Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 7d2cd2272299b94b01c8d22c0c1f7f5cbfb2b91a
https://github.com/galaxyproject/galaxy/commit/7d2cd2272299b94b01c8d22c0c1f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M static/maps/mvc/library/library-dataset-view.js.map
M static/scripts/mvc/library/library-dataset-view.js
Log Message:
-----------
replace colon and comma in role names since they are also separators
Commit: 3b4bd3bb6fa922c9e2156fe87660de409acf3367
https://github.com/galaxyproject/galaxy/commit/3b4bd3bb6fa922c9e2156fe87660…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M static/maps/mvc/library/library-dataset-view.js.map
M static/scripts/bundled/admin.bundled.js.map
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/library/library-dataset-view.js
Log Message:
-----------
make client
Commit: 153dfaa68080481607a90731c5a0825754cf713d
https://github.com/galaxyproject/galaxy/commit/153dfaa68080481607a90731c5a0…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-09-16 (Sat, 16 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M static/maps/mvc/library/library-dataset-view.js.map
M static/scripts/bundled/admin.bundled.js.map
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/library/library-dataset-view.js
Log Message:
-----------
Merge pull request #4621 from martenson/library-sharing-roles
replace separators in library sharing role names
Compare: https://github.com/galaxyproject/galaxy/compare/ea7b27443715...153dfaa68080
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1c1ca9bd91298e2265cb4a9e6982f18c3e4ae39d
https://github.com/galaxyproject/galaxy/commit/1c1ca9bd91298e2265cb4a9e6982…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M static/maps/mvc/library/library-dataset-view.js.map
M static/scripts/bundled/admin.bundled.js.map
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/library/library-dataset-view.js
Log Message:
-----------
Fix loose->lose in help text for library dataset view.
Commit: d5aba7da15f5a05821e7659828bd701fd438769e
https://github.com/galaxyproject/galaxy/commit/d5aba7da15f5a05821e7659828bd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/util/maf_utilities.py
Log Message:
-----------
Three more looses.
Commit: 7831b9889897e1d51ba2004cc8fcc5df079c0594
https://github.com/galaxyproject/galaxy/commit/7831b9889897e1d51ba2004cc8fc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M static/maps/mvc/library/library-dataset-view.js.map
M static/scripts/mvc/library/library-dataset-view.js
Log Message:
-----------
Occurred, spelling.
Commit: 0ea6272f5d35a769bc63a4706c503793fa903fe2
https://github.com/galaxyproject/galaxy/commit/0ea6272f5d35a769bc63a4706c50…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/toolshed/scripts/mvc/groups/group-detail-view.js
M client/toolshed/scripts/mvc/groups/group-list-view.js
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/maps/mvc/library/library-librarylist-view.js.map
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/toolshed/scripts/mvc/groups/group-detail-view.js
M static/toolshed/scripts/mvc/groups/group-list-view.js
Log Message:
-----------
More spelling.
Commit: 540322e38856cc86a4a3d91aa3ac670418378d90
https://github.com/galaxyproject/galaxy/commit/540322e38856cc86a4a3d91aa3ac…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/toolshed/scripts/mvc/groups/group-detail-view.js
M client/toolshed/scripts/mvc/groups/group-list-view.js
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/util/maf_utilities.py
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/maps/mvc/library/library-librarylist-view.js.map
M static/scripts/bundled/admin.bundled.js.map
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/library/library-dataset-view.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/toolshed/scripts/mvc/groups/group-detail-view.js
M static/toolshed/scripts/mvc/groups/group-list-view.js
Log Message:
-----------
Merge pull request #4626 from dannon/loose_use
Misc. spelling/grammatical error fixes.
