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[ADAM-1616] Resolve installation directory if scripts are symlinks. #1617

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heuermh commented Jul 21, 2017

Fixes #1616

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Coverage Status

Coverage decreased (-0.5%) to 84.248% when pulling 2b215a3 on heuermh:resolve-symlinks into 7652536 on bigdatagenomics:master.

coveralls commented Jul 21, 2017

Coverage Status

Coverage decreased (-0.5%) to 84.248% when pulling 2b215a3 on heuermh:resolve-symlinks into 7652536 on bigdatagenomics:master.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2254/

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/1617/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 247206f # timeout=10Checking out Revision 247206f (origin/pr/1617/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 247206fda42d11e373979828a387306f046ebff6First time build. Skipping changelog.Triggering 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 FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Jul 21, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2254/

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/1617/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 247206f # timeout=10Checking out Revision 247206f (origin/pr/1617/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 247206fda42d11e373979828a387306f046ebff6First time build. Skipping changelog.Triggering 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 FAILUREADAM-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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Coverage Status

Coverage remained the same at 84.743% when pulling 2b215a3 on heuermh:resolve-symlinks into 7652536 on bigdatagenomics:master.

coveralls commented Jul 21, 2017

Coverage Status

Coverage remained the same at 84.743% when pulling 2b215a3 on heuermh:resolve-symlinks into 7652536 on bigdatagenomics:master.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2256/

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/1617/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains e52ec73 # timeout=10Checking out Revision e52ec73 (origin/pr/1617/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f e52ec738db6264da9498f2b5de1627f153649e07First time build. Skipping changelog.Triggering 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 SUCCESSADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-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 FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Jul 21, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2256/

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/1617/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains e52ec73 # timeout=10Checking out Revision e52ec73 (origin/pr/1617/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f e52ec738db6264da9498f2b5de1627f153649e07First time build. Skipping changelog.Triggering 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 SUCCESSADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-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 FAILUREADAM-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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Coverage Status

Coverage remained the same at 84.743% when pulling 2b215a3 on heuermh:resolve-symlinks into 7652536 on bigdatagenomics:master.

coveralls commented Jul 21, 2017

Coverage Status

Coverage remained the same at 84.743% when pulling 2b215a3 on heuermh:resolve-symlinks into 7652536 on bigdatagenomics:master.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2257/

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/1617/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains e52ec73 # timeout=10Checking out Revision e52ec73 (origin/pr/1617/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f e52ec738db6264da9498f2b5de1627f153649e07First time build. Skipping changelog.Triggering 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 FAILUREADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result SUCCESSADAM-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 FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Jul 21, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2257/

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/1617/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains e52ec73 # timeout=10Checking out Revision e52ec73 (origin/pr/1617/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f e52ec738db6264da9498f2b5de1627f153649e07First time build. Skipping changelog.Triggering 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 FAILUREADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result SUCCESSADAM-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 FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Jul 21, 2017

Jenkins, test this please.

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Two small misspellings here. If this passes tests, I'll just merge manually and fix those.

# does the user have ADAM_OPTS set? if yes, then warn
if [[ -z $@ && -n "$ADAM_OPTS" ]]; then
echo "WARNING: Passing Spark arguments via ADAM_OPTS was recently removed."
echo "Run adam-shell instead as adam-shell <spark-args>"
fi
# Find original directory of this script, resovling symlinks

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resovling -> resolving

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resovling -> resolving

@@ -49,15 +49,23 @@ if [[ $DD == False && -n "$ADAM_OPTS" ]]; then
echo "Run adam-submit instead as adam-submit <spark-args> -- <adam-args>"
fi
# Figure out where ADAM is installed
SCRIPT_DIR="$(cd `dirname $0`/..; pwd)"
# Find original directory of this script, resovling symlinks

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resovling -> resolving

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resovling -> resolving

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Coverage Status

Coverage remained the same at 84.743% when pulling 2b215a3 on heuermh:resolve-symlinks into 7652536 on bigdatagenomics:master.

coveralls commented Jul 21, 2017

Coverage Status

Coverage remained the same at 84.743% when pulling 2b215a3 on heuermh:resolve-symlinks into 7652536 on bigdatagenomics:master.

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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2266/
Test PASSed.

AmplabJenkins commented Jul 21, 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/2266/
Test PASSed.

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Merged manually as e3fa6bf. Thanks @heuermh!

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fnothaft commented Jul 21, 2017

Merged manually as e3fa6bf. Thanks @heuermh!

@fnothaft fnothaft closed this Jul 21, 2017

@heuermh heuermh deleted the heuermh:resolve-symlinks branch Jul 21, 2017

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Thank you!

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heuermh commented Jul 21, 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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