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[ADAM-1974] Close unclosed stream in FastqInputFormat. #1975

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merged 1 commit into from Apr 11, 2018

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fnothaft commented Apr 5, 2018

Resolves #1974.

@fnothaft fnothaft added this to the 0.24.1 milestone Apr 5, 2018

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AmplabJenkins commented Apr 5, 2018

Test PASSed.
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Test PASSed.

@@ -74,6 +74,8 @@
// why htsjdk doesn't make the function take a buffered input stream instead of
// an input stream, i do not know
splittable = BlockCompressedInputStream.isValidFile(new BufferedInputStream(is));

is.close();

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harsha2010 Apr 5, 2018

this should probably be in the finally block

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@fnothaft fnothaft force-pushed the fnothaft:issues/1974-fastq-stream-leak branch from 3e61542 to 3b6ba33 Apr 9, 2018

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coveralls commented Apr 9, 2018

Coverage Status

Coverage remained the same at 79.067% when pulling 3b6ba33 on fnothaft:issues/1974-fastq-stream-leak into 5328a8f on bigdatagenomics:master.

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coveralls commented Apr 9, 2018

Coverage Status

Coverage remained the same at 79.067% when pulling 3b6ba33 on fnothaft:issues/1974-fastq-stream-leak into 5328a8f on bigdatagenomics:master.

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coveralls commented Apr 9, 2018

Coverage Status

Coverage remained the same at 79.067% when pulling 3b6ba33 on fnothaft:issues/1974-fastq-stream-leak into 5328a8f on bigdatagenomics:master.

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heuermh commented Apr 9, 2018

Linking to #1719.

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heuermh approved these changes Apr 9, 2018

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AmplabJenkins commented Apr 9, 2018

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

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1975/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains a841cc9 # timeout=10Checking out Revision a841cc9 (origin/pr/1975/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f a841cc928d5c776b7a7de84a9bdae618310c7debFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result ABORTEDADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result ABORTEDNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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heuermh commented Apr 9, 2018

Jenkins, retest this please.

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AmplabJenkins commented Apr 9, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2744/
Test PASSed.

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heuermh commented Apr 9, 2018

@harsha2010 could you test with this branch and mark as Approved if it works for you? Thank you.

@heuermh heuermh merged commit ad37f5f into bigdatagenomics:master Apr 11, 2018

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Codacy/PR Quality Review Good work! A positive pull request.
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heuermh commented Apr 11, 2018

Thank you, @fnothaft! Thank you, @harsha2010 for the review!

@fnothaft fnothaft deleted the fnothaft:issues/1974-fastq-stream-leak branch Apr 11, 2018

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fnothaft commented Apr 11, 2018

Cherry-picked over to maint_spark2_2.11-0.24.0 as 8f20f0a.

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