- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] d9f21f: Only fail through to client mapping when it exists...
by GitHub 05 Apr '17

05 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9f21fd34c059d422e63d31e9fb94660e826c4ff https://github.com/galaxyproject/galaxy/commit/d9f21fd34c059d422e63d31e9fb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Only fail through to client mapping when it exists. Commit: c27dac65c882906aa87c364961ac7783f1babd17 https://github.com/galaxyproject/galaxy/commit/c27dac65c882906aa87c364961ac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Merge pull request #3783 from dannon/routing_bug_exception_propagation Layered routing fix for when controller route fails and client route does not exist. Compare: https://github.com/galaxyproject/galaxy/compare/6251b51aebc8...c27dac65c882

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[galaxyproject/galaxy] 200994: Revert "Allows to drag-and-drop history items into...
by GitHub 05 Apr '17

05 Apr '17

Branch: refs/heads/revert-3871-history_drag_drop Home: https://github.com/galaxyproject/galaxy Commit: 200994536e6110fffb586a968edf7edd3c04e4f2 https://github.com/galaxyproject/galaxy/commit/200994536e6110fffb586a968edf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less M static/maps/mvc/history/history-view-edit.js.map 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/history/history-view-edit.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css Log Message: ----------- Revert "Allows to drag-and-drop history items into the content selector"

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[galaxyproject/galaxy] 2b0ac9: Enable drag drop for history items
by GitHub 05 Apr '17

05 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b0ac9a098b7ca2c207c3d00be698a993e4130ff https://github.com/galaxyproject/galaxy/commit/2b0ac9a098b7ca2c207c3d00be69… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/history/history-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js Log Message: ----------- Enable drag drop for history items Commit: 97d5a86a585b2c9ac159c9db255dd0389f83ab3b https://github.com/galaxyproject/galaxy/commit/97d5a86a585b2c9ac159c9db255d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 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 Log Message: ----------- Catch drag and drop basic event handlers for content selector Commit: aa7bed3b7270db18505e1dc7a8f84600482114cb https://github.com/galaxyproject/galaxy/commit/aa7bed3b7270db18505e1dc7a8f8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less 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 static/style/blue/base.css Log Message: ----------- Add basic styles to highlight drop area on drag over Commit: f56651b9ea8b20e34d1cb0604888d3de2e49e2c4 https://github.com/galaxyproject/galaxy/commit/f56651b9ea8b20e34d1cb0604888… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 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 Log Message: ----------- Access drop data Commit: 642002854c2abd312e917632191c7db638234ad7 https://github.com/galaxyproject/galaxy/commit/642002854c2abd312e917632191c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 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 Log Message: ----------- Move drop handler, support datasets and collections Commit: 5bbc91289b0d5cd69a00a487751f4782f298932a https://github.com/galaxyproject/galaxy/commit/5bbc91289b0d5cd69a00a487751f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less 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 static/style/blue/base.css Log Message: ----------- Display success and error colors Commit: 039f706bd7395f8b0350453936f2e82f98fa4e93 https://github.com/galaxyproject/galaxy/commit/039f706bd7395f8b0350453936f2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix style color on inital dragover Commit: af066197b9b9a4ff6f804fe4cc588611eab0ddd9 https://github.com/galaxyproject/galaxy/commit/af066197b9b9a4ff6f804fe4cc58… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 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 Log Message: ----------- Improve validation Commit: da0d53728be70d26123a748546a8c0d6cb8d67c3 https://github.com/galaxyproject/galaxy/commit/da0d53728be70d26123a748546a8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 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 Log Message: ----------- Move delay timer value to attributes, rename status handler Commit: e05036a6a02c396c207c9ea80dc056a58c9f7f08 https://github.com/galaxyproject/galaxy/commit/e05036a6a02c396c207c9ea80dc0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 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 static/style/blue/base.css Log Message: ----------- Avoid flickering due to bubbling events from children without masking div Commit: 5c85fe1c9821a12caaef30df37eeac3c1fcb2a66 https://github.com/galaxyproject/galaxy/commit/5c85fe1c9821a12caaef30df37ee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 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 Log Message: ----------- Remove unused default behavior blockers Commit: 2c3cdfb6d0355667909a40a79c8e02a76b6dca97 https://github.com/galaxyproject/galaxy/commit/2c3cdfb6d0355667909a40a79c8e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 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 Log Message: ----------- Fix code style, improve readability Commit: 071186d520fdd0069b182dd77aeaad4bddd1e323 https://github.com/galaxyproject/galaxy/commit/071186d520fdd0069b182dd77aea… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less 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 static/style/blue/base.css Log Message: ----------- Improve support for multiple dataset selector Commit: 383db9bb3bedef57f490dff4feb1bd74188c798b https://github.com/galaxyproject/galaxy/commit/383db9bb3bedef57f490dff4feb1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 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 Log Message: ----------- Trigger change to update current selection if value has not actually changed Commit: 6251b51aebc8719b64122e1311175e683e55bbb3 https://github.com/galaxyproject/galaxy/commit/6251b51aebc8719b64122e131117… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less M static/maps/mvc/history/history-view-edit.js.map 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/history/history-view-edit.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css Log Message: ----------- Merge pull request #3871 from guerler/history_drag_drop Allows to drag-and-drop history items into the content selector Compare: https://github.com/galaxyproject/galaxy/compare/5937a677d57e...6251b51aebc8

