[ADAM-416] Removing 'ADAM' prefix #418

tdanford · 2014-10-14T12:46:20Z

This initial commit includes just the change for the ADAMFeaturesContext
class/object.

I'll add more commits (and accept PRs to this PR!) which remove the prefix from other classes.

Fixes #416.

AmplabJenkins · 2014-10-14T13:03:10Z

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fnothaft · 2014-10-14T13:14:31Z

+1; LGTM!

AmplabJenkins · 2014-10-14T13:18:08Z

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GitHub pull request #418 of commit 5f7d259 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/418/merge^{commit} # timeout=10Checking out Revision 1dcfbb8c88204752ca032bf98fdf0ad480c735cb (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 1dcfbb8c88204752ca032bf98fdf0ad480c735cb > git rev-list fa32bbf # timeout=10First time build. Skipping changelog.Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result SUCCESSADAM-prb » 2.3.0,centos completed with result FAILURE
Test FAILed.

fnothaft · 2014-10-14T13:26:25Z

Jenkins, retest this please.

AmplabJenkins · 2014-10-14T13:43:12Z

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tdanford · 2014-10-14T15:00:55Z

This fixes the obvious classes/objects that I can see. I also cleaned up some of the method names that contained extraneous 'adam' particles. Anyone see anything else I missed?

tdanford · 2014-10-14T15:01:05Z

When this builds, I'll squash down into a single commit.

fnothaft · 2014-10-14T15:09:25Z

I'd say it's pretty clean now:

adam fnothaft$ git status
HEAD detached at tdanford/remove-adam-prefix
nothing added to commit (use "git add" to track)
adam fnothaft$ grep -i adam -R adam-core/src/ | grep -v org.bdgenomics.adam | grep -v adamLoad
adam-core/src//main/resources/git.properties:git.commit.message.full=Merge pull request \#404 from tdanford/gene-models\n\n[ADAM-327] Adding gene, transcript, and exon models.
adam-core/src//main/resources/git.properties:git.commit.id.describe=adam-parent-0.14.0-31-gbeec466
adam-core/src//main/resources/git.properties:git.remote.origin.url=git@github.com\:fnothaft/adam.git
adam-core/src//main/resources/log4j.properties:log4j.appender.logfile.file=adam.log
Binary file adam-core/src//test/resources/parquet_lister_dir/small_adam_A.fgenotype matches
Binary file adam-core/src//test/resources/parquet_lister_dir/small_adam_B.fgenotype matches
adam fnothaft$

fnothaft · 2014-10-14T15:12:33Z

Sorry, ignore the above; that was grep used incorrectly...

fnothaft · 2014-10-14T15:15:00Z

adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/VCFOutputFormat.scala

@@ -22,7 +22,7 @@ import org.bdgenomics.adam.converters.VariantAnnotationConverter
 import org.seqdoop.hadoop_bam.{ VCFFormat, KeyIgnoringVCFOutputFormat }
 import scala.collection.JavaConversions._

-object ADAMVCFOutputFormat extends Serializable {


I would actually not rename this file, to make it obvious that this is distinct from the VCF output formats provided by Hadoop-BAM.

AmplabJenkins · 2014-10-14T15:17:43Z

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GitHub pull request #418 of commit 40fea82 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/418/merge^{commit} # timeout=10Checking out Revision 8d63104b079f827f990af9f354f6039fd485d413 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 8d63104b079f827f990af9f354f6039fd485d413 > git rev-list 1dcfbb8c88204752ca032bf98fdf0ad480c735cb # timeout=10Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result SUCCESSADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILURE
Test FAILed.

fnothaft · 2014-10-14T15:17:57Z

Here are a few ones I saw that I'm not sure about:

ADAMPredicate <-- IMO, these should ultimately be moved out of ADAM and into bdg-utils
ADAMMetrics/ADAMMetricsListener <-- I think these are OK

Otherwise, looks good here!

fnothaft · 2014-10-14T15:18:48Z

@tdanford can you squash? This looks like some wonkyness with the new Jenkins setup; I'll ping @shaneknapp.

tdanford · 2014-10-14T15:21:56Z

I'll squash it when I'm back at my computer :-)

On Tue, Oct 14, 2014 at 11:18 AM, Frank Austin Nothaft
notifications@github.com wrote:

@tdanford can you squash? This looks like some wonkyness with the new Jenkins setup; I'll ping @shaneknapp.

