Branch: refs/heads/release_18.01
Home: https://github.com/galaxyproject/galaxy
Commit: 7490fd452046b4a4578f6401501439773cbf2f28
https://github.com/galaxyproject/galaxy/commit/7490fd452046b4a4578f64015014…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/model_operations.py
Log Message:
-----------
More robust nametag discovery and propagation.
- Nametags weren't being picked up on collection inputs - so for instance tools that take in a single collection and produce a dataset or file weren't propagating nametags (unless the collection contents had tags). To see this create two unnamed datasets without tags, create a pair from them, add a tag to the pair, and run the pair through the "paired_test" test tool.
- Nametags weren't being propagated to the outputs of collection operations.
Commit: 6f40f7098d507895c6c6608aff6a698289f2eeb6
https://github.com/galaxyproject/galaxy/commit/6f40f7098d507895c6c6608aff6a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Cleanup collection operation tagging implementation thanks to @mvdbeek comments.
Commit: 6022fe7d7e90b0da0cad83589d5d630f6dd1d386
https://github.com/galaxyproject/galaxy/commit/6022fe7d7e90b0da0cad83589d5d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Handle optional inputs when collecting preserved tags.
https://github.com/galaxyproject/galaxy/pull/5403/files#r165283450
Commit: 60561c20307cf0585e553d0fa5cd612716ab7975
https://github.com/galaxyproject/galaxy/commit/60561c20307cf0585e553d0fa5cd…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/model_operations.py
Log Message:
-----------
Merge pull request #5403 from jmchilton/collection_operation_tags
[18.01] More robust nametag discovery and propagation.
Compare: https://github.com/galaxyproject/galaxy/compare/f24043e8a74e...60561c20307c
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6bdd755aafbb008422db46231949ad3c6e4e608f
https://github.com/galaxyproject/galaxy/commit/6bdd755aafbb008422db46231949…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-01-25 (Thu, 25 Jan 2018)
Changed paths:
M doc/source/admin/framework_dependencies.rst
Log Message:
-----------
WIP framework dependencies doc update
Commit: fd96864bd6fca8f4ff149ca0ba270ebb164254ac
https://github.com/galaxyproject/galaxy/commit/fd96864bd6fca8f4ff149ca0ba27…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-01-25 (Thu, 25 Jan 2018)
Changed paths:
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/scaling.md
R lib/galaxy/dependencies/conda-environment.txt
A lib/galaxy/dependencies/conda-file.sh
M scripts/common_startup.sh
Log Message:
-----------
Finish updates to framework dependencies doc
Commit: 6333e83a6517830599d17e42707f0bead367d135
https://github.com/galaxyproject/galaxy/commit/6333e83a6517830599d17e42707f…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-01-26 (Fri, 26 Jan 2018)
Changed paths:
M doc/source/admin/framework_dependencies.rst
Log Message:
-----------
Doc corrections from @nsoranzo
Commit: 6070bf07e18b0d3ebc210f3c4c44a1ed14b1dd27
https://github.com/galaxyproject/galaxy/commit/6070bf07e18b0d3ebc210f3c4c44…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/onload.js
A config/plugins/webhooks/demo/search/config.yml
R config/plugins/webhooks/demo/search/config/searchover.yaml
A config/plugins/webhooks/demo/search/script.js
R config/plugins/webhooks/demo/search/static/script.js
R config/plugins/webhooks/demo/search/static/styles.css
A config/plugins/webhooks/demo/search/styles.css
A config/plugins/webhooks/demo/tool_list/__init__.py
A config/plugins/webhooks/demo/tool_list/config.yml
R config/plugins/webhooks/demo/tool_list/config/tool_list.yml
R config/plugins/webhooks/demo/tool_list/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/__init__.py
A config/plugins/webhooks/demo/tour_generator/config.yml
R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml
R config/plugins/webhooks/demo/tour_generator/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/script.js
R config/plugins/webhooks/demo/tour_generator/static/script.js
R config/plugins/webhooks/demo/tour_generator/static/styles.css
A config/plugins/webhooks/demo/tour_generator/styles.css
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webhooks/__init__.py
A test/functional/webhooks/history_test1/config.yml
R test/functional/webhooks/history_test1/config/history_test1.yml
A test/functional/webhooks/history_test2/config.yml
R test/functional/webhooks/history_test2/config/history_test2.yml
A test/functional/webhooks/masthead_test/config.yml
R test/functional/webhooks/masthead_test/config/masthead_test.yml
A test/functional/webhooks/phdcomics/__init__.py
A test/functional/webhooks/phdcomics/config.yaml
R test/functional/webhooks/phdcomics/config/phdcomics.yaml
R test/functional/webhooks/phdcomics/helper/__init__.py
A test/functional/webhooks/phdcomics/script.js
R test/functional/webhooks/phdcomics/static/script.js
R test/functional/webhooks/phdcomics/static/styles.css
A test/functional/webhooks/phdcomics/styles.css
A test/functional/webhooks/trans_object/__init__.py
A test/functional/webhooks/trans_object/config.yaml
R test/functional/webhooks/trans_object/config/trans_object.yaml
R test/functional/webhooks/trans_object/helper/__init__.py
A test/functional/webhooks/xkcd/config.yml
R test/functional/webhooks/xkcd/config/xkcd.yml
A test/functional/webhooks/xkcd/script.js
R test/functional/webhooks/xkcd/static/script.js
R test/functional/webhooks/xkcd/static/styles.css
A test/functional/webhooks/xkcd/styles.css
Log Message:
-----------
simplify Webhooks' structure
Commit: ada76931d8231a83ff15667ccec652b06bd793d4
https://github.com/galaxyproject/galaxy/commit/ada76931d8231a83ff15667ccec6…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/onload.js
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
add weighted random webhook pick
Commit: 90d59ac9234d7a756eb3040cccb35c6e181826ec
https://github.com/galaxyproject/galaxy/commit/90d59ac9234d7a756eb3040cccb3…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M test/api/test_webhooks.py
M test/selenium_tests/test_tool_describing_tours.py
Log Message:
-----------
fix webhooks tests
Commit: 57c1fc78043220ec16081255c2b15e854cac976c
https://github.com/galaxyproject/galaxy/commit/57c1fc78043220ec16081255c2b1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/onload.js
Log Message:
-----------
Client formatting of webhooks changes.