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[galaxyproject/galaxy] d1974a: Use detect_errors="exit_code" in Trim tool
by GitHub 04 Apr '17

04 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d1974a42e5787ef06d4c4d25dbe7178eb26284d5 https://github.com/galaxyproject/galaxy/commit/d1974a42e5787ef06d4c4d25dbe7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M tools/filters/trimmer.py M tools/filters/trimmer.xml Log Message: ----------- Use detect_errors="exit_code" in Trim tool Prevent job failures due to spurious messages on stderr from the cluster scheduler. Commit: 5937a677d57e6180aaeabcd737e70aac0809fbd5 https://github.com/galaxyproject/galaxy/commit/5937a677d57e6180aaeabcd737e7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M tools/filters/trimmer.py M tools/filters/trimmer.xml Log Message: ----------- Merge pull request #3869 from nsoranzo/trimmer Use detect_errors="exit_code" in Trim tool Compare: https://github.com/galaxyproject/galaxy/compare/41a88de7527c...5937a677d57e

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[galaxyproject/infrastructure-playbook] 03eb97: Update common roles and fixes for that update
by GitHub 04 Apr '17

04 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 03eb97c687114238d4afaf4d20c53019ee7c7f17 https://github.com/galaxyproject/infrastructure-playbook/commit/03eb97c6871… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M common_roles M galaxyenv/host_vars/chouffe.galaxyproject.org.yml M galaxyenv/host_vars/delirium.galaxyproject.org.yml R library/yum_repository Log Message: ----------- Update common roles and fixes for that update Commit: 275b525e0c21fb3f45e61873dbb6d95c1b4b85ec https://github.com/galaxyproject/infrastructure-playbook/commit/275b525e0c2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M roles/cvmfs/tasks/client.yml Log Message: ----------- Don't unnecessarily run cvmfs_config setup Commit: b3db2254a57dfc2a75fdc8ec4317eaae24118b62 https://github.com/galaxyproject/infrastructure-playbook/commit/b3db2254a57… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M roles/slurm/tasks/main.yml M taccenv/group_vars/slurmclients.yml Log Message: ----------- Slurm role improvements: - Have it create its own user account if so configured, since relying on the users common role tramples other group_users configs. - Don't have it set up its own yum repo since the same yum repo is used by other things and was being used multiple times. Commit: b17840d747965b873fd0e0d84c37b320b98f64a3 https://github.com/galaxyproject/infrastructure-playbook/commit/b17840d7479… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M taccenv/playbook.yml Log Message: ----------- Better use of tags Commit: 6318da492b5cda52693332e462d4fd9da7acc083 https://github.com/galaxyproject/infrastructure-playbook/commit/6318da492b5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M galaxyenv/host_vars/cvmfs0-psu0.galaxyproject.org.yml M galaxyenv/host_vars/cvmfs0-tacc0.galaxyproject.org.yml M taccenv/group_vars/galaxyservers.yml Log Message: ----------- Install the Galaxy EL yum repo via the packages role Commit: 21601edfc91d2ade0bf96b53d201ff64ba15d937 https://github.com/galaxyproject/infrastructure-playbook/commit/21601edfc91… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M taccenv/secret_group_vars/testgalaxyservers.yml Log Message: ----------- Update Test access lists Commit: 0a9963fe69db97a7e66f36cf02d6af069dc21332 https://github.com/galaxyproject/infrastructure-playbook/commit/0a9963fe69d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: A taccenv/host_vars/galaxy07.tacc.utexas.edu.yml M taccenv/inventory Log Message: ----------- Set up galaxy07 as new Galaxy Test server Commit: 09b1b64d0e35d3399668b2b5181b94b9c7649b3b https://github.com/galaxyproject/infrastructure-playbook/commit/09b1b64d0e3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M jetstreamdockerenv/group_vars/baseinstances.yml Log Message: ----------- Switch base instance for Jetstream GIE docker swarm Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/922a0a6e94…

