- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] eee4a1: Update version to 17.09.rc1
by GitHub 19 Sep '17

19 Sep '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: eee4a17a4cb45b6d79e610c00cbdf37df0988993 https://github.com/galaxyproject/galaxy/commit/eee4a17a4cb45b6d79e610c00cbd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.09.rc1 Commit: a25b6e5b0eb5ed97e789e1b4b8643be775a55e05 https://github.com/galaxyproject/galaxy/commit/a25b6e5b0eb5ed97e789e1b4b864… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #4648 from martenson/version-17.09 [17.09]Update version to 17.09.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/f15405877601...a25b6e5b0eb5

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[galaxyproject/galaxy]
by GitHub 19 Sep '17

19 Sep '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 0df4db: Replace spaces with newlines in multi url upload r...
by GitHub 19 Sep '17

19 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0df4db5175bec7653aaa855a5d873b3e6de14fcb https://github.com/galaxyproject/galaxy/commit/0df4db5175bec7653aaa855a5d87… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Replace spaces with newlines in multi url upload requests Commit: 2bcd46c7234aba06a871b6a824e49f5e39057239 https://github.com/galaxyproject/galaxy/commit/2bcd46c7234aba06a871b6a824e4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Split by space instead of newline Commit: 6af7661fb181a90b31f50e055ac99b9113d1b287 https://github.com/galaxyproject/galaxy/commit/6af7661fb181a90b31f50e055ac9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Drop manual string replacements, rely on split without parameters Commit: 8b517e7a036f0df3666e6d89f1aa0e885835225c https://github.com/galaxyproject/galaxy/commit/8b517e7a036f0df3666e6d89f1aa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Restore previous behavior Commit: 403cd3ffca23fc91c6f8976e1734fcf96af26a78 https://github.com/galaxyproject/galaxy/commit/403cd3ffca23fc91c6f8976e1734… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- Remove line wrap Commit: f1540587760184b0f622c94802d0c8f84b885833 https://github.com/galaxyproject/galaxy/commit/f1540587760184b0f622c94802d0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- Merge pull request #4639 from guerler/replace_spaces_url do not wrap lines in the upload url fetch Compare: https://github.com/galaxyproject/galaxy/compare/7d394f202d84...f15405877601

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[galaxyproject/galaxy] 8a4c63: optimize the process of identifying public librari...
by GitHub 19 Sep '17

19 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8a4c63738897a7324e31683076f4e77253ef3408 https://github.com/galaxyproject/galaxy/commit/8a4c63738897a7324e31683076f4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M lib/galaxy/managers/libraries.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- optimize the process of identifying public libraries this aims to speed up the library loading considerably Commit: c5d29be0a2c2c2d16be13d0fa528ad01e5022e1d https://github.com/galaxyproject/galaxy/commit/c5d29be0a2c2c2d16be13d0fa528… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- avoid mutable default, improve docs switch to set comprehension Commit: 7d394f202d84200e9b4a3c63ce42bf7baf53ccc8 https://github.com/galaxyproject/galaxy/commit/7d394f202d84200e9b4a3c63ce42… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/managers/libraries.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- Merge pull request #4640 from martenson/datalibs-optimize-access-checks optimize the process of identifying public libraries Compare: https://github.com/galaxyproject/galaxy/compare/3f51e7dc1ef9...7d394f202d84

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[galaxyproject/usegalaxy-playbook] 0ae5e1: Remove warning banner
by GitHub 19 Sep '17

19 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0ae5e1d1b5074af07d6be10a86b871e275f6fb01 https://github.com/galaxyproject/usegalaxy-playbook/commit/0ae5e1d1b5074af0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Remove warning banner

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[galaxyproject/usegalaxy-playbook] fa48a9: Reenable nginx upload module post-maintenance.
by GitHub 19 Sep '17

19 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fa48a9c6add55b5f44865e0ff9f31cb1db4b0b42 https://github.com/galaxyproject/usegalaxy-playbook/commit/fa48a9c6add55b5f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M env/main/templates/nginx/usegalaxy.j2 Log Message: ----------- Reenable nginx upload module post-maintenance.