Compare: https://github.com/galaxyproject/galaxy/compare/64af1bd9e962...540322e38856
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: fc90aec7fe4a3267868fdf3cc2c2123f935f15a2
https://github.com/galaxyproject/galaxy/commit/fc90aec7fe4a3267868fdf3cc2c2…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M create_db.sh
M extract_dataset_parts.sh
M manage_db.sh
M manage_tools.sh
Log Message:
-----------
Fix virtualenv activation for some scripts
In particular add virtualenv activation to extract_dataset_parts.sh
to fix the following error when running tools which use
`<parallelism>`:
```
Fatal error:
/tmp/tmpOoQ01k/job_working_directory/000/12/task_0:
Traceback (most recent call last):
File "./scripts/extract_dataset_part.py", line 17, in <module>
import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers
File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module>
from six import string_types
ModuleNotFoundError: No module named 'six'
```
Commit: 97e8e36185312ff6e1afea15fec7e83aadafd25b
https://github.com/galaxyproject/galaxy/commit/97e8e36185312ff6e1afea15fec7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M create_db.sh
M extract_dataset_parts.sh
M manage_db.sh
M manage_tools.sh
Log Message:
-----------
Merge pull request #4624 from nsoranzo/release_17.05_fix_scripts
[17.05] Backport of #4616
Commit: 64af1bd9e96265cbd6b21faadbad5adea4a2d613
https://github.com/galaxyproject/galaxy/commit/64af1bd9e96265cbd6b21faadbad…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Log Message:
-----------
Merge branch 'release_17.05' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/c5ff555ec4ef...64af1bd9e962
Branch: refs/heads/master
Home: https://github.com/galaxyproject/galaxy
Commit: 6c6c804ab63866c6239299f4221fa436dd4a9591
https://github.com/galaxyproject/galaxy/commit/6c6c804ab63866c6239299f4221f…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
When a page is involved, the ID will be wrong
Commit: 33a0c7fac3a0624d26efd8d08dabbca5f7e8c226
https://github.com/galaxyproject/galaxy/commit/33a0c7fac3a0624d26efd8d08dab…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Make client
Commit: a2229783177b76786f581cc78040b059cbd2aab5
https://github.com/galaxyproject/galaxy/commit/a2229783177b76786f581cc78040…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Merge pull request #4355 from erasche/patch-wrong-folder-id
[release_17.05] Patch bug preventing creation of dataset library folders
Commit: ecfb90ef9f8037575db2e62ae49d8bbb7e4e427b
https://github.com/galaxyproject/galaxy/commit/ecfb90ef9f8037575db2e62ae49d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
R static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
R static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Revert "[release_17.05] Patch bug preventing creation of dataset library folders"
Commit: 163e4ebbe1fbfc5f1f97b5aabc804621fdd426c9
https://github.com/galaxyproject/galaxy/commit/163e4ebbe1fbfc5f1f97b5aabc80…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
R static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
R static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Merge pull request #4356 from galaxyproject/revert-4355-patch-wrong-folder-id
Revert "[release_17.05] Patch bug preventing creation of dataset library folders"
Commit: 12f0acba1dc1b81bb621ea130a75ec7dfac0fdaa
https://github.com/galaxyproject/galaxy/commit/12f0acba1dc1b81bb621ea130a75…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Revert "Revert "[release_17.05] Patch bug preventing creation of dataset library folders""
Commit: 10efd7fac6e38c5ca07d94c351d10473811c7d6c
https://github.com/galaxyproject/galaxy/commit/10efd7fac6e38c5ca07d94c351d1…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-07-31 (Mon, 31 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Merge pull request #4357 from galaxyproject/revert-4356-revert-4355-patch-wrong-folder-id
[release_17.05] Patch bug preventing creation of dataset library folders
Commit: ba3249acf07ca1a44a813e2c68a9d6074d2b7c4c
https://github.com/galaxyproject/galaxy/commit/ba3249acf07ca1a44a813e2c68a9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/molecules.py
Log Message:
-----------
Add missing chemical formats to datatypes_conf.xml.sample
Commit: 61d172f18d8f7740585b038dd786e81178ca1831
https://github.com/galaxyproject/galaxy/commit/61d172f18d8f7740585b038dd786…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M setup.cfg
M tox.ini
Log Message:
-----------
Update pin for flake8-docstrings
Similar to commit 2586df45637d794c63252838573b2d1e6d692243 .
Commit: a249dc01a5d0afa42474a6e4075ed2a3ad80400f
https://github.com/galaxyproject/galaxy/commit/a249dc01a5d0afa42474a6e4075e…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M .travis.yml
Log Message:
-----------
Use container-based infrastructure (sudo: false) in TravisCI
Commit: d0b06a3b1da09ff3394e9ea036d788676817b58f
https://github.com/galaxyproject/galaxy/commit/d0b06a3b1da09ff3394e9ea036d7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Don't cast tool_version to string if tool_version is None-type
If a version is not specifically requested a wrong version (`None` cast to
`'None'`) of a tool will be loaded in the workflow editor instead of the
latest version.
