SeqWare/seqware — pull request #4 by briandoconnor (2012-09-28 01:42:54+00:00)
Title: Feature/seqware 1214 hotfix 0.12.5.1

This is a pull request to test fixes to BundleManager so it supports testing again via the --test param. See https://jira.oicr.on.ca/browse/SEQWARE-1214

Unfortunately, we don't have the full subversion history so we're essentially creating 0.12.5.1 using 0.13.3 SNAPSHOT.

Here's how I tested this:

1) download and run our SeqWare VM: https://s3.amazonaws.com/nimbusinformatics.exchange/public/SeqWareVM_0.12.5_r5163_CentOS_6.2_20120904b.ova

2) setup a git repo on this machine and sync to this branch:

git checkout feature/SEQWARE-1214_hotfix_0.12.5.1
git pull

3) build normally (I skipped tests, I still need to verify our tests all work).

4) create a new HelloWorld bundle using the 0.12.5 on this VM as a template, and replace the previous jar with the 0.13.3-SNAPSHOT

5) run the new HelloWorld bundle with:

java -jar Workflow_Bundle_helloworld/1.0/lib/seqware-pipeline-0.13.3.jar -p net.sourceforge.seqware.pipeline.plugins.BundleManager -- -b `pwd` -t

This now waits for the workflow to finish and correctly reports progress.

TODO:

I still need to make sure all our tests run on this branch on the VM. We should also test by creating a release branch with this, installing DB and web service on sqwstage.hpc, testing, and then doing a real push to master. Once finished this bug will be closed and the 0.13.3-SNAPSHOT will be pushed to artifactory (manually) to be 0.12.5.1, the web service/db will be updated, and Morgan's team notified of the new URLs and jar file.