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

[galaxyproject/galaxy] 5c4840: Various fixes for test image Docker user switching...
by GitHub 22 Jan '17

22 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c48402b0202e438d663c4dc151d835c7725a4f6 https://github.com/galaxyproject/galaxy/commit/5c48402b0202e438d663c4dc151d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Various fixes for test image Docker user switching. - Fix if testing as user with GID 109 (fixes #3425). - Fix if testing as a user with any UID or GID that already exists in the container. - More logging to indicate the "problems" being printed to standard output in these cases are not problems. - Fix sqlite being readonly in the container for the test user. Commit: d9f9a31c32b9d1a2121d5db6e2b8f81dbf12d7c8 https://github.com/galaxyproject/galaxy/commit/d9f9a31c32b9d1a2121d5db6e2b8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #3443 from jmchilton/test_docker_fix Various fixes for test image Docker user switching. Compare: https://github.com/galaxyproject/galaxy/compare/3945f3b885a2...d9f9a31c32b9

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[galaxyproject/galaxy] f8552c: Document shared_inputs for parallelism tag in tool...
by GitHub 20 Jan '17

20 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8552c19dc55ddeeeb7441190891f52cdd9d9ef3 https://github.com/galaxyproject/galaxy/commit/f8552c19dc55ddeeeb7441190891… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Document shared_inputs for parallelism tag in tool XSD. Commit: 22f4696f7d54a90a31f253d05a7ed1314db4b943 https://github.com/galaxyproject/galaxy/commit/22f4696f7d54a90a31f253d05a7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: A test/functional/tools/explicit_conversion.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement tool testing and documenting explicit conversion tags. Commit: 074e10ac00a7dde7c2fc5e76928392e073791b30 https://github.com/galaxyproject/galaxy/commit/074e10ac00a7dde7c2fc5e769283… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/explicit_conversion.xml M test/functional/tools/implicit_conversion.xml Log Message: ----------- Fix tool XSD to document <conversion> tag for data parameters. Rebased with English fixes and small tool cleanups thanks to @nsoranzo. Commit: dba4d95961a3ccadd4a0822f13f0f02730889a8a https://github.com/galaxyproject/galaxy/commit/dba4d95961a3ccadd4a0822f13f0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: M test/functional/tools/column_param.xml M test/functional/tools/explicit_conversion.xml M test/functional/tools/implicit_conversion.xml Log Message: ----------- Reduced usage of from_work_dir in test tools. Per recommendation of @bgruening. Commit: 3945f3b885a291c9b1a1ebf85a56137e2d1b22e2 https://github.com/galaxyproject/galaxy/commit/3945f3b885a291c9b1a1ebf85a56… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/column_param.xml A test/functional/tools/explicit_conversion.xml M test/functional/tools/implicit_conversion.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3457 from jmchilton/xsd_fixes_2 Tool Documentation and Testing Improvements Compare: https://github.com/galaxyproject/galaxy/compare/d8f23b393527...3945f3b885a2

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[galaxyproject/galaxy] 1af158: Fix various transiently failing Selenium tests.
by GitHub 19 Jan '17

19 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1af1583caa1b5c62c92573fe42693338ba457fcf https://github.com/galaxyproject/galaxy/commit/1af1583caa1b5c62c92573fe4269… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Fix various transiently failing Selenium tests. I'm pretty sure the problem is that I was waiting on conditions (e.g. datasets to become "ok") using the API and then assuming the state of the GUI elements was the same. Obviously though the GUI is polling the API and there is some lag there. This commit changes things to specifically wait on history panel GUI changes - obviously the better thing to wait on in a GUI test. Commit: d8f23b393527e2ea5b495cc850eeec25fdc64a8b https://github.com/galaxyproject/galaxy/commit/d8f23b393527e2ea5b495cc850ee… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #3450 from jmchilton/selenium_fixes_2 Fix various transiently failing Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/60b57397e7f8...d8f23b393527

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[galaxyproject/galaxy] f50826: Do not wrap __class__ attribute of SafeStringWrapp...
by GitHub 19 Jan '17

19 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f5082604f7282587bb8385dbdb3bb91905bee87b https://github.com/galaxyproject/galaxy/commit/f5082604f7282587bb8385dbdb3b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Do not wrap __class__ attribute of SafeStringWrapper Fix #3353 by not recursing on the parent classes, which may lead to an abstract class. Also fix a method name of "object" class. Commit: c9fdb6e3efd2721dc193ea5f1d5cfe6c014ad94e https://github.com/galaxyproject/galaxy/commit/c9fdb6e3efd2721dc193ea5f1d5c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Merge pull request #3449 from dannon/backport_mistargeted_3429 [16.10] Backport of 3429, safestringwrapper Commit: 60b57397e7f8227f0a5017141c81fdcc81d59ede https://github.com/galaxyproject/galaxy/commit/60b57397e7f8227f0a5017141c81… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-19 (Thu, 19 Jan 2017) Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/b4475ba9df9b...60b57397e7f8

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[galaxyproject/galaxy] f50826: Do not wrap __class__ attribute of SafeStringWrapp...
by GitHub 19 Jan '17

19 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: f5082604f7282587bb8385dbdb3bb91905bee87b https://github.com/galaxyproject/galaxy/commit/f5082604f7282587bb8385dbdb3b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Do not wrap __class__ attribute of SafeStringWrapper Fix #3353 by not recursing on the parent classes, which may lead to an abstract class. Also fix a method name of "object" class. Commit: c9fdb6e3efd2721dc193ea5f1d5cfe6c014ad94e https://github.com/galaxyproject/galaxy/commit/c9fdb6e3efd2721dc193ea5f1d5c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Merge pull request #3449 from dannon/backport_mistargeted_3429 [16.10] Backport of 3429, safestringwrapper Compare: https://github.com/galaxyproject/galaxy/compare/02a8a7da0a0f...c9fdb6e3efd2

