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

[galaxyproject/galaxy] de624b: Sync non-CWL galaxy-lib changes.
by GitHub 01 Sep '17

01 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: de624b48b14f491841921363e4ef7d1ba72db3f3 https://github.com/galaxyproject/galaxy/commit/de624b48b14f491841921363e4ef… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/linters/help.py M lib/galaxy/util/__init__.py Log Message: ----------- Sync non-CWL galaxy-lib changes. Covers https://github.com/galaxyproject/galaxy-lib/pull/71 and https://github.com/galaxyproject/galaxy-lib/pull/69. Commit: 558e22a49cbd9a1622a6b7db77ad6f66f17b5229 https://github.com/galaxyproject/galaxy/commit/558e22a49cbd9a1622a6b7db77ad… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/linters/help.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #4535 from jmchilton/galaxy-lib Sync non-CWL galaxy-lib changes. Compare: https://github.com/galaxyproject/galaxy/compare/dd9c757a15e9...558e22a49cbd

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[galaxyproject/galaxy] a0bd78: Optimize loading of StoredWorkflow attributes
by GitHub 01 Sep '17

01 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a0bd78034defb11adf2140f7c6dd90e63bc7da43 https://github.com/galaxyproject/galaxy/commit/a0bd78034defb11adf2140f7c6dd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Optimize loading of StoredWorkflow attributes WorkflowsManager.get_stored_workflow is used when exporting or editing workflows. In these cases we iterate over the related workflow objects steps as well as the related tags and annotation objects. Each iteration will emit a new SQL statement. Joinedloading these relations here speeds up the workflow run form and the editor. With sqlite as backend this speeds up exporting a workflow for the workflow editor by about 5X. Commit: 62204de0aeb4a833e43e5a1f81657293853ffb03 https://github.com/galaxyproject/galaxy/commit/62204de0aeb4a833e43e5a1f8165… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/model/item_attrs.py Log Message: ----------- Use pre-existing annotations object if possible This avoids additional requests to the database. Commit: db04f295d34e8ca03b151f462e7ffd1d613a1321 https://github.com/galaxyproject/galaxy/commit/db04f295d34e8ca03b151f462e7f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Do not provide a history in workflow_building_mode Commit: cb1392fd2d707587859bcbbb3e1744fb472ebf22 https://github.com/galaxyproject/galaxy/commit/cb1392fd2d707587859bcbbb3e17… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Use WorkflowManager to get StoredWorkflow in workflow web controller Commit: 83bb7b108e90086ae0f421d63107c3870dea5d73 https://github.com/galaxyproject/galaxy/commit/83bb7b108e90086ae0f421d63107… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Avoid ToolShedRepository attributes where possible Commit: d5eee194252270ebf4be008c6cf0492d5c6c3340 https://github.com/galaxyproject/galaxy/commit/d5eee194252270ebf4be008c6cf0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Use workflow_building_modes.ENABLED instead of True Commit: e4f4dc91eebe7d5e4fbf8667bff52079498d88ea https://github.com/galaxyproject/galaxy/commit/e4f4dc91eebe7d5e4fbf8667bff5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Cache edam_data and edam_formats Commit: 17246225d962f4d1494b4b718440f42631fd6210 https://github.com/galaxyproject/galaxy/commit/17246225d962f4d1494b4b718440… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Use joinedload for latest_workflow.steps when building workflow editor config Commit: 1a1232e11dd31b96284d2842292d13f9b67ee22e https://github.com/galaxyproject/galaxy/commit/1a1232e11dd31b96284d2842292d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Use get_item_annotation_str instead of get_item_annotation_obj Commit: 2faa56eefe7a8b029ed62b9b4402894c2a26248f https://github.com/galaxyproject/galaxy/commit/2faa56eefe7a8b029ed62b9b4402… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Rework if statement to be more explicit Commit: dd9c757a15e929be2ab6d138fb181f0ed543c156 https://github.com/galaxyproject/galaxy/commit/dd9c757a15e929be2ab6d138fb18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/item_attrs.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4500 from mvdbeek/workflow_loading_speedup Workflow loading speedup Compare: https://github.com/galaxyproject/galaxy/compare/9fb78b1010f8...dd9c757a15e9

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[galaxyproject/galaxy] a85d65: Another fix for Selenium worklow tests.
by GitHub 31 Aug '17

31 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a85d65c6a2ce3fd0a166e130f8a89dc198c3e0c7 https://github.com/galaxyproject/galaxy/commit/a85d65c6a2ce3fd0a166e130f8a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/selenium_tests/test_workflow_run.py Log Message: ----------- Another fix for Selenium worklow tests. This time for the workflow upgrade message test, mirrors the fix in #4524 - the content we are searching for in on this page is no longer in the iframe. Commit: 9fb78b1010f8e106d34bf0b44888265b980521fd https://github.com/galaxyproject/galaxy/commit/9fb78b1010f8e106d34bf0b44888… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #4531 from jmchilton/selenium_fixes_17 Another fix for Selenium worklow tests. Compare: https://github.com/galaxyproject/galaxy/compare/7db1a3fb3e6f...9fb78b1010f8

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