main/java/org/cbioportal/web/parameter/PageSettingsIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/PageSettingsIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.Set; diff --git a/src/main/java/org/cbioportal/web/parameter/PagingConstants.java b/src/main/java/org/cbioportal/legacy/web/parameter/PagingConstants.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/PagingConstants.java rename to src/main/java/org/cbioportal/legacy/web/parameter/PagingConstants.java index 0c26098758c..a65cbcaa799 100644 --- a/src/main/java/org/cbioportal/web/parameter/PagingConstants.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/PagingConstants.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public class PagingConstants { diff --git a/src/main/java/org/cbioportal/web/parameter/PatientFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/PatientFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/PatientFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/PatientFilter.java index 7f69fb048de..3a44271b583 100644 --- a/src/main/java/org/cbioportal/web/parameter/PatientFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/PatientFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/PatientIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/PatientIdentifier.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/PatientIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/PatientIdentifier.java index b7a9117a031..4109d747b02 100644 --- a/src/main/java/org/cbioportal/web/parameter/PatientIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/PatientIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/Projection.java b/src/main/java/org/cbioportal/legacy/web/parameter/Projection.java similarity index 61% rename from src/main/java/org/cbioportal/web/parameter/Projection.java rename to src/main/java/org/cbioportal/legacy/web/parameter/Projection.java index d17103c18ba..b62b2cbd2a7 100644 --- a/src/main/java/org/cbioportal/web/parameter/Projection.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/Projection.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public enum Projection { diff --git a/src/main/java/org/cbioportal/web/parameter/ResultsPageSettings.java b/src/main/java/org/cbioportal/legacy/web/parameter/ResultsPageSettings.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/ResultsPageSettings.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ResultsPageSettings.java index b549ed25c51..bb4205cf4f0 100644 --- a/src/main/java/org/cbioportal/web/parameter/ResultsPageSettings.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ResultsPageSettings.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.annotation.JsonInclude; diff --git a/src/main/java/org/cbioportal/web/parameter/SampleFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/SampleFilter.java similarity index 93% rename from src/main/java/org/cbioportal/web/parameter/SampleFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/SampleFilter.java index 701dc6181ac..c8dea2bc1db 100644 --- a/src/main/java/org/cbioportal/web/parameter/SampleFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/SampleFilter.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; -import org.cbioportal.web.SampleController; +import org.cbioportal.legacy.web.SampleController; import java.util.List; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/SampleIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/SampleIdentifier.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/SampleIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/SampleIdentifier.java index 95b78e36763..71abb67cffb 100644 --- a/src/main/java/org/cbioportal/web/parameter/SampleIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/SampleIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.Objects; diff --git a/src/main/java/org/cbioportal/web/parameter/SampleMolecularIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/SampleMolecularIdentifier.java similarity index 92% rename from src/main/java/org/cbioportal/web/parameter/SampleMolecularIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/SampleMolecularIdentifier.java index 12103116941..9c484eae79d 100644 --- a/src/main/java/org/cbioportal/web/parameter/SampleMolecularIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/SampleMolecularIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/SessionPage.java b/src/main/java/org/cbioportal/legacy/web/parameter/SessionPage.java similarity index 58% rename from src/main/java/org/cbioportal/web/parameter/SessionPage.java rename to src/main/java/org/cbioportal/legacy/web/parameter/SessionPage.java index bdffd95307f..527f34f7371 100644 --- a/src/main/java/org/cbioportal/web/parameter/SessionPage.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/SessionPage.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public enum SessionPage { results_view, diff --git a/src/main/java/org/cbioportal/web/parameter/StructuralVariantFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/StructuralVariantFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/StructuralVariantFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/StructuralVariantFilter.java index 7d3c831196c..ad87e3bc58a 100644 --- a/src/main/java/org/cbioportal/web/parameter/StructuralVariantFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/StructuralVariantFilter.java @@ -21,13 +21,13 @@ * along with this program. If not, see . */ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.Valid; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; import org.apache.commons.collections4.CollectionUtils; -import org.cbioportal.model.StructuralVariantQuery; +import org.cbioportal.legacy.model.StructuralVariantQuery; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/StudyPageSettings.java b/src/main/java/org/cbioportal/legacy/web/parameter/StudyPageSettings.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/StudyPageSettings.java rename to src/main/java/org/cbioportal/legacy/web/parameter/StudyPageSettings.java index 5dcbc8b3887..49a62f3274f 100644 --- a/src/main/java/org/cbioportal/web/parameter/StudyPageSettings.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/StudyPageSettings.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.annotation.JsonInclude; diff --git a/src/main/java/org/cbioportal/web/parameter/StudyViewFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/StudyViewFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/StudyViewFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/StudyViewFilter.java index 738d3632a70..61d3f7f5356 100644 --- a/src/main/java/org/cbioportal/web/parameter/StudyViewFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/StudyViewFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; @@ -10,10 +10,11 @@ import jakarta.validation.Valid; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.GeneFilter; -import org.cbioportal.model.StudyViewStructuralVariantFilter; -import org.cbioportal.web.parameter.filter.*; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.GeneFilter; +import org.cbioportal.legacy.model.StudyViewStructuralVariantFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedPatientTreatmentFilters; +import org.cbioportal.legacy.web.parameter.filter.AndedSampleTreatmentFilters; @JsonIgnoreProperties(ignoreUnknown = true) @JsonInclude(Include.NON_NULL) diff --git a/src/main/java/org/cbioportal/web/parameter/SurvivalRequest.java b/src/main/java/org/cbioportal/legacy/web/parameter/SurvivalRequest.java similarity index 97% rename from src/main/java/org/cbioportal/web/parameter/SurvivalRequest.java rename to src/main/java/org/cbioportal/legacy/web/parameter/SurvivalRequest.java index 7f770d9cd42..c4301c52a98 100644 --- a/src/main/java/org/cbioportal/web/parameter/SurvivalRequest.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/SurvivalRequest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.Valid; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/web/parameter/VariantCountIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/VariantCountIdentifier.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/VariantCountIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/VariantCountIdentifier.java index 1b6ace73404..4a9090ce935 100644 --- a/src/main/java/org/cbioportal/web/parameter/VariantCountIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/VariantCountIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public class VariantCountIdentifier { diff --git a/src/main/java/org/cbioportal/web/parameter/VirtualStudy.java b/src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudy.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/VirtualStudy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudy.java index d5613860982..c4a5e6a1593 100644 --- a/src/main/java/org/cbioportal/web/parameter/VirtualStudy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.IOException; @@ -8,7 +8,7 @@ import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.utils.removeme.Session; +import org.cbioportal.legacy.utils.removeme.Session; @JsonIgnoreProperties(ignoreUnknown = true) public class VirtualStudy extends Session { diff --git a/src/main/java/org/cbioportal/web/parameter/VirtualStudyData.java b/src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudyData.java similarity index 98% rename from src/main/java/org/cbioportal/web/parameter/VirtualStudyData.java rename to src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudyData.java index f3f60dfb360..b6add15bafd 100644 --- a/src/main/java/org/cbioportal/web/parameter/VirtualStudyData.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudyData.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.HashSet; diff --git a/src/main/java/org/cbioportal/web/parameter/VirtualStudySamples.java b/src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudySamples.java similarity index 89% rename from src/main/java/org/cbioportal/web/parameter/VirtualStudySamples.java rename to src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudySamples.java index 5cfb36afa3b..ed4e6e9d96c 100644 --- a/src/main/java/org/cbioportal/web/parameter/VirtualStudySamples.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudySamples.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.util.Set; diff --git a/src/main/java/org/cbioportal/web/parameter/filter/AndedPatientTreatmentFilters.java b/src/main/java/org/cbioportal/legacy/web/parameter/filter/AndedPatientTreatmentFilters.java similarity index 76% rename from src/main/java/org/cbioportal/web/parameter/filter/AndedPatientTreatmentFilters.java rename to src/main/java/org/cbioportal/legacy/web/parameter/filter/AndedPatientTreatmentFilters.java index eaf81744f5c..a06cd30d509 100644 --- a/src/main/java/org/cbioportal/web/parameter/filter/AndedPatientTreatmentFilters.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/filter/AndedPatientTreatmentFilters.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.parameter.filter; +package org.cbioportal.legacy.web.parameter.filter; -import org.cbioportal.model.ClinicalEventSample; -import org.cbioportal.model.PatientTreatmentRow; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/filter/AndedSampleTreatmentFilters.java b/src/main/java/org/cbioportal/legacy/web/parameter/filter/AndedSampleTreatmentFilters.java similarity index 75% rename from src/main/java/org/cbioportal/web/parameter/filter/AndedSampleTreatmentFilters.java rename to src/main/java/org/cbioportal/legacy/web/parameter/filter/AndedSampleTreatmentFilters.java index 93960cc7541..1d0f23720fb 100644 --- a/src/main/java/org/cbioportal/web/parameter/filter/AndedSampleTreatmentFilters.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/filter/AndedSampleTreatmentFilters.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.parameter.filter; +package org.cbioportal.legacy.web.parameter.filter; -import org.cbioportal.model.PatientTreatmentRow; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/filter/OredPatientTreatmentFilters.java b/src/main/java/org/cbioportal/legacy/web/parameter/filter/OredPatientTreatmentFilters.java similarity index 75% rename from src/main/java/org/cbioportal/web/parameter/filter/OredPatientTreatmentFilters.java rename to src/main/java/org/cbioportal/legacy/web/parameter/filter/OredPatientTreatmentFilters.java index 57ae0d3797e..f41fb5faa6e 100644 --- a/src/main/java/org/cbioportal/web/parameter/filter/OredPatientTreatmentFilters.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/filter/OredPatientTreatmentFilters.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.parameter.filter; +package org.cbioportal.legacy.web.parameter.filter; -import org.cbioportal.model.ClinicalEventSample; -import org.cbioportal.model.PatientTreatmentRow; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/filter/OredSampleTreatmentFilters.java b/src/main/java/org/cbioportal/legacy/web/parameter/filter/OredSampleTreatmentFilters.java similarity index 80% rename from src/main/java/org/cbioportal/web/parameter/filter/OredSampleTreatmentFilters.java rename to src/main/java/org/cbioportal/legacy/web/parameter/filter/OredSampleTreatmentFilters.java index 388ab0113a4..497561e4a1e 100644 --- a/src/main/java/org/cbioportal/web/parameter/filter/OredSampleTreatmentFilters.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/filter/OredSampleTreatmentFilters.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.parameter.filter; +package org.cbioportal.legacy.web.parameter.filter; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/filter/PatientTreatmentFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/filter/PatientTreatmentFilter.java similarity index 87% rename from src/main/java/org/cbioportal/web/parameter/filter/PatientTreatmentFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/filter/PatientTreatmentFilter.java index fb4d8095ce9..d78da03a5cf 100644 --- a/src/main/java/org/cbioportal/web/parameter/filter/PatientTreatmentFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/filter/PatientTreatmentFilter.java @@ -1,10 +1,10 @@ -package org.cbioportal.web.parameter.filter; +package org.cbioportal.legacy.web.parameter.filter; import java.io.Serializable; import java.util.Map; import java.util.Set; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; public class PatientTreatmentFilter implements Serializable { private String treatment; diff --git a/src/main/java/org/cbioportal/web/parameter/filter/SampleTreatmentFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/filter/SampleTreatmentFilter.java similarity index 82% rename from src/main/java/org/cbioportal/web/parameter/filter/SampleTreatmentFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/filter/SampleTreatmentFilter.java index f4c2dcf1027..6975e744aac 100644 --- a/src/main/java/org/cbioportal/web/parameter/filter/SampleTreatmentFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/filter/SampleTreatmentFilter.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.parameter.filter; +package org.cbioportal.legacy.web.parameter.filter; -import org.cbioportal.model.TemporalRelation; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.TemporalRelation; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import java.io.Serializable; import java.util.Map; diff --git a/src/main/java/org/cbioportal/web/parameter/sort/CancerTypeSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/CancerTypeSortBy.java similarity index 88% rename from src/main/java/org/cbioportal/web/parameter/sort/CancerTypeSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/CancerTypeSortBy.java index 31305e393bd..68152cf1cde 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/CancerTypeSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/CancerTypeSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum CancerTypeSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/ClinicalAttributeSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalAttributeSortBy.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/sort/ClinicalAttributeSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalAttributeSortBy.java index 5b6ef9c8021..b30e1e6374a 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/ClinicalAttributeSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalAttributeSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum ClinicalAttributeSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/ClinicalDataSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalDataSortBy.java similarity index 85% rename from src/main/java/org/cbioportal/web/parameter/sort/ClinicalDataSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalDataSortBy.java index 9da6465c5af..a738c93271c 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/ClinicalDataSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalDataSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum ClinicalDataSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/ClinicalEventSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalEventSortBy.java similarity index 88% rename from src/main/java/org/cbioportal/web/parameter/sort/ClinicalEventSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalEventSortBy.java index 44508aba81f..84bba1dce25 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/ClinicalEventSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalEventSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum ClinicalEventSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/CopyNumberSegmentSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/CopyNumberSegmentSortBy.java similarity index 88% rename from src/main/java/org/cbioportal/web/parameter/sort/CopyNumberSegmentSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/CopyNumberSegmentSortBy.java index 2d662dbd005..b647b770c3e 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/CopyNumberSegmentSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/CopyNumberSegmentSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum CopyNumberSegmentSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/DiscreteCopyNumberSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/DiscreteCopyNumberSortBy.java similarity index 86% rename from src/main/java/org/cbioportal/web/parameter/sort/DiscreteCopyNumberSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/DiscreteCopyNumberSortBy.java index 41e4128c4a9..9cf89c89bfc 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/DiscreteCopyNumberSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/DiscreteCopyNumberSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum DiscreteCopyNumberSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/GenePanelSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/GenePanelSortBy.java similarity index 85% rename from src/main/java/org/cbioportal/web/parameter/sort/GenePanelSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/GenePanelSortBy.java index 1b2750f9386..f554dcfb891 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/GenePanelSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/GenePanelSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum GenePanelSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/GeneSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/GeneSortBy.java similarity index 88% rename from src/main/java/org/cbioportal/web/parameter/sort/GeneSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/GeneSortBy.java index 233f92864b5..d5062e29314 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/GeneSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/GeneSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum GeneSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/MolecularProfileSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/MolecularProfileSortBy.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/sort/MolecularProfileSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/MolecularProfileSortBy.java index c089ee90fea..b7b063892b8 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/MolecularProfileSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/MolecularProfileSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum MolecularProfileSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/MutationSortBy.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/MutationSortBy.java index ce2caf51cdb..0e27aae5a7c 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/MutationSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum MutationSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/PatientSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/PatientSortBy.java similarity index 84% rename from src/main/java/org/cbioportal/web/parameter/sort/PatientSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/PatientSortBy.java index eca583a6e6e..885dc00b3d0 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/PatientSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/PatientSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum PatientSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/ResourceDataSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ResourceDataSortBy.java similarity index 85% rename from src/main/java/org/cbioportal/web/parameter/sort/ResourceDataSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/ResourceDataSortBy.java index aa0d097020a..cc0fe176435 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/ResourceDataSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ResourceDataSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum ResourceDataSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/ResourceDefinitionSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ResourceDefinitionSortBy.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/sort/ResourceDefinitionSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/ResourceDefinitionSortBy.java index 92163a2350b..2f02cfd4656 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/ResourceDefinitionSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ResourceDefinitionSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum ResourceDefinitionSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/SampleListSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SampleListSortBy.java similarity index 88% rename from src/main/java/org/cbioportal/web/parameter/sort/SampleListSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/SampleListSortBy.java index 924ca559177..838cabd135b 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/SampleListSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SampleListSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum SampleListSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/SampleSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SampleSortBy.java similarity index 85% rename from src/main/java/org/cbioportal/web/parameter/sort/SampleSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/SampleSortBy.java index d42dc7b7f53..1730df00189 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/SampleSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SampleSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum SampleSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/SignificantCopyNumberRegionSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SignificantCopyNumberRegionSortBy.java similarity index 89% rename from src/main/java/org/cbioportal/web/parameter/sort/SignificantCopyNumberRegionSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/SignificantCopyNumberRegionSortBy.java index 8003d56a9ef..823af50bd23 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/SignificantCopyNumberRegionSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SignificantCopyNumberRegionSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum SignificantCopyNumberRegionSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/SignificantlyMutatedGeneSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SignificantlyMutatedGeneSortBy.java similarity index 89% rename from src/main/java/org/cbioportal/web/parameter/sort/SignificantlyMutatedGeneSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/SignificantlyMutatedGeneSortBy.java index eb2a9003756..4fdb049969b 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/SignificantlyMutatedGeneSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SignificantlyMutatedGeneSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum SignificantlyMutatedGeneSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/StudySortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/StudySortBy.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/sort/StudySortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/StudySortBy.java index d13a09d9535..0f0122cf85f 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/StudySortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/StudySortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum StudySortBy { diff --git a/src/main/java/org/cbioportal/web/studyview/CustomDataController.java b/src/main/java/org/cbioportal/legacy/web/studyview/CustomDataController.java similarity index 85% rename from src/main/java/org/cbioportal/web/studyview/CustomDataController.java rename to src/main/java/org/cbioportal/legacy/web/studyview/CustomDataController.java index 9df5f7acf14..cc9544cbfa8 100644 --- a/src/main/java/org/cbioportal/web/studyview/CustomDataController.java +++ b/src/main/java/org/cbioportal/legacy/web/studyview/CustomDataController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.studyview; +package org.cbioportal.legacy.web.studyview; import io.swagger.v3.oas.annotations.Operation; @@ -9,18 +9,18 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.Patient; -import org.cbioportal.service.CustomDataService; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.ClinicalDataCountFilter; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.StudyViewFilterApplier; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.service.CustomDataService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.ClinicalDataCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -56,7 +56,7 @@ public class CustomDataController { @Autowired private PatientService patientService; - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/custom-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch custom data counts by study view filter") @ApiResponse(responseCode = "200", description = "OK", diff --git a/src/main/java/org/cbioportal/web/util/BinningData.java b/src/main/java/org/cbioportal/legacy/web/util/BinningData.java similarity index 88% rename from src/main/java/org/cbioportal/web/util/BinningData.java rename to src/main/java/org/cbioportal/legacy/web/util/BinningData.java index 82edafd1edd..e6d93f8eee1 100644 --- a/src/main/java/org/cbioportal/web/util/BinningData.java +++ b/src/main/java/org/cbioportal/legacy/web/util/BinningData.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.google.common.collect.ImmutableList; -import org.cbioportal.model.Binnable; -import org.cbioportal.model.ClinicalData; +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalData; import java.util.Collection; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/util/BinningIds.java b/src/main/java/org/cbioportal/legacy/web/util/BinningIds.java similarity index 98% rename from src/main/java/org/cbioportal/web/util/BinningIds.java rename to src/main/java/org/cbioportal/legacy/web/util/BinningIds.java index 6d19d79051b..95c65c22070 100644 --- a/src/main/java/org/cbioportal/web/util/BinningIds.java +++ b/src/main/java/org/cbioportal/legacy/web/util/BinningIds.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.util.ArrayList; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataBinUtil.java b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataBinUtil.java similarity index 94% rename from src/main/java/org/cbioportal/web/util/ClinicalDataBinUtil.java rename to src/main/java/org/cbioportal/legacy/web/util/ClinicalDataBinUtil.java index bf90b2de08b..f946b7a855b 100644 --- a/src/main/java/org/cbioportal/web/util/ClinicalDataBinUtil.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataBinUtil.java @@ -1,17 +1,22 @@ -package org.cbioportal.web.util; - -import org.cbioportal.model.Binnable; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataBin; -import org.cbioportal.service.AttributeByStudyService; -import org.cbioportal.service.CustomDataService; -import org.cbioportal.service.util.BinnableCustomDataValue; -import org.cbioportal.service.util.CustomAttributeWithData; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.service.util.CustomDataValue; -import org.cbioportal.web.columnar.util.NewClinicalDataBinUtil; -import org.cbioportal.web.parameter.*; +package org.cbioportal.legacy.web.util; + +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataBin; +import org.cbioportal.legacy.service.AttributeByStudyService; +import org.cbioportal.legacy.service.CustomDataService; +import org.cbioportal.legacy.service.util.BinnableCustomDataValue; +import org.cbioportal.legacy.service.util.CustomAttributeWithData; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.service.util.CustomDataValue; +import org.cbioportal.legacy.web.columnar.util.NewClinicalDataBinUtil; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.DataBinMethod; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataEnrichmentUtil.java b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataEnrichmentUtil.java similarity index 95% rename from src/main/java/org/cbioportal/web/util/ClinicalDataEnrichmentUtil.java rename to src/main/java/org/cbioportal/legacy/web/util/ClinicalDataEnrichmentUtil.java index 50ab61aafa1..ac07f9fce5e 100644 --- a/src/main/java/org/cbioportal/web/util/ClinicalDataEnrichmentUtil.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataEnrichmentUtil.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.math.BigDecimal; import java.util.*; @@ -7,15 +7,15 @@ import java.util.stream.Stream; import org.apache.commons.lang3.math.NumberUtils; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalDataEnrichment; -import org.cbioportal.model.Sample; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.util.ClinicalAttributeUtil; -import org.cbioportal.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalDataEnrichment; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataEqualityFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataEqualityFilterApplier.java similarity index 87% rename from src/main/java/org/cbioportal/web/util/ClinicalDataEqualityFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/ClinicalDataEqualityFilterApplier.java index 251b9f96e56..b2842e8c078 100644 --- a/src/main/java/org/cbioportal/web/util/ClinicalDataEqualityFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataEqualityFilterApplier.java @@ -1,10 +1,10 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.PatientService; -import org.cbioportal.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataFetcher.java b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataFetcher.java similarity index 93% rename from src/main/java/org/cbioportal/web/util/ClinicalDataFetcher.java rename to src/main/java/org/cbioportal/legacy/web/util/ClinicalDataFetcher.java index 56dcbef0573..943b511f3ae 100644 --- a/src/main/java/org/cbioportal/web/util/ClinicalDataFetcher.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataFetcher.java @@ -1,10 +1,10 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import org.apache.commons.collections4.CollectionUtils; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.Projection; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataFilterApplier.java similarity index 89% rename from src/main/java/org/cbioportal/web/util/ClinicalDataFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/ClinicalDataFilterApplier.java index 5a46baca9c2..af1fb6e97de 100644 --- a/src/main/java/org/cbioportal/web/util/ClinicalDataFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataFilterApplier.java @@ -1,17 +1,17 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.util.ArrayList; import java.util.List; import java.util.stream.Collectors; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.Patient; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.PatientService; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; public abstract class ClinicalDataFilterApplier implements DataFilterApplier { private PatientService patientService; diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataIntervalFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataIntervalFilterApplier.java similarity index 93% rename from src/main/java/org/cbioportal/web/util/ClinicalDataIntervalFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/ClinicalDataIntervalFilterApplier.java index 66d310a2511..9886c1af64d 100644 --- a/src/main/java/org/cbioportal/web/util/ClinicalDataIntervalFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataIntervalFilterApplier.java @@ -1,12 +1,12 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.google.common.collect.Range; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.PatientService; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.DataFilterValue; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.DataFilterValue; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/CustomDataFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/CustomDataFilterApplier.java similarity index 94% rename from src/main/java/org/cbioportal/web/util/CustomDataFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/CustomDataFilterApplier.java index ed37c9a13a4..28be6574666 100644 --- a/src/main/java/org/cbioportal/web/util/CustomDataFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/CustomDataFilterApplier.java @@ -1,10 +1,10 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.service.CustomDataService; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.service.CustomDataService; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/CustomDatatype.java b/src/main/java/org/cbioportal/legacy/web/util/CustomDatatype.java similarity index 76% rename from src/main/java/org/cbioportal/web/util/CustomDatatype.java rename to src/main/java/org/cbioportal/legacy/web/util/CustomDatatype.java index 9aaac0ebd15..0e59d8c9bbc 100644 --- a/src/main/java/org/cbioportal/web/util/CustomDatatype.java +++ b/src/main/java/org/cbioportal/legacy/web/util/CustomDatatype.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; public enum CustomDatatype { /** diff --git a/src/main/java/org/cbioportal/web/util/DataBinHelper.java b/src/main/java/org/cbioportal/legacy/web/util/DataBinHelper.java similarity index 99% rename from src/main/java/org/cbioportal/web/util/DataBinHelper.java rename to src/main/java/org/cbioportal/legacy/web/util/DataBinHelper.java index 9138aef2572..d6a817afa70 100644 --- a/src/main/java/org/cbioportal/web/util/DataBinHelper.java +++ b/src/main/java/org/cbioportal/legacy/web/util/DataBinHelper.java @@ -1,6 +1,6 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; -import org.cbioportal.model.DataBin; +import org.cbioportal.legacy.model.DataBin; import com.google.common.collect.Range; import java.math.BigDecimal; import java.math.RoundingMode; diff --git a/src/main/java/org/cbioportal/web/util/DataBinner.java b/src/main/java/org/cbioportal/legacy/web/util/DataBinner.java similarity index 98% rename from src/main/java/org/cbioportal/web/util/DataBinner.java rename to src/main/java/org/cbioportal/legacy/web/util/DataBinner.java index 85e21f2e69c..d5340b47613 100644 --- a/src/main/java/org/cbioportal/web/util/DataBinner.java +++ b/src/main/java/org/cbioportal/legacy/web/util/DataBinner.java @@ -1,13 +1,13 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.google.common.collect.Range; import org.apache.commons.lang3.math.NumberUtils; -import org.cbioportal.model.Binnable; -import org.cbioportal.model.DataBin; -import org.cbioportal.web.parameter.BinsGeneratorConfig; -import org.cbioportal.web.parameter.ClinicalDataBinFilter; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.DataBinFilter; +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.DataBin; +import org.cbioportal.legacy.web.parameter.BinsGeneratorConfig; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.DataBinFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/DataFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/DataFilterApplier.java similarity index 60% rename from src/main/java/org/cbioportal/web/util/DataFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/DataFilterApplier.java index ad5d6521658..62caf776304 100644 --- a/src/main/java/org/cbioportal/web/util/DataFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/DataFilterApplier.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; -import org.cbioportal.web.parameter.DataFilter; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.DataFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/util/DensityPlotParameters.java b/src/main/java/org/cbioportal/legacy/web/util/DensityPlotParameters.java similarity index 98% rename from src/main/java/org/cbioportal/web/util/DensityPlotParameters.java rename to src/main/java/org/cbioportal/legacy/web/util/DensityPlotParameters.java index 47e65543680..fba7f8d0a6d 100644 --- a/src/main/java/org/cbioportal/web/util/DensityPlotParameters.java +++ b/src/main/java/org/cbioportal/legacy/web/util/DensityPlotParameters.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/util/DiscreteDataBinner.java b/src/main/java/org/cbioportal/legacy/web/util/DiscreteDataBinner.java similarity index 91% rename from src/main/java/org/cbioportal/web/util/DiscreteDataBinner.java rename to src/main/java/org/cbioportal/legacy/web/util/DiscreteDataBinner.java index d6eaf334f82..b7a2552740c 100644 --- a/src/main/java/org/cbioportal/web/util/DiscreteDataBinner.java +++ b/src/main/java/org/cbioportal/legacy/web/util/DiscreteDataBinner.java @@ -1,6 +1,6 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; -import org.cbioportal.model.DataBin; +import org.cbioportal.legacy.model.DataBin; import org.springframework.stereotype.Component; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/util/GoogleAnalyticsInterceptor.java b/src/main/java/org/cbioportal/legacy/web/util/GoogleAnalyticsInterceptor.java similarity index 99% rename from src/main/java/org/cbioportal/web/util/GoogleAnalyticsInterceptor.java rename to src/main/java/org/cbioportal/legacy/web/util/GoogleAnalyticsInterceptor.java index 540e8f2ab79..c40de9b87e3 100644 --- a/src/main/java/org/cbioportal/web/util/GoogleAnalyticsInterceptor.java +++ b/src/main/java/org/cbioportal/legacy/web/util/GoogleAnalyticsInterceptor.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.util.Arrays; import java.util.concurrent.CompletableFuture; diff --git a/src/main/java/org/cbioportal/web/util/GzippedInputStreamRequestWrapper.java b/src/main/java/org/cbioportal/legacy/web/util/GzippedInputStreamRequestWrapper.java similarity index 98% rename from src/main/java/org/cbioportal/web/util/GzippedInputStreamRequestWrapper.java rename to src/main/java/org/cbioportal/legacy/web/util/GzippedInputStreamRequestWrapper.java index 2d8b4bc9b90..5e0f3b74f20 100644 --- a/src/main/java/org/cbioportal/web/util/GzippedInputStreamRequestWrapper.java +++ b/src/main/java/org/cbioportal/legacy/web/util/GzippedInputStreamRequestWrapper.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import jakarta.servlet.ReadListener; import jakarta.servlet.ServletInputStream; diff --git a/src/main/java/org/cbioportal/web/util/HttpRequestUtils.java b/src/main/java/org/cbioportal/legacy/web/util/HttpRequestUtils.java similarity index 96% rename from src/main/java/org/cbioportal/web/util/HttpRequestUtils.java rename to src/main/java/org/cbioportal/legacy/web/util/HttpRequestUtils.java index 325a5cf35bf..f1e9318a448 100644 --- a/src/main/java/org/cbioportal/web/util/HttpRequestUtils.java +++ b/src/main/java/org/cbioportal/legacy/web/util/HttpRequestUtils.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.util.Enumeration; diff --git a/src/main/java/org/cbioportal/web/util/IdPopulator.java b/src/main/java/org/cbioportal/legacy/web/util/IdPopulator.java similarity index 89% rename from src/main/java/org/cbioportal/web/util/IdPopulator.java rename to src/main/java/org/cbioportal/legacy/web/util/IdPopulator.java index e7c02227bdf..d43f5a3286d 100644 --- a/src/main/java/org/cbioportal/web/util/IdPopulator.java +++ b/src/main/java/org/cbioportal/legacy/web/util/IdPopulator.java @@ -1,9 +1,9 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.util.ClinicalAttributeUtil; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java b/src/main/java/org/cbioportal/legacy/web/util/InvolvedCancerStudyExtractorInterceptor.java similarity index 96% rename from src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java rename to src/main/java/org/cbioportal/legacy/web/util/InvolvedCancerStudyExtractorInterceptor.java index e0ee3961f71..9cc19225fe2 100644 --- a/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java +++ b/src/main/java/org/cbioportal/legacy/web/util/InvolvedCancerStudyExtractorInterceptor.java @@ -30,43 +30,43 @@ * along with this program. If not, see . */ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.fasterxml.jackson.databind.ObjectMapper; import jakarta.servlet.http.HttpServletRequest; import jakarta.servlet.http.HttpServletResponse; import org.apache.commons.lang3.StringUtils; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.SampleList; -import org.cbioportal.persistence.cachemaputil.CacheMapUtil; -import org.cbioportal.web.parameter.ClinicalAttributeCountFilter; -import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; -import org.cbioportal.web.parameter.ClinicalDataCountFilter; -import org.cbioportal.web.parameter.ClinicalDataIdentifier; -import org.cbioportal.web.parameter.ClinicalDataMultiStudyFilter; -import org.cbioportal.web.parameter.ClinicalEventAttributeRequest; -import org.cbioportal.web.parameter.GenePanelDataMultipleStudyFilter; -import org.cbioportal.web.parameter.GenericAssayDataBinCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataMultipleStudyFilter; -import org.cbioportal.web.parameter.GenomicDataBinCountFilter; -import org.cbioportal.web.parameter.GenomicDataCountFilter; -import org.cbioportal.web.parameter.GroupFilter; -import org.cbioportal.web.parameter.MolecularDataMultipleStudyFilter; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupAndAlterationTypeFilter; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupFilter; -import org.cbioportal.web.parameter.MolecularProfileFilter; -import org.cbioportal.web.parameter.MutationMultipleStudyFilter; -import org.cbioportal.web.parameter.PatientFilter; -import org.cbioportal.web.parameter.PatientIdentifier; -import org.cbioportal.web.parameter.SampleFilter; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; -import org.cbioportal.web.parameter.StructuralVariantFilter; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.SurvivalRequest; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.persistence.cachemaputil.CacheMapUtil; +import org.cbioportal.legacy.web.parameter.ClinicalAttributeCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataIdentifier; +import org.cbioportal.legacy.web.parameter.ClinicalDataMultiStudyFilter; +import org.cbioportal.legacy.web.parameter.ClinicalEventAttributeRequest; +import org.cbioportal.legacy.web.parameter.GenePanelDataMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataCountFilter; +import org.cbioportal.legacy.web.parameter.GroupFilter; +import org.cbioportal.legacy.web.parameter.MolecularDataMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupAndAlterationTypeFilter; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupFilter; +import org.cbioportal.legacy.web.parameter.MolecularProfileFilter; +import org.cbioportal.legacy.web.parameter.MutationMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.PatientFilter; +import org.cbioportal.legacy.web.parameter.PatientIdentifier; +import org.cbioportal.legacy.web.parameter.SampleFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.web.parameter.StructuralVariantFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.SurvivalRequest; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/cbioportal/web/util/LinearDataBinner.java b/src/main/java/org/cbioportal/legacy/web/util/LinearDataBinner.java similarity index 98% rename from src/main/java/org/cbioportal/web/util/LinearDataBinner.java rename to src/main/java/org/cbioportal/legacy/web/util/LinearDataBinner.java index 34bea85d9e4..2af45cc9271 100644 --- a/src/main/java/org/cbioportal/web/util/LinearDataBinner.java +++ b/src/main/java/org/cbioportal/legacy/web/util/LinearDataBinner.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.google.common.collect.Range; -import org.cbioportal.model.DataBin; +import org.cbioportal.legacy.model.DataBin; import org.springframework.stereotype.Component; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/util/LogScaleDataBinner.java b/src/main/java/org/cbioportal/legacy/web/util/LogScaleDataBinner.java similarity index 97% rename from src/main/java/org/cbioportal/web/util/LogScaleDataBinner.java rename to src/main/java/org/cbioportal/legacy/web/util/LogScaleDataBinner.java index febeb34ebb8..8732533da92 100644 --- a/src/main/java/org/cbioportal/web/util/LogScaleDataBinner.java +++ b/src/main/java/org/cbioportal/legacy/web/util/LogScaleDataBinner.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.google.common.collect.Range; -import org.cbioportal.model.DataBin; +import org.cbioportal.legacy.model.DataBin; import org.springframework.stereotype.Component; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/util/RequestBodyGZipFilter.java b/src/main/java/org/cbioportal/legacy/web/util/RequestBodyGZipFilter.java similarity index 98% rename from src/main/java/org/cbioportal/web/util/RequestBodyGZipFilter.java rename to src/main/java/org/cbioportal/legacy/web/util/RequestBodyGZipFilter.java index 7c68698c38c..7812abc932d 100644 --- a/src/main/java/org/cbioportal/web/util/RequestBodyGZipFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/util/RequestBodyGZipFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import jakarta.servlet.*; import jakarta.servlet.http.HttpServletRequest; diff --git a/src/main/java/org/cbioportal/web/util/ResettableHttpServletRequestFilter.java b/src/main/java/org/cbioportal/legacy/web/util/ResettableHttpServletRequestFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/util/ResettableHttpServletRequestFilter.java rename to src/main/java/org/cbioportal/legacy/web/util/ResettableHttpServletRequestFilter.java index b34fe2eaaab..0b65f6e148b 100644 --- a/src/main/java/org/cbioportal/web/util/ResettableHttpServletRequestFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ResettableHttpServletRequestFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.io.IOException; diff --git a/src/main/java/org/cbioportal/web/util/ScientificSmallDataBinner.java b/src/main/java/org/cbioportal/legacy/web/util/ScientificSmallDataBinner.java similarity index 97% rename from src/main/java/org/cbioportal/web/util/ScientificSmallDataBinner.java rename to src/main/java/org/cbioportal/legacy/web/util/ScientificSmallDataBinner.java index f3766164ef8..854867db4d7 100644 --- a/src/main/java/org/cbioportal/web/util/ScientificSmallDataBinner.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ScientificSmallDataBinner.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.google.common.collect.Range; -import org.cbioportal.model.DataBin; +import org.cbioportal.legacy.model.DataBin; import org.springframework.stereotype.Component; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterApplier.java similarity index 95% rename from src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterApplier.java index 43980c99f90..05a64c9f755 100644 --- a/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterApplier.java @@ -1,63 +1,63 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.model.Binnable; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.DataBin; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneFilter; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.GenericAssayDataBin; -import org.cbioportal.model.GenomicDataBin; -import org.cbioportal.model.MolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfile.MolecularAlterationType; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationFilterOption; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.UniqueKeyBase; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.StructuralVariantService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.util.MolecularProfileUtil; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.DataBinCountFilter; -import org.cbioportal.web.parameter.DataBinFilter; -import org.cbioportal.web.parameter.DataBinMethod; -import org.cbioportal.web.parameter.DataFilter; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.DiscreteCopyNumberEventType; -import org.cbioportal.web.parameter.GeneIdType; -import org.cbioportal.web.parameter.GenericAssayDataBinCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataBinFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinCountFilter; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.MutationDataFilter; -import org.cbioportal.web.parameter.MutationOption; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.appliers.StudyViewSubFilterApplier; +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.DataBin; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneFilter; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.GenericAssayDataBin; +import org.cbioportal.legacy.model.GenomicDataBin; +import org.cbioportal.legacy.model.MolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfile.MolecularAlterationType; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationFilterOption; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.UniqueKeyBase; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.DiscreteCopyNumberService; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StructuralVariantService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.DataBinCountFilter; +import org.cbioportal.legacy.web.parameter.DataBinFilter; +import org.cbioportal.legacy.web.parameter.DataBinMethod; +import org.cbioportal.legacy.web.parameter.DataFilter; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.DiscreteCopyNumberEventType; +import org.cbioportal.legacy.web.parameter.GeneIdType; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.MutationDataFilter; +import org.cbioportal.legacy.web.parameter.MutationOption; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.appliers.StudyViewSubFilterApplier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.context.ApplicationContext; diff --git a/src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java b/src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterUtil.java similarity index 92% rename from src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java rename to src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterUtil.java index b44b8bd8a63..1895e081225 100644 --- a/src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java +++ b/src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterUtil.java @@ -1,20 +1,33 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.model.Binnable; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Patient; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariantSpecialValue; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.service.util.CustomDataValue; -import org.cbioportal.web.parameter.*; +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantSpecialValue; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.service.util.CustomDataValue; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.DataBinFilter; +import org.cbioportal.legacy.web.parameter.DataFilter; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.GeneIdType; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.MutationDataFilter; +import org.cbioportal.legacy.web.parameter.MutationOption; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/UniqueKeyExtractor.java b/src/main/java/org/cbioportal/legacy/web/util/UniqueKeyExtractor.java similarity index 91% rename from src/main/java/org/cbioportal/web/util/UniqueKeyExtractor.java rename to src/main/java/org/cbioportal/legacy/web/util/UniqueKeyExtractor.java index 90d99dfe0a0..6e5ffce4049 100644 --- a/src/main/java/org/cbioportal/web/util/UniqueKeyExtractor.java +++ b/src/main/java/org/cbioportal/legacy/web/util/UniqueKeyExtractor.java @@ -1,6 +1,6 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; -import org.cbioportal.utils.Encoder; +import org.cbioportal.legacy.utils.Encoder; import java.util.List; import java.util.Collection; diff --git a/src/main/java/org/cbioportal/web/util/appliers/AbstractPatientTreatmentFilter.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/AbstractPatientTreatmentFilter.java similarity index 81% rename from src/main/java/org/cbioportal/web/util/appliers/AbstractPatientTreatmentFilter.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/AbstractPatientTreatmentFilter.java index 30d507d297a..0b8389fd522 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/AbstractPatientTreatmentFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/AbstractPatientTreatmentFilter.java @@ -1,11 +1,11 @@ -package org.cbioportal.web.util.appliers; - -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.model.PatientTreatmentRow; -import org.cbioportal.service.TreatmentService; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedPatientTreatmentFilters; +package org.cbioportal.legacy.web.util.appliers; + +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.service.TreatmentService; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedPatientTreatmentFilters; import org.springframework.beans.factory.annotation.Autowired; import java.util.ArrayList; diff --git a/src/main/java/org/cbioportal/web/util/appliers/AbstractSampleTreatmentFilter.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/AbstractSampleTreatmentFilter.java similarity index 80% rename from src/main/java/org/cbioportal/web/util/appliers/AbstractSampleTreatmentFilter.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/AbstractSampleTreatmentFilter.java index c28dcefbcbd..e10673e7d50 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/AbstractSampleTreatmentFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/AbstractSampleTreatmentFilter.java @@ -1,11 +1,11 @@ -package org.cbioportal.web.util.appliers; - -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.service.TreatmentService; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedSampleTreatmentFilters; +package org.cbioportal.legacy.web.util.appliers; + +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.service.TreatmentService; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedSampleTreatmentFilters; import org.springframework.beans.factory.annotation.Autowired; import java.util.ArrayList; diff --git a/src/main/java/org/cbioportal/web/util/appliers/ClinicalEventFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/ClinicalEventFilterApplier.java similarity index 89% rename from src/main/java/org/cbioportal/web/util/appliers/ClinicalEventFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/ClinicalEventFilterApplier.java index adf70d4a782..65a93432d53 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/ClinicalEventFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/ClinicalEventFilterApplier.java @@ -1,10 +1,10 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.web.parameter.DataFilter; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.web.parameter.DataFilter; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.lang.NonNull; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentFilterApplier.java similarity index 62% rename from src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentFilterApplier.java index c97c313ec8b..b2377277368 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentFilterApplier.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedPatientTreatmentFilters; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedPatientTreatmentFilters; import org.springframework.stereotype.Component; @Component diff --git a/src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentGroupFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentGroupFilterApplier.java similarity index 63% rename from src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentGroupFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentGroupFilterApplier.java index 6110d4aa8e3..d63a68a65f7 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentGroupFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentGroupFilterApplier.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedPatientTreatmentFilters; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedPatientTreatmentFilters; import org.springframework.stereotype.Component; @Component diff --git a/src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentTargetFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentTargetFilterApplier.java similarity index 63% rename from src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentTargetFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentTargetFilterApplier.java index 87c69ea8fbc..494bbd651d2 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentTargetFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentTargetFilterApplier.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedPatientTreatmentFilters; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedPatientTreatmentFilters; import org.springframework.stereotype.Component; @Component diff --git a/src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentFilterApplier.java similarity index 62% rename from src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentFilterApplier.java index 83e6bd7301a..ed42f31a8a2 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentFilterApplier.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedSampleTreatmentFilters; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedSampleTreatmentFilters; import org.springframework.stereotype.Component; @Component diff --git a/src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentGroupFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentGroupFilterApplier.java similarity index 63% rename from src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentGroupFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentGroupFilterApplier.java index 9f0e3aa0b31..a2ed8cf5cbd 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentGroupFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentGroupFilterApplier.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedSampleTreatmentFilters; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedSampleTreatmentFilters; import org.springframework.stereotype.Component; @Component diff --git a/src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentTargetFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentTargetFilterApplier.java similarity index 63% rename from src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentTargetFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentTargetFilterApplier.java index d7d6c37b449..6fbf49a044d 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentTargetFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentTargetFilterApplier.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedSampleTreatmentFilters; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedSampleTreatmentFilters; import org.springframework.stereotype.Component; @Component diff --git a/src/main/java/org/cbioportal/web/util/appliers/StructuralVariantSubFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/StructuralVariantSubFilterApplier.java similarity index 89% rename from src/main/java/org/cbioportal/web/util/appliers/StructuralVariantSubFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/StructuralVariantSubFilterApplier.java index 9367c54884b..716c4205b3b 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/StructuralVariantSubFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/StructuralVariantSubFilterApplier.java @@ -1,13 +1,13 @@ -package org.cbioportal.web.util.appliers; - -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StudyViewStructuralVariantFilter; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.StructuralVariantService; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.StudyViewFilterUtil; +package org.cbioportal.legacy.web.util.appliers; + +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StudyViewStructuralVariantFilter; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.StructuralVariantService; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/appliers/StudyViewSubFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/StudyViewSubFilterApplier.java similarity index 57% rename from src/main/java/org/cbioportal/web/util/appliers/StudyViewSubFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/StudyViewSubFilterApplier.java index 8ba7dc037ef..358df77207b 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/StudyViewSubFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/StudyViewSubFilterApplier.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/util/appliers/TreatmentRowExtractor.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/TreatmentRowExtractor.java similarity index 69% rename from src/main/java/org/cbioportal/web/util/appliers/TreatmentRowExtractor.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/TreatmentRowExtractor.java index f260304356a..82d816dcf80 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/TreatmentRowExtractor.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/TreatmentRowExtractor.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.model.ClinicalEventSample; -import org.cbioportal.model.TreatmentRow; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.TreatmentRow; import org.springframework.stereotype.Service; import java.util.Set; diff --git a/src/main/java/org/cbioportal/service/ServerStatusService.java b/src/main/java/org/cbioportal/service/ServerStatusService.java deleted file mode 100644 index ac77b693c08..00000000000 --- a/src/main/java/org/cbioportal/service/ServerStatusService.java +++ /dev/null @@ -1,7 +0,0 @@ -package org.cbioportal.service; - -import org.cbioportal.service.impl.ServerStatusServiceImpl.ServerStatusMessage; - -public interface ServerStatusService { - ServerStatusMessage getServerStatus(); -} diff --git a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java b/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java deleted file mode 100644 index 66305eb5fe8..00000000000 --- a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java +++ /dev/null @@ -1,14 +0,0 @@ -package org.cbioportal.service.treatment; - -import org.cbioportal.model.PatientTreatmentReport; -import org.cbioportal.model.SampleTreatmentReport; -import org.cbioportal.model.StudyViewFilterContext; -import org.cbioportal.web.parameter.CustomSampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; - -import java.util.List; - -public interface TreatmentCountReportService { - PatientTreatmentReport getPatientTreatmentReport(StudyViewFilterContext studyViewFilterContext); - SampleTreatmentReport getSampleTreatmentReport(StudyViewFilterContext studyViewFilterContext); -} diff --git a/src/main/java/org/cbioportal/shared/SortAndSearchCriteria.java b/src/main/java/org/cbioportal/shared/SortAndSearchCriteria.java new file mode 100644 index 00000000000..49c4aa6ae43 --- /dev/null +++ b/src/main/java/org/cbioportal/shared/SortAndSearchCriteria.java @@ -0,0 +1,12 @@ +package org.cbioportal.shared; + +public record SortAndSearchCriteria(String searchTerm, String sortField, String sortOrder) { + boolean isSortable() { + return (sortField != null && !sortField.isEmpty()) + && (sortOrder != null && !sortOrder.isEmpty()); + } + + boolean isSearchable() { + return searchTerm != null && !searchTerm.isEmpty(); + } +} diff --git a/src/main/java/org/cbioportal/shared/enums/ProjectionType.java b/src/main/java/org/cbioportal/shared/enums/ProjectionType.java new file mode 100644 index 00000000000..21f12e0d7ba --- /dev/null +++ b/src/main/java/org/cbioportal/shared/enums/ProjectionType.java @@ -0,0 +1,88 @@ +package org.cbioportal.shared.enums; +/** + * Enum representing different levels of data projection for API responses. + *