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[galaxyproject/galaxy] 87bb57: Improved state handling for @anatskiy-style Seleni...
by GitHub 19 Sep '17

19 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87bb576c39dadadbf119167dee581a6801a54cea https://github.com/galaxyproject/galaxy/commit/87bb576c39dadadbf119167dee58… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M test/selenium_tests/framework.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Improved state handling for @anatskiy-style Selenium tests. These tests aren't idealized unittest.TestCase because they initialize class level data in instance level methods. While this isn't ideal, it is seems an entirely fair workaround given that SeleniumTestCase setups up the Selenium connection itself in an instance method - so class-level initializers would not be able to setup Galaxy data. Since I think we will continue using this pattern then, probably best to formalize it a bit and improve error handling. This provides a formal super class for these test cases that provides a uniform method for setting up the class level data and tracks whether this is successful or not. This serves a couple purposes beyond simple uniformity. First, it tracks if the state has actually been setup or not and will skip subsequent tests if it hasn't. Some of these tests aren't passing very consistently on Jenkins and so we get a bunch of extra noise for tests that are attempting to run without their preconditions met - this will fix that and make the original errors much more clear. Moving the "hacky" part of this into the framework itself also means the tests themselves don't have to repeat hacks like seeing if variables are set with ``getattr`` and such - I always prefer one framework hack to a dozen application hacks. Commit: 3f51e7dc1ef99a68aa8694cfe6858a70e9482e50 https://github.com/galaxyproject/galaxy/commit/3f51e7dc1ef99a68aa8694cfe685… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M test/selenium_tests/framework.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #4647 from jmchilton/selenium_fixes_28 Improved state handling for @anatskiy-style Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/844f083c7b8c...3f51e7dc1ef9

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[galaxyproject/infrastructure-playbook] 93db85: Add starforge image build deps
by GitHub 19 Sep '17

19 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 93db85f559a8196e368f669b777bfb5c1aa3ad74 https://github.com/galaxyproject/infrastructure-playbook/commit/93db85f559a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M galaxyenv/group_vars/starforgebuilders.yml Log Message: ----------- Add starforge image build deps

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[galaxyproject/usegalaxy-playbook] bc1f26: Prevent nginx on Main from touching Corral
by GitHub 19 Sep '17

19 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bc1f26988f2d34ae877e6285651feb98f213f674 https://github.com/galaxyproject/usegalaxy-playbook/commit/bc1f26988f2d34ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M env/main/templates/nginx/usegalaxy.j2 Log Message: ----------- Prevent nginx on Main from touching Corral

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[galaxyproject/galaxy] 2c128b: add custom builds tests
by GitHub 19 Sep '17

19 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2c128b097a07057f4d5a6f9c622eab0f5dabcf3b https://github.com/galaxyproject/galaxy/commit/2c128b097a07057f4d5a6f9c622e… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: A test/selenium_tests/test_custom_builds.py Log Message: ----------- add custom builds tests Commit: 260a8346197e4a8997f7033f1d99be7acdf302c6 https://github.com/galaxyproject/galaxy/commit/260a8346197e4a8997f7033f1d99… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M create_db.sh M extract_dataset_parts.sh M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webhooks/__init__.py M manage_db.sh M manage_tools.sh M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/user/user-custom-builds.js M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Merge branch 'dev' into custom_builds_tests Commit: db67d254ed02f628254464f8b60d2043b871f282 https://github.com/galaxyproject/galaxy/commit/db67d254ed02f628254464f8b60d… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M test/selenium_tests/test_custom_builds.py Log Message: ----------- don't test the uploading of fasta files Commit: e01b57da58d55763870ad7943a3c04b0e6a34c5b https://github.com/galaxyproject/galaxy/commit/e01b57da58d55763870ad7943a3c… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M test/selenium_tests/test_custom_builds.py Log Message: ----------- small improvement Commit: 844f083c7b8c9d29d95a4bca3817db3f918273a4 https://github.com/galaxyproject/galaxy/commit/844f083c7b8c9d29d95a4bca3817… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: A test/selenium_tests/test_custom_builds.py Log Message: ----------- Merge pull request #4641 from anatskiy/custom_builds_tests Custom Builds tests Compare: https://github.com/galaxyproject/galaxy/compare/a17ae7b90cda...844f083c7b8c

