Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 952f3f9b7a04a6e7d3185da76d84dea0fa9bca8d
https://github.com/galaxyproject/galaxy/commit/952f3f9b7a04a6e7d3185da76d84…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-12-11 (Fri, 11 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-select-default.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-default.js
M static/style/blue/base.css
Log Message:
-----------
Open select2 dropdown on click
Commit: bca004eff8607e347d440ce5fc5d086d7acb45f9
https://github.com/galaxyproject/galaxy/commit/bca004eff8607e347d440ce5fc5d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-11 (Fri, 11 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-select-default.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-default.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #1298 from guerler/fix_select2_open_000
Open select2 drop down on caret click
Compare: https://github.com/galaxyproject/galaxy/compare/f8d95abf0616...bca004eff860
Branch: refs/heads/master
Home: https://github.com/galaxyproject/galaxy
Commit: 8334593de11e915389b1da58c3b5db26121c7bef
https://github.com/galaxyproject/galaxy/commit/8334593de11e915389b1da58c3b5…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/workflow/extract.py
Log Message:
-----------
Fixes for dataset 'cleanup'/association linking when extracting workflows from a history.
Commit: 7923360dcec48b2e98d7c2a5bcae5f47187d6bf6
https://github.com/galaxyproject/galaxy/commit/7923360dcec48b2e98d7c2a5bcae…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
M test/api/test_tools.py
Log Message:
-----------
"Fix" collection outputs to hide the HDAs in the history.
Long term this is just not a solution, but it is the strategy we use for mapped over output HDAs also.
Rebased and fixed based on comments from @nsoranzo indicating the previous attempt did absolutely nothing to fix the problem.
xref https://github.com/galaxyproject/tools-iuc/pull/412/files
Commit: 41a56ead749bd25c6bc46107201b0e62bb65af9a
https://github.com/galaxyproject/galaxy/commit/41a56ead749bd25c6bc46107201b…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-12-07 (Mon, 07 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M static/maps/mvc/collection/list-collection-creator.js.map
M static/scripts/mvc/collection/list-collection-creator.js
Log Message:
-----------
Fix list collection creator being cutoff by restoring height: 100%
Commit: 94b049926d844a8aa54017b6d7a9983b94203316
https://github.com/galaxyproject/galaxy/commit/94b049926d844a8aa54017b6d7a9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-08 (Tue, 08 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M static/maps/mvc/collection/list-collection-creator.js.map
M static/scripts/mvc/collection/list-collection-creator.js
Log Message:
-----------
Merge pull request #1258 from carlfeberhard/release_15.10
[15.10] Fix list collection creator being cutoff by restoring height: 100%
Commit: 2be17071f35bb5db2298883aff107134a53701d1
https://github.com/galaxyproject/galaxy/commit/2be17071f35bb5db2298883aff10…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-08 (Tue, 08 Dec 2015)
Changed paths:
M lib/galaxy/workflow/extract.py
Log Message:
-----------
Merge pull request #1228 from blankenberg/wf_extrac_15.10
[15.10] Fixes for dataset 'cleanup'/association linking when extracting workflows from a history.
Commit: 0d98cf8ab76a374362302547b5699fa024d5ce21
https://github.com/galaxyproject/galaxy/commit/0d98cf8ab76a374362302547b569…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-12-09 (Wed, 09 Dec 2015)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Log a warning for missing tool whitelist file only if explicitly defined.
Also fix the log message.
Commit: a9034b5df3f3c80144727ebc161caa38b64ba7a1
https://github.com/galaxyproject/galaxy/commit/a9034b5df3f3c80144727ebc161c…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-12-09 (Wed, 09 Dec 2015)
Changed paths:
M eggs.ini
Log Message:
-----------
Update Kombu and AMQP eggs to fix problems with El Capitan's System
Integrity Protection.
Commit: b6e7b9a33b5dec7fdad2ad2f863bbf88980626ec
https://github.com/galaxyproject/galaxy/commit/b6e7b9a33b5dec7fdad2ad2f863b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-10 (Thu, 10 Dec 2015)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Adjustments to sanitize_whitelist reloading.
Commit: 2835aead8f949e3ac8b5c2ece0dc00c872950bde
https://github.com/galaxyproject/galaxy/commit/2835aead8f949e3ac8b5c2ece0dc…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2015-12-10 (Thu, 10 Dec 2015)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Merge pull request #2 from dannon/release_15.10_config
Adjustments to sanitize_whitelist reloading.
Commit: f13e9298de2eba4bee36ecb8336477a63345294b
https://github.com/galaxyproject/galaxy/commit/f13e9298de2eba4bee36ecb83364…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-10 (Thu, 10 Dec 2015)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Merge pull request #1278 from nsoranzo/release_15.10_config
[15.10] Log a warning for missing tool whitelist file only if explicitly defined.
Commit: fba354cb87754450ac41e58252dd405ac073557d
https://github.com/galaxyproject/galaxy/commit/fba354cb87754450ac41e58252dd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-10 (Thu, 10 Dec 2015)
Changed paths:
M eggs.ini
Log Message:
-----------
Merge pull request #1282 from natefoo/kombu-el-cap
[15.10] Update Kombu and AMQP eggs to fix problems with El Capitan's System Integrity Protection
Commit: 6a47d2d3a7f27b659e5de5fb1b37c7c1f9d04302
https://github.com/galaxyproject/galaxy/commit/6a47d2d3a7f27b659e5de5fb1b37…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-10 (Thu, 10 Dec 2015)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
M test/api/test_tools.py
Log Message:
-----------
Merge pull request #1239 from jmchilton/collection_outputs_hidden
[15.10] "Fix" collection outputs to hide the HDAs in the history.
