Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1d16200759895b6ede6c38655d085fa7bb0a1e17
https://github.com/galaxyproject/galaxy/commit/1d16200759895b6ede6c38655d08…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Refactor recent toolbox changes for galaxy-lib.
The abstracttoolbox class is supposed to shield Galaxy from the internals of the toolbox organization and vice versa, so having a reload method that uses Galaxy-specific queueing stuff is less than ideal. The concrete toolbox class is where I have been putting such functionality.
In addition to this being the abstract design I prefer, it is definitely needed for galaxy-lib which contains the abstracttoolbox but not the concrete toolbox or the queue worker functionality.
xref #2840
Commit: 780473a751ae52868e29b4e34ba2b0894598dc7b
https://github.com/galaxyproject/galaxy/commit/780473a751ae52868e29b4e34ba2…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Merge pull request #2971 from jmchilton/galaxy-lib-import-fix
Refactor recent toolbox changes for galaxy-lib.
Compare: https://github.com/galaxyproject/galaxy/compare/7f19ba817c4d...780473a751ae
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: d7ab1c5cfbfcdff3ce3e201f6fb0684fdb914096
https://github.com/galaxyproject/galaxy/commit/d7ab1c5cfbfcdff3ce3e201f6fb0…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-modal.js
M static/maps/mvc/ui/ui-modal.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-modal.js
Log Message:
-----------
UI, Modal: re-build dom on render
Moves templating to render (and updates dom node attributes after)
to reset modal and prevent inline styling and other modifications
to the singleton from persisting between calls to show.
Commit: 04d62e242412d0eb6e739f3577256d99b1aaa5bf
https://github.com/galaxyproject/galaxy/commit/04d62e242412d0eb6e739f357725…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-modal.js
M static/maps/mvc/ui/ui-modal.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-modal.js
Log Message:
-----------
Merge pull request #2955 from carlfeberhard/fix.modal-resetting
[16.07] UI, Modal: re-build dom on render
Compare: https://github.com/galaxyproject/galaxy/compare/e667f9f36038...04d62e242412
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c0e8a7608351679b8ebdb71207339384161d6616
https://github.com/galaxyproject/galaxy/commit/c0e8a7608351679b8ebdb7120733…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/util/metadata_util.py
Log Message:
-----------
[16.07] Fix tool dependencies handling in Tool Shed model (#2950)
* Fix the cause of toolshed test 1400 failing.
* Fix handling of repositories without tool dependencies.
* Fix tool dependency retrieval.
In some cases, a process might attempt to fetch tool dependencies for revision
1:7334f6d0ac17, but the repository has been updated, and tool dependency
metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves
that issue.
* Correct the logic that returns an empty string for an empty dict.
* Fix getting latest revision with tool dependencies.
* Use self.app instead of trans.app
Commit: 9b3c061addb4f3e61d72465cf492396b9e07464e
https://github.com/galaxyproject/galaxy/commit/9b3c061addb4f3e61d72465cf492…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/util/metadata_util.py
Log Message:
-----------
[16.07] Fix tool dependencies handling in Tool Shed model (#2950)
* Fix the cause of toolshed test 1400 failing.
* Fix handling of repositories without tool dependencies.
* Fix tool dependency retrieval.
In some cases, a process might attempt to fetch tool dependencies for revision
1:7334f6d0ac17, but the repository has been updated, and tool dependency
metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves
that issue.
* Correct the logic that returns an empty string for an empty dict.
* Fix getting latest revision with tool dependencies.
* Use self.app instead of trans.app
Conflicts:
lib/galaxy/webapps/tool_shed/controllers/repository.py
Commit: a78b8bcd2aa02abf787f0974fe567ab4f70f41a1
https://github.com/galaxyproject/galaxy/commit/a78b8bcd2aa02abf787f0974fe56…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/managers/rbac_secured.py
M test/unit/managers/test_DatasetManager.py
Log Message:
-----------
Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04
Commit: c06f8c29968971c6c1e0dfc6847b3baf755f3a96
https://github.com/galaxyproject/galaxy/commit/c06f8c29968971c6c1e0dfc6847b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/model/__init__.py
Log Message:
-----------
correct the method call
Commit: 5e7ee28e0d6937fa53f39b350e04357b554ce9ae
https://github.com/galaxyproject/galaxy/commit/5e7ee28e0d6937fa53f39b350e04…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M test/shed_functional/functional/test_1400_review_migration_stages.py
Log Message:
-----------
bump freebayes in test (since it was updated)
Commit: 45e6949eeae88c0d3c4c3f6341ddc5695d329bb2
https://github.com/galaxyproject/galaxy/commit/45e6949eeae88c0d3c4c3f6341dd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/util/metadata_util.py
M test/shed_functional/functional/test_1400_review_migration_stages.py
Log Message:
-----------
Merge pull request #2959 from martenson/release_16.04
[16.04] backport of model tool dependencies fix
Commit: 3b3e2e3358aa73a5374345686581310d37349ff9
https://github.com/galaxyproject/galaxy/commit/3b3e2e3358aa73a5374345686581…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M test/shed_functional/functional/test_1400_review_migration_stages.py
Log Message:
-----------
Merge branch 'release_16.04' into release_16.07
Conflicts:
lib/galaxy/webapps/tool_shed/controllers/repository.py
lib/galaxy/webapps/tool_shed/model/__init__.py
Commit: 317fb472c96296c6de4d094b7236b9c3f25610da
https://github.com/galaxyproject/galaxy/commit/317fb472c96296c6de4d094b7236…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/util/metadata_util.py
M test/shed_functional/functional/test_1400_review_migration_stages.py
Log Message:
-----------
Merge branch 'release_16.07' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/51a6d849342f...317fb472c962
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: 9b3c061addb4f3e61d72465cf492396b9e07464e
https://github.com/galaxyproject/galaxy/commit/9b3c061addb4f3e61d72465cf492…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/util/metadata_util.py
Log Message:
-----------
[16.07] Fix tool dependencies handling in Tool Shed model (#2950)
* Fix the cause of toolshed test 1400 failing.
* Fix handling of repositories without tool dependencies.
* Fix tool dependency retrieval.
In some cases, a process might attempt to fetch tool dependencies for revision
1:7334f6d0ac17, but the repository has been updated, and tool dependency
metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves
that issue.
* Correct the logic that returns an empty string for an empty dict.
* Fix getting latest revision with tool dependencies.
* Use self.app instead of trans.app
Conflicts:
lib/galaxy/webapps/tool_shed/controllers/repository.py
Commit: a78b8bcd2aa02abf787f0974fe567ab4f70f41a1
https://github.com/galaxyproject/galaxy/commit/a78b8bcd2aa02abf787f0974fe56…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/managers/rbac_secured.py
M test/unit/managers/test_DatasetManager.py
Log Message:
-----------
Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04
Commit: c06f8c29968971c6c1e0dfc6847b3baf755f3a96
https://github.com/galaxyproject/galaxy/commit/c06f8c29968971c6c1e0dfc6847b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/model/__init__.py
Log Message:
-----------
correct the method call
Commit: 5e7ee28e0d6937fa53f39b350e04357b554ce9ae
https://github.com/galaxyproject/galaxy/commit/5e7ee28e0d6937fa53f39b350e04…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M test/shed_functional/functional/test_1400_review_migration_stages.py
Log Message:
-----------
bump freebayes in test (since it was updated)
Commit: 45e6949eeae88c0d3c4c3f6341ddc5695d329bb2
https://github.com/galaxyproject/galaxy/commit/45e6949eeae88c0d3c4c3f6341dd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/util/metadata_util.py
M test/shed_functional/functional/test_1400_review_migration_stages.py
Log Message:
-----------
Merge pull request #2959 from martenson/release_16.04
[16.04] backport of model tool dependencies fix
Commit: 3b3e2e3358aa73a5374345686581310d37349ff9
https://github.com/galaxyproject/galaxy/commit/3b3e2e3358aa73a5374345686581…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M test/shed_functional/functional/test_1400_review_migration_stages.py
Log Message:
-----------
Merge branch 'release_16.04' into release_16.07
Conflicts:
lib/galaxy/webapps/tool_shed/controllers/repository.py
lib/galaxy/webapps/tool_shed/model/__init__.py
Compare: https://github.com/galaxyproject/galaxy/compare/c0e8a7608351...3b3e2e3358aa