February 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] d7de19: fix toolbox filters
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: d7de19b072745ab96a68428281e186cd4c755e45 https://github.com/galaxyproject/galaxy/commit/d7de19b072745ab96a68428281e1… Author: Bjoern Gruening <bjoern.gruening(a)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/d5687bc418664bd05e4034a1beea… Author: John Chilton <jmchilton(a)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/ea2bac8a12ad220d39f7e851f708… Author: Björn Grüning <bjoern(a)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: 6b0e20a7a9006aec997b9e60aae793d5d2fb8915 https://github.com/galaxyproject/galaxy/commit/6b0e20a7a9006aec997b9e60aae7… Author: Dannon Baker <dannon.baker(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/a269a95cf0ae...6b0e20a7a900

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[galaxyproject/infrastructure-playbook] 1cfe00: Use `cvmfs_server snapshot -a` instead of snapshot...
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1cfe001988c2692eed4cbfa04eaf5acfbf194e06 https://github.com/galaxyproject/infrastructure-playbook/commit/1cfe001988c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M env/galaxy/inventory M roles/cvmfs/tasks/stratum1.yml Log Message: ----------- Use `cvmfs_server snapshot -a` instead of snapshotting each repo individually

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[galaxyproject/galaxy] 8ecdde: WIP for linking doc versions
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8ecddefd09ce70cab2f275d95832a0901fd4dd94 https://github.com/galaxyproject/galaxy/commit/8ecddefd09ce70cab2f275d95832… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M doc/source/conf.py Log Message: ----------- WIP for linking doc versions Commit: 141ac1eabc64b11444a31bbd7c8c0d91436a9d29 https://github.com/galaxyproject/galaxy/commit/141ac1eabc64b11444a31bbd7c8c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M doc/source/conf.py A doc/source/conf.versioning.py Log Message: ----------- Move simpleversioning config to a separate file that can be written to conf.py by Jenkins Commit: 59c6d6957e6bfd3500c2967cb9a86d8c87731a4f https://github.com/galaxyproject/galaxy/commit/59c6d6957e6bfd3500c2967cb9a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Fix string slicing error Commit: 98e369c9a730090fb99975d9904484c749a6ea50 https://github.com/galaxyproject/galaxy/commit/98e369c9a730090fb99975d99044… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Use $TARGET_GIT_BRANCH instead of $GIT_BRANCH (which is a lie for matrix configs) Commit: 4bdebe018648bc28a3029368849c82cc786ae650 https://github.com/galaxyproject/galaxy/commit/4bdebe018648bc28a3029368849c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Conditional fixes for the documentation message box Commit: d238b0f25bba2319d414f3de4a48dc1a887b6051 https://github.com/galaxyproject/galaxy/commit/d238b0f25bba2319d414f3de4a48… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Fix linting error and avoid double import Commit: a54681e8c67c3bc9b1dff993a1445c23d87275dd https://github.com/galaxyproject/galaxy/commit/a54681e8c67c3bc9b1dff993a144… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M doc/source/conf.py A doc/source/conf.versioning.py Log Message: ----------- Merge pull request #5334 from natefoo/doc-versioning Documentation version selection Compare: https://github.com/galaxyproject/galaxy/compare/92826fe5e763...a54681e8c67c

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[galaxyproject/galaxy] a269a9: Fix the bug
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: a269a95cf0aef62b1f1dbca8de698d7b2f61f52b https://github.com/galaxyproject/galaxy/commit/a269a95cf0aef62b1f1dbca8de69… Author: anup kumar <anup.rulez(a)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

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[galaxyproject/galaxy] 83cf06: Fix the bug
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83cf06e3614b5463e3aaac74f314e3d04ad46f9a https://github.com/galaxyproject/galaxy/commit/83cf06e3614b5463e3aaac74f314… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Fix the bug Commit: 92826fe5e763a0938cf4710955be4d1e4e5cf967 https://github.com/galaxyproject/galaxy/commit/92826fe5e763a0938cf4710955be… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Merge pull request #5531 from bgruening/bugfix_#5522 Fix search overlay JS errors Compare: https://github.com/galaxyproject/galaxy/compare/298ef7ee1951...92826fe5e763

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[galaxyproject/galaxy] 8c941a: Fix for: https://github.com/galaxyproject/galaxy/i...
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 8c941ae35a37f8dd087222c6827c122ddfdcc966 https://github.com/galaxyproject/galaxy/commit/8c941ae35a37f8dd087222c6827c… Author: Nuwan Goonasekera <nuwan.ag(a)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

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[galaxyproject/galaxy] 8a721f: Fix for: https://github.com/galaxyproject/galaxy/i...
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8a721f6f37741d07fbe709112fa03c51b4697a49 https://github.com/galaxyproject/galaxy/commit/8a721f6f37741d07fbe709112fa0… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-02-13 (Tue, 13 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: 298ef7ee1951cf64fe42b4cc44ce83b4257aace6 https://github.com/galaxyproject/galaxy/commit/298ef7ee1951cf64fe42b4cc44ce… Author: Martin Cech <marten(a)bx.psu.edu> 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: ----------- Merge pull request #5528 from gvlproject/genomespace_18.01_bugfix Fix for GenomeSpace importer/exporter Compare: https://github.com/galaxyproject/galaxy/compare/78ee5f8451e0...298ef7ee1951

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[galaxyproject/galaxy] 7663de: Remove unused methods.
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7663de745f5df827f7873960c9ec341eb88e86a2 https://github.com/galaxyproject/galaxy/commit/7663de745f5df827f7873960c9ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/execute.py Log Message: ----------- Remove unused methods. Commit: aed2b4a239ebbcd4081426599023867eed94f63b https://github.com/galaxyproject/galaxy/commit/aed2b4a239ebbcd4081426599023… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py Log Message: ----------- remove unused import Commit: 78ee5f8451e022515e75e9ca5888bf598d2d3414 https://github.com/galaxyproject/galaxy/commit/78ee5f8451e022515e75e9ca5888… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #5450 from jmchilton/collection_mapping_cleanup Remove unused mapping code. Compare: https://github.com/galaxyproject/galaxy/compare/41a31967540e...78ee5f8451e0

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[galaxyproject/galaxy] 283ab0: Improve performance bugs and misleading summary in...
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 283ab0459fe25cc26606ccae86bdd99e1c6765b9 https://github.com/galaxyproject/galaxy/commit/283ab0459fe25cc26606ccae86bd… Author: John Chilton <jmchilton(a)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: 755fb9fb21581f29ba96a1465ca73e72eb68b610 https://github.com/galaxyproject/galaxy/commit/755fb9fb21581f29ba96a1465ca7… Author: Martin Cech <marten(a)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: 42c12c51884454c60a8b109f1ae7e814eeeaf7a4 https://github.com/galaxyproject/galaxy/commit/42c12c51884454c60a8b109f1ae7… Author: Martin Cech <marten(a)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. Compare: https://github.com/galaxyproject/galaxy/compare/1ccd55a500e5...42c12c518844

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[galaxyproject/galaxy] 712073: [18.01] Fix missing job stdout/stderr on Pulsar tr...
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 7120739230255c63bf9786fb735016292b57dcfd https://github.com/galaxyproject/galaxy/commit/7120739230255c63bf9786fb7350… Author: John Chilton <jmchilton(a)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: 1ccd55a500e59c98a910f783e5fcc01913beef54 https://github.com/galaxyproject/galaxy/commit/1ccd55a500e59c98a910f783e5fc… Author: Nate Coraor <nate(a)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. Compare: https://github.com/galaxyproject/galaxy/compare/296af58c3d3f...1ccd55a500e5

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