Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8e0be5089c63d94b841babfffcd70f2d8ab9b27c https://github.com/galaxyproject/galaxy/commit/8e0be5089c63d94b841babfffcd70... Author: John Chilton <jmchilton@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/9234420cd770661b58ee91051015e... Author: John Chilton <jmchilton@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/6c82cf3c22445e97621429591e729... Author: Dannon Baker <dannon.baker@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/779156111a117f5513ae10af04d0b... Author: Martin Cech <marten@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/7e4f805d479acc8f362ed651330f9... Author: Martin Cech <marten@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/02bdc7495d80d4fb085de26e07e20... Author: Martin Cech <marten@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/1d0ace1452aa9d5e334ee89aca07f... Author: Nicola Soranzo <nsoranzo@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/f75a72aee80680537dad802944585... Author: Dannon Baker <dannon.baker@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)@example.org users. Commit: 09ba27543b8726fb61cd998bf9614018a9ba7316 https://github.com/galaxyproject/galaxy/commit/09ba27543b8726fb61cd998bf9614... Author: Dannon Baker <dannon.baker@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/b779977cdc31d50183e7b0f356e94... Author: Dannon Baker <dannon.baker@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/eb9a940a2dd69574b5fbaca06ffdc... Author: Dannon Baker <dannon.baker@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/f3c134abcb04ee2885f247ba79e95... Author: Nicola Soranzo <nsoranzo@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/d398c90dbd70fff91a672935997bc... Author: Nicola Soranzo <nicola.soranzo@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