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

[galaxyproject/galaxy] b12b95: Attempted fix for transiently failing API test_job...
by GitHub 30 Apr '17

30 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b12b951e91e6b8472f81d73f184c40aac7f9aad8 https://github.com/galaxyproject/galaxy/commit/b12b951e91e6b8472f81d73f184c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Attempted fix for transiently failing API test_jobs introduced in #3619. A couple things need to occur while the jobs are "running" and it seems that 60 seconds wasn't enough time to sleep for all that to happen on Jenkins. I checked the timing in the raw logs (they are for some reasons being filtered out in the Jenkins display of the XUnit) - and indeed the jobs are properly sleeping the correct amount of time but the client API calls need some more time it seems. My initial thought was maybe the jobs were being interrupted or something - and that does not appear to be the case. Commit: ffed281c33be5bcb1006cd3e94055fa01e5c3d18 https://github.com/galaxyproject/galaxy/commit/ffed281c33be5bcb1006cd3e9405… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-30 (Sun, 30 Apr 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Merge pull request #3988 from jmchilton/job_test_timing_improvements Attempted fix for transiently failing API test_jobs introduced in #3619. Compare: https://github.com/galaxyproject/galaxy/compare/c93afcec64d5...ffed281c33be

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[galaxyproject/galaxy] 85a9b3: Setup framework for retrying failed Selenium tests...
by GitHub 28 Apr '17

28 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85a9b37d80fcc503d674e4f3322b9e618f5e87c5 https://github.com/galaxyproject/galaxy/commit/85a9b37d80fcc503d674e4f3322b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh M run_tests.sh M test/selenium_tests/framework.py Log Message: ----------- Setup framework for retrying failed Selenium tests. - By default this won't occur locally, but you can set GALAXY_TEST_SELENIUM_RETRIES to a non-zero number to enable auto retrying tests that many times. - Capture the stack trace in the Selenium test error report directory - this will be useful for debugging problems that may fail once but pass on a subsequence attempt. Jenkins now captures these directories and includes their content in the test reports. - Document the Selenium test error report directory in run_tests.sh as well as this new retry variable. - Update the Jenkins test script to set this new variable to 1 so transient failures break the build much less frequently. Commit: c93afcec64d5f4036bf75011c35b4c8497068238 https://github.com/galaxyproject/galaxy/commit/c93afcec64d5f4036bf75011c35b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh M run_tests.sh M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #3993 from jmchilton/selenium_fixes_10 Setup framework for retrying failed Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/a32e78585c84...c93afcec64d5

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[galaxyproject/usegalaxy-playbook] dc487e: Increase Main uWSGI buffer-size to hopefully elimi...
by GitHub 28 Apr '17

28 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dc487e2a2f585554dc5140660c2536e505eedca9 https://github.com/galaxyproject/usegalaxy-playbook/commit/dc487e2a2f585554… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/uwsgi.ini.j2 Log Message: ----------- Increase Main uWSGI buffer-size to hopefully eliminate (104: Connection reset by peer) while reading response header from upstream

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[galaxyproject/usegalaxy-playbook] 55280c: Main mutable configs
by GitHub 28 Apr '17

28 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 55280cc37e5906cc0f2cb74caca0c293fe5d2bd6 https://github.com/galaxyproject/usegalaxy-playbook/commit/55280cc37e5906cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Main mutable configs

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[galaxyproject/usegalaxy-playbook] 7684bd: Increase Test uWSGI buffer-size to hopefully elimi...
by GitHub 28 Apr '17

28 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7684bd4ff0f0222dbb82a16c95cc4b9dc606e9a7 https://github.com/galaxyproject/usegalaxy-playbook/commit/7684bd4ff0f0222d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M env/test/templates/galaxy/config/uwsgi.ini.j2 Log Message: ----------- Increase Test uWSGI buffer-size to hopefully eliminate (104: Connection reset by peer) while reading response header from upstream

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[galaxyproject/infrastructure-playbook] 50f9fe: Add a key to jenkins
by GitHub 28 Apr '17

28 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 50f9fef3797dd8706f85a78c16ce8537ef5b4eb9 https://github.com/galaxyproject/infrastructure-playbook/commit/50f9fef3797… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml Log Message: ----------- Add a key to jenkins

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[galaxyproject/galaxy] 414abb: Add a validator that ensures a dataset's extra_fil...
by GitHub 28 Apr '17

