- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 2c4977: Separate condensed user preference form into three...
by GitHub 15 Mar '17

15 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2c49779d81b8eb2eae1e9f4dd74de7e01647f675 https://github.com/galaxyproject/galaxy/commit/2c49779d81b8eb2eae1e9f4dd74d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-preferences.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/user/user-preferences.js Log Message: ----------- Separate condensed user preference form into three components, improve route handling Commit: 84f9d3c5c9dc27af1d121e9b84504109d9291ff0 https://github.com/galaxyproject/galaxy/commit/84f9d3c5c9dc27af1d121e9b8450… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.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/user/user-preferences.js Log Message: ----------- Fix basic routing between main preference panel and individual user forms Commit: 3c31cbd21ed222060c31400eb0e0d0ea90b33ec0 https://github.com/galaxyproject/galaxy/commit/3c31cbd21ed222060c31400eb0e0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.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/user/user-preferences.js Log Message: ----------- Fix error message Commit: 88b4b7a7182fb48904d587b7a049e099169c7ccf https://github.com/galaxyproject/galaxy/commit/88b4b7a7182fb48904d587b7a049… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.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/user/user-preferences.js Log Message: ----------- Properly handle openid redirect and sign out feature Commit: ceb11577bde43e6ee61ee1c89e6c002037039510 https://github.com/galaxyproject/galaxy/commit/ceb11577bde43e6ee61ee1c89e6c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.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/user/user-preferences.js Log Message: ----------- Place row template into separate function Commit: 365c56f77f6b57c8930641864924ec9a67fdf174 https://github.com/galaxyproject/galaxy/commit/365c56f77f6b57c8930641864924… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/web/base/controllers/admin.py M static/maps/mvc/user/user-preferences.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/user/user-preferences.js Log Message: ----------- Redirect admin user manager route to js-based preference forms Commit: efa856dbb91766dbf80c447c241dd37e1a5401ca https://github.com/galaxyproject/galaxy/commit/efa856dbb91766dbf80c447c241d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M templates/grid_base.mako Log Message: ----------- Attempt to fix grid routing options Commit: 8a8603be7f697c065382d61fb0539552d15d1f3f https://github.com/galaxyproject/galaxy/commit/8a8603be7f697c065382d61fb053… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M templates/grid_base.mako Log Message: ----------- Enhance grid target handling for links Commit: cc6fa6a4c8607c0c2f33b2271a963da54756334f https://github.com/galaxyproject/galaxy/commit/cc6fa6a4c8607c0c2f33b2271a96… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/grid/grid-view.js M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M doc/source/releases/17.01_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M scripts/bootstrap_history.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js M templates/grid_base.mako A templates/webapps/galaxy/user/manage_info.mako M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into ui_pref_routing Commit: f0b03a59b51bd02a07b591900147d0e9a79053f7 https://github.com/galaxyproject/galaxy/commit/f0b03a59b51bd02a07b591900147… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py R templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Strip old user manager mako Commit: c281dd87ed83934ffe2654130d8c709892796142 https://github.com/galaxyproject/galaxy/commit/c281dd87ed83934ffe2654130d8c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js R client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.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/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'dev' into ui_pref_routing Commit: fa1f81cbcf5ac4c026bb624ee003f56405ef358e https://github.com/galaxyproject/galaxy/commit/fa1f81cbcf5ac4c026bb624ee003… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-preferences.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/user/user-preferences.js Log Message: ----------- Users -> user in menu/interface usage. Commit: 42c090cb20e82bee50b8931aeeedca4e735f766b https://github.com/galaxyproject/galaxy/commit/42c090cb20e82bee50b8931aeeed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Update users->user in the menu as well Commit: 2ee81a3faaef38547295f9a47f9f063423b40394 https://github.com/galaxyproject/galaxy/commit/2ee81a3faaef38547295f9a47f9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Client route priority is *last* Commit: b00dfc8a7b7bc739a84c5a229c161a917601d68a https://github.com/galaxyproject/galaxy/commit/b00dfc8a7b7bc739a84c5a229c16… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Remove extra empty line. Commit: 0fb9fbc3885eb11b7e49f97f6a129f9c0343e780 https://github.com/galaxyproject/galaxy/commit/0fb9fbc3885eb11b7e49f97f6a12… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/layout/menu.js.map M static/maps/mvc/user/user-preferences.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/layout/menu.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Merge pull request #18 from dannon/ui_pref_routing User->Users Commit: 6e32b0f7c119ca6c3d54a761e64f49fe6a7f8280 https://github.com/galaxyproject/galaxy/commit/6e32b0f7c119ca6c3d54a761e64f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tool/tools.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tool/tools.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/dataset/dataset-li-edit.js M static/scripts/mvc/tool/tools.js Log Message: ----------- Use routing helper to navigate to tool form Commit: 5df0187d42d19c5a930bf067a52a2ef4cf9d3ec8 https://github.com/galaxyproject/galaxy/commit/5df0187d42d19c5a930bf067a52a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/history.less M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/static/script.js A config/plugins/webhooks/demo/search/static/styles.css A cron/clean_docker_swarm_mode_services.sh M doc/source/admin/interactive_environments.rst M lib/galaxy/config.