Commit: 0ac7b7830dd06ef474002a57c677ca429913d766
https://github.com/galaxyproject/galaxy/commit/0ac7b7830dd06ef474002a57c677…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
Fix import order in webhooks/__init__.py
Commit: 3b7daece0460286288a8678c5020dd6530d5457f
https://github.com/galaxyproject/galaxy/commit/3b7daece0460286288a8678c5020…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/webhooks.js
Log Message:
-----------
Delay interpolation of webhook url template; Galaxy won't exist as a configured object necessarily when this is imported.
Commit: 22b0b2f2e90249feacacd0f8cfb60a9335bb40e9
https://github.com/galaxyproject/galaxy/commit/22b0b2f2e90249feacacd0f8cfb6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/qunit/tests/page_tests.js
Log Message:
-----------
Minor tweaks/fixes while trying to sort out qunit test failures related to webhook changes.
Commit: fa0ba22f97cbf69c30828205ea94358094b654e0
https://github.com/galaxyproject/galaxy/commit/fa0ba22f97cbf69c30828205ea94…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/qunit/test-app.js
Log Message:
-----------
Fix webhook filtering, make it a bit more defensive. Minor other tweaks.
Commit: 9b4465efd37fe7c27276971a2348283e41cc9027
https://github.com/galaxyproject/galaxy/commit/9b4465efd37fe7c27276971a2348…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M client/galaxy/scripts/layout/menu.js
Log Message:
-----------
fix webhook's property name
Commit: 29c766167a64f302341101b0a7301fcd29634698
https://github.com/galaxyproject/galaxy/commit/29c766167a64f302341101b0a730…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M doc/source/admin/special_topics/webhooks.rst
Log Message:
-----------
update webhooks docs
Commit: a37b638491bc1d04be266bf9a14852fcfb62c342
https://github.com/galaxyproject/galaxy/commit/a37b638491bc1d04be266bf9a148…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/scaling.md
R lib/galaxy/dependencies/conda-environment.txt
A lib/galaxy/dependencies/conda-file.sh
M scripts/common_startup.sh
Log Message:
-----------
Merge pull request #5390 from natefoo/framework-dependencies-doc-update
[18.01] Update framework dependencies documentation
Commit: ffaabe0a63f47c57cd9785de84cf9e77e398b95c
https://github.com/galaxyproject/galaxy/commit/ffaabe0a63f47c57cd9785de84cf…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/onload.js
M client/galaxy/scripts/qunit/test-app.js
M client/galaxy/scripts/qunit/tests/page_tests.js
A config/plugins/webhooks/demo/search/config.yml
R config/plugins/webhooks/demo/search/config/searchover.yaml
A config/plugins/webhooks/demo/search/script.js
R config/plugins/webhooks/demo/search/static/script.js
R config/plugins/webhooks/demo/search/static/styles.css
A config/plugins/webhooks/demo/search/styles.css
A config/plugins/webhooks/demo/tool_list/__init__.py
A config/plugins/webhooks/demo/tool_list/config.yml
R config/plugins/webhooks/demo/tool_list/config/tool_list.yml
R config/plugins/webhooks/demo/tool_list/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/__init__.py
A config/plugins/webhooks/demo/tour_generator/config.yml
R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml
R config/plugins/webhooks/demo/tour_generator/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/script.js
R config/plugins/webhooks/demo/tour_generator/static/script.js
R config/plugins/webhooks/demo/tour_generator/static/styles.css
A config/plugins/webhooks/demo/tour_generator/styles.css
M doc/source/admin/special_topics/webhooks.rst
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webhooks/__init__.py
M test/api/test_webhooks.py
A test/functional/webhooks/history_test1/config.yml
R test/functional/webhooks/history_test1/config/history_test1.yml
A test/functional/webhooks/history_test2/config.yml
R test/functional/webhooks/history_test2/config/history_test2.yml
A test/functional/webhooks/masthead_test/config.yml
R test/functional/webhooks/masthead_test/config/masthead_test.yml
A test/functional/webhooks/phdcomics/__init__.py
A test/functional/webhooks/phdcomics/config.yaml
R test/functional/webhooks/phdcomics/config/phdcomics.yaml
