galaxy-commits May 2016

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[galaxyproject/galaxy] 168ba1: Follow up on @nsoranzo comment...
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 168ba1b130cfa306f050aacc3d7d4a0bb260421e https://github.com/galaxyproject/galaxy/commit/168ba1b130cfa306f050aacc3d7d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Follow up on @nsoranzo comment... https://github.com/galaxyproject/galaxy/pull/2409#discussion_r64588439 \minor Commit: b16ad40bee213a861085dc7e6a0bb762caee4adf https://github.com/galaxyproject/galaxy/commit/b16ad40bee213a861085dc7e6a0b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Merge pull request #2412 from jmchilton/2409_followup Follow up on @nsoranzo comment... Compare: https://github.com/galaxyproject/galaxy/compare/b41e03994e48...b16ad40bee21

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[galaxyproject/galaxy] 4765f5: Enhancements to tool test output verification.
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4765f5876eddf8855395b9d1bd8dd82f19ab4ce5 https://github.com/galaxyproject/galaxy/commit/4765f5876eddf8855395b9d1bd8d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/tools/parser/xml.py A lib/galaxy/tools/verify/__init__.py A lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/tabular.py A lib/galaxy/tools/verify/asserts/text.py A lib/galaxy/tools/verify/asserts/xml.py A lib/galaxy/tools/verify/test_data.py M test/api/test_tools.py M test/api/test_workflows.py R test/base/asserts/__init__.py R test/base/asserts/tabular.py R test/base/asserts/text.py R test/base/asserts/xml.py R test/base/test_data.py M test/base/twilltestcase.py M test/functional/test_toolbox.py A test/functional/tools/composite_output_tests.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Enhancements to tool test output verification. Refactor test verification into galaxy-lib-compat module. - Refactor a bunch class methods in ``test.base.twilltestcase`` into module functions in ``galaxy.tools.verify``. - Move ``test.base.test_data`` to ``galaxy.tools.verify.test_data``. - Move ``test.base.asserts`` to ``galaxy.tools.verify.asserts``. Remove duplication in execution of these methods between composite and normal test outputs. This also entailed reworking the parsing of the composite test outputs to bring them inline with normal outputs. In addition to simplify removing duplication, this means many more tests can be made over composite outputs - such as md5 checks and test assertions. I've added a new framework test tool to verify this. Commit: b41e03994e48abfb15c375f43a5de0cf3605e462 https://github.com/galaxyproject/galaxy/commit/b41e03994e48abfb15c375f43a5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/tools/parser/xml.py A lib/galaxy/tools/verify/__init__.py A lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/tabular.py A lib/galaxy/tools/verify/asserts/text.py A lib/galaxy/tools/verify/asserts/xml.py A lib/galaxy/tools/verify/test_data.py M test/api/test_tools.py M test/api/test_workflows.py R test/base/asserts/__init__.py R test/base/asserts/tabular.py R test/base/asserts/text.py R test/base/asserts/xml.py R test/base/test_data.py M test/base/twilltestcase.py M test/functional/test_toolbox.py A test/functional/tools/composite_output_tests.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2409 from jmchilton/test_assertions_lib Enhancements to tool test output verification. Compare: https://github.com/galaxyproject/galaxy/compare/d72031869d9c...b41e03994e48

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[galaxyproject/galaxy] 5dcd04: UI, datasets: show hid in 'view details' page
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5dcd04b0b2955a1908db3f35b3a18969a307dc8a https://github.com/galaxyproject/galaxy/commit/5dcd04b0b2955a1908db3f35b3a1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M templates/show_params.mako Log Message: ----------- UI, datasets: show hid in 'view details' page Adds the hid to the list of dataset/job information on the show_params/ view details/info page. Commit: d72031869d9c4885cada462bc77de54c9c52ea64 https://github.com/galaxyproject/galaxy/commit/d72031869d9c4885cada462bc77d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #2411 from carlfeberhard/show-params.add-hid UI, datasets: show hid in 'view details' page Compare: https://github.com/galaxyproject/galaxy/compare/7479dddb8562...d72031869d9c

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[galaxyproject/usegalaxy-playbook] 932903: Remove embedded Pulsar from Main job config
by GitHub 25 May '16

25 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 932903a67a949a69009387803136ba6784a7275f https://github.com/galaxyproject/usegalaxy-playbook/commit/932903a67a949a69… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M files/galaxy/usegalaxy.org/config/pulsar_jetstream.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Remove embedded Pulsar from Main job config

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[galaxyproject/infrastructure-playbook] 4033cc: New slurm controller for IU
by GitHub 25 May '16

25 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4033cc2de2b67cbfc5868ac6661f28adde535d59 https://github.com/galaxyproject/infrastructure-playbook/commit/4033cc2de2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M jetstreamiuenv/group_vars/all.yml M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamiuenv/group_vars/slurmclients.yml Log Message: ----------- New slurm controller for IU

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[galaxyproject/infrastructure-playbook] 3d8b05: Move duvel nginx config from private playbook and ...
by GitHub 25 May '16

25 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3d8b059560f2be93ca6c41993bad02cc48f7f958 https://github.com/galaxyproject/infrastructure-playbook/commit/3d8b059560f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: A galaxyenv/host_vars/duvel.galaxyproject.org.yml M galaxyenv/inventory A galaxyenv/templates/nginx/duvel.j2 A galaxyenv/templates/nginx/jenkins.j2 Log Message: ----------- Move duvel nginx config from private playbook and add an http proxy timeout

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[galaxyproject/usegalaxy-playbook] 8f6768: Update Main
by GitHub 25 May '16

25 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8f676862eb0f770da0e655bfe87e87fbbdc2b49c https://github.com/galaxyproject/usegalaxy-playbook/commit/8f676862eb0f770d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main

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[galaxyproject/galaxy] 5fbb65: Catch all exceptions in slurm's _complete_terminal...
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5fbb65e5033d23b9751251a4a935b4c76ffd65d5 https://github.com/galaxyproject/galaxy/commit/5fbb65e5033d23b9751251a4a935… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Catch all exceptions in slurm's _complete_terminal_job() to prevent looping job completion Commit: b6d65da83d77167482a3fe3a706c249abad6dbfa https://github.com/galaxyproject/galaxy/commit/b6d65da83d77167482a3fe3a706c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix linting error Commit: 2a29e92ef9d8e560988d6e64d06c5cbbf79098a1 https://github.com/galaxyproject/galaxy/commit/2a29e92ef9d8e560988d6e64d06c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- API, history: fix order in most_recently_used - Fix ascending order used in HistoryManager.most_recent to descending - Slightly update the docs to reflect actual value better - Add tests Commit: 47a65160960003244091d4fd441111c257e9e8d9 https://github.com/galaxyproject/galaxy/commit/47a65160960003244091d4fd4411… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #2407 from carlfeberhard/fix.most_recently_used [16.01] API, history: fix order in most_recently_used Commit: 7dcf850ed5203196371fa3d20800b0b864c01158 https://github.com/galaxyproject/galaxy/commit/7dcf850ed5203196371fa3d20800… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2402 from natefoo/slurm-fixes [16.04] Catch all exceptions in slurm's _complete_terminal_job() to prevent looping job completion Commit: 5db5e1395880876ac3066fc91397e7cb1618ea62 https://github.com/galaxyproject/galaxy/commit/5db5e1395880876ac3066fc91397… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: test/unit/managers/test_HistoryManager.py Commit: 7479dddb8562dc063db16bc4eb3de3d4053548d6 https://github.com/galaxyproject/galaxy/commit/7479dddb8562dc063db16bc4eb3d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c033544a7e73...7479dddb8562

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[galaxyproject/galaxy] 2a29e9: API, history: fix order in most_recently_used
by GitHub 25 May '16

25 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 2a29e92ef9d8e560988d6e64d06c5cbbf79098a1 https://github.com/galaxyproject/galaxy/commit/2a29e92ef9d8e560988d6e64d06c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- API, history: fix order in most_recently_used - Fix ascending order used in HistoryManager.most_recent to descending - Slightly update the docs to reflect actual value better - Add tests Commit: 47a65160960003244091d4fd441111c257e9e8d9 https://github.com/galaxyproject/galaxy/commit/47a65160960003244091d4fd4411… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #2407 from carlfeberhard/fix.most_recently_used [16.01] API, history: fix order in most_recently_used Commit: 5db5e1395880876ac3066fc91397e7cb1618ea62 https://github.com/galaxyproject/galaxy/commit/5db5e1395880876ac3066fc91397… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: test/unit/managers/test_HistoryManager.py Compare: https://github.com/galaxyproject/galaxy/compare/7dcf850ed520...5db5e1395880

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[galaxyproject/galaxy] 3330a2: increase range to 5, Jenkins still fails to push s...
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3330a25c7538d375c9c1331353e8608f164076f0 https://github.com/galaxyproject/galaxy/commit/3330a25c7538d375c9c1331353e8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- increase range to 5, Jenkins still fails to push sometimes Commit: c033544a7e7330a93d9d4a7bb2577325090948ab https://github.com/galaxyproject/galaxy/commit/c033544a7e7330a93d9d4a7bb257… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #2410 from martenson/more-tspus-attempts increase range to 5, Jenkins still fails to push sometimes Compare: https://github.com/galaxyproject/galaxy/compare/caec8c838a7d...c033544a7e73

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galaxy-commits May 2016