February 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 812ad3: Fix transiently failing Selenium upload test.
by GitHub 10 Feb '17

10 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 812ad3af18b087372b31188ac173b7e9238d712b https://github.com/galaxyproject/galaxy/commit/812ad3af18b087372b31188ac173… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M test/selenium_tests/test_uploads.py Log Message: ----------- Fix transiently failing Selenium upload test. Commit: 66a24c8830f5a87579f5e6e4f55c8efbf9073b0f https://github.com/galaxyproject/galaxy/commit/66a24c8830f5a87579f5e6e4f55c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #3587 from jmchilton/selenium_fixes Fix transiently failing Selenium upload test. Compare: https://github.com/galaxyproject/galaxy/compare/2ad612349683...66a24c8830f5

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[galaxyproject/galaxy] 1922d5: Increase patience of Galaxy tests throughout.
by GitHub 10 Feb '17

10 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1922d50f903f0c6ad1440d9128a1a23d37cc529c https://github.com/galaxyproject/galaxy/commit/1922d50f903f0c6ad1440d9128a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Increase patience of Galaxy tests throughout. This should help reduce various API and Selenium transient failures. Commit: 2ad612349683dd4ab3bde476f9153e90415f0b53 https://github.com/galaxyproject/galaxy/commit/2ad612349683dd4ab3bde476f915… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #3589 from jmchilton/test_timeout_increases Increase patience of Galaxy tests throughout. Compare: https://github.com/galaxyproject/galaxy/compare/ed52230952a1...2ad612349683

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[galaxyproject/galaxy] a7d05a: Prevent make_html_table() datatype methods from ra...
by GitHub 10 Feb '17

10 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a7d05a47da592e76fd88ed699f034e13e2dba08e https://github.com/galaxyproject/galaxy/commit/a7d05a47da592e76fd88ed699f03… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Prevent make_html_table() datatype methods from raising Exceptions This was preventing the browse of a data library which contained a purged dataset of gg datatype. Also fix import order and Python3 compatibility. Commit: f8dcae95364b79a1612c7a0d04b489d874512aa7 https://github.com/galaxyproject/galaxy/commit/f8dcae95364b79a1612c7a0d04b4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Remove edam_format for Genbank from config/datatypes_conf.xml.sample This was preventing the loading of the datatype: WARNING 2017-02-10 11:07:05,162 Cannot specify edam_format without setting subclass to True, skipping datatype. Bug introduced in commit c36fbebb443ae5b5263ba6cad6ad36113bb52f44 . Also backport commit 5657a8b809e5938d3d996a77c826811e1176c108 from dev. Commit: 087c75e76ff44cf49eb0b458520d2df4db31e32e https://github.com/galaxyproject/galaxy/commit/087c75e76ff44cf49eb0b458520d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #3585 from nsoranzo/release_17.01_datatypes_fixes [17.01] Two datatypes fixes Commit: ed52230952a1411a39cff3bde7a7ed66e1344f6f https://github.com/galaxyproject/galaxy/commit/ed52230952a1411a39cff3bde7a7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: config/datatypes_conf.xml.sample Compare: https://github.com/galaxyproject/galaxy/compare/6f5743d052fb...ed52230952a1

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[galaxyproject/galaxy] a7d05a: Prevent make_html_table() datatype methods from ra...
by GitHub 10 Feb '17

10 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: a7d05a47da592e76fd88ed699f034e13e2dba08e https://github.com/galaxyproject/galaxy/commit/a7d05a47da592e76fd88ed699f03… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Prevent make_html_table() datatype methods from raising Exceptions This was preventing the browse of a data library which contained a purged dataset of gg datatype. Also fix import order and Python3 compatibility. Commit: f8dcae95364b79a1612c7a0d04b489d874512aa7 https://github.com/galaxyproject/galaxy/commit/f8dcae95364b79a1612c7a0d04b4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Remove edam_format for Genbank from config/datatypes_conf.xml.sample This was preventing the loading of the datatype: WARNING 2017-02-10 11:07:05,162 Cannot specify edam_format without setting subclass to True, skipping datatype. Bug introduced in commit c36fbebb443ae5b5263ba6cad6ad36113bb52f44 . Also backport commit 5657a8b809e5938d3d996a77c826811e1176c108 from dev. Commit: 087c75e76ff44cf49eb0b458520d2df4db31e32e https://github.com/galaxyproject/galaxy/commit/087c75e76ff44cf49eb0b458520d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #3585 from nsoranzo/release_17.01_datatypes_fixes [17.01] Two datatypes fixes Compare: https://github.com/galaxyproject/galaxy/compare/884cff33fa04...087c75e76ff4

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[galaxyproject/galaxy] f33098: add option to send API key in header
by GitHub 10 Feb '17

