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Adding examples of how to use joins in the real world #1605

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merged 15 commits into from Jul 21, 2017

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devin-petersohn commented Jul 13, 2017

Resolves #890.

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Coverage Status

Coverage remained the same at 84.157% when pulling 77ad223 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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Coverage Status

Coverage remained the same at 84.157% when pulling 77ad223 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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Somehow, I am skeptical that this PR decreased coverage by 0.5%.

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fnothaft commented Jul 13, 2017

Somehow, I am skeptical that this PR decreased coverage by 0.5%.

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fnothaft requested changes Jul 13, 2017 edited

Thanks @devin-petersohn! I've dropped a few specific notes inline. As a generalization, code isn't great standalone documentation. For each query, I'd like to see:

  1. Brief synopsis of the query (why would I run this?)
  2. The code for the query
  3. A brief discussion about the query (why it was written in a specific way, any non-obvious nits, performance implications, etc.)

E.g., for use case 2:

This query joins an RDD of Variants against an RDD of Features, and immediately performs a group-by on the Feature. This produces an RDD whose elements are a tuple containing a Feature, and all of the Variants overlapping the Feature. This query is useful for trying to identify annotated variants that may interact (identifying frameshift mutations within a transcript that may act as a pair to shift and then restore the reading frame) or as the start of a query that computes variant density over a set of genomic features.

... code ...

One important implication with this query is that the broadcast region join strategy only supports a group-by on the right side of the tuple. This means that we need to structure our query so that the variant table is the broadcast table. Since we typically expect our variant dataset to be much larger than our feature dataset, this may perform substantially worse than the shuffle join.

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@fnothaft fnothaft added this to the 0.23.0 milestone Jul 13, 2017

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Coverage remained the same at 84.157% when pulling f1183b3 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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Coverage Status

Coverage remained the same at 84.157% when pulling f1183b3 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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devin-petersohn Jul 13, 2017

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I pushed this a little early, I'll push another update shortly.

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devin-petersohn commented Jul 13, 2017

I pushed this a little early, I'll push another update shortly.

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// We can use ShuffleRegionJoin…
val joinedGenotypesShuffle = genotypes.shuffleRegionJoin(features)
// …or BroadcastRegionJoin

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heuermh Jul 13, 2017

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A separate code block for the broadcast region join would be helpful. I know folks like to copy and paste from docs. ;)

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heuermh Jul 13, 2017

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A separate code block for the broadcast region join would be helpful. I know folks like to copy and paste from docs. ;)

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I would rather leave it as is. It makes it easier to visually inspect the differences between the broadcast and shuffle versions of the joins.

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fnothaft Jul 13, 2017

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I would rather leave it as is. It makes it easier to visually inspect the differences between the broadcast and shuffle versions of the joins.

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// As a ShuffleRegionJoin, it can be implemented as follows:
val variantsByFeatureShuffle = features.shuffleRegionJoinAndGroupByLeft(variants)
// As a BroadcastRegionJoin, it can be implemented as follows:

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heuermh Jul 13, 2017

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...and separate broadcast code block

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heuermh Jul 13, 2017

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...and separate broadcast code block

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fnothaft Jul 13, 2017

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-1 on separating into two blocks, please keep as is

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fnothaft Jul 13, 2017

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-1 on separating into two blocks, please keep as is

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heuermh Jul 13, 2017

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Sorry about the outdated comments, was reviewing inbetween yer pushes :)

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heuermh commented Jul 13, 2017

Sorry about the outdated comments, was reviewing inbetween yer pushes :)

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Coverage Status

Coverage remained the same at 84.157% when pulling ff0b84e on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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Coverage Status

Coverage remained the same at 84.157% when pulling ff0b84e on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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// We can use ShuffleRegionJoin…
val joinedGenotypesShuffle = genotypes.shuffleRegionJoin(features)
// …or BroadcastRegionJoin

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fnothaft Jul 13, 2017

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I would rather leave it as is. It makes it easier to visually inspect the differences between the broadcast and shuffle versions of the joins.

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fnothaft Jul 13, 2017

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I would rather leave it as is. It makes it easier to visually inspect the differences between the broadcast and shuffle versions of the joins.

