- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 85a9b3: Setup framework for retrying failed Selenium tests...
by GitHub 29 Apr '17

29 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-data/new_labels_1.txt A test-data/new_labels_2.txt A test-data/new_labels_bad_1.txt A test-data/new_labels_bad_2.txt M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/api_asserts.py M test/base/data/test_workflow_pause.ga M test/base/driver_util.py M test/base/populators.py M test/docker/base/run_test_wrapper.sh M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml A test/functional/tools/identifier_multiple_in_conditional.xml A test/functional/tools/identifier_multiple_in_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py A test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_workflow_handler_configuration.py A 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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[galaxyproject/infrastructure-playbook] 97fe8f: Two more redirects for hub
by GitHub 28 Apr '17

28 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 97fe8f28d0e9f91fd422db185706d1e39214c9e4 https://github.com/galaxyproject/infrastructure-playbook/commit/97fe8f28d0e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Two more redirects for hub

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[galaxyproject/infrastructure-playbook] 32d21f: Admin/Interface redirect
by GitHub 28 Apr '17

28 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 32d21f9efdbd2ca03532d0fa38184fde4db21d89 https://github.com/galaxyproject/infrastructure-playbook/commit/32d21f9efdb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Admin/Interface redirect

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[galaxyproject/galaxy] 4b5311: Add missing imports for documentation builds
by GitHub 27 Apr '17

27 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b531179b0a19a45902f40f49e823cf5260bbd56 https://github.com/galaxyproject/galaxy/commit/4b531179b0a19a45902f40f49e82… Author: Athos Ribeiro <athoscr(a)fedoraproject.org> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Add missing imports for documentation builds As mentioned in #3075, the build requirements for the project documentation were only listed in the Jenkins job. This commit adds those missing requirements to the project. Note that they should also be removed from the Jenkins build * fixes #3075 Commit: 647b4901c30d356f13f851a76c2a7c7ed8bfd808 https://github.com/galaxyproject/galaxy/commit/647b4901c30d356f13f851a76c2a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M Makefile M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- move reqs to dev-requirements and touch makefile Commit: d42fc9ae71b26caed30d6b904681a6b2065febbc https://github.com/galaxyproject/galaxy/commit/d42fc9ae71b26caed30d6b904681… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A 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test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_fasta.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.py R tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/pasteWrapper.xml M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/trimmer.xml M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.py M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.py M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.py M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.py M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.py M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.py M tools/maf/vcf_to_maf_customtrack.xml M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/fastq_gen_conv.xml M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.xml M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge branch 'dev' into fix_documentation_build Commit: 7edfe39f20024f161a30be14406c0baa2a9807bf https://github.com/galaxyproject/galaxy/commit/7edfe39f20024f161a30be14406c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M Makefile Log Message: ----------- fix makefile help for docs thanks nsoranzo Commit: 7ba3662d29f0f8d9c6a24ea3fa66eee421f6059d https://github.com/galaxyproject/galaxy/commit/7ba3662d29f0f8d9c6a24ea3fa66… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M Makefile M lib/galaxy/dependencies/dev-requirements.txt Log Message: ----------- Merge pull request #3104 from athos-ribeiro/fix_documentation_build Add missing imports for documentation builds Compare: https://github.com/galaxyproject/galaxy/compare/26afd36a4d13...7ba3662d29f0

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[galaxyproject/galaxy] f369ab: Add login redirect for backbone router
by GitHub 27 Apr '17

27 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f369ab0668fcedf572346553d3e0b70564f81796 https://github.com/galaxyproject/galaxy/commit/f369ab0668fcedf572346553d3e0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add login redirect for backbone router Commit: e431af074f4bb8a0d70f6a387af2654bfa21790b https://github.com/galaxyproject/galaxy/commit/e431af074f4bb8a0d70f6a387af2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Redirect through push Commit: 26afd36a4d1336825fa47e2e8f3921c4ee8e1486 https://github.com/galaxyproject/galaxy/commit/26afd36a4d1336825fa47e2e8f39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge remote-tracking branch 'guerler/login_routes' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3e14cd532074...26afd36a4d13

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[galaxyproject/galaxy] 60e000: Fix edge case for workflow mapping handling when t...
by GitHub 27 Apr '17

27 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 60e00088c8b27c04734c7f7adb3cdae6a9a9580f https://github.com/galaxyproject/galaxy/commit/60e00088c8b27c04734c7f7adb3c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix edge case for workflow mapping handling when tools not available. Fixes #3960. Commit: 3fcd78564630fae9c4670cfbe198572f94f688c0 https://github.com/galaxyproject/galaxy/commit/3fcd78564630fae9c4670cfbe198… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #3962 from jmchilton/workflow_editor_mapping_test [17.01] Fix edge case for workflow mapping handling when tools not available. Compare: https://github.com/galaxyproject/galaxy/compare/f3c134abcb04...3fcd78564630