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/text.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/json.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/workflow/steps.py M run_tests.sh A static/maps/analysis.js.map A static/maps/app.js.map A static/maps/app/analysis.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/onload.js.map A static/scripts/analysis.js A static/scripts/app.js A static/scripts/app/analysis.js 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 M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/onload.js M static/style/blue/base.css M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/tool_shed/repository/common.mako M test/TESTING.md M test/api/test_workflows.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/selenium_tests/test_collection_builders.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge branch 'dev' into ui_pref_routing Commit: 9f498f9c4be7d1ba6cfba38a2cc8993f732c013b https://github.com/galaxyproject/galaxy/commit/9f498f9c4be7d1ba6cfba38a2cc8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Avoid reusing 'map' builtin Commit: 3ef22d2e6728bf890f14ef6465e88f757bd88b94 https://github.com/galaxyproject/galaxy/commit/3ef22d2e6728bf890f14ef6465e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Slightly more accurate check to verify we have a controller match Commit: 675c375cad69affacda74521d7e88f5227160cb6 https://github.com/galaxyproject/galaxy/commit/675c375cad69affacda74521d7e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- A try at two layer routing with failthrough to clientside routes. Commit: 036d35ac643ace26f1bad289d1989d3db8971ff2 https://github.com/galaxyproject/galaxy/commit/036d35ac643ace26f1bad289d198… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Slight refactoring to reduce duplication in map matching Commit: 66e6be890bedbf59f98b1d10a54146175524df8a https://github.com/galaxyproject/galaxy/commit/66e6be890bedbf59f98b1d10a541… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- No need to check API routes against clientside mapper, catch specific exception Commit: bf88e891977da140d36ba9a627ffebf19178b290 https://github.com/galaxyproject/galaxy/commit/bf88e891977da140d36ba9a627ff… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Merge pull request #20 from dannon/ui_pref_routing Ui pref routing Commit: df73622becc820017a1873db00f64fdcbb6de27a https://github.com/galaxyproject/galaxy/commit/df73622becc820017a1873db00f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py Log Message: ----------- Fix route used in admin controller Commit: 05a689e2adf455f461556fa1aa9229cf4f0454ff https://github.com/galaxyproject/galaxy/commit/05a689e2adf455f461556fa1aa92… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/onload.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/onload.js Log Message: ----------- Merge branch 'dev' into ui_pref_routing Commit: 20916c16a9861cf1f491173cbded2bac0b61f378 https://github.com/galaxyproject/galaxy/commit/20916c16a9861cf1f491173cbded… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/layout/menu.js.map M static/maps/mvc/user/user-preferences.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/layout/menu.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Remove back button to simplify routing, avoid failing returns Commit: 7523ff6983bd6511725509ae4f4d744b36223b97 https://github.com/galaxyproject/galaxy/commit/7523ff6983bd6511725509ae4f4d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-10 (Fri, 10 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 random identifier to request url in order to allow proper reload upon multiple navigation requests Commit: 38336e7e94b15b1580e32e4d0b4321836791db9b https://github.com/galaxyproject/galaxy/commit/38336e7e94b15b1580e32e4d0b43… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/webapps/galaxy/admin/manage_dependencies.mako M test/integration/test_resolvers.py Log Message: ----------- Merge branch 'dev' into ui_pref_routing Commit: e9c98e46ed580463a4f7a4ed989d11f7714ac13f https://github.com/galaxyproject/galaxy/commit/e9c98e46ed580463a4f7a4ed989d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Don't have the clientside mapper register itself Commit: 3b0be252e3485b413d7978a91b14242b589702c5 https://github.com/galaxyproject/galaxy/commit/3b0be252e3485b413d7978a91b14… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Remove old deprecated option (explicit is defined at mapper instantiation, and we wat the default Commit: 93c2286442bbb27e9dd3db708064e6f3deb45287 https://github.com/galaxyproject/galaxy/commit/93c2286442bbb27e9dd3db708064… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Initialize clientside_routes regexes. Commit: 061b7d78f26d4aa1298a3a072fcc420d214d4f7b https://github.com/galaxyproject/galaxy/commit/061b7d78f26d4aa1298a3a072fcc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Refactor failthrough mapping logic Commit: 550bc423af0cb036d1a870c0c419533f25517bbf https://github.com/galaxyproject/galaxy/commit/550bc423af0cb036d1a870c0c419… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Rename parameter, make it a bit more clear what this failthrough logic is doing. Commit: 44fd8aa9bbc77680083eb71d30840a41ce1f79ee https://github.com/galaxyproject/galaxy/commit/44fd8aa9bbc77680083eb71d3084… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Merge pull request #21 from dannon/ui_pref_routing Don't have the clientside mapper register itself Commit: 0498c7f833fad513e2ca878843938e378475202b https://github.com/galaxyproject/galaxy/commit/0498c7f833fad513e2ca87884393… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M static/maps/layout/menu.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/user/user-preferences.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/layout/menu.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/user/user-preferences.js M templates/grid_base.mako R templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Merge pull request #3446 from guerler/ui_pref_routing Improve routing for user preference views Compare: https://github.com/galaxyproject/galaxy/compare/149bbf87e3d5...0498c7f833fa

