March 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 8d71c3: Change to sentry middleware to work with modern ra...
by GitHub 09 Mar '16

09 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d71c3dc1b7ed1ad33f60af1f1fe71e4c7ece108 https://github.com/galaxyproject/galaxy/commit/8d71c3dc1b7ed1ad33f60af1f1fe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Change to sentry middleware to work with modern raven clients. This allows us to upgrade raven and actually show the entire event_id to users on the guru meditation page. Commit: cd26a567e84bbe736d3dcfbcbe37da7070045823 https://github.com/galaxyproject/galaxy/commit/cd26a567e84bbe736d3dcfbcbe37… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Merge pull request #1895 from dannon/sentry_event_id Change to sentry middleware to work with modern raven clients. Compare: https://github.com/galaxyproject/galaxy/compare/36d85e81eecd...cd26a567e84b

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[galaxyproject/usegalaxy-playbook] 14427d: Mutable configs on Test + fix the Test config to r...
by GitHub 08 Mar '16

08 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 14427de5dd473ae9020b4ea2118e6f91c6f2d715 https://github.com/galaxyproject/usegalaxy-playbook/commit/14427de5dd473ae9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M stage/group_vars/galaxyservers.yml Log Message: ----------- Mutable configs on Test + fix the Test config to remove a duplication

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[galaxyproject/usegalaxy-playbook] 195454: Update Test
by GitHub 08 Mar '16

08 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 195454dc2362dee23e9170e2990cba5f875ef016 https://github.com/galaxyproject/usegalaxy-playbook/commit/195454dc2362dee2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test

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[galaxyproject/infrastructure-playbook] 9e9077: Install sentry on galaxy06
by GitHub 08 Mar '16

08 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 9e9077c991fc7ec0b6ef5ab317d7262723a6a6b4 https://github.com/galaxyproject/infrastructure-playbook/commit/9e9077c991f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M common_roles A roles/sentry/defaults/main.yml A roles/sentry/tasks/main.yml A roles/sentry/templates/redis.conf.j2 A roles/sentry/templates/sentry.conf.py.j2 A roles/sentry/templates/uwsgi.ini.j2 M taccenv/group_vars/statsservers.yml M taccenv/host_vars/galaxy06.tacc.utexas.edu.yml M taccenv/playbook.yml M taccenv/secret_group_vars/ssl.yml M taccenv/templates/nginx/sentry.j2 A taccenv/templates/supervisor/sentry.j2 Log Message: ----------- Install sentry on galaxy06

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[galaxyproject/usegalaxy-playbook] 39d151: Move the supervisor module to the common_roles sub...
by GitHub 08 Mar '16

08 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 39d151d8207a6b829918bf3061dfab35b7c8feff https://github.com/galaxyproject/usegalaxy-playbook/commit/39d151d8207a6b82… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M common_roles M production/group_vars/galaxyservers.yml M production/group_vars/toolshedservers.yml M production/host_vars/galaxy-web-01.tacc.utexas.edu.yml R roles/supervisor/defaults/main.yml R roles/supervisor/handlers/main.yml R roles/supervisor/tasks/main.yml R roles/supervisor/templates/centos.init.j2 R roles/supervisor/templates/debian.init.j2 R roles/supervisor/templates/redhat.init.j2 R roles/supervisor/templates/supervisord.conf.j2 R roles/supervisor/templates/systemd.init.j2 R roles/supervisor/templates/ubuntu.init.j2 M stage/group_vars/galaxyservers.yml M stage/group_vars/toolshedservers.yml R templates/supervisor/galaxy.conf.j2 A templates/supervisor/galaxy.j2 R templates/supervisor/galaxy_datamanager.conf.j2 A templates/supervisor/galaxy_datamanager.j2 R templates/supervisor/galaxy_group.conf.j2 A templates/supervisor/galaxy_group.j2 R templates/supervisor/galaxy_impersonate.conf.j2 A templates/supervisor/galaxy_impersonate.j2 R templates/supervisor/galaxy_installer.conf.j2 A templates/supervisor/galaxy_installer.j2 R templates/supervisor/galaxy_reports.conf.j2 A templates/supervisor/galaxy_reports.j2 R templates/supervisor/testtoolshed.conf.j2 A templates/supervisor/testtoolshed.j2 R templates/supervisor/toolshed.conf.j2 A templates/supervisor/toolshed.j2 Log Message: ----------- Move the supervisor module to the common_roles submodule.

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[galaxyproject/galaxy] 3241fe: Click-to-center functionality for the workflow edi...
by GitHub 08 Mar '16

08 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3241fe3cad8ad19ac5265a02482919ea60cfb0c5 https://github.com/galaxyproject/galaxy/commit/3241fe3cad8ad19ac5265a024829… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M static/maps/mvc/workflow/workflow-canvas.js.map M static/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- Click-to-center functionality for the workflow editor overview box. Commit: 517be33229efec0fc5410e544260fed93a2f815f https://github.com/galaxyproject/galaxy/commit/517be33229efec0fc5410e544260… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M static/maps/mvc/workflow/workflow-canvas.js.map M static/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- Block the extra click that happens just after drag-end; we don't want to move/recenter an additional time. Commit: 365e20733156d8873243c5c86770605259d472ab https://github.com/galaxyproject/galaxy/commit/365e20733156d8873243c5c86770… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- Fix positional calculation to work regardless of event-source element. Commit: f2043a2142106f33ebfb5260705ca686583a2219 https://github.com/galaxyproject/galaxy/commit/f2043a2142106f33ebfb5260705c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M static/maps/mvc/workflow/workflow-canvas.js.map M static/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- rebuild client Commit: 5561c8c2ea5243c31eb5fdea08c388444ce4ee45 https://github.com/galaxyproject/galaxy/commit/5561c8c2ea5243c31eb5fdea08c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove stray debug statement (I think) Commit: 36d85e81eecde5a4ae2d8b3252f8f13295585adc https://github.com/galaxyproject/galaxy/commit/36d85e81eecde5a4ae2d8b3252f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M static/maps/mvc/workflow/workflow-canvas.js.map M static/scripts/mvc/workflow/workflow-canvas.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #1843 from dannon/click_workflow_overview Workflow editor overview click navigation Compare: https://github.com/galaxyproject/galaxy/compare/57c25731492a...36d85e81eecd