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[galaxyproject/galaxy] 78c263: Udpate Babel to a version compat. with sphinx.
by GitHub 27 Apr '17

27 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78c263ac7c6beb1b93269f252897b0dd6336b450 https://github.com/galaxyproject/galaxy/commit/78c263ac7c6beb1b93269f252897… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Udpate Babel to a version compat. with sphinx. Commit: 3e14cd532074d190def283ed2cce61ae22c0eee9 https://github.com/galaxyproject/galaxy/commit/3e14cd532074d190def283ed2cce… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #3986 from jmchilton/babel_update Udpate Babel to a version compat. with sphinx. Compare: https://github.com/galaxyproject/galaxy/compare/92d93c7ef964...3e14cd532074

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[galaxyproject/galaxy] 852fb4: Leasing container sometimes breaks things in docke...
by GitHub 27 Apr '17

27 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 852fb42945bc5176d15b22dbe624523b7b571035 https://github.com/galaxyproject/galaxy/commit/852fb42945bc5176d15b22dbe624… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-12-03 (Sat, 03 Dec 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Leasing container sometimes breaks things in docker galaxy Commit: 92d93c7ef96452ba343a43502fe519e0dea3f8bf https://github.com/galaxyproject/galaxy/commit/92d93c7ef96452ba343a43502fe5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Merge pull request #3263 from zfrenchee/patch-1 Azure - Leasing container sometimes breaks things in docker galaxy Compare: https://github.com/galaxyproject/galaxy/compare/291426a5dcd7...92d93c7ef964

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[galaxyproject/galaxy] c0fd3c: Display input parameters default value for runtime...
by GitHub 27 Apr '17

27 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c0fd3c7c6ddef01b0546b485a1a4e88d215042e2 https://github.com/galaxyproject/galaxy/commit/c0fd3c7c6ddef01b0546b485a1a4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-19 (Wed, 19 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Display input parameters default value for runtime values Commit: fba860f689d1af5e6727a946e20e1521f83620ed https://github.com/galaxyproject/galaxy/commit/fba860f689d1af5e6727a946e20e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-19 (Wed, 19 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Use local flag to handle runtime values Commit: 291426a5dcd7941e1d6711b5926418bf0dab0c4c https://github.com/galaxyproject/galaxy/commit/291426a5dcd7941e1d6711b59264… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3943 from guerler/show_default_value_for_runtime_values Show default value for runtime values Compare: https://github.com/galaxyproject/galaxy/compare/b7a8bea3cd67...291426a5dcd7

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[galaxyproject/galaxy] be7d12: Fix Travix builds which use flake8-docstrings
by GitHub 26 Apr '17

26 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be7d1294fd69618cbd415df4c562ce2c4ef88808 https://github.com/galaxyproject/galaxy/commit/be7d1294fd69618cbd415df4c562… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M tox.ini Log Message: ----------- Fix Travix builds which use flake8-docstrings flake8-docstrings is broken due to the release of pydocstyle 2.0.0 (see https://gitlab.com/pycqa/flake8-docstrings/issues/19 ), so temporarily add an extra dep in tox.ini to pin it. Commit: b7a8bea3cd67b8e889f44fd88b8529e47fe53cbc https://github.com/galaxyproject/galaxy/commit/b7a8bea3cd67b8e889f44fd88b85… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #3981 from nsoranzo/fix_py27-lint_build Fix Travix builds which use flake8-docstrings Compare: https://github.com/galaxyproject/galaxy/compare/d398c90dbd70...b7a8bea3cd67

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[galaxyproject/infrastructure-playbook] ebd39c: Redirects for both GetGalaxy and Get%20Galaxy
by GitHub 26 Apr '17

26 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ebd39cdbf1066fd30b8e4df370f7fb7d291f5213 https://github.com/galaxyproject/infrastructure-playbook/commit/ebd39cdbf10… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Redirects for both GetGalaxy and Get%20Galaxy

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[galaxyproject/galaxy] 8e0be5: [17.01] Fix collection operations in workflows.
by GitHub 26 Apr '17

