Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 62fdbd526ae34357d3fbb44cedc46635c4df7cbb
https://github.com/galaxyproject/galaxy/commit/62fdbd526ae34357d3fbb44cedc4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-29 (Fri, 29 Jul 2016)
Changed paths:
M lib/galaxy/util/__init__.py
Log Message:
-----------
Fix the sanitization of None values in utils. This had previously not happened because Params had only been sanitizing strings coming in as part of the request, but if you're passing off (potentially manipulated, as in adding None default params) to a secondary request for a response, this can happen.
Commit: ed7c357668df5bbb3381fae94353465594c7e184
https://github.com/galaxyproject/galaxy/commit/ed7c357668df5bbb3381fae94353…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-07-29 (Fri, 29 Jul 2016)
Changed paths:
M lib/galaxy/util/__init__.py
Log Message:
-----------
Merge pull request #2693 from dannon/utils_fix_sanitization_of_none
[16.07] Fix the sanitization of None values in utils. This had previously no…
Commit: 7bf0cc72418308e54b6ec180a8913623004c8288
https://github.com/galaxyproject/galaxy/commit/7bf0cc72418308e54b6ec180a891…
Author: Remi Marenco <remi.marenco(a)gmail.com>
Date: 2016-08-02 (Tue, 02 Aug 2016)
Changed paths:
M lib/galaxy/datatypes/tracks.py
Log Message:
-----------
Remove the old HubAssembly class
Commit: 3206199652330659aa9f1cebe75c6940787f85d4
https://github.com/galaxyproject/galaxy/commit/3206199652330659aa9f1cebe75c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-03 (Wed, 03 Aug 2016)
Changed paths:
M lib/galaxy/datatypes/tracks.py
Log Message:
-----------
Merge pull request #2701 from remimarenco/release_16.07
[16.07] Fix: Remove the old HubAssembly class
Commit: 48849b814aac6bb70a1651f063f0789da4022ce7
https://github.com/galaxyproject/galaxy/commit/48849b814aac6bb70a1651f063f0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-03 (Wed, 03 Aug 2016)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/pulsar.py
Log Message:
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Fixup metadata collection on workdir outputs for Pulsar.
https://github.com/galaxyproject/galaxy/pull/1688/commits/a2e31403753c407e7… which gave tool's clean working directories made the function get_workdir_outputs a big sloppy. Pulsar would send it the actual remote working directory for jobs and Galaxy would send it the job directory (expecting it to append 'working').
Commit: 82430c024378e15729e5d2b52e50ad49930e5dd2
https://github.com/galaxyproject/galaxy/commit/82430c024378e15729e5d2b52e50…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-03 (Wed, 03 Aug 2016)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/pulsar.py
Log Message:
-----------
Merge pull request #2721 from jmchilton/working_pulsar_metadata
[16.07] Fix metadata collection on workdir outputs for Pulsar.
Commit: 2affd08647c723014182552b09bcb4402d30d9b3
https://github.com/galaxyproject/galaxy/commit/2affd08647c723014182552b09bc…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2016-08-03 (Wed, 03 Aug 2016)
Changed paths:
M lib/galaxy/dataset_collections/subcollections.py
Log Message:
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Fix for splitting dataset collections
Commit: 8b0d88b30e62997ec9b33fec402379b8e2033e5c
https://github.com/galaxyproject/galaxy/commit/8b0d88b30e62997ec9b33fec4023…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-03 (Wed, 03 Aug 2016)
Changed paths:
M lib/galaxy/dataset_collections/subcollections.py
Log Message:
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Merge pull request #2723 from jmchilton/backport_2708
[16.07] Backport #2708
Commit: 3206a54055620cb524fb5265ab91c979d3a520b2
https://github.com/galaxyproject/galaxy/commit/3206a54055620cb524fb5265ab91…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-08-04 (Thu, 04 Aug 2016)
Changed paths:
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/util/__init__.py
Log Message:
-----------
Merge branch 'release_16.07' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/7efa1e0e4dd0...3206a5405562
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 9f75926e4dfc8c4d644d191ba324a5f8a40e2e7d
https://github.com/galaxyproject/galaxy/commit/9f75926e4dfc8c4d644d191ba324…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
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Inject data module values in connected steps on initialization
Commit: db4b78baad9d246d34b77f0e032cd35344f75587
https://github.com/galaxyproject/galaxy/commit/db4b78baad9d246d34b77f0e032c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
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Use same dom append call for tool and data steps
Commit: 7b2d71e86ee9d57db0a4412b908448f03ec333a8
https://github.com/galaxyproject/galaxy/commit/7b2d71e86ee9d57db0a4412b9084…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
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Add missing get_initial_value for collection parameters, remove unused repeat avoiding mechanism for now
Commit: b34757b6b1dd71d189ea1fd2c44c6f938b9344b3