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[galaxyproject/galaxy] 3f38e8: Update tables to watch when installing new data ma...
by GitHub 19 Sep '17

19 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3f38e81cb7bb2246cc3c79dd10dc5992685f1337 https://github.com/galaxyproject/galaxy/commit/3f38e81cb7bb2246cc3c79dd10dc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/config_watchers.py A test/integration/test_data_manager_table_reload.py Log Message: ----------- Update tables to watch when installing new data manager Commit: 843d2e420011cde58e3742cacc58d3c6f1ab6255 https://github.com/galaxyproject/galaxy/commit/843d2e420011cde58e3742cacc58… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Assign correct guids to DM tools after TS install Commit: d06fb09f4bb93906ef36faf0c947eb5625c457e9 https://github.com/galaxyproject/galaxy/commit/d06fb09f4bb93906ef36faf0c947… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py M lib/tool_shed/tools/tool_validator.py A test/integration/tool_sheds_conf.xml Log Message: ----------- Make DynamicOptions use updated tool_data_tables Otherwise a restart would be necessary after adding items to a data table. Commit: 2e6654b18bd2a38f39d202e35ee5d24562122b3a https://github.com/galaxyproject/galaxy/commit/2e6654b18bd2a38f39d202e35ee5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py M test/integration/test_data_manager_table_reload.py Log Message: ----------- Linting fixes Commit: a4c4d826dca64b2d85bd8c38cccf9cf6f7762008 https://github.com/galaxyproject/galaxy/commit/a4c4d826dca64b2d85bd8c38cccf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Make watchdog a conditional dependency Commit: 4b403008270bf26e29f037ae902526641dea8e3e https://github.com/galaxyproject/galaxy/commit/4b403008270bf26e29f037ae9025… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/config.py M lib/tool_shed/tool_shed_registry.py Log Message: ----------- Remove unused root_dir argument Commit: 2d844a86e7b1534c4211d4a3de7de6e367b5fd44 https://github.com/galaxyproject/galaxy/commit/2d844a86e7b1534c4211d4a3de7d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt Log Message: ----------- Add watchdog to dev-requirements so it is available for integration tests Commit: 9d3af63660461c8738782f0a3903e8112e1e5c93 https://github.com/galaxyproject/galaxy/commit/9d3af63660461c8738782f0a3903… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M test/integration/test_data_manager_table_reload.py Log Message: ----------- Skip DataManagerIntegrationTestCase when watchdog unavailable Commit: 706434da41e70922f3d723b8cc390f3d0e5d984a https://github.com/galaxyproject/galaxy/commit/706434da41e70922f3d723b8cc39… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M test/integration/test_data_manager_table_reload.py M test/integration/test_resolvers.py Log Message: ----------- Append temp dirs to test_driver list of temp dirs Thanks for the hint @jmchilton. Commit: 642aaa811bb99a0ef3b532eac3fd5d245972994a https://github.com/galaxyproject/galaxy/commit/642aaa811bb99a0ef3b532eac3fd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Do cleanup if skip_cleanup is not set Commit: a17ae7b90cda7c6c71875f0a7b332410dab15a43 https://github.com/galaxyproject/galaxy/commit/a17ae7b90cda7c6c71875f0a7b33… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/queue_worker.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/config_watchers.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/tool_validator.py M test/base/driver_util.py A test/integration/test_data_manager_table_reload.py M test/integration/test_resolvers.py A test/integration/tool_sheds_conf.xml Log Message: ----------- Merge pull request #4617 from mvdbeek/data_manager_watch_new_tables Allow adding new data tables without restart Compare: https://github.com/galaxyproject/galaxy/compare/d9a805536840...a17ae7b90cda

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[galaxyproject/usegalaxy-playbook] dc9378: Mutable configs
by GitHub 18 Sep '17

18 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dc937857d6d8b64cff4b801eaaeaf331baaedd24 https://github.com/galaxyproject/usegalaxy-playbook/commit/dc937857d6d8b64c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Mutable configs

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[galaxyproject/usegalaxy-playbook] ce7349: Downtime message for Main
by GitHub 18 Sep '17

18 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ce7349c409580d6a59eee9e3d2135ac95d2f1537 https://github.com/galaxyproject/usegalaxy-playbook/commit/ce7349c409580d6a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Downtime message for Main

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[galaxyproject/galaxy] 5f635b: remove .git and .hg from recursive file search
by GitHub 18 Sep '17

18 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5f635bda100d7d8f93564c442c5f2d354ae453d0 https://github.com/galaxyproject/galaxy/commit/5f635bda100d7d8f93564c442c5f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-17 (Sun, 17 Sep 2017) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- remove .git and .hg from recursive file search Commit: cfb0d06575dc7523a8f7496e930b6c530e341a5c https://github.com/galaxyproject/galaxy/commit/cfb0d06575dc7523a8f7496e930b… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Exclude venv Commit: d9a805536840f9e606caee9abc0f4e2a64ffe8ea https://github.com/galaxyproject/galaxy/commit/d9a805536840f9e606caee9abc0f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Merge pull request #4636 from bgruening/find_file remove .git and .hg from recursive file search Compare: https://github.com/galaxyproject/galaxy/compare/ef602e1d1a1e...d9a805536840

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[galaxyproject/galaxy] 2c77d3: Write out registry once per job
by GitHub 18 Sep '17

18 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2c77d386def0dc21b8aa40d5d7cf5f8934c16a74 https://github.com/galaxyproject/galaxy/commit/2c77d386def0dc21b8aa40d5d7cf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/evaluation.py Log Message: ----------- Write out registry once per job Commit: e03ee53f3c398fe429ba1fe8693782a06b20cd73 https://github.com/galaxyproject/galaxy/commit/e03ee53f3c398fe429ba1fe86937… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py Log Message: ----------- Remove references to integrated_datatypes_config Commit: 03d9a9c6fba0e26fae080a7ebb65fd6f0676477e https://github.com/galaxyproject/galaxy/commit/03d9a9c6fba0e26fae080a7ebb65… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/evaluation.py Log Message: ----------- Merge pull request #4633 from mvdbeek/backport_registry_to_working_dir [17.05] Backport #4600: Write datatypes registry xml to working directory Commit: ef602e1d1a1e2b4f90d4d4ac58fb6968424b5bf6 https://github.com/galaxyproject/galaxy/commit/ef602e1d1a1e2b4f90d4d4ac58fb… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M lib/galaxy/tools/actions/metadata.py Log Message: ----------- Merge branch 'release_17.05' into dev Conflicts: lib/galaxy/datatypes/registry.py lib/galaxy/jobs/__init__.py lib/galaxy/jobs/command_factory.py lib/galaxy/tools/actions/metadata.py lib/galaxy/tools/evaluation.py Compare: https://github.com/galaxyproject/galaxy/compare/8f337f692f2a...ef602e1d1a1e

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[galaxyproject/galaxy] f3c593: fix column order in Custom Builds
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3c593fc59f0c1a43ddc992feed582cc7668caee https://github.com/galaxyproject/galaxy/commit/f3c593fc59f0c1a43ddc992feed5… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- fix column order in Custom Builds Commit: 8f337f692f2aa2a5aef766bc525929c51cad7324 https://github.com/galaxyproject/galaxy/commit/8f337f692f2aa2a5aef766bc5259… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-17 (Sun, 17 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Merge pull request #4634 from anatskiy/custom_builds_fix Fix data order in Custom Builds Compare: https://github.com/galaxyproject/galaxy/compare/13881bd264eb...8f337f692f2a

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[galaxyproject/galaxy] 2c77d3: Write out registry once per job
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 2c77d386def0dc21b8aa40d5d7cf5f8934c16a74 https://github.com/galaxyproject/galaxy/commit/2c77d386def0dc21b8aa40d5d7cf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/evaluation.py Log Message: ----------- Write out registry once per job Commit: e03ee53f3c398fe429ba1fe8693782a06b20cd73 https://github.com/galaxyproject/galaxy/commit/e03ee53f3c398fe429ba1fe86937… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py Log Message: ----------- Remove references to integrated_datatypes_config Commit: 03d9a9c6fba0e26fae080a7ebb65fd6f0676477e https://github.com/galaxyproject/galaxy/commit/03d9a9c6fba0e26fae080a7ebb65… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/evaluation.py Log Message: ----------- Merge pull request #4633 from mvdbeek/backport_registry_to_working_dir [17.05] Backport #4600: Write datatypes registry xml to working directory Compare: https://github.com/galaxyproject/galaxy/compare/97e8e3618531...03d9a9c6fba0

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[galaxyproject/galaxy] ac0844: Swap sanitize whitelist form to use a post.
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac084495978a8e5b607d90cf45dfb36c853aaf79 https://github.com/galaxyproject/galaxy/commit/ac084495978a8e5b607d90cf45df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Swap sanitize whitelist form to use a post. Commit: 13881bd264eb647bff4019ebbbf52aabf134f92b https://github.com/galaxyproject/galaxy/commit/13881bd264eb647bff4019ebbbf5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Merge pull request #4625 from dannon/sanitize_whitelist_post Swap sanitize whitelist form to use a post. Compare: https://github.com/galaxyproject/galaxy/compare/4c9cc67a8f10...13881bd264eb

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[galaxyproject/galaxy] 289799: Refactored a dataset variable to hda
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2897992ab56b69164a916ec400a2ed92b9c72d20 https://github.com/galaxyproject/galaxy/commit/2897992ab56b69164a916ec400a2… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Refactored a dataset variable to hda Commit: 4c9cc67a8f107887f341b1e386b2ac994acc2ba5 https://github.com/galaxyproject/galaxy/commit/4c9cc67a8f107887f341b1e386b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #4630 from VJalili/patch-4 Refactored a dataset variable to hda Compare: https://github.com/galaxyproject/galaxy/compare/6dbd47e66197...4c9cc67a8f10

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[galaxyproject/galaxy] 432d7f: Restore correct metadata path in setup_external_me...
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 432d7f44053a7c7d1fde1504e3f382edf2a539ec https://github.com/galaxyproject/galaxy/commit/432d7f44053a7c7d1fde1504e3f3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Restore correct metadata path in setup_external_metdata This is a change I shouldn't have touched in https://github.com/galaxyproject/galaxy/pull/4600 Commit: 6dbd47e661971969c734a46938a06c42b85eea8f https://github.com/galaxyproject/galaxy/commit/6dbd47e661971969c734a46938a0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #4632 from mvdbeek/fix_unintended_change [BUG] Restore tool provided metadata path in setup_external_metdata Compare: https://github.com/galaxyproject/galaxy/compare/22b0542d0bb7...6dbd47e66197

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[galaxyproject/galaxy] 0624a0: remove macos testing
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0624a043a73f1a16fc36621b1c61a5cf52c67ba4 https://github.com/galaxyproject/galaxy/commit/0624a043a73f1a16fc36621b1c61… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M .travis.yml Log Message: ----------- remove macos testing Commit: 22b0542d0bb7a2f88b1503b53a8950d236be0f25 https://github.com/galaxyproject/galaxy/commit/22b0542d0bb7a2f88b1503b53a89… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #4631 from martenson/disable-macos-travis disable MacOS CI on travis Compare: https://github.com/galaxyproject/galaxy/compare/153dfaa68080...22b0542d0bb7

