Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c8573888232f15ef3641bfeb2f0d92a7aa80387f
https://github.com/galaxyproject/galaxy/commit/c8573888232f15ef3641bfeb2f0d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Merge ToolConfWatchers and separate from Toolbox
This should avoid some complexities associated with managing threads.
I would also like to eliminate the separate reload_tool_data_tables
and reload_data_managers callbacks and do this when reloading the
toolbox, but every tool data table reload triggers twice the download of
http://igv.broadinstitute.org/genomes/genomes.txt, which each time takes
2 seconds.
Commit: 1a5e337420e4832593b6e30089c0022291fd6078
https://github.com/galaxyproject/galaxy/commit/1a5e337420e4832593b6e30089c0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/app.py
M lib/galaxy/tools/toolbox/watcher.py
A lib/galaxy/webapps/galaxy/config_watchers.py
Log Message:
-----------
Move ConfigWatchers into galaxy.webapps.galaxy.config_watchers
Commit: f79fb9075a4f724d5bad95163a6450c9ffb89b84
https://github.com/galaxyproject/galaxy/commit/f79fb9075a4f724d5bad95163a64…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/config_watchers.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Move ToolWatcher from Toolbox to ConfigWatchers class
Commit: 63f1efd15a6903526406ff8d643fb3d6f4a5e678
https://github.com/galaxyproject/galaxy/commit/63f1efd15a6903526406ff8d643f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Fix toolshed startup
Commit: c4e6671ce50a64ba561a3ef815816426183adf4d
https://github.com/galaxyproject/galaxy/commit/c4e6671ce50a64ba561a3ef81581…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/config_watchers.py
Log Message:
-----------
Fix import order in config_watchers.py
Commit: b037332e943edbf9cf65f4799a1226bf53e8476a
https://github.com/galaxyproject/galaxy/commit/b037332e943edbf9cf65f4799a12…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/config_watchers.py
Log Message:
-----------
Avoid race-condition between multiple instances of ToolConfWatchers
Commit: 2c7089df46fa0a5178a1e0f72cc87514e8a97142
https://github.com/galaxyproject/galaxy/commit/2c7089df46fa0a5178a1e0f72cc8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Fix TS tests
Commit: e7a4ae5c154e5a9a9d2767c76ea043c5fd846fe8
https://github.com/galaxyproject/galaxy/commit/e7a4ae5c154e5a9a9d2767c76ea0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-07 (Fri, 07 Apr 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
A lib/galaxy/webapps/galaxy/config_watchers.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Merge pull request #3821 from mvdbeek/repository_updates
Merge ToolConfWatchers and separate from Toolbox
Compare: https://github.com/galaxyproject/galaxy/compare/b5323e714726...e7a4ae5c154e
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 2b4b431d0a4f300c1af3d9ac4a105e7887ec09c6
https://github.com/galaxyproject/galaxy/commit/2b4b431d0a4f300c1af3d9ac4a10…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-06 (Thu, 06 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:
-----------
Add missing trigger event to drop handler in content selector
Commit: ea17f2dacf8b00e579741676deb33a98d0c234ef
https://github.com/galaxyproject/galaxy/commit/ea17f2dacf8b00e579741676deb3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/tag.js
M client/package.json
M client/webpack.config.js
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/tags.py
M lib/galaxy/tools/actions/__init__.py
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/tag.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/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/tag.js
Log Message:
-----------
Merge branch 'dev' into fix_refresh_trigger
Commit: f5ade2b5daab6fbf3fa924cbda89fbf21e7373a9
https://github.com/galaxyproject/galaxy/commit/f5ade2b5daab6fbf3fa924cbda89…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-07 (Fri, 07 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:
-----------
Merge pull request #3897 from guerler/fix_refresh_trigger
Add missing trigger event to drop handler in content selector
Compare: https://github.com/galaxyproject/galaxy/compare/408906efb118...f5ade2b5daab
Branch: refs/heads/master
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: 3a24bb310885f6a529e28aa6c8424e991223a45d
https://github.com/galaxyproject/infrastructure-playbook/commit/3a24bb31088…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-04-07 (Fri, 07 Apr 2017)
Changed paths:
A common_env/group_vars/dockersslclients.yml
A common_env/secret_group_vars/dockersslclients.yml
M roles/docker/defaults/main.yml
M roles/docker/tasks/ssl-ca.yml
M roles/docker/tasks/ssl-client.yml
M roles/docker/tasks/ssl-server.yml
A taccenv/group_vars/dockersslclients.yml
M taccenv/host_vars/galaxy07.tacc.utexas.edu.yml
M taccenv/inventory
M taccenv/playbook.yml
A taccenv/secret_group_vars/dockersslclients.yml
Log Message:
-----------
Docker SSL fixes (distribute from playbook if necessary, e.g. for cases where
the docker ssl master cannot ssh directly to ansible_user@client).
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f88d893562112223553ba069eff2a1f42fe7d69b
https://github.com/galaxyproject/galaxy/commit/f88d893562112223553ba069eff2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M lib/galaxy/managers/tags.py
Log Message:
-----------
Add HistoryDatasetCollectionAssociation as a possible tagged item in the galaxy tag manager. Should refactor this down the road, feels weird to register everything here in the manager.
