Figure out how to set up bitbucket pipeline build for App repositories

Done with the creation of JAR file as well as the OBR index for the app. Setup pipeline to copy both the files to downloads section of the bitbucket.
Now investigating on how we can provide a URL of the bitbucket repository's download section directly to the app manager in IGB for testing.
Following exception thrown when we check on the downloads repository path from IGB's app manager :
10:53:12.286 ERROR o.l.i.p.m.RepositoryInfoManager - Expected element 'repository' at the root of the document
java.lang.Exception: Expected element 'repository' at the root of the document
at org.apache.felix.bundlerepository.impl.PullParser.parseRepository(PullParser.java:50) ~[na:na]
at org.apache.felix.bundlerepository.impl.DataModelHelperImpl.repository(DataModelHelperImpl.java:168) ~[na:na]
at org.apache.felix.bundlerepository.impl.DataModelHelperImpl.repository(DataModelHelperImpl.java:141) ~[na:na]
at org.apache.felix.bundlerepository.impl.RepositoryAdminImpl$1.run(RepositoryAdminImpl.java:114) ~[na:na]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_101]
at org.apache.felix.bundlerepository.impl.RepositoryAdminImpl.addRepository(RepositoryAdminImpl.java:110) ~[na:na]
at org.apache.felix.bundlerepository.impl.RepositoryAdminImpl.addRepository(RepositoryAdminImpl.java:98) ~[na:na]
at org.lorainelab.igb.plugin.manager.RepositoryInfoManager$1.runInBackground(RepositoryInfoManager.java:59) [plugins-manager-9.1.0.jar:na]
at org.lorainelab.igb.plugin.manager.RepositoryInfoManager$1.runInBackground(RepositoryInfoManager.java:55) [plugins-manager-9.1.0.jar:na]
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) [genometry-9.1.0.jar:na]
at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [na:1.8.0_101]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_101]
at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_101]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_101]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_101]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_101]

Debugging for the same.

A potentially usful suggestion:

• It will probably be easier to make a fork and use that for testing the build and copy to downloads location.

Reason:

I think you will be less likely to encounter permissions problems since you would "own" the fork in that case. I'm not sure if bitbucket will allow a non-admin user to modify a team repository, and both 23andMe and "Hello World" App repositories are "owned" by the Loraine Lab team. You are a member and have write-access but not admin-access to same.

If you do make a fork, it is completely fine to issue pull requests from your fork's master to the team repo's master and then accept your own pulls – or you could ask another devloper to review if you want another pair of eyes.

Another possibly useful suggestion:

• From the error, it looks like the repository.xml file – which IGB expects to find at URL https://bitbucket.org/.../downloads/repository.xml – is not present or accessible from that address.

Sure Prof. [~aloraine] I will fork the 23andMe repository to avoid permission problems.
Also, the repository.xml is present at that location but I guess it is not accessible. I'll try to investigate on that.

Thanks for the suggestion Prof. [~aloraine]. It worked.
So, I forked the 23andme-snp-converter repository and setup the pipeline for the same.
It is creating the required files under the download section and we can directly provide the "downloads" section path in the IGB app manager in order to test the app.
Now submitting a pull request to push those changes onto the master.

For testing:
1) Create a for the 23andMe app repository.
2) You can just set up the repository variables for 23andMe. As the configuration file is already there in the repository, you just need to enable pipelines in the repository.
Once it is enabled the build setup will start and after its completion you can check the downloads section for the JAR and repository.xml
3) You can copy this downloads section link and paste it into the manage repositories section of the IGB app manager.
4) Install the app and test it in IGB.
For more details on the testing steps, please refer the comments section of IGBF-1822 ticket.

IGB Apps now have example bitbucket_pipeline.yml files demonstrating how to

• build App jar file and OBR index file "repository.xml"
• copy same to downloads section

Currently, a user can add the downloads URL to IGB (using App Manager GUI or Settings) to check that the App can be installed.

Example:

https://bitbucket.org/lorainelab/merge-annotation-operator/downloads/

Note: Final slash character is required! (We may fix in later versions of IGB)