Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Merged
merged 2 commits into from Jul 21, 2017

Conversation

@fnothaft
Copy link
Member

@fnothaft 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.

@coveralls
Copy link

@coveralls 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.

@AmplabJenkins
Copy link

@AmplabJenkins 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.

@heuermh
Copy link
Member

@heuermh heuermh commented Jul 21, 2017

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

fnothaft added 2 commits Jul 21, 2017
Resolves bigdatagenomics#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.
@fnothaft fnothaft force-pushed the issues/1611-pype branch from 1bedfe9 to 74baf8d Jul 21, 2017
@fnothaft
Copy link
Member Author

@fnothaft fnothaft commented Jul 21, 2017

Rebased.

@fnothaft
Copy link
Member Author

@fnothaft fnothaft commented Jul 21, 2017

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

@coveralls
Copy link

@coveralls 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.

@AmplabJenkins
Copy link

@AmplabJenkins 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.

Copy link
Member

@devin-petersohn devin-petersohn left a comment

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

@fnothaft
Copy link
Member Author

@fnothaft fnothaft commented Jul 21, 2017

Jenkins, test this please.

@coveralls
Copy link

@coveralls 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.

@AmplabJenkins
Copy link

@AmplabJenkins 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
@heuermh
Copy link
Member

@heuermh heuermh commented Jul 21, 2017

Thank you, @fnothaft!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Linked issues

Successfully merging this pull request may close these issues.

None yet

5 participants