https://github.com/galaxyproject/galaxy/commit/b34757b6b1dd71d189ea1fd2c44c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Use hda representative agent if collections are parsed
Commit: bccf3d58f5afa0b95187583c099ba67d3cc60552
https://github.com/galaxyproject/galaxy/commit/bccf3d58f5afa0b95187583c099b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/dynamic_options.py
Log Message:
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Add hda agent generation to dynamic options
Commit: bd194a885db94b0655c5781a25c3e0b292484cd7
https://github.com/galaxyproject/galaxy/commit/bd194a885db94b0655c5781a25c3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Use one line if to determine atomic versus listed hda agents
Commit: 65328ff3b7a9b2342b3acdc822a7620eb247b23d
https://github.com/galaxyproject/galaxy/commit/65328ff3b7a9b2342b3acdc822a7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/workflow/modules.py
Log Message:
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Rename to_hda_agent to to_hda_representative
Commit: 24ecf34c4f49b93d79d7d6b5f5d21aeec89733e0
https://github.com/galaxyproject/galaxy/commit/24ecf34c4f49b93d79d7d6b5f5d2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Enhance collection to regular data field injection when multiple collections are parsed
Commit: 4d6754f4a4e81b8dc3f90a32d72cfd9190077a2d
https://github.com/galaxyproject/galaxy/commit/4d6754f4a4e81b8dc3f90a32d72c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M templates/webapps/galaxy/workflow/run.mako
Log Message:
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Remove get initial value without repeats call from workflow run mako
Commit: 15aba09847b03940167c38eb8e3a24214db4f92f
https://github.com/galaxyproject/galaxy/commit/15aba09847b03940167c38eb8e3a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
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Align spacing style of get_column_list function
Commit: c8de0edc96d37be7ee7b32c11be74f39cb616b23
https://github.com/galaxyproject/galaxy/commit/c8de0edc96d37be7ee7b32c11be7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M static/maps/mvc/tool/tool-form-composite.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/tool/tool-form-composite.js
Log Message:
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Instantly display workflow form upgrade messages, avoid fade in
Commit: 6bff8ce48b8fc19bec2d0b02aefc617f93a2d2e8
https://github.com/galaxyproject/galaxy/commit/6bff8ce48b8fc19bec2d0b02aefc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-misc.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/tool/tool-form-composite.js
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Instantly display workflow form upgrade messages, avoid fade in
Commit: 52879750a7c297f6fb45c8aeec2c14712d302343
https://github.com/galaxyproject/galaxy/commit/52879750a7c297f6fb45c8aeec2c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M test/unit/tools/test_data_parameters.py
Log Message:
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Align data tool parameter test cases for initial values
Commit: efc850c32e15490df33dee5e164542791bc0b21c
https://github.com/galaxyproject/galaxy/commit/efc850c32e15490df33dee5e1645…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
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Fix padding to avoid scroll bar
Commit: 24573f7ffb8e5797ae1589a9353f5937d114417c
https://github.com/galaxyproject/galaxy/commit/24573f7ffb8e5797ae1589a9353f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-03 (Wed, 03 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-misc.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/tool/tool-form-composite.js
M static/scripts/mvc/ui/ui-misc.js
M templates/webapps/galaxy/workflow/run.mako
M test/unit/tools/test_data_parameters.py
Log Message:
-----------
Merge branch 'inject_connected_inputs' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/66d5560da569...24573f7ffb8e
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: bf0ac1cc3e24f93f1f7948689a90c0b2424d61aa
https://github.com/galaxyproject/galaxy/commit/bf0ac1cc3e24f93f1f7948689a90…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-03 (Wed, 03 Aug 2016)
Changed paths:
M client/galaxy/style/less/upload.less
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/style/blue/base.css
Log Message:
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Slight styling tweak to prevent overflow on the right edge in composite upload dialog.
Commit: 66d5560da5696113bcaec612a3e5b9c375a44ce3
https://github.com/galaxyproject/galaxy/commit/66d5560da5696113bcaec612a3e5…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-03 (Wed, 03 Aug 2016)
Changed paths:
M client/galaxy/style/less/upload.less
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/style/blue/base.css
Log Message:
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Merge pull request #2716 from dannon/slight_upload_style_tweak
Slight styling tweak to prevent overflow on the right edge in composi…
Compare: https://github.com/galaxyproject/galaxy/compare/b2ab62b21f21...66d5560da569