fix develop nightly builds (#297)

* Test with final webservice release * iterate things to 1.17 and new avro * adapt test
dockstore · Nov 25, 2024 · f73108d · f73108d
1 parent 760937c
commit f73108d
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diff --git a/THIRD-PARTY-LICENSES.txt b/THIRD-PARTY-LICENSES.txt
@@ -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/)
@@ -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)

diff --git a/dockstore-cli-integration-testing/generated/src/main/resources/pom.xml b/dockstore-cli-integration-testing/generated/src/main/resources/pom.xml
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>

diff --git a/dockstore-cli-reports/generated/src/main/resources/pom.xml b/dockstore-cli-reports/generated/src/main/resources/pom.xml
@@ -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>
@@ -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>

diff --git a/dockstore-client/generated/src/main/resources/pom.xml b/dockstore-client/generated/src/main/resources/pom.xml
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>

diff --git a/dockstore-client/src/main/java/io/dockstore/client/cli/nested/AbstractEntryClient.java b/dockstore-client/src/main/java/io/dockstore/client/cli/nested/AbstractEntryClient.java
@@ -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();

diff --git a/dockstore-client/src/main/java/io/github/collaboratory/cwl/CWLClient.java b/dockstore-client/src/main/java/io/github/collaboratory/cwl/CWLClient.java
@@ -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;

diff --git a/dockstore-client/src/test/java/io/dockstore/client/cli/YamlValidatorTest.java b/dockstore-client/src/test/java/io/dockstore/client/cli/YamlValidatorTest.java
@@ -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"));
         }
 
     }
@@ -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"));
         }
 
     }

diff --git a/dockstore-file-plugin-parent/generated/src/main/resources/pom.xml b/dockstore-file-plugin-parent/generated/src/main/resources/pom.xml
@@ -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>

diff --git a/openapi-java-wes-client/generated/src/main/resources/pom.xml b/openapi-java-wes-client/generated/src/main/resources/pom.xml
@@ -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>

diff --git a/pom.xml b/pom.xml
@@ -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>
@@ -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>
@@ -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>
 

diff --git a/support/generated/src/main/resources/pom.xml b/support/generated/src/main/resources/pom.xml
@@ -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>