28 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 414abb00d1e5b25516d9ad714575b591ea503c2c https://github.com/galaxyproject/galaxy/commit/414abb00d1e5b25516d9ad714575… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Add a validator that ensures a dataset's extra_files_path directory exists and is non-empty Commit: f3c8edea83e537281e830fe8fa6d9de3da836489 https://github.com/galaxyproject/galaxy/commit/f3c8edea83e537281e830fe8fa6d… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Use abstract dataset functions for testing Commit: 4a5c8823173a125fd3eade1693a23ba6e6b73aa5 https://github.com/galaxyproject/galaxy/commit/4a5c8823173a125fd3eade1693a2… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Remove unused import Commit: 5b9bc76cac7f8ad4dd859af97e9ae1199cf6e62a https://github.com/galaxyproject/galaxy/commit/5b9bc76cac7f8ad4dd859af97e9a… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Change validator name Commit: a32e78585c843517d5ae091ce03e08427214f2ff https://github.com/galaxyproject/galaxy/commit/a32e78585c843517d5ae091ce03e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Merge pull request #3918 from gregvonkuster/fpv Add a validator that ensures a dataset's extra_files_path Compare: https://github.com/galaxyproject/galaxy/compare/2b09fe149dc7...a32e78585c84

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[galaxyproject/galaxy] 54b9d7: Use the configured tool_path when loading data man...
by GitHub 28 Apr '17

28 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 54b9d7ac10535e56caf9389da00125664a9a779e https://github.com/galaxyproject/galaxy/commit/54b9d7ac10535e56caf9389da001… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Use the configured tool_path when loading data managers. Commit: 92f3841bee3a473b85661779790a40f773b0f86d https://github.com/galaxyproject/galaxy/commit/92f3841bee3a473b85661779790a… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Remove dev remnant. Commit: 6e1daab992c27fa22b7682bcf5609fcea75aa800 https://github.com/galaxyproject/galaxy/commit/6e1daab992c27fa22b7682bcf560… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Fix errors discovered by Nicola. Commit: 5fd7f8bdf728356ee1aeafb36996392dd91b9e46 https://github.com/galaxyproject/galaxy/commit/5fd7f8bdf728356ee1aeafb36996… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Explicit is better than implicit. Commit: 2b09fe149dc7b65718f4a74f288cfe27cf6fcf82 https://github.com/galaxyproject/galaxy/commit/2b09fe149dc7b65718f4a74f288c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Merge pull request #3989 from davebx/fix_managers Use the configured tool_path when loading data managers Compare: https://github.com/galaxyproject/galaxy/compare/dab18fb2387d...2b09fe149dc7

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[galaxyproject/galaxy] 417d1d: Initial commit to get this rolling, library-securi...
by GitHub 28 Apr '17

