[ADAM-2304] Provide access to header to model conversions

[heuermh]

Fixes #2304

[AmplabJenkins]

Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3158/

Build result: FAILURE

[...truncated 926 B...]Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Using reference repository: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --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 --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse 90e0f83^{commit} # timeout=10Checking out Revision 90e0f83 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 90e0f83 # timeout=10Commit message: "Provide access to header to model conversions." > git rev-list --no-walk e6332ef # timeout=10Triggering ADAM-prb » 3.2.1,2.12,3.0.2,ubuntuADAM-prb » 3.2.1,2.12,3.0.2,ubuntu completed with result FAILURENotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Failed to evaluate macro ''Setting status of 90e0f83 to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3158/ and message: 'Build finished. '

[heuermh]

Jenkins, retest this please

[AmplabJenkins]

Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3159/

Build result: FAILURE

[...truncated 911 B...]Wiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Using reference repository: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --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 --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse 90e0f83^{commit} # timeout=10Checking out Revision 90e0f83 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 90e0f83 # timeout=10Commit message: "Provide access to header to model conversions." > git rev-list --no-walk 90e0f83 # timeout=10Triggering ADAM-prb » 3.2.1,2.12,3.0.2,ubuntuADAM-prb » 3.2.1,2.12,3.0.2,ubuntu completed with result FAILURENotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of 90e0f83 to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3159/ and message: 'Build finished. '

[heuermh]

...
Recording test results
[Checks API] No suitable checks publisher found.
ERROR: [GitHub Commit Status Setter] - Error creating extended parser class: null, setting build result to FAILURE
Build step 'Set build status on GitHub commit [deprecated]' changed build result to FAILURE
Finished: FAILURE

[heuermh]

Same issue as bigdatagenomics/cannoli#293

[AmplabJenkins]

Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3160/

Build result: FAILURE

[...truncated 911 B...]Wiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Using reference repository: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --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 --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse 439c714^{commit} # timeout=10Checking out Revision 439c714 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 439c714 # timeout=10Commit message: "refactor SAMRecordConverter into AlignmetConverter" > git rev-list --no-walk 90e0f83 # timeout=10Triggering ADAM-prb » 3.2.1,2.12,3.0.2,ubuntuADAM-prb » 3.2.1,2.12,3.0.2,ubuntu completed with result FAILURENotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of 439c714 to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3160/ and message: 'Build finished. '

[AmplabJenkins]

Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3161/

Build result: FAILURE

[...truncated 936 B...]Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Using reference repository: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --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 --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse 8f5d44d^{commit} # timeout=10Checking out Revision 8f5d44d (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 8f5d44d # timeout=10Commit message: "Provide access to header to model conversions." > git rev-list --no-walk 439c714 # timeout=10First time build. Skipping changelog.Triggering ADAM-prb » 3.2.1,2.12,3.0.2,ubuntuADAM-prb » 3.2.1,2.12,3.0.2,ubuntu completed with result FAILURENotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of 8f5d44d to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3161/ and message: 'Build finished. '