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

[galaxyproject/galaxy] fd90d7: Cleanup delayed action in history-view.js.
by GitHub 03 Oct '17

03 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fd90d764531cec90347cb53699914d4f3fcffa8f https://github.com/galaxyproject/galaxy/commit/fd90d764531cec90347cb5369991… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js Log Message: ----------- Cleanup delayed action in history-view.js. Might fix #4698 but who knows. Commit: e132521255ca1349a556a337ee8e6b031bb1c382 https://github.com/galaxyproject/galaxy/commit/e132521255ca1349a556a337ee8e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Selenium - bug fix for grabbing history name during transition. xref https://jenkins.galaxyproject.org/job/selenium/654/artifact/654-test-errors… Commit: 2e3c6e8941b72aedf9704435e9aa83bd602aa97d https://github.com/galaxyproject/galaxy/commit/2e3c6e8941b72aedf9704435e9aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Selenium - bug fix for checking workflow names on workflow index page. xref https://jenkins.galaxyproject.org/job/selenium/654/artifact/654-test-errors… Commit: 27ef24601ca1147cfa51990a7460d4f3ac49e829 https://github.com/galaxyproject/galaxy/commit/27ef24601ca1147cfa51990a7460… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix typo. Commit: cce59aeb558873c1229f91dca6d21ee11da33d08 https://github.com/galaxyproject/galaxy/commit/cce59aeb558873c1229f91dca6d2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py Log Message: ----------- Remove deprecated method click_hda_title in navigates_galaxy. Commit: 3f28f847703b18e6098d33eabe2fa46bcacc1692 https://github.com/galaxyproject/galaxy/commit/3f28f847703b18e6098d33eabe2f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- NavigatesGalaxy class docs. Commit: 28c8644f02a6080e0305b6c8caf46bd15c2517f4 https://github.com/galaxyproject/galaxy/commit/28c8644f02a6080e0305b6c8caf4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_panel.py Log Message: ----------- More history panel abstractions in NavigatesGalaxy. Commit: afaea964cf0e980f41aa0d9c4a259efbf6613144 https://github.com/galaxyproject/galaxy/commit/afaea964cf0e980f41aa0d9c4a25… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M test/selenium_tests/framework.py M test/selenium_tests/test_registration.py Log Message: ----------- Selenium - cleanup duplication of DEFAULT_PASSWORD variable. Commit: c9915fc7e6617b8c8f0b3103028008e5f37e79d1 https://github.com/galaxyproject/galaxy/commit/c9915fc7e6617b8c8f0b31030280… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Switch to configurable, scaling approach to Selenium timeouts. Implement different "WAIT_TYPES" and try to sleep for different amounts of time based on what is being waited for. Replace sleep statements in addition to Selenium wait on statements. Commit: 14d4367cc47720d2a8c24250707655d9f40687fd https://github.com/galaxyproject/galaxy/commit/14d4367cc47720d2a8c242507076… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Allow forcing a particular user for some Selenium tests. Commit: 395eefcbb250ea682f27b4056a48ed416abd935c https://github.com/galaxyproject/galaxy/commit/395eefcbb250ea682f27b4056a48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Selenium - implement managed_history decorator for tests. Creates and deletes a history for tests - good for tests meant to aim at production servers that need to have useful metadata and need to be cleaned up. Commit: cc3c3a9b92c64f4daffbcc6f2257c090044c7e3e https://github.com/galaxyproject/galaxy/commit/cc3c3a9b92c64f4daffbcc6f2257… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: A test-data/selenium-test-notebook.ipynb M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py A test/selenium_tests/test_jupyter.py Log Message: ----------- Implement outline of Jupyter testing. Commit: bff364753a6c3c77baa3a1a20ba3e0e2dcbc843a https://github.com/galaxyproject/galaxy/commit/bff364753a6c3c77baa3a1a20ba3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: A test/selenium_tests/test_navigates_galaxy.py Log Message: ----------- Add Selenium test case for testing bits of navigates_galaxy.py. Commit: 2d521ff927a10b1820363527a8422362e0a7bb74 https://github.com/galaxyproject/galaxy/commit/2d521ff927a10b1820363527a842… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Capture screenshots and such for setUp problems in Selenium tests as well. Commit: e709000206d516d92fb23f24e2a7179aa8b3ed22 https://github.com/galaxyproject/galaxy/commit/e709000206d516d92fb23f24e2a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M test/galaxy_selenium/navigation-data.yml Log Message: ----------- Remove unused navigation data YAML thing... Commit: 0650978a9171866aeda4be0aedbd0090fd8649ec https://github.com/galaxyproject/galaxy/commit/0650978a9171866aeda4be0aedbd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/navigation.yml M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_uploads.py Log Message: ----------- Switch to a new more structured YAML format for navigation data. Break everything into components. Commit: d685b49ef2dcea480e93c4b4ea532861a815a8e0 https://github.com/galaxyproject/galaxy/commit/d685b49ef2dcea480e93c4b4ea53… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js A test-data/selenium-test-notebook.ipynb M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py A test/selenium_tests/test_jupyter.py A test/selenium_tests/test_navigates_galaxy.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #4732 from jmchilton/selenium Selenium Overhaul Compare: https://github.com/galaxyproject/galaxy/compare/3d87afbb4174...d685b49ef2dc