26 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8e0be5089c63d94b841babfffcd70f2d8ab9b27c https://github.com/galaxyproject/galaxy/commit/8e0be5089c63d94b841babfffcd7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py M test/api/test_workflows.py Log Message: ----------- [17.01] Fix collection operations in workflows. Due to a couple bugs things weren't being delayed correctly for some of these tools in some workflows. Commit: 9234420cd770661b58ee91051015e9580505ca47 https://github.com/galaxyproject/galaxy/commit/9234420cd770661b58ee91051015… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.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/ui/ui-select-content.js M test/qunit/tests/ui_tests.js Log Message: ----------- Fix multiple collection reductions on multiple data parameters. Was introduced in #805 but there was a small bug (maybe a last minute change before opening the PR) in the client code so this never was exposed to the users the way it was intended. This should largely negate the need for hacks such as in cuffmerge that allow multiple list collections in addition to main multiple data selector. xref galaxyproject/tools-iuc#1225. Commit: 6c82cf3c22445e97621429591e72951a0941104e https://github.com/galaxyproject/galaxy/commit/6c82cf3c22445e97621429591e72… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M templates/user/logout.mako Log Message: ----------- Remove logout hack -- logout should always be a redirect or full page action, leaving it free of any JS side-effects this would be necessary for. Commit: 779156111a117f5513ae10af04d0b12052627a32 https://github.com/galaxyproject/galaxy/commit/779156111a117f5513ae10af04d0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- add two tools from str_fm repository to galaxy module whitelist we broke them so we are fixing it Commit: 7e4f805d479acc8f362ed651330f91fb8e2c9c40 https://github.com/galaxyproject/galaxy/commit/7e4f805d479acc8f362ed651330f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #3848 from jmchilton/collection_operation_check_inputs_bug [17.01] Fix collection operations in workflows. Commit: 02bdc7495d80d4fb085de26e07e200a95a20ec56 https://github.com/galaxyproject/galaxy/commit/02bdc7495d80d4fb085de26e07e2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.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/ui/ui-select-content.js M test/qunit/tests/ui_tests.js Log Message: ----------- Merge pull request #3875 from jmchilton/fix_multi_collection_multi_data_param_reductions [17.01] Fix multiple collection reductions on multiple data parameters. Commit: 1d0ace1452aa9d5e334ee89aca07fa401db37806 https://github.com/galaxyproject/galaxy/commit/1d0ace1452aa9d5e334ee89aca07… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3973 from martenson/strfm-fix [17.01] add two tools from str_fm repository to galaxy module whitelist Commit: f75a72aee80680537dad802944585d6007d237c9 https://github.com/galaxyproject/galaxy/commit/f75a72aee80680537dad80294458… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- Rework logic for remote_user/session handling. This should fix issues @erasche reported regarding (null)(a)example.org users. Commit: 09ba27543b8726fb61cd998bf9614018a9ba7316 https://github.com/galaxyproject/galaxy/commit/09ba27543b8726fb61cd998bf961… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Slightly adjust logic for discarding headers; this shouldn't try to throw away empty headers anymore. Commit: b779977cdc31d50183e7b0f356e9489a43eb755d https://github.com/galaxyproject/galaxy/commit/b779977cdc31d50183e7b0f356e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Slightly improve error message under remote auth with anon session attempt. Commit: eb9a940a2dd69574b5fbaca06ffdc9beea4d4153 https://github.com/galaxyproject/galaxy/commit/eb9a940a2dd69574b5fbaca06ffd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M templates/user/logout.mako Log Message: ----------- Put back old hack; necessary for now. Commit: f3c134abcb04ee2885f247ba79e95a354e4bb32b https://github.com/galaxyproject/galaxy/commit/f3c134abcb04ee2885f247ba79e9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #3976 from dannon/fix_logout [17.01] Remote user logout fixes, rework header handling a bit. Commit: d398c90dbd70fff91a672935997bc21e949e8767 https://github.com/galaxyproject/galaxy/commit/d398c90dbd70fff91a672935997b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M static/maps/mvc/ui/ui-select-content.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/ui/ui-select-content.js M test/api/test_workflows.py M test/qunit/tests/ui_tests.js Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: static/maps/mvc/ui/ui-select-content.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/ui/ui-select-content.js Compare: https://github.com/galaxyproject/galaxy/compare/740d85a6a6f8...d398c90dbd70

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[galaxyproject/galaxy] 6c82cf: Remove logout hack -- logout should always be a re...
by GitHub 26 Apr '17

