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[ADAM-1676] Add more finely grained validation for INFO/FORMAT fields. #1677

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merged 1 commit into from Sep 14, 2017

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fnothaft commented Aug 22, 2017

Resolves #1676. Pushes validation checking down to the single field conversion level, which keeps a variant/genotype record around even if a bad INFO/FORMAT field was attached to that record.

WIP, needs more testing, not ready for merge.

@fnothaft fnothaft requested a review from heuermh Aug 22, 2017

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coveralls Aug 22, 2017

Coverage Status

Coverage decreased (-0.5%) to 82.948% when pulling cf2aa38 on fnothaft:issues/1676-validate-fields into b46b583 on bigdatagenomics:master.

coveralls commented Aug 22, 2017

Coverage Status

Coverage decreased (-0.5%) to 82.948% when pulling cf2aa38 on fnothaft:issues/1676-validate-fields into b46b583 on bigdatagenomics:master.

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Test PASSed.
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Ping for review.

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fnothaft commented Sep 6, 2017

Ping for review.

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The code here looks reasonable, I'm not sure the conversation in issue #1676 has been resolved.

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heuermh commented Sep 6, 2017

The code here looks reasonable, I'm not sure the conversation in issue #1676 has been resolved.

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Rebased. Ready for merge once tests pass.

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fnothaft commented Sep 12, 2017

Rebased. Ready for merge once tests pass.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1677/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 16f2efe # timeout=10Checking out Revision 16f2efe (origin/pr/1677/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 16f2efe3faa47ae85a79d0f8072f96e77b7db812First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Sep 12, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2363/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1677/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 16f2efe # timeout=10Checking out Revision 16f2efe (origin/pr/1677/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 16f2efe3faa47ae85a79d0f8072f96e77b7db812First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[ADAM-1676] Add more finely grained validation for INFO/FORMAT fields.
Resolves #1676. Pushes validation checking down to the single field conversion
level, which keeps a variant/genotype record around even if a bad INFO/FORMAT
field was attached to that record.
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Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2365/
Test PASSed.

AmplabJenkins commented Sep 13, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2365/
Test PASSed.

@heuermh heuermh merged commit 547f92d into bigdatagenomics:master Sep 14, 2017

1 of 2 checks passed

codacy/pr Not so good... This pull request quality could be better.
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heuermh Sep 14, 2017

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Thank you, @fnothaft!

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heuermh commented Sep 14, 2017

Thank you, @fnothaft!

@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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