[~aloraine] -

Could you help me figure out the repositories which needs an upgrade?

Sure. Here are some options:

• If you log in to bitbucket and visit https://bitbucket.org/lorainelab/ you *may* see a green check (or exclamation point) in the "Builds" column. But you might not – I am not sure if your user would be able to view build status. Anyway, any repo with a check mark is getting built using the Docker image and needs to be updated.
• Any repository with a "bitbucket_pipelines.yml" file. Unfortunately there does not seem to be a way to search for repositories with that file using the bitbucket interface.
• Go to: https://bitbucket.org/lorainelab/profile/projects. Every repository in the "IGB Apps" project should have a bitbucket_pipelines.yml" file which needs to be updated to use the new Docker image.
• Also go to: https://bitbucket.org/account/user/lorainelab/projects/IGB. Projects that need to be updated include: GenoViz SDK, GenoViz SDK Demos, IGB for Testing App Workflow, Integrated Genome Browser.

Also, I see you have updated "JRE Bundles Install4j" Downloads section. Thanks!

Code changes to the repositories -

https://bitbucket.org/noorzahara/2bit-reader-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/genoviz-sdk-demos-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/igb-for-testing-app-workflow-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/app-for-testing-app-workflow-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/get-average-score-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/23andme-snp-converter-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/bundlemarkdownencoder-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/command-socket-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/experimental-apps-for-igb-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/geometric-mean-operator-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/merge-annotation-operator-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/protannot-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/super-simple-igb-app-local/branch/IGBF-2291#diff

https://bitbucket.org/nzahara/genoviz-sdk-local/branch/IGBF-2291#diff

Testing steps - Follow the readme in each repositories.

I have reviewed each of the above links. I was not able to test the 'App for testing App workflow' since the downloads link did not contain repository.xml file. Noor Zahara can you please look into it and rebuild your branch? Rest all are working fine.

I have tested the 'App for testing App workflow' using Appstore. It is working fine. Noor Zahara please submit a PR for the same.

PR Created

https://bitbucket.org/lorainelab/2bit-reader/pull-requests/4/igbf-2291/diff
https://bitbucket.org/lorainelab/genoviz-sdk-demos/pull-requests/3/upgrade-jdk-version-to-180241/diff
https://bitbucket.org/lorainelab/igb-for-testing-app-workflow/pull-requests/1/upgrade-jdk-version-to-180241/diff
https://bitbucket.org/lorainelab/app-for-testing-app-workflow/pull-requests/1/upgrade-jdk-version-to-180241/diff
https://bitbucket.org/lorainelab/get-average-score/pull-requests/7/upgrade-jdk-version-to-180241/diff
https://bitbucket.org/lorainelab/23andme-snp-converter/pull-requests/9/upgrade-jdk-version-to-180241/diff
https://bitbucket.org/lorainelab/bundlemarkdownencoder/pull-requests/2/upgrade-jdk-version-to-180241/diff
https://bitbucket.org/lorainelab/command-socket/pull-requests/15/upgrade-jdk-version-to-180241/diff
https://bitbucket.org/lorainelab/experimental-apps-for-igb/pull-requests/11/upgrade-jdk-version-to-180241/diff
https://bitbucket.org/lorainelab/geometric-mean-operator/pull-requests/10/upgrade-jdk-version-to-180241/diff
https://bitbucket.org/lorainelab/protannot/pull-requests/13/igbf-2291-upgrade-jdk-version-to-180241/diff
https://bitbucket.org/lorainelab/super-simple-igb-app/pull-requests/10/upgrade-jdk-version-to-180241/diff
https://bitbucket.org/lorainelab/genoviz-sdk/pull-requests/19/upgrade-jdk-version-to-180241/diff
https://bitbucket.org/lorainelab/merge-annotation-operator/pull-requests/12/upgrade-jdk-version-to-180241/diff

Please check Command Socket PR for comment.
cc: Noor Zahara

I have removed the git.properties file

Command socket merged.
Moving to "Ready for Testing" as all PRs are now merged to their respective master branches.

All projects were successfully built, except for 'igb-for-testing-app-workflow', which fails at genometry tests, with the following exception:

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.19:test (default-test) on project genometry: There are test failures.

All project except the above that failed to build can be successfully installed using IGB app manager. Tested on macOS

Update: The error seems to the same one that was fixed in IGBF-2357. However, the repo below is behind the main IGB repo containing the merged fix.

https://bitbucket.org/lorainelab/igb-for-testing-app-workflow/src/Mock-rel-9.1.0/

To fix, Loraine needs to pull changes from main repo into this fork.

Pull changes and now the fork builds. Moving to closed.