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[ADAM-439] Fix ADAM to account for BDG-FORMATS-35: Avro uses Strings #440

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merged 1 commit into from Nov 17, 2014

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laserson commented Oct 28, 2014

Just changed a bunch of CharSequences to Strings.

Some tests fail, though not sure why, as I'm not familiar with that part of the codebase.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #440 of commit 3ff93b3 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (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/440/merge^{commit} # timeout=10Checking out Revision 88a1fcd (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 88a1fcd > git rev-list 77ea367 # timeout=10Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILURE
Test FAILed.

AmplabJenkins commented Oct 28, 2014

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Build result: FAILURE

GitHub pull request #440 of commit 3ff93b3 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (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/440/merge^{commit} # timeout=10Checking out Revision 88a1fcd (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 88a1fcd > git rev-list 77ea367 # timeout=10Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILURE
Test FAILed.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #440 of commit f0441ef automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (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/440/merge^{commit} # timeout=10Checking out Revision a16515a (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f a16515a > git rev-list 77ea367 # timeout=10Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILURE
Test FAILed.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #440 of commit f0441ef automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (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/440/merge^{commit} # timeout=10Checking out Revision a16515a (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f a16515a > git rev-list 77ea367 # timeout=10Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILURE
Test FAILed.

@@ -31,8 +31,8 @@ object ImplicitJavaConversions {
seqAsJavaList(list.map(i => i: java.lang.Integer))
}
implicit def charSequenceToString(cs: CharSequence): String = cs.toString
// implicit def charSequenceToString(cs: CharSequence): String = cs.toString

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fnothaft Oct 29, 2014

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Shall we just remove these?

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Shall we just remove these?

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Oh, yeah, that was exactly what I wanted to ask. Any objections?

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Oh, yeah, that was exactly what I wanted to ask. Any objections?

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No objections here!

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No objections here!

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@laserson @tdanford pointed out the failing test to me, I'm looking at it now...

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fnothaft commented Oct 29, 2014

@laserson @tdanford pointed out the failing test to me, I'm looking at it now...

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@fnothaft get a chance to look at the failure?

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laserson commented Oct 30, 2014

@fnothaft get a chance to look at the failure?

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@laserson yeah, I'm still looking into it. I think I've figured it out, but haven't been able to fix it yet.

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fnothaft commented Oct 30, 2014

@laserson yeah, I'm still looking into it. I think I've figured it out, but haven't been able to fix it yet.

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Just following up on this

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laserson commented Nov 16, 2014

Just following up on this

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@laserson just pushed a fix towards your fork.

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fnothaft commented Nov 16, 2014

@laserson just pushed a fix towards your fork.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #440 of commit 65d18a9 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (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/440/merge^{commit} # timeout=10Checking out Revision f214a4407bbbb2172945bc3fc4f411b44908b0f4 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f f214a4407bbbb2172945bc3fc4f411b44908b0f4 > git rev-list f211b54 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
Test FAILed.

AmplabJenkins commented Nov 16, 2014

Test FAILed.
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Build result: FAILURE

GitHub pull request #440 of commit 65d18a9 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (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/440/merge^{commit} # timeout=10Checking out Revision f214a4407bbbb2172945bc3fc4f411b44908b0f4 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f f214a4407bbbb2172945bc3fc4f411b44908b0f4 > git rev-list f211b54 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
Test FAILed.

@laserson laserson changed the title from [ADAM-439] Fix ADAM to account for BDG-FORMATS-35 to [ADAM-439] Fix ADAM to account for BDG-FORMATS-35: Avro uses Strings Nov 17, 2014

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Yikes, sorry about the ugly commit history. Let me know if you'd prefer me to squash this.

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laserson commented Nov 17, 2014

Yikes, sorry about the ugly commit history. Let me know if you'd prefer me to squash this.

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Test FAILed.
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Build result: ABORTED

GitHub pull request #440 of commit e12c48d automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (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/440/merge^{commit} # timeout=10Checking out Revision ba78b0d16b230b789f55674b67464908f626ca20 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f ba78b0d16b230b789f55674b67464908f626ca20 > git rev-list f211b54 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result ABORTEDADAM-prb » 1.0.4,centos completed with result ABORTEDADAM-prb » 2.2.0,centos completed with result ABORTED
Test FAILed.

AmplabJenkins commented Nov 17, 2014

Test FAILed.
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Build result: ABORTED

GitHub pull request #440 of commit e12c48d automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (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/440/merge^{commit} # timeout=10Checking out Revision ba78b0d16b230b789f55674b67464908f626ca20 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f ba78b0d16b230b789f55674b67464908f626ca20 > git rev-list f211b54 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result ABORTEDADAM-prb » 1.0.4,centos completed with result ABORTEDADAM-prb » 2.2.0,centos completed with result ABORTED
Test FAILed.

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:-/ builds fine on my machine

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laserson commented Nov 17, 2014

:-/ builds fine on my machine

Uri Laserson
[ADAM-439] Fix ADAM to account for BDG-FORMATS-35
Includes commit by @fnothaft: Fixed flipped index in indel realigner.

Fixes #439
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Building locally now...

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fnothaft commented Nov 17, 2014

Building locally now...

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Just did the same...passed for me

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laserson commented Nov 17, 2014

Just did the same...passed for me

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Test PASSed.
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Test PASSed.

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fnothaft added a commit that referenced this pull request Nov 17, 2014

Merge pull request #440 from laserson/ADAM-439
[ADAM-439] Fix ADAM to account for BDG-FORMATS-35: Avro uses Strings

@fnothaft fnothaft merged commit 087378b into bigdatagenomics:master Nov 17, 2014

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Merged! Thanks @laserson!

BTW, it turns out that our builds on Jenkins have been trending towards 30 minutes and are now flirting dangerously with the build timeout. I've upped the build timeout for now; #478 and #481 should get our build times down to <10 minutes when merged.

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fnothaft commented Nov 17, 2014

Merged! Thanks @laserson!

BTW, it turns out that our builds on Jenkins have been trending towards 30 minutes and are now flirting dangerously with the build timeout. I've upped the build timeout for now; #478 and #481 should get our build times down to <10 minutes when merged.

@laserson laserson deleted the laserson:ADAM-439 branch Dec 2, 2014

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