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[galaxyproject/galaxy] c51adf: Insert update caller/helper for options
by GitHub 04 Apr '17

04 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c51adf781a1a711c4e54d89fbdca7ea9d3331f08 https://github.com/galaxyproject/galaxy/commit/c51adf781a1a711c4e54d89fbdca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M static/maps/mvc/ui/ui-options.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/ui/ui-options.js Log Message: ----------- Insert update caller/helper for options Commit: c8eb2c186def4b505143a5a6b0d971549b15d19a https://github.com/galaxyproject/galaxy/commit/c8eb2c186def4b505143a5a6b0d9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M static/maps/mvc/ui/ui-options.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/ui/ui-options.js Log Message: ----------- Merge pull request #3851 from guerler/add_lost_update_caller [17.01] Fix update caller/helper for options Commit: 99c8f2c9fc6f335863f134a5b8b4055d5079cfe1 https://github.com/galaxyproject/galaxy/commit/99c8f2c9fc6f335863f134a5b8b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix setting UUID on steps when copying steps from another workflow. It seems like the client is correctly setting the UUID to None, but the backend is treating the None as a UUID because it was (incorrectly IMO) making a distinction between ``uuid`` being absent and being set to ``None``. Fixes #3845. Commit: 268aac29526b3526a42457576e8de7867c2bfe1f https://github.com/galaxyproject/galaxy/commit/268aac29526b3526a42457576e8d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #3856 from jmchilton/1701_uuid_on_copy_fix [17.01] Fix setting UUID on steps when copying steps from another workflow. Commit: 5b46c431b416e619a7ac5467527ab30743eabd33 https://github.com/galaxyproject/galaxy/commit/5b46c431b416e619a7ac5467527a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py 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 Log Message: ----------- Fix certain aspects of dataset reductions in conditionals/repeats. For instance, fixes #3859 restoring the correct ``element_identifier`` for reduces collections in conditionals. Add tests for combinations of repeats and conditionals. Commit: 3c080cae96aadccd824aa7cf6fda9c4b5bf7471a https://github.com/galaxyproject/galaxy/commit/3c080cae96aadccd824aa7cf6fda… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py 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 Log Message: ----------- Merge pull request #3864 from jmchilton/fix_identifiers_in_conditionals [17.01] Fix certain aspects of collection reductions in conditionals/repeats. Commit: 41a88de7527c4e5f38070fe31e0dfe78ad817603 https://github.com/galaxyproject/galaxy/commit/41a88de7527c4e5f38070fe31e0d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/actions/__init__.py M static/maps/mvc/ui/ui-options.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-options.js M test/api/test_tools.py 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 Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/5d810d5908ac...41a88de7527c

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[galaxyproject/galaxy] 1e7021: Touch up #3559 based on post-merge discussions.
by GitHub 04 Apr '17

04 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1e70211fa4827badf4bd3fe1f1703004d369afec https://github.com/galaxyproject/galaxy/commit/1e70211fa4827badf4bd3fe1f170… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M test/api/test_libraries.py Log Message: ----------- Touch up #3559 based on post-merge discussions. Commit: 5d810d5908ac851e398ebc7fcd7d54c5a892fd04 https://github.com/galaxyproject/galaxy/commit/5d810d5908ac851e398ebc7fcd7d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M test/api/test_libraries.py Log Message: ----------- Merge pull request #3857 from jmchilton/3559_touchups Touch up #3559 based on post-merge discussions. Compare: https://github.com/galaxyproject/galaxy/compare/6f4e242b1648...5d810d5908ac

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[galaxyproject/galaxy] 283915: Adding Phylocanvas visualization for the Galaxy ch...
by GitHub 04 Apr '17

