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fix develop nightly builds #297

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merged 4 commits into from
Nov 25, 2024
Merged

fix develop nightly builds #297

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9ea6e49
Test with final webservice release
denis-yuen Nov 22, 2024
c361c37
iterate things to 1.17 and new avro
denis-yuen Nov 22, 2024
6e1e74e
adapt test
denis-yuen Nov 22, 2024
9789fd1
Merge branch 'develop' into feature/fix_develop
denis-yuen Nov 22, 2024
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10 changes: 5 additions & 5 deletions THIRD-PARTY-LICENSES.txt
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Expand Up @@ -9,16 +9,16 @@ Lists of 403 third-party dependencies.
(Apache License 2.0) Annotations for Metrics (io.dropwizard.metrics:metrics-annotation:4.2.19 - https://metrics.dropwizard.io/metrics-annotation)
(The BSD License) ANTLR 4 Runtime (org.antlr:antlr4-runtime:4.10.1 - http://www.antlr.org/antlr4-runtime)
(EPL 2.0) (GPL2 w/ CPE) aopalliance version 1.0 repackaged as a module (org.glassfish.hk2.external:aopalliance-repackaged:3.0.4 - https://github.com/eclipse-ee4j/glassfish-hk2/external/aopalliance-repackaged)
(Apache-2.0) Apache Avro (org.apache.avro:avro:1.11.3 - https://avro.apache.org)
(Apache-2.0) Apache Avro (org.apache.avro:avro:1.11.4 - https://avro.apache.org)
(Apache License, Version 2.0) Apache Commons BeanUtils (commons-beanutils:commons-beanutils:1.9.4 - https://commons.apache.org/proper/commons-beanutils/)
(Apache-2.0) Apache Commons Codec (commons-codec:commons-codec:1.17.1 - https://commons.apache.org/proper/commons-codec/)
(Apache License, Version 2.0) Apache Commons Collections (commons-collections:commons-collections:3.2.2 - http://commons.apache.org/collections/)
(Apache License, Version 2.0) Apache Commons Collections (org.apache.commons:commons-collections4:4.4 - https://commons.apache.org/proper/commons-collections/)
(Apache-2.0) Apache Commons Compress (org.apache.commons:commons-compress:1.26.0 - https://commons.apache.org/proper/commons-compress/)
(Apache-2.0) Apache Commons Compress (org.apache.commons:commons-compress:1.26.2 - https://commons.apache.org/proper/commons-compress/)
(Apache-2.0) Apache Commons Configuration (org.apache.commons:commons-configuration2:2.10.1 - https://commons.apache.org/proper/commons-configuration/)
(Apache License, Version 2.0) Apache Commons CSV (org.apache.commons:commons-csv:1.5 - http://commons.apache.org/proper/commons-csv/)
(Apache License, Version 2.0) Apache Commons Exec (org.apache.commons:commons-exec:1.3 - http://commons.apache.org/proper/commons-exec/)
(Apache-2.0) Apache Commons IO (commons-io:commons-io:2.15.1 - https://commons.apache.org/proper/commons-io/)
(Apache-2.0) Apache Commons IO (commons-io:commons-io:2.16.1 - https://commons.apache.org/proper/commons-io/)
(Apache-2.0) Apache Commons Lang (org.apache.commons:commons-lang3:3.14.0 - https://commons.apache.org/proper/commons-lang/)
(Apache-2.0) Apache Commons Logging (commons-logging:commons-logging:1.3.0 - https://commons.apache.org/proper/commons-logging/)
(Apache License, Version 2.0) Apache Commons Net (commons-net:commons-net:3.9.0 - https://commons.apache.org/proper/commons-net/)
Expand Down Expand Up @@ -132,8 +132,8 @@ Lists of 403 third-party dependencies.
(Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-wdl-transforms-new-base (org.broadinstitute:cromwell-wdl-transforms-new-base_2.13:85 - no url defined)
(Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-wdl-transforms-shared (org.broadinstitute:cromwell-wdl-transforms-shared_2.13:85 - no url defined)
(Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-wom (org.broadinstitute:cromwell-wom_2.13:85 - no url defined)
(Apache License, Version 2.0) cwlavro-generated (io.cwl:cwlavro-generated:2.0.4.9 - no url defined)
(Apache License, Version 2.0) cwlavro-tools (io.cwl:cwlavro-tools:2.0.4.9 - no url defined)
(Apache License, Version 2.0) cwlavro-generated (io.cwl:cwlavro-generated:2.1.0 - no url defined)
(Apache License, Version 2.0) cwlavro-tools (io.cwl:cwlavro-tools:2.1.0 - no url defined)
(The Apache Software License, Version 2.0) docker-java-api (com.github.docker-java:docker-java-api:3.3.6 - https://github.com/docker-java/docker-java)
(The Apache Software License, Version 2.0) docker-java-core (com.github.docker-java:docker-java-core:3.3.6 - https://github.com/docker-java/docker-java)
(The Apache Software License, Version 2.0) docker-java-transport (com.github.docker-java:docker-java-transport:3.3.6 - https://github.com/docker-java/docker-java)
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14 changes: 7 additions & 7 deletions dockstore-cli-integration-testing/generated/src/main/resources/pom.xml