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[galaxyproject/infrastructure-playbook] 80aaa8: Restore original GDC2010/GCC2011 pages.
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 80aaa80b9619f225146cebdf4538855e823e39a2 https://github.com/galaxyproject/infrastructure-playbook/commit/80aaa80b961… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M galaxyenv/templates/nginx/galaxydomains.j2 M galaxyenv/templates/nginx/galaxyproject.j2 Log Message: ----------- Restore original GDC2010/GCC2011 pages.

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[galaxyproject/usegalaxy-playbook] c89e74: Mutable configs for updated sequence utils
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c89e7450f0f4efe65ab8a906f1b054bf8bb87e4c https://github.com/galaxyproject/usegalaxy-playbook/commit/c89e7450f0f4efe6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 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 for updated sequence utils

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[galaxyproject/usegalaxy-playbook] 0a38e3: Split the mutable config backup tasks out from the...
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0a38e3f57ffecf3f54a95f5886b0001e7e8b7127 https://github.com/galaxyproject/usegalaxy-playbook/commit/0a38e3f57ffecf3f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: A env/common/backup.yml M env/common/config.yml A env/main/backup.yml A env/test/backup.yml M roles/usegalaxy/tasks/main.yml A roles/usegalaxy_backup/defaults A roles/usegalaxy_backup/tasks/main.yml Log Message: ----------- Split the mutable config backup tasks out from the usegalaxy role into a usegalaxy_backup role for faster runtimes after tool installs. Fixes #40.

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[galaxyproject/usegalaxy-playbook] b64ae9: Pull mutable configs after upgrading sequence tool...
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b64ae9b37a0d3a7837f75d414eecbf0ed7d0d338 https://github.com/galaxyproject/usegalaxy-playbook/commit/b64ae9b37a0d3a78… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Pull mutable configs after upgrading sequence tools

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[galaxyproject/usegalaxy-playbook] 762ef1: Update galaxy role
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 762ef1077115adb867ae4a74eea904d814c0edb7 https://github.com/galaxyproject/usegalaxy-playbook/commit/762ef1077115adb8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M roles/galaxyproject.galaxy/README.md M roles/galaxyproject.galaxy/meta/.galaxy_install_info M roles/galaxyproject.galaxy/tasks/dependencies.yml Log Message: ----------- Update galaxy role Commit: 1c2a0203088a9a83b5e3107ff9d375f685936b17 https://github.com/galaxyproject/usegalaxy-playbook/commit/1c2a0203088a9a83… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: 38ed456a1485acabbc0726063cf288a973d8a38a https://github.com/galaxyproject/usegalaxy-playbook/commit/38ed456a1485acab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/4cd46aea3fbf...…

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[galaxyproject/ansible-galaxy]
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/tags/0.7.4 Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] 6544db: Add --extra-index-url for explicit PyPI fetching
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 6544db9b17cc4db6cfbaf6940545fb57edc37cdf https://github.com/galaxyproject/ansible-galaxy/commit/6544db9b17cc4db6cfba… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M tasks/dependencies.yml Log Message: ----------- Add --extra-index-url for explicit PyPI fetching

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[galaxyproject/ansible-galaxy] db7efd: Change role names to match ansible galaxy
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: db7efda5860fc38ae7f82b543fd44be4a072a02d https://github.com/galaxyproject/ansible-galaxy/commit/db7efda5860fc38ae7f8… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-06-29 (Thu, 29 Jun 2017) Changed paths: M defaults/main.yml M handlers/main.yml M tasks/main.yml Log Message: ----------- Change role names to match ansible galaxy Commit: 53fd5fd243e0cb8108d6a6c008e0b0031076abd8 https://github.com/galaxyproject/ansible-galaxy/commit/53fd5fd243e0cb8108d6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M defaults/main.yml M handlers/main.yml M tasks/main.yml Log Message: ----------- Merge pull request #22 from gvlproject/master Change role names to match ansible galaxy Compare: https://github.com/galaxyproject/ansible-galaxy/compare/317e925b8dd4...53fd…

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[galaxyproject/infrastructure-playbook] 75c7cf: Update access lists
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 75c7cf09fd0194816447e8967c5ff9fd5badcf8a https://github.com/galaxyproject/infrastructure-playbook/commit/75c7cf09fd0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M galaxyenv/secret_host_vars/cvmfs1-iu0.galaxyproject.org.yml M galaxyenv/secret_host_vars/cvmfs1-psu0.galaxyproject.org.yml M galaxyenv/secret_host_vars/cvmfs1-tacc0.galaxyproject.org.yml Log Message: ----------- Update access lists

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