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October 2017
- 1 participants
- 196 discussions
31 Oct '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ccb5f6184502dbc2ebdf05e05e46eee2a2d675ad
https://github.com/galaxyproject/galaxy/commit/ccb5f6184502dbc2ebdf05e05e46…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-26 (Thu, 26 Oct 2017)
Changed paths:
A .ci/tox_envs/flake8/Pipfile
A .ci/tox_envs/flake8/requirements.txt
A .ci/tox_envs/flake8_imports/Pipfile
A .ci/tox_envs/flake8_imports/requirements.txt
A .ci/tox_envs/update.sh
M Makefile
M scripts/bootstrap_history.py
M tox.ini
Log Message:
-----------
Absolute pins on linting dependencies.
- Use completely pinned and hashed dependencies for more consistent, reproducible linting.
- Leverage the awesomeness of pipenv to automate updating these.
- These will always be locked now so builds don't break randomly on other people updating their software. When we finally have the bot up and running that forward merges fixes for Galaxy we can add another if statement that runs this check against dev once a day and opens a PR if needed.
Commit: b25de8c685977eb8a8f2d689e9d20b8378449a66
https://github.com/galaxyproject/galaxy/commit/b25de8c685977eb8a8f2d689e9d2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-27 (Fri, 27 Oct 2017)
Changed paths:
M .ci/tox_envs/update.sh
Log Message:
-----------
Fix bashism (spotted by @nsoranzo).
Commit: 04dc1470f0b26f1f495a446f0c1549635fedc5a3
https://github.com/galaxyproject/galaxy/commit/04dc1470f0b26f1f495a446f0c15…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-10-31 (Tue, 31 Oct 2017)
Changed paths:
M .ci/tox_envs/update.sh
Log Message:
-----------
Fix more bashims
Commit: 0ad92e830b2134f768796e96c8c6d03bc5f65115
https://github.com/galaxyproject/galaxy/commit/0ad92e830b2134f768796e96c8c6…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-10-31 (Tue, 31 Oct 2017)
Changed paths:
M .ci/tox_envs/flake8_imports/requirements.txt
Log Message:
-----------
Rev and re-lock linting dependencies.
Commit: 07d11c6d0b78e683c2bae35318789db229957c4d
https://github.com/galaxyproject/galaxy/commit/07d11c6d0b78e683c2bae3531878…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-10-31 (Tue, 31 Oct 2017)
Changed paths:
A .ci/tox_envs/flake8/Pipfile
A .ci/tox_envs/flake8/requirements.txt
A .ci/tox_envs/flake8_imports/Pipfile
A .ci/tox_envs/flake8_imports/requirements.txt
A .ci/tox_envs/update.sh
M Makefile
M scripts/bootstrap_history.py
M tox.ini
Log Message:
-----------
Merge pull request #4876 from jmchilton/update_linting_deps
Absolute pins on linting dependencies.
Compare: https://github.com/galaxyproject/galaxy/compare/9bd9e04572cc...07d11c6d0b78
1
0
[galaxyproject/galaxy] d2394a: Merge pull request #4198 from fabio-cumbo/data-sou...
by GitHub 31 Oct '17
by GitHub 31 Oct '17
31 Oct '17
Branch: refs/heads/master
Home: https://github.com/galaxyproject/galaxy
Commit: d2394aa172e2030c301f7b50863fb3d96664a2db
https://github.com/galaxyproject/galaxy/commit/d2394aa172e2030c301f7b50863f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/async.py
Log Message:
-----------
Merge pull request #4198 from fabio-cumbo/data-source-async
Async update: support to collections
Commit: d698d32ceb043fdb9820b68615748ca13e0825c8
https://github.com/galaxyproject/galaxy/commit/d698d32ceb043fdb9820b6861574…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Manage users and groups for role
Commit: 9ee062bd4622481165d4cb1e783454a49fcdd704
https://github.com/galaxyproject/galaxy/commit/9ee062bd4622481165d4cb1e7834…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Show current name and description when renaming roles
Commit: 183176a05c95e063a710ff469a368c463e18db2f
https://github.com/galaxyproject/galaxy/commit/183176a05c95e063a710ff469a36…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Add create role form
Commit: 663c6c13975b01cf0472a083a68164d9bd010871
https://github.com/galaxyproject/galaxy/commit/663c6c13975b01cf0472a083a681…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
R templates/admin/dataset_security/role/role.mako
R templates/admin/dataset_security/role/role_create.mako
R templates/admin/dataset_security/role/role_rename.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako
Log Message:
-----------
Fix boolean title, and move unused role makos to toolshed
Commit: e77fd47b034e6af5b19756bd778f5081332e7c85
https://github.com/galaxyproject/galaxy/commit/e77fd47b034e6af5b19756bd778f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix boolean handling
Commit: 419f3db64fb3614d5a70ed9a9eea8a260b6f5865
https://github.com/galaxyproject/galaxy/commit/419f3db64fb3614d5a70ed9a9eea…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/tool_shed/util/admin_util.py
Log Message:
-----------
Remove unused information feature for toolshed
Commit: 7b423e19c92868a6a3e7abee2a4ad6e92a03aad8
https://github.com/galaxyproject/galaxy/commit/7b423e19c92868a6a3e7abee2a4a…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
Log Message:
-----------
Merge pull request #1 from dannon/library_tags
Swap two more spots initializing TagManagers to new session
Commit: c49e749534f76c8bb2d0ea8bb629a6ee236ff5cc
https://github.com/galaxyproject/galaxy/commit/c49e749534f76c8bb2d0ea8bb629…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/tool_shed/util/admin_util.py
Log Message:
-----------
Fix user info link for toolshed
Commit: 733e225ec96b058dd159dda4e18ba1f7572573fd
https://github.com/galaxyproject/galaxy/commit/733e225ec96b058dd159dda4e18b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M client/galaxy/scripts/utils/query-string-parsing.js
M static/maps/utils/query-string-parsing.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/utils/query-string-parsing.js
Log Message:
-----------
Fix message handