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

[galaxyproject/usegalaxy-playbook] 13310f: Workaround for SLASH2 incompatibilities with OpenJ...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 13310f470d7ff256da5d75b766233ad6d7372527 https://github.com/galaxyproject/usegalaxy-playbook/commit/13310f470d7ff256… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: A CHANGELOG.md M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Workaround for SLASH2 incompatibilities with OpenJDK < 9. Commit: 49b8d60e5ce91a82343a69b49e1fb406a3d41276 https://github.com/galaxyproject/usegalaxy-playbook/commit/49b8d60e5ce91a82… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M env/main/group_vars/ftpservers/vars.yml M env/test/group_vars/ftpservers/vars.yml Log Message: ----------- Workaround for the issue described in proftpd/proftpd#568 Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/0a5fe4b44250...…

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[galaxyproject/galaxy] c67158: Prevent unbound variable error history controller.
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c6715819006256e429bf4e589dd456835b8d349c https://github.com/galaxyproject/galaxy/commit/c6715819006256e429bf4e589dd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Prevent unbound variable error history controller. Fixes #4423 I suppose - thanks @erasche. Commit: 7db47e7e3c012d34fd27cfb7aadfca17469b2480 https://github.com/galaxyproject/galaxy/commit/7db47e7e3c012d34fd27cfb7aadf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #4557 from jmchilton/shared_histories_unbound Prevent unbound variable error history controller. Compare: https://github.com/galaxyproject/galaxy/compare/b734581495f4...7db47e7e3c01

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[galaxyproject/galaxy] 254192: Revert "Remove Selenium test that is broken becaus...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2541928855159504caf049dd58ffca9570b8bde1 https://github.com/galaxyproject/galaxy/commit/2541928855159504caf049dd58ff… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Revert "Remove Selenium test that is broken because Galaxy is broken." This reverts commit a91c03d4403ad57336ce5cc235b22cf4be5ebd6d. Commit: b734581495f4bf39da16013ce8ae5536d0cc4437 https://github.com/galaxyproject/galaxy/commit/b734581495f4bf39da16013ce8ae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #4561 from mvdbeek/reintroduce_missing_tool_test Revert "Remove Selenium test that is broken because Galaxy is broken." Compare: https://github.com/galaxyproject/galaxy/compare/3962ba94d756...b734581495f4

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[galaxyproject/galaxy] 4d3452: Update the default testing Selenium Chrome Docker ...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4d3452c09e67be62812a13ea7ad803f62ce76fbb https://github.com/galaxyproject/galaxy/commit/4d3452c09e67be62812a13ea7ad8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-04 (Mon, 04 Sep 2017) Changed paths: M .ci/jenkins/selenium/docker-compose.yml Log Message: ----------- Update the default testing Selenium Chrome Docker target. Some recent changes was incompatible with some bug in the older version (possibly this bug https://bugs.chromium.org/p/chromedriver/issues/detail?id=1552) the result is a huge number of failures in Jenkins as some persistent session error occurs. For example the older (https://jenkins.galaxyproject.org/job/selenium/209/testReport/) but with me hacking the Jenkins job to make this change only two tests fail (https://jenkins.galaxyproject.org/job/selenium/210/testReport/) Commit: ebcb4aa623dce9f92b904bf1f2ad58f59f07dbaf https://github.com/galaxyproject/galaxy/commit/ebcb4aa623dce9f92b904bf1f2ad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-04 (Mon, 04 Sep 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Possible fix for a transient failure in the published histories grid tests. See failure here (https://jenkins.galaxyproject.org/job/selenium/210/testReport/selenium_test…) Uses technique to retry atomic assertions that may not be immediately true but will settle as the DOM is updated in response to changes to be true (added in https://github.com/galaxyproject/galaxy/commit/d0df3886fa7acaa3d5f63360e2af…) Commit: a91c03d4403ad57336ce5cc235b22cf4be5ebd6d https://github.com/galaxyproject/galaxy/commit/a91c03d4403ad57336ce5cc235b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-04 (Mon, 04 Sep 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Remove Selenium test that is broken because Galaxy is broken. See (https://github.com/galaxyproject/galaxy/issues/4548) for more information on the underlying issue. Commit: 3962ba94d756defce37b49375d77e221890904d7 https://github.com/galaxyproject/galaxy/commit/3962ba94d756defce37b49375d77… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M .ci/jenkins/selenium/docker-compose.yml M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #4549 from jmchilton/selenium_fixes_18 Assorted Selenium test fixes Compare: https://github.com/galaxyproject/galaxy/compare/235bdca1eb94...3962ba94d756

