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[ADAM-1611] Extend pipe APIs to Java, Python, and R. #1613

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merged 2 commits into from Jul 21, 2017

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fnothaft commented Jul 21, 2017

Resolves #1611. Depends on #1397. Adds a Java-friendly pipe method onto GenomicRDD, and conversion functions in the org.bdgenomics.adam.api.java package. Simultaneously, we add a GenomicRDD base type in the R bindings. With these additions, we then add the pipe method to the GenomicRDD class that exists in both Python and R. The language bindings use reflection to construct the in/out-formatters and conversion functions.

While I was at it, I also made the toDF implementation in R generic.

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Coverage Status

Coverage decreased (-0.9%) to 83.874% when pulling 1bedfe9 on fnothaft:issues/1611-pype into 7652536 on bigdatagenomics:master.

coveralls commented Jul 21, 2017

Coverage Status

Coverage decreased (-0.9%) to 83.874% when pulling 1bedfe9 on fnothaft:issues/1611-pype into 7652536 on bigdatagenomics:master.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2252/

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/1613/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 3f20508 # timeout=10Checking out Revision 3f20508 (origin/pr/1613/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 3f2050816edc17afe4ae5547dc7165b042cbacc4First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Jul 21, 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/2252/

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/1613/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 3f20508 # timeout=10Checking out Revision 3f20508 (origin/pr/1613/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 3f2050816edc17afe4ae5547dc7165b042cbacc4First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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heuermh Jul 21, 2017

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Looks good to me, will review further after conflicts are resolved.

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heuermh commented Jul 21, 2017

Looks good to me, will review further after conflicts are resolved.

fnothaft added some commits Jul 20, 2017

[ADAM-1611] Extend pipe APIs to Java, Python, and R.
Resolves #1611. Adds a Java-friendly pipe method onto `GenomicRDD`, and
conversion functions in the `org.bdgenomics.adam.api.java` package.
Simultaneously, we add a `GenomicRDD` base type in the R bindings. With
these additions, we then add the pipe method to the `GenomicRDD` class
that exists in both Python and R. The language bindings use reflection
to construct the in/out-formatters and conversion functions.
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Rebased.

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fnothaft commented Jul 21, 2017

Rebased.

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@heuermh btw the meat of the interesting stuff is the changes to GenomicRDD.

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fnothaft commented Jul 21, 2017

@heuermh btw the meat of the interesting stuff is the changes to GenomicRDD.

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Coverage Status

Coverage decreased (-0.4%) to 83.874% when pulling 74baf8d on fnothaft:issues/1611-pype into 640c44b on bigdatagenomics:master.

coveralls commented Jul 21, 2017

Coverage Status

Coverage decreased (-0.4%) to 83.874% when pulling 74baf8d on fnothaft:issues/1611-pype into 640c44b on bigdatagenomics:master.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2261/

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/1613/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains a433274 # timeout=10Checking out Revision a433274 (origin/pr/1613/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f a433274da4081f0cf4bbf0a5e05c1811c6c0e0a1First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Jul 21, 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/2261/

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/1613/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains a433274 # timeout=10Checking out Revision a433274 (origin/pr/1613/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f a433274da4081f0cf4bbf0a5e05c1811c6c0e0a1First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@devin-petersohn

This looks good to me, but it's failing with Jenkins.

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Jenkins, test this please.

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fnothaft commented Jul 21, 2017

Jenkins, test this please.

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coveralls Jul 21, 2017

Coverage Status

Coverage decreased (-0.4%) to 83.874% when pulling 74baf8d on fnothaft:issues/1611-pype into 640c44b on bigdatagenomics:master.

coveralls commented Jul 21, 2017

Coverage Status

Coverage decreased (-0.4%) to 83.874% when pulling 74baf8d on fnothaft:issues/1611-pype into 640c44b on bigdatagenomics:master.

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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2268/
Test PASSed.

AmplabJenkins commented Jul 21, 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/2268/
Test PASSed.

@heuermh heuermh merged commit 271c388 into bigdatagenomics:master Jul 21, 2017

2 of 3 checks passed

codacy/pr Not so good... This pull request quality could be better.
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coverage/coveralls Coverage decreased (-0.4%) to 83.874%
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default Merged build finished.
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Thank you, @fnothaft!

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heuermh commented Jul 21, 2017

Thank you, @fnothaft!

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

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