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[galaxyproject/galaxy] 08f66a: GIE container waiting and swarm management.
by GitHub 15 Mar '17

15 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 08f66a924b8a46d673fc6237dec3a4e8fcb34f21 https://github.com/galaxyproject/galaxy/commit/08f66a924b8a46d673fc6237dec3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/galaxy.ini.sample M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/neo/static/js/neo.js M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A config/swarm_manager_conf.yml.sample R cron/clean_docker_swarm_mode_services.sh M doc/source/admin/interactive_environments.rst M lib/galaxy/config.py A lib/galaxy/container/__init__.py A lib/galaxy/container/docker_swarm.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/lib/mapper.js A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M static/maps/galaxy.interactive_environments.js.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- GIE container waiting and swarm management. 1. Create a new API endpoint and client spin to wait for GIE containers to become ready. IEs are not required to use it, but usage does require a slight change to their `load_notebook()` functions. 2. Add a Docker swarm manager daemon that runs automatically to add nodes when services are waiting, clean up exited services, and remove idle nodes. Shuts down automatically when there's nothing to do. The format of the GIE proxy session database has changed, if GIEs are running when you restart Galaxy, they will be interrupted. If you run the GIE proxy separate from Galaxy, you should restart it after upgrading. Commit: 149bbf87e3d57ffe22c51c283a94fbec33542f05 https://github.com/galaxyproject/galaxy/commit/149bbf87e3d57ffe22c51c283a94… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/galaxy.ini.sample M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/neo/static/js/neo.js M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A config/swarm_manager_conf.yml.sample R cron/clean_docker_swarm_mode_services.sh M doc/source/admin/interactive_environments.rst M lib/galaxy/config.py A lib/galaxy/container/__init__.py A lib/galaxy/container/docker_swarm.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/lib/mapper.js A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M static/maps/galaxy.interactive_environments.js.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- Merge pull request #3740 from natefoo/docker-swarm-mode-wait Interactive Environment container waiting and swarm management Compare: https://github.com/galaxyproject/galaxy/compare/aaa28071b3ac...149bbf87e3d5

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[galaxyproject/galaxy] 88fb86: Bump routes to 2.4.1, fix (newly?) broken archive ...
by GitHub 15 Mar '17

15 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 88fb8650b9699a50348ddece8d336797aacd03c5 https://github.com/galaxyproject/galaxy/commit/88fb8650b9699a50348ddece8d33… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Bump routes to 2.4.1, fix (newly?) broken archive route. Commit: 6700c08a96467d322e917347a63f1ec8c932700e https://github.com/galaxyproject/galaxy/commit/6700c08a96467d322e917347a63f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt Log Message: ----------- Update Routes 2.4.1 hash Commit: aaa28071b3acaad514157dae856cb2f5a4895eef https://github.com/galaxyproject/galaxy/commit/aaa28071b3acaad514157dae856c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #3752 from dannon/routes-bump Bump routes to 2.4.1 Compare: https://github.com/galaxyproject/galaxy/compare/4f27240ef760...aaa28071b3ac