28 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 417d1d251e7e7c735a8d4aefd53edcec941db1f4 https://github.com/galaxyproject/galaxy/commit/417d1d251e7e7c735a8d4aefd53e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M CITATION M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js Log Message: ----------- Initial commit to get this rolling, library-security does not exist and needs to be created, among others. Commit: bc870cdf66ecaaf218cd20debdbcc68b20e7f959 https://github.com/galaxyproject/galaxy/commit/bc870cdf66ecaaf218cd20debdbc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Update galaxy.ini.sample and config. Commit: 11829c4f9df12cf8e8e3e7a14dc11e9a02afe6a4 https://github.com/galaxyproject/galaxy/commit/11829c4f9df12cf8e8e3e7a14dc1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/managers/configuration.py M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- More defaults, these should be consolidated. Commit: e12c07cacd12fbf4a2fb148242be5bea7c13221e https://github.com/galaxyproject/galaxy/commit/e12c07cacd12fbf4a2fb148242be… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako Log Message: ----------- Use config.py for defaults used in managers/configuration. Commit: ed1d19a967989416caebd3588fe6b8b6460764e2 https://github.com/galaxyproject/galaxy/commit/ed1d19a967989416caebd3588fe6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Update reports and toolshed app configs as well. Commit: 72cd0ba00ad05793751105dccf434c9868791b2a https://github.com/galaxyproject/galaxy/commit/72cd0ba00ad05793751105dccf43… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Adjust link to the new Galaxy HUB site Commit: b4fda2ccd49fd7b406a5521bce3243ff6ffb7950 https://github.com/galaxyproject/galaxy/commit/b4fda2ccd49fd7b406a5521bce32… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Merge pull request #16 from bgruening/wf_link /learn/advanced-workflow/variables-edit Commit: ea3796152a01aad87f0585bf83ceb661392ba4d4 https://github.com/galaxyproject/galaxy/commit/ea3796152a01aad87f0585bf83ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Replace wiki.galaxyproject.org links in /lib Commit: 04a32064f1d553c01828092b445175a9c7d8a53d https://github.com/galaxyproject/galaxy/commit/04a32064f1d553c01828092b4451… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/viz/phyloviz.js M static/maps/mvc/citation/citation-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-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/viz/phyloviz.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/citation/citation-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-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/viz/phyloviz.js Log Message: ----------- Update wiki.galaxyproject.org links in client Commit: a5143ce7a86cb64c81b0ffa36a90742b872cec15 https://github.com/galaxyproject/galaxy/commit/a5143ce7a86cb64c81b0ffa36a90… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/data_manager/index.mako Log Message: ----------- Convert wiki.galaxyproject.org links in templates Commit: 29aa00e42129bec564a9f1009547e3b740b29709 https://github.com/galaxyproject/galaxy/commit/29aa00e42129bec564a9f1009547… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .travis.yml M CONTRIBUTING.md M README.rst M client/galaxy/scripts/apps/analysis.js M 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client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-table.js A client/galaxy/scripts/mvc/upload/collection/collection-row.js A client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-view.js A client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js A client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/ui/paired-collection-creator.less M client/galaxy/style/less/upload.less M client/package.json M 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test/integration/workflow_handler_configuration_job_conf.xml A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml M test/qunit/package.json M test/qunit/test-data/paired-collection-creator.data.js M test/qunit/tests/ui_tests.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/filters/trimmer.py M tools/filters/trimmer.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into wiki-to-hub Commit: 0dd75e6cdd985ec3711987ef8adb3fe6365b8501 https://github.com/galaxyproject/galaxy/commit/0dd75e6cdd985ec3711987ef8adb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako A templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Attempt to rectify bad merge. Commit: 05e81192bd91559876da1a82b734c7e49e15f43e https://github.com/galaxyproject/galaxy/commit/05e81192bd91559876da1a82b734… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M test/qunit/tests/form_tests.js Log Message: ----------- Update tool form qunit test text. Commit: 89e692d980965f5a1963818180ccaf62ae2c207f https://github.com/galaxyproject/galaxy/commit/89e692d980965f5a1963818180cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M CITATION M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M config/galaxy.ini.sample M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/workflow/workflow-forms.js M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Tweaks for @nsoranzo. Commit: 5fe7b7208c8668b7d4dd9dc31568c77a0a8c2562 https://github.com/galaxyproject/galaxy/commit/5fe7b7208c8668b7d4dd9dc31568… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Fix support link Commit: f0740136831623adf8b2c1fe9ed17dbf4327ebc4 https://github.com/galaxyproject/galaxy/commit/f0740136831623adf8b2c1fe9ed1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M config/galaxy.ini.sample Log Message: ----------- Small tweaks for data-libraries URLS Commit: dab18fb2387d737f859637bbd37d9b0ce3ec658c https://github.com/galaxyproject/galaxy/commit/dab18fb2387d737f859637bbd37d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M CITATION M client/galaxy/scripts/mvc/citation/citation-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-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/viz/phyloviz.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M static/maps/mvc/citation/citation-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-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/viz/phyloviz.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/mvc/citation/citation-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-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/viz/phyloviz.js M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako M test/qunit/tests/form_tests.js Log Message: ----------- Merge branch 'wiki-to-hub' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/760160a02cd9...dab18fb2387d

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[galaxyproject/galaxy] 8b21e6: Improve implicit workflow connection test case.
by GitHub 28 Apr '17

28 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b21e651969fff8cff41f736c47312f099cc5ee9 https://github.com/galaxyproject/galaxy/commit/8b21e651969fff8cff41f736c473… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Improve implicit workflow connection test case. I think https://jenkins.galaxyproject.org/job/docker-api/7316/testReport/junit/api.… may be the first time I have seen it fail - but still it has some other problems. - Eliminate the sleep - instead wait on explicitly on the desired condition (first two jobs are complete and the workflow is ready for unpause). This is likely why the test case failed. - Improve the other assertions to provide more details in the test case ever fails again. Commit: 760160a02cd925168eefb0b05a4471bd5dbc7b61 https://github.com/galaxyproject/galaxy/commit/760160a02cd925168eefb0b05a44… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #3991 from jmchilton/workflow_connection_test_case_improvement Improve implicit workflow connection test case. Compare: https://github.com/galaxyproject/galaxy/compare/7ba3662d29f0...760160a02cd9

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