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Updating cwltool dependencies #291

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merged 11 commits into from
Aug 15, 2024
Merged

Updating cwltool dependencies #291

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d637e80
Remove dead ICGC link and update synapse link
david4096 Aug 7, 2024
852c7fb
Bump artifact version
david4096 Aug 7, 2024
fb0161d
Try updating circle image
david4096 Aug 7, 2024
24ea29f
Update encrypted bundle for gitlab/bitbucket keys
david4096 Aug 7, 2024
e1850f2
Add .DS_Store to gitignore
david4096 Aug 7, 2024
abcb568
Update version installed for integration testing
david4096 Aug 8, 2024
dcd7d72
Try reverting docker image
david4096 Aug 8, 2024
5ad72e5
Set back webservice version
david4096 Aug 15, 2024
4f18ce9
other POM updates as well
david4096 Aug 15, 2024
aa74b5b
Typos in README and point to new script
david4096 Aug 15, 2024
190e61e
Point to new release off hotfix branch
david4096 Aug 15, 2024
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -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
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3 changes: 1 addition & 2 deletions README.md
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Expand Up @@ -45,8 +45,7 @@ server-url = https://www.dockstore.org/api

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, [Synapse](http://docs.synapse.org/articles/downloading_data.html), and
[ICGC Score Client](https://docs.icgc.org/download/guide/#score-client-usage) via [plugins](https://github.com/dockstore).
the Amazon S3 and [Synapse](https://help.synapse.org/docs/Downloading-Data-Programmatically.2003796248.html), and via [plugins](https://github.com/dockstore).

Download the above set of default plugins via:
```
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Binary file modified circle_ci_test_data.zip.enc
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8 changes: 4 additions & 4 deletions dockstore-cli-integration-testing/generated/src/main/resources/pom.xml
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Expand Up @@ -36,7 +36,7 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-integration-testing</artifactId>
<version>1.15.0-rc.1</version>
<version>1.15.4-alpha.1</version>
<classifier>tests</classifier>
<scope>compile</scope>
<exclusions>
Expand All @@ -49,13 +49,13 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-common</artifactId>
<version>1.15.0-rc.1</version>
<version>1.15.4-alpha.1</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-webservice</artifactId>
<version>1.15.0-rc.1</version>
<version>1.15.4-alpha.1</version>
<scope>compile</scope>
<exclusions>
<exclusion>
Expand All @@ -67,7 +67,7 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>openapi-java-client</artifactId>
<version>1.15.0-rc.1</version>
<version>1.15.4-alpha.1</version>
<scope>compile</scope>
</dependency>
<dependency>
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4 changes: 2 additions & 2 deletions dockstore-cli-reports/generated/src/main/resources/pom.xml
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Expand Up @@ -30,13 +30,13 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-webservice</artifactId>
<version>1.15.0-rc.1</version>
<version>1.15.4-alpha.1</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-common</artifactId>
<version>1.15.0-rc.1</version>
<version>1.15.4-alpha.1</version>
<scope>compile</scope>
</dependency>
<dependency>
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4 changes: 2 additions & 2 deletions dockstore-client/generated/src/main/resources/pom.xml
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Expand Up @@ -66,7 +66,7 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-common</artifactId>
<version>1.15.0-rc.1</version>
<version>1.15.4-alpha.1</version>
<scope>compile</scope>
<exclusions>
<exclusion>
Expand All @@ -78,7 +78,7 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>openapi-java-client</artifactId>
<version>1.15.0-rc.1</version>
<version>1.15.4-alpha.1</version>
<scope>compile</scope>
</dependency>
<dependency>
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2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -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>1.15.0-rc.1</dockstore-core.version>
<dockstore-core.version>1.15.4-alpha.1</dockstore-core.version>
<maven-failsafe.version>2.22.2</maven-failsafe.version>
<maven-surefire.version>2.22.2</maven-surefire.version>
<skipTests>false</skipTests>
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2 changes: 1 addition & 1 deletion scripts/install-tests.sh
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Expand Up @@ -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/feature/dock-2539/cwltool-deps/dockstore-webservice/src/main/resources/requirements/1.15.0/requirements3.txt
fi

if [ "${TESTING_PROFILE}" = "singularity-tests" ]; then
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