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Resolve #1508, #1509 for Pipe API #1511

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merged 2 commits into from May 11, 2017

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fnothaft commented Apr 29, 2017

Resolves #1508, #1509. WIP, still being tested.

@fnothaft fnothaft added this to the 0.23.0 milestone Apr 29, 2017

@fnothaft fnothaft self-assigned this Apr 29, 2017

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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/1969/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1511/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 27bfbd61210c7c232d861d0313cad70259907354 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1511/merge^{commit} # timeout=10Checking out Revision 27bfbd61210c7c232d861d0313cad70259907354 (origin/pr/1511/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 27bfbd61210c7c232d861d0313cad70259907354First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Apr 29, 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/1969/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1511/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 27bfbd61210c7c232d861d0313cad70259907354 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1511/merge^{commit} # timeout=10Checking out Revision 27bfbd61210c7c232d861d0313cad70259907354 (origin/pr/1511/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 27bfbd61210c7c232d861d0313cad70259907354First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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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/1970/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1511/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains a71d88fad84fb6b9b1573ed45414ccfece1cf395 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1511/merge^{commit} # timeout=10Checking out Revision a71d88fad84fb6b9b1573ed45414ccfece1cf395 (origin/pr/1511/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f a71d88fad84fb6b9b1573ed45414ccfece1cf395First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Apr 30, 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/1970/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1511/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains a71d88fad84fb6b9b1573ed45414ccfece1cf395 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1511/merge^{commit} # timeout=10Checking out Revision a71d88fad84fb6b9b1573ed45414ccfece1cf395 (origin/pr/1511/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f a71d88fad84fb6b9b1573ed45414ccfece1cf395First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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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/1971/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1511/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains d90d575309a668b84adc29cdef045f3840c48096 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1511/merge^{commit} # timeout=10Checking out Revision d90d575309a668b84adc29cdef045f3840c48096 (origin/pr/1511/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d90d575309a668b84adc29cdef045f3840c48096First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Apr 30, 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/1971/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1511/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains d90d575309a668b84adc29cdef045f3840c48096 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1511/merge^{commit} # timeout=10Checking out Revision d90d575309a668b84adc29cdef045f3840c48096 (origin/pr/1511/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d90d575309a668b84adc29cdef045f3840c48096First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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coveralls Apr 30, 2017

Coverage Status

Coverage increased (+0.2%) to 81.88% when pulling 2ab0657 on fnothaft:issues/1508-1509-pipe-files into dbe5c97 on bigdatagenomics:master.

coveralls commented Apr 30, 2017

Coverage Status

Coverage increased (+0.2%) to 81.88% when pulling 2ab0657 on fnothaft:issues/1508-1509-pipe-files into dbe5c97 on bigdatagenomics:master.

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Test PASSed.
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Test PASSed.

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Test PASSed.
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Test PASSed.

@heuermh

LGTM, could you add a unit test that looks for $root?

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@heuermh can do! I'll be testing this later today, and will add the unit test as well.

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fnothaft commented Apr 30, 2017

@heuermh can do! I'll be testing this later today, and will add the unit test as well.

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+1

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heuermh commented Apr 30, 2017

+1

fnothaft added a commit to fnothaft/cannoli-1 that referenced this pull request May 1, 2017

fnothaft added a commit to fnothaft/cannoli-1 that referenced this pull request May 1, 2017

fnothaft added some commits Apr 29, 2017

[ADAM-1509] Adding root dir path to pipe API.
Resolves #1509. This allows the directory where the SparkFiles are copied
to be accessed and included in a piped command.
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@heuermh Rebased and added the test.

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fnothaft commented May 11, 2017

@heuermh Rebased and added the test.

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coveralls May 11, 2017

Coverage Status

Coverage increased (+0.009%) to 81.881% when pulling 7291bd8 on fnothaft:issues/1508-1509-pipe-files into ea9ce6c on bigdatagenomics:master.

coveralls commented May 11, 2017

Coverage Status

Coverage increased (+0.009%) to 81.881% when pulling 7291bd8 on fnothaft:issues/1508-1509-pipe-files into ea9ce6c 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/1982/
Test PASSed.

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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/1982/
Test PASSed.

@heuermh heuermh merged commit 0dd09b2 into bigdatagenomics:master May 11, 2017

3 checks passed

codacy/pr Good work! A positive pull request.
Details
coverage/coveralls Coverage increased (+0.009%) to 81.881%
Details
default Merged build finished.
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Thank you, @fnothaft

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heuermh commented May 11, 2017

Thank you, @fnothaft

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