Fixed: Issue 90 #560

jvivian · 2015-01-27T21:14:59Z

Removed Required=true from @arguments
Supplied control statement in run method to handle -list_comparisons exception

AmplabJenkins · 2015-01-27T21:18:00Z

Can one of the admins verify this patch?

jvivian · 2015-01-27T21:18:29Z

adam-cli/src/main/scala/org/bdgenomics/adam/cli/CompareADAM.scala

      println("\nAvailable comparisons:")
      DefaultComparisons.comparisons.foreach {
        generator =>
          println("\t%10s : %s".format(generator.name, generator.description))
      }
-
      return


Commenting this return statement out produces an error. What exactly does it do?

It terminate the run() method. Unless the caller has something else to do (which I don't think is the case) it will return also, and so on until the current thread's main run method returns. That will terminate the thread and if it is the last non-daemon thread, the equivalent of sys.exit(0) will be performed, i.e. the JVM process terminates with a zero status code.

fnothaft · 2015-01-27T21:47:56Z

Jenkins, add to whitelist and test this please.

AmplabJenkins · 2015-01-27T21:59:57Z

Test PASSed.
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Test PASSed.

AmplabJenkins · 2015-01-27T23:39:29Z

Test PASSed.
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Test PASSed.

fnothaft · 2015-02-05T15:19:35Z

@jvivian can you rebase this on master? I would merge but am getting merge conflicts.

fnothaft · 2015-02-05T18:48:35Z

Also, can you squash these commits down to a single commit?

jvivian · 2015-02-05T18:49:41Z

Should I close this request and open another? I've committed the changes to the master branch (as one commit).

fnothaft · 2015-02-05T18:50:55Z

You should be able to do the squash and rebase on the original branch that the PR is from. If you do that and then push that branch, then you won't need to open a new PR.

AmplabJenkins · 2015-02-05T23:10:30Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #560 of commit c0093ad.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse c0093ad^{commit} # timeout=10Checking out Revision c0093ad (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f c0093ad > git rev-list d8e02d9 # timeout=10Triggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.2.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,centos completed with result SUCCESSADAM-prb ? 1.0.4,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

fnothaft · 2015-02-05T23:23:38Z

Jenkins, retest this please.

jvivian · 2015-02-05T23:47:40Z

Sorry Frank, I'm in the meeting Matt is in -- I'll squash and rebase ASAP.

fnothaft · 2015-02-05T23:48:06Z

@jvivian no worries! Take your time.

AmplabJenkins · 2015-02-06T00:13:30Z

Test FAILed.
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Build result: ABORTED

GitHub pull request #560 of commit c0093ad.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse c0093ad^{commit} # timeout=10Checking out Revision c0093ad (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f c0093ad > git rev-list c0093ad # timeout=10Triggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.2.0,centos completed with result ABORTEDADAM-prb ? 2.3.0,centos completed with result SUCCESSADAM-prb ? 1.0.4,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

…nomics#90) Added control flow in CompareADAM.scala to return options for -list_arguments flag when no arguments (files) are provided.

AmplabJenkins · 2015-02-06T01:08:52Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #560 of commit e4f3520 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/560/merge^{commit} # timeout=10Checking out Revision 66bb29e (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 66bb29e > git rev-list c0093ad # timeout=10Triggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 2.3.0,centos completed with result FAILUREADAM-prb ? 1.0.4,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

jvivian · 2015-02-06T01:11:09Z

I rebased and squashed, but I had to force push. Given that my previous commits were built successfully, I'm not sure the current build failure is due to my commits.

fnothaft · 2015-02-06T02:21:13Z

@jvivian this isn't an issue on your side; there's a known bug in our CI system that causes the system to intermittently fail to correctly check out a fork after a force push. We just try rerunning the tests until the CI system checks out the fork and builds correctly.

fnothaft · 2015-02-06T02:21:19Z

Jenkins, retest this please.

AmplabJenkins · 2015-02-06T02:33:01Z

Test PASSed.
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Test PASSed.

fnothaft · 2015-02-06T16:50:31Z

Thanks @jvivian! I've manually committed this via 1956ac9.

jvivian changed the title ~~Issue 90 experiment~~ Fixed: Issue 90 Jan 27, 2015

jvivian reviewed Jan 27, 2015
View reviewed changes

Fix the -list_comparisons argument in CompareAdam (resolves bigdatage…

e4f3520

…nomics#90) Added control flow in CompareADAM.scala to return options for -list_arguments flag when no arguments (files) are provided.

jvivian force-pushed the Issue-90-experiment branch from c0093ad to e4f3520 Compare February 6, 2015 01:07

fnothaft closed this Feb 6, 2015

This was referenced Feb 6, 2015

Fix the -list_comparisons argument in CompareAdam #90

Closed

Unit test failure: take10 works correctly on example SAM *** FAILED *** #537

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Fixed: Issue 90 #560

Fixed: Issue 90 #560

jvivian commented Jan 27, 2015

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jvivian Jan 27, 2015

hannes-ucsc Jan 27, 2015

fnothaft commented Jan 27, 2015

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jvivian commented Feb 5, 2015

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AmplabJenkins commented Feb 6, 2015

AmplabJenkins commented Feb 6, 2015

jvivian commented Feb 6, 2015

fnothaft commented Feb 6, 2015

fnothaft commented Feb 6, 2015

AmplabJenkins commented Feb 6, 2015

fnothaft commented Feb 6, 2015

Fixed: Issue 90 #560

Fixed: Issue 90 #560

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Build result: FAILURE

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AmplabJenkins commented Feb 6, 2015

Build result: ABORTED

AmplabJenkins commented Feb 6, 2015

Build result: FAILURE

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