That should address @martenson's remark in
https://github.com/galaxyproject/galaxy/pull/4373#issuecomment-321896674
(and maybe also
https://github.com/galaxyproject/galaxy/issues/557#issuecomment-213498153).
Commit: 6ad6fd9252bf5ec44beb00cb434876e170dc9548
https://github.com/galaxyproject/galaxy/commit/6ad6fd9252bf5ec44beb00cb4348…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M lib/galaxy/model/tool_shed_install/__init__.py
Log Message:
-----------
Rebuild tool_version_cache on DetachedInstanceError
Commit: 0f5ad34eaf6b65a2d258f308aa6fea8b4f39a52a
https://github.com/galaxyproject/galaxy/commit/0f5ad34eaf6b65a2d258f308aa6f…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M .travis.yml
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/molecules.py
M setup.cfg
M tox.ini
Log Message:
-----------
Merge pull request #4413 from nsoranzo/release_17.01_really_add_datatypes
[17.01] Add missing chemical formats to datatypes_conf.xml.sample
Commit: 4faf496c9898786e8f504bd36b28dc70df4e3e26
https://github.com/galaxyproject/galaxy/commit/4faf496c9898786e8f504bd36b28…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/molecules.py
Log Message:
-----------
Merge branch 'release_17.01' into release_17.05
Conflicts:
tox.ini
Commit: 7f78ee7b18b83961b305cac19aa8949a4452710d
https://github.com/galaxyproject/galaxy/commit/7f78ee7b18b83961b305cac19aa8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Merge pull request #4420 from mvdbeek/fix_wrong_tool_version_cast
[17.05] Don't cast tool_version to string if tool_version is None-type
Commit: 1e1c549e695cf6541c4dcac5d554c852165e7b6a
https://github.com/galaxyproject/galaxy/commit/1e1c549e695cf6541c4dcac5d554…
Author: Matthias Bernt <m.bernt(a)ufz.de>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/installable.py
Log Message:
-----------
added missing parameter to function ensure_installed
Commit: a1b8a54ef8009ccf9ac64a699ed848cd56bba283
https://github.com/galaxyproject/galaxy/commit/a1b8a54ef8009ccf9ac64a699ed8…
Author: Matthias Bernt <m.bernt(a)ufz.de>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/installable.py
Log Message:
-----------
ensure_installed is now iterative instead of recursive
Commit: 349c9c8f10f6f5eeac45c1a14e3b4a6c23cc373e
https://github.com/galaxyproject/galaxy/commit/349c9c8f10f6f5eeac45c1a14e3b…
Author: Matthias Bernt <m.bernt(a)ufz.de>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/installable.py
Log Message:
-----------
version with no repetition at all
Commit: a76547281f59b80acd27ddfa098c97e65a72d81a
https://github.com/galaxyproject/galaxy/commit/a76547281f59b80acd27ddfa098c…
Author: Matthias Bernt <m.bernt(a)ufz.de>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/installable.py
Log Message:
-----------
Set timeout for aquiring lock to 5min
Commit: 748539a3a671552eea60e114a6c6e4dd7b48c7de
https://github.com/galaxyproject/galaxy/commit/748539a3a671552eea60e114a6c6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/installable.py
Log Message:
-----------
Merge pull request #4450 from mvdbeek/fix_file_lock_error
[17.01] Fix file lock error handling
Commit: 685b9de09bca5a2973de336b93865273c9fa975c
https://github.com/galaxyproject/galaxy/commit/685b9de09bca5a2973de336b9386…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/installable.py
Log Message:
-----------
Merge remote-tracking branch 'origin/release_17.01' into release_17.05
Commit: ce7d8a2fc1bcc1f9241028b3d437c653edccda0c
https://github.com/galaxyproject/galaxy/commit/ce7d8a2fc1bcc1f9241028b3d437…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-23 (Wed, 23 Aug 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Validate workflow step after step argument injection
Commit: 3ef39b390c8d2f66ff890a29b712f785b6376601
https://github.com/galaxyproject/galaxy/commit/3ef39b390c8d2f66ff890a29b712…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-25 (Fri, 25 Aug 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
Log Message:
-----------
Fix drag and drop from history for firefox
Commit: cf897795fe8b544bc4cb5899585b1be2ee0063e6
https://github.com/galaxyproject/galaxy/commit/cf897795fe8b544bc4cb5899585b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-25 (Fri, 25 Aug 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
Log Message:
-----------
Merge pull request #4496 from guerler/fix_drag_drop_firefox
[17.05] Fix drag and drop from history for Firefox
Commit: c70926445fb7518e1f2ebf755477ca3327dea6a3
https://github.com/galaxyproject/galaxy/commit/c70926445fb7518e1f2ebf755477…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-25 (Fri, 25 Aug 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Merge pull request #4483 from guerler/fix_workflow_validation
[17.05] Validate workflow step after step argument injection
Commit: 47ba644de78dd82cfaed205128bd34056aa99078
https://github.com/galaxyproject/galaxy/commit/47ba644de78dd82cfaed205128bd…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/web/framework/base.py
Log Message:
-----------
2017-08 Security Patch
Commit: 5a18464d547d7497285ee25067050ee4cd665eda
https://github.com/galaxyproject/galaxy/commit/5a18464d547d7497285ee2506705…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/web/framework/base.py
Log Message:
-----------
2017-08 Security Patch
Commit: 1d485390b0af80441c4e577f8fb7ddde265f9618
https://github.com/galaxyproject/galaxy/commit/1d485390b0af80441c4e577f8fb7…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/web/framework/base.py
Log Message:
-----------
2017-08 Security Patch
Commit: 02c77929852d99ed837e0599140d2b3f40d89767
https://github.com/galaxyproject/galaxy/commit/02c77929852d99ed837e0599140d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
[16.01] Backport uwsgi fix from #2836.
Now that newer releases require a library that the mere presence of breaks an older version of Galaxy, I think this will be encountered more during development. It is breaking Planemo's ability to switch between different versions of Galaxy.
https://github.com/galaxyproject/galaxy/pull/2836
Commit: 2207e7f8aa20702fd3074fec63977520d3213299
https://github.com/galaxyproject/galaxy/commit/2207e7f8aa20702fd3074fec6397…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Merge pull request #4565 from jmchilton/backport_uwsgi_fix
[16.01] Backport uwsgi fix from #2836.
Commit: dad5563cac852971776d6670c8401b0cb6a2ce6a
https://github.com/galaxyproject/galaxy/commit/dad5563cac852971776d6670c840…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Merge branch 'release_16.01' into release_16.04
Commit: 4345d8e7d7a3f27a46b6a06ce54637b74951915a
https://github.com/galaxyproject/galaxy/commit/4345d8e7d7a3f27a46b6a06ce546…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
M lib/galaxy/util/postfork.py
Log Message:
-----------
Merge branch 'release_16.04' into release_16.07
Conflicts:
lib/galaxy/config.py
Commit: 140c570517df5c9c0728c6d5be442d82b2f78ae9
https://github.com/galaxyproject/galaxy/commit/140c570517df5c9c0728c6d5be44…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Log Message:
-----------
Merge branch 'release_16.07' into release_16.10
Commit: 759780b72c03efd6563c0c53efc9edff9505979c
https://github.com/galaxyproject/galaxy/commit/759780b72c03efd6563c0c53efc9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Log Message:
-----------
Merge branch 'release_16.10' into release_17.01
Commit: 41fe55129a3af95d7ef84ecb387b954b14509843
https://github.com/galaxyproject/galaxy/commit/41fe55129a3af95d7ef84ecb387b…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Log Message:
-----------
Merge branch 'release_17.01' into release_17.05
Conflicts:
lib/galaxy/datatypes/data.py
Commit: b17fbfb968b8921729798c909220e522abfb29fd
https://github.com/galaxyproject/galaxy/commit/b17fbfb968b8921729798c909220…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
Fix startup of galaxy when wehbooks dir is empty
Reported by @alpapan on gitter.
Commit: c86bf78c6a966b52d3c9e21ffae71bbf134ecdb4
https://github.com/galaxyproject/galaxy/commit/c86bf78c6a966b52d3c9e21ffae7…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
Merge pull request #4570 from mvdbeek/webhook_loading_fix
[17.05] Bug: Fix startup of galaxy when wehbooks dir is empty
Commit: 7fdce2efd951f79e8ad5a4e2cf9fe8d04340454d
https://github.com/galaxyproject/galaxy/commit/7fdce2efd951f79e8ad5a4e2cf9f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/package.json
M static/maps/mvc/base/controlled-fetch-collection.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/base/controlled-fetch-collection.js
Log Message:
-----------
Allow fetchMore to actually specify a 0 offset when intentional. This should fix the mysterious missing history in multiview bug.
Commit: 14ceb6d91b57563f1203ccd82312b96fdafa8698
https://github.com/galaxyproject/galaxy/commit/14ceb6d91b57563f1203ccd82312…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/package.json
M static/maps/mvc/base/controlled-fetch-collection.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/base/controlled-fetch-collection.js
Log Message:
-----------
Merge pull request #4615 from dannon/release_16.10_backport2
[16.10] Allow fetchMore to actually specify a 0 offset when intentional, fixes multiview
Commit: a9facdc7568f68af06ba7474611feeeabf60466b
https://github.com/galaxyproject/galaxy/commit/a9facdc7568f68af06ba7474611f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/package.json
M static/maps/mvc/base/controlled-fetch-collection.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/base/controlled-fetch-collection.js
Log Message:
-----------
Merge branch 'release_16.10' into release_17.01
Commit: 83b363d5207625b916523b7d08b4fff26e8379ed
https://github.com/galaxyproject/galaxy/commit/83b363d5207625b916523b7d08b4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M static/maps/mvc/base/controlled-fetch-collection.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/base/controlled-fetch-collection.js
Log Message:
-----------
Merge branch 'release_17.01' into release_17.05
Commit: fc90aec7fe4a3267868fdf3cc2c2123f935f15a2
https://github.com/galaxyproject/galaxy/commit/fc90aec7fe4a3267868fdf3cc2c2…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M create_db.sh
M extract_dataset_parts.sh
M manage_db.sh
M manage_tools.sh
Log Message:
-----------
Fix virtualenv activation for some scripts
In particular add virtualenv activation to extract_dataset_parts.sh
to fix the following error when running tools which use
`<parallelism>`:
```
Fatal error:
/tmp/tmpOoQ01k/job_working_directory/000/12/task_0:
Traceback (most recent call last):
File "./scripts/extract_dataset_part.py", line 17, in <module>
import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers
File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module>
from six import string_types
ModuleNotFoundError: No module named 'six'
```
Commit: 97e8e36185312ff6e1afea15fec7e83aadafd25b
https://github.com/galaxyproject/galaxy/commit/97e8e36185312ff6e1afea15fec7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M create_db.sh
M extract_dataset_parts.sh
M manage_db.sh
M manage_tools.sh
Log Message:
-----------
Merge pull request #4624 from nsoranzo/release_17.05_fix_scripts
[17.05] Backport of #4616
Commit: 0a39bfcbf7dcd5d2801be4a6b36a4c34a2ff9b5d
https://github.com/galaxyproject/galaxy/commit/0a39bfcbf7dcd5d2801be4a6b36a…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M config/datatypes_conf.xml.sample
M create_db.sh
M extract_dataset_parts.sh
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/tools/deps/installable.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/webhooks/__init__.py
M lib/galaxy/workflow/modules.py
M manage_db.sh
M manage_tools.sh
M static/maps/mvc/base/controlled-fetch-collection.js.map
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
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/base/controlled-fetch-collection.js
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Merge branch 'release_17.05'
Compare: https://github.com/galaxyproject/galaxy/compare/4a7045c8d210...0a39bfcbf7dc
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: fc90aec7fe4a3267868fdf3cc2c2123f935f15a2
https://github.com/galaxyproject/galaxy/commit/fc90aec7fe4a3267868fdf3cc2c2…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M create_db.sh
M extract_dataset_parts.sh
M manage_db.sh
M manage_tools.sh
Log Message:
-----------
Fix virtualenv activation for some scripts
In particular add virtualenv activation to extract_dataset_parts.sh
to fix the following error when running tools which use
`<parallelism>`:
```
Fatal error:
/tmp/tmpOoQ01k/job_working_directory/000/12/task_0:
Traceback (most recent call last):
File "./scripts/extract_dataset_part.py", line 17, in <module>
import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers
File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module>
from six import string_types
ModuleNotFoundError: No module named 'six'
```
Commit: 97e8e36185312ff6e1afea15fec7e83aadafd25b
https://github.com/galaxyproject/galaxy/commit/97e8e36185312ff6e1afea15fec7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M create_db.sh
M extract_dataset_parts.sh
M manage_db.sh
M manage_tools.sh
Log Message:
-----------
Merge pull request #4624 from nsoranzo/release_17.05_fix_scripts
[17.05] Backport of #4616
Compare: https://github.com/galaxyproject/galaxy/compare/83b363d52076...97e8e3618531
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d8dfbe56c427e73f359595609c932105114950eb
https://github.com/galaxyproject/galaxy/commit/d8dfbe56c427e73f359595609c93…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M static/maps/mvc/library/library-dataset-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-dataset-view.js
Log Message:
-----------
unify library dataset permission frontend for all users
also refactor
Commit: 028aac0a3dabe31a5392feaf35a93900ac7eb8b7
https://github.com/galaxyproject/galaxy/commit/028aac0a3dabe31a5392feaf35a9…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M lib/galaxy/security/__init__.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
Log Message:
-----------
respect expose_user_email when offering roles to datalib permissions
Commit: a1cd3bd1e41d4da17d116c1a8cde1eedb6143ab9
https://github.com/galaxyproject/galaxy/commit/a1cd3bd1e41d4da17d116c1a8cde…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M static/maps/mvc/library/library-dataset-view.js.map
M static/scripts/bundled/admin.bundled.js.map
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/library/library-dataset-view.js
Log Message:
-----------
rebuild client
Commit: 1b2221cd5600823285737fae5d7819c3f2670cfb
https://github.com/galaxyproject/galaxy/commit/1b2221cd5600823285737fae5d78…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M lib/galaxy/security/__init__.py
Log Message:
-----------
fix indent
Commit: 9084edd8200cc7c7387d62ae969921daf3feec86
https://github.com/galaxyproject/galaxy/commit/9084edd8200cc7c7387d62ae9699…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M static/maps/mvc/library/library-dataset-view.js.map
M static/scripts/mvc/library/library-dataset-view.js
Log Message:
-----------
fix typo
thanks @dannon
Commit: c5ff555ec4ef32e0d12020c4ea4e0f52f214e31e
https://github.com/galaxyproject/galaxy/commit/c5ff555ec4ef32e0d12020c4ea4e…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M lib/galaxy/security/__init__.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
M static/maps/mvc/library/library-dataset-view.js.map
M static/scripts/bundled/admin.bundled.js.map
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/library/library-dataset-view.js
Log Message:
-----------
Merge pull request #4611 from martenson/respect-email-exposure
respect expose_user_email configuration in datalibraries permissions list
Compare: https://github.com/galaxyproject/galaxy/compare/c677621481ab...c5ff555ec4ef
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e1be66312b536a419383746b8e702b6148edeeec
https://github.com/galaxyproject/galaxy/commit/e1be66312b536a419383746b8e70…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M create_db.sh
M extract_dataset_parts.sh
M manage_db.sh
M manage_tools.sh
Log Message:
-----------
Fix virtualenv activation for some scripts
In particular add virtualenv activation to extract_dataset_parts.sh
to fix the following error when running tools which use
`<parallelism>`:
```
Fatal error:
/tmp/tmpOoQ01k/job_working_directory/000/12/task_0:
Traceback (most recent call last):
File "./scripts/extract_dataset_part.py", line 17, in <module>
import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers
File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module>
from six import string_types
ModuleNotFoundError: No module named 'six'
```
Commit: 90eed104f0d80fed13ac6b5cfc13f96d28d01771
https://github.com/galaxyproject/galaxy/commit/90eed104f0d80fed13ac6b5cfc13…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M create_db.sh
M extract_dataset_parts.sh
M manage_db.sh
M manage_tools.sh
Log Message:
-----------
Merge pull request #4616 from nsoranzo/fix_scripts
Fix virtualenv activation for some scripts
Compare: https://github.com/galaxyproject/galaxy/compare/8b9e91310fd9...90eed104f0d8