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

[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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