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[galaxyproject/galaxy] 932a3a: Make chronos dependency conditional.
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 932a3aa3be3327938b619b6c7f97d837264a12a6 https://github.com/galaxyproject/galaxy/commit/932a3aa3be3327938b619b6c7f97… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Make chronos dependency conditional. Fixes #4085. Commit: 235bdca1eb942605eadedf719190de54559fde3a https://github.com/galaxyproject/galaxy/commit/235bdca1eb942605eadedf719190… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #4556 from jmchilton/conditional_chronos Make chronos dependency conditional. Compare: https://github.com/galaxyproject/galaxy/compare/65b86e3eb015...235bdca1eb94

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[galaxyproject/galaxy] bff6b5: Allow exporting workflows when tool is uninstalled
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bff6b58a1ba356f904af7ec17735a88be4b348de https://github.com/galaxyproject/galaxy/commit/bff6b58a1ba356f904af7ec17735… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Allow exporting workflows when tool is uninstalled Commit: 65b86e3eb0152f872a4d30b3be6741972f2fe7f7 https://github.com/galaxyproject/galaxy/commit/65b86e3eb0152f872a4d30b3be67… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #4553 from mvdbeek/allow_exporting_workflow_with_uninstalled_tools Allow exporting workflows when tool is uninstalled Compare: https://github.com/galaxyproject/galaxy/compare/338b0c994cf8...65b86e3eb015

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[galaxyproject/galaxy] 6deff3: import of history works even if we use symlink in ...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6deff3f9e518a1c7b51cea584ced1e4755ba9254 https://github.com/galaxyproject/galaxy/commit/6deff3f9e518a1c7b51cea584ced… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- import of history works even if we use symlink in database directory Commit: d76e304d9bec3d09867c2c264af3f73eabcd17dc https://github.com/galaxyproject/galaxy/commit/d76e304d9bec3d09867c2c264af3… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- remove the redundant call to os.path.abspath(), which is called internally by os.path.realpath() Commit: 338b0c994cf8f249ac2f4cd7dce2ced811e3a58a https://github.com/galaxyproject/galaxy/commit/338b0c994cf8f249ac2f4cd7dce2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge pull request #4511 from FredericBGA/import_history_and_symlink import of history works even if we use symlink in database directory Compare: https://github.com/galaxyproject/galaxy/compare/a13bd06f48eb...338b0c994cf8

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[galaxyproject/galaxy] 96cf1b: Lower threshold for auto-matching dataset pairs in...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 96cf1b94f14b7c92c767943fa4595e638eb322e3 https://github.com/galaxyproject/galaxy/commit/96cf1b94f14b7c92c767943fa459… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Lower threshold for auto-matching dataset pairs in the collection builder. Thanks to @mvdbeek for originally testing this and verifying it works. Fixes #4349. Commit: a13bd06f48eb1eda43c034e3fe0a3d9363d8cda4 https://github.com/galaxyproject/galaxy/commit/a13bd06f48eb1eda43c034e3fe0a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #4555 from jmchilton/lower_matching_threshold Lower threshold for auto-matching dataset pairs in the collection builder Compare: https://github.com/galaxyproject/galaxy/compare/1e3bd2d4e831...a13bd06f48eb