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[galaxyproject/galaxy] 01e1bc: Added percolator proteomics datatypes for input an...
by GitHub 15 Mar '17

15 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 01e1bc6f3007aff1234e518977115c97bd20e1eb https://github.com/galaxyproject/galaxy/commit/01e1bc6f3007aff1234e51897711… Author: Jorrit Boekel <jorrit.boekel(a)scilifelab.se> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Added percolator proteomics datatypes for input and output Commit: 4f27240ef760446743b7b774404f159b713ae3ce https://github.com/galaxyproject/galaxy/commit/4f27240ef760446743b7b774404f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3737 from glormph/percolator_datatypes Percolator out datatypes Compare: https://github.com/galaxyproject/galaxy/compare/65e7ee0c78e5...4f27240ef760

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[galaxyproject/usegalaxy-playbook]
by GitHub 14 Mar '17

14 Mar '17

Branch: refs/heads/wiki-to-hub Home: https://github.com/galaxyproject/usegalaxy-playbook

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[galaxyproject/usegalaxy-playbook] 05f954: Revert "Revert "Changed wiki links to Hub links, a...
by GitHub 14 Mar '17

14 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 05f954da66802d33b36a85540eef3a19939bc4d3 https://github.com/galaxyproject/usegalaxy-playbook/commit/05f954da66802d33… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: A files/galaxy/common/static/welcome_img/ohsu_logo.png M files/galaxy/usegalaxy.org/config/job_resource_params_conf.xml M production/group_vars/galaxyservers.yml M production/group_vars/toolshedservers.yml M roles/galaxyprojectdotorg.galaxy/tasks/main.yml M roles/galaxyprojectdotorg.galaxy_toolshed/tasks/main.yml M roles/galaxyprojectdotorg.tools/files/README.md M stage/group_vars/galaxyservers.yml M stage/group_vars/toolshedservers.yml M templates/galaxy/common/static/welcome.html.j2 M templates/nginx/usegalaxy_rewrites.conf.j2 Log Message: ----------- Revert "Revert "Changed wiki links to Hub links, added OHSU to home page."" This reverts commit 5ee89a7583f1be6bdd9e440a1c2d1e6718d0fc28. Commit: d6122393ad9cb251a820c77799de49960a32eeb8 https://github.com/galaxyproject/usegalaxy-playbook/commit/d6122393ad9cb251… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: A files/galaxy/common/static/welcome_img/ohsu_logo.png M files/galaxy/usegalaxy.org/config/job_resource_params_conf.xml M production/group_vars/galaxyservers.yml M production/group_vars/toolshedservers.yml M roles/galaxyprojectdotorg.galaxy/tasks/main.yml M roles/galaxyprojectdotorg.galaxy_toolshed/tasks/main.yml M roles/galaxyprojectdotorg.tools/files/README.md M stage/group_vars/galaxyservers.yml M stage/group_vars/toolshedservers.yml M templates/galaxy/common/static/welcome.html.j2 M templates/nginx/usegalaxy_rewrites.conf.j2 Log Message: ----------- Merge pull request #24 from galaxyproject/wiki-to-hub Changed wiki links to Hub links, added OHSU to home page Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/5ee89a7583f1...…

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[galaxyproject/usegalaxy-playbook] 05f954: Revert "Revert "Changed wiki links to Hub links, a...
by GitHub 14 Mar '17

14 Mar '17

Branch: refs/heads/wiki-to-hub Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 05f954da66802d33b36a85540eef3a19939bc4d3 https://github.com/galaxyproject/usegalaxy-playbook/commit/05f954da66802d33… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: A files/galaxy/common/static/welcome_img/ohsu_logo.png M files/galaxy/usegalaxy.org/config/job_resource_params_conf.xml M production/group_vars/galaxyservers.yml M production/group_vars/toolshedservers.yml M roles/galaxyprojectdotorg.galaxy/tasks/main.yml M roles/galaxyprojectdotorg.galaxy_toolshed/tasks/main.yml M roles/galaxyprojectdotorg.tools/files/README.md M stage/group_vars/galaxyservers.yml M stage/group_vars/toolshedservers.yml M templates/galaxy/common/static/welcome.html.j2 M templates/nginx/usegalaxy_rewrites.conf.j2 Log Message: ----------- Revert "Revert "Changed wiki links to Hub links, added OHSU to home page."" This reverts commit 5ee89a7583f1be6bdd9e440a1c2d1e6718d0fc28.