04 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2839153eb4b08f0b9a536059912d39fd3ee902a0 https://github.com/galaxyproject/galaxy/commit/2839153eb4b08f0b9a536059912d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Adding Phylocanvas visualization for the Galaxy charts Commit: 876c7a2d3df70b1c4edcf4fe738eb51c6e76bcfa https://github.com/galaxyproject/galaxy/commit/876c7a2d3df70b1c4edcf4fe738e… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js Log Message: ----------- Adding more features like colors, collapse, prune and resize of the tree Commit: 8e1d761beccfc301129070f2c5c0a79939d290a0 https://github.com/galaxyproject/galaxy/commit/8e1d761beccfc301129070f2c5c0… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js M display_applications/igv/bigwig.xml M doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst A doc/source/admin/reports.md M doc/source/admin/useful_scripts.rst A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/galaxy.webapps.galaxy.api.rst R doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/releases/_header.rst M doc/source/ts_api_doc.rst M lib/galaxy/tools/__init__.py Log Message: ----------- Merging with dev Commit: 2f66d4563e02e8b585e5c1529b4e414117846858 https://github.com/galaxyproject/galaxy/commit/2f66d4563e02e8b585e5c1529b4e… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js Log Message: ----------- Adding shapes for leaves of phylogenetic tree Commit: e67dc45c26e77d3f2b85ac7e2ab80ac5fdab0cf9 https://github.com/galaxyproject/galaxy/commit/e67dc45c26e77d3f2b85ac7e2ab8… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.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 M client/galaxy/style/less/upload.less M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js 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/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into phylocanvas Commit: fa086edf22c725b8a98cff92ac6ca6a4ab210237 https://github.com/galaxyproject/galaxy/commit/fa086edf22c725b8a98cff92ac6c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js Log Message: ----------- Adding support for .nhx files (Newick) and removing txt files support Commit: 0c3f7989bb913842e28a8fbb267d1280420caa92 https://github.com/galaxyproject/galaxy/commit/0c3f7989bb913842e28a8fbb267d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M .ci/flake8_lint_include_list.txt M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/model/__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/workflow/modules.py M lib/galaxy/workflow/run.py M templates/webapps/galaxy/admin/manage_dependencies.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- Merging wtih dev Commit: 339566bc03f1a51c7a4c60c2d6a100f43e1d3c15 https://github.com/galaxyproject/galaxy/commit/339566bc03f1a51c7a4c60c2d6a1… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M CONTRIBUTING.md M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/scheduling_manager.py M test/api/test_users.py M test/api/test_workflows.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- Merging with dev Commit: 6f4e242b16487b6032347dad3f60fef00f60464f https://github.com/galaxyproject/galaxy/commit/6f4e242b16487b6032347dad3f60… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js Log Message: ----------- Merge pull request #3850 from bgruening/phylocanvas Phylocanvas as a BioJS component for the Galaxy charts Compare: https://github.com/galaxyproject/galaxy/compare/5169fbe917c9...6f4e242b1648

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[galaxyproject/galaxy] 5b46c4: Fix certain aspects of dataset reductions in condi...
by GitHub 03 Apr '17

03 Apr '17

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 5b46c431b416e619a7ac5467527ab30743eabd33 https://github.com/galaxyproject/galaxy/commit/5b46c431b416e619a7ac5467527a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py 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 Log Message: ----------- Fix certain aspects of dataset reductions in conditionals/repeats. For instance, fixes #3859 restoring the correct ``element_identifier`` for reduces collections in conditionals. Add tests for combinations of repeats and conditionals. Commit: 3c080cae96aadccd824aa7cf6fda9c4b5bf7471a https://github.com/galaxyproject/galaxy/commit/3c080cae96aadccd824aa7cf6fda… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py 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 Log Message: ----------- Merge pull request #3864 from jmchilton/fix_identifiers_in_conditionals [17.01] Fix certain aspects of collection reductions in conditionals/repeats. Commit: 83c8291976048ee1bec4047963b82ae805292b99 https://github.com/galaxyproject/galaxy/commit/83c8291976048ee1bec4047963b8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py 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 Log Message: ----------- Merge pull request #3867 from galaxyproject/release_17.01 [usegalaxy] merge Release 17.01 Compare: https://github.com/galaxyproject/galaxy/compare/aafb8e305ace...83c829197604

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[galaxyproject/galaxy] 5b46c4: Fix certain aspects of dataset reductions in condi...
by GitHub 03 Apr '17

03 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 5b46c431b416e619a7ac5467527ab30743eabd33 https://github.com/galaxyproject/galaxy/commit/5b46c431b416e619a7ac5467527a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py 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 Log Message: ----------- Fix certain aspects of dataset reductions in conditionals/repeats. For instance, fixes #3859 restoring the correct ``element_identifier`` for reduces collections in conditionals. Add tests for combinations of repeats and conditionals. Commit: 3c080cae96aadccd824aa7cf6fda9c4b5bf7471a https://github.com/galaxyproject/galaxy/commit/3c080cae96aadccd824aa7cf6fda… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py 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 Log Message: ----------- Merge pull request #3864 from jmchilton/fix_identifiers_in_conditionals [17.01] Fix certain aspects of collection reductions in conditionals/repeats. Compare: https://github.com/galaxyproject/galaxy/compare/268aac29526b...3c080cae96aa

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[galaxyproject/usegalaxy-playbook] 883f97: Forgot to commit updated GIE versions
by GitHub 03 Apr '17

03 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 883f977bf56f25af1aec54f81a19efb46e5e70e1 https://github.com/galaxyproject/usegalaxy-playbook/commit/883f977bf56f25af… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- Forgot to commit updated GIE versions

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[galaxyproject/usegalaxy-playbook] e19fdc: Update Test and Main
by GitHub 03 Apr '17

03 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e19fdc9ee821c9dee451555fef1a12ef75f9ed93 https://github.com/galaxyproject/usegalaxy-playbook/commit/e19fdc9ee821c9de… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M production/galaxy_version.yml M stage/galaxy_version.yml Log Message: ----------- Update Test and Main

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[galaxyproject/galaxy] 1fbdb3: Have IGV bigWig display application make use of bu...
by GitHub 03 Apr '17

