Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 9d736dd42eba2e8bd116d575c7d1278e15183ba3
https://github.com/galaxyproject/galaxy/commit/9d736dd42eba2e8bd116d575c7d1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/container_resolvers/__init__.py
Log Message:
-----------
Fix container resolution.
Without these decorators swapped - resolving containers results in the following Exception:
```
TypeError: unbound method __str__() must be called with ContainerResolver instance as first argument (got nothing instead)
```
I think this recent merge commit 3ed60db5ce9bf2acb954c843c14f8983b11ffbd9 introduced this problem as it merged the two decorators together.
Commit: 8a033b720b370a7e7e9049fa22a5c7a78f0d5a85
https://github.com/galaxyproject/galaxy/commit/8a033b720b370a7e7e9049fa22a5…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/container_resolvers/__init__.py
Log Message:
-----------
Merge pull request #3805 from jmchilton/container_resolution_fix
Fix container resolution.
Compare: https://github.com/galaxyproject/galaxy/compare/f8950feb30ca...8a033b720b37
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 2eefe8571a00497c6faefff64cf86224bae05825
https://github.com/galaxyproject/galaxy/commit/2eefe8571a00497c6faefff64cf8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.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/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
Log Message:
-----------
Fix usage of _.extend in joint collection builder templates.
Fixes bug introduced in #3781. #minor
Commit: f8950feb30ca3caa94d48f487d9d7079839143a0
https://github.com/galaxyproject/galaxy/commit/f8950feb30ca3caa94d48f487d9d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.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/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
Log Message:
-----------
Merge pull request #3799 from jmchilton/fix_extend_usage
Fix usage of _.extend in joint collection builder templates.
Compare: https://github.com/galaxyproject/galaxy/compare/3ed60db5ce9b...f8950feb30ca
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: dda11d21c2e88f6b935f9f90f270a7aeccd929da
https://github.com/galaxyproject/galaxy/commit/dda11d21c2e88f6b935f9f90f270…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/requirements.py
Log Message:
-----------
[17.01] Fix container resolver log statements exposing pointers.
These log statements:
```
2017-02-27 12:11:50,959 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.explicit.ExplicitContainerResolver object at 0x10b211590>] found description [None]
2017-02-27 12:11:51,062 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.mulled.CachedMulledContainerResolver object at 0x10b2115d0>] found description [None]
2017-02-27 12:11:51,490 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.mulled.MulledContainerResolver object at 0x10b211610>] found description [<galaxy.tools.deps.requirements.ContainerDescription object at 0x10d6f1550>]
```
Become:
```
2017-02-27 13:19:06,201 INFO [galaxy.tools.deps.containers] Checking with container resolver [ExplicitContainerResolver[]] found description [None]
2017-02-27 13:19:06,251 INFO [galaxy.tools.deps.containers] Checking with container resolver [CachedMulledContainerResolver[namespace=None]] found description [None]
2017-02-27 13:19:06,679 INFO [galaxy.tools.deps.containers] Checking with container resolver [MulledContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/seqtk:1.2--0,type=docker]]
```
Rebased with suggestion from @nsoranzo :eagle::eyes:
Commit: ca5bb99ee043587fe37cc9354885d3de6fbd5ce3
https://github.com/galaxyproject/galaxy/commit/ca5bb99ee043587fe37cc9354885…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/requirements.py
Log Message:
-----------
Merge pull request #3679 from jmchilton/fix_logs
[17.01] Fix container resolver log statements exposing pointers.
Commit: ce7f9e91ca8893ce290aeeac4836e18db07af3a5
https://github.com/galaxyproject/galaxy/commit/ce7f9e91ca8893ce290aeeac4836…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Annotate converters that appear to need galaxy on PYTHONPATH.
Should fix #3499 (thanks for the explicit heads up @mvdbeek).