1 0

[galaxyproject/usegalaxy-playbook]
by GitHub 14 Mar '17

14 Mar '17

Branch: refs/heads/wiki-to-hub Home: https://github.com/galaxyproject/usegalaxy-playbook

1 0

[galaxyproject/usegalaxy-playbook] 5ee89a: Revert "Changed wiki links to Hub links, added OHS...
by GitHub 14 Mar '17

14 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5ee89a7583f1be6bdd9e440a1c2d1e6718d0fc28 https://github.com/galaxyproject/usegalaxy-playbook/commit/5ee89a7583f1be6b… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: R files/galaxy/common/static/welcome_img/ohsu_logo.png M files/galaxy/usegalaxy.org/config/job_resource_params_conf.xml M production/group_vars/galaxyservers.yml M production/group_vars/toolshedservers.yml M roles/galaxyprojectdotorg.galaxy/tasks/main.yml M roles/galaxyprojectdotorg.galaxy_toolshed/tasks/main.yml M roles/galaxyprojectdotorg.tools/files/README.md M stage/group_vars/galaxyservers.yml M stage/group_vars/toolshedservers.yml M templates/galaxy/common/static/welcome.html.j2 M templates/nginx/usegalaxy_rewrites.conf.j2 Log Message: ----------- Revert "Changed wiki links to Hub links, added OHSU to home page." This reverts commit 25ae442b80c9b4069655b6a03d4066dd300dc8db.

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[galaxyproject/usegalaxy-playbook] 25ae44: Changed wiki links to Hub links, added OHSU to hom...
by GitHub 14 Mar '17

14 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 25ae442b80c9b4069655b6a03d4066dd300dc8db https://github.com/galaxyproject/usegalaxy-playbook/commit/25ae442b80c9b406… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: A files/galaxy/common/static/welcome_img/ohsu_logo.png M files/galaxy/usegalaxy.org/config/job_resource_params_conf.xml M production/group_vars/galaxyservers.yml M production/group_vars/toolshedservers.yml M roles/galaxyprojectdotorg.galaxy/tasks/main.yml M roles/galaxyprojectdotorg.galaxy_toolshed/tasks/main.yml M roles/galaxyprojectdotorg.tools/files/README.md M stage/group_vars/galaxyservers.yml M stage/group_vars/toolshedservers.yml M templates/galaxy/common/static/welcome.html.j2 M templates/nginx/usegalaxy_rewrites.conf.j2 Log Message: ----------- Changed wiki links to Hub links, added OHSU to home page. But, something is not quite right yet. Links in the help menu still show the old links, and the support link does not work at all.

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[galaxyproject/infrastructure-playbook] 00d193: Valid rules are good rules.
by GitHub 14 Mar '17

14 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 00d193621eb89003899b2399e55420dc9ddd7dbd https://github.com/galaxyproject/infrastructure-playbook/commit/00d193621eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M galaxyenv/templates/nginx/galaxyproject.j2 Log Message: ----------- Valid rules are good rules.

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[galaxyproject/infrastructure-playbook] 3591f5: Slight reformat of galaxyproject includes.
by GitHub 14 Mar '17

14 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3591f5234501cc2175099945cffd6d18e4d90e7d https://github.com/galaxyproject/infrastructure-playbook/commit/3591f523450… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M galaxyenv/templates/nginx/galaxyproject.j2 Log Message: ----------- Slight reformat of galaxyproject includes.

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[galaxyproject/infrastructure-playbook] 50b066: Redirect old searches.
by GitHub 14 Mar '17

14 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 50b06618adf73529b7f2580da1a0f447b6527106 https://github.com/galaxyproject/infrastructure-playbook/commit/50b06618adf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M galaxyenv/templates/nginx/galaxyproject.j2 Log Message: ----------- Redirect old searches.