Reply to this email directly or view it on GitHub:
#418 (comment)

tdanford · 2014-10-14T15:49:02Z

I don't think I renamed ADAMPredicate or the metrics stuff, right? (I agree with you, I would leave those.)

fnothaft · 2014-10-14T15:52:58Z

@tdanford ah, sorry, my comment was unclear; I was just pointing out classes that still had prefixes. I think we should drop the prefix from ADAMPredicate. I agree with you that the prefixes should stay on the metrics work.

tdanford · 2014-10-14T15:59:18Z

I think "Predicate" is so generic, I'm going ot leave the ADAM prefix on it for right now. It probably should be a different prefix in the future.

fnothaft · 2014-10-14T16:00:24Z

@tdanford agreed; that's fine with me. I'm thinking we can reevaluate the predicate prefix if/when we move it to bdg-utils.

tdanford · 2014-10-14T16:00:54Z

yup, sounds good.

AmplabJenkins · 2014-10-14T16:08:42Z

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GitHub pull request #418 of commit 2df26b3 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/418/merge^{commit} # timeout=10Checking out Revision 2e436e08fbbf47c4bc13f76e4fc6242aade72735 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 2e436e08fbbf47c4bc13f76e4fc6242aade72735 > git rev-list 8d63104b079f827f990af9f354f6039fd485d413 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

Includes renames for: * ADAMFeaturesContext class/object. * ADAMNucleotideContigFragmentContext/RDDFunctions * ADAMPileupContext/RDDFunctions and ADAMRODRDDFunctions * AlignmentRecordContext, AlignmentRecordRDDFunctions * Variation/GenotypeContext ADAMContext, ADAMRDDFunctions, ADAMVCFInput/OutputFormats, ADAMMetric*, and ADAMPredicate were all intentionally left unchanged. Some method names were also changed, to remove the 'adam' prefix as a particle within the name.

fnothaft · 2014-10-14T16:09:42Z

Jenkins, retest this please.

tdanford · 2014-10-14T16:10:43Z

Squashed and rebased.

AmplabJenkins · 2014-10-14T16:28:28Z

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Build result: FAILURE

GitHub pull request #418 of commit a957395 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/418/merge^{commit} # timeout=10Checking out Revision db0f900 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f db0f900 > git rev-list 2e436e08fbbf47c4bc13f76e4fc6242aade72735 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result SUCCESSADAM-prb » 1.0.4,centos completed with result SUCCESS
Test FAILed.

shaneknapp · 2014-10-14T17:19:41Z

Jenkins, test this please

shaneknapp · 2014-10-14T17:34:45Z

Jenkins, retest this please.

AmplabJenkins · 2014-10-14T17:53:07Z

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[ADAM-416] Removing 'ADAM' prefix

fnothaft · 2014-10-14T17:55:05Z

Merged! Thanks @tdanford!

tdanford · 2014-10-14T18:08:57Z

Thanks @fnothaft!

fnothaft reviewed Oct 14, 2014
View reviewed changes

tdanford force-pushed the remove-adam-prefix branch from 40fea82 to 2df26b3 Compare October 14, 2014 16:05

tdanford force-pushed the remove-adam-prefix branch from 2df26b3 to a957395 Compare October 14, 2014 16:10

fnothaft added a commit that referenced this pull request Oct 14, 2014

Merge pull request #418 from tdanford/remove-adam-prefix

d7bba84

[ADAM-416] Removing 'ADAM' prefix

fnothaft merged commit d7bba84 into bigdatagenomics:master Oct 14, 2014

tdanford deleted the remove-adam-prefix branch October 14, 2014 18:08

fnothaft mentioned this pull request Oct 15, 2014

Do we need the GA prefix on all objects? ga4gh/ga4gh-schemas#87

Closed

tdanford mentioned this pull request Oct 15, 2014

Fix the dependencies which were broken by removing the ADAM* prefixes bigdatagenomics/avocado#112

Closed

fnothaft mentioned this pull request Oct 16, 2014

Fix broken build due to upstream changes bigdatagenomics/rice#38

Closed

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[ADAM-416] Removing 'ADAM' prefix #418

[ADAM-416] Removing 'ADAM' prefix #418

tdanford commented Oct 14, 2014

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fnothaft commented Oct 14, 2014

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fnothaft Oct 14, 2014

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fnothaft commented Oct 14, 2014

tdanford commented Oct 14, 2014

@tdanford can you squash? This looks like some wonkyness with the new Jenkins setup; I'll ping @shaneknapp.

tdanford commented Oct 14, 2014

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tdanford commented Oct 14, 2014

[ADAM-416] Removing 'ADAM' prefix #418

[ADAM-416] Removing 'ADAM' prefix #418

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AmplabJenkins commented Oct 14, 2014

Build result: FAILURE

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tdanford commented Oct 14, 2014

@tdanford can you squash? This looks like some wonkyness with the new Jenkins setup; I'll ping @shaneknapp.

tdanford commented Oct 14, 2014

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Build result: FAILURE

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Build result: FAILURE

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