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Resolve #1508, #1509 for Pipe API #1511

Merged
merged 2 commits into from
May 11, 2017
Merged

Resolve #1508, #1509 for Pipe API #1511

merged 2 commits into from
May 11, 2017

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fnothaft
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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.

@fnothaft fnothaft force-pushed the issues/1508-1509-pipe-files branch from 54d1fb0 to 1f48cb9 Compare April 30, 2017 04:31
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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.

@fnothaft fnothaft force-pushed the issues/1508-1509-pipe-files branch from 1f48cb9 to dd5f01c Compare April 30, 2017 18:01
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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.

@fnothaft fnothaft force-pushed the issues/1508-1509-pipe-files branch from dd5f01c to 2ab0657 Compare April 30, 2017 21:51
@fnothaft fnothaft mentioned this pull request Apr 30, 2017
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coveralls commented Apr 30, 2017 •
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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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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1972/
Test PASSed.

heuermh
heuermh approved these changes Apr 30, 2017
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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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heuermh commented Apr 30, 2017

+1

fnothaft added a commit to fnothaft/cannoli-1 that referenced this pull request May 1, 2017
@fnothaft
Bump to ADAM 0.23.0-SNAPSHOT.
84a07ad 
To pick up bigdatagenomics/adam#1511.
@fnothaft fnothaft mentioned this pull request May 1, 2017
Merged
fnothaft added a commit to fnothaft/cannoli-1 that referenced this pull request May 1, 2017
@fnothaft
Bump to ADAM 0.23.0-SNAPSHOT.
0bd30b4 
To pick up bigdatagenomics/adam#1511.
fnothaft added 2 commits May 10, 2017 20:45
@fnothaft
[ADAM-1508] Use file name, not full path, with SparkFiles.get
7c8f5bb 
Resolves bigdatagenomics#1508.
@fnothaft
[ADAM-1509] Adding root dir path to pipe API.
7291bd8 
Resolves bigdatagenomics#1509. This allows the directory where the SparkFiles are copied
to be accessed and included in a piped command.
@fnothaft fnothaft force-pushed the issues/1508-1509-pipe-files branch from 2ab0657 to 7291bd8 Compare May 11, 2017 03:52
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@heuermh Rebased and added the test.

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coveralls commented May 11, 2017 •
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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.

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

Thank you, @fnothaft

@fnothaft fnothaft mentioned this pull request May 12, 2017
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