Compare: https://github.com/galaxyproject/galaxy/compare/7d4eac1535fc...6a47d2d3a7f2
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a22c09b11f5a16b4c429cf88ebd74faa433da97c
https://github.com/galaxyproject/galaxy/commit/a22c09b11f5a16b4c429cf88ebd7…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-12-08 (Tue, 08 Dec 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M test/docker/base/Dockerfile
M test/tool_shed/functional/test_1460_data_managers.py
Log Message:
-----------
Fix typos.
Commit: f974b0f740d4ed8c44ebafde74908cdea1748a1a
https://github.com/galaxyproject/galaxy/commit/f974b0f740d4ed8c44ebafde7490…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-12-08 (Tue, 08 Dec 2015)
Changed paths:
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/util/tool_dependency_util.py
Log Message:
-----------
Extend the logging of tool dependency status changes.
Also merge handle_tool_dependency_installation_error() in
set_tool_dependency_attributes() and consolidate its use.
Commit: f8d95abf061608e2dc544e56fc5b83ad3d54d1bd
https://github.com/galaxyproject/galaxy/commit/f8d95abf061608e2dc544e56fc5b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-10 (Thu, 10 Dec 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/util/tool_dependency_util.py
M test/docker/base/Dockerfile
M test/tool_shed/functional/test_1460_data_managers.py
Log Message:
-----------
Merge pull request #1263 from nsoranzo/dev_tool_shed_fixes
Extend the logging of tool dependency status changes.
Compare: https://github.com/galaxyproject/galaxy/compare/b455157bd6f3...f8d95abf0616
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: bb23701fa80c74a6621b1826b050d9e42c12455f
https://github.com/galaxyproject/galaxy/commit/bb23701fa80c74a6621b1826b050…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M lib/galaxy/datatypes/text.py
Log Message:
-----------
White space in BIOM1 datatype.
Commit: 64506bbd43e21b299a8b42ee3cfd2ef8e40c06d2
https://github.com/galaxyproject/galaxy/commit/64506bbd43e21b299a8b42ee3cfd…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Prevent unneccessary extra read in BIOM1 sniffer.
Commit: b5c77a8e8c0255f61ca62a7ff2311d443e224bec
https://github.com/galaxyproject/galaxy/commit/b5c77a8e8c0255f61ca62a7ff231…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Add metadata for BIOM1 datatype. I am not yet sure that we should store table_rows and table_columns, as these could grow quite large, but could be useful in tools.
Commit: f41540f6137a2f63a6dcb27327e33bf73752f954
https://github.com/galaxyproject/galaxy/commit/f41540f6137a2f63a6dcb27327e3…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Most of these should probably not be user visible.
Commit: b20fb71e33c1779e42dd67bb68aa9b31b69ffca2
https://github.com/galaxyproject/galaxy/commit/b20fb71e33c1779e42dd67bb68aa…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Fix extraneous white space.
Commit: 2c6c5236323dbea196cfd2e8fe3915f0c7e4c6df
https://github.com/galaxyproject/galaxy/commit/2c6c5236323dbea196cfd2e8fe39…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-12-02 (Wed, 02 Dec 2015)
Changed paths:
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Only store ids for row and column in BIOM1 datatype.
Commit: 3acfa9c786e1fa5567cf313b294b68ab4c508c1b
https://github.com/galaxyproject/galaxy/commit/3acfa9c786e1fa5567cf313b294b…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-12-02 (Wed, 02 Dec 2015)
Changed paths:
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Add blank lines around internal function.
Commit: b455157bd6f3f23ce2de81d5145b6268e4da77f3
https://github.com/galaxyproject/galaxy/commit/b455157bd6f3f23ce2de81d5145b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-10 (Thu, 10 Dec 2015)
Changed paths:
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Merge pull request #1198 from blankenberg/dt-biom
BIOM1 Datatype enhancements
Compare: https://github.com/galaxyproject/galaxy/compare/7a3aa044fbf9...b455157bd6f3
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 133e5f2e24eed9650a0862ced42092d35f8a6566
https://github.com/galaxyproject/galaxy/commit/133e5f2e24eed9650a0862ced420…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-10 (Thu, 10 Dec 2015)
Changed paths:
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/interactor.py
Log Message:
-----------
Various small API testing fixes/improvements.
Commit: 09a68adb1e2a837f4ae01ca9ec25b4d6d0fab446
https://github.com/galaxyproject/galaxy/commit/09a68adb1e2a837f4ae01ca9ec25…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-10 (Thu, 10 Dec 2015)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Add another API test verifying validation of workflow substitions.
A little different because it targets a different tool, validation, and is inside a repeat.
Commit: 928ff581efa3ace63a57e97db80e7a9c21c09841
https://github.com/galaxyproject/galaxy/commit/928ff581efa3ace63a57e97db80e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-10 (Thu, 10 Dec 2015)
Changed paths:
M test/base/interactor.py
Log Message:
-----------
Fix typo spotted by @nsoranzo.
Commit: bce8140bd9f9c3e069c83f765ae892d0fd1656b7
https://github.com/galaxyproject/galaxy/commit/bce8140bd9f9c3e069c83f765ae8…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2015-12-10 (Thu, 10 Dec 2015)
Changed paths:
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/interactor.py
Log Message:
-----------
Merge pull request #1285 from jmchilton/test_improvemnts_1
Small API Test Improvements
Compare: https://github.com/galaxyproject/galaxy/compare/183c3c11b60a...bce8140bd9f9