03 Apr '17

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 1fbdb35d6edb84a3700ea1392dcf32f1a42f8225 https://github.com/galaxyproject/galaxy/commit/1fbdb35d6edb84a3700ea1392dcf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml Log Message: ----------- Have IGV bigWig display application make use of build_sites/ site_type config instead of direct filename. Commit: a2b5c41de00505179c7ce5a5f28ac0d9f0f1dee7 https://github.com/galaxyproject/galaxy/commit/a2b5c41de00505179c7ce5a5f28a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml Log Message: ----------- Merge pull request #3828 from blankenberg/17.01_bigwig_igv [17.01] Have IGV bigWig display application make use of build_sites/ site_typ… Commit: 5d3250fac03b32f4d14213cd6039aac884a1307e https://github.com/galaxyproject/galaxy/commit/5d3250fac03b32f4d14213cd6039… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- [17.01] Order processing evaluation of workflow invocations when scheduling. xref https://github.com/galaxyproject/galaxy/pull/3820#issuecomment-289725795 Also optimize the query to just pull out workflow invocation IDs per the suggestion of @nsoranzo [here](https://github.com/galaxyproject/galaxy/pull/3830#pullrequestreview-2…. Commit: 4beb98e973000e0bd51b06ad35301ddb8b905ec1 https://github.com/galaxyproject/galaxy/commit/4beb98e973000e0bd51b06ad3530… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- [17.01] By default, do not allow workflow invocations to schedule indefinitely. Give up after a month but allow admins to reduce this amount as well. Commit: aba31bc0d484f3729b46a10b2b357b92fa826fae https://github.com/galaxyproject/galaxy/commit/aba31bc0d484f3729b46a10b2b35… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- [17.01] Restrict workflow scheduling within a history to a fixed, random handler. Lets revisit the problem that background scheduling workflows (as is the default UI behavior as of 16.10) makes it easier for histories to contain datasets interleaved from different workflow invocations under certain reasonable conditions (https://github.com/galaxyproject/galaxy/issues/3474) Considering only a four year old workflow and tool feature set (no collection operations, no dynamic dataset discovery, only tool and input workflow modules), all workflows can and will fully schedule on the first scheduling iteration. Under those circumstances, this solution is functionally equivalent to history_local_serial_workflow_scheduling introduced #3520 - but should be more performant because all such workflows fully schedule in the first iteration and the double loop introduced here https://github.com/galaxyproject/galaxy/pull/3520/files#diff-d7e80a366f3965… is avoided for each workflow invocation for each iteration. This addresses both concerns I outlined [here](https://github.com/galaxyproject/galaxy/issues/3816#issuecomment-2893…. For workflows that use certain classes of newer tools or newer workflow features - I'd argue this approach will not degrade as harshly as enabling history_local_serial_workflow_scheduling. For instance, imagine a workflow with a dynamic dataset collection output step (such as used by IUC tools Deseq2, Trinity, Stacks, and various Mothur tools) half way through that takes 24 hour of queue time to reach. Now imagine a user running 5 such workflows at once. - Without this and without history_local_serial_workflow_scheduling, the 5 workflows will each run as fast as possible and the UI will show as much of each workflow as can be scheduled but the order of the datsets may be shuffled. The workflows will be complete for the users in 48 hours. - With history_local_serial_workflow_scheduling enabled, only 1 workflow will be scheduled only half way for the first 24 hours and the user will be given no visual indication for why the other workflows are not running for 1 day. The final workflow output will take nearly a week to be complete for the users. - With this enabled - the new default in this commit - each workflow will be scheduled in two chunks but these chunks will be contingious and it should be fairly clear to the user what tool caused the discontinuity of the datasets in the history. So things are still mostly ordered, but the draw backs of history_local_serial_workflow_scheduling are avoided entirely. Namely, the other four workflows aren't hidden from the user without a UI indication and the workflows will still only take 48 hours to be complete and outputs ready for the user. The only drawback of this new default behavior is that you could potentially see some performance improvements by scheduling multiple workflow invocations within one history - but this was never a design goal in my mind when implementing background scheduling and under typical Galaxy use cases I don't think this would be worth the UI problems. So, the older behavior can be re-enabled by setting parallelize_workflow_scheduling_within_histories to True in galaxy.ini but it won't be on by default or really recommended if the Galaxy UI is being used. Commit: 8f8526bf307d083c64330859793c112a9823b5d8 https://github.com/galaxyproject/galaxy/commit/8f8526bf307d083c64330859793c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- Merge pull request #3659 from jmchilton/1701_maximum_workflow_invocation_duration [17.01] By default, do not allow workflow invocations to schedule indefinitely. Commit: c51adf781a1a711c4e54d89fbdca7ea9d3331f08 https://github.com/galaxyproject/galaxy/commit/c51adf781a1a711c4e54d89fbdca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M static/maps/mvc/ui/ui-options.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/ui/ui-options.js Log Message: ----------- Insert update caller/helper for options Commit: 07887be3a162678859e32c063dae024f0a8da25c https://github.com/galaxyproject/galaxy/commit/07887be3a162678859e32c063dae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- Merge pull request #3820 from jmchilton/fixed_history_handler [17.01] Restrict workflow scheduling within a history to a fixed, random handler. Commit: bf6b65f005965eff9d01f432bf52f5d1104294b7 https://github.com/galaxyproject/galaxy/commit/bf6b65f005965eff9d01f432bf52… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #3830 from jmchilton/1701_order_collection_invocation_processing [17.01] Order processing evaluation of workflow invocations when scheduling. Commit: c8eb2c186def4b505143a5a6b0d971549b15d19a https://github.com/galaxyproject/galaxy/commit/c8eb2c186def4b505143a5a6b0d9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M static/maps/mvc/ui/ui-options.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/ui/ui-options.js Log Message: ----------- Merge pull request #3851 from guerler/add_lost_update_caller [17.01] Fix update caller/helper for options Commit: 99c8f2c9fc6f335863f134a5b8b4055d5079cfe1 https://github.com/galaxyproject/galaxy/commit/99c8f2c9fc6f335863f134a5b8b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix setting UUID on steps when copying steps from another workflow. It seems like the client is correctly setting the UUID to None, but the backend is treating the None as a UUID because it was (incorrectly IMO) making a distinction between ``uuid`` being absent and being set to ``None``. Fixes #3845. Commit: 268aac29526b3526a42457576e8de7867c2bfe1f https://github.com/galaxyproject/galaxy/commit/268aac29526b3526a42457576e8d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #3856 from jmchilton/1701_uuid_on_copy_fix [17.01] Fix setting UUID on steps when copying steps from another workflow. Commit: aafb8e305ace53af9aebd67626f8127b60b1219a https://github.com/galaxyproject/galaxy/commit/aafb8e305ace53af9aebd67626f8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M config/galaxy.ini.sample M display_applications/igv/bigwig.xml M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/scheduling_manager.py M static/maps/mvc/ui/ui-options.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/ui/ui-options.js M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.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 Log Message: ----------- Merge branch 'release_17.01' of https://github.com/galaxyproject/galaxy into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/812b04bb3abe...aafb8e305ace

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[galaxyproject/galaxy] 99c8f2: Fix setting UUID on steps when copying steps from ...
by GitHub 03 Apr '17