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[galaxyproject/galaxy] 9f5b7a: Revise tool state encryption, remove copy/paste ha...
by GitHub 08 Mar '16

08 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f5b7a5f66e053b502c20aaaac588b604897ebaf https://github.com/galaxyproject/galaxy/commit/9f5b7a5f66e053b502c20aaaac58… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-05 (Sat, 05 Mar 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/util/workflow_util.py M templates/webapps/galaxy/workflow/run.mako M test/unit/workflows/test_modules.py Log Message: ----------- Revise tool state encryption, remove copy/paste hacks Commit: 96b1274b12a465c2ba0311124428aa929129af2c https://github.com/galaxyproject/galaxy/commit/96b1274b12a465c2ba0311124428… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-05 (Sat, 05 Mar 2016) Changed paths: M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M templates/webapps/galaxy/workflow/run.mako M test/unit/workflows/test_modules.py Log Message: ----------- Remove encode_runtime_state Commit: 57c25731492a7441b528dbf5de877c96d9cb30d5 https://github.com/galaxyproject/galaxy/commit/57c25731492a7441b528dbf5de87… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/util/workflow_util.py M templates/webapps/galaxy/workflow/run.mako M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #1838 from guerler/remove_decoding_000 Remove decryption/encryption of tool states Compare: https://github.com/galaxyproject/galaxy/compare/0f06dfe670ac...57c25731492a

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[galaxyproject/galaxy] 4dc403: Replace get_tool_shed_repository_by_tool_shed_name...
by GitHub 08 Mar '16

08 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4dc40352de31babba69ca06618d6ac64add15c56 https://github.com/galaxyproject/galaxy/commit/4dc40352de31babba69ca06618d6… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Replace get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision with get_repository_for_dependency_relationship Commit: 28595613dcada855f2675b4c57710486aadcdc73 https://github.com/galaxyproject/galaxy/commit/28595613dcada855f2675b4c5771… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- remove unused import Commit: 0f06dfe670ac53ffc0b648883f33dc4e622068f7 https://github.com/galaxyproject/galaxy/commit/0f06dfe670ac53ffc0b648883f33… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Merge pull request #1868 from mvdbeek/update_troubleshooting Replace get_tool_shed_repository_by_tool_shed_name_owner_changeset_re… Compare: https://github.com/galaxyproject/galaxy/compare/eb832cae6a73...0f06dfe670ac

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[galaxyproject/galaxy] 0d7c6c: Resolves https://github.com/galaxyproject/galaxy/i...
by GitHub 07 Mar '16

07 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0d7c6c2ddf6721dd0a7b6eaed5ec8a1f6c85bb18 https://github.com/galaxyproject/galaxy/commit/0d7c6c2ddf6721dd0a7b6eaed5ec… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Resolves https://github.com/galaxyproject/galaxy/issues/1878 by adding a dedicated client endpoint on the root controller. Commit: eb832cae6a73d748abe54a5ed1d828d04f28d72e https://github.com/galaxyproject/galaxy/commit/eb832cae6a73d748abe54a5ed1d8… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #1879 from dannon/multiple_aliased_routes_fix Add dedicated client endpoint to the root controller. Compare: https://github.com/galaxyproject/galaxy/compare/4cf90643580c...eb832cae6a73

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[galaxyproject/galaxy] e14e8a: Allow rerun of datasets new yet queued by job mana...
by GitHub 07 Mar '16

07 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e14e8a074c1344ab62dae2254f1e4a250e963b22 https://github.com/galaxyproject/galaxy/commit/e14e8a074c1344ab62dae2254f1e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-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/dataset/dataset-li-edit.js Log Message: ----------- Allow rerun of datasets new yet queued by job manager. Commit: 0445fcda51cad08a0b2969140b48948a9e7d759b https://github.com/galaxyproject/galaxy/commit/0445fcda51cad08a0b2969140b48… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add workflow building mode check to collection parameter handling Commit: 8905bafe10845545bedbd1c6b9e758e1b9523b4d https://github.com/galaxyproject/galaxy/commit/8905bafe10845545bedbd1c6b9e7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-06 (Sun, 06 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1859 from guerler/fix_collection_000 [16.01] Add workflow building mode check to collection parameter handling Commit: 0c34d5bd3ff414d6beb669e106306066f663d75f https://github.com/galaxyproject/galaxy/commit/0c34d5bd3ff414d6beb669e10630… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-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/dataset/dataset-li-edit.js Log Message: ----------- Merge pull request #1858 from jmchilton/rerun_new_datasets [16.01] Allow rerun of datasets new yet queued by job manager. Commit: 4cf90643580c4cda20b2076e9ebe2bb5660a4c75 https://github.com/galaxyproject/galaxy/commit/4cf90643580c4cda20b2076e9ebe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/dataset/dataset-li-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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge, rebuild client. Compare: https://github.com/galaxyproject/galaxy/compare/cff3eb8073ea...4cf90643580c

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