Commit: 73bfb57abf5ba728e4145731f91d0b222d74f5df
https://github.com/galaxyproject/galaxy/commit/73bfb57abf5ba728e4145731f91d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M lib/galaxy/managers/collections.py
Log Message:
-----------
Use the correct tag manager instance from the Collections manager.
Commit: 5ceca34344b92d6bfa63ad1eb433a1cdea893f4f
https://github.com/galaxyproject/galaxy/commit/5ceca34344b92d6bfa63ad1eb433…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M lib/galaxy/managers/collections.py
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-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/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
Log Message:
-----------
Add basic tag rendering to expanded collection
Commit: 821ee5bbcbfdd9a79c52ac60a20a51e20898b573
https://github.com/galaxyproject/galaxy/commit/821ee5bbcbfdd9a79c52ac60a20a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M static/maps/mvc/collection/collection-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/collection/collection-view-edit.js
Log Message:
-----------
Simplify tags usage, since this editor's display is static.
Commit: 4a45c9097e5c7d19977196d3ade1cd949af5af03
https://github.com/galaxyproject/galaxy/commit/4a45c9097e5c7d19977196d3ade1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M client/package.json
M client/webpack.config.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.map
Log Message:
-----------
Add babel loader.
Commit: 2a86f8e54c95da45b59fe166d515fc40b06f3c26
https://github.com/galaxyproject/galaxy/commit/2a86f8e54c95da45b59fe166d515…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M lib/galaxy/managers/hdcas.py
Log Message:
-----------
Add tags to hdca serializer. TODO: Details only.
Commit: 225393a30006ca0313585de1a4bd93b3f0d88566
https://github.com/galaxyproject/galaxy/commit/225393a30006ca0313585de1a4bd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M lib/galaxy/managers/hdcas.py
Log Message:
-----------
Add nametags to dataset collection serializer
Commit: c4fd96092bcabd869f8c4a4427489d0b2c6209a3
https://github.com/galaxyproject/galaxy/commit/c4fd96092bcabd869f8c4a442748…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-30 (Thu, 30 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/tag.js
M static/maps/mvc/tag.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/tag.js
Log Message:
-----------
Make TagEditor label optional.
Commit: c452af01bd16cf85e7459f767ee77c381e527a9a
https://github.com/galaxyproject/galaxy/commit/c452af01bd16cf85e7459f767ee7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/hdca-li.js
M static/maps/mvc/history/hdca-li.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/hdca-li.js
Log Message:
-----------
Render 'nametags' for hdcas
Commit: 2f4aa1a763146e980f9c1c929f07ffd4b7bf7ff3
https://github.com/galaxyproject/galaxy/commit/2f4aa1a763146e980f9c1c929f07…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M static/maps/mvc/collection/collection-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/collection/collection-view-edit.js
Log Message:
-----------
Toggle tags prompt on collection view
Commit: 01655895174eb14530d27452789682335b2f7197
https://github.com/galaxyproject/galaxy/commit/01655895174eb14530d274527896…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view.js
M static/maps/mvc/collection/collection-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.map
M static/scripts/mvc/collection/collection-view.js
Log Message:
-----------
Tags editor location/styling fix for collection view.
Commit: c9bbaa30f7400f547e8549ae8d0d3bed5ccbf0c5
https://github.com/galaxyproject/galaxy/commit/c9bbaa30f7400f547e8549ae8d0d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M CONTRIBUTING.md
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-contents.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-options.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/ui/paired-collection-creator.less
M client/galaxy/style/less/upload.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample
M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
A 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
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/utilities/sifjson.js
M config/plugins/visualizations/charts/static/repository/utilities/utils.js
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
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/config.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/scheduling_manager.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-contents.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-options.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-contents.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-options.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 templates/webapps/galaxy/admin/manage_dependencies.mako
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/api_asserts.py
M test/base/data/test_workflow_pause.ga
M test/base/driver_util.py
M test/base/populators.py
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
A test/functional/tools/identifier_multiple_in_conditional.xml
A test/functional/tools/identifier_multiple_in_repeat.xml
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/sizzle.py
A test/integration/test_maximum_worklfow_invocation_duration.py
A test/integration/test_workflow_handler_configuration.py
A test/integration/workflow_handler_configuration_job_conf.xml
M test/qunit/test-data/paired-collection-creator.data.js
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into tags_improvements
Commit: 439444e65ad9c79a0a2553a5eb916405b1910e93
https://github.com/galaxyproject/galaxy/commit/439444e65ad9c79a0a2553a5eb91…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Preserve tags for collection outputs. This is one step forward, also need to address non-output handled collectinos, like those automatically created in workflow execution with collection inputs.
Commit: bfbca68b4e70cc380398e364dd8abdd5ac1a360e
https://github.com/galaxyproject/galaxy/commit/bfbca68b4e70cc380398e364dd8a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Don't wrap tags up in element_kwds -- this prevents them being sent to non-hda collections.