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Coverage Status

Coverage remained the same at 84.157% when pulling 0704601 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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Coverage Status

Coverage remained the same at 84.157% when pulling 0704601 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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Coverage Status

Coverage remained the same at 84.157% when pulling 4fbe0a6 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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Coverage Status

Coverage remained the same at 84.157% when pulling 4fbe0a6 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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Coverage Status

Coverage increased (+0.03%) to 84.191% when pulling d2e4371 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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gunjanbaid and others added some commits Jul 17, 2017

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Coverage Status

Coverage increased (+0.4%) to 84.58% when pulling 0a51d85 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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Coverage Status

Coverage increased (+0.4%) to 84.58% when pulling 0a51d85 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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[...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/1605/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains d2e7c9740e82adc9aca2caf53026a71b347c48fa # timeout=10Checking out Revision d2e7c9740e82adc9aca2caf53026a71b347c48fa (origin/pr/1605/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d2e7c9740e82adc9aca2caf53026a71b347c48faFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosADAM-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 FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,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 FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
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@fnothaft

A couple more nits; this is pretty close! Thanks @devin-petersohn.

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Coverage Status

Coverage increased (+0.4%) to 84.58% when pulling cd98e93 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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Coverage Status

Coverage increased (+0.4%) to 84.58% when pulling cd98e93 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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1 really small typo, otherwise LGTM. Thanks @devin-petersohn!

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LGTM. Thanks @devin-petersohn!

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Coverage Status

Coverage increased (+0.4%) to 84.58% when pulling a49cd04 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

coveralls commented Jul 19, 2017

Coverage Status

Coverage increased (+0.4%) to 84.58% when pulling a49cd04 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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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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@heuermh just going to ping you for a review. As an FYI, @devin-petersohn is going to clean up the history on the commit, so don't merge until you get an OK from him.

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fnothaft commented Jul 19, 2017

@heuermh just going to ping you for a review. As an FYI, @devin-petersohn is going to clean up the history on the commit, so don't merge until you get an OK from him.

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fnothaft commented Jul 21, 2017

Ping @heuermh

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Few minor suggestions, otherwise looks good

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Ok to squash. I talked to @gunjanbaid and she ok'ed squash.

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devin-petersohn commented Jul 21, 2017

Ok to squash. I talked to @gunjanbaid and she ok'ed squash.

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Thanks @devin-petersohn and @gunjanbaid! @heuermh if the latest changes look good to you, please squash-and-merge.

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fnothaft commented Jul 21, 2017

Thanks @devin-petersohn and @gunjanbaid! @heuermh if the latest changes look good to you, please squash-and-merge.

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coveralls Jul 21, 2017

Coverage Status

Coverage decreased (-0.1%) to 84.016% when pulling 6f3fe74 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

coveralls commented Jul 21, 2017

Coverage Status

Coverage decreased (-0.1%) to 84.016% when pulling 6f3fe74 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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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/1605/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 90b0b6cd6ecfdcbe2b521b4ffc71a5f92c27b5a1 # timeout=10Checking out Revision 90b0b6cd6ecfdcbe2b521b4ffc71a5f92c27b5a1 (origin/pr/1605/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 90b0b6cd6ecfdcbe2b521b4ffc71a5f92c27b5a1 > /home/jenkins/git2/bin/git rev-list 8704718 # timeout=10Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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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/1605/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 90b0b6cd6ecfdcbe2b521b4ffc71a5f92c27b5a1 # timeout=10Checking out Revision 90b0b6cd6ecfdcbe2b521b4ffc71a5f92c27b5a1 (origin/pr/1605/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 90b0b6cd6ecfdcbe2b521b4ffc71a5f92c27b5a1 > /home/jenkins/git2/bin/git rev-list 8704718 # timeout=10Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, retest this please

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heuermh commented Jul 21, 2017

Jenkins, retest this please

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coveralls Jul 21, 2017

Coverage Status

Coverage increased (+0.6%) to 84.743% when pulling 6f3fe74 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

coveralls commented Jul 21, 2017

Coverage Status

Coverage increased (+0.6%) to 84.743% when pulling 6f3fe74 on devin-petersohn:issue#890joinDocExamples into 607cd50 on bigdatagenomics:master.

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Test PASSed.
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Test PASSed.

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@fnothaft fnothaft merged commit 6abe7a6 into bigdatagenomics:master Jul 21, 2017

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codacy/pr Good work! A positive pull request.
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coverage/coveralls Coverage increased (+0.6%) to 84.743%
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Merged! Thanks @devin-petersohn!

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fnothaft commented Jul 21, 2017

Merged! Thanks @devin-petersohn!

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

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