Commit: 93a802bd450658f0c66d4226c626112e8163d5a6
https://github.com/galaxyproject/galaxy/commit/93a802bd450658f0c66d4226c626…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3690 from jmchilton/converter_galaxy_lib_fixes
[17.01] Annotate converters that appear to need galaxy on PYTHONPATH.
Commit: 02f3a2737dd1c48574df9bf8e51ce43e6789bf1e
https://github.com/galaxyproject/galaxy/commit/02f3a2737dd1c48574df9bf8e51c…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Bug fix for masthead webhook if Galaxy.page is undefined for workflow, data libraries etc pages
Commit: 7988ae59f5b94b952bd1965b76250ad3f21525d6
https://github.com/galaxyproject/galaxy/commit/7988ae59f5b94b952bd1965b7625…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
Log Message:
-----------
Allow display of install_resolver_checkbox when installing data manager tools
by merging select_shed_tool_panel_config.mako functionality into
select_tool_panel_section.mako (thx @nsoranzo for this suggestion).
Commit: e8922295bd5753e0be262f141b25a05622972ee6
https://github.com/galaxyproject/galaxy/commit/e8922295bd5753e0be262f141b25…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message:
-----------
Remove checks
for `includes_tools_for_display_in_tool_panel` and
`includes_tools_for_display_in_tool_panel` when determining if
initiate_repository_installation.mako should be posted to. It is
sufficient to check that select_tool_panel_section_button has been
clicked.
Commit: 2df727cb05d8d15e14a23a4f8c1da920bfde999d
https://github.com/galaxyproject/galaxy/commit/2df727cb05d8d15e14a23a4f8c1d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M test/shed_functional/functional/test_1150_datatype_converters.py
Log Message:
-----------
Adjust wording of datatype converter install test.
Commit: 1b9a2868a17899787bf65181f96892596b16b51b
https://github.com/galaxyproject/galaxy/commit/1b9a2868a17899787bf65181f968…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Merge pull request #3728 from martenson/backport-masthead-fix
[16.10] backport of webhook masthead fix for datalibs and workflows
Commit: 376212eff900d28450165ddf715f3d9a29870ca9
https://github.com/galaxyproject/galaxy/commit/376212eff900d28450165ddf715f…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Fix for uploading rdata datasets when explicitly declaring datatype.
Now that ext's are forced to be all lowercase, you cannot upload a dataset with any uppercase characters in the extension.
TODO: An additional fix directly for the upload tool/datatype widget should be pursued that will prevent these issues.
Commit: fa37f67786b88b5d1c4138a142efccf3cc42d219
https://github.com/galaxyproject/galaxy/commit/fa37f67786b88b5d1c4138a142ef…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Merge branch 'release_16.10' into release_17.01
Conflicts:
static/maps/layout/menu.js.map
static/scripts/bundled/libs.bundled.js
static/scripts/bundled/libs.bundled.js.map
static/scripts/layout/menu.js
Commit: 7429ded33e1af8214f2ca20563698f73dd3869d3
https://github.com/galaxyproject/galaxy/commit/7429ded33e1af8214f2ca2056369…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
fix datetime import
Commit: aaafbe956f343eb6d34dbdcec0b8b937e439334a
https://github.com/galaxyproject/galaxy/commit/aaafbe956f343eb6d34dbdcec0b8…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
add the activation functionality to API users controller
it was invoked but not included resulting in errors
Commit: 642956a899ea2b97348be698bd81dd11a85d113e
https://github.com/galaxyproject/galaxy/commit/642956a899ea2b97348be698bd81…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
remove unused import
Commit: 54fb1a433d061d398d67a0cb3e80ea1406226898
https://github.com/galaxyproject/galaxy/commit/54fb1a433d061d398d67a0cb3e80…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
only request verificaion when needed
thanks @nsoranzo
Commit: 56c710adbc1f10579511c506503493241df4176c
https://github.com/galaxyproject/galaxy/commit/56c710adbc1f10579511c5065034…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
reqork the activation logic when email is changed
thanks to @nsoranzo for help
Commit: cfa3e29cadf0960f01735a2ad43b64ac9c17e031
https://github.com/galaxyproject/galaxy/commit/cfa3e29cadf0960f01735a2ad43b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M test/shed_functional/functional/test_1150_datatype_converters.py
Log Message:
-----------
Merge pull request #3686 from mvdbeek/datamanager_conda_install
[17.01] Allow display of install_resolver_checkbox when installing data manag…
Commit: 6ab5cc1caf8c9fc0d4ce311c43988d12ea2ae6bb
https://github.com/galaxyproject/galaxy/commit/6ab5cc1caf8c9fc0d4ce311c4398…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-18 (Sat, 18 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Merge pull request #3771 from martenson/fix-users-api
[17.01] Fixes for users API
Commit: e3e24facc72103dadeca2dc72c9d038f907eb10e
https://github.com/galaxyproject/galaxy/commit/e3e24facc72103dadeca2dc72c9d…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Merge pull request #3766 from blankenberg/17.01-rdata-upload-fix
[17.01] Fix for uploading rdata datasets when explicitly declaring datatype.