03 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 99c8f2c9fc6f335863f134a5b8b4055d5079cfe1 https://github.com/galaxyproject/galaxy/commit/99c8f2c9fc6f335863f134a5b8b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix setting UUID on steps when copying steps from another workflow. It seems like the client is correctly setting the UUID to None, but the backend is treating the None as a UUID because it was (incorrectly IMO) making a distinction between ``uuid`` being absent and being set to ``None``. Fixes #3845. Commit: 268aac29526b3526a42457576e8de7867c2bfe1f https://github.com/galaxyproject/galaxy/commit/268aac29526b3526a42457576e8d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #3856 from jmchilton/1701_uuid_on_copy_fix [17.01] Fix setting UUID on steps when copying steps from another workflow. Compare: https://github.com/galaxyproject/galaxy/compare/c8eb2c186def...268aac29526b

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[galaxyproject/galaxy]
by GitHub 01 Apr '17

01 Apr '17

Branch: refs/heads/contrib_changes Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] b5fe42: Small changes to links and add gitter
by GitHub 01 Apr '17

01 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b5fe42c462ebcbf4fb9f0a09fd63e11c2a68fd7e https://github.com/galaxyproject/galaxy/commit/b5fe42c462ebcbf4fb9f0a09fd63… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-01 (Sat, 01 Apr 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- Small changes to links and add gitter Commit: ffce14e65d70441827086c1eccdae46a28819df3 https://github.com/galaxyproject/galaxy/commit/ffce14e65d70441827086c1eccda… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- change devteam to iuc Commit: 224a5b39004e93c7ced8a6ce317e2ac85b553b40 https://github.com/galaxyproject/galaxy/commit/224a5b39004e93c7ced8a6ce317e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- fix contribute pdf link Commit: 5169fbe917c90ee6b13a345e869bf88bf51f6512 https://github.com/galaxyproject/galaxy/commit/5169fbe917c90ee6b13a345e869b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- Merge pull request #3861 from galaxyproject/contrib_changes Small changes to links and add gitter Compare: https://github.com/galaxyproject/galaxy/compare/6af5334f1254...5169fbe917c9

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[galaxyproject/galaxy] 224a5b: fix contribute pdf link
by GitHub 01 Apr '17

01 Apr '17

Branch: refs/heads/contrib_changes Home: https://github.com/galaxyproject/galaxy Commit: 224a5b39004e93c7ced8a6ce317e2ac85b553b40 https://github.com/galaxyproject/galaxy/commit/224a5b39004e93c7ced8a6ce317e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- fix contribute pdf link

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[galaxyproject/galaxy] ffce14: change devteam to iuc
by GitHub 01 Apr '17

01 Apr '17

Branch: refs/heads/contrib_changes Home: https://github.com/galaxyproject/galaxy Commit: ffce14e65d70441827086c1eccdae46a28819df3 https://github.com/galaxyproject/galaxy/commit/ffce14e65d70441827086c1eccda… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- change devteam to iuc

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[galaxyproject/galaxy] b5fe42: Small changes to links and add gitter
by GitHub 01 Apr '17

01 Apr '17

Branch: refs/heads/contrib_changes Home: https://github.com/galaxyproject/galaxy Commit: b5fe42c462ebcbf4fb9f0a09fd63e11c2a68fd7e https://github.com/galaxyproject/galaxy/commit/b5fe42c462ebcbf4fb9f0a09fd63… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-01 (Sat, 01 Apr 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- Small changes to links and add gitter

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[galaxyproject/usegalaxy-playbook] 46a503: Display protocol for ftp upload site.
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 46a503d82374c0a3cae7427de15f302d6f3bd44d https://github.com/galaxyproject/usegalaxy-playbook/commit/46a503d82374c0a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Display protocol for ftp upload site.

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[galaxyproject/galaxy] 5dcc0e: Clean up old TODO into history tests.
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5dcc0ed04376d08deb960f309e21fc14a6d29ce8 https://github.com/galaxyproject/galaxy/commit/5dcc0ed04376d08deb960f309e21… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M test/api/test_users.py Log Message: ----------- Clean up old TODO into history tests. We upgraded the module a long time ago now that was referenced in the Trello card. Commit: 6af5334f125461fba1ea1735bf06eed516bd6754 https://github.com/galaxyproject/galaxy/commit/6af5334f125461fba1ea1735bf06… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M test/api/test_users.py Log Message: ----------- Merge pull request #3855 from jmchilton/user_api_tests Clean up old TODO into history tests. Compare: https://github.com/galaxyproject/galaxy/compare/ad2e6473bc07...6af5334f1254