26 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 6c82cf3c22445e97621429591e72951a0941104e https://github.com/galaxyproject/galaxy/commit/6c82cf3c22445e97621429591e72… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M templates/user/logout.mako Log Message: ----------- Remove logout hack -- logout should always be a redirect or full page action, leaving it free of any JS side-effects this would be necessary for. Commit: f75a72aee80680537dad802944585d6007d237c9 https://github.com/galaxyproject/galaxy/commit/f75a72aee80680537dad80294458… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- Rework logic for remote_user/session handling. This should fix issues @erasche reported regarding (null)(a)example.org users. Commit: 09ba27543b8726fb61cd998bf9614018a9ba7316 https://github.com/galaxyproject/galaxy/commit/09ba27543b8726fb61cd998bf961… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Slightly adjust logic for discarding headers; this shouldn't try to throw away empty headers anymore. Commit: b779977cdc31d50183e7b0f356e9489a43eb755d https://github.com/galaxyproject/galaxy/commit/b779977cdc31d50183e7b0f356e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Slightly improve error message under remote auth with anon session attempt. Commit: eb9a940a2dd69574b5fbaca06ffdc9beea4d4153 https://github.com/galaxyproject/galaxy/commit/eb9a940a2dd69574b5fbaca06ffd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M templates/user/logout.mako Log Message: ----------- Put back old hack; necessary for now. Commit: f3c134abcb04ee2885f247ba79e95a354e4bb32b https://github.com/galaxyproject/galaxy/commit/f3c134abcb04ee2885f247ba79e9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #3976 from dannon/fix_logout [17.01] Remote user logout fixes, rework header handling a bit. Compare: https://github.com/galaxyproject/galaxy/compare/1d0ace1452aa...f3c134abcb04

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[galaxyproject/galaxy] 80324d: 17.01 version of rstudio
by GitHub 26 Apr '17

26 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 80324d08a5270b4961f706b1951c3b0f8c7ffe57 https://github.com/galaxyproject/galaxy/commit/80324d08a5270b4961f706b1951c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- 17.01 version of rstudio Commit: b1c6d3363d6bccbc53c689543efa4460d796c814 https://github.com/galaxyproject/galaxy/commit/b1c6d3363d6bccbc53c689543efa… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample Log Message: ----------- remove old versions Commit: 60a05c1811c3716e47c28ecec6f2ab25d3b56d97 https://github.com/galaxyproject/galaxy/commit/60a05c1811c3716e47c28ecec6f2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- more touch-ups and easier vimdiffing with jupyter configs Commit: 740d85a6a6f8b3877faf75fa3488a1a1d2a10c1e https://github.com/galaxyproject/galaxy/commit/740d85a6a6f8b3877faf75fa3488… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3975 from erasche/17.05-gie-fixes 17.05 rstudio fixes / one small gie fix Compare: https://github.com/galaxyproject/galaxy/compare/c84b5725e63a...740d85a6a6f8

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[galaxyproject/galaxy] 427343: Use container-based infrastructure (sudo: false) i...
by GitHub 26 Apr '17

26 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 42734350d2e44fce1b2e699f643d755e7e4441be https://github.com/galaxyproject/galaxy/commit/42734350d2e44fce1b2e699f643d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M .travis.yml Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI Commit: c84b5725e63a3b93b5c798d23b277df27d63cd6f https://github.com/galaxyproject/galaxy/commit/c84b5725e63a3b93b5c798d23b27… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #3977 from nsoranzo/travis Use container-based infrastructure (sudo: false) in TravisCI Compare: https://github.com/galaxyproject/galaxy/compare/910c22b7a1c7...c84b5725e63a

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[galaxyproject/galaxy] ec22b1: Fixes to get IEs working on Mac OS X.
by GitHub 26 Apr '17

26 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ec22b1d3ecd85cff65d232d0997703ee096d5ce1 https://github.com/galaxyproject/galaxy/commit/ec22b1d3ecd85cff65d232d09977… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Fixes to get IEs working on Mac OS X. - Fix logic error related to config parsing (OS non-specific). - Don't trust GatewayAddress from Docker if on Mac OS X - it is probably a Docker host VM specific address. - Update sqlite dependency for the newest version of Node available from Mac OS X Homebrew. - Add a little blurb about how to configure galaxy_infrastructure_url in this case. Commit: 910c22b7a1c759a651186f13e6c6707d91becfec https://github.com/galaxyproject/galaxy/commit/910c22b7a1c759a651186f13e6c6… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Merge pull request #3978 from jmchilton/ie_for_mac_os_x_fixes Fixes to get GIEs working on Mac OS X. Compare: https://github.com/galaxyproject/galaxy/compare/2f518e5ee444...910c22b7a1c7

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[galaxyproject/galaxy] e9eba8: Small selenium hack.
by GitHub 25 Apr '17

25 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e9eba8625d7922a9e7e7f759fc797d4fab8ddb7d https://github.com/galaxyproject/galaxy/commit/e9eba8625d7922a9e7e7f759fc79… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Small selenium hack. Commit: 2f518e5ee4444e3a95b6f4967366a1b38b1ca3b4 https://github.com/galaxyproject/galaxy/commit/2f518e5ee4444e3a95b6f4967366… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #3967 from jmchilton/selenium_fixes_8 Small selenium hack to fix occasionally failing collection upload tests. Compare: https://github.com/galaxyproject/galaxy/compare/399c7f061cef...2f518e5ee444

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