Commit: 12eb3838496f373e429235cd8e75117baf682005
https://github.com/galaxyproject/galaxy/commit/12eb3838496f373e429235cd8e75…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
fix xss thanks to @erasche
Commit: 2528a89bd087786c458c86d6ac78c24e8fb7f51d
https://github.com/galaxyproject/galaxy/commit/2528a89bd087786c458c86d6ac78…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Merge pull request #3776 from martenson/xss-fix
[16.04] fix xss vuln in grids
Commit: e3255fd3cb7c1b0cf9ce9fa82f0a4a9c39719f19
https://github.com/galaxyproject/galaxy/commit/e3255fd3cb7c1b0cf9ce9fa82f0a…
Author: nekrut <anton(a)nekrut.org>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/unzip_collection.xml
M lib/galaxy/tools/zip_collection.xml
Log Message:
-----------
made collection ops help sections slightly more readable
Commit: d9c3a0bb57e63a1849bb3f55c056ae0384a2279a
https://github.com/galaxyproject/galaxy/commit/d9c3a0bb57e63a1849bb3f55c056…
Author: Anton Nekrutenko <anekrut(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/tools/unzip_collection.xml
Log Message:
-----------
Update unzip_collection.xml
fixed typos identified by @mvdbeek
Commit: 80ecc79a4cb8fa3dbaf9b3348216df6f9387a91c
https://github.com/galaxyproject/galaxy/commit/80ecc79a4cb8fa3dbaf9b3348216…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Merge pull request #3789 from galaxyproject/release_16.04
merge 16.04 into 16.07
Commit: 490e565611b5e3a22124d937e22cf0363afb62f6
https://github.com/galaxyproject/galaxy/commit/490e565611b5e3a22124d937e22c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Merge pull request #3790 from galaxyproject/release_16.07
merge 16.07 into 16.10
Commit: ec88dda1e9c926341b87bc7e19b7b5842eb92ddb
https://github.com/galaxyproject/galaxy/commit/ec88dda1e9c926341b87bc7e19b7…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Merge pull request #3791 from galaxyproject/release_16.10
merge 16.10 into 17.01
Commit: c84b3ba0b8f9de983d43ea17c165856d23960911
https://github.com/galaxyproject/galaxy/commit/c84b3ba0b8f9de983d43ea17c165…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/unzip_collection.xml
M lib/galaxy/tools/zip_collection.xml
Log Message:
-----------
Merge pull request #3788 from jmchilton/backport_collection_option_help_fixes
[17.01] Backport collection operation help fixes
Commit: 3ed60db5ce9bf2acb954c843c14f8983b11ffbd9
https://github.com/galaxyproject/galaxy/commit/3ed60db5ce9bf2acb954c843c14f…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M test/shed_functional/functional/test_1150_datatype_converters.py
Log Message:
-----------
Merge branch 'release_17.01' into dev
Conflicts:
lib/galaxy/tools/deps/container_resolvers/__init__.py
static/scripts/bundled/libs.bundled.js
static/scripts/bundled/libs.bundled.js.map
Compare: https://github.com/galaxyproject/galaxy/compare/279548574136...3ed60db5ce9b
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e0f80db701b2c843c78074b9957452aa2eb3fe58
https://github.com/galaxyproject/galaxy/commit/e0f80db701b2c843c78074b99574…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-04 (Sat, 04 Feb 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M test/api/test_libraries.py
Log Message:
-----------
Add possibility to load collections into library
and to conserve element_identifier.
