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[ADAM-1481] Refactor ADAMContext loadXxx methods for consistency #1487

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merged 8 commits into from Apr 19, 2017

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heuermh commented Apr 12, 2017

Fixes #1481.

I flagged most of the pathName method parameter param doc strings with (todo: confirm) because it is not immediately clear which support glob/directories and which do not.

There is also some inconsistency wrt when .gz is supported and when it is not.

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Coverage increased (+0.03%) to 81.667% when pulling 072ccf5 on heuermh:load-cleanup into 93b32c6 on bigdatagenomics:master.

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Coverage Status

Coverage increased (+0.03%) to 81.667% when pulling 072ccf5 on heuermh:load-cleanup into 93b32c6 on bigdatagenomics:master.

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Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1487/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains b99480b8032090dce76fdfb1cce900bb7800a5ff # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1487/merge^{commit} # timeout=10Checking out Revision b99480b8032090dce76fdfb1cce900bb7800a5ff (origin/pr/1487/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f b99480b8032090dce76fdfb1cce900bb7800a5ffFirst 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'
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[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1487/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains b99480b8032090dce76fdfb1cce900bb7800a5ff # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1487/merge^{commit} # timeout=10Checking out Revision b99480b8032090dce76fdfb1cce900bb7800a5ff (origin/pr/1487/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f b99480b8032090dce76fdfb1cce900bb7800a5ffFirst 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'
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Coverage decreased (-0.1%) to 81.508% when pulling 8082b2c on heuermh:load-cleanup into 93b32c6 on bigdatagenomics:master.

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Coverage Status

Coverage decreased (-0.1%) to 81.508% when pulling 8082b2c on heuermh:load-cleanup into 93b32c6 on bigdatagenomics:master.

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Coverage increased (+0.04%) to 81.674% when pulling 8082b2c on heuermh:load-cleanup into 93b32c6 on bigdatagenomics:master.

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Coverage Status

Coverage increased (+0.04%) to 81.674% when pulling 8082b2c on heuermh:load-cleanup into 93b32c6 on bigdatagenomics:master.

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@heuermh After merging #1482, this branch has conflicts. Can you rebase?

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fnothaft commented Apr 13, 2017

@heuermh After merging #1482, this branch has conflicts. Can you rebase?

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Will do. I have more changes coming.

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heuermh commented Apr 13, 2017

Will do. I have more changes coming.

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Sounds good! Would you like me to hold off on reviewing until you're done with the changes?

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fnothaft commented Apr 13, 2017

Sounds good! Would you like me to hold off on reviewing until you're done with the changes?

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If you have feedback on some of the open questions now, that would be helpful.

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heuermh commented Apr 13, 2017

If you have feedback on some of the open questions now, that would be helpful.

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What are the open questions? Are they the following? If so, answers below:

I flagged most of the pathName method parameter param doc strings with (todo: confirm) because it is not immediately clear which support glob/directories and which do not.

All of the loadX methods should support globs and directories.

There is also some inconsistency wrt when .gz is supported and when it is not.

  • GZIPed VCF is loaded (and even split if BGZIPed)
  • All of the files that use sc.textFile (FASTA, all of the feature formats) will load both GZIPed files (as a single split) and BZIP2 files
  • FileInputFormat (FASTQ) will load GZIPed data, but there is an issue, see #1457

I'm not sure about GZIPed SAM.

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fnothaft commented Apr 13, 2017

What are the open questions? Are they the following? If so, answers below:

I flagged most of the pathName method parameter param doc strings with (todo: confirm) because it is not immediately clear which support glob/directories and which do not.

All of the loadX methods should support globs and directories.

There is also some inconsistency wrt when .gz is supported and when it is not.

  • GZIPed VCF is loaded (and even split if BGZIPed)
  • All of the files that use sc.textFile (FASTA, all of the feature formats) will load both GZIPed files (as a single split) and BZIP2 files
  • FileInputFormat (FASTQ) will load GZIPed data, but there is an issue, see #1457

I'm not sure about GZIPed SAM.

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All of the loadX methods should support globs and directories.

Some clearly do not, loadIndexedBam, for example.

Others forward to loadAvro and sc.newAPIHadoopFile without going through getFsAndFiles and related, do those support globs and directories? E.g. loadInterleavedFastq forwards pathName: String to sc.newAPIHadoopFile.

There is also some inconsistency wrt when .gz is supported and when it is not.

Thanks, we need to make sure .gz and .bz2 extensions pass format guessing checks where appropriate then.

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heuermh commented Apr 13, 2017

All of the loadX methods should support globs and directories.

Some clearly do not, loadIndexedBam, for example.

Others forward to loadAvro and sc.newAPIHadoopFile without going through getFsAndFiles and related, do those support globs and directories? E.g. loadInterleavedFastq forwards pathName: String to sc.newAPIHadoopFile.

There is also some inconsistency wrt when .gz is supported and when it is not.

Thanks, we need to make sure .gz and .bz2 extensions pass format guessing checks where appropriate then.

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All of the loadX methods should support globs and directories.

Some clearly do not, loadIndexedBam, for example.

https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala#L369-L375 ;)

Others forward to loadAvro and sc.newAPIHadoopFile without going through getFsAndFiles and related, do those support globs and directories? E.g. loadInterleavedFastq forwards pathName: String to sc.newAPIHadoopFile.

In general, they should, unless the underlying InputFormat is doing something funny.

Thanks, we need to make sure .gz and .bz2 extensions pass format guessing checks where appropriate then.

+1

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fnothaft commented Apr 13, 2017

All of the loadX methods should support globs and directories.

Some clearly do not, loadIndexedBam, for example.

https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala#L369-L375 ;)

Others forward to loadAvro and sc.newAPIHadoopFile without going through getFsAndFiles and related, do those support globs and directories? E.g. loadInterleavedFastq forwards pathName: String to sc.newAPIHadoopFile.

In general, they should, unless the underlying InputFormat is doing something funny.

Thanks, we need to make sure .gz and .bz2 extensions pass format guessing checks where appropriate then.

+1

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All of the loadX methods should support globs and directories.

Some clearly do not, loadIndexedBam, for example.

https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala#L369-L375 ;)

Dang it! Who made that work and forgot to update the @param docs? :)

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heuermh commented Apr 13, 2017

All of the loadX methods should support globs and directories.

Some clearly do not, loadIndexedBam, for example.

https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala#L369-L375 ;)

Dang it! Who made that work and forgot to update the @param docs? :)

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Dang it! Who made that work and forgot to update the @param docs? :)

My bad! ;)

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fnothaft commented Apr 13, 2017

Dang it! Who made that work and forgot to update the @param docs? :)

My bad! ;)

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Coverage Status

Coverage increased (+0.04%) to 81.674% when pulling 579126a on heuermh:load-cleanup into 93b32c6 on bigdatagenomics:master.

coveralls commented Apr 13, 2017

Coverage Status

Coverage increased (+0.04%) to 81.674% when pulling 579126a on heuermh:load-cleanup into 93b32c6 on bigdatagenomics:master.

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Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse 579126a^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 579126a # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1487/head^{commit} # timeout=10Checking out Revision 579126a (origin/pr/1487/head) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 579126af17f2b882c715080dd75e309bfda3ebf5First 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'
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[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse 579126a^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 579126a # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1487/head^{commit} # timeout=10Checking out Revision 579126a (origin/pr/1487/head) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 579126af17f2b882c715080dd75e309bfda3ebf5First 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'
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Coverage increased (+0.3%) to 81.854% when pulling c7814c9 on heuermh:load-cleanup into 6c32a02 on bigdatagenomics:master.

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Coverage Status

Coverage increased (+0.3%) to 81.854% when pulling c7814c9 on heuermh:load-cleanup into 6c32a02 on bigdatagenomics:master.

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Coverage increased (+0.2%) to 81.809% when pulling f3d1d3c on heuermh:load-cleanup into 6c32a02 on bigdatagenomics:master.

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Coverage increased (+0.2%) to 81.809% when pulling f3d1d3c on heuermh:load-cleanup into 6c32a02 on bigdatagenomics:master.

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This one is ready to review!

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heuermh commented Apr 14, 2017

This one is ready to review!

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Let's check for compressors using the Hadoop factory, but otherwise this LGTM! Thanks @heuermh! This is a great cleanup.

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Coverage increased (+0.4%) to 81.942% when pulling b021e2c on heuermh:load-cleanup into 6c32a02 on bigdatagenomics:master.

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Coverage increased (+0.4%) to 81.942% when pulling b021e2c on heuermh:load-cleanup into 6c32a02 on bigdatagenomics:master.

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This LGTM from a code perspective, but I think we should mention in each of the docstrings that we do support compressed text files, and where that comes from. I think we're very close here; thanks for driving this @heuermh!

Show outdated Hide outdated ...-apis/src/main/scala/org/bdgenomics/adam/apis/java/JavaADAMContext.scala Outdated
Show outdated Hide outdated ...-apis/src/main/scala/org/bdgenomics/adam/apis/java/JavaADAMContext.scala Outdated
Show outdated Hide outdated ...-apis/src/main/scala/org/bdgenomics/adam/apis/java/JavaADAMContext.scala Outdated
* * .gff3 as GFF3 format,
* * .gtf/.gff as GTF/GFF2 format,
* * .narrow[pP]eak as NarrowPeak format, and
* * .interval_list as IntervalList format.

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Ditto.

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Ditto.

* * .gff3 as GFF3 format,
* * .gtf/.gff as GTF/GFF2 format,
* * .narrow[pP]eak as NarrowPeak format, and
* * .interval_list as IntervalList format.

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Ditto.

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Ditto.

* * .gff3 as GFF3 format,
* * .gtf/.gff as GTF/GFF2 format,
* * .narrow[pP]eak as NarrowPeak format, and
* * .interval_list as IntervalList format.

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Ditto.

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Ditto.

* * .gff3 as GFF3 format,
* * .gtf/.gff as GTF/GFF2 format,
* * .narrow[pP]eak as NarrowPeak format, and
* * .interval_list as IntervalList format.

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Ditto.

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Ditto.

Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala Outdated
Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala Outdated
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Coverage Status

Coverage increased (+0.4%) to 82.018% when pulling 9b13e6e on heuermh:load-cleanup into 6c32a02 on bigdatagenomics:master.

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Coverage Status

Coverage increased (+0.4%) to 82.018% when pulling 9b13e6e on heuermh:load-cleanup into 6c32a02 on bigdatagenomics:master.

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Test PASSed.

AmplabJenkins commented Apr 19, 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/1955/
Test PASSed.

@fnothaft

LGTM! Do you want to squash in any specific way, or would you like me to hit the green squash button?

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Green squash is fine!

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heuermh commented Apr 19, 2017

Green squash is fine!

@fnothaft fnothaft merged commit 93d17b4 into bigdatagenomics:master Apr 19, 2017

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codacy/pr Good work! A positive pull request.
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coverage/coveralls Coverage increased (+0.4%) to 82.018%
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default Merged build finished.
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@heuermh heuermh deleted the heuermh:load-cleanup branch Apr 19, 2017

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Thank you!

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heuermh commented Apr 19, 2017

Thank you!

@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017

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

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