Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8e0be5089c63d94b841babfffcd70f2d8ab9b27c
https://github.com/galaxyproject/galaxy/commit/8e0be5089c63d94b841babfffcd7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/execute.py
M test/api/test_workflows.py
Log Message:
-----------
[17.01] Fix collection operations in workflows.
Due to a couple bugs things weren't being delayed correctly for some of these tools in some workflows.
Commit: 9234420cd770661b58ee91051015e9580505ca47
https://github.com/galaxyproject/galaxy/commit/9234420cd770661b58ee91051015…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Fix multiple collection reductions on multiple data parameters.
Was introduced in #805 but there was a small bug (maybe a last minute change before opening the PR) in the client code so this never was exposed to the users the way it was intended.
This should largely negate the need for hacks such as in cuffmerge that allow multiple list collections in addition to main multiple data selector. xref galaxyproject/tools-iuc#1225.
Commit: 6c82cf3c22445e97621429591e72951a0941104e
https://github.com/galaxyproject/galaxy/commit/6c82cf3c22445e97621429591e72…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-11 (Tue, 11 Apr 2017)
Changed paths:
M templates/user/logout.mako
Log Message:
-----------
Remove logout hack -- logout should always be a redirect or full page action, leaving it free of any JS side-effects this would be necessary for.
Commit: 779156111a117f5513ae10af04d0b12052627a32
https://github.com/galaxyproject/galaxy/commit/779156111a117f5513ae10af04d0…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
add two tools from str_fm repository to galaxy module whitelist
we broke them so we are fixing it
Commit: 7e4f805d479acc8f362ed651330f91fb8e2c9c40
https://github.com/galaxyproject/galaxy/commit/7e4f805d479acc8f362ed651330f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/execute.py
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #3848 from jmchilton/collection_operation_check_inputs_bug
[17.01] Fix collection operations in workflows.
Commit: 02bdc7495d80d4fb085de26e07e200a95a20ec56
https://github.com/galaxyproject/galaxy/commit/02bdc7495d80d4fb085de26e07e2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Merge pull request #3875 from jmchilton/fix_multi_collection_multi_data_param_reductions
[17.01] Fix multiple collection reductions on multiple data parameters.
Commit: 1d0ace1452aa9d5e334ee89aca07fa401db37806
https://github.com/galaxyproject/galaxy/commit/1d0ace1452aa9d5e334ee89aca07…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3973 from martenson/strfm-fix
[17.01] add two tools from str_fm repository to galaxy module whitelist
Commit: f75a72aee80680537dad802944585d6007d237c9
https://github.com/galaxyproject/galaxy/commit/f75a72aee80680537dad80294458…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
Log Message:
-----------
Rework logic for remote_user/session handling. This should fix issues @erasche reported regarding (null)(a)example.org users.
Commit: 09ba27543b8726fb61cd998bf9614018a9ba7316
https://github.com/galaxyproject/galaxy/commit/09ba27543b8726fb61cd998bf961…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
Log Message:
-----------
Slightly adjust logic for discarding headers; this shouldn't try to throw away empty headers anymore.
Commit: b779977cdc31d50183e7b0f356e9489a43eb755d
https://github.com/galaxyproject/galaxy/commit/b779977cdc31d50183e7b0f356e9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M lib/galaxy/web/framework/webapp.py
Log Message:
-----------
Slightly improve error message under remote auth with anon session attempt.
Commit: eb9a940a2dd69574b5fbaca06ffdc9beea4d4153
https://github.com/galaxyproject/galaxy/commit/eb9a940a2dd69574b5fbaca06ffd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M templates/user/logout.mako
Log Message:
-----------
Put back old hack; necessary for now.
Commit: f3c134abcb04ee2885f247ba79e95a354e4bb32b
https://github.com/galaxyproject/galaxy/commit/f3c134abcb04ee2885f247ba79e9…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
Log Message:
-----------
Merge pull request #3976 from dannon/fix_logout
[17.01] Remote user logout fixes, rework header handling a bit.