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[galaxyproject/galaxy] 10d276: Do not wrap __class__ attribute of SafeStringWrapp...
by GitHub 19 Jan '17

19 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10d27609af607208e182b7ce18b0447281de942c https://github.com/galaxyproject/galaxy/commit/10d27609af607208e182b7ce18b0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Do not wrap __class__ attribute of SafeStringWrapper Fix #3353 by not recursing on the parent classes, which may lead to an abstract class. Also fix a method name of "object" class. Commit: b4475ba9df9b9425b5791e15c8c070b638768286 https://github.com/galaxyproject/galaxy/commit/b4475ba9df9b9425b5791e15c8c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Merge pull request #3429 from nsoranzo/release_16.10_fix_3353 [16.10] Do not wrap __class__ attribute of SafeStringWrapper Compare: https://github.com/galaxyproject/galaxy/compare/4071b3eb79e4...b4475ba9df9b

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[galaxyproject/galaxy] 7f62eb: Fix history sharing test broken with #3417.
by GitHub 19 Jan '17

19 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7f62eb0c83c18949fdf945c4c194b89d74e66cae https://github.com/galaxyproject/galaxy/commit/7f62eb0c83c18949fdf945c4c194… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M test/selenium_tests/test_history_sharing.py Log Message: ----------- Fix history sharing test broken with #3417. Commit: 6fdd0014d38ac8455f26e12b9f44b55d46bc9ee6 https://github.com/galaxyproject/galaxy/commit/6fdd0014d38ac8455f26e12b9f44… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Remove debugging "assert False" in workflow editor test. Commit: e1612d24eaf67f7dd517caa210131a54f141d2cd https://github.com/galaxyproject/galaxy/commit/e1612d24eaf67f7dd517caa21013… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M test/selenium_tests/test_workflow_management.py Log Message: ----------- Update URL used by Selenium tests that changed with a recent commit. Commit: 4071b3eb79e49806a6cd8df141be452366ba1942 https://github.com/galaxyproject/galaxy/commit/4071b3eb79e49806a6cd8df141be… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merge pull request #3440 from jmchilton/selenium_fixes_1 Fix most broken Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/c4f5a2cfb8b7...4071b3eb79e4

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[galaxyproject/galaxy] b00887: Fixup circular dependency in #3427.
by GitHub 19 Jan '17

19 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b00887b9d7e471c65155740db548effd75dc4703 https://github.com/galaxyproject/galaxy/commit/b00887b9d7e471c65155740db548… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fixup circular dependency in #3427. Unfortunately the "root" of the problem is that galaxy.tools.deps.requirements.ToolRequirement should be importable without importing galaxy.tools - but it cannot be currently just because of the way things are structured. Commit: c4f5a2cfb8b7a34faf05367a5f4d8073ab229b98 https://github.com/galaxyproject/galaxy/commit/c4f5a2cfb8b7a34faf05367a5f4d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #3447 from jmchilton/ts_import_cycle Fixup circular dependency in #3427. Compare: https://github.com/galaxyproject/galaxy/compare/94150df087b2...c4f5a2cfb8b7

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[galaxyproject/galaxy] 4a3c6c: Add nice css to error email
by GitHub 18 Jan '17

18 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a3c6c871d75a2e457b5ceb6cd081df827d60425 https://github.com/galaxyproject/galaxy/commit/4a3c6c871d75a2e457b5ceb6cd08… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Add nice css to error email Apparently you have to inline it for certain web email clients to show it.. Commit: 94150df087b29810111952853a03fdb6ddd34631 https://github.com/galaxyproject/galaxy/commit/94150df087b29810111952853a03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #3445 from erasche/email-template-css Inline CSS in error report email Compare: https://github.com/galaxyproject/galaxy/compare/9646d264a1a9...94150df087b2

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[galaxyproject/galaxy] e0990e: extend API version information
by GitHub 18 Jan '17

18 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e0990e2ab58895e9667438aa3207f1a15e9ec3bf https://github.com/galaxyproject/galaxy/commit/e0990e2ab58895e9667438aa3207… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- extend API version information extend API version information #1907 https://github.com/galaxyproject/galaxy/issues/1907 output json file contents with version_major ``` {"extra": {"user_tag": "_fix_job_runner_issue", "commit-id": "abcde123"}, "version_major": "16.10"} ``` First check environment value GALAXY_VERSION_JSON_FILE. if it's not set, try "galaxy root direcotory"/version.json. if json file is not find, extra set empty. Commit: c2d1a2a1897ba05e5067433fcecdfcd60c761009 https://github.com/galaxyproject/galaxy/commit/c2d1a2a1897ba05e5067433fcecd… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- fix lint Commit: 0c0e58d5fb6c48418c36e547e976dde1dfd79942 https://github.com/galaxyproject/galaxy/commit/0c0e58d5fb6c48418c36e547e976… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- fix lint Commit: 8c34293602ec99b7deb128f60e2086f89f25e64a https://github.com/galaxyproject/galaxy/commit/8c34293602ec99b7deb128f60e20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- More idiomatic Python for extended version information. - Eliminate the use of a bare except. - Use a ``with`` to ensure file handling is cleaned up. Commit: 9646d264a1a9d9d9107c2311deb4e6f319bb417d https://github.com/galaxyproject/galaxy/commit/9646d264a1a9d9d9107c2311deb4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Merge pull request #3411 from manabuishii/extend_api_version extend API version information Compare: https://github.com/galaxyproject/galaxy/compare/29cdd6007fa3...9646d264a1a9

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