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[galaxyproject/galaxy] c51adf: Insert update caller/helper for options
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: c51adf781a1a711c4e54d89fbdca7ea9d3331f08 https://github.com/galaxyproject/galaxy/commit/c51adf781a1a711c4e54d89fbdca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M static/maps/mvc/ui/ui-options.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/ui/ui-options.js Log Message: ----------- Insert update caller/helper for options Commit: c8eb2c186def4b505143a5a6b0d971549b15d19a https://github.com/galaxyproject/galaxy/commit/c8eb2c186def4b505143a5a6b0d9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M static/maps/mvc/ui/ui-options.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/ui/ui-options.js Log Message: ----------- Merge pull request #3851 from guerler/add_lost_update_caller [17.01] Fix update caller/helper for options Compare: https://github.com/galaxyproject/galaxy/compare/bf6b65f00596...c8eb2c186def

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[galaxyproject/galaxy] 5d3250: [17.01] Order processing evaluation of workflow in...
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 5d3250fac03b32f4d14213cd6039aac884a1307e https://github.com/galaxyproject/galaxy/commit/5d3250fac03b32f4d14213cd6039… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- [17.01] Order processing evaluation of workflow invocations when scheduling. xref https://github.com/galaxyproject/galaxy/pull/3820#issuecomment-289725795 Also optimize the query to just pull out workflow invocation IDs per the suggestion of @nsoranzo [here](https://github.com/galaxyproject/galaxy/pull/3830#pullrequestreview-2…. Commit: bf6b65f005965eff9d01f432bf52f5d1104294b7 https://github.com/galaxyproject/galaxy/commit/bf6b65f005965eff9d01f432bf52… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #3830 from jmchilton/1701_order_collection_invocation_processing [17.01] Order processing evaluation of workflow invocations when scheduling. Commit: 7e64fa395c6c56a0973f56ecc1aa615f15d9fe80 https://github.com/galaxyproject/galaxy/commit/7e64fa395c6c56a0973f56ecc1aa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' Compare: https://github.com/galaxyproject/galaxy/compare/dd439530509f...7e64fa395c6c

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[galaxyproject/galaxy] 5d3250: [17.01] Order processing evaluation of workflow in...
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5d3250fac03b32f4d14213cd6039aac884a1307e https://github.com/galaxyproject/galaxy/commit/5d3250fac03b32f4d14213cd6039… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- [17.01] Order processing evaluation of workflow invocations when scheduling. xref https://github.com/galaxyproject/galaxy/pull/3820#issuecomment-289725795 Also optimize the query to just pull out workflow invocation IDs per the suggestion of @nsoranzo [here](https://github.com/galaxyproject/galaxy/pull/3830#pullrequestreview-2…. Commit: bf6b65f005965eff9d01f432bf52f5d1104294b7 https://github.com/galaxyproject/galaxy/commit/bf6b65f005965eff9d01f432bf52… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #3830 from jmchilton/1701_order_collection_invocation_processing [17.01] Order processing evaluation of workflow invocations when scheduling. Commit: ad2e6473bc07a5b229d50f85c28cad0363a40f11 https://github.com/galaxyproject/galaxy/commit/ad2e6473bc07a5b229d50f85c28c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/190d1901a43a...ad2e6473bc07

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[galaxyproject/galaxy] 5d3250: [17.01] Order processing evaluation of workflow in...
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 5d3250fac03b32f4d14213cd6039aac884a1307e https://github.com/galaxyproject/galaxy/commit/5d3250fac03b32f4d14213cd6039… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- [17.01] Order processing evaluation of workflow invocations when scheduling. xref https://github.com/galaxyproject/galaxy/pull/3820#issuecomment-289725795 Also optimize the query to just pull out workflow invocation IDs per the suggestion of @nsoranzo [here](https://github.com/galaxyproject/galaxy/pull/3830#pullrequestreview-2…. Commit: bf6b65f005965eff9d01f432bf52f5d1104294b7 https://github.com/galaxyproject/galaxy/commit/bf6b65f005965eff9d01f432bf52… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #3830 from jmchilton/1701_order_collection_invocation_processing [17.01] Order processing evaluation of workflow invocations when scheduling. Compare: https://github.com/galaxyproject/galaxy/compare/07887be3a162...bf6b65f00596

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