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[galaxyproject/infrastructure-playbook] 7d0fdc: Update rewrites, redirect to page-not-found for va...
by GitHub 14 Mar '17

14 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 7d0fdc5ac1f2fc20bb4ed6ef0be6fda04d3406e5 https://github.com/galaxyproject/infrastructure-playbook/commit/7d0fdc5ac1f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Update rewrites, redirect to page-not-found for various things instead of root (/)

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[galaxyproject/galaxy] f21f96: Change API path in docstrings to correct /api/depe...
by GitHub 14 Mar '17

14 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f21f963a23427e2b5aa1f58a7d9b0fb85aed7607 https://github.com/galaxyproject/galaxy/commit/f21f963a23427e2b5aa1f58a7d9b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_dependencies.py Log Message: ----------- Change API path in docstrings to correct /api/dependency_resolvers/* Commit: 65e7ee0c78e5c61a6ef9d9eaa8ccd6d8666014ad https://github.com/galaxyproject/galaxy/commit/65e7ee0c78e5c61a6ef9d9eaa8cc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_dependencies.py Log Message: ----------- Merge pull request #3749 from mvdbeek/docstring_fix_api Change API path in docstrings to correct /api/dependency_resolvers/* Compare: https://github.com/galaxyproject/galaxy/compare/7d08f8f2fecf...65e7ee0c78e5

1 0

[galaxyproject/galaxy] 90b300: Return empty list if resolve_all() has failed
by GitHub 14 Mar '17

14 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 90b300cbd731df2e6005ca1dcd2f5c1c59a34e0e https://github.com/galaxyproject/galaxy/commit/90b300cbd731df2e6005ca1dcd2f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Return empty list if resolve_all() has failed This should solve the problems pointed out by :eyes: @nsoranzo introduced in https://github.com/galaxyproject/galaxy/pull/3725. This commit also clarifies this behaviour in the docstrings. Commit: 8192d3562937d07410aa5d7dd73727efc5832634 https://github.com/galaxyproject/galaxy/commit/8192d3562937d07410aa5d7dd737… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Add `:returns: list of resolved dependencies` to docstring of `resolve_all` method Commit: 7d08f8f2fecf08743a58f71c431e1d71f84f0d76 https://github.com/galaxyproject/galaxy/commit/7d08f8f2fecf08743a58f71c431e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3746 from mvdbeek/resolve_all_fix_3725 BUG: Return empty list if resolve_all() has failed Compare: https://github.com/galaxyproject/galaxy/compare/7e1c04cc6df8...7d08f8f2fecf

1 0

[galaxyproject/galaxy] f94174: update xsd codefile doc with info from moin
by GitHub 13 Mar '17

13 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f94174912a09a56eebe2e14e63238c3f3f172327 https://github.com/galaxyproject/galaxy/commit/f94174912a09a56eebe2e14e6323… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- update xsd codefile doc with info from moin Commit: 7e1c04cc6df810ca3a4e726a85cc9566d9d1ff61 https://github.com/galaxyproject/galaxy/commit/7e1c04cc6df810ca3a4e726a85cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3739 from martenson/update-codefile-schema update xsd codefile doc with info from moin Compare: https://github.com/galaxyproject/galaxy/compare/fc1df7bad17e...7e1c04cc6df8

1 0

[galaxyproject/galaxy] 46e452: Fix typo in install_dependencies docstring
by GitHub 13 Mar '17

13 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 46e452bfe820ddbb329e694d0eb2b7b755594910 https://github.com/galaxyproject/galaxy/commit/46e452bfe820ddbb329e694d0eb2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Fix typo in install_dependencies docstring Commit: 8b5d408e438c346f04088374d70eaca65e06c292 https://github.com/galaxyproject/galaxy/commit/8b5d408e438c346f04088374d70e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/integration/test_resolvers.py Log Message: ----------- Add API to remove requirements installed by Conda This is currently limited to the Conda dependency resolver, but other resolver would only need to implement the resolver.uninstall method and set can_uninstall_dependencies to True. To use this endpoint, POST to <galaxy_url>/tools/<tool_id>/uninstall_dependencies'. Commit: 3b067ef62a4dfa8af54bc4c75c6260f98d660aeb https://github.com/galaxyproject/galaxy/commit/3b067ef62a4dfa8af54bc4c75c62… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Return last non-zero returncode Commit: d5b5d29137ee1e5577530ed2c56579b9394520b3 https://github.com/galaxyproject/galaxy/commit/d5b5d29137ee1e5577530ed2c565… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/integration/test_resolvers.py Log Message: ----------- Change endpoint to `api/tools/<tool_id>/dependencies` A POST will trigger installation and DELETE will trigger uninstalling the dependencies (Thx for the suggestion @jmchilton). Commit: 6902e62d38e3c5741a238736f640b5b847c5e8c2 https://github.com/galaxyproject/galaxy/commit/6902e62d38e3c5741a238736f640… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix uninstall when not all dependencies are resolved by all-in-one resolver Commit: 95106ea3c9ad875ce35b16c6b9bb8556f3d82076 https://github.com/galaxyproject/galaxy/commit/95106ea3c9ad875ce35b16c6b9bb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Add UI for Conda dependency uninstall Commit: fc1df7bad17e53c54bd57602b82bbec22cc0e074 https://github.com/galaxyproject/galaxy/commit/fc1df7bad17e53c54bd57602b82b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/webapps/galaxy/admin/manage_dependencies.mako M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3725 from mvdbeek/remove_env_conda Add API and UI to remove requirements installed by Conda Compare: https://github.com/galaxyproject/galaxy/compare/33ff2754cc75...fc1df7bad17e

