Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d7de19b072745ab96a68428281e186cd4c755e45 https://github.com/galaxyproject/galaxy/commit/d7de19b072745ab96a68428281e18... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- fix toolbox filters Commit: d5687bc418664bd05e4034a1beea603890128f5e https://github.com/galaxyproject/galaxy/commit/d5687bc418664bd05e4034a1beea6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- PEP8 fixes. Commit: ea2bac8a12ad220d39f7e851f70821836da4bbdb https://github.com/galaxyproject/galaxy/commit/ea2bac8a12ad220d39f7e851f7082... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- yes, the name is tool not tools :( Commit: 7120739230255c63bf9786fb735016292b57dcfd https://github.com/galaxyproject/galaxy/commit/7120739230255c63bf9786fb73501... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/jobs/runners/pulsar.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- [18.01] Fix missing job stdout/stderr on Pulsar transfer failures. Shouldn't break backward compatiblity at all without it - but to get the outputs Pulsar requires an update (https://github.com/galaxyproject/pulsar/pull/159) as well. Commit: 283ab0459fe25cc26606ccae86bdd99e1c6765b9 https://github.com/galaxyproject/galaxy/commit/283ab0459fe25cc26606ccae86bdd... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Improve performance bugs and misleading summary info in history list. Prefetch shared user information as counts instead of objects and do so in initial query to eliminate an extra 15 SQL queries per page and load less data related to sharing. Replace columns that would cause HDA information to be joined into the query (history size and HDA state counts) with a spinner that will be fetched in subsequent queries on the client end. There can hundreds of thousands of datasets per history - this information shouldn't be summarized to get the initial page to render - it can be fetched one history at a time once the page is rendered. This commit also adds a new column "Items" that corresponds to the next HID - and that I think is a good summary of the "history size" before the dataset state information is loaded and even gives additional information because that count includes collections. This also renders state information for deleted and hidden datasets that was previously missing and could cause confusion. That said I don't like the dataset summaries - I'd rather just have the item count and then job state summaries. Commit: 7457ce426f0563464dff2313249381afa9378f28 https://github.com/galaxyproject/galaxy/commit/7457ce426f0563464dff231324938... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/managers/libraries.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- optimize nonadmin and nonanon library list permission queries Before, the code would emit extra queries per each library to find out whether the current user has permissions on it. By pre-fetching all of them in one query and passing around as a dict object we should see a considerable speedup on Galaxies with many libraries. Commit: 296af58c3d3f6fdb19560f1c8ab58290c9742b8b https://github.com/galaxyproject/galaxy/commit/296af58c3d3f6fdb19560f1c8ab58... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/managers/libraries.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- Merge pull request #5542 from martenson/optimize-nonadmin-nonanon-datalibs [18.01] optimize nonadmin and nonanon library list permission queries Commit: 755fb9fb21581f29ba96a1465ca73e72eb68b610 https://github.com/galaxyproject/galaxy/commit/755fb9fb21581f29ba96a1465ca73... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_variables.less Log Message: ----------- style changes for history lists * include title for all state indicators * shorten title * change style of deleted indicator * comment out unused less variables Commit: 1ccd55a500e59c98a910f783e5fcc01913beef54 https://github.com/galaxyproject/galaxy/commit/1ccd55a500e59c98a910f783e5fcc... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/jobs/runners/pulsar.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5535 from jmchilton/pulsar_error_handling_1 [18.01] Fix missing job stdout/stderr on Pulsar transfer failures. Commit: 42c12c51884454c60a8b109f1ae7e814eeeaf7a4 https://github.com/galaxyproject/galaxy/commit/42c12c51884454c60a8b109f1ae7e... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_variables.less M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #5533 from jmchilton/history_list_opts [18.01] Improve performance bugs and misleading summary info in history list. Commit: 8c941ae35a37f8dd087222c6827c122ddfdcc966 https://github.com/galaxyproject/galaxy/commit/8c941ae35a37f8dd087222c6827c1... Author: Nuwan Goonasekera <nuwan.ag@gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- Fix for: https://github.com/galaxyproject/galaxy/issues/5527 Commit: a269a95cf0aef62b1f1dbca8de698d7b2f61f52b https://github.com/galaxyproject/galaxy/commit/a269a95cf0aef62b1f1dbca8de698... Author: anup kumar <anup.rulez@gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Fix the bug Commit: 6b0e20a7a9006aec997b9e60aae793d5d2fb8915 https://github.com/galaxyproject/galaxy/commit/6b0e20a7a9006aec997b9e60aae79... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #5526 from bgruening/user_filter [18.01] fix toolbox filters Commit: f7b505e68dad6cee53ba884dce258f659d7da33a https://github.com/galaxyproject/galaxy/commit/f7b505e68dad6cee53ba884dce258... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_variables.less M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/history.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a54681e8c67c...f7b505e68dad