+ * This enum is used in the domain layer to control the amount of data + * included in API responses, ensuring that only the necessary fields are + * returned based on the specific use case. By limiting the data returned, + * this enum helps improve performance, reduce network overhead, and simplify + * client-side processing. + *

+ *

+ * Each projection level corresponds to a specific set of fields or data + * representation, allowing the domain layer to tailor responses to the + * requirements of the client or the context of the request. + *

+ *

+ * Usage Example: + * 

+ * {@code
+ * public ResponseEntity getEntity(@RequestParam Projection projection) {
+ *     Entity entity = entityService.getEntity(projection);
+ *     EntityDto dto = entityMapper.toDto(entity, projection);
+ *     return ResponseEntity.ok(dto);
+ * }
+ * }
+ *
+ *

+ */ +public enum ProjectionType { + + /** + * ID Projection - Includes only the essential identifier fields of the entity. + *

+ * This projection is suitable for scenarios where only the unique identifier + * of the entity is required, such as when referencing the entity in another + * context or performing lightweight operations. + *

+ *

+ * Example Use Case: Fetching entity IDs for batch processing or + * creating relationships between entities. + *

+ */ + ID, + + /** + * SUMMARY Projection - Includes a limited set of fields to provide + * a high-level overview of the entity. + *

+ * This projection is useful for lightweight data representations, such as + * displaying a list of entities in a UI or providing a quick summary without + * the full details. + *

+ *

+ * Example Use Case: Displaying a list of entities in a dropdown or + * search results. + *

+ */ + SUMMARY, + + /** + * DETAILED Projection - Includes all available fields of the entity. + *

+ * This projection provides a complete representation of the entity, including + * all attributes and relationships. It is best suited for scenarios where + * the client requires a full view of the entity. + *

+ *

+ * Example Use Case: Viewing the full details of an entity in a + * detailed view or edit form. + *

+ */ + DETAILED, + + /** + * META Projection - Focuses on metadata, such as counts, statistics, + * or aggregated information about the underlying data. + *

+ * This projection is useful for scenarios where the client needs summary + * information rather than individual records, such as displaying totals, + * averages, or other aggregated data. + *