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[galaxyproject/infrastructure-playbook] 53c6ff: Ansible 2.0+ updates
by GitHub 13 Mar '17

13 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 53c6ff16eedab22e0abe472f7096de56da94f2cc https://github.com/galaxyproject/infrastructure-playbook/commit/53c6ff16eed… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M galaxyenv/group_vars/starforgebuilders.yml M roles/linuxbrew/tasks/main.yml Log Message: ----------- Ansible 2.0+ updates

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[galaxyproject/galaxy] 5818bb: Prefer versioned Conda dependencies to unversioned...
by GitHub 10 Mar '17

10 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5818bbcbaaeca54a85bef9acaadd41d12386a6ad https://github.com/galaxyproject/galaxy/commit/5818bbcbaaeca54a85bef9acaadd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Prefer versioned Conda dependencies to unversioned Galaxy ones. Commit: 45971b29bd8b93825fe48134750bd866c82f7a9f https://github.com/galaxyproject/galaxy/commit/45971b29bd8b93825fe48134750b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Update dependency resolver docs for new default order Commit: 33ff2754cc75981796176b7e7ae75ce362db62a0 https://github.com/galaxyproject/galaxy/commit/33ff2754cc75981796176b7e7ae7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3708 from natefoo/dep-resolve-order Prefer versioned Conda dependencies to unversioned Galaxy ones Compare: https://github.com/galaxyproject/galaxy/compare/5a7eab0f06b4...33ff2754cc75

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[galaxyproject/galaxy] 90108e: tool-form needs to not be required at the top leve...
by GitHub 10 Mar '17

10 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 90108e450fd2d13d3010e05a2fcb1224a2549a2a https://github.com/galaxyproject/galaxy/commit/90108e450fd2d13d3010e05a2fcb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/onload.js Log Message: ----------- tool-form needs to not be required at the top level of the Galaxy webapp Commit: 2134d6c3856edf8358c185178f9efe35a232c03b https://github.com/galaxyproject/galaxy/commit/2134d6c3856edf8358c185178f9e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Use a redirect (which will get routed, soon) instead of instantiating a toolform within the overlay -- this is much lighter weight Commit: da9ee941afa604586cfc6dfdacb2594284b3e6f0 https://github.com/galaxyproject/galaxy/commit/da9ee941afa604586cfc6dfdacb2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Standardize tabs/spaces in webhook overlay search Commit: 3d33586d4a5758e566dc5d1eceda91e97cd3d73a https://github.com/galaxyproject/galaxy/commit/3d33586d4a5758e566dc5d1eceda… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Cleanup pass on formatting/unused vars in webhooks Commit: 5a7eab0f06b4eb9f877c8e582bb6e078622be1ad https://github.com/galaxyproject/galaxy/commit/5a7eab0f06b4eb9f877c8e582bb6… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/search/static/script.js M static/maps/onload.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/onload.js Log Message: ----------- Merge pull request #3731 from dannon/fix_webhook_search_overlay Fix webhook search overlay interfering with masthead load Compare: https://github.com/galaxyproject/galaxy/compare/8911e491a56c...5a7eab0f06b4

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[galaxyproject/infrastructure-playbook] 3111f6: Galaxy site moved to athena
by GitHub 09 Mar '17