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Expand Up @@ -19,7 +19,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-cli-integration-testing</artifactId>
<version>1.16.0</version>
<version>1.17.0-SNAPSHOT</version>
<licenses>
<license>
<name>Apache Software License, Version 2.0</name>
Expand All @@ -30,13 +30,13 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-client</artifactId>
<version>1.16.0</version>
<version>1.17.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-integration-testing</artifactId>
<version>1.16.0</version>
<version>1.17.0-alpha.0</version>
<classifier>tests</classifier>
<scope>compile</scope>
<exclusions>
Expand All @@ -49,13 +49,13 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-common</artifactId>
<version>1.16.0</version>
<version>1.17.0-alpha.0</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-webservice</artifactId>
<version>1.16.0</version>
<version>1.17.0-alpha.0</version>
<scope>compile</scope>
<exclusions>
<exclusion>
Expand All @@ -67,7 +67,7 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>openapi-java-client</artifactId>
<version>1.16.0</version>
<version>1.17.0-alpha.0</version>
<scope>compile</scope>
</dependency>
<dependency>
Expand All @@ -79,7 +79,7 @@
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.15.1</version>
<version>2.16.1</version>
<scope>compile</scope>
</dependency>
<dependency>
Expand Down
10 changes: 5 additions & 5 deletions dockstore-cli-reports/generated/src/main/resources/pom.xml
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Expand Up @@ -19,7 +19,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-cli-reports</artifactId>
<version>1.16.0</version>
<version>1.17.0-SNAPSHOT</version>
<licenses>
<license>
<name>Apache Software License, Version 2.0</name>
Expand All @@ -30,25 +30,25 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-webservice</artifactId>
<version>1.16.0</version>
<version>1.17.0-alpha.0</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-common</artifactId>
<version>1.16.0</version>
<version>1.17.0-alpha.0</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-client</artifactId>
<version>1.16.0</version>
<version>1.17.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-cli-integration-testing</artifactId>
<version>1.16.0</version>
<version>1.17.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
</dependencies>
Expand Down
16 changes: 8 additions & 8 deletions dockstore-client/generated/src/main/resources/pom.xml
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Expand Up @@ -19,7 +19,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-client</artifactId>
<version>1.16.0</version>
<version>1.17.0-SNAPSHOT</version>
<licenses>
<license>
<name>Apache Software License, Version 2.0</name>
Expand Down Expand Up @@ -66,7 +66,7 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-common</artifactId>
<version>1.16.0</version>
<version>1.17.0-alpha.0</version>
<scope>compile</scope>
<exclusions>
<exclusion>
Expand All @@ -78,19 +78,19 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>openapi-java-client</artifactId>
<version>1.16.0</version>
<version>1.17.0-alpha.0</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>openapi-java-wes-client</artifactId>
<version>1.16.0</version>
<version>1.17.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-file-plugin-parent</artifactId>
<version>1.16.0</version>
<version>1.17.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
Expand Down Expand Up @@ -126,7 +126,7 @@
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.15.1</version>
<version>2.16.1</version>
<scope>compile</scope>
</dependency>
<dependency>
Expand Down Expand Up @@ -162,7 +162,7 @@
<dependency>
<groupId>io.cwl</groupId>
<artifactId>cwlavro-tools</artifactId>
<version>2.0.4.9</version>
<version>2.1.0</version>
<scope>compile</scope>
<exclusions>
<exclusion>
Expand All @@ -178,7 +178,7 @@
<dependency>
<groupId>io.cwl</groupId>
<artifactId>cwlavro-generated</artifactId>
<version>2.0.4.9</version>
<version>2.1.0</version>
<scope>compile</scope>
<exclusions>
<exclusion>
Expand Down
2 changes: 1 addition & 1 deletion dockstore-client/src/main/java/io/dockstore/client/cli/nested/AbstractEntryClient.java
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Expand Up @@ -221,7 +221,7 @@ boolean getIgnoreChecksums() {
public CWL getCwlUtil() {
// TODO: may be reactivated if we find a different way to read CWL into Java
// String cwlrunner = CWLRunnerFactory.getCWLRunner();
return new CWL(false, Utilities.parseConfig(getConfigFile()));
return new CWL(Utilities.parseConfig(getConfigFile()));
}

public abstract String getConfigFile();
Expand Down
2 changes: 1 addition & 1 deletion dockstore-client/src/main/java/io/github/collaboratory/cwl/CWLClient.java
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Expand Up @@ -177,7 +177,7 @@ public File provisionInputFiles() {
Class cwlClassTarget = getCWLClassTarget();