+ *

+ * Example Use Case: Displaying dashboard metrics or summary reports. + *

+ */ + META +} + diff --git a/src/main/java/org/cbioportal/utils/security/AccessLevel.java b/src/main/java/org/cbioportal/utils/security/AccessLevel.java deleted file mode 100644 index bdd3c9024f0..00000000000 --- a/src/main/java/org/cbioportal/utils/security/AccessLevel.java +++ /dev/null @@ -1,5 +0,0 @@ -package org.cbioportal.utils.security; - -public enum AccessLevel { - READ, LIST -} diff --git a/src/main/java/org/cbioportal/web/mixin/GeneMixin.java b/src/main/java/org/cbioportal/web/mixin/GeneMixin.java deleted file mode 100644 index fb4445cfcb2..00000000000 --- a/src/main/java/org/cbioportal/web/mixin/GeneMixin.java +++ /dev/null @@ -1,5 +0,0 @@ -package org.cbioportal.web.mixin; - -public class GeneMixin { - -} diff --git a/src/main/resources/mappers/clickhouse/cancerstudy/CancerStudyMapper.xml b/src/main/resources/mappers/clickhouse/cancerstudy/CancerStudyMapper.xml new file mode 100644 index 00000000000..fbdc8b4c720 --- /dev/null +++ b/src/main/resources/mappers/clickhouse/cancerstudy/CancerStudyMapper.xml @@ -0,0 +1,199 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/AlterationCountsMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/AlterationCountsMapper.xml similarity index 98% rename from src/main/resources/org/cbioportal/persistence/mybatis/AlterationCountsMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/AlterationCountsMapper.xml index f9e53a35b08..c2bc086ada4 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/AlterationCountsMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/AlterationCountsMapper.xml @@ -1,9 +1,9 @@ - + - SELECT ENTREZ_GENE_ID AS "entrezGeneId", HUGO_GENE_SYMBOL AS "hugoGeneSymbol", @@ -37,7 +37,7 @@ GROUP BY ENTREZ_GENE_ID, HUGO_GENE_SYMBOL; - SELECT ENTREZ_GENE_ID AS entrezGeneId, HUGO_GENE_SYMBOL AS hugoGeneSymbol, @@ -71,7 +71,7 @@ GROUP BY ENTREZ_GENE_ID, HUGO_GENE_SYMBOL; - SELECT cna_event.ENTREZ_GENE_ID AS entrezGeneId, gene.HUGO_GENE_SYMBOL AS hugoGeneSymbol, @@ -111,7 +111,7 @@ GROUP BY cna_event.ENTREZ_GENE_ID, cna_event.ALTERATION, reference_genome_gene.CYTOBAND, gene.HUGO_GENE_SYMBOL - SELECT cna_event.ENTREZ_GENE_ID AS entrezGeneId, gene.HUGO_GENE_SYMBOL AS hugoGeneSymbol, @@ -148,7 +148,7 @@ GROUP BY cna_event.ENTREZ_GENE_ID, cna_event.ALTERATION, gene.HUGO_GENE_SYMBOL - SELECT gene1.ENTREZ_GENE_ID AS gene1EntrezGeneId, gene1.HUGO_GENE_SYMBOL AS gene1HugoGeneSymbol, @@ -176,7 +176,7 @@ GROUP BY gene1.ENTREZ_GENE_ID, gene2.ENTREZ_GENE_ID - SELECT gene1.ENTREZ_GENE_ID AS gene1EntrezGeneId, gene1.HUGO_GENE_SYMBOL AS gene1HugoGeneSymbol, @@ -579,7 +579,7 @@ caseUniqueId - SELECT genetic_profile.GENETIC_PROFILE_ID AS molecularProfileId, diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMapper.xml similarity index 90% rename from src/main/resources/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMapper.xml index 6d133f365d7..85e9d73a9e6 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMapper.xml @@ -1,9 +1,9 @@ - + - SELECT alteration_driver_annotation.ALTERATION_EVENT_ID as alterationEventId, alteration_driver_annotation.GENETIC_PROFILE_ID as geneticProfileId, diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/CancerTypeMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/CancerTypeMapper.xml similarity index 80% rename from src/main/resources/org/cbioportal/persistence/mybatis/CancerTypeMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/CancerTypeMapper.xml index 138ae3932bc..f1a93ec450a 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/CancerTypeMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/CancerTypeMapper.xml @@ -1,7 +1,7 @@ - + type_of_cancer.TYPE_OF_CANCER_ID AS "${prefix}typeOfCancerId" @@ -14,7 +14,7 @@ - SELECT @@ -31,13 +31,13 @@ - SELECT COUNT(*) AS "totalCount" FROM type_of_cancer - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMapper.xml similarity index 95% rename from src/main/resources/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMapper.xml index 8dbdbc9a942..a552a83ffa2 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMapper.xml @@ -1,7 +1,7 @@ - + clinical_attribute_meta.ATTR_ID AS "${prefix}attrId", @@ -64,7 +64,7 @@ - SELECT @@ -90,7 +90,7 @@ - SELECT COUNT(*) AS "totalCount" FROM clinical_attribute_meta @@ -105,7 +105,7 @@ - SELECT @@ -116,7 +116,7 @@ AND cancer_study.CANCER_STUDY_IDENTIFIER = #{studyId} - SELECT count(*) as "count", clinical_sample.ATTR_ID as "attrId" FROM clinical_sample @@ -134,7 +134,7 @@ GROUP BY clinical_patient.ATTR_ID - SELECT count(*) as "count", clinical_sample.ATTR_ID as "attrId" FROM clinical_sample @@ -152,7 +152,7 @@ GROUP BY clinical_patient.ATTR_ID - SELECT clinical_attribute_meta.ATTR_ID AS "attrId", cancer_study.CANCER_STUDY_IDENTIFIER AS "cancerStudyIdentifier", diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalDataMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMapper.xml similarity index 96% rename from src/main/resources/org/cbioportal/persistence/mybatis/ClinicalDataMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMapper.xml index bfe06321aff..129fdce9494 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalDataMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMapper.xml @@ -1,7 +1,7 @@ - + clinical_sample.INTERNAL_ID AS "${prefix}internalId", @@ -15,7 +15,7 @@ , - + @@ -33,7 +33,7 @@ , - + @@ -115,7 +115,7 @@ - SELECT sample.INTERNAL_ID internalId, sample.STABLE_ID sampleId, patient.STABLE_ID patientId, cancer_study.CANCER_STUDY_IDENTIFIER studyId, clinical_patient.ATTR_ID attrId, clinical_patient.ATTR_VALUE attrValue FROM clinical_patient @@ -128,7 +128,7 @@ - SELECT sample.INTERNAL_ID internalId, sample.STABLE_ID sampleId, patient.STABLE_ID patientId, cancer_study.CANCER_STUDY_IDENTIFIER studyId, clinical_sample.ATTR_ID attrId, clinical_sample.ATTR_VALUE attrValue FROM clinical_sample @@ -141,7 +141,7 @@ - SELECT @@ -164,14 +164,14 @@ - SELECT COUNT(*) AS "totalCount" - SELECT @@ -194,7 +194,7 @@ - SELECT @@ -219,14 +219,14 @@ - SELECT COUNT(*) AS "totalCount" - SELECT count(*) as count, clinical_sample.ATTR_ID as attributeId, clinical_sample.ATTR_VALUE as value @@ -235,7 +235,7 @@ GROUP BY clinical_sample.ATTR_ID, clinical_sample.ATTR_VALUE - SELECT count(*) as count, clinical_patient.ATTR_ID as attributeId, clinical_patient.ATTR_VALUE as value diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMapper.xml similarity index 96% rename from src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMapper.xml index 48e446aeccb..badc8b79702 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMapper.xml @@ -1,7 +1,7 @@ - + clinical_event.CLINICAL_EVENT_ID AS "clinicalEventId", @@ -34,7 +34,7 @@ - SELECT @@ -50,14 +50,14 @@ - SELECT COUNT(*) AS totalCount - SELECT clinical_event_data.CLINICAL_EVENT_ID AS clinicalEventId, clinical_event_data.KEY AS "key", @@ -73,7 +73,7 @@ - SELECT @@ -89,14 +89,14 @@ - SELECT COUNT(*) AS totalCount - SELECT clinical_event.CLINICAL_EVENT_ID as clinicalEventId, clinical_event.EVENT_TYPE as eventType, @@ -140,7 +140,7 @@ - SELECT @@ -184,7 +184,7 @@ Group by clinical_event.EVENT_TYPE, patient.INTERNAL_ID - SELECT patient.STABLE_ID AS patientId, cancer_study.CANCER_STUDY_IDENTIFIER AS studyId, @@ -240,9 +240,9 @@ clinical_event.PATIENT_ID, cancer_study.CANCER_STUDY_IDENTIFIER; - + - + diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMapper.xml similarity index 94% rename from src/main/resources/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMapper.xml index 58e2a37da07..0d3503c6fd5 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMapper.xml @@ -1,7 +1,7 @@ - + copy_number_seg.SEG_ID AS "segId", @@ -50,7 +50,7 @@ - SELECT @@ -69,7 +69,7 @@ - SELECT COUNT(*) AS totalCount @@ -79,7 +79,7 @@ - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/CosmicCountMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/CosmicCountMapper.xml similarity index 87% rename from src/main/resources/org/cbioportal/persistence/mybatis/CosmicCountMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/CosmicCountMapper.xml index df0fe7e0fe3..5541cb31f7b 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/CosmicCountMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/CosmicCountMapper.xml @@ -1,9 +1,9 @@ - + - SELECT cosmic_mutation.COSMIC_MUTATION_ID AS "cosmicMutationId", cosmic_mutation.PROTEIN_CHANGE AS "proteinChange", diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/DataAccessTokenMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMapper.xml similarity index 85% rename from src/main/resources/org/cbioportal/persistence/mybatis/DataAccessTokenMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMapper.xml index f6aea8ca139..9aa8776df70 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/DataAccessTokenMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMapper.xml @@ -1,7 +1,7 @@ - + data_access_tokens.TOKEN AS "${prefix}token", @@ -10,7 +10,7 @@ data_access_tokens.CREATION AS "${prefix}creation" - SELECT @@ -20,7 +20,7 @@ ORDER BY data_access_tokens.EXPIRATION ASC - SELECT @@ -41,7 +41,7 @@ WHERE USERNAME = #{username} - + INSERT INTO data_access_tokens(TOKEN, USERNAME, EXPIRATION, CREATION) VALUES (#{token}, #{username}, #{expiration}, #{creation}) diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMapper.xml similarity index 95% rename from src/main/resources/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMapper.xml index 3060a8a389e..338347d24ef 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMapper.xml @@ -1,7 +1,7 @@ - + cna_event.ENTREZ_GENE_ID as entrezGeneId, @@ -17,7 +17,7 @@ alteration_driver_annotation.DRIVER_TIERS_FILTER_ANNOTATION AS "driverTiersFilterAnnotation" , - + @@ -193,7 +193,7 @@ - SELECT @@ -203,14 +203,14 @@ - SELECT COUNT(*) AS "totalCount" - SELECT @@ -220,7 +220,7 @@ - SELECT @@ -230,7 +230,7 @@ - SELECT @@ -240,14 +240,14 @@ - SELECT COUNT(*) AS "totalCount" - SELECT cna_event.ENTREZ_GENE_ID AS "entrezGeneId", gene.HUGO_GENE_SYMBOL AS "hugoGeneSymbol", diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/GeneMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/GeneMapper.xml similarity index 91% rename from src/main/resources/org/cbioportal/persistence/mybatis/GeneMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/GeneMapper.xml index eb9bbf1f24a..eab4878cfb3 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/GeneMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/GeneMapper.xml @@ -1,7 +1,7 @@ - + gene.ENTREZ_GENE_ID AS "${prefix}entrezGeneId", @@ -32,7 +32,7 @@ - SELECT @@ -53,14 +53,14 @@ - SELECT COUNT(*) AS "totalCount" - SELECT @@ -69,7 +69,7 @@ WHERE gene.GENETIC_ENTITY_ID = #{geneticEntityId} - SELECT @@ -78,7 +78,7 @@ WHERE gene.ENTREZ_GENE_ID = #{entrezGeneId} - SELECT @@ -100,14 +100,14 @@ WHERE gene.HUGO_GENE_SYMBOL = #{hugoGeneSymbol} - SELECT gene_alias.ENTREZ_GENE_ID AS "entrezGeneId", LOWER(gene_alias.GENE_ALIAS) AS "geneAlias" FROM gene_alias - SELECT @@ -126,7 +126,7 @@ - SELECT COUNT(*) AS "totalCount" FROM gene @@ -143,7 +143,7 @@ - SELECT @@ -162,7 +162,7 @@ - SELECT COUNT(*) AS totalCount FROM gene diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/GenePanelMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/GenePanelMapper.xml similarity index 90% rename from src/main/resources/org/cbioportal/persistence/mybatis/GenePanelMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/GenePanelMapper.xml index 96a1d434c15..289f4df0127 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/GenePanelMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/GenePanelMapper.xml @@ -1,7 +1,7 @@ - + gene_panel.INTERNAL_ID AS "internalId", @@ -30,7 +30,7 @@ LEFT JOIN gene_panel ON sample_profile.PANEL_ID = gene_panel.INTERNAL_ID - SELECT FROM gene_panel @@ -45,20 +45,20 @@ - SELECT COUNT(*) AS totalCount FROM gene_panel - SELECT FROM gene_panel WHERE gene_panel.STABLE_ID = #{genePanelId} - SELECT FROM gene_panel @@ -72,7 +72,7 @@ - SELECT gene_panel.STABLE_ID AS genePanelId, gene_panel_list.GENE_ID AS entrezGeneId, @@ -91,7 +91,7 @@ ORDER BY hugoGeneSymbol ASC - SELECT @@ -102,7 +102,7 @@ AND sample_list_query.STABLE_ID = #{sampleListId} - SELECT @@ -116,7 +116,7 @@ - SELECT @@ -127,7 +127,7 @@ - SELECT @@ -157,7 +157,7 @@ - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/GenericAssayMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/GenericAssayMapper.xml similarity index 93% rename from src/main/resources/org/cbioportal/persistence/mybatis/GenericAssayMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/GenericAssayMapper.xml index 5b767fb93b3..461d855ef02 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/GenericAssayMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/GenericAssayMapper.xml @@ -1,10 +1,10 @@ - + - SELECT genetic_entity.STABLE_ID as stableId, genetic_entity.ENTITY_TYPE as entityType FROM genetic_entity @@ -16,7 +16,7 @@ - SELECT generic_entity_properties.NAME as name, generic_entity_properties.VALUE as value, genetic_entity.STABLE_ID as stableId diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/GenesetHierarchyMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMapper.xml similarity index 87% rename from src/main/resources/org/cbioportal/persistence/mybatis/GenesetHierarchyMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMapper.xml index 6ed4252ada4..f8e105e4e64 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/GenesetHierarchyMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMapper.xml @@ -1,7 +1,7 @@ - + a.NODE_ID AS nodeId, @@ -10,7 +10,7 @@ b.NODE_NAME AS parentNodeName - SELECT FROM geneset_hierarchy_node as a left join geneset_hierarchy_node as b ON a.PARENT_ID = b.NODE_ID @@ -27,7 +27,7 @@ ORDER BY b.NODE_NAME, a.NODE_NAME - SELECT FROM geneset_hierarchy_node as a LEFT join geneset_hierarchy_node as b ON a.PARENT_ID = b.NODE_ID @@ -44,9 +44,9 @@ ORDER BY b.NODE_NAME, a.NODE_NAME - SELECT - + FROM geneset diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/GenesetMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/GenesetMapper.xml similarity index 82% rename from src/main/resources/org/cbioportal/persistence/mybatis/GenesetMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/GenesetMapper.xml index 8c1fe553431..5a6674a2be4 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/GenesetMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/GenesetMapper.xml @@ -1,7 +1,7 @@ - + geneset.ID AS "${prefix}internalId", @@ -11,7 +11,7 @@ geneset.REF_LINK as "${prefix}refLink" - SELECT @@ -28,13 +28,13 @@ - SELECT COUNT(*) AS totalCount FROM geneset - SELECT @@ -43,7 +43,7 @@ WHERE geneset.EXTERNAL_ID = #{genesetId} - SELECT @@ -56,9 +56,9 @@ ORDER BY geneset.EXTERNAL_ID ASC - SELECT - + FROM gene diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/MolecularDataMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/MolecularDataMapper.xml similarity index 91% rename from src/main/resources/org/cbioportal/persistence/mybatis/MolecularDataMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/MolecularDataMapper.xml index 45a1e222e63..e6f22dcdf63 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/MolecularDataMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/MolecularDataMapper.xml @@ -1,7 +1,7 @@ - + @@ -20,7 +20,7 @@ - SELECT genetic_profile.STABLE_ID AS "molecularProfileId", genetic_profile_samples.ORDERED_SAMPLE_LIST AS "commaSeparatedSampleIds" @@ -37,13 +37,13 @@ - SELECT gene.ENTREZ_GENE_ID AS "entrezGeneId", genetic_alteration.`VALUES` AS "values" , - + @@ -67,13 +67,13 @@ (Attempts where made to share getGeneMolecularAlterations between methods in MolecularDataMapper.java all of which have failed). --> - SELECT gene.ENTREZ_GENE_ID AS "entrezGeneId", genetic_alteration.`VALUES` AS "values" , - + @@ -92,7 +92,7 @@ - SELECT gene.ENTREZ_GENE_ID AS "entrezGeneId", genetic_alteration.`VALUES` AS "values" @@ -104,14 +104,14 @@ - SELECT gene.ENTREZ_GENE_ID AS "entrezGeneId", genetic_alteration.`VALUES` AS "values", genetic_profile.STABLE_ID AS "molecularProfileId" , - + @@ -121,7 +121,7 @@ - SELECT geneset.EXTERNAL_ID AS genesetId, @@ -145,7 +145,7 @@ - SELECT genetic_entity.STABLE_ID AS genericAssayStableId, genetic_profile.STABLE_ID AS molecularProfileId, @@ -175,7 +175,7 @@ (Attempts where made to share getGenericAssayMolecularAlterations between methods in MolecularDataMapper.java all of which have failed). --> - SELECT genetic_entity.STABLE_ID AS genericAssayStableId, genetic_profile.STABLE_ID AS molecularProfileId, diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/MolecularProfileMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMapper.xml similarity index 93% rename from src/main/resources/org/cbioportal/persistence/mybatis/MolecularProfileMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMapper.xml index b51a2f9b5ab..bf59ea76beb 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/MolecularProfileMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMapper.xml @@ -1,7 +1,7 @@ - + genetic_profile.GENETIC_PROFILE_ID AS "${prefix}molecularProfileId", @@ -22,13 +22,13 @@ , - + - SELECT @@ -58,7 +58,7 @@ - SELECT COUNT(*) AS totalCount FROM genetic_profile @@ -72,7 +72,7 @@ - SELECT @@ -83,7 +83,7 @@ WHERE genetic_profile.STABLE_ID = #{molecularProfileId} - SELECT @@ -101,7 +101,7 @@ - SELECT COUNT(*) AS totalCount FROM genetic_profile @@ -115,7 +115,7 @@ - SELECT @@ -133,7 +133,7 @@ ) - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/MutationMapper.xml similarity index 96% rename from src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/MutationMapper.xml index de6a18dc104..eb82f54b0e0 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/MutationMapper.xml @@ -1,7 +1,7 @@ - + genetic_profile.STABLE_ID AS "molecularProfileId", @@ -40,7 +40,7 @@ , - + , @@ -275,13 +275,13 @@ AND mutation.SAMPLE_ID = allele_specific_copy_number.SAMPLE_ID - + - + - + @@ -289,7 +289,7 @@ - SELECT @@ -310,7 +310,7 @@ - SELECT COUNT(*) AS "totalCount", COUNT(DISTINCT(mutation.SAMPLE_ID)) AS "sampleCount" @@ -319,7 +319,7 @@ - SELECT @@ -332,7 +332,7 @@ - SELECT @@ -345,7 +345,7 @@ - SELECT COUNT(*) AS "totalCount", COUNT(DISTINCT(mutation.SAMPLE_ID)) AS "sampleCount" @@ -354,7 +354,7 @@ - SELECT COUNT(*) AS "totalCount", COUNT(DISTINCT(mutation.SAMPLE_ID)) AS "sampleCount" @@ -363,7 +363,7 @@ - SELECT mutation.ENTREZ_GENE_ID AS "entrezGeneId", gene.HUGO_GENE_SYMBOL AS "hugoGeneSymbol", @@ -378,7 +378,7 @@ GROUP BY mutation.ENTREZ_GENE_ID - SELECT #{entrezGeneId} AS "entrezGeneId", #{proteinPosStart} AS "proteinPosStart", diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/PatientMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/PatientMapper.xml similarity index 91% rename from src/main/resources/org/cbioportal/persistence/mybatis/PatientMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/PatientMapper.xml index 3b396bdfa6a..009a363d46f 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/PatientMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/PatientMapper.xml @@ -1,7 +1,7 @@ - + patient.INTERNAL_ID AS "${prefix}internalId", @@ -10,7 +10,7 @@ cancer_study.CANCER_STUDY_IDENTIFIER AS "${prefix}cancerStudyIdentifier" , - + @@ -45,7 +45,7 @@ - SELECT @@ -69,7 +69,7 @@ - SELECT COUNT(*) AS totalCount @@ -79,7 +79,7 @@ - SELECT @@ -89,7 +89,7 @@ AND cancer_study.CANCER_STUDY_IDENTIFIER = #{studyId} - SELECT DISTINCT(patient.STABLE_ID) AS stableId, cancer_study.CANCER_STUDY_IDENTIFIER AS cancerStudyIdentifier FROM sample diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMapper.xml similarity index 93% rename from src/main/resources/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMapper.xml index 0888d5d06be..0e2cbc981bd 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMapper.xml @@ -1,7 +1,7 @@ - + @@ -18,7 +18,7 @@ - SELECT @@ -31,7 +31,7 @@ - SELECT @@ -53,7 +53,7 @@ - SELECT @@ -75,7 +75,7 @@ - SELECT @@ -89,7 +89,7 @@ - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/ResourceDataMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/ResourceDataMapper.xml similarity index 92% rename from src/main/resources/org/cbioportal/persistence/mybatis/ResourceDataMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/ResourceDataMapper.xml index 051634e0e86..cfba5e33523 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/ResourceDataMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/ResourceDataMapper.xml @@ -1,7 +1,7 @@ - + sample.STABLE_ID AS "${prefix}sampleId", @@ -13,7 +13,7 @@ , - + @@ -28,7 +28,7 @@ , - + @@ -42,7 +42,7 @@ , - + @@ -105,7 +105,7 @@ - SELECT @@ -127,7 +127,7 @@ - SELECT @@ -149,7 +149,7 @@ - SELECT @@ -171,7 +171,7 @@ - SELECT @@ -188,7 +188,7 @@ - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/ResourceDefinitionMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMapper.xml similarity index 94% rename from src/main/resources/org/cbioportal/persistence/mybatis/ResourceDefinitionMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMapper.xml index a10818544ec..3910f6ce29c 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/ResourceDefinitionMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMapper.xml @@ -1,7 +1,7 @@ - + resource_definition.RESOURCE_ID AS "${prefix}resourceId", @@ -17,7 +17,7 @@ - SELECT @@ -48,7 +48,7 @@ - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/SampleListMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml similarity index 88% rename from src/main/resources/org/cbioportal/persistence/mybatis/SampleListMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml index ffb47f850f5..3cbce6bf85c 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/SampleListMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml @@ -1,7 +1,7 @@ - + sample_list.LIST_ID AS "${prefix}listId", @@ -16,13 +16,13 @@ , - + - SELECT @@ -53,7 +53,7 @@ - SELECT COUNT(*) AS totalCount FROM sample_list @@ -63,7 +63,7 @@ - SELECT @@ -74,7 +74,7 @@ WHERE sample_list.STABLE_ID = #{sampleListId} - SELECT @@ -101,7 +101,7 @@ WHERE sample_list.STABLE_ID = #{sampleListId} - SELECT sample_list_list.LIST_ID as sampleListId, sample.STABLE_ID as sampleId diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/SampleMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleMapper.xml similarity index 92% rename from src/main/resources/org/cbioportal/persistence/mybatis/SampleMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleMapper.xml index 21f4e86da37..291946fe0ed 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/SampleMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleMapper.xml @@ -1,7 +1,7 @@ - + sample.INTERNAL_ID AS "${prefix}internalId", @@ -15,7 +15,7 @@ , - + @@ -68,7 +68,7 @@ - SELECT @@ -89,7 +89,7 @@ - SELECT @@ -107,14 +107,14 @@ ) - SELECT COUNT(*) AS "totalCount" - SELECT COUNT(*) AS "totalCount" @@ -130,7 +130,7 @@ ) - SELECT @@ -140,7 +140,7 @@ AND cancer_study.CANCER_STUDY_IDENTIFIER = #{studyId} - SELECT @@ -149,7 +149,7 @@ WHERE sample.INTERNAL_ID = #{internalId} - SELECT @@ -165,7 +165,7 @@ - SELECT @@ -181,7 +181,7 @@ - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/SecurityMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SecurityMapper.xml similarity index 88% rename from src/main/resources/org/cbioportal/persistence/mybatis/SecurityMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/SecurityMapper.xml index 77eb4a73004..8c2c7694833 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/SecurityMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SecurityMapper.xml @@ -1,18 +1,18 @@ - + - + - SELECT LOWER(email) AS email, name, diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMapper.xml similarity index 88% rename from src/main/resources/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMapper.xml index eeea7c87f8c..c4cbfb34809 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMapper.xml @@ -1,7 +1,7 @@ - + gistic.GISTIC_ROI_ID AS "gisticRoiId", @@ -25,7 +25,7 @@ - SELECT @@ -41,14 +41,14 @@ - SELECT COUNT(*) AS totalCount - SELECT gistic_to_gene.GISTIC_ROI_ID AS gisticRoiId, gistic_to_gene.ENTREZ_GENE_ID AS entrezGeneId, diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMapper.xml similarity index 90% rename from src/main/resources/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMapper.xml index 51d26473570..a3b4a463011 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMapper.xml @@ -1,7 +1,7 @@ - + mut_sig.ENTREZ_GENE_ID AS "entrezGeneId", @@ -26,7 +26,7 @@ - SELECT @@ -43,7 +43,7 @@ - SELECT COUNT(*) AS totalCount diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/StaticDataTimestampMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/StaticDataTimestampMapper.xml similarity index 80% rename from src/main/resources/org/cbioportal/persistence/mybatis/StaticDataTimestampMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/StaticDataTimestampMapper.xml index d1e69e5d8b7..fd058d34c0d 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/StaticDataTimestampMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/StaticDataTimestampMapper.xml @@ -1,9 +1,9 @@ - + - SELECT TABLE_NAME AS "tableName", diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/StructuralVariantMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMapper.xml similarity index 96% rename from src/main/resources/org/cbioportal/persistence/mybatis/StructuralVariantMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMapper.xml index 0fe8bbe8955..45ea024fca7 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/StructuralVariantMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMapper.xml @@ -1,7 +1,7 @@ - + genetic_profile.STABLE_ID AS "${prefix}molecularProfileId", @@ -92,20 +92,20 @@ - + AND structural_variant.SITE1_ENTREZ_GENE_ID IS NULL - + AND structural_variant.SITE1_ENTREZ_GENE_ID = ${geneFilterQuery.getGene1Query().getEntrezId()} - + AND structural_variant.SITE2_ENTREZ_GENE_ID IS NULL - + AND structural_variant.SITE2_ENTREZ_GENE_ID = ${geneFilterQuery.getGene2Query().getEntrezId()} @@ -243,7 +243,7 @@ - SELECT @@ -269,7 +269,7 @@ ORDER BY gene1.HUGO_GENE_SYMBOL, gene2.HUGO_GENE_SYMBOL - SELECT @@ -295,7 +295,7 @@ ORDER BY gene1.HUGO_GENE_SYMBOL, gene2.HUGO_GENE_SYMBOL - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/StudyMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/StudyMapper.xml similarity index 95% rename from src/main/resources/org/cbioportal/persistence/mybatis/StudyMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/StudyMapper.xml index 9b580a23507..eff6ccbd3b5 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/StudyMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/StudyMapper.xml @@ -1,7 +1,7 @@ - + cancer_study.CANCER_STUDY_ID AS "${prefix}cancerStudyId", @@ -95,7 +95,7 @@ - SELECT @@ -125,7 +125,7 @@ - SELECT COUNT(*) AS totalCount FROM cancer_study @@ -135,7 +135,7 @@ - SELECT @@ -152,7 +152,7 @@ GROUP BY cancer_study.CANCER_STUDY_ID - SELECT cancer_study_tags.CANCER_STUDY_ID AS cancerStudyId, cancer_study_tags.TAGS AS tags @@ -161,7 +161,7 @@ WHERE cancer_study.CANCER_STUDY_IDENTIFIER = #{studyId} - SELECT cancer_study_tags.CANCER_STUDY_ID AS cancerStudyId, cancer_study_tags.TAGS AS tags, diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/TreatmentMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/TreatmentMapper.xml similarity index 95% rename from src/main/resources/org/cbioportal/persistence/mybatis/TreatmentMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/TreatmentMapper.xml index 58c93613077..91037a138f4 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/TreatmentMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/TreatmentMapper.xml @@ -1,9 +1,9 @@ - + - SELECT clinical_event_data.VALUE as treatment, patient.STABLE_ID as patientId, @@ -21,7 +21,7 @@ AND clinical_event_data.KEY = #{key} - SELECT sample.STABLE_ID as sampleId, patient.STABLE_ID as patientId, @@ -38,7 +38,7 @@ AND (clinical_event.EVENT_TYPE LIKE 'Sample Acquisition' OR clinical_event.EVENT_TYPE LIKE 'SPECIMEN') - SELECT sample.STABLE_ID as sampleId, patient.STABLE_ID as patientId, diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/VariantCountMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/VariantCountMapper.xml similarity index 89% rename from src/main/resources/org/cbioportal/persistence/mybatis/VariantCountMapper.xml rename to src/main/resources/org/cbioportal/legacy/persistence/mybatis/VariantCountMapper.xml index 92dcfc2788b..35376d31c39 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/VariantCountMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/VariantCountMapper.xml @@ -1,9 +1,9 @@ - + - SELECT genetic_profile.STABLE_ID AS molecularProfileId, mutation_count_by_keyword.KEYWORD AS keyword, diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewAlterationFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewAlterationFilterMapper.xml index 7f003505381..ead231b0236 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewAlterationFilterMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewAlterationFilterMapper.xml @@ -1,7 +1,7 @@ - + NULL diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml index 74eca303a81..96d572c12b1 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml @@ -1,7 +1,7 @@ - + @@ -645,7 +645,7 @@ - + WITH all_samples AS ( SELECT sample_unique_id FROM sample_derived @@ -704,7 +704,8 @@ - + SELECT DISTINCT sample_unique_id FROM genomic_event_derived diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml index ce2fd9bf6ed..60ce0f90dce 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml @@ -1,10 +1,10 @@ - + - SELECT internal_id as internalId, patient_stable_id as patientStableId, @@ -33,7 +33,7 @@ - SELECT hugo_gene_symbol as hugoGeneSymbol, entrez_gene_id as entrezGeneId, @@ -55,7 +55,7 @@ - SELECT hugo_gene_symbol as hugoGeneSymbol, entrez_gene_id as entrezGeneId, @@ -76,7 +76,7 @@ GROUP BY entrez_gene_id, hugo_gene_symbol, alteration, cytoband - SELECT hugo_gene_symbol as hugoGeneSymbol, entrez_gene_id as entrezGeneId, @@ -92,7 +92,7 @@ GROUP BY entrez_gene_id, hugo_gene_symbol - SELECT internal_id as internalId, replaceOne(sample_unique_id, concat(cancer_study_identifier, '_'), '') as sampleId, @@ -115,7 +115,7 @@ AND type = 'sample' - SELECT internal_id as internalId, replaceOne(patient_unique_id, concat(cancer_study_identifier, '_'), '') as patientId, @@ -149,7 +149,7 @@ - --we need to derive the alteration type from the stable_id by removing cancer study id --this should probaby be refactored at some point but we need to maintain api interface SELECT replaceOne(genetic_profile.stable_id, @@ -168,7 +168,7 @@ - SELECT name AS label, REPLACE(stable_id, CONCAT(cancer_study_identifier, '_'), '') AS value, @@ -415,10 +415,10 @@ hugo_gene_symbol - + - + @@ -426,17 +426,17 @@ - + - + - + - + @@ -451,7 +451,7 @@ - SELECT attr_id as attrId, datatype as dataType, @@ -461,7 +461,7 @@ JOIN cancer_study cs on cs.cancer_study_id = cam.cancer_study_id - SELECT attr_id as attrId, datatype as dataType, @@ -486,7 +486,7 @@ We compute the WES counts by using the query getSampleProfileCountWithoutPanelData and adding this value to the totalProfiled Count per gene in java. --> - SELECT gene as hugoGeneSymbol, COUNT(*) as numberOfProfiledCases @@ -546,7 +546,7 @@ - SELECT gene as hugoGeneSymbol, gene_panel_id as genePanelId @@ -567,7 +567,7 @@ GROUP BY gene, gene_panel_id - SELECT event_type as eventType, count(DISTINCT patient_unique_id) as count @@ -601,7 +601,7 @@ - + @@ -649,7 +649,7 @@ - + @@ -699,7 +699,7 @@ GROUP BY treatments.treatment - WITH genomic_numerical_query AS ( @@ -742,7 +742,7 @@ cast(((SELECT * FROM ()) - coalesce((SELECT genomic_numerical_count FROM genomic_numerical_sum LIMIT 1), 0)) as INTEGER) as count - WITH generic_assay_query AS ( @@ -785,7 +785,7 @@ cast(((SELECT * FROM ()) - coalesce((SELECT generic_assay_count FROM generic_assay_sum LIMIT 1), 0)) as INTEGER) as count - SELECT genetic_profile.genetic_profile_id AS "molecularProfileId", genetic_profile.stable_id AS "stableId", @@ -806,7 +806,7 @@ WHERE genetic_profile.genetic_alteration_type = 'GENERIC_ASSAY' - WITH unique_study_ids AS ( SELECT DISTINCT cancer_study_identifier diff --git a/src/main/resources/templates/tracking_include.html b/src/main/resources/templates/tracking_include.html index 6c0f1070639..bdcb02f7a0f 100644 --- a/src/main/resources/templates/tracking_include.html +++ b/src/main/resources/templates/tracking_include.html @@ -1,6 +1,9 @@ - diff --git a/src/test/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCaseTest.java b/src/test/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCaseTest.java new file mode 100644 index 00000000000..771ae3b040e --- /dev/null +++ b/src/test/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCaseTest.java @@ -0,0 +1,41 @@ +package org.cbioportal.cancerstudy.usecase; + +import org.cbioportal.cancerstudy.repository.CancerStudyRepository; +import org.cbioportal.shared.SortAndSearchCriteria; +import org.cbioportal.shared.enums.ProjectionType; +import org.junit.Assert; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.mockito.InjectMocks; +import org.mockito.Mock; +import org.mockito.junit.MockitoJUnitRunner; + +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.Mockito.verify; + + +@RunWith(MockitoJUnitRunner.class) +public class GetCancerStudyMetadataUseCaseTest { + + @InjectMocks + private GetCancerStudyMetadataUseCase getCancerStudyMetadataUseCase; + + @Mock + CancerStudyRepository cancerStudyRepository; + + @Test + public void testExecuteWithProjectionTypeSummary() { + getCancerStudyMetadataUseCase.execute(ProjectionType.SUMMARY, new SortAndSearchCriteria("","","")); + verify(cancerStudyRepository).getCancerStudiesMetadataSummary(any(SortAndSearchCriteria.class)); + } + @Test + public void testExecuteWithProjectionTypeDetailed() { + getCancerStudyMetadataUseCase.execute(ProjectionType.DETAILED, new SortAndSearchCriteria("","", "")); + verify(cancerStudyRepository).getCancerStudiesMetadata(any(SortAndSearchCriteria.class)); + } + @Test + public void testExecuteWithProjectionTypeDefault() { + Assert.assertTrue(getCancerStudyMetadataUseCase.execute(ProjectionType.META, new SortAndSearchCriteria("","","" + )).isEmpty()); + } +} \ No newline at end of file diff --git a/src/test/java/org/cbioportal/persistence/helper/AlterationFilterHelperTest.java b/src/test/java/org/cbioportal/legacy/persistence/helper/AlterationFilterHelperTest.java similarity index 96% rename from src/test/java/org/cbioportal/persistence/helper/AlterationFilterHelperTest.java rename to src/test/java/org/cbioportal/legacy/persistence/helper/AlterationFilterHelperTest.java index c2884acab53..ac88988613b 100644 --- a/src/test/java/org/cbioportal/persistence/helper/AlterationFilterHelperTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/helper/AlterationFilterHelperTest.java @@ -1,7 +1,8 @@ -package org.cbioportal.persistence.helper; +package org.cbioportal.legacy.persistence.helper; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.MutationEventType; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.persistence.helper.AlterationFilterHelper; import org.junit.Test; import java.util.HashMap; diff --git a/src/test/java/org/cbioportal/persistence/helper/StudyViewFilterHelperTest.java b/src/test/java/org/cbioportal/legacy/persistence/helper/StudyViewFilterHelperTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/helper/StudyViewFilterHelperTest.java rename to src/test/java/org/cbioportal/legacy/persistence/helper/StudyViewFilterHelperTest.java index 1f0e10225a1..5be83440772 100644 --- a/src/test/java/org/cbioportal/persistence/helper/StudyViewFilterHelperTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/helper/StudyViewFilterHelperTest.java @@ -1,7 +1,8 @@ -package org.cbioportal.persistence.helper; +package org.cbioportal.legacy.persistence.helper; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; import org.junit.Test; import java.math.BigDecimal; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMyBatisRepositoryTest.java similarity index 91% rename from src/test/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMyBatisRepositoryTest.java index 242103d2f1d..fd9b171e1b1 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMyBatisRepositoryTest.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.AlterationDriverAnnotation; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.AlterationDriverAnnotation; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepositoryTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepositoryTest.java index 440624b753b..b9e00e99dae 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepositoryTest.java @@ -1,23 +1,18 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import java.sql.SQLException; -import java.util.ArrayList; import java.util.Arrays; -import java.util.HashSet; import java.util.List; import java.util.Set; import java.util.TreeSet; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.model.QueryElement; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.mybatis.config.TestConfig; -import org.h2.tools.Server; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/CancerTypeMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMyBatisRepositoryTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/mybatis/CancerTypeMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMyBatisRepositoryTest.java index bb071cb76bb..2ee0234598b 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/CancerTypeMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMyBatisRepositoryTest.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMyBatisRepositoryTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMyBatisRepositoryTest.java index 2166b2d0ab1..ea428caa1b4 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMyBatisRepositoryTest.java @@ -1,13 +1,13 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Optional; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java index 254efa47463..539c16b2c2b 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.Arrays; @@ -6,13 +6,12 @@ import java.util.Optional; import java.util.stream.Collectors; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalAttributeRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.config.TestConfig; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/ClinicalEventMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMyBatisRepositoryTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatis/ClinicalEventMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMyBatisRepositoryTest.java index 60a8d1067de..6d3f8f6ebda 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/ClinicalEventMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMyBatisRepositoryTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; -import org.cbioportal.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMyBatisRepositoryTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMyBatisRepositoryTest.java index b8e72afac33..f8843db0725 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMyBatisRepositoryTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/CosmicCountMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMyBatisRepositoryTest.java similarity index 90% rename from src/test/java/org/cbioportal/persistence/mybatis/CosmicCountMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMyBatisRepositoryTest.java index 585463834d3..7ff6bc65558 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/CosmicCountMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMyBatisRepositoryTest.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.CosmicMutation; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CosmicMutation; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/DataAccessTokenMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMyBatisRepositoryTest.java similarity index 95% rename from src/test/java/org/cbioportal/persistence/mybatis/DataAccessTokenMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMyBatisRepositoryTest.java index 1bce1c32c8a..c9687bdd4ea 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/DataAccessTokenMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMyBatisRepositoryTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Calendar; import java.util.Date; import java.util.List; import java.util.UUID; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMyBatisRepositoryTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMyBatisRepositoryTest.java index ef098188c8c..92687a9e770 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMyBatisRepositoryTest.java @@ -1,18 +1,18 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.Arrays; import java.util.Comparator; import java.util.List; -import org.cbioportal.model.CNA; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GeneMyBatisRepositoryTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/GeneMyBatisRepositoryTest.java index 796bb0348aa..4359a729846 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GeneMyBatisRepositoryTest.java @@ -30,13 +30,13 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/GenePanelMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMyBatisRepositoryTest.java similarity index 93% rename from src/test/java/org/cbioportal/persistence/mybatis/GenePanelMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMyBatisRepositoryTest.java index 3e51b7bf9e5..a8b3b013126 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/GenePanelMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMyBatisRepositoryTest.java @@ -1,14 +1,14 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/GenericAssayMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMyBatisRepositoryTest.java similarity index 89% rename from src/test/java/org/cbioportal/persistence/mybatis/GenericAssayMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMyBatisRepositoryTest.java index 98dcdb0c8d6..c8637fae4f6 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/GenericAssayMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMyBatisRepositoryTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.GenericAssayAdditionalProperty; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.GenericAssayAdditionalProperty; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMyBatisRepositoryTest.java similarity index 95% rename from src/test/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMyBatisRepositoryTest.java index 8b27fe13768..3e3e0b96641 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMyBatisRepositoryTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetHierarchyInfo; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/GenesetMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenesetMyBatisRepositoryTest.java similarity index 93% rename from src/test/java/org/cbioportal/persistence/mybatis/GenesetMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/GenesetMyBatisRepositoryTest.java index 7580baf8393..a40b5340c1d 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/GenesetMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenesetMyBatisRepositoryTest.java @@ -30,15 +30,15 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java similarity index 95% rename from src/test/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java index d3241bcd6cd..ee81451fb89 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java @@ -1,14 +1,14 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.List; import java.util.Map; import java.util.stream.Collectors; import java.util.stream.Stream; -import org.cbioportal.model.GeneMolecularAlteration; -import org.cbioportal.model.GenesetMolecularAlteration; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GenesetMolecularAlteration; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/MolecularProfileMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMyBatisRepositoryTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/mybatis/MolecularProfileMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMyBatisRepositoryTest.java index 2b4db775c3d..fa6d70a9438 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/MolecularProfileMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMyBatisRepositoryTest.java @@ -1,13 +1,13 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/MutationMyBatisRepositoryTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/MutationMyBatisRepositoryTest.java index 723f200c30f..c589cf20ad3 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/MutationMyBatisRepositoryTest.java @@ -1,15 +1,15 @@ -package org.cbioportal.persistence.mybatis; - -import org.cbioportal.model.AlleleSpecificCopyNumber; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.mybatis.config.TestConfig; -import org.cbioportal.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; +package org.cbioportal.legacy.persistence.mybatis; + +import org.cbioportal.legacy.model.AlleleSpecificCopyNumber; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/PatientMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/PatientMyBatisRepositoryTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatis/PatientMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/PatientMyBatisRepositoryTest.java index 3661a80043e..00b26192d96 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/PatientMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/PatientMyBatisRepositoryTest.java @@ -1,14 +1,14 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; import java.util.stream.Collectors; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMyBatisRepositoryTest.java similarity index 91% rename from src/test/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMyBatisRepositoryTest.java index 939548f1135..ec62463d207 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMyBatisRepositoryTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.ReferenceGenome; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.ReferenceGenome; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/ResourceDataMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMyBatisRepositoryTest.java similarity index 96% rename from src/test/java/org/cbioportal/persistence/mybatis/ResourceDataMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMyBatisRepositoryTest.java index 888c80e7602..01c451ca803 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/ResourceDataMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMyBatisRepositoryTest.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ResourceData; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.model.ResourceType; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.ResourceData; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.model.ResourceType; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMyBatisRepositoryTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMyBatisRepositoryTest.java index 36b3c5d7021..e10034dc65d 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMyBatisRepositoryTest.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.model.ResourceType; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.model.ResourceType; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/SampleListMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SampleListMyBatisRepositoryTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatis/SampleListMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/SampleListMyBatisRepositoryTest.java index 9103ba5fc7d..4358ef95bfe 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/SampleListMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SampleListMyBatisRepositoryTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/SampleMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SampleMyBatisRepositoryTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/mybatis/SampleMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/SampleMyBatisRepositoryTest.java index 1d4614cecd4..a39b8ee0435 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/SampleMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SampleMyBatisRepositoryTest.java @@ -1,15 +1,15 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; import java.util.stream.Collectors; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.Patient; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepositoryTest.java similarity index 95% rename from src/test/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepositoryTest.java index 197afb2dc6b..965f86ab722 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepositoryTest.java @@ -1,12 +1,12 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepositoryTest.java similarity index 95% rename from src/test/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepositoryTest.java index 3d92ac2ff52..216a0e93e8c 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepositoryTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.math.BigDecimal; import java.util.List; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/StructuralVariantMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMyBatisRepositoryTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/mybatis/StructuralVariantMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMyBatisRepositoryTest.java index 149d2327f01..48d4b7e48db 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/StructuralVariantMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMyBatisRepositoryTest.java @@ -21,21 +21,21 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantGeneSubQuery; -import org.cbioportal.model.StructuralVariantQuery; -import org.cbioportal.model.StructuralVariantSpecialValue; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.mybatis.config.TestConfig; -import org.cbioportal.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantGeneSubQuery; +import org.cbioportal.legacy.model.StructuralVariantQuery; +import org.cbioportal.legacy.model.StructuralVariantSpecialValue; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; import org.junit.Assert; import org.junit.Before; import org.junit.Test; @@ -44,12 +44,8 @@ import org.springframework.boot.test.context.SpringBootTest; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import java.util.ArrayList; -import java.util.Arrays; import java.util.Collections; -import java.util.List; import java.util.Objects; -import java.util.stream.Collectors; @RunWith(SpringJUnit4ClassRunner.class) @SpringBootTest(classes = {StructuralVariantMyBatisRepository.class, StructuralVariantMapper.class, diff --git a/src/test/java/org/cbioportal/persistence/mybatis/StudyMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/StudyMyBatisRepositoryTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatis/StudyMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/StudyMyBatisRepositoryTest.java index f3bd2772229..9042c49aaa8 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/StudyMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/StudyMyBatisRepositoryTest.java @@ -1,14 +1,14 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.text.SimpleDateFormat; import java.util.Arrays; import java.util.List; import java.util.TimeZone; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/TreatmentMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMyBatisRepositoryTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/mybatis/TreatmentMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMyBatisRepositoryTest.java index 5cdc3506c34..bbbb9859840 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/TreatmentMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMyBatisRepositoryTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.model.ClinicalEventSample; -import org.cbioportal.model.Treatment; -import org.cbioportal.persistence.TreatmentRepository; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.Treatment; +import org.cbioportal.legacy.persistence.TreatmentRepository; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/VariantCountMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMyBatisRepositoryTest.java similarity index 92% rename from src/test/java/org/cbioportal/persistence/mybatis/VariantCountMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMyBatisRepositoryTest.java index 1dd6b241105..1ae262a031a 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/VariantCountMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMyBatisRepositoryTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Arrays; import java.util.List; import java.util.Optional; -import org.cbioportal.model.VariantCount; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.VariantCount; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/config/TestConfig.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/config/TestConfig.java similarity index 92% rename from src/test/java/org/cbioportal/persistence/mybatis/config/TestConfig.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/config/TestConfig.java index bd86b27af83..12e46a8f3f7 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/config/TestConfig.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/config/TestConfig.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis.config; +package org.cbioportal.legacy.persistence.mybatis.config; import javax.sql.DataSource; import org.apache.ibatis.mapping.DatabaseIdProvider; import org.apache.ibatis.mapping.VendorDatabaseIdProvider; import org.apache.ibatis.session.SqlSessionFactory; -import org.cbioportal.persistence.mybatis.typehandler.SampleTypeTypeHandler; +import org.cbioportal.legacy.persistence.mybatis.typehandler.SampleTypeTypeHandler; import org.mybatis.spring.SqlSessionFactoryBean; import org.mybatis.spring.annotation.MapperScan; import org.springframework.boot.test.context.TestConfiguration; @@ -18,7 +18,7 @@ import java.util.Properties; @TestConfiguration -@MapperScan("org.cbioportal.persistence.mybatis") +@MapperScan("org.cbioportal.legacy.persistence.mybatis") public class TestConfig { @Bean diff --git a/src/test/java/org/cbioportal/persistence/mybatis/util/MolecularProfileCaseIdentifierUtilTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/util/MolecularProfileCaseIdentifierUtilTest.java similarity index 93% rename from src/test/java/org/cbioportal/persistence/mybatis/util/MolecularProfileCaseIdentifierUtilTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/util/MolecularProfileCaseIdentifierUtilTest.java index 7163f5300db..bb658c1957f 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/util/MolecularProfileCaseIdentifierUtilTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/util/MolecularProfileCaseIdentifierUtilTest.java @@ -1,9 +1,11 @@ -package org.cbioportal.persistence.mybatis.util; +package org.cbioportal.legacy.persistence.mybatis.util; import java.util.ArrayList; import java.util.Arrays; import java.util.Map; import java.util.Set; + +import org.cbioportal.legacy.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/util/PaginationCalculatorTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/util/PaginationCalculatorTest.java similarity index 90% rename from src/test/java/org/cbioportal/persistence/mybatis/util/PaginationCalculatorTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/util/PaginationCalculatorTest.java index 0f8bc654e1c..df3ccab4edc 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/util/PaginationCalculatorTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/util/PaginationCalculatorTest.java @@ -1,5 +1,6 @@ -package org.cbioportal.persistence.mybatis.util; +package org.cbioportal.legacy.persistence.mybatis.util; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; @@ -7,7 +8,7 @@ import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; @RunWith(SpringJUnit4ClassRunner.class) -@ContextConfiguration(classes=PaginationCalculator.class) +@ContextConfiguration(classes= PaginationCalculator.class) public class PaginationCalculatorTest { diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/AbstractTestcontainers.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/AbstractTestcontainers.java similarity index 96% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/AbstractTestcontainers.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/AbstractTestcontainers.java index a4c04e4aedb..fb1d8117aff 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/AbstractTestcontainers.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/AbstractTestcontainers.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; import org.junit.BeforeClass; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/CNAGenesTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/CNAGenesTest.java similarity index 87% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/CNAGenesTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/CNAGenesTest.java index 18df4041406..210d448534c 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/CNAGenesTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/CNAGenesTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.persistence.helper.AlterationFilterHelper; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.persistence.helper.AlterationFilterHelper; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java similarity index 85% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java index 00bf968c29d..24684b768dc 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.DataFilter; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.DataFilter; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; @@ -13,6 +13,7 @@ import org.springframework.context.annotation.Import; import org.springframework.test.annotation.DirtiesContext; import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.TestPropertySource; import org.springframework.test.context.junit4.SpringRunner; import java.util.List; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/FilteredSamplesTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/FilteredSamplesTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/FilteredSamplesTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/FilteredSamplesTest.java index d4926855e97..6d95950fafc 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/FilteredSamplesTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/FilteredSamplesTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.CustomSampleIdentifier; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.CustomSampleIdentifier; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java similarity index 87% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java index 086b18593df..d1e5165ab86 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.model.GenericAssayDataCount; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.GenericAssayDataCount; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/GenomicDataCountsTest.java similarity index 87% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/GenomicDataCountsTest.java index 9e569b0e4a1..c2594b589a9 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/GenomicDataCountsTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MolecularProfileCountTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MolecularProfileCountTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/MolecularProfileCountTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MolecularProfileCountTest.java index f9748a09110..b46492bf09a 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MolecularProfileCountTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MolecularProfileCountTest.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutatedGenesTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MutatedGenesTest.java similarity index 90% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutatedGenesTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MutatedGenesTest.java index dd8001ded6f..86658bc8dfb 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutatedGenesTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MutatedGenesTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.persistence.helper.AlterationFilterHelper; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.persistence.helper.AlterationFilterHelper; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutationDataCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MutationDataCountsTest.java similarity index 87% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutationDataCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MutationDataCountsTest.java index d04adb06575..a7c7959a0b4 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutationDataCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MutationDataCountsTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java similarity index 84% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java index b23fc8f266f..f83ea3f263a 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; - -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedPatientTreatmentFilters; -import org.cbioportal.web.parameter.filter.OredPatientTreatmentFilters; -import org.cbioportal.web.parameter.filter.PatientTreatmentFilter; +package org.cbioportal.legacy.persistence.mybatisclickhouse; + +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedPatientTreatmentFilters; +import org.cbioportal.legacy.web.parameter.filter.OredPatientTreatmentFilters; +import org.cbioportal.legacy.web.parameter.filter.PatientTreatmentFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProfiledCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ProfiledCountsTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProfiledCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ProfiledCountsTest.java index aa3e4a12f4f..6edfada6bec 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProfiledCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ProfiledCountsTest.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java similarity index 89% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java index 332dff493b4..9d352d15b0e 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java @@ -1,12 +1,12 @@ -package org.cbioportal.persistence.mybatisclickhouse; - -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.StudyViewFilter; +package org.cbioportal.legacy.persistence.mybatisclickhouse; + +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java similarity index 83% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java index 5baa9149739..8cfd8977da4 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java @@ -1,12 +1,12 @@ -package org.cbioportal.persistence.mybatisclickhouse; - -import org.cbioportal.model.TemporalRelation; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedSampleTreatmentFilters; -import org.cbioportal.web.parameter.filter.OredSampleTreatmentFilters; -import org.cbioportal.web.parameter.filter.SampleTreatmentFilter; +package org.cbioportal.legacy.persistence.mybatisclickhouse; + +import org.cbioportal.legacy.model.TemporalRelation; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedSampleTreatmentFilters; +import org.cbioportal.legacy.web.parameter.filter.OredSampleTreatmentFilters; +import org.cbioportal.legacy.web.parameter.filter.SampleTreatmentFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StructuralVariantGenesTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StructuralVariantGenesTest.java similarity index 86% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/StructuralVariantGenesTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StructuralVariantGenesTest.java index f3a1dc6db00..f5abdcb578f 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StructuralVariantGenesTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StructuralVariantGenesTest.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.persistence.helper.AlterationFilterHelper; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.persistence.helper.AlterationFilterHelper; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java similarity index 93% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java index 66d72a34a88..4ec4993d5e2 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.service.util.StudyViewColumnarServiceUtil; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.service.util.StudyViewColumnarServiceUtil; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java similarity index 96% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java index 2e48da4cb1d..a7d74ae3b3d 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; - -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.StudyViewFilter; +package org.cbioportal.legacy.persistence.mybatisclickhouse; + +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/config/MyBatisConfig.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/config/MyBatisConfig.java similarity index 93% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/config/MyBatisConfig.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/config/MyBatisConfig.java index 25d1e098c64..174c55207ff 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/config/MyBatisConfig.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/config/MyBatisConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.mybatisclickhouse.config; +package org.cbioportal.legacy.persistence.mybatisclickhouse.config; import org.mybatis.spring.SqlSessionFactoryBean; import org.mybatis.spring.annotation.MapperScan; @@ -12,7 +12,7 @@ import java.io.IOException; @TestConfiguration -@MapperScan("org.cbioportal.persistence.mybatisclickhouse") +@MapperScan("org.cbioportal.legacy.persistence.mybatisclickhouse") public class MyBatisConfig { @Bean diff --git a/src/test/java/org/cbioportal/persistence/util/CustomKeyGeneratorTest.java b/src/test/java/org/cbioportal/legacy/persistence/util/CustomKeyGeneratorTest.java similarity index 93% rename from src/test/java/org/cbioportal/persistence/util/CustomKeyGeneratorTest.java rename to src/test/java/org/cbioportal/legacy/persistence/util/CustomKeyGeneratorTest.java index 94eb9170dd0..8606a4c0f96 100644 --- a/src/test/java/org/cbioportal/persistence/util/CustomKeyGeneratorTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/CustomKeyGeneratorTest.java @@ -1,8 +1,9 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.persistence.CacheEnabledConfig; -import org.cbioportal.persistence.StudyRepository; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.persistence.CacheEnabledConfig; +import org.cbioportal.legacy.persistence.StudyRepository; +import org.cbioportal.legacy.persistence.util.CustomKeyGenerator; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/persistence/util/CustomRedisCacheIntegrationTest.java b/src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheIntegrationTest.java similarity index 89% rename from src/test/java/org/cbioportal/persistence/util/CustomRedisCacheIntegrationTest.java rename to src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheIntegrationTest.java index 0a52d338217..2c59ff38256 100644 --- a/src/test/java/org/cbioportal/persistence/util/CustomRedisCacheIntegrationTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheIntegrationTest.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; -import org.cbioportal.persistence.util.fakeclient.MockInMemoryRedissonClient; +import org.cbioportal.legacy.persistence.util.fakeclient.MockInMemoryRedissonClient; import org.junit.Test; import static org.junit.Assert.assertEquals; diff --git a/src/test/java/org/cbioportal/persistence/util/CustomRedisCacheManagerTest.java b/src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheManagerTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/util/CustomRedisCacheManagerTest.java rename to src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheManagerTest.java index 02578ed04df..975084d0cd5 100644 --- a/src/test/java/org/cbioportal/persistence/util/CustomRedisCacheManagerTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheManagerTest.java @@ -1,5 +1,6 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; +import org.cbioportal.legacy.persistence.util.CustomRedisCacheManager; import org.junit.Test; import org.junit.runner.RunWith; import org.mockito.Mock; diff --git a/src/test/java/org/cbioportal/persistence/util/CustomRedisCacheTest.java b/src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheTest.java similarity index 99% rename from src/test/java/org/cbioportal/persistence/util/CustomRedisCacheTest.java rename to src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheTest.java index e680e476a41..3e5ced0c2c0 100644 --- a/src/test/java/org/cbioportal/persistence/util/CustomRedisCacheTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheTest.java @@ -1,8 +1,10 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import java.util.Arrays; import java.util.HashMap; import java.util.List; + +import org.cbioportal.legacy.persistence.util.CustomRedisCache; import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/util/EhCacheUtilsTest.java b/src/test/java/org/cbioportal/legacy/persistence/util/EhCacheUtilsTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/util/EhCacheUtilsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/util/EhCacheUtilsTest.java index b60760037b8..c0c59f1fb18 100644 --- a/src/test/java/org/cbioportal/persistence/util/EhCacheUtilsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/EhCacheUtilsTest.java @@ -1,5 +1,6 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; +import org.cbioportal.legacy.persistence.util.EhCacheUtils; import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/util/RedisCacheUtilsTest.java b/src/test/java/org/cbioportal/legacy/persistence/util/RedisCacheUtilsTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/util/RedisCacheUtilsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/util/RedisCacheUtilsTest.java index 8ea296623b8..12d32fae832 100644 --- a/src/test/java/org/cbioportal/persistence/util/RedisCacheUtilsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/RedisCacheUtilsTest.java @@ -1,5 +1,6 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; +import org.cbioportal.legacy.persistence.util.RedisCacheUtils; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/persistence/util/fakeclient/MockInMemoryRedissonClient.java b/src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockInMemoryRedissonClient.java similarity index 99% rename from src/test/java/org/cbioportal/persistence/util/fakeclient/MockInMemoryRedissonClient.java rename to src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockInMemoryRedissonClient.java index 145be13601c..25ee4c46eae 100644 --- a/src/test/java/org/cbioportal/persistence/util/fakeclient/MockInMemoryRedissonClient.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockInMemoryRedissonClient.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.util.fakeclient; +package org.cbioportal.legacy.persistence.util.fakeclient; import org.redisson.api.*; import org.redisson.api.redisnode.BaseRedisNodes; diff --git a/src/test/java/org/cbioportal/persistence/util/fakeclient/MockRBucket.java b/src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockRBucket.java similarity index 99% rename from src/test/java/org/cbioportal/persistence/util/fakeclient/MockRBucket.java rename to src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockRBucket.java index 642509fd28a..32c48bd8bf9 100644 --- a/src/test/java/org/cbioportal/persistence/util/fakeclient/MockRBucket.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockRBucket.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.util.fakeclient; +package org.cbioportal.legacy.persistence.util.fakeclient; import org.redisson.api.ObjectListener; import org.redisson.api.RBucket; diff --git a/src/test/java/org/cbioportal/persistence/util/fakeclient/MockRKeys.java b/src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockRKeys.java similarity index 99% rename from src/test/java/org/cbioportal/persistence/util/fakeclient/MockRKeys.java rename to src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockRKeys.java index 3866c31ddca..68fec768cf3 100644 --- a/src/test/java/org/cbioportal/persistence/util/fakeclient/MockRKeys.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockRKeys.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.util.fakeclient; +package org.cbioportal.legacy.persistence.util.fakeclient; import org.redisson.api.*; diff --git a/src/test/java/org/cbioportal/proxy/MonkifierTest.java b/src/test/java/org/cbioportal/legacy/proxy/MonkifierTest.java similarity index 96% rename from src/test/java/org/cbioportal/proxy/MonkifierTest.java rename to src/test/java/org/cbioportal/legacy/proxy/MonkifierTest.java index 9fb7d5da515..85cc121b53a 100644 --- a/src/test/java/org/cbioportal/proxy/MonkifierTest.java +++ b/src/test/java/org/cbioportal/legacy/proxy/MonkifierTest.java @@ -1,5 +1,6 @@ -package org.cbioportal.proxy; +package org.cbioportal.legacy.proxy; +import org.cbioportal.application.proxy.Monkifier; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/AlterationCountServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/AlterationCountServiceImplTest.java similarity index 91% rename from src/test/java/org/cbioportal/service/impl/AlterationCountServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/AlterationCountServiceImplTest.java index 0497e4e1d37..cd2c9e0648e 100644 --- a/src/test/java/org/cbioportal/service/impl/AlterationCountServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/AlterationCountServiceImplTest.java @@ -1,22 +1,20 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.AlterationRepository; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.persistence.StudyViewRepository; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.util.AlterationEnrichmentUtil; -import org.cbioportal.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.AlterationRepository; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.util.AlterationEnrichmentUtil; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/AlterationDriverAnnotationServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/AlterationDriverAnnotationServiceImplTest.java similarity index 95% rename from src/test/java/org/cbioportal/service/impl/AlterationDriverAnnotationServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/AlterationDriverAnnotationServiceImplTest.java index 7fc93118464..da6445f678c 100644 --- a/src/test/java/org/cbioportal/service/impl/AlterationDriverAnnotationServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/AlterationDriverAnnotationServiceImplTest.java @@ -1,8 +1,9 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.AlterationDriverAnnotation; -import org.cbioportal.model.CustomDriverAnnotationReport; -import org.cbioportal.persistence.AlterationDriverAnnotationRepository; +import org.cbioportal.legacy.model.AlterationDriverAnnotation; +import org.cbioportal.legacy.model.CustomDriverAnnotationReport; +import org.cbioportal.legacy.persistence.AlterationDriverAnnotationRepository; +import org.cbioportal.legacy.service.impl.AlterationDriverAnnotationServiceImpl; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/AlterationEnrichmentServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/AlterationEnrichmentServiceImplTest.java similarity index 85% rename from src/test/java/org/cbioportal/service/impl/AlterationEnrichmentServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/AlterationEnrichmentServiceImplTest.java index 0c645bb2620..c1af5e5d2ad 100644 --- a/src/test/java/org/cbioportal/service/impl/AlterationEnrichmentServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/AlterationEnrichmentServiceImplTest.java @@ -1,17 +1,17 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationEnrichment; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MutationCountByGene; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.model.util.Select; -import org.cbioportal.service.AlterationCountService; -import org.cbioportal.service.util.AlterationEnrichmentUtil; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationEnrichment; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MutationCountByGene; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.service.AlterationCountService; +import org.cbioportal.legacy.service.util.AlterationEnrichmentUtil; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/BaseServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/BaseServiceImplTest.java similarity index 98% rename from src/test/java/org/cbioportal/service/impl/BaseServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/BaseServiceImplTest.java index 827a7b752a5..d6d0f436854 100644 --- a/src/test/java/org/cbioportal/service/impl/BaseServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/BaseServiceImplTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; public class BaseServiceImplTest { diff --git a/src/test/java/org/cbioportal/service/impl/CacheServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/CacheServiceImplTest.java similarity index 91% rename from src/test/java/org/cbioportal/service/impl/CacheServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/CacheServiceImplTest.java index d2a686f9b1d..8e61eb38b9d 100644 --- a/src/test/java/org/cbioportal/service/impl/CacheServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/CacheServiceImplTest.java @@ -1,10 +1,11 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.persistence.StudyRepository; -import org.cbioportal.persistence.cachemaputil.StaticRefCacheMapUtil; -import org.cbioportal.persistence.util.CacheUtils; -import org.cbioportal.service.exception.CacheOperationException; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.persistence.StudyRepository; +import org.cbioportal.legacy.persistence.cachemaputil.StaticRefCacheMapUtil; +import org.cbioportal.legacy.persistence.util.CacheUtils; +import org.cbioportal.legacy.service.exception.CacheOperationException; +import org.cbioportal.legacy.service.impl.CacheServiceImpl; import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/CancerTypeServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/CancerTypeServiceImplTest.java similarity index 88% rename from src/test/java/org/cbioportal/service/impl/CancerTypeServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/CancerTypeServiceImplTest.java index 72cd6eb40e0..40f30816ba4 100644 --- a/src/test/java/org/cbioportal/service/impl/CancerTypeServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/CancerTypeServiceImplTest.java @@ -1,9 +1,9 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CancerTypeRepository; -import org.cbioportal.service.exception.CancerTypeNotFoundException; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CancerTypeRepository; +import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/ClinicalAttributeServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ClinicalAttributeServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/ClinicalAttributeServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ClinicalAttributeServiceImplTest.java index 8d07226f80d..759f2c4cbe4 100644 --- a/src/test/java/org/cbioportal/service/impl/ClinicalAttributeServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ClinicalAttributeServiceImplTest.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalAttributeRepository; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.ClinicalAttributeNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalAttributeRepository; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.ClinicalAttributeNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.Before; diff --git a/src/test/java/org/cbioportal/service/impl/ClinicalDataServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ClinicalDataServiceImplTest.java similarity index 95% rename from src/test/java/org/cbioportal/service/impl/ClinicalDataServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ClinicalDataServiceImplTest.java index 1a272ae3075..4d4f73ca0c5 100755 --- a/src/test/java/org/cbioportal/service/impl/ClinicalDataServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ClinicalDataServiceImplTest.java @@ -1,13 +1,23 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.lang3.tuple.ImmutablePair; -import org.cbioportal.model.*; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalDataRepository; -import org.cbioportal.service.*; -import org.cbioportal.service.exception.*; -import org.cbioportal.service.util.ClinicalAttributeUtil; -import org.cbioportal.utils.Encoder; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.SampleClinicalDataCollection; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalDataRepository; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.utils.Encoder; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/ClinicalEventServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ClinicalEventServiceImplTest.java similarity index 95% rename from src/test/java/org/cbioportal/service/impl/ClinicalEventServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ClinicalEventServiceImplTest.java index e6fe83f8c7e..a84e7471b41 100644 --- a/src/test/java/org/cbioportal/service/impl/ClinicalEventServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ClinicalEventServiceImplTest.java @@ -1,18 +1,18 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalEventRepository; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.web.parameter.ClinicalEventRequest; -import org.cbioportal.web.parameter.ClinicalEventRequestIdentifier; -import org.cbioportal.web.parameter.OccurrencePosition; -import org.cbioportal.web.parameter.SurvivalRequest; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalEventRepository; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.web.parameter.ClinicalEventRequest; +import org.cbioportal.legacy.web.parameter.ClinicalEventRequestIdentifier; +import org.cbioportal.legacy.web.parameter.OccurrencePosition; +import org.cbioportal.legacy.web.parameter.SurvivalRequest; import org.junit.Test; import org.junit.runner.RunWith; import org.mockito.InjectMocks; diff --git a/src/test/java/org/cbioportal/service/impl/CoExpressionServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/CoExpressionServiceImplTest.java similarity index 96% rename from src/test/java/org/cbioportal/service/impl/CoExpressionServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/CoExpressionServiceImplTest.java index 711b5f43888..46b07fcc26d 100644 --- a/src/test/java/org/cbioportal/service/impl/CoExpressionServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/CoExpressionServiceImplTest.java @@ -1,19 +1,19 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.CoExpression; -import org.cbioportal.model.EntityType; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.GenesetService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.util.CoExpressionAsyncMethods; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.CoExpression; +import org.cbioportal.legacy.model.EntityType; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.GenesetService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.util.CoExpressionAsyncMethods; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/CopyNumberSegmentServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/CopyNumberSegmentServiceImplTest.java similarity index 93% rename from src/test/java/org/cbioportal/service/impl/CopyNumberSegmentServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/CopyNumberSegmentServiceImplTest.java index a5412473c32..876aecbbc8b 100644 --- a/src/test/java/org/cbioportal/service/impl/CopyNumberSegmentServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/CopyNumberSegmentServiceImplTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CopyNumberSegmentRepository; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CopyNumberSegmentRepository; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/CosmicCountServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/CosmicCountServiceImplTest.java similarity index 87% rename from src/test/java/org/cbioportal/service/impl/CosmicCountServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/CosmicCountServiceImplTest.java index d8c1df4e26b..ef269ee4bd8 100644 --- a/src/test/java/org/cbioportal/service/impl/CosmicCountServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/CosmicCountServiceImplTest.java @@ -1,7 +1,7 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.CosmicMutation; -import org.cbioportal.persistence.CosmicCountRepository; +import org.cbioportal.legacy.model.CosmicMutation; +import org.cbioportal.legacy.persistence.CosmicCountRepository; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/DiscreteCopyNumberServiceImplTest.java similarity index 96% rename from src/test/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/DiscreteCopyNumberServiceImplTest.java index 199865c11bd..87448cccfed 100644 --- a/src/test/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/DiscreteCopyNumberServiceImplTest.java @@ -1,11 +1,16 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.*; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.DiscreteCopyNumberRepository; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.DiscreteCopyNumberRepository; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/ExpressionEnrichmentServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ExpressionEnrichmentServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/ExpressionEnrichmentServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ExpressionEnrichmentServiceImplTest.java index 0b612d5f9ea..8aed57a4ef7 100644 --- a/src/test/java/org/cbioportal/service/impl/ExpressionEnrichmentServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ExpressionEnrichmentServiceImplTest.java @@ -1,16 +1,30 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.math.BigDecimal; import java.util.*; -import org.cbioportal.model.*; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.util.ExpressionEnrichmentUtil; + +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.ExpressionEnrichment; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GenericAssayEnrichment; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.GenomicEnrichment; +import org.cbioportal.legacy.model.GroupStatistics; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.ReferenceGenome; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.util.ExpressionEnrichmentUtil; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/GeneMemoizerServiceTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GeneMemoizerServiceTest.java similarity index 91% rename from src/test/java/org/cbioportal/service/impl/GeneMemoizerServiceTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GeneMemoizerServiceTest.java index 04f81101215..13d1a52f437 100644 --- a/src/test/java/org/cbioportal/service/impl/GeneMemoizerServiceTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GeneMemoizerServiceTest.java @@ -1,7 +1,8 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.service.StaticDataTimestampService; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.service.StaticDataTimestampService; +import org.cbioportal.legacy.service.impl.GeneMemoizerServiceImpl; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/GenePanelServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GenePanelServiceImplTest.java similarity index 95% rename from src/test/java/org/cbioportal/service/impl/GenePanelServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GenePanelServiceImplTest.java index 19b65920131..0a5944f0eea 100644 --- a/src/test/java/org/cbioportal/service/impl/GenePanelServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GenePanelServiceImplTest.java @@ -1,14 +1,18 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.*; import java.util.stream.Collectors; -import org.cbioportal.model.*; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GenePanelRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.exception.GenePanelNotFoundException; -import org.cbioportal.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GenePanelRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.exception.GenePanelNotFoundException; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/GeneServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GeneServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/GeneServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GeneServiceImplTest.java index 10e3ada5269..d195b257136 100644 --- a/src/test/java/org/cbioportal/service/impl/GeneServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GeneServiceImplTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.Gene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GeneRepository; -import org.cbioportal.service.exception.GeneNotFoundException; -import org.cbioportal.service.util.ChromosomeCalculator; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GeneRepository; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.service.util.ChromosomeCalculator; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/GenericAssayEnrichmentServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GenericAssayEnrichmentServiceImplTest.java similarity index 93% rename from src/test/java/org/cbioportal/service/impl/GenericAssayEnrichmentServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GenericAssayEnrichmentServiceImplTest.java index ea9e489e13a..9f3dd12f5bd 100644 --- a/src/test/java/org/cbioportal/service/impl/GenericAssayEnrichmentServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GenericAssayEnrichmentServiceImplTest.java @@ -1,25 +1,25 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.ExpressionEnrichment; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.ReferenceGenome; -import org.cbioportal.model.Sample; -import org.cbioportal.model.GenericAssayMolecularAlteration; -import org.cbioportal.model.GenericAssayBinaryEnrichment; -import org.cbioportal.model.GenericAssayCategoricalEnrichment; -import org.cbioportal.model.GroupStatistics; - -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.util.ExpressionEnrichmentUtil; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.ExpressionEnrichment; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.ReferenceGenome; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.GenericAssayBinaryEnrichment; +import org.cbioportal.legacy.model.GenericAssayCategoricalEnrichment; +import org.cbioportal.legacy.model.GroupStatistics; + +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.util.ExpressionEnrichmentUtil; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/GenericAssayServiceImpTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GenericAssayServiceImpTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/GenericAssayServiceImpTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GenericAssayServiceImpTest.java index 14bcf9adbdf..db6b344a86d 100644 --- a/src/test/java/org/cbioportal/service/impl/GenericAssayServiceImpTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GenericAssayServiceImpTest.java @@ -1,24 +1,24 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.*; import java.util.stream.Collectors; import java.util.stream.Stream; -import org.cbioportal.model.GenericAssayAdditionalProperty; -import org.cbioportal.model.GenericAssayData; -import org.cbioportal.model.GenericAssayMolecularAlteration; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.model.Sample; -import org.cbioportal.model.MolecularProfile.MolecularAlterationType; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.persistence.GenericAssayRepository; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.GenericAssayNotFoundException; +import org.cbioportal.legacy.model.GenericAssayAdditionalProperty; +import org.cbioportal.legacy.model.GenericAssayData; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.MolecularProfile.MolecularAlterationType; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.persistence.GenericAssayRepository; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.GenericAssayNotFoundException; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/GenesetCorrelationServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GenesetCorrelationServiceImplTest.java similarity index 92% rename from src/test/java/org/cbioportal/service/impl/GenesetCorrelationServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GenesetCorrelationServiceImplTest.java index 65bc425fd04..27e35c359b7 100644 --- a/src/test/java/org/cbioportal/service/impl/GenesetCorrelationServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GenesetCorrelationServiceImplTest.java @@ -1,19 +1,19 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.GenesetCorrelation; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.service.GenesetService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.GenesetCorrelation; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.GenesetService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/GenesetDataServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GenesetDataServiceImplTest.java similarity index 91% rename from src/test/java/org/cbioportal/service/impl/GenesetDataServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GenesetDataServiceImplTest.java index fc67d32bfba..c76233fea0b 100644 --- a/src/test/java/org/cbioportal/service/impl/GenesetDataServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GenesetDataServiceImplTest.java @@ -1,17 +1,17 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.GenesetMolecularAlteration; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.model.Sample; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; +import org.cbioportal.legacy.model.GenesetMolecularAlteration; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/GenesetHierarchyServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GenesetHierarchyServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/GenesetHierarchyServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GenesetHierarchyServiceImplTest.java index 5e13e9b2c9a..7e41f965ba0 100644 --- a/src/test/java/org/cbioportal/service/impl/GenesetHierarchyServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GenesetHierarchyServiceImplTest.java @@ -1,19 +1,19 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.GenesetHierarchyInfo; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.persistence.GenesetHierarchyRepository; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.service.GenesetService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.persistence.GenesetHierarchyRepository; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.GenesetService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/GenesetServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GenesetServiceImplTest.java similarity index 89% rename from src/test/java/org/cbioportal/service/impl/GenesetServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GenesetServiceImplTest.java index 90a73ae3c3e..7186a7c7c8f 100644 --- a/src/test/java/org/cbioportal/service/impl/GenesetServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GenesetServiceImplTest.java @@ -1,15 +1,15 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GenesetRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GenesetRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/MolecularDataServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/MolecularDataServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/MolecularDataServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/MolecularDataServiceImplTest.java index d63ef1216c2..f58d8c6b913 100644 --- a/src/test/java/org/cbioportal/service/impl/MolecularDataServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/MolecularDataServiceImplTest.java @@ -1,17 +1,17 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.GeneMolecularAlteration; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.DiscreteCopyNumberRepository; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.DiscreteCopyNumberRepository; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/MolecularProfileServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/MolecularProfileServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/MolecularProfileServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/MolecularProfileServiceImplTest.java index ab68f88124a..5272283df94 100644 --- a/src/test/java/org/cbioportal/service/impl/MolecularProfileServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/MolecularProfileServiceImplTest.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.service.util.MolecularProfileUtil; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/MrnaPercentileServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/MrnaPercentileServiceImplTest.java similarity index 93% rename from src/test/java/org/cbioportal/service/impl/MrnaPercentileServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/MrnaPercentileServiceImplTest.java index 4a21c6a8688..ce9f6469687 100644 --- a/src/test/java/org/cbioportal/service/impl/MrnaPercentileServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/MrnaPercentileServiceImplTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MrnaPercentile; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MrnaPercentile; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/MutationServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/MutationServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/MutationServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/MutationServiceImplTest.java index e89edc0627f..b4f28bb14ce 100644 --- a/src/test/java/org/cbioportal/service/impl/MutationServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/MutationServiceImplTest.java @@ -1,17 +1,17 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.persistence.MutationRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.persistence.MutationRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/MutationSpectrumServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/MutationSpectrumServiceImplTest.java similarity index 96% rename from src/test/java/org/cbioportal/service/impl/MutationSpectrumServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/MutationSpectrumServiceImplTest.java index c27bbcdb830..f4960f142d5 100644 --- a/src/test/java/org/cbioportal/service/impl/MutationSpectrumServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/MutationSpectrumServiceImplTest.java @@ -1,8 +1,8 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationSpectrum; -import org.cbioportal.service.MutationService; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationSpectrum; +import org.cbioportal.legacy.service.MutationService; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/PatientServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/PatientServiceImplTest.java similarity index 93% rename from src/test/java/org/cbioportal/service/impl/PatientServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/PatientServiceImplTest.java index 9d15499e55f..f2ecca2e8c8 100644 --- a/src/test/java/org/cbioportal/service/impl/PatientServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/PatientServiceImplTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.PatientRepository; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.PatientRepository; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/ReadPermissionServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ReadPermissionServiceImplTest.java similarity index 89% rename from src/test/java/org/cbioportal/service/impl/ReadPermissionServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ReadPermissionServiceImplTest.java index 5f781f0d9ce..406e8f22152 100644 --- a/src/test/java/org/cbioportal/service/impl/ReadPermissionServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ReadPermissionServiceImplTest.java @@ -1,8 +1,9 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.security.CancerStudyPermissionEvaluator; -import org.cbioportal.utils.security.AccessLevel; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.application.security.CancerStudyPermissionEvaluator; +import org.cbioportal.legacy.service.impl.ReadPermissionServiceImpl; +import org.cbioportal.legacy.utils.security.AccessLevel; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/ReferenceGenomeGeneServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ReferenceGenomeGeneServiceImplTest.java similarity index 91% rename from src/test/java/org/cbioportal/service/impl/ReferenceGenomeGeneServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ReferenceGenomeGeneServiceImplTest.java index 7ce4bb6a6bc..1d20e73e9e9 100644 --- a/src/test/java/org/cbioportal/service/impl/ReferenceGenomeGeneServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ReferenceGenomeGeneServiceImplTest.java @@ -1,11 +1,9 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.Gene; -import org.cbioportal.model.ReferenceGenome; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ReferenceGenomeGeneRepository; -import org.cbioportal.service.exception.GeneNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.ReferenceGenome; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.persistence.ReferenceGenomeGeneRepository; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; @@ -15,7 +13,6 @@ import org.mockito.junit.MockitoJUnitRunner; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; @RunWith(MockitoJUnitRunner.class) diff --git a/src/test/java/org/cbioportal/service/impl/SampleListServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/SampleListServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/SampleListServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/SampleListServiceImplTest.java index 42b639e5a0a..b6c64f0ceb3 100644 --- a/src/test/java/org/cbioportal/service/impl/SampleListServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/SampleListServiceImplTest.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.SampleList; -import org.cbioportal.model.SampleListToSampleId; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.SampleListToSampleId; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.Before; diff --git a/src/test/java/org/cbioportal/service/impl/SampleServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/SampleServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/SampleServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/SampleServiceImplTest.java index 374368d1718..c4dbb9f9060 100644 --- a/src/test/java/org/cbioportal/service/impl/SampleServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/SampleServiceImplTest.java @@ -1,17 +1,17 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CopyNumberSegmentRepository; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.persistence.SampleRepository; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CopyNumberSegmentRepository; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.persistence.SampleRepository; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/ServerStatusServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ServerStatusServiceImplTest.java similarity index 86% rename from src/test/java/org/cbioportal/service/impl/ServerStatusServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ServerStatusServiceImplTest.java index 03fc7c35db0..e60862b7486 100644 --- a/src/test/java/org/cbioportal/service/impl/ServerStatusServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ServerStatusServiceImplTest.java @@ -1,11 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.persistence.CancerTypeRepository; -import org.cbioportal.service.impl.ServerStatusServiceImpl.ServerStatusMessage; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.persistence.CancerTypeRepository; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/SignificantCopyNumberRegionServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/SignificantCopyNumberRegionServiceImplTest.java similarity index 89% rename from src/test/java/org/cbioportal/service/impl/SignificantCopyNumberRegionServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/SignificantCopyNumberRegionServiceImplTest.java index cf7a4ae0e8b..ecbc2cf7aa4 100644 --- a/src/test/java/org/cbioportal/service/impl/SignificantCopyNumberRegionServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/SignificantCopyNumberRegionServiceImplTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SignificantCopyNumberRegionRepository; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SignificantCopyNumberRegionRepository; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/SignificantlyMutatedGeneServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/SignificantlyMutatedGeneServiceImplTest.java similarity index 87% rename from src/test/java/org/cbioportal/service/impl/SignificantlyMutatedGeneServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/SignificantlyMutatedGeneServiceImplTest.java index 30076855c7f..1dcca401c3f 100644 --- a/src/test/java/org/cbioportal/service/impl/SignificantlyMutatedGeneServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/SignificantlyMutatedGeneServiceImplTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SignificantlyMutatedGeneRepository; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SignificantlyMutatedGeneRepository; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/StaticDataTimestampServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/StaticDataTimestampServiceImplTest.java similarity index 86% rename from src/test/java/org/cbioportal/service/impl/StaticDataTimestampServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/StaticDataTimestampServiceImplTest.java index 498ae771bb5..945d44fc899 100644 --- a/src/test/java/org/cbioportal/service/impl/StaticDataTimestampServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/StaticDataTimestampServiceImplTest.java @@ -1,7 +1,7 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.TableTimestampPair; -import org.cbioportal.persistence.StaticDataTimeStampRepository; +import org.cbioportal.legacy.model.TableTimestampPair; +import org.cbioportal.legacy.persistence.StaticDataTimeStampRepository; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/StructuralVariantServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/StructuralVariantServiceImplTest.java similarity index 91% rename from src/test/java/org/cbioportal/service/impl/StructuralVariantServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/StructuralVariantServiceImplTest.java index 71e2d2d4efb..c7f1b1f1554 100644 --- a/src/test/java/org/cbioportal/service/impl/StructuralVariantServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/StructuralVariantServiceImplTest.java @@ -21,16 +21,16 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.Collections; import java.util.List; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantQuery; -import org.cbioportal.persistence.StructuralVariantRepository; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantQuery; +import org.cbioportal.legacy.persistence.StructuralVariantRepository; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/StudyServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/StudyServiceImplTest.java similarity index 88% rename from src/test/java/org/cbioportal/service/impl/StudyServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/StudyServiceImplTest.java index ae97ac38e4c..c5dbcec60f5 100644 --- a/src/test/java/org/cbioportal/service/impl/StudyServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/StudyServiceImplTest.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.StudyRepository; -import org.cbioportal.service.CancerTypeService; -import org.cbioportal.service.ReadPermissionService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.utils.security.AccessLevel; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.StudyRepository; +import org.cbioportal.legacy.service.CancerTypeService; +import org.cbioportal.legacy.service.ReadPermissionService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.utils.security.AccessLevel; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/StudyViewServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/StudyViewServiceImplTest.java similarity index 95% rename from src/test/java/org/cbioportal/service/impl/StudyViewServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/StudyViewServiceImplTest.java index e714ec3ea0d..c7d6e122e13 100644 --- a/src/test/java/org/cbioportal/service/impl/StudyViewServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/StudyViewServiceImplTest.java @@ -1,32 +1,32 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenericAssayData; -import org.cbioportal.model.GenericAssayDataCount; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.model.util.Select; -import org.cbioportal.service.AlterationCountService; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.SignificantCopyNumberRegionService; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenericAssayData; +import org.cbioportal.legacy.model.GenericAssayDataCount; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.service.AlterationCountService; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.SignificantCopyNumberRegionService; +import org.cbioportal.legacy.service.SignificantlyMutatedGeneService; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/TreatmentServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/TreatmentServiceImplTest.java similarity index 96% rename from src/test/java/org/cbioportal/service/impl/TreatmentServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/TreatmentServiceImplTest.java index 8a86e465d3f..cf4a01a066f 100644 --- a/src/test/java/org/cbioportal/service/impl/TreatmentServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/TreatmentServiceImplTest.java @@ -1,7 +1,13 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.*; -import org.cbioportal.persistence.TreatmentRepository; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.model.TemporalRelation; +import org.cbioportal.legacy.model.Treatment; +import org.cbioportal.legacy.service.impl.TreatmentServiceImpl; +import org.cbioportal.legacy.persistence.TreatmentRepository; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTest.java similarity index 93% rename from src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTest.java index 89b34a50c95..9a225e610f1 100644 --- a/src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTest.java @@ -46,31 +46,22 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; //TODO package org.cbioportal.security.spring.authentication.token; import java.util.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; + import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.beans.factory.annotation.Value; -import org.springframework.stereotype.Component; -import org.springframework.context.annotation.Import; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.TestPropertySource; import org.springframework.test.context.junit4.SpringRunner; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.Mockito; -import org.mockito.junit.MockitoJUnitRunner; -import org.cbioportal.persistence.DataAccessTokenRepository; -import org.cbioportal.service.exception.InvalidDataAccessTokenException; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.impl.UuidDataAccessTokenServiceImpl; +import org.cbioportal.legacy.persistence.DataAccessTokenRepository; +import org.cbioportal.legacy.model.DataAccessToken; @TestPropertySource( properties = { "dat.jwt.secret_key = +NbopXzb/AIQNrVEGzxzP5CF42e5drvrXTQot3gfW/s=", diff --git a/src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTestConfiguration.java b/src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTestConfiguration.java similarity index 97% rename from src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTestConfiguration.java rename to src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTestConfiguration.java index d83ff6994fe..c2905a58f87 100644 --- a/src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTestConfiguration.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTestConfiguration.java @@ -46,19 +46,20 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; //TODO package org.cbioportal.security.spring.authentication.token; import java.util.*; +import org.cbioportal.legacy.service.impl.UuidDataAccessTokenServiceImpl; import org.springframework.boot.test.context.TestConfiguration; import org.springframework.context.annotation.Bean; import org.mockito.ArgumentMatchers; import org.mockito.Mockito; import org.mockito.stubbing.Answer; import org.mockito.invocation.InvocationOnMock; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.persistence.DataAccessTokenRepository; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.persistence.DataAccessTokenRepository; @TestConfiguration public class UuidDataAccessTokenServiceImplTestConfiguration { diff --git a/src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTestFiveTokenLimit.java b/src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTestFiveTokenLimit.java similarity index 91% rename from src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTestFiveTokenLimit.java rename to src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTestFiveTokenLimit.java index 46a43245032..063a654a85d 100644 --- a/src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTestFiveTokenLimit.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTestFiveTokenLimit.java @@ -46,31 +46,22 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; //TODO package org.cbioportal.security.spring.authentication.token; import java.util.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.cbioportal.service.exception.InvalidDataAccessTokenException; + import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.beans.factory.annotation.Value; -import org.springframework.stereotype.Component; -import org.springframework.context.annotation.Import; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.TestPropertySource; import org.springframework.test.context.junit4.SpringRunner; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.Mockito; -import org.mockito.junit.MockitoJUnitRunner; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.persistence.DataAccessTokenRepository; -import org.cbioportal.service.impl.UuidDataAccessTokenServiceImpl; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.persistence.DataAccessTokenRepository; @TestPropertySource( properties = { "dat.jwt.secret_key = +NbopXzb/AIQNrVEGzxzP5CF42e5drvrXTQot3gfW/s=", diff --git a/src/test/java/org/cbioportal/service/impl/VariantCountServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/VariantCountServiceImplTest.java similarity index 82% rename from src/test/java/org/cbioportal/service/impl/VariantCountServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/VariantCountServiceImplTest.java index 2b828629d62..14cd72b79ee 100644 --- a/src/test/java/org/cbioportal/service/impl/VariantCountServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/VariantCountServiceImplTest.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.VariantCount; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.persistence.VariantCountRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.SampleListService; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.VariantCount; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.persistence.VariantCountRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.SampleListService; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/ViolinPlotServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ViolinPlotServiceImplTest.java similarity index 97% rename from src/test/java/org/cbioportal/service/impl/ViolinPlotServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ViolinPlotServiceImplTest.java index 2b00e7f2c66..e879097dccb 100644 --- a/src/test/java/org/cbioportal/service/impl/ViolinPlotServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ViolinPlotServiceImplTest.java @@ -1,10 +1,11 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalViolinPlotData; -import org.cbioportal.model.ClinicalViolinPlotRowData; -import org.cbioportal.model.Sample; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalViolinPlotData; +import org.cbioportal.legacy.model.ClinicalViolinPlotRowData; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.impl.ViolinPlotServiceImpl; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/util/AlterationCountServiceUtilTest.java b/src/test/java/org/cbioportal/legacy/service/util/AlterationCountServiceUtilTest.java similarity index 97% rename from src/test/java/org/cbioportal/service/util/AlterationCountServiceUtilTest.java rename to src/test/java/org/cbioportal/legacy/service/util/AlterationCountServiceUtilTest.java index 31f09303271..4ec37645110 100644 --- a/src/test/java/org/cbioportal/service/util/AlterationCountServiceUtilTest.java +++ b/src/test/java/org/cbioportal/legacy/service/util/AlterationCountServiceUtilTest.java @@ -1,13 +1,14 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MutSig; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.service.util.AlterationCountServiceUtil; import org.junit.Test; import java.math.BigDecimal; diff --git a/src/test/java/org/cbioportal/service/util/AlterationEnrichmentUtilTest.java b/src/test/java/org/cbioportal/legacy/service/util/AlterationEnrichmentUtilTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/util/AlterationEnrichmentUtilTest.java rename to src/test/java/org/cbioportal/legacy/service/util/AlterationEnrichmentUtilTest.java index 7020d01ef0e..6751bfd1dd4 100644 --- a/src/test/java/org/cbioportal/service/util/AlterationEnrichmentUtilTest.java +++ b/src/test/java/org/cbioportal/legacy/service/util/AlterationEnrichmentUtilTest.java @@ -1,11 +1,17 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.math.BigDecimal; import java.util.*; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.*; -import org.cbioportal.service.GeneService; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationEnrichment; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.util.AlterationEnrichmentUtil; +import org.cbioportal.legacy.service.util.FisherExactTestCalculator; +import org.cbioportal.legacy.service.util.ProfiledCasesCounter; +import org.cbioportal.legacy.service.GeneService; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/util/CoExpressionAsyncMethodsTest.java b/src/test/java/org/cbioportal/legacy/service/util/CoExpressionAsyncMethodsTest.java similarity index 96% rename from src/test/java/org/cbioportal/service/util/CoExpressionAsyncMethodsTest.java rename to src/test/java/org/cbioportal/legacy/service/util/CoExpressionAsyncMethodsTest.java index 28fb4c43c13..9c2daebb3ec 100644 --- a/src/test/java/org/cbioportal/service/util/CoExpressionAsyncMethodsTest.java +++ b/src/test/java/org/cbioportal/legacy/service/util/CoExpressionAsyncMethodsTest.java @@ -1,6 +1,7 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; -import org.cbioportal.model.CoExpression; +import org.cbioportal.legacy.model.CoExpression; +import org.cbioportal.legacy.service.util.CoExpressionAsyncMethods; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/util/JwtUtilsTest.java b/src/test/java/org/cbioportal/legacy/service/util/JwtUtilsTest.java similarity index 98% rename from src/test/java/org/cbioportal/service/util/JwtUtilsTest.java rename to src/test/java/org/cbioportal/legacy/service/util/JwtUtilsTest.java index 13d848d098d..954144b73de 100644 --- a/src/test/java/org/cbioportal/service/util/JwtUtilsTest.java +++ b/src/test/java/org/cbioportal/legacy/service/util/JwtUtilsTest.java @@ -46,11 +46,11 @@ * along with this program. If not, see . */ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; //TODO package org.cbioportal.security.spring.authentication.token; import java.util.*; -import org.cbioportal.service.exception.InvalidDataAccessTokenException; +import org.cbioportal.legacy.service.exception.InvalidDataAccessTokenException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.TestPropertySource; diff --git a/src/test/java/org/cbioportal/service/util/JwtUtilsTestConfiguration.java b/src/test/java/org/cbioportal/legacy/service/util/JwtUtilsTestConfiguration.java similarity index 96% rename from src/test/java/org/cbioportal/service/util/JwtUtilsTestConfiguration.java rename to src/test/java/org/cbioportal/legacy/service/util/JwtUtilsTestConfiguration.java index 5322922a2d6..5e235ffe341 100644 --- a/src/test/java/org/cbioportal/service/util/JwtUtilsTestConfiguration.java +++ b/src/test/java/org/cbioportal/legacy/service/util/JwtUtilsTestConfiguration.java @@ -46,9 +46,10 @@ * along with this program. If not, see . */ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; //TODO package org.cbioportal.security.spring.authentication.token; +import org.cbioportal.legacy.service.util.JwtUtils; import org.springframework.boot.test.context.TestConfiguration; import org.springframework.context.annotation.Bean; diff --git a/src/test/java/org/cbioportal/service/util/MolecularProfileUtilTest.java b/src/test/java/org/cbioportal/legacy/service/util/MolecularProfileUtilTest.java similarity index 97% rename from src/test/java/org/cbioportal/service/util/MolecularProfileUtilTest.java rename to src/test/java/org/cbioportal/legacy/service/util/MolecularProfileUtilTest.java index 078acc83e06..5a23eef4325 100644 --- a/src/test/java/org/cbioportal/service/util/MolecularProfileUtilTest.java +++ b/src/test/java/org/cbioportal/legacy/service/util/MolecularProfileUtilTest.java @@ -1,8 +1,8 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.service.impl.BaseServiceImplTest; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.impl.BaseServiceImplTest; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/util/ProfiledCasesCounterTest.java b/src/test/java/org/cbioportal/legacy/service/util/ProfiledCasesCounterTest.java similarity index 93% rename from src/test/java/org/cbioportal/service/util/ProfiledCasesCounterTest.java rename to src/test/java/org/cbioportal/legacy/service/util/ProfiledCasesCounterTest.java index a0303a80c7a..e5bc4fb1971 100644 --- a/src/test/java/org/cbioportal/service/util/ProfiledCasesCounterTest.java +++ b/src/test/java/org/cbioportal/legacy/service/util/ProfiledCasesCounterTest.java @@ -1,15 +1,16 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.SampleListService; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.util.ProfiledCasesCounter; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java b/src/test/java/org/cbioportal/legacy/service/util/StudyViewColumnarServiceUtilTest.java similarity index 96% rename from src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java rename to src/test/java/org/cbioportal/legacy/service/util/StudyViewColumnarServiceUtilTest.java index 0c9687d6e59..cdbc893ecbb 100644 --- a/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java +++ b/src/test/java/org/cbioportal/legacy/service/util/StudyViewColumnarServiceUtilTest.java @@ -1,12 +1,13 @@ -package org.cbioportal.service.util; - -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.web.parameter.GenomicDataFilter; +package org.cbioportal.legacy.service.util; + +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.service.util.StudyViewColumnarServiceUtil; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; import org.junit.Assert; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/utils/config/PropertyConditionTest.java b/src/test/java/org/cbioportal/legacy/utils/config/PropertyConditionTest.java similarity index 97% rename from src/test/java/org/cbioportal/utils/config/PropertyConditionTest.java rename to src/test/java/org/cbioportal/legacy/utils/config/PropertyConditionTest.java index 79dd1ba5e48..b6a950fe7b4 100644 --- a/src/test/java/org/cbioportal/utils/config/PropertyConditionTest.java +++ b/src/test/java/org/cbioportal/legacy/utils/config/PropertyConditionTest.java @@ -1,5 +1,6 @@ -package org.cbioportal.utils.config; +package org.cbioportal.legacy.utils.config; +import org.cbioportal.legacy.utils.config.PropertyCondition; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/web/AlterationDriverAnnotationControllerTest.java b/src/test/java/org/cbioportal/legacy/web/AlterationDriverAnnotationControllerTest.java similarity index 93% rename from src/test/java/org/cbioportal/web/AlterationDriverAnnotationControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/AlterationDriverAnnotationControllerTest.java index cfa208c397f..7b0efce0839 100644 --- a/src/test/java/org/cbioportal/web/AlterationDriverAnnotationControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/AlterationDriverAnnotationControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.mockito.ArgumentMatchers.anyList; import static org.mockito.Mockito.when; @@ -11,9 +11,9 @@ import java.util.Collections; import java.util.HashSet; import java.util.List; -import org.cbioportal.model.CustomDriverAnnotationReport; -import org.cbioportal.service.AlterationDriverAnnotationService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.CustomDriverAnnotationReport; +import org.cbioportal.legacy.service.AlterationDriverAnnotationService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/web/AlterationEnrichmentControllerTest.java b/src/test/java/org/cbioportal/legacy/web/AlterationEnrichmentControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/AlterationEnrichmentControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/AlterationEnrichmentControllerTest.java index 54ab0b76405..25b39a16e93 100644 --- a/src/test/java/org/cbioportal/web/AlterationEnrichmentControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/AlterationEnrichmentControllerTest.java @@ -1,17 +1,17 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.AlterationEnrichment; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.CountSummary; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.service.AlterationEnrichmentService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupAndAlterationTypeFilter; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupFilter; -import org.cbioportal.web.util.AlterationFilterMockitoArgumentMatcher; +import org.cbioportal.legacy.model.AlterationEnrichment; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CountSummary; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.service.AlterationEnrichmentService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupAndAlterationTypeFilter; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupFilter; +import org.cbioportal.legacy.web.util.AlterationFilterMockitoArgumentMatcher; import org.hamcrest.Matchers; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/web/CacheControllerTest.java b/src/test/java/org/cbioportal/legacy/web/CacheControllerTest.java similarity index 92% rename from src/test/java/org/cbioportal/web/CacheControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/CacheControllerTest.java index cf40aee1d37..c09783784a7 100644 --- a/src/test/java/org/cbioportal/web/CacheControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/CacheControllerTest.java @@ -1,7 +1,5 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; -import static org.mockito.ArgumentMatchers.anyBoolean; -import static org.mockito.ArgumentMatchers.anyString; import static org.mockito.ArgumentMatchers.eq; import static org.mockito.Mockito.doThrow; import static org.mockito.Mockito.never; @@ -10,10 +8,8 @@ import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; -import org.cbioportal.service.CacheService; -import org.cbioportal.service.exception.CacheOperationException; -import org.junit.Ignore; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.service.CacheService; +import org.cbioportal.legacy.web.config.TestConfig; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/web/CacheStatsControllerTest.java b/src/test/java/org/cbioportal/legacy/web/CacheStatsControllerTest.java similarity index 94% rename from src/test/java/org/cbioportal/web/CacheStatsControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/CacheStatsControllerTest.java index 904b76f8d03..bfd5d45fc2a 100644 --- a/src/test/java/org/cbioportal/web/CacheStatsControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/CacheStatsControllerTest.java @@ -1,8 +1,8 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; -import org.cbioportal.service.CacheStatisticsService; -import org.cbioportal.service.exception.CacheNotFoundException; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.service.CacheStatisticsService; +import org.cbioportal.legacy.service.exception.CacheNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/CancerTypeControllerTest.java b/src/test/java/org/cbioportal/legacy/web/CancerTypeControllerTest.java similarity index 94% rename from src/test/java/org/cbioportal/web/CancerTypeControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/CancerTypeControllerTest.java index fb53ae94c76..babad36579b 100644 --- a/src/test/java/org/cbioportal/web/CancerTypeControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/CancerTypeControllerTest.java @@ -1,13 +1,13 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.CancerTypeService; -import org.cbioportal.service.exception.CancerTypeNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.CancerTypeService; +import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ClinicalAttributeControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ClinicalAttributeControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/ClinicalAttributeControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ClinicalAttributeControllerTest.java index 8433b5018fa..468f39accac 100644 --- a/src/test/java/org/cbioportal/web/ClinicalAttributeControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ClinicalAttributeControllerTest.java @@ -1,18 +1,15 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.exception.ClinicalAttributeNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.ClinicalAttributeCountFilter; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.exception.ClinicalAttributeNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ClinicalAttributeCountControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ClinicalAttributeCountControllerTest.java similarity index 92% rename from src/test/java/org/cbioportal/web/ClinicalAttributeCountControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ClinicalAttributeCountControllerTest.java index e59b46f760e..a074445caeb 100644 --- a/src/test/java/org/cbioportal/web/ClinicalAttributeCountControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ClinicalAttributeCountControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,15 +6,12 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.exception.ClinicalAttributeNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.ClinicalAttributeCountFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.SampleIdentifier; + +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.ClinicalAttributeCountFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ClinicalDataControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ClinicalDataControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/ClinicalDataControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ClinicalDataControllerTest.java index 86d56d7accb..7747ac721cb 100644 --- a/src/test/java/org/cbioportal/web/ClinicalDataControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ClinicalDataControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,15 +6,15 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.web.config.CustomObjectMapper; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.ClinicalDataIdentifier; -import org.cbioportal.web.parameter.ClinicalDataMultiStudyFilter; -import org.cbioportal.web.parameter.ClinicalDataSingleStudyFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.web.config.CustomObjectMapper; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.ClinicalDataIdentifier; +import org.cbioportal.legacy.web.parameter.ClinicalDataMultiStudyFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataSingleStudyFilter; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ClinicalDataEnrichmentControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ClinicalDataEnrichmentControllerTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/ClinicalDataEnrichmentControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ClinicalDataEnrichmentControllerTest.java index 8e9ab0fa5ef..f7ea9e12e05 100644 --- a/src/test/java/org/cbioportal/web/ClinicalDataEnrichmentControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ClinicalDataEnrichmentControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -8,16 +8,16 @@ import java.util.Arrays; import java.util.List; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalDataEnrichment; -import org.cbioportal.model.Sample; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.SampleService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.Group; -import org.cbioportal.web.parameter.GroupFilter; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.util.ClinicalDataEnrichmentUtil; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalDataEnrichment; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.Group; +import org.cbioportal.legacy.web.parameter.GroupFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.util.ClinicalDataEnrichmentUtil; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ClinicalEventControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ClinicalEventControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/ClinicalEventControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ClinicalEventControllerTest.java index bdbda3ca306..b2d41aaff2e 100644 --- a/src/test/java/org/cbioportal/web/ClinicalEventControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ClinicalEventControllerTest.java @@ -1,15 +1,15 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.ClinicalEventAttributeRequest; -import org.cbioportal.web.parameter.ClinicalEventRequest; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PatientIdentifier; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.ClinicalEventAttributeRequest; +import org.cbioportal.legacy.web.parameter.ClinicalEventRequest; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PatientIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/CoExpressionControllerTest.java b/src/test/java/org/cbioportal/legacy/web/CoExpressionControllerTest.java similarity index 93% rename from src/test/java/org/cbioportal/web/CoExpressionControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/CoExpressionControllerTest.java index ae97e59d1d6..a2b61a606cf 100644 --- a/src/test/java/org/cbioportal/web/CoExpressionControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/CoExpressionControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -8,11 +8,11 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.CoExpression; -import org.cbioportal.model.EntityType; -import org.cbioportal.service.CoExpressionService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.CoExpressionFilter; +import org.cbioportal.legacy.model.CoExpression; +import org.cbioportal.legacy.model.EntityType; +import org.cbioportal.legacy.service.CoExpressionService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.CoExpressionFilter; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/CopyNumberSegmentControllerTest.java b/src/test/java/org/cbioportal/legacy/web/CopyNumberSegmentControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/CopyNumberSegmentControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/CopyNumberSegmentControllerTest.java index 88e10e11eaa..cd242c8bed1 100644 --- a/src/test/java/org/cbioportal/web/CopyNumberSegmentControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/CopyNumberSegmentControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -7,12 +7,12 @@ import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.CopyNumberSegmentService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.CopyNumberSegmentService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/CosmicCountControllerTest.java b/src/test/java/org/cbioportal/legacy/web/CosmicCountControllerTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/CosmicCountControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/CosmicCountControllerTest.java index e1cd3cb52e3..b39948136d7 100644 --- a/src/test/java/org/cbioportal/web/CosmicCountControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/CosmicCountControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,9 +6,9 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.CosmicMutation; -import org.cbioportal.service.CosmicCountService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.CosmicMutation; +import org.cbioportal.legacy.service.CosmicCountService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/DataAccessTokenControllerTest.java b/src/test/java/org/cbioportal/legacy/web/DataAccessTokenControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/DataAccessTokenControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/DataAccessTokenControllerTest.java index 917a2908184..66065e76223 100644 --- a/src/test/java/org/cbioportal/web/DataAccessTokenControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/DataAccessTokenControllerTest.java @@ -15,7 +15,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.mockito.Mockito.*; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -23,12 +23,11 @@ import com.fasterxml.jackson.databind.ObjectMapper; import jakarta.servlet.http.HttpSession; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.service.exception.TokenNotFoundException; -import org.cbioportal.web.config.DataAccessTokenControllerConfig; -import org.cbioportal.web.config.DataAccessTokenControllerTestConfig; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.service.exception.TokenNotFoundException; +import org.cbioportal.legacy.web.config.DataAccessTokenControllerTestConfig; +import org.cbioportal.legacy.web.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; @@ -44,7 +43,6 @@ import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.TestPropertySource; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import org.springframework.test.util.ReflectionTestUtils; import org.springframework.test.web.servlet.MockMvc; import org.springframework.test.web.servlet.MvcResult; import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; diff --git a/src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java b/src/test/java/org/cbioportal/legacy/web/DiscreteCopyNumberControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/DiscreteCopyNumberControllerTest.java index 126c183c204..d0a5629ef84 100644 --- a/src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/DiscreteCopyNumberControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,16 +6,15 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.CopyNumberCount; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.Gene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.CopyNumberCountIdentifier; -import org.cbioportal.web.parameter.DiscreteCopyNumberEventType; -import org.cbioportal.web.parameter.DiscreteCopyNumberFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; + +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.DiscreteCopyNumberService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.DiscreteCopyNumberEventType; +import org.cbioportal.legacy.web.parameter.DiscreteCopyNumberFilter; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/DiscreteCopyNumberCountControllerTest.java b/src/test/java/org/cbioportal/legacy/web/DiscreteCopyNumberCountControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/DiscreteCopyNumberCountControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/DiscreteCopyNumberCountControllerTest.java index e90866f12f8..81946bc5c1c 100644 --- a/src/test/java/org/cbioportal/web/DiscreteCopyNumberCountControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/DiscreteCopyNumberCountControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,10 +6,10 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.CopyNumberCount; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.CopyNumberCountIdentifier; +import org.cbioportal.legacy.model.CopyNumberCount; +import org.cbioportal.legacy.service.DiscreteCopyNumberService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.CopyNumberCountIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/DocRedirectControllerTest.java b/src/test/java/org/cbioportal/legacy/web/DocRedirectControllerTest.java similarity index 85% rename from src/test/java/org/cbioportal/web/DocRedirectControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/DocRedirectControllerTest.java index 3765936985d..3c0257d37b9 100644 --- a/src/test/java/org/cbioportal/web/DocRedirectControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/DocRedirectControllerTest.java @@ -1,21 +1,15 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import junit.framework.TestCase; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.web.config.TestConfig; import org.junit.Before; import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; -import org.mockito.Mockito; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest; -import org.springframework.context.annotation.Bean; -import org.springframework.context.annotation.Configuration; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import org.springframework.test.context.web.WebAppConfiguration; import org.springframework.test.web.servlet.MockMvc; import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; import org.springframework.test.web.servlet.result.MockMvcResultMatchers; diff --git a/src/test/java/org/cbioportal/web/ExpressionEnrichmentControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ExpressionEnrichmentControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/ExpressionEnrichmentControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ExpressionEnrichmentControllerTest.java index 2f73e1ca80b..f0742f96f07 100644 --- a/src/test/java/org/cbioportal/web/ExpressionEnrichmentControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ExpressionEnrichmentControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,12 +6,12 @@ import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.GenericAssayEnrichment; -import org.cbioportal.model.GenomicEnrichment; -import org.cbioportal.model.GroupStatistics; -import org.cbioportal.service.ExpressionEnrichmentService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.GenericAssayEnrichment; +import org.cbioportal.legacy.model.GenomicEnrichment; +import org.cbioportal.legacy.model.GroupStatistics; +import org.cbioportal.legacy.service.ExpressionEnrichmentService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/GeneControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GeneControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/GeneControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GeneControllerTest.java index c4b78fb7fde..56498842a63 100644 --- a/src/test/java/org/cbioportal/web/GeneControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GeneControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.mockito.ArgumentMatchers.eq; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -7,14 +7,13 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.exception.GeneNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; import org.mockito.Mockito; diff --git a/src/test/java/org/cbioportal/web/GenePanelControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenePanelControllerTest.java similarity index 93% rename from src/test/java/org/cbioportal/web/GenePanelControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenePanelControllerTest.java index 50a5a7f09a5..20e3ea084c4 100644 --- a/src/test/java/org/cbioportal/web/GenePanelControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenePanelControllerTest.java @@ -1,22 +1,16 @@ -package org.cbioportal.web; - -import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.exception.GenePanelNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.GenePanelDataFilter; -import org.cbioportal.web.parameter.GenePanelDataMultipleStudyFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.exception.GenePanelNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/GenePanelDataControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenePanelDataControllerTest.java similarity index 92% rename from src/test/java/org/cbioportal/web/GenePanelDataControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenePanelDataControllerTest.java index 824223ef8a9..72d8b76b92a 100644 --- a/src/test/java/org/cbioportal/web/GenePanelDataControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenePanelDataControllerTest.java @@ -1,17 +1,12 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.exception.GenePanelNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.GenePanelDataFilter; -import org.cbioportal.web.parameter.GenePanelDataMultipleStudyFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.GenePanelDataFilter; +import org.cbioportal.legacy.web.parameter.GenePanelDataMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; import org.hamcrest.Matchers; import org.junit.Before; import org.junit.Test; @@ -20,13 +15,10 @@ import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest; import org.springframework.boot.test.mock.mockito.MockBean; -import org.springframework.context.annotation.Bean; -import org.springframework.context.annotation.Configuration; import org.springframework.http.MediaType; import org.springframework.security.test.context.support.WithMockUser; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import org.springframework.test.context.web.WebAppConfiguration; import org.springframework.test.web.servlet.MockMvc; import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; import org.springframework.test.web.servlet.result.MockMvcResultMatchers; @@ -34,7 +26,6 @@ import org.springframework.web.context.WebApplicationContext; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; @RunWith(SpringJUnit4ClassRunner.class) diff --git a/src/test/java/org/cbioportal/web/GenericAssayControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenericAssayControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/GenericAssayControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenericAssayControllerTest.java index a3f81f70a38..8ee7612398a 100644 --- a/src/test/java/org/cbioportal/web/GenericAssayControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenericAssayControllerTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.GenericAssayMetaFilter; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.GenericAssayMetaFilter; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/GenericAssayDataControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenericAssayDataControllerTest.java similarity index 94% rename from src/test/java/org/cbioportal/web/GenericAssayDataControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenericAssayDataControllerTest.java index ee7fc0d285c..9a8742ba05d 100644 --- a/src/test/java/org/cbioportal/web/GenericAssayDataControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenericAssayDataControllerTest.java @@ -1,14 +1,12 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.GenericAssayData; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.GenericAssayDataMultipleStudyFilter; -import org.cbioportal.web.parameter.GenericAssayFilter; -import org.cbioportal.web.parameter.GenericAssayMetaFilter; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.model.GenericAssayData; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.GenericAssayDataMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayFilter; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; import org.hamcrest.Matchers; import org.junit.Before; import org.junit.Test; @@ -17,12 +15,9 @@ import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest; import org.springframework.boot.test.mock.mockito.MockBean; -import org.springframework.context.annotation.Bean; -import org.springframework.context.annotation.Configuration; import org.springframework.http.MediaType; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import org.springframework.test.context.web.WebAppConfiguration; import org.springframework.test.web.servlet.MockMvc; import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; import org.springframework.test.web.servlet.result.MockMvcResultMatchers; diff --git a/src/test/java/org/cbioportal/web/GenesetControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenesetControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/GenesetControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenesetControllerTest.java index e58da5d8fa0..426ccee931d 100644 --- a/src/test/java/org/cbioportal/web/GenesetControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenesetControllerTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Geneset; -import org.cbioportal.service.GenesetService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.service.GenesetService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/GenesetCorrelationControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenesetCorrelationControllerTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/GenesetCorrelationControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenesetCorrelationControllerTest.java index a0bc3244d65..bc515cc5ec1 100644 --- a/src/test/java/org/cbioportal/web/GenesetCorrelationControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenesetCorrelationControllerTest.java @@ -1,13 +1,13 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.GenesetCorrelation; -import org.cbioportal.service.GenesetCorrelationService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.GenesetCorrelation; +import org.cbioportal.legacy.service.GenesetCorrelationService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/GenesetDataControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenesetDataControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/GenesetDataControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenesetDataControllerTest.java index 843d3aaa771..fcdf0b8b2d9 100644 --- a/src/test/java/org/cbioportal/web/GenesetDataControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenesetDataControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -7,10 +7,10 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.GenesetDataFilterCriteria; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.GenesetDataFilterCriteria; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/GenesetHierarchyControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenesetHierarchyControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/GenesetHierarchyControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenesetHierarchyControllerTest.java index e9a951ce15d..c7674a50352 100644 --- a/src/test/java/org/cbioportal/web/GenesetHierarchyControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenesetHierarchyControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,10 +6,10 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetHierarchyInfo; -import org.cbioportal.service.GenesetHierarchyService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.service.GenesetHierarchyService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/InfoControllerTest.java b/src/test/java/org/cbioportal/legacy/web/InfoControllerTest.java similarity index 94% rename from src/test/java/org/cbioportal/web/InfoControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/InfoControllerTest.java index af78e860bb1..c7cbe258570 100644 --- a/src/test/java/org/cbioportal/web/InfoControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/InfoControllerTest.java @@ -1,6 +1,6 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.web.config.TestConfig; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/web/MolecularDataControllerTest.java b/src/test/java/org/cbioportal/legacy/web/MolecularDataControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/MolecularDataControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/MolecularDataControllerTest.java index 3793079fe80..8fc0cdbc64b 100644 --- a/src/test/java/org/cbioportal/web/MolecularDataControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/MolecularDataControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -7,12 +7,12 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.MolecularDataFilter; -import org.cbioportal.web.parameter.MolecularDataMultipleStudyFilter; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.MolecularDataFilter; +import org.cbioportal.legacy.web.parameter.MolecularDataMultipleStudyFilter; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/MolecularProfileControllerTest.java b/src/test/java/org/cbioportal/legacy/web/MolecularProfileControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/MolecularProfileControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/MolecularProfileControllerTest.java index b999ec5ebe8..0fd88754f6a 100644 --- a/src/test/java/org/cbioportal/web/MolecularProfileControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/MolecularProfileControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -7,14 +7,14 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.MolecularProfileFilter; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.MolecularProfileFilter; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/MrnaPercentileControllerTest.java b/src/test/java/org/cbioportal/legacy/web/MrnaPercentileControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/MrnaPercentileControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/MrnaPercentileControllerTest.java index 1056c2d0336..728b6ae2c60 100644 --- a/src/test/java/org/cbioportal/web/MrnaPercentileControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/MrnaPercentileControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -7,9 +7,9 @@ import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.MrnaPercentile; -import org.cbioportal.service.MrnaPercentileService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.MrnaPercentile; +import org.cbioportal.legacy.service.MrnaPercentileService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/MutationControllerTest.java b/src/test/java/org/cbioportal/legacy/web/MutationControllerTest.java similarity index 98% rename from src/test/java/org/cbioportal/web/MutationControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/MutationControllerTest.java index b68a15106ca..bf76fdf2e6b 100644 --- a/src/test/java/org/cbioportal/web/MutationControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/MutationControllerTest.java @@ -1,18 +1,18 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.AlleleSpecificCopyNumber; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.service.MutationService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.MutationFilter; -import org.cbioportal.web.parameter.MutationMultipleStudyFilter; -import org.cbioportal.web.parameter.MutationPositionIdentifier; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.model.AlleleSpecificCopyNumber; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.MutationFilter; +import org.cbioportal.legacy.web.parameter.MutationMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.MutationPositionIdentifier; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/MutationCountControllerTest.java b/src/test/java/org/cbioportal/legacy/web/MutationCountControllerTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/MutationCountControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/MutationCountControllerTest.java index 26607dd2827..9bb8ed51c25 100644 --- a/src/test/java/org/cbioportal/web/MutationCountControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/MutationCountControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,10 +6,10 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.service.MutationService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.MutationPositionIdentifier; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.MutationPositionIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/MutationSpectrumControllerTest.java b/src/test/java/org/cbioportal/legacy/web/MutationSpectrumControllerTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/MutationSpectrumControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/MutationSpectrumControllerTest.java index 84b562c6a4e..a348e5cc1da 100644 --- a/src/test/java/org/cbioportal/web/MutationSpectrumControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/MutationSpectrumControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -7,10 +7,10 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.MutationSpectrum; -import org.cbioportal.service.MutationSpectrumService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.MutationSpectrumFilter; +import org.cbioportal.legacy.model.MutationSpectrum; +import org.cbioportal.legacy.service.MutationSpectrumService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.MutationSpectrumFilter; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/PatientControllerTest.java b/src/test/java/org/cbioportal/legacy/web/PatientControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/PatientControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/PatientControllerTest.java index 906e8df119e..cf4a1d3c409 100644 --- a/src/test/java/org/cbioportal/web/PatientControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/PatientControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,15 +6,15 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PatientFilter; -import org.cbioportal.web.parameter.PatientIdentifier; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PatientFilter; +import org.cbioportal.legacy.web.parameter.PatientIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ReferenceGenomeGeneControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ReferenceGenomeGeneControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/ReferenceGenomeGeneControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ReferenceGenomeGeneControllerTest.java index 958f4643ee4..1d01421497f 100644 --- a/src/test/java/org/cbioportal/web/ReferenceGenomeGeneControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ReferenceGenomeGeneControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.mockito.Mockito.times; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -8,10 +8,10 @@ import java.util.ArrayList; import java.util.Collections; import java.util.List; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.service.GeneMemoizerService; -import org.cbioportal.service.ReferenceGenomeGeneService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.service.GeneMemoizerService; +import org.cbioportal.legacy.service.ReferenceGenomeGeneService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ResourceDataControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ResourceDataControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/ResourceDataControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ResourceDataControllerTest.java index c5fb2af22a2..31c7df70063 100644 --- a/src/test/java/org/cbioportal/web/ResourceDataControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ResourceDataControllerTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.ResourceData; -import org.cbioportal.service.ResourceDataService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.ResourceData; +import org.cbioportal.legacy.service.ResourceDataService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ResourceDefinitionControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ResourceDefinitionControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/ResourceDefinitionControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ResourceDefinitionControllerTest.java index d76045645d2..b92849fffeb 100644 --- a/src/test/java/org/cbioportal/web/ResourceDefinitionControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ResourceDefinitionControllerTest.java @@ -1,13 +1,13 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.service.ResourceDefinitionService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.service.ResourceDefinitionService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/SampleControllerTest.java b/src/test/java/org/cbioportal/legacy/web/SampleControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/SampleControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/SampleControllerTest.java index 7756f33acdf..d8f8ffecb3c 100644 --- a/src/test/java/org/cbioportal/web/SampleControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/SampleControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,16 +6,16 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.SampleFilter; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.SampleFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/SampleListControllerTest.java b/src/test/java/org/cbioportal/legacy/web/SampleListControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/SampleListControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/SampleListControllerTest.java index 5f2900fb057..579b5e5842f 100644 --- a/src/test/java/org/cbioportal/web/SampleListControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/SampleListControllerTest.java @@ -1,15 +1,15 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ServerStatusControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ServerStatusControllerTest.java similarity index 93% rename from src/test/java/org/cbioportal/web/ServerStatusControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ServerStatusControllerTest.java index f4ec9e1da59..5ad72442cd0 100644 --- a/src/test/java/org/cbioportal/web/ServerStatusControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ServerStatusControllerTest.java @@ -1,6 +1,6 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; -import org.cbioportal.service.ServerStatusService; +import org.cbioportal.legacy.service.ServerStatusService; import org.junit.Before; import org.junit.Ignore; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/SessionServiceControllerTest.java b/src/test/java/org/cbioportal/legacy/web/SessionServiceControllerTest.java similarity index 91% rename from src/test/java/org/cbioportal/web/SessionServiceControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/SessionServiceControllerTest.java index 0f9e751d826..dc1eb97c091 100644 --- a/src/test/java/org/cbioportal/web/SessionServiceControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/SessionServiceControllerTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; -import org.cbioportal.service.util.SessionServiceRequestHandler; -import org.cbioportal.utils.removeme.Session; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.service.util.SessionServiceRequestHandler; +import org.cbioportal.legacy.utils.removeme.Session; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/SignificantCopyNumberRegionControllerTest.java b/src/test/java/org/cbioportal/legacy/web/SignificantCopyNumberRegionControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/SignificantCopyNumberRegionControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/SignificantCopyNumberRegionControllerTest.java index f91c5aaa539..d2aaa08abf9 100644 --- a/src/test/java/org/cbioportal/web/SignificantCopyNumberRegionControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/SignificantCopyNumberRegionControllerTest.java @@ -1,14 +1,14 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.SignificantCopyNumberRegionService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.SignificantCopyNumberRegionService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/SignificantlyMutatedGenesControllerTest.java b/src/test/java/org/cbioportal/legacy/web/SignificantlyMutatedGenesControllerTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/SignificantlyMutatedGenesControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/SignificantlyMutatedGenesControllerTest.java index a8bd79a8fe2..22abdd4e06d 100644 --- a/src/test/java/org/cbioportal/web/SignificantlyMutatedGenesControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/SignificantlyMutatedGenesControllerTest.java @@ -1,13 +1,13 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.SignificantlyMutatedGeneService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/StaticDataTimestampControllerTest.java b/src/test/java/org/cbioportal/legacy/web/StaticDataTimestampControllerTest.java similarity index 91% rename from src/test/java/org/cbioportal/web/StaticDataTimestampControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/StaticDataTimestampControllerTest.java index 1b555c2fbce..52bea19eaea 100644 --- a/src/test/java/org/cbioportal/web/StaticDataTimestampControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/StaticDataTimestampControllerTest.java @@ -1,8 +1,8 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import java.util.HashMap; -import org.cbioportal.service.StaticDataTimestampService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.service.StaticDataTimestampService; +import org.cbioportal.legacy.web.config.TestConfig; import org.junit.Test; import org.junit.runner.RunWith; import org.mockito.Mockito; diff --git a/src/test/java/org/cbioportal/web/StructuralVariantControllerTest.java b/src/test/java/org/cbioportal/legacy/web/StructuralVariantControllerTest.java similarity index 98% rename from src/test/java/org/cbioportal/web/StructuralVariantControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/StructuralVariantControllerTest.java index 0be3faf380a..e2b29dc0189 100644 --- a/src/test/java/org/cbioportal/web/StructuralVariantControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/StructuralVariantControllerTest.java @@ -21,7 +21,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -32,16 +32,15 @@ import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.node.ObjectNode; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantQuery; -import org.cbioportal.model.StructuralVariantSpecialValue; -import org.cbioportal.service.StructuralVariantService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; -import org.cbioportal.web.parameter.StructuralVariantFilter; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantQuery; +import org.cbioportal.legacy.model.StructuralVariantSpecialValue; +import org.cbioportal.legacy.service.StructuralVariantService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.web.parameter.StructuralVariantFilter; import org.hamcrest.Matchers; import org.junit.Assert; -import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; import org.mockito.ArgumentCaptor; @@ -54,8 +53,6 @@ import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; import org.springframework.test.web.servlet.MockMvc; -import org.springframework.test.context.web.WebAppConfiguration; -import org.springframework.test.web.servlet.*; import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; import org.springframework.test.web.servlet.result.MockMvcResultMatchers; diff --git a/src/test/java/org/cbioportal/web/StudyControllerTest.java b/src/test/java/org/cbioportal/legacy/web/StudyControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/StudyControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/StudyControllerTest.java index 1540bf6244c..29ff2258354 100644 --- a/src/test/java/org/cbioportal/web/StudyControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/StudyControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -10,15 +10,15 @@ import java.util.Arrays; import java.util.List; import java.util.TimeZone; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.utils.security.AccessLevel; -import org.cbioportal.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.utils.security.AccessLevel; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; @@ -30,7 +30,6 @@ import org.springframework.security.test.context.support.WithMockUser; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import org.springframework.test.context.web.WebAppConfiguration; import org.springframework.test.util.ReflectionTestUtils; import org.springframework.test.web.servlet.MockMvc; import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; diff --git a/src/test/java/org/cbioportal/web/StudyViewControllerTest.java b/src/test/java/org/cbioportal/legacy/web/StudyViewControllerTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/StudyViewControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/StudyViewControllerTest.java index 19f607bf154..2956a6fb356 100644 --- a/src/test/java/org/cbioportal/web/StudyViewControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/StudyViewControllerTest.java @@ -1,64 +1,64 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; import org.apache.commons.lang3.tuple.ImmutablePair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.GenericAssayDataCount; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleClinicalDataCollection; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariantSpecialValue; -import org.cbioportal.model.StudyViewStructuralVariantFilter; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.AlterationRepository; -import org.cbioportal.service.AlterationCountService; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.StudyViewService; -import org.cbioportal.service.TreatmentService; -import org.cbioportal.service.ViolinPlotService; -import org.cbioportal.service.util.ClinicalAttributeUtil; -import org.cbioportal.service.util.MolecularProfileUtil; -import org.cbioportal.utils.Encoder; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; -import org.cbioportal.web.parameter.ClinicalDataBinFilter; -import org.cbioportal.web.parameter.ClinicalDataCountFilter; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.GenericAssayDataCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataCountFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.ClinicalDataBinUtil; -import org.cbioportal.web.util.ClinicalDataFetcher; -import org.cbioportal.web.util.DataBinHelper; -import org.cbioportal.web.util.DataBinner; -import org.cbioportal.web.util.DiscreteDataBinner; -import org.cbioportal.web.util.LinearDataBinner; -import org.cbioportal.web.util.LogScaleDataBinner; -import org.cbioportal.web.util.ScientificSmallDataBinner; -import org.cbioportal.web.util.StudyViewFilterApplier; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.GenericAssayDataCount; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleClinicalDataCollection; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantSpecialValue; +import org.cbioportal.legacy.model.StudyViewStructuralVariantFilter; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.AlterationRepository; +import org.cbioportal.legacy.service.AlterationCountService; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.service.DiscreteCopyNumberService; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyViewService; +import org.cbioportal.legacy.service.TreatmentService; +import org.cbioportal.legacy.service.ViolinPlotService; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.utils.Encoder; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.ClinicalDataBinUtil; +import org.cbioportal.legacy.web.util.ClinicalDataFetcher; +import org.cbioportal.legacy.web.util.DataBinHelper; +import org.cbioportal.legacy.web.util.DataBinner; +import org.cbioportal.legacy.web.util.DiscreteDataBinner; +import org.cbioportal.legacy.web.util.LinearDataBinner; +import org.cbioportal.legacy.web.util.LogScaleDataBinner; +import org.cbioportal.legacy.web.util.ScientificSmallDataBinner; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.junit.Before; import org.junit.Ignore; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/web/SurvivalControllerTest.java b/src/test/java/org/cbioportal/legacy/web/SurvivalControllerTest.java similarity index 92% rename from src/test/java/org/cbioportal/web/SurvivalControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/SurvivalControllerTest.java index 7c8532c515d..0ae7f22e5aa 100644 --- a/src/test/java/org/cbioportal/web/SurvivalControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/SurvivalControllerTest.java @@ -1,14 +1,14 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.ClinicalEventRequest; -import org.cbioportal.web.parameter.ClinicalEventRequestIdentifier; -import org.cbioportal.web.parameter.OccurrencePosition; -import org.cbioportal.web.parameter.PatientIdentifier; -import org.cbioportal.web.parameter.SurvivalRequest; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.ClinicalEventRequest; +import org.cbioportal.legacy.web.parameter.ClinicalEventRequestIdentifier; +import org.cbioportal.legacy.web.parameter.OccurrencePosition; +import org.cbioportal.legacy.web.parameter.PatientIdentifier; +import org.cbioportal.legacy.web.parameter.SurvivalRequest; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/TreatmentControllerTest.java b/src/test/java/org/cbioportal/legacy/web/TreatmentControllerTest.java similarity index 92% rename from src/test/java/org/cbioportal/web/TreatmentControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/TreatmentControllerTest.java index 85ba345b6fb..6a45b72d422 100644 --- a/src/test/java/org/cbioportal/web/TreatmentControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/TreatmentControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,15 +6,15 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.PatientTreatmentRow; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.model.TemporalRelation; -import org.cbioportal.service.TreatmentService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.StudyViewFilterApplier; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.model.TemporalRelation; +import org.cbioportal.legacy.service.TreatmentService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.junit.Test; import org.junit.runner.RunWith; import org.mockito.Mockito; diff --git a/src/test/java/org/cbioportal/web/VariantCountControllerTest.java b/src/test/java/org/cbioportal/legacy/web/VariantCountControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/VariantCountControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/VariantCountControllerTest.java index 34a0f8753f2..6a973f433a9 100644 --- a/src/test/java/org/cbioportal/web/VariantCountControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/VariantCountControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,10 +6,10 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.VariantCount; -import org.cbioportal.service.VariantCountService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.VariantCountIdentifier; +import org.cbioportal.legacy.model.VariantCount; +import org.cbioportal.legacy.service.VariantCountService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.VariantCountIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/config/CacheMapUtilConfig.java b/src/test/java/org/cbioportal/legacy/web/config/CacheMapUtilConfig.java similarity index 78% rename from src/test/java/org/cbioportal/web/config/CacheMapUtilConfig.java rename to src/test/java/org/cbioportal/legacy/web/config/CacheMapUtilConfig.java index fe044aec44f..948be9ea9b2 100644 --- a/src/test/java/org/cbioportal/web/config/CacheMapUtilConfig.java +++ b/src/test/java/org/cbioportal/legacy/web/config/CacheMapUtilConfig.java @@ -15,16 +15,16 @@ * along with this program. If not, see . */ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; -import org.cbioportal.persistence.CancerTypeRepository; -import org.cbioportal.persistence.GenericAssayRepository; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.persistence.PatientRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.persistence.StudyRepository; -import org.cbioportal.persistence.cachemaputil.CacheMapUtil; -import org.cbioportal.service.StaticDataTimestampService; +import org.cbioportal.legacy.persistence.CancerTypeRepository; +import org.cbioportal.legacy.persistence.GenericAssayRepository; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.persistence.PatientRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.persistence.StudyRepository; +import org.cbioportal.legacy.persistence.cachemaputil.CacheMapUtil; +import org.cbioportal.legacy.service.StaticDataTimestampService; import org.mockito.Mockito; import org.springframework.boot.test.context.TestConfiguration; import org.springframework.context.annotation.Bean; diff --git a/src/test/java/org/cbioportal/web/config/DataAccessTokenControllerConfig.java b/src/test/java/org/cbioportal/legacy/web/config/DataAccessTokenControllerConfig.java similarity index 91% rename from src/test/java/org/cbioportal/web/config/DataAccessTokenControllerConfig.java rename to src/test/java/org/cbioportal/legacy/web/config/DataAccessTokenControllerConfig.java index cf4f53f3efb..21efb05416d 100644 --- a/src/test/java/org/cbioportal/web/config/DataAccessTokenControllerConfig.java +++ b/src/test/java/org/cbioportal/legacy/web/config/DataAccessTokenControllerConfig.java @@ -30,10 +30,10 @@ * along with this program. If not, see . */ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.web.DataAccessTokenController; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.web.DataAccessTokenController; import org.mockito.Mockito; import org.springframework.boot.test.context.TestConfiguration; import org.springframework.context.annotation.Bean; diff --git a/src/test/java/org/cbioportal/web/config/DataAccessTokenControllerTestConfig.java b/src/test/java/org/cbioportal/legacy/web/config/DataAccessTokenControllerTestConfig.java similarity index 98% rename from src/test/java/org/cbioportal/web/config/DataAccessTokenControllerTestConfig.java rename to src/test/java/org/cbioportal/legacy/web/config/DataAccessTokenControllerTestConfig.java index 484ab71b742..647f5edfb12 100644 --- a/src/test/java/org/cbioportal/web/config/DataAccessTokenControllerTestConfig.java +++ b/src/test/java/org/cbioportal/legacy/web/config/DataAccessTokenControllerTestConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import org.springframework.boot.test.context.TestConfiguration; import org.springframework.context.annotation.Bean; diff --git a/src/test/java/org/cbioportal/web/config/RestAuthenticationEntryPoint.java b/src/test/java/org/cbioportal/legacy/web/config/RestAuthenticationEntryPoint.java similarity index 98% rename from src/test/java/org/cbioportal/web/config/RestAuthenticationEntryPoint.java rename to src/test/java/org/cbioportal/legacy/web/config/RestAuthenticationEntryPoint.java index 7984d3445df..d02e4ea6828 100644 --- a/src/test/java/org/cbioportal/web/config/RestAuthenticationEntryPoint.java +++ b/src/test/java/org/cbioportal/legacy/web/config/RestAuthenticationEntryPoint.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import java.io.IOException; diff --git a/src/test/java/org/cbioportal/web/config/TestConfig.java b/src/test/java/org/cbioportal/legacy/web/config/TestConfig.java similarity index 83% rename from src/test/java/org/cbioportal/web/config/TestConfig.java rename to src/test/java/org/cbioportal/legacy/web/config/TestConfig.java index dee57c0420d..f6ec8c650ae 100644 --- a/src/test/java/org/cbioportal/web/config/TestConfig.java +++ b/src/test/java/org/cbioportal/legacy/web/config/TestConfig.java @@ -1,8 +1,9 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; -import org.cbioportal.persistence.cachemaputil.CacheMapUtil; -import org.cbioportal.web.error.GlobalExceptionHandler; -import org.cbioportal.web.util.InvolvedCancerStudyExtractorInterceptor; +import org.cbioportal.legacy.persistence.cachemaputil.CacheMapUtil; +import org.cbioportal.legacy.web.config.CustomObjectMapper; +import org.cbioportal.legacy.web.error.GlobalExceptionHandler; +import org.cbioportal.legacy.web.util.InvolvedCancerStudyExtractorInterceptor; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.test.context.TestConfiguration; import org.springframework.boot.test.mock.mockito.MockBean; diff --git a/src/test/java/org/cbioportal/web/config/TokenAuthenticationSuccessHandler.java b/src/test/java/org/cbioportal/legacy/web/config/TokenAuthenticationSuccessHandler.java similarity index 98% rename from src/test/java/org/cbioportal/web/config/TokenAuthenticationSuccessHandler.java rename to src/test/java/org/cbioportal/legacy/web/config/TokenAuthenticationSuccessHandler.java index 4fdadbc0c13..ce9ecba4d53 100644 --- a/src/test/java/org/cbioportal/web/config/TokenAuthenticationSuccessHandler.java +++ b/src/test/java/org/cbioportal/legacy/web/config/TokenAuthenticationSuccessHandler.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import jakarta.servlet.http.HttpServletRequest; diff --git a/src/test/java/org/cbioportal/web/util/AlterationFilterMockitoArgumentMatcher.java b/src/test/java/org/cbioportal/legacy/web/util/AlterationFilterMockitoArgumentMatcher.java similarity index 94% rename from src/test/java/org/cbioportal/web/util/AlterationFilterMockitoArgumentMatcher.java rename to src/test/java/org/cbioportal/legacy/web/util/AlterationFilterMockitoArgumentMatcher.java index 59d97866bd2..c999e097ccc 100644 --- a/src/test/java/org/cbioportal/web/util/AlterationFilterMockitoArgumentMatcher.java +++ b/src/test/java/org/cbioportal/legacy/web/util/AlterationFilterMockitoArgumentMatcher.java @@ -1,6 +1,6 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; -import org.cbioportal.model.AlterationFilter; +import org.cbioportal.legacy.model.AlterationFilter; import org.mockito.ArgumentMatcher; public class AlterationFilterMockitoArgumentMatcher implements ArgumentMatcher { diff --git a/src/test/java/org/cbioportal/web/util/ClinicalDataBinUtilTest.java b/src/test/java/org/cbioportal/legacy/web/util/ClinicalDataBinUtilTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/util/ClinicalDataBinUtilTest.java rename to src/test/java/org/cbioportal/legacy/web/util/ClinicalDataBinUtilTest.java index b25def51f5b..4b65b4c37bc 100644 --- a/src/test/java/org/cbioportal/web/util/ClinicalDataBinUtilTest.java +++ b/src/test/java/org/cbioportal/legacy/web/util/ClinicalDataBinUtilTest.java @@ -1,19 +1,37 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.fasterxml.jackson.core.TreeNode; import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataBin; -import org.cbioportal.model.Patient; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.impl.CustomDataServiceImpl; -import org.cbioportal.service.util.ClinicalAttributeUtil; -import org.cbioportal.service.util.SessionServiceRequestHandler; -import org.cbioportal.web.parameter.*; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataBin; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.impl.CustomDataServiceImpl; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.service.util.SessionServiceRequestHandler; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.DataBinFilter; +import org.cbioportal.legacy.web.parameter.DataBinMethod; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.ClinicalDataBinUtil; +import org.cbioportal.legacy.web.util.ClinicalDataFetcher; +import org.cbioportal.legacy.web.util.DataBinHelper; +import org.cbioportal.legacy.web.util.DataBinner; +import org.cbioportal.legacy.web.util.DiscreteDataBinner; +import org.cbioportal.legacy.web.util.IdPopulator; +import org.cbioportal.legacy.web.util.LinearDataBinner; +import org.cbioportal.legacy.web.util.LogScaleDataBinner; +import org.cbioportal.legacy.web.util.ScientificSmallDataBinner; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/util/ClinicalDataEnrichmentUtilTest.java b/src/test/java/org/cbioportal/legacy/web/util/ClinicalDataEnrichmentUtilTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/util/ClinicalDataEnrichmentUtilTest.java rename to src/test/java/org/cbioportal/legacy/web/util/ClinicalDataEnrichmentUtilTest.java index cc4cc5cf5d7..667143b008a 100644 --- a/src/test/java/org/cbioportal/web/util/ClinicalDataEnrichmentUtilTest.java +++ b/src/test/java/org/cbioportal/legacy/web/util/ClinicalDataEnrichmentUtilTest.java @@ -1,19 +1,20 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalDataEnrichment; -import org.cbioportal.model.Sample; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalDataEnrichment; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.web.util.ClinicalDataEnrichmentUtil; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/util/DataBinHelperTest.java b/src/test/java/org/cbioportal/legacy/web/util/DataBinHelperTest.java similarity index 99% rename from src/test/java/org/cbioportal/web/util/DataBinHelperTest.java rename to src/test/java/org/cbioportal/legacy/web/util/DataBinHelperTest.java index 792cecfd6e2..934e2c22e5c 100644 --- a/src/test/java/org/cbioportal/web/util/DataBinHelperTest.java +++ b/src/test/java/org/cbioportal/legacy/web/util/DataBinHelperTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import static org.junit.Assert.*; @@ -9,6 +9,8 @@ import java.util.Collections; import java.util.List; import java.util.stream.Collectors; + +import org.cbioportal.legacy.web.util.DataBinHelper; import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/util/DataBinnerMocker.java b/src/test/java/org/cbioportal/legacy/web/util/DataBinnerMocker.java similarity index 99% rename from src/test/java/org/cbioportal/web/util/DataBinnerMocker.java rename to src/test/java/org/cbioportal/legacy/web/util/DataBinnerMocker.java index e3090402073..c35ef521942 100644 --- a/src/test/java/org/cbioportal/web/util/DataBinnerMocker.java +++ b/src/test/java/org/cbioportal/legacy/web/util/DataBinnerMocker.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.util.LinkedHashMap; import java.util.Map; diff --git a/src/test/java/org/cbioportal/web/util/DataBinnerTest.java b/src/test/java/org/cbioportal/legacy/web/util/DataBinnerTest.java similarity index 99% rename from src/test/java/org/cbioportal/web/util/DataBinnerTest.java rename to src/test/java/org/cbioportal/legacy/web/util/DataBinnerTest.java index 5ed86de169b..d643891bf67 100644 --- a/src/test/java/org/cbioportal/web/util/DataBinnerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/util/DataBinnerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.math.BigDecimal; import java.math.MathContext; @@ -9,19 +9,19 @@ import java.util.Map; import java.util.stream.Collectors; import java.util.stream.Stream; -import static org.cbioportal.web.parameter.DataBinFilter.*; +import static org.cbioportal.legacy.web.parameter.DataBinFilter.*; import java.util.stream.IntStream; -import org.cbioportal.model.Binnable; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.DataBin; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.util.MolecularProfileUtil; -import org.cbioportal.web.parameter.BinsGeneratorConfig; -import org.cbioportal.web.parameter.ClinicalDataBinFilter; -import org.cbioportal.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.DataBin; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.web.parameter.BinsGeneratorConfig; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/web/util/SelectMockitoArgumentMatcher.java b/src/test/java/org/cbioportal/legacy/web/util/SelectMockitoArgumentMatcher.java similarity index 87% rename from src/test/java/org/cbioportal/web/util/SelectMockitoArgumentMatcher.java rename to src/test/java/org/cbioportal/legacy/web/util/SelectMockitoArgumentMatcher.java index bcd6d021e1b..ca1ed05c043 100644 --- a/src/test/java/org/cbioportal/web/util/SelectMockitoArgumentMatcher.java +++ b/src/test/java/org/cbioportal/legacy/web/util/SelectMockitoArgumentMatcher.java @@ -1,6 +1,6 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; -import org.cbioportal.model.util.Select; +import org.cbioportal.legacy.model.util.Select; import org.mockito.ArgumentMatcher; public class SelectMockitoArgumentMatcher implements ArgumentMatcher