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[galaxyproject/galaxy] 946d64: LMOD Dependency resolver - Initial commit (lib lmo...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 946d64b8f7dc08b92ebb03f34a91cab8aa7ecfbb https://github.com/galaxyproject/galaxy/commit/946d64b8f7dc08b92ebb03f34a91… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: A lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- LMOD Dependency resolver - Initial commit (lib lmod.py) Initial commit of a prototype dependency resolver based on the LMOD environment modules system. Commit: 4d143479d5998531cc4803af11579e12d160c87b https://github.com/galaxyproject/galaxy/commit/4d143479d5998531cc4803af1157… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample Log Message: ----------- Update of the dependency_resolvers_conf.xml.sample file Addition of the LMOD Dependency resolver to the appropriate sample configuration file (dependency_resolvers_conf.xml.sample). Comment lines have also been added to describe the possible attributes of the resolver as well as their default values. Commit: e84284c477182b3c03e785b79f93dd88d63e6ebd https://github.com/galaxyproject/galaxy/commit/e84284c477182b3c03e785b79f93… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample A config/lmod_modules_mapping.yml.sample M lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- LMOD Dependency resolver - Default mapping file If a lmod_modules_mapping.yml file exists in the config folder then it will be taken into consideration automatically to map Galaxy requirements to LMOD modules. Commit: fed3206a87e4ae4ede380c90cfa3409220847cf7 https://github.com/galaxyproject/galaxy/commit/fed3206a87e4ae4ede380c90cfa3… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- Fix errors reported by the initial Travis tests Fix incorrect numbers of blank lines. Fix deprecated syntax. Commit: 09887529765ba88adb70e739d1b9d8896cb86229 https://github.com/galaxyproject/galaxy/commit/09887529765ba88adb70e739d1b9… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- Syntax fix in the shell_commands method The built command now reflect more directly the command that is really executed by the the LMOD "module" bash function when a user execute "module load package_name/package_version". Commit: 574e697a4d66a53f298f37f4987d31db96ff8e14 https://github.com/galaxyproject/galaxy/commit/574e697a4d66a53f298f37f4987d… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample Log Message: ----------- Dependency_resolvers_conf.xml - More explanations Some more explanations about the versionless mode have been added. Commit: db5efdaa7cbc197eaf6a777d4d390de24b212e88 https://github.com/galaxyproject/galaxy/commit/db5efdaa7cbc197eaf6a777d4d39… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- Clearer comment lines in the has_module method A comment of the has_module method of the AvailModuleChecker class has been modified to be clearer and more explicit. Commit: eda36ffb99a1abec8f878c0b7ae194938781c8d6 https://github.com/galaxyproject/galaxy/commit/eda36ffb99a1abec8f878c0b7ae1… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- LMOD Dependency resolver - Unit tests added The unit/tools/tests_tool_deps.py script has been updated to includ unit tests for the LMOD dependency resolver. Commit: bbec357bbd744b9e0d760e8d0903adfa43d1b7e2 https://github.com/galaxyproject/galaxy/commit/bbec357bbd744b9e0d760e8d0903… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Fix the import order error raised by Travis The order of the import statements in the test_tool_deps script was incorrect (as stated by travis). That should no longer be the case. Commit: 9822f5f2a91fae7e3420a06c58f2621a2cf084ac https://github.com/galaxyproject/galaxy/commit/9822f5f2a91fae7e3420a06c58f2… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Fix attempt for the modulepath issue in unit tests On a computer where LMOD is not installed, the MODULEPATH variable is not defined and the modulepath attributes of the LMOD dependency resolver must be used. Commit: 1e3bd2d4e831331b8e3b314bac287288fa4533fc https://github.com/galaxyproject/galaxy/commit/1e3bd2d4e831331b8e3b314bac28… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample A config/lmod_modules_mapping.yml.sample A lib/galaxy/tools/deps/resolvers/lmod.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #4489 from arbernard/LMOD_Dependency_resolver New Dependency resolver for the LMOD environment modules system Compare: https://github.com/galaxyproject/galaxy/compare/6e6845b4987a...1e3bd2d4e831

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[galaxyproject/galaxy] cfefee: Refactor history import/export tests to allow coll...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cfefeebdd713552c9e0776b932fca59fe65961a3 https://github.com/galaxyproject/galaxy/commit/cfefeebdd713552c9e0776b932fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/api/test_histories.py Log Message: ----------- Refactor history import/export tests to allow collection testing (not yet implemented). xref #4345, #4532 Commit: 6e6845b4987ab2de5608e216b1f537ad9b1f0fd5 https://github.com/galaxyproject/galaxy/commit/6e6845b4987ab2de5608e216b1f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M test/api/test_histories.py Log Message: ----------- Merge pull request #4534 from jmchilton/collection_import_export_test_case Refactor history import/export tests to allow collection testing. Compare: https://github.com/galaxyproject/galaxy/compare/af9173d7cfa8...6e6845b4987a

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