R test/functional/webhooks/phdcomics/helper/__init__.py
A test/functional/webhooks/phdcomics/script.js
R test/functional/webhooks/phdcomics/static/script.js
R test/functional/webhooks/phdcomics/static/styles.css
A test/functional/webhooks/phdcomics/styles.css
A test/functional/webhooks/trans_object/__init__.py
A test/functional/webhooks/trans_object/config.yaml
R test/functional/webhooks/trans_object/config/trans_object.yaml
R test/functional/webhooks/trans_object/helper/__init__.py
A test/functional/webhooks/xkcd/config.yml
R test/functional/webhooks/xkcd/config/xkcd.yml
A test/functional/webhooks/xkcd/script.js
R test/functional/webhooks/xkcd/static/script.js
R test/functional/webhooks/xkcd/static/styles.css
A test/functional/webhooks/xkcd/styles.css
M test/selenium_tests/test_tool_describing_tours.py
Log Message:
-----------
Merge pull request #5342 from dannon/integration.webhooks_improvements
[18.01] Webhooks improvements
Commit: b4cdce925bf485ecdb24868bacdcffe2f4e7a717
https://github.com/galaxyproject/galaxy/commit/b4cdce925bf485ecdb24868bacdc…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/onload.js
M client/galaxy/scripts/qunit/test-app.js
M client/galaxy/scripts/qunit/tests/page_tests.js
A config/plugins/webhooks/demo/search/config.yml
R config/plugins/webhooks/demo/search/config/searchover.yaml
A config/plugins/webhooks/demo/search/script.js
R config/plugins/webhooks/demo/search/static/script.js
R config/plugins/webhooks/demo/search/static/styles.css
A config/plugins/webhooks/demo/search/styles.css
A config/plugins/webhooks/demo/tool_list/__init__.py
A config/plugins/webhooks/demo/tool_list/config.yml
R config/plugins/webhooks/demo/tool_list/config/tool_list.yml
R config/plugins/webhooks/demo/tool_list/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/__init__.py
A config/plugins/webhooks/demo/tour_generator/config.yml
R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml
R config/plugins/webhooks/demo/tour_generator/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/script.js
R config/plugins/webhooks/demo/tour_generator/static/script.js
R config/plugins/webhooks/demo/tour_generator/static/styles.css
A config/plugins/webhooks/demo/tour_generator/styles.css
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/scaling.md
M doc/source/admin/special_topics/webhooks.rst
A lib/galaxy/dependencies/conda-file.sh
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webhooks/__init__.py
M scripts/common_startup.sh
M test/api/test_webhooks.py
A test/functional/webhooks/history_test1/config.yml
R test/functional/webhooks/history_test1/config/history_test1.yml
A test/functional/webhooks/history_test2/config.yml
R test/functional/webhooks/history_test2/config/history_test2.yml
A test/functional/webhooks/masthead_test/config.yml
R test/functional/webhooks/masthead_test/config/masthead_test.yml
A test/functional/webhooks/phdcomics/__init__.py
A test/functional/webhooks/phdcomics/config.yaml
R test/functional/webhooks/phdcomics/config/phdcomics.yaml
R test/functional/webhooks/phdcomics/helper/__init__.py
A test/functional/webhooks/phdcomics/script.js
R test/functional/webhooks/phdcomics/static/script.js
R test/functional/webhooks/phdcomics/static/styles.css
A test/functional/webhooks/phdcomics/styles.css
A test/functional/webhooks/trans_object/__init__.py
A test/functional/webhooks/trans_object/config.yaml
R test/functional/webhooks/trans_object/config/trans_object.yaml
R test/functional/webhooks/trans_object/helper/__init__.py
A test/functional/webhooks/xkcd/config.yml
R test/functional/webhooks/xkcd/config/xkcd.yml
A test/functional/webhooks/xkcd/script.js
R test/functional/webhooks/xkcd/static/script.js
R test/functional/webhooks/xkcd/static/styles.css
A test/functional/webhooks/xkcd/styles.css
M test/selenium_tests/test_tool_describing_tours.py
Log Message:
-----------
Merge branch 'release_18.01' into dev
I removed the conflicted file that was modified
in dev after removal in 18.01
Compare: https://github.com/galaxyproject/galaxy/compare/a76614486be3...b4cdce925bf4