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[galaxyproject/galaxy] 7d2cd2: replace colon and comma in role names since they a...
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7d2cd2272299b94b01c8d22c0c1f7f5cbfb2b91a https://github.com/galaxyproject/galaxy/commit/7d2cd2272299b94b01c8d22c0c1f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- replace colon and comma in role names since they are also separators Commit: 3b4bd3bb6fa922c9e2156fe87660de409acf3367 https://github.com/galaxyproject/galaxy/commit/3b4bd3bb6fa922c9e2156fe87660… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- make client Commit: 153dfaa68080481607a90731c5a0825754cf713d https://github.com/galaxyproject/galaxy/commit/153dfaa68080481607a90731c5a0… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- Merge pull request #4621 from martenson/library-sharing-roles replace separators in library sharing role names Compare: https://github.com/galaxyproject/galaxy/compare/ea7b27443715...153dfaa68080

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[galaxyproject/galaxy] 860f0a: Some function description updates
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 860f0ab6ba6c45c98b5c9f3f002096cc9ef0c7b6 https://github.com/galaxyproject/galaxy/commit/860f0ab6ba6c45c98b5c9f3f0020… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Some function description updates Commit: e3e26ae202369876eb1523562b2582f2a15495cb https://github.com/galaxyproject/galaxy/commit/e3e26ae202369876eb1523562b25… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Updated a comment Commit: 3cca06a153253f65f752d1f80aae2fd2e3cf221e https://github.com/galaxyproject/galaxy/commit/3cca06a153253f65f752d1f80aae… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- updated a comment. Commit: 604fdde4248dc2d7f261e63449ab5530463058a3 https://github.com/galaxyproject/galaxy/commit/604fdde4248dc2d7f261e63449ab… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- typo Commit: ea7b27443715730597e273b315dce875910738ce https://github.com/galaxyproject/galaxy/commit/ea7b27443715730597e273b315dc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #4629 from VJalili/patch-3 Updated function description and fix some typos Compare: https://github.com/galaxyproject/galaxy/compare/fe88dab79b0b...ea7b27443715

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[galaxyproject/galaxy] 69af37: Typo fix
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 69af37f653569117371413bfadd06e5428486526 https://github.com/galaxyproject/galaxy/commit/69af37f653569117371413bfadd0… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Typo fix Commit: fe88dab79b0b47245c079ebc372563392c917f30 https://github.com/galaxyproject/galaxy/commit/fe88dab79b0b47245c079ebc3725… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Merge pull request #4628 from VJalili/patch-3 Typo fix Compare: https://github.com/galaxyproject/galaxy/compare/540322e38856...fe88dab79b0b

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[galaxyproject/galaxy] 1c1ca9: Fix loose->lose in help text for library dataset v...
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1c1ca9bd91298e2265cb4a9e6982f18c3e4ae39d https://github.com/galaxyproject/galaxy/commit/1c1ca9bd91298e2265cb4a9e6982… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- Fix loose->lose in help text for library dataset view. Commit: d5aba7da15f5a05821e7659828bd701fd438769e https://github.com/galaxyproject/galaxy/commit/d5aba7da15f5a05821e7659828bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/util/maf_utilities.py Log Message: ----------- Three more looses. Commit: 7831b9889897e1d51ba2004cc8fcc5df079c0594 https://github.com/galaxyproject/galaxy/commit/7831b9889897e1d51ba2004cc8fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- Occurred, spelling. Commit: 0ea6272f5d35a769bc63a4706c503793fa903fe2 https://github.com/galaxyproject/galaxy/commit/0ea6272f5d35a769bc63a4706c50… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js Log Message: ----------- More spelling. Commit: 540322e38856cc86a4a3d91aa3ac670418378d90 https://github.com/galaxyproject/galaxy/commit/540322e38856cc86a4a3d91aa3ac… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/util/maf_utilities.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js Log Message: ----------- Merge pull request #4626 from dannon/loose_use Misc. spelling/grammatical error fixes. Compare: https://github.com/galaxyproject/galaxy/compare/64af1bd9e962...540322e38856

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