Merge pull request #6 from qbicsoftware/development

Release PR

measurement-provider/pom.xml

@@ -5,11 +5,11 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>life.qbic</groupId>
-    <artifactId>data-access-server</artifactId>
+    <artifactId>data-download-server</artifactId>
     <version>0.1.0</version>
   </parent>
 
-  <groupId>life.qbic.data-access</groupId>
+  <groupId>life.qbic.data-download</groupId>
   <artifactId>measurement-provider</artifactId>
   <version>0.1.0</version>
   <packaging>jar</packaging>
@@ -23,7 +23,7 @@
         <configuration>
           <archive>
             <manifestEntries>
-              <Automatic-Module-Name>life.qbic.data_access.measurement.provider</Automatic-Module-Name>
+              <Automatic-Module-Name>life.qbic.data_download.measurement.provider</Automatic-Module-Name>
             </manifestEntries>
           </archive>
         </configuration>

measurement-provider/src/main/java/life/qbic/data_access/measurements/api/DataFile.java → measurement-provider/src/main/java/life/qbic/data_download/measurements/api/DataFile.java

@@ -1,4 +1,4 @@
-package life.qbic.data_access.measurements.api;
+package life.qbic.data_download.measurements.api;
 
 import static java.util.Objects.requireNonNull;
 
@@ -7,12 +7,7 @@
 import java.util.StringJoiner;
 
 /**
- * TODO!
- * <b>short description</b>
- *
- * <p>detailed description</p>
- *
- * @since <version tag>
+ * A file with data
  */
 public class DataFile {
 

measurement-provider/src/main/java/life/qbic/data_download/measurements/api/FileInfo.java

@@ -0,0 +1,8 @@
+package life.qbic.data_download.measurements.api;
+
+/**
+ * Information about a file
+ */
+public record FileInfo(String path, long length, long crc32, long registrationMillis, long lastModifiedMillis) {
+
+}

measurement-provider/src/main/java/life/qbic/data_download/measurements/api/Measurement.java

@@ -0,0 +1,8 @@
+package life.qbic.data_download.measurements.api;
+
+/**
+ * A measurement
+ */
+public record Measurement(MeasurementId id, MeasurementInfo info, MeasurementData data) {
+
+}

measurement-provider/src/main/java/life/qbic/data_download/measurements/api/MeasurementData.java

@@ -0,0 +1,10 @@
+package life.qbic.data_download.measurements.api;
+
+import java.io.InputStream;
+
+/**
+ * Measurement data
+ */
+public interface MeasurementData {
+  InputStream stream();
+}

measurement-provider/src/main/java/life/qbic/data_download/measurements/api/MeasurementDataProvider.java

@@ -0,0 +1,10 @@
+package life.qbic.data_download.measurements.api;
+
+/**
+ * Provides measurement data given a measurement
+ */
+public interface MeasurementDataProvider {
+
+  MeasurementData loadData(MeasurementId measurementId);
+
+}

measurement-provider/src/main/java/life/qbic/data_access/measurements/api/MeasurementDataReader.java → measurement-provider/src/main/java/life/qbic/data_download/measurements/api/MeasurementDataReader.java

@@ -1,14 +1,9 @@
-package life.qbic.data_access.measurements.api;
+package life.qbic.data_download.measurements.api;
 
 import java.io.InputStream;
 
 /**
- * TODO!
- * <b>short description</b>
- *
- * <p>detailed description</p>
- *
- * @since <version tag>
+ * Reads measurement data
  */
 public interface MeasurementDataReader extends AutoCloseable {
 

measurement-provider/src/main/java/life/qbic/data_access/measurements/api/MeasurementFinder.java → measurement-provider/src/main/java/life/qbic/data_download/measurements/api/MeasurementFinder.java

@@ -1,4 +1,4 @@
-package life.qbic.data_access.measurements.api;
+package life.qbic.data_download.measurements.api;
 
 public interface MeasurementFinder {
   MeasurementInfo findById(MeasurementId measurementId);

measurement-provider/src/main/java/life/qbic/data_access/measurements/api/MeasurementId.java → measurement-provider/src/main/java/life/qbic/data_download/measurements/api/MeasurementId.java

@@ -1,4 +1,4 @@
-package life.qbic.data_access.measurements.api;
+package life.qbic.data_download.measurements.api;
 
 /**
  * The ID of a measurement.

measurement-provider/src/main/java/life/qbic/data_download/measurements/api/MeasurementInfo.java

@@ -0,0 +1,8 @@
+package life.qbic.data_download.measurements.api;
+
+/**
+ * Information about a measurement
+ */
+public record MeasurementInfo(long size, int fileCount) {
+
+}

measurement-provider/src/main/java/module-info.java

@@ -1,3 +1,3 @@
-module life.qbic.data_access.measurements {
-  exports life.qbic.data_access.measurements.api;
+module life.qbic.data_download.measurements {
+  exports life.qbic.data_download.measurements.api;
 }

openbis-connector/pom.xml

@@ -6,11 +6,11 @@
 
   <parent>
     <groupId>life.qbic</groupId>
-    <artifactId>data-access-server</artifactId>
+    <artifactId>data-download-server</artifactId>
     <version>0.1.0</version>
   </parent>
 
-  <groupId>life.qbic.data-access</groupId>
+  <groupId>life.qbic.data-download</groupId>
   <artifactId>openbis-connector</artifactId>
   <packaging>jar</packaging>
   <version>0.1.0</version>
@@ -64,7 +64,7 @@
       <classifier>r1700646105</classifier>
     </dependency>
     <dependency>
-      <groupId>life.qbic.data-access</groupId>
+      <groupId>life.qbic.data-download</groupId>
       <artifactId>measurement-provider</artifactId>
       <version>0.1.0</version>
     </dependency>
@@ -84,7 +84,7 @@
         <configuration>
           <archive>
             <manifestEntries>
-              <Automatic-Module-Name>life.qbic.data_access.openbis.connector</Automatic-Module-Name>
+              <Automatic-Module-Name>life.qbic.data_download.openbis.connector</Automatic-Module-Name>
             </manifestEntries>
           </archive>
         </configuration>

openbis-connector/src/main/java/deactivated.module-info.java

@@ -1,5 +1,5 @@
-//import life.qbic.data_access.measurements.api.MeasurementDataReader;
-//import life.qbic.data_access.openbis.DatasetFileStreamReaderImpl;
+//import life.qbic.data_download.measurements.api.MeasurementDataReader;
+//import life.qbic.data_download.openbis.DatasetFileStreamReaderImpl;
 //
 ///**
 // * TODO!
@@ -9,8 +9,8 @@
 // *
 // * @since <version tag>
 // */
-//module life.qbic.data_access.openbis {
-//  requires life.qbic.data_access.measurements;
+//module life.qbic.data_download.openbis {
+//  requires life.qbic.data_download.measurements;
 //  requires spring.context;
 //  requires spring.beans;
 //  requires org.slf4j;

openbis-connector/src/main/java/life/qbic/data_access/openbis/ApiV3.java → openbis-connector/src/main/java/life/qbic/data_download/openbis/ApiV3.java

@@ -1,24 +1,27 @@
-package life.qbic.data_access.openbis;
+package life.qbic.data_download.openbis;
 
 import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
 import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
 import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
+import java.time.Duration;
+import java.time.temporal.ChronoUnit;
 
 /**
- * TODO!
- * <b>short description</b>
- *
- * <p>detailed description</p>
- *
- * @since <version tag>
+ * A provider for openbis apis v3
  */
 public class ApiV3 {
 
+  private static final Duration TIMEOUT = Duration.of(5, ChronoUnit.DAYS);
+
+  private ApiV3() {
+    //hide the implicit constructor
+  }
+
   public static IApplicationServerApi applicationServer(String url) {
-    return HttpInvokerUtils.createServiceStub(IApplicationServerApi.class, url + IApplicationServerApi.SERVICE_URL, 100_000L);
+    return HttpInvokerUtils.createServiceStub(IApplicationServerApi.class, url + IApplicationServerApi.SERVICE_URL, TIMEOUT.toMillis());
   }
   public static IDataStoreServerApi dataStoreServer(String url) {
-    return HttpInvokerUtils.createStreamSupportingServiceStub(IDataStoreServerApi.class, url + IDataStoreServerApi.SERVICE_URL, 100_000L);
+    return HttpInvokerUtils.createStreamSupportingServiceStub(IDataStoreServerApi.class, url + IDataStoreServerApi.SERVICE_URL, TIMEOUT.toMillis());
   }
 
 }

openbis-connector/src/main/java/life/qbic/data_access/openbis/DatasetFileStreamReaderImpl.java → openbis-connector/src/main/java/life/qbic/data_download/openbis/DatasetFileStreamReaderImpl.java

@@ -1,28 +1,27 @@
-package life.qbic.data_access.openbis;
+package life.qbic.data_download.openbis;
 
 import static java.util.Objects.nonNull;
 
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.DataStore;
 import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownload;
 import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadReader;
 import java.io.InputStream;
-import life.qbic.data_access.measurements.api.DataFile;
-import life.qbic.data_access.measurements.api.FileInfo;
-import life.qbic.data_access.measurements.api.MeasurementDataReader;
+import java.util.Optional;
+import life.qbic.data_download.measurements.api.DataFile;
+import life.qbic.data_download.measurements.api.FileInfo;
+import life.qbic.data_download.measurements.api.MeasurementDataReader;
 
 /**
- * TODO!
- * <b>short description</b>
- *
- * <p>detailed description</p>
- *
- * @since <version tag>
+ * Reads openbis data streams
  */
 public class DatasetFileStreamReaderImpl implements MeasurementDataReader {
 
   private DataSetFileDownloadReader dataSetFileDownloadReader;
-  public DatasetFileStreamReaderImpl() {
+  private final String ignoredPrefix;
+
+  public DatasetFileStreamReaderImpl(String ignoredPrefix) {
     dataSetFileDownloadReader = null;
+    this.ignoredPrefix = Optional.ofNullable(ignoredPrefix).orElse("");
   }
 
 
@@ -56,7 +55,7 @@ public DataFile nextDataFile() {
         .toEpochMilli() : -1;
     long lastModifiedMillis = nonNull(dataStore) ? dataStore.getModificationDate().toInstant()
         .toEpochMilli() : -1;
-    FileInfo fileInfo = new FileInfo(fileDownload.getDataSetFile().getPath(),
+    FileInfo fileInfo = new FileInfo(fileDownload.getDataSetFile().getPath().replaceFirst(ignoredPrefix, ""),
         fileDownload.getDataSetFile().getFileLength(),
         Integer.toUnsignedLong(fileDownload.getDataSetFile().getChecksumCRC32()),
         creationMillis,

openbis-connector/src/main/java/life/qbic/data_access/openbis/OpenBisConnector.java → openbis-connector/src/main/java/life/qbic/data_download/openbis/OpenBisConnector.java

@@ -1,4 +1,4 @@
-package life.qbic.data_access.openbis;
+package life.qbic.data_download.openbis;
 
 import static java.util.Objects.requireNonNull;
 import static java.util.function.Predicate.not;
@@ -20,23 +20,18 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.stream.Collectors;
-import life.qbic.data_access.measurements.api.MeasurementData;
-import life.qbic.data_access.measurements.api.MeasurementDataProvider;
-import life.qbic.data_access.measurements.api.MeasurementFinder;
-import life.qbic.data_access.measurements.api.MeasurementId;
-import life.qbic.data_access.measurements.api.MeasurementInfo;
-import life.qbic.data_access.openbis.SessionFactory.OpenBisSession;
+import life.qbic.data_download.measurements.api.MeasurementData;
+import life.qbic.data_download.measurements.api.MeasurementDataProvider;
+import life.qbic.data_download.measurements.api.MeasurementFinder;
+import life.qbic.data_download.measurements.api.MeasurementId;
+import life.qbic.data_download.measurements.api.MeasurementInfo;
+import life.qbic.data_download.openbis.SessionFactory.OpenBisSession;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Component;
 
 /**
- * TODO!
- * <b>short description</b>
- *
- * <p>detailed description</p>
- *
- * @since <version tag>
+ * A connector to the openBIS system.
  */
 @Component("openbisConnector")
 public class OpenBisConnector implements MeasurementFinder, MeasurementDataProvider {

openbis-connector/src/main/java/life/qbic/data_access/openbis/SessionFactory.java → openbis-connector/src/main/java/life/qbic/data_download/openbis/SessionFactory.java

@@ -1,4 +1,4 @@
-package life.qbic.data_access.openbis;
+package life.qbic.data_download.openbis;
 
 import static java.util.Objects.requireNonNull;
 import static org.slf4j.LoggerFactory.getLogger;
@@ -10,12 +10,7 @@
 import org.springframework.stereotype.Service;
 
 /**
- * TODO!
- * <b>short description</b>
- *
- * <p>detailed description</p>
- *
- * @since <version tag>
+ * Creates openbis sessions
  */
 @Service("openbisSessionFactory")
 public class SessionFactory {