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[ADAM-1169] Write GFF header line pragma in single file mode. #1529

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merged 1 commit into from May 16, 2017

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@fnothaft fnothaft commented May 15, 2017

Resolves #1169.

@fnothaft fnothaft added this to the 0.23.0 milestone May 15, 2017
@fnothaft fnothaft requested a review from heuermh May 15, 2017
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@coveralls coveralls commented May 15, 2017

Coverage Status

Coverage decreased (-0.3%) to 81.754% when pulling 3197212 on fnothaft:issues/1169-gff-pragma into 18191f9 on bigdatagenomics:master.

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@coveralls coveralls commented May 15, 2017

Coverage Status

Coverage decreased (-0.08%) to 81.93% when pulling 3197212 on fnothaft:issues/1169-gff-pragma into 18191f9 on bigdatagenomics:master.

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@heuermh heuermh left a comment

Looks good, minor GFF → GFF3 changes requested

@@ -390,10 +394,18 @@ case class FeatureRDD(rdd: RDD[Feature],
def saveAsGff3(fileName: String,
asSingleFile: Boolean = false,
disableFastConcat: Boolean = false) = {
val optHeaderPath = if (asSingleFile) {
val headerPath = "%s_head".format(fileName)
GFFHeaderWriter(headerPath, rdd.context)

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heuermh May 15, 2017
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GFFHeaderWriter should be GFF3HeaderWriter to match GFF3InFormatter and elsewhere. The GFF2/GTF specifications do not require a version pragma in the header.

import org.apache.spark.SparkContext

/**
* Writes the header for a GFF file to an otherwise empty file.

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GFF → GFF3

class GFFHeaderWriterSuite extends ADAMFunSuite {

sparkTest("write gff header pragma") {
val tmp = tmpFile(".gff")

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heuermh May 15, 2017
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".gff"".gff3"

val HEADER_STRING = "##gff-version 3.2.1"

/**
* Writes a GFF Header pragma to a file.

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heuermh May 15, 2017
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GFF → GFF3

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@AmplabJenkins AmplabJenkins commented May 15, 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/2011/
Test PASSed.

@fnothaft fnothaft force-pushed the fnothaft:issues/1169-gff-pragma branch from 3197212 to 789ad99 May 15, 2017
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@fnothaft fnothaft commented May 15, 2017

@heuermh addressed comments.

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@AmplabJenkins AmplabJenkins commented May 15, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1529/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 3fe7fe43c4e94f4646dbe923d04f7950a15a7b9a # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1529/merge^{commit} # timeout=10Checking out Revision 3fe7fe43c4e94f4646dbe923d04f7950a15a7b9a (origin/pr/1529/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 3fe7fe43c4e94f4646dbe923d04f7950a15a7b9aFirst 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 fnothaft:issues/1169-gff-pragma branch from 789ad99 to a13ff4a May 15, 2017
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@coveralls coveralls commented May 15, 2017

Coverage Status

Coverage decreased (-0.08%) to 81.93% when pulling a13ff4a on fnothaft:issues/1169-gff-pragma into 18191f9 on bigdatagenomics:master.

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@AmplabJenkins AmplabJenkins commented May 15, 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/2013/
Test PASSed.

@heuermh heuermh merged commit e8f9bed into bigdatagenomics:master May 16, 2017
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codacy/pr Not so good... This pull request quality could be better.
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coverage/coveralls Coverage decreased (-0.08%) to 81.93%
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@heuermh heuermh commented May 16, 2017

Thank you, @fnothaft!

@heuermh heuermh added this to Completed in Release 0.23.0 May 30, 2017
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