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update to _replaceRdd with tests #1749

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merged 1 commit into from Sep 27, 2017

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@akmorrow13
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akmorrow13 commented Sep 26, 2017

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Test FAILed.
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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/1749/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 3e638b5b1b55dfaa8062aad2e879745f06f1e1b0 # timeout=10Checking out Revision 3e638b5b1b55dfaa8062aad2e879745f06f1e1b0 (origin/pr/1749/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 3e638b5b1b55dfaa8062aad2e879745f06f1e1b0First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Sep 26, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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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/1749/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 3e638b5b1b55dfaa8062aad2e879745f06f1e1b0 # timeout=10Checking out Revision 3e638b5b1b55dfaa8062aad2e879745f06f1e1b0 (origin/pr/1749/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 3e638b5b1b55dfaa8062aad2e879745f06f1e1b0First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Test PASSed.
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Test PASSed.

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Test PASSed.
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Test PASSed.

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Test PASSed.
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Test PASSed.

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Test PASSed.
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Test PASSed.

@@ -692,6 +692,11 @@ def _inferConversionFn(self, destClass):
class FeatureRDD(GenomicDataset):
def _replaceRdd(self, newRdd):

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heuermh Sep 27, 2017

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Is this only necessary in class FeatureRDD?

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heuermh Sep 27, 2017

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Is this only necessary in class FeatureRDD?

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akmorrow13 Sep 27, 2017

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@heuermh if it is not present transform will fail (_replaceRdd is not a function)

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akmorrow13 Sep 27, 2017

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@heuermh if it is not present transform will fail (_replaceRdd is not a function)

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akmorrow13 Sep 27, 2017

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https://github.com/akmorrow13/adam/blob/eec00a545dca3e4cd4e258023c99a1afa8a8974e/adam-python/bdgenomics/adam/rdd.py#L104 is defined in GenomicRDD, calling _replaceRDD, which FeatureRDD does not have

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heuermh Sep 27, 2017

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Thanks!

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heuermh Sep 27, 2017

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Thanks!

@@ -692,6 +692,11 @@ def _inferConversionFn(self, destClass):
class FeatureRDD(GenomicDataset):
def _replaceRdd(self, newRdd):

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@heuermh

heuermh Sep 27, 2017

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Thanks!

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heuermh Sep 27, 2017

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Thanks!

@heuermh heuermh merged commit b2c243f into bigdatagenomics:master Sep 27, 2017

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codacy/pr Good work! A positive pull request.
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heuermh Sep 27, 2017

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Thank you, @akmorrow13

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heuermh commented Sep 27, 2017

Thank you, @akmorrow13

@heuermh heuermh added this to the 0.23.0 milestone Oct 4, 2017

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

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