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[ADAM-2112] Refactor org.bdgenomics.adam.rdd package to org.bdgenomics.adam.ds #2137

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commented Mar 14, 2019

Fixes #2112

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commented Mar 14, 2019

Coverage Status

Coverage increased (+0.06%) to 79.047% when pulling 2c0a20e on heuermh:rdd-to-ds into e78cceb on bigdatagenomics:master.

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commented Mar 14, 2019

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2958/

Build result: FAILURE

GitHub pull request #2137 of commit a4eba9a automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2137/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains a23bceb # timeout=10Checking out Revision a23bceb (origin/pr/2137/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f a23bcebb83bf27b5a83510a475c739666690f11fFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.11,2.2.3,ubuntuADAM-prb ? 2.7.5,2.11,2.2.3,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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commented Mar 15, 2019

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2959/

Build result: FAILURE

GitHub pull request #2137 of commit 842bbfd automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2137/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 6fc19ee # timeout=10Checking out Revision 6fc19ee (origin/pr/2137/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6fc19ee923db20c262571db2e1d40ff67de9039cFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.11,2.2.3,ubuntuADAM-prb ? 2.7.5,2.11,2.2.3,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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commented Mar 15, 2019

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2960/
Test PASSed.

@heuermh heuermh requested review from fnothaft and akmorrow13 Mar 15, 2019

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commented Mar 15, 2019

Ready for review. Will need squash before merge.

I was thinking of adding a @deprecated ADAMContext back to the rdd package that forwards to the real one in ds package along with a log message about deprecation, but I haven't been clever enough to make that work yet.

@heuermh heuermh force-pushed the heuermh:rdd-to-ds branch from 2dfad2b to 2c0a20e Apr 24, 2019

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commented Apr 24, 2019

Rebased to pick up Jenkins fixes.

I was thinking of adding a @deprecated ADAMContext back to the rdd package that forwards to the real one in ds package along with a log message about deprecation, but I haven't been clever enough to make that work yet.

@fnothaft any thoughts on the forwarding ADAMContext or is ok to simply break?

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commented Apr 24, 2019

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2965/
Test PASSed.

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