09 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3111f6620693c4145f942fc916a9786140cd5314 https://github.com/galaxyproject/infrastructure-playbook/commit/3111f662069… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M common_env/secret_group_vars/sslwebservers.yml M galaxyenv/files/jenkins/jenkins_server_user_ssh_config M galaxyenv/files/jenkins/jenkins_slave_user_ssh_config A galaxyenv/files/ssl/athena.galaxyproject.org_cert.pem M galaxyenv/host_vars/athena.galaxyproject.org.yml M galaxyenv/host_vars/chouffe.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/secret_group_vars/all.yml M galaxyenv/secret_group_vars/jenkinsslaves.yml M galaxyenv/secret_host_vars/athena.galaxyproject.org.yml M galaxyenv/secret_host_vars/chouffe.galaxyproject.org.yml M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml A galaxyenv/templates/nginx/cloudlaunch.j2 A galaxyenv/templates/nginx/galaxyproject.j2 A galaxyenv/templates/nginx/moin.j2 M galaxyenv/templates/nginx/new.j2 M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Galaxy site moved to athena

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[galaxyproject/usegalaxy-playbook] 29479b: Move all athena stuff to infrastructure-playbook
by GitHub 09 Mar '17

09 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 29479b5ca735b13b5b5716c5858f1966e57125a6 https://github.com/galaxyproject/usegalaxy-playbook/commit/29479b5ca735b13b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: R common/host_vars/athena.galaxyproject.org.yml M common/inventory M common/secret_vars/ssl.yml R files/ssl/athena.galaxyproject.org_cert.pem R templates/nginx/cloudlaunch.j2 R templates/nginx/galaxyproject.j2 Log Message: ----------- Move all athena stuff to infrastructure-playbook

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[galaxyproject/galaxy] 33abab: Move the user calculate_and_set_disk_usage functio...
by GitHub 09 Mar '17

09 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 33ababaeb48e8ecfad487a54e96550ce7e43bc78 https://github.com/galaxyproject/galaxy/commit/33ababaeb48e8ecfad487a54e965… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py Log Message: ----------- Move the user calculate_and_set_disk_usage functionality to the model instead of the queue worker. Commit: c928f15b4d00bb798453d42a6f6a79042692edfc https://github.com/galaxyproject/galaxy/commit/c928f15b4d00bb798453d42a6f6a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Robustify calculate_and_set_disk_usage for handling changes during the long calc Commit: cd6e7f73d8a54698aa63d670e8aba6e45f8eef1b https://github.com/galaxyproject/galaxy/commit/cd6e7f73d8a54698aa63d670e8ab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Swap admin recalculate to use model-based recalc-and-set Commit: 751182640d1a76962cbac872ae31c0ce471872dd https://github.com/galaxyproject/galaxy/commit/751182640d1a76962cbac872ae31… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove now-unused import of pgcalc Commit: 8002ef31ea6f4cb52d6e907dcdf1d002ced45eb6 https://github.com/galaxyproject/galaxy/commit/8002ef31ea6f4cb52d6e907dcdf1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Ensure there's a user before calling calculate_and_set_disk_usage Commit: e088a48323a06e80d55e85944a4c09cf368b8391 https://github.com/galaxyproject/galaxy/commit/e088a48323a06e80d55e85944a4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Add error logging to recalculate task. Commit: 2d964eb50c9f2f2246044a1d7b83e0f920046510 https://github.com/galaxyproject/galaxy/commit/2d964eb50c9f2f2246044a1d7b83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- I have no idea what I would be doing without Nicola. Commit: 8911e491a56cdc3b8fb327bc702b4843d7d22a4d https://github.com/galaxyproject/galaxy/commit/8911e491a56cdc3b8fb327bc702b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge pull request #3734 from dannon/queue_worker_trim Quota recalculation logic consolidation Compare: https://github.com/galaxyproject/galaxy/compare/bcc4e025c36c...8911e491a56c

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[galaxyproject/infrastructure-playbook] 6353ac: Redirect wiki pages to hub
by GitHub 09 Mar '17

09 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6353ac6c8ebad10bcf8b72f144f0a4f7b9173b0f https://github.com/galaxyproject/infrastructure-playbook/commit/6353ac6c8eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M galaxyenv/host_vars/chouffe.galaxyproject.org.yml M galaxyenv/templates/nginx/wiki.j2 A galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Redirect wiki pages to hub

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