Commit: 8906f515e1df604c62a0faf6744b309b396431d5
https://github.com/galaxyproject/galaxy/commit/8906f515e1df604c62a0faf6744b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-04 (Sat, 04 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Add first working version of js needed for collection import
Commit: 08449059f4e3c62fd281fcbeae67cdce149241c0
https://github.com/galaxyproject/galaxy/commit/08449059f4e3c62fd281fcbeae67…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M test/api/test_libraries.py
Log Message:
-----------
Test adding a single dataset to a folder and test creating library using from_hdca_id
Commit: 8b9fd288bc4a05b177a56665229cbd9b58f4de3c
https://github.com/galaxyproject/galaxy/commit/8b9fd288bc4a05b177a56665229c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M test/api/test_libraries.py
Log Message:
-----------
Test creating library datatsets fails when not owning HDA
Commit: 26050f6deafe51fc38632dc4a02c284ec0ea993d
https://github.com/galaxyproject/galaxy/commit/26050f6deafe51fc38632dc4a02c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
Log Message:
-----------
Move functionality shared between folder and library api into UsesLibraryMixinItems
Commit: e7a0c186a9494f3589364dfc5f76e25bcd97dbad
https://github.com/galaxyproject/galaxy/commit/e7a0c186a9494f3589364dfc5f76…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
Log Message:
-----------
Simplify exception handling
Commit: 46af8ba4c3007f33f68c0b0d95f2dc166e69a14f
https://github.com/galaxyproject/galaxy/commit/46af8ba4c3007f33f68c0b0d95f2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
Log Message:
-----------
Simplify exceptions some more
Commit: 6e7d290d0c462772cf51118f83e3f6c39a170ede
https://github.com/galaxyproject/galaxy/commit/6e7d290d0c462772cf51118f83e3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
Log Message:
-----------
Remove unused rval variable
Commit: 828422fe5e6d419ec1af28e0c62b7a8759bae9b8
https://github.com/galaxyproject/galaxy/commit/828422fe5e6d419ec1af28e0c62b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Only show items in selector if item is visible and state is ok
Commit: 75994c8816cdac0af80614db629553495dcb6bff
https://github.com/galaxyproject/galaxy/commit/75994c8816cdac0af80614db6295…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
Log Message:
-----------
Always set new ldda's to visible
Commit: 7a6579878a09862e1cd5919ba7d94c527f3b0e56
https://github.com/galaxyproject/galaxy/commit/7a6579878a09862e1cd5919ba7d9…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
fix markup and add a stylistic space
Commit: 234361253a168eaf4b4c86fe4a1963a511271c86
https://github.com/galaxyproject/galaxy/commit/234361253a168eaf4b4c86fe4a19…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
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M .ci/jenkins/selenium/run_tests.sh
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M README.rst
M client/galaxy/scripts/apps/analysis.js
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M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js
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M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
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M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
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M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/user/user-quotameter.js
A client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
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M config/plugins/interactive_environments/common/templates/ie.mako
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M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/plugins/interactive_environments/neo/static/js/neo.js
M config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/interactive_environments/phinch/config/phinch.ini.sample
M config/plugins/interactive_environments/phinch/static/js/phinch.js
M config/plugins/interactive_environments/phinch/templates/phinch.mako
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
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M config/plugins/tours/core.history.yaml
A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js
A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map
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A config/plugins/webhooks/demo/search/config/searchover.yaml