10 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3309822c856e50c61d94c2e021859342d40c5fb https://github.com/galaxyproject/galaxy/commit/f3309822c856e50c61d94c2e0218… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- add option to send API key in header Commit: 6f5743d052fb4c2ee227d71bf6106f2be9f4428a https://github.com/galaxyproject/galaxy/commit/6f5743d052fb4c2ee227d71bf610… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #3584 from jvolkening/http_header_api_key add option to send API key in header Compare: https://github.com/galaxyproject/galaxy/compare/7d35a029174d...6f5743d052fb

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[galaxyproject/galaxy] f7092b: Clean up Selenium resources better.
by GitHub 09 Feb '17

09 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f7092bd959cfae7f6ee0262a993a2dc5867416e4 https://github.com/galaxyproject/galaxy/commit/f7092bd959cfae7f6ee0262a993a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Clean up Selenium resources better. Commit: 7d35a029174da0e3c8f481c0662139b9a59b3051 https://github.com/galaxyproject/galaxy/commit/7d35a029174da0e3c8f481c06621… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Merge pull request #3583 from jmchilton/selenium_fixes Clean up docker-compose resources better for Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/be09b7c2ccf2...7d35a029174d

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[galaxyproject/galaxy] 139bac: Remove broken tour step.
by GitHub 09 Feb '17

09 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 139bacb7d3e507ea56b8c8997e47408db87b5fa3 https://github.com/galaxyproject/galaxy/commit/139bacb7d3e507ea56b8c8997e47… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Remove broken tour step. This causes the Selenium tests to fail under various conditions - but legimately so. The referenced target link disappears pretty quickly after the step in the previous click. When I run them in the web browser and this step is "disconnected" and in the center of the screen and as a result it isn't clear what links are being referred to. Commit: be09b7c2ccf2ef861927795c16fb1306ef37ff1a https://github.com/galaxyproject/galaxy/commit/be09b7c2ccf2ef861927795c16fb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Merge pull request #3582 from jmchilton/selenium_fixes Remove broken tour step. Compare: https://github.com/galaxyproject/galaxy/compare/ca847e2d588d...be09b7c2ccf2

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[galaxyproject/usegalaxy-playbook] 2e21c5: update submodule
by GitHub 09 Feb '17

09 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2e21c55a4645d808ce369104453d38e348f6f6b4 https://github.com/galaxyproject/usegalaxy-playbook/commit/2e21c55a4645d808… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M common_roles Log Message: ----------- update submodule

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[galaxyproject/galaxy] 86a788: Update Nagios check
by GitHub 08 Feb '17

08 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 86a7880e48b81dec9a480600da9f918f7380c3bf https://github.com/galaxyproject/galaxy/commit/86a7880e48b81dec9a480600da9f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M contrib/nagios/check_galaxy M contrib/nagios/check_galaxy.py Log Message: ----------- Update Nagios check Commit: ca847e2d588db417bb66664a76ecfdb2105ccc41 https://github.com/galaxyproject/galaxy/commit/ca847e2d588db417bb66664a76ec… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M contrib/nagios/check_galaxy M contrib/nagios/check_galaxy.py Log Message: ----------- Merge pull request #3568 from natefoo/nagios Update Nagios check Compare: https://github.com/galaxyproject/galaxy/compare/ed3062b41de4...ca847e2d588d

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[galaxyproject/galaxy] 3b7890: Set 'deleted' to True when purging a history datas...
by GitHub 08 Feb '17

08 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3b78907fdbbf2f26ea89f4459901e59164a033b7 https://github.com/galaxyproject/galaxy/commit/3b78907fdbbf2f26ea89f4459901… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/managers/deletable.py A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M test/api/test_history_contents.py M test/unit/managers/test_HDAManager.py Log Message: ----------- Set 'deleted' to True when purging a history dataset association Fix https://github.com/galaxyproject/galaxy/issues/3548 Add API and unit test cases. Add migration to fix misaligned databases. Commit: b215ea1eed127e61421cccb8ff5ddb68963e28ae https://github.com/galaxyproject/galaxy/commit/b215ea1eed127e61421cccb8ff5d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/webapps/galaxy/api/histories.py M test/api/test_histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Sync API history purge with hda implementation Add API and unit test cases. Import order and Python3 fixes. Commit: ed3062b41de47d77974bfae97bac21b2d9806432 https://github.com/galaxyproject/galaxy/commit/ed3062b41de47d77974bfae97bac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/managers/deletable.py A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/webapps/galaxy/api/histories.py M test/api/test_histories.py M test/api/test_history_contents.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #3572 from nsoranzo/fix_3548 Set 'deleted' to True when purging a history dataset association Compare: https://github.com/galaxyproject/galaxy/compare/3b3bfad8e0af...ed3062b41de4

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