Merge branch 'develop' into feature/move_doc

.gitignore

@@ -2,6 +2,7 @@
 .idea
 *.class
 *.swp
+.DS_Store
 
 # Contains SQL statements to initialize testing DB with a confidential user and tokens
 # Contains SQL statements to initialize testing DB with a confidential user, assuming they followed the dockstore setup tutorial

README.md

@@ -47,7 +47,7 @@ For developers, if you are working with a custom-built or updated Dockstore clie
 
 By default, cwltool reads input files from the local filesystem. Dockstore also adds support for additional file systems
 such as http, https, and ftp. Through a plug-in system, Dockstore also supports 
-the Amazon S3 and [Synapse](https://help.synapse.org/docs/Downloading-Data-Programmatically.2003796248.html), and via [plugins](https://github.com/dockstore).
+Amazon S3 and [Synapse](https://help.synapse.org/docs/Downloading-Data-Programmatically.2003796248.html) via [plugins](https://github.com/dockstore).
 
 Download the above set of default plugins via: 
 ```

THIRD-PARTY-LICENSES.txt

@@ -158,7 +158,7 @@ Lists of 394 third-party dependencies.
      (The Apache Software License, Version 2.0) FindBugs-jsr305 (com.google.code.findbugs:jsr305:3.0.2 - http://findbugs.sourceforge.net/)
      (The Apache Software License, Version 2.0) GeantyRef (io.leangen.geantyref:geantyref:1.3.14 - https://github.com/leangen/geantyref)
      (Apache 2.0) genericExtras (io.circe:circe-generic-extras_2.13:0.14.1 - https://github.com/circe/circe-generic-extras)
-     (The MIT license) GitHub API for Java (org.kohsuke:github-api:1.313 - https://github-api.kohsuke.org/)
+     (The MIT license) GitHub API for Java (org.kohsuke:github-api:1.322 - https://github-api.kohsuke.org/)
      (The Apache Software License, Version 2.0) Gitlab Java API Wrapper (org.gitlab:java-gitlab-api:4.0.0 - http://nexus.sonatype.org/oss-repository-hosting.html/java-gitlab-api)
      (The Apache Software License, Version 2.0) Google APIs Client Library for Java (com.google.api-client:google-api-client:1.35.0 - https://github.com/googleapis/google-api-java-client/google-api-client)
      (BSD New license) Google Auth Library for Java - Credentials (com.google.auth:google-auth-library-credentials:1.5.3 - https://github.com/googleapis/google-auth-library-java/google-auth-library-credentials)

dockstore-cli-integration-testing/generated/src/main/resources/pom.xml

@@ -36,7 +36,7 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-integration-testing</artifactId>
-      <version>1.16.0-alpha.11</version>
+      <version>1.16.0-alpha.15</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-alpha.11</version>
+      <version>1.16.0-alpha.15</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-webservice</artifactId>
-      <version>1.16.0-alpha.11</version>
+      <version>1.16.0-alpha.15</version>
       <scope>compile</scope>
       <exclusions>
         <exclusion>
@@ -67,7 +67,7 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>openapi-java-client</artifactId>
-      <version>1.16.0-alpha.11</version>
+      <version>1.16.0-alpha.15</version>
       <scope>compile</scope>
     </dependency>
     <dependency>

dockstore-cli-reports/generated/src/main/resources/pom.xml

@@ -30,13 +30,13 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-webservice</artifactId>
-      <version>1.16.0-alpha.11</version>
+      <version>1.16.0-alpha.15</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-common</artifactId>
-      <version>1.16.0-alpha.11</version>
+      <version>1.16.0-alpha.15</version>
       <scope>compile</scope>
     </dependency>
     <dependency>

dockstore-client/generated/src/main/resources/pom.xml

@@ -66,7 +66,7 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-common</artifactId>
-      <version>1.16.0-alpha.11</version>
+      <version>1.16.0-alpha.15</version>
       <scope>compile</scope>
       <exclusions>
         <exclusion>
@@ -78,7 +78,7 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>openapi-java-client</artifactId>
-      <version>1.16.0-alpha.11</version>
+      <version>1.16.0-alpha.15</version>
       <scope>compile</scope>
     </dependency>
     <dependency>

pom.xml

@@ -38,7 +38,7 @@
 
         <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-alpha.11</dockstore-core.version>
+        <dockstore-core.version>1.16.0-alpha.15</dockstore-core.version>
         <maven-failsafe.version>2.22.2</maven-failsafe.version>
         <maven-surefire.version>2.22.2</maven-surefire.version>
         <skipTests>false</skipTests>

scripts/install-tests.sh

@@ -14,7 +14,7 @@ fi
 if [ "${TESTING_PROFILE}" = "toil-integration-tests" ]; then
     pip3 install --user toil[cwl]==3.15.0
 else
-    pip3 install --user -r https://raw.githubusercontent.com/dockstore/dockstore/develop/dockstore-webservice/src/main/resources/requirements/1.14.0/requirements3.txt
+    pip3 install --user -r https://raw.githubusercontent.com/dockstore/dockstore/develop/dockstore-webservice/src/main/resources/requirements/1.15.0/requirements3.txt
 fi
 
 if [ "${TESTING_PROFILE}" = "singularity-tests" ]; then