Commit: 6ce47ddbf4ed0046f52cd6c7d4f140c893d9b1e3
https://github.com/galaxyproject/galaxy/commit/6ce47ddbf4ed0046f52cd6c7d4f1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M lib/galaxy/managers/collections.py
Log Message:
-----------
Also include implicit_collection_info in collection tag creation logic.
Commit: bdcc474d3666fd08f0032629e1882a4441b35244
https://github.com/galaxyproject/galaxy/commit/bdcc474d3666fd08f0032629e188…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-table.js
A client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/ui.less
M lib/galaxy/web/framework/base.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A static/GruntFile.js
A static/GruntFile.js.map
M static/maps/layout/menu.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-table.js.map
A static/maps/mvc/user/user-custom-builds.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/form/form-parameters.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-table.js
A static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
M static/style/blue/base.css
R templates/user/dbkeys.mako
M tools/filters/trimmer.py
M tools/filters/trimmer.xml
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into tags_improvements
Commit: 54b7c32bd2913c236c4eacfaf45bdef3ba4c2e7d
https://github.com/galaxyproject/galaxy/commit/54b7c32bd2913c236c4eacfaf45b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li.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/hda-li.js
M static/scripts/mvc/history/hdca-li.js
Log Message:
-----------
Render nametags from core tag data instead of a different field. This actually should be somewhat faster, along with being easier to track/update.
Commit: 2215869f2d68c1839091dc23cf303bf43fa29078
https://github.com/galaxyproject/galaxy/commit/2215869f2d68c1839091dc23cf30…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/tag.js
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/tag.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/hda-li.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/tag.js
Log Message:
-----------
Listen to tag change events, rerender list item for nametags.
Commit: 5a513b20bbc371cf9a51483b1cf468d9126a45fe
https://github.com/galaxyproject/galaxy/commit/5a513b20bbc371cf9a51483b1cf4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/tag.js
M static/maps/mvc/tag.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/tag.js
Log Message:
-----------
Remove (previously) never-invoked change code which now double-invokes. Parents will handle this.
Commit: d41a4efd8822c46aa9f236937d4fc74678ba0dfd
https://github.com/galaxyproject/galaxy/commit/d41a4efd8822c46aa9f236937d4f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M static/maps/mvc/dataset/dataset-li.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.js
Log Message:
-----------
For datasets, only rerender title bar if tags have changed (for nametags)
Commit: 2ab68fea8b20c256c30afd7e18bcf2647c978396
https://github.com/galaxyproject/galaxy/commit/2ab68fea8b20c256c30afd7e18bc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/hda-li.js
M static/maps/mvc/history/hda-li.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/hda-li.js
Log Message:
-----------
Remove redundant listener, handled in parent.
Commit: 9e9a2d8312990c11ff7d9df6e71927bdc3210514
https://github.com/galaxyproject/galaxy/commit/9e9a2d8312990c11ff7d9df6e719…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M static/maps/mvc/dataset/dataset-li.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.js
Log Message:
-----------
Rerender specifically subtitle iff it's the only changed attribute.
Commit: cad62b1f8b5d289dc27ec88303118dadddbbbc52
https://github.com/galaxyproject/galaxy/commit/cad62b1f8b5d289dc27ec8830311…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-06 (Thu, 06 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 config/tool_destinations.yml.sample
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
R lib/galaxy/webapps/galaxy/controllers/search.py
M run_tests.sh
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
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 remote-tracking branch 'upstream/dev' into tags_improvements
Commit: 1a5d570704da50bdca0ca3194f5549f1338f2c6b
https://github.com/galaxyproject/galaxy/commit/1a5d570704da50bdca0ca3194f55…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M static/maps/mvc/collection/collection-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
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Remove comment, rebuild.
Commit: 8ea4cf29f812d8ce29b31efa18495aad5d5fca44
https://github.com/galaxyproject/galaxy/commit/8ea4cf29f812d8ce29b31efa1849…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/tag.js
M client/package.json
M client/webpack.config.js
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/tags.py
M lib/galaxy/tools/actions/__init__.py
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/tag.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/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/tag.js
Log Message:
-----------
Merge pull request #3868 from dannon/tags_improvements
Adding tagging to collections.
Compare: https://github.com/galaxyproject/galaxy/compare/483f25c5c2c8...8ea4cf29f812
Branch: refs/heads/master
Home: https://github.com/galaxyproject/ansible-galaxy
Commit: c9f923ad2691df71df75658cebd87f4249ab268c
https://github.com/galaxyproject/ansible-galaxy/commit/c9f923ad2691df71df75…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M README.md
M defaults/main.yml
M files/makepyc.py
M handlers/main.yml
M tasks/clone.yml
M tasks/database.yml
M tasks/dependencies.yml
M tasks/download.yml
M tasks/main.yml
M tasks/mutable_setup.yml
M tasks/static_setup.yml
M tasks/virtualenv.yml
Log Message:
-----------
Remove a lot of cruft, switch to yaml-style task params, and update for
Ansible 2.2 compatibility