Commit: d398c90dbd70fff91a672935997bc21e949e8767
https://github.com/galaxyproject/galaxy/commit/d398c90dbd70fff91a672935997b…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/execute.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M test/api/test_workflows.py
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Merge branch 'release_17.01' into dev
Conflicts:
static/maps/mvc/ui/ui-select-content.js.map
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
static/scripts/mvc/ui/ui-select-content.js
Compare: https://github.com/galaxyproject/galaxy/compare/740d85a6a6f8...d398c90dbd70
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ec22b1d3ecd85cff65d232d0997703ee096d5ce1
https://github.com/galaxyproject/galaxy/commit/ec22b1d3ecd85cff65d232d09977…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/proxy/js/package.json
Log Message:
-----------
Fixes to get IEs working on Mac OS X.
- Fix logic error related to config parsing (OS non-specific).
- Don't trust GatewayAddress from Docker if on Mac OS X - it is probably a Docker host VM specific address.
- Update sqlite dependency for the newest version of Node available from Mac OS X Homebrew.
- Add a little blurb about how to configure galaxy_infrastructure_url in this case.
Commit: 910c22b7a1c759a651186f13e6c6707d91becfec
https://github.com/galaxyproject/galaxy/commit/910c22b7a1c759a651186f13e6c6…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/proxy/js/package.json
Log Message:
-----------
Merge pull request #3978 from jmchilton/ie_for_mac_os_x_fixes
Fixes to get GIEs working on Mac OS X.
Compare: https://github.com/galaxyproject/galaxy/compare/2f518e5ee444...910c22b7a1c7
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d41ad577617da2577b5dabadb47cb37a7edc5cb1
https://github.com/galaxyproject/galaxy/commit/d41ad577617da2577b5dabadb47c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Fix margin style values for color picker element
Commit: a6a920cb5ebb71a8f0349e733b31ffdd70ffab27
https://github.com/galaxyproject/galaxy/commit/a6a920cb5ebb71a8f0349e733b31…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-color-picker.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-color-picker.js
M static/style/blue/base.css
Log Message:
-----------
Remove unused label attribute, fix styles within color selector, remove encoded style attributes
Commit: 9aa7c6d2e905fc83bb9aee2c06f85f6aa7e1ad8c
https://github.com/galaxyproject/galaxy/commit/9aa7c6d2e905fc83bb9aee2c06f8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/repository_registry.py
M static/maps/layout/menu.js.map
M static/maps/nls/fr/locale.js.map
M static/maps/nls/locale.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/nls/fr/locale.js
M static/scripts/nls/locale.js
Log Message:
-----------
Merge branch 'dev' into fix_color_input_style
Commit: 722c294165eb40aad9d8f4a3d02e383563064b3e
https://github.com/galaxyproject/galaxy/commit/722c294165eb40aad9d8f4a3d02e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Use first/last child selector
Commit: 6c51f5232a7af4b0a73d803b4a3e7c64b23ec9c7
https://github.com/galaxyproject/galaxy/commit/6c51f5232a7af4b0a73d803b4a3e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M static/maps/mvc/ui/ui-color-picker.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-color-picker.js
Log Message:
-----------
Remove unused classes from code file
Commit: 399c7f061ceff36c355536abd499362edc6f90d5
https://github.com/galaxyproject/galaxy/commit/399c7f061ceff36c355536abd499…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-color-picker.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-color-picker.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #3965 from guerler/fix_color_input_style
Fix margin style values for color picker element
Compare: https://github.com/galaxyproject/galaxy/compare/45e40a184a41...399c7f061cef
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: 9234420cd770661b58ee91051015e9580505ca47
https://github.com/galaxyproject/galaxy/commit/9234420cd770661b58ee91051015…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Fix multiple collection reductions on multiple data parameters.
Was introduced in #805 but there was a small bug (maybe a last minute change before opening the PR) in the client code so this never was exposed to the users the way it was intended.
This should largely negate the need for hacks such as in cuffmerge that allow multiple list collections in addition to main multiple data selector. xref galaxyproject/tools-iuc#1225.
Commit: 02bdc7495d80d4fb085de26e07e200a95a20ec56
https://github.com/galaxyproject/galaxy/commit/02bdc7495d80d4fb085de26e07e2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Merge pull request #3875 from jmchilton/fix_multi_collection_multi_data_param_reductions
[17.01] Fix multiple collection reductions on multiple data parameters.
Compare: https://github.com/galaxyproject/galaxy/compare/7e4f805d479a...02bdc7495d80