// Load CWL from JSON to object
CWL cwlUtil = new CWL(false, config);
CWL cwlUtil = new CWL(config);
// This won't work since I am using zip files, it is expecting files to be unzipped
final String imageDescriptorContent = cwlUtil.parseCWL(localPrimaryDescriptorFile.getAbsolutePath()).getLeft();
Object cwlObject = null;
Expand Down
4 changes: 2 additions & 2 deletions dockstore-client/src/test/java/io/dockstore/client/cli/YamlValidatorTest.java
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Expand Up @@ -90,7 +90,7 @@ void relativePrimaryPathYml() {
YamlVerifyUtility.dockstoreValidate(relativePathDockstoreYmlDirectory);
fail("Invalid YAML not caught");
} catch (YamlVerifyUtility.ValidateYamlException ex) {
assertTrue(ex.getMessage().contains("the path must be an absolute path to be valid"));
assertTrue(ex.getMessage().contains("must be an absolute path to be valid"));
}

}
Expand All @@ -103,7 +103,7 @@ void relativeTestDescriptorPathYml() {
YamlVerifyUtility.dockstoreValidate(relativePathDockstoreYmlDirectory);
fail("Invalid YAML not caught");
} catch (YamlVerifyUtility.ValidateYamlException ex) {
assertTrue(ex.getMessage().contains("the path must be an absolute path to be valid"));
assertTrue(ex.getMessage().contains("must be an absolute path to be valid"));
}

}
Expand Down
2 changes: 1 addition & 1 deletion dockstore-file-plugin-parent/generated/src/main/resources/pom.xml
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Expand Up @@ -19,7 +19,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-file-plugin-parent</artifactId>
<version>1.16.0</version>
<version>1.17.0-SNAPSHOT</version>
<licenses>
<license>
<name>Apache Software License, Version 2.0</name>
Expand Down
2 changes: 1 addition & 1 deletion openapi-java-wes-client/generated/src/main/resources/pom.xml
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Expand Up @@ -19,7 +19,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>io.dockstore</groupId>
<artifactId>openapi-java-wes-client</artifactId>
<version>1.16.0</version>
<version>1.17.0-SNAPSHOT</version>
<licenses>
<license>
<name>Apache Software License, Version 2.0</name>
Expand Down
28 changes: 3 additions & 25 deletions pom.xml
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Expand Up @@ -33,12 +33,12 @@
-->
<properties>
<!-- the following properties set sane defaults when no revision properties are set from the command-line -->
<revision>1.16</revision>
<revision>1.17</revision>
<changelist>.0-SNAPSHOT</changelist>

<github.url>scm:git:[email protected]:dockstore/dockstore-cli.git</github.url>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<dockstore-core.version>1.16.0</dockstore-core.version>
<dockstore-core.version>1.17.0-alpha.0</dockstore-core.version>
<maven-failsafe.version>2.22.2</maven-failsafe.version>
<maven-surefire.version>2.22.2</maven-surefire.version>
<skipTests>false</skipTests>
Expand All @@ -53,7 +53,7 @@
${project.basedir}/target/jacoco.xml,${project.basedir}/target/jacoco-it.xml,${project.basedir}/../dockstore-cli-reports/target/site/jacoco-aggregate/jacoco.xml
</sonar.coverage.jacoco.xmlReportPaths>
<!-- end sonarcloud properties -->
<cwlavro.version>2.0.4.9</cwlavro.version>
<cwlavro.version>2.1.0</cwlavro.version>
</properties>

<organization>
Expand Down Expand Up @@ -200,28 +200,6 @@
</exclusion>
</exclusions>
</dependency>
<!-- remove after bom is updated with Dockstore or above 1.14.0 -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
<version>1.26.0</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>1.11.0</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.15.1</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.14.0</version>
</dependency>

</dependencies>
</dependencyManagement>

Expand Down
2 changes: 1 addition & 1 deletion support/generated/src/main/resources/pom.xml
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Expand Up @@ -19,7 +19,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>io.dockstore</groupId>
<artifactId>support</artifactId>
<version>1.16.0</version>
<version>1.17.0-SNAPSHOT</version>
<licenses>
<license>
<name>Apache Software License, Version 2.0</name>
Expand Down