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A config/plugins/webhooks/demo/search/static/styles.css
A config/plugins/webhooks/demo/tool_list/config/tool_list.yml
A config/plugins/webhooks/demo/tool_list/helper/__init__.py
A config/swarm_manager_conf.yml.sample
M contrib/nagios/check_galaxy
M contrib/nagios/check_galaxy.py
A doc/source/admin/authentication.md
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M doc/source/admin/dependency_resolvers.rst
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R doc/source/admin/interactive_environments.png
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A doc/source/admin/tool_panel.rst
R doc/source/admin/webhooks.rst
M doc/source/conf.py
M doc/source/dev/index.rst
M doc/source/dev/interactive_environments.rst
M doc/source/index.rst
R doc/source/lib/galaxy_utils.rst
R doc/source/lib/galaxy_utils.sequence.rst
M doc/source/lib/modules.rst
M doc/source/project/issues.rst
A doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
A doc/source/releases/17.05_announce.rst
M doc/source/releases/_thanks.rst
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M doc/source/slideshow/architecture/galaxy_architecture.md
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M lib/galaxy/app.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/config.py
A lib/galaxy/container/__init__.py
A lib/galaxy/container/docker_swarm.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/managers/deletable.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
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M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
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M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
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M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
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A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
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M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
A lib/galaxy/tools/fetcher.py
M lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/loader_directory.py
A lib/galaxy/tools/locations/__init__.py
A lib/galaxy/tools/locations/dockstore.py
A lib/galaxy/tools/locations/file.py
A lib/galaxy/tools/locations/http.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/json.py
R lib/galaxy/util/postfork.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/lib/mapper.js
A lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/util.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/steps.py
R lib/galaxy_utils/__init__.py
R lib/galaxy_utils/sequence/__init__.py
R lib/galaxy_utils/sequence/fasta.py
R lib/galaxy_utils/sequence/fastq.py
R lib/galaxy_utils/sequence/sequence.py
R lib/galaxy_utils/sequence/transform.py
R lib/galaxy_utils/sequence/vcf.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/util/workflow_util.py
M run_tests.sh
M scripts/api/README
M scripts/bootstrap_history.py
A scripts/secret_decoder_ring.py
M scripts/slideshow/slideshow_template.html
A static/maps/analysis.js.map
A static/maps/app.js.map
A static/maps/app/analysis.js.map
M static/maps/galaxy.interactive_environments.js.map
M static/maps/layout/menu.js.map
M static/maps/libs/jquery/jquery.autocomplete.js.map
A static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
R static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/user/user-quotameter.js.map
A static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-node.js.map
M static/maps/mvc/workflow/workflow-view.js.map
R static/maps/mvc/workflow/workflow.js.map
M static/maps/ui/autocom_tagging.js.map
A static/scripts/analysis.js
A static/scripts/app.js
A static/scripts/app/analysis.js
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
M static/scripts/bundled/login.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
M static/scripts/layout/menu.js
M static/scripts/libs/jquery/jquery.autocomplete.js
A static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
R static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/user/user-quotameter.js
A static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/ui/autocom_tagging.js
M static/style/blue/base.css
M templates/admin/reload_tool.mako
M templates/grid_base.mako
M templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M test/TESTING.md
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_tools.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/base/populators.py
M test/docker/base/run_test_wrapper.sh
A test/functional/tools/mulled_example_multi_incomplete.xml
A test/functional/tools/output_format_deprecated_when.xml
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation-data.yml
M test/integration/test_resolvers.py
M test/qunit/tests/form_tests.js
M test/selenium_tests/framework.py
A test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_uploads.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_execution.py
M test/unit/workflows/test_modules.py
M tools/data_source/upload.py
Log Message:
-----------
Merge branch 'dev' into add_hdca_to_library
Commit: 3dcd174f2b2f0e78d58b3e9d7e19103bd299b128
https://github.com/galaxyproject/galaxy/commit/3dcd174f2b2f0e78d58b3e9d7e19…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
repack
Commit: 279548574136817c226fad61c52168cfab199fb8
https://github.com/galaxyproject/galaxy/commit/279548574136817c226fad61c521…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M lib/galaxy/model/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/mvc/library/library-foldertoolbar-view.js
M test/api/test_libraries.py
Log Message:
-----------
Merge pull request #3559 from mvdbeek/add_hdca_to_library
Add possibility to load collection into library
Compare: https://github.com/galaxyproject/galaxy/compare/eadbb16462f2...279548574136
Branch: refs/heads/usegalaxy
Home: https://github.com/galaxyproject/galaxy
Commit: 12eb3838496f373e429235cd8e75117baf682005
https://github.com/galaxyproject/galaxy/commit/12eb3838496f373e429235cd8e75…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
fix xss thanks to @erasche
Commit: 2528a89bd087786c458c86d6ac78c24e8fb7f51d
https://github.com/galaxyproject/galaxy/commit/2528a89bd087786c458c86d6ac78…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Merge pull request #3776 from martenson/xss-fix
[16.04] fix xss vuln in grids
Commit: e3255fd3cb7c1b0cf9ce9fa82f0a4a9c39719f19
https://github.com/galaxyproject/galaxy/commit/e3255fd3cb7c1b0cf9ce9fa82f0a…
Author: nekrut <anton(a)nekrut.org>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/unzip_collection.xml
M lib/galaxy/tools/zip_collection.xml
Log Message:
-----------
made collection ops help sections slightly more readable
Commit: d9c3a0bb57e63a1849bb3f55c056ae0384a2279a
https://github.com/galaxyproject/galaxy/commit/d9c3a0bb57e63a1849bb3f55c056…
Author: Anton Nekrutenko <anekrut(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/tools/unzip_collection.xml
Log Message:
-----------
Update unzip_collection.xml
fixed typos identified by @mvdbeek
Commit: 80ecc79a4cb8fa3dbaf9b3348216df6f9387a91c
https://github.com/galaxyproject/galaxy/commit/80ecc79a4cb8fa3dbaf9b3348216…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Merge pull request #3789 from galaxyproject/release_16.04
merge 16.04 into 16.07
Commit: 490e565611b5e3a22124d937e22cf0363afb62f6
https://github.com/galaxyproject/galaxy/commit/490e565611b5e3a22124d937e22c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Merge pull request #3790 from galaxyproject/release_16.07
merge 16.07 into 16.10
Commit: ec88dda1e9c926341b87bc7e19b7b5842eb92ddb
https://github.com/galaxyproject/galaxy/commit/ec88dda1e9c926341b87bc7e19b7…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Merge pull request #3791 from galaxyproject/release_16.10
merge 16.10 into 17.01
Commit: c84b3ba0b8f9de983d43ea17c165856d23960911
https://github.com/galaxyproject/galaxy/commit/c84b3ba0b8f9de983d43ea17c165…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/unzip_collection.xml
M lib/galaxy/tools/zip_collection.xml
Log Message:
-----------
Merge pull request #3788 from jmchilton/backport_collection_option_help_fixes
[17.01] Backport collection operation help fixes
Commit: f9b8e6a51a179a0c41e1657e1b9eb92e017a0a1a
https://github.com/galaxyproject/galaxy/commit/f9b8e6a51a179a0c41e1657e1b9e…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/unzip_collection.xml
M lib/galaxy/tools/zip_collection.xml
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Merge pull request #3792 from galaxyproject/release_17.01
[usegalaxy] merge 17.01
Compare: https://github.com/galaxyproject/galaxy/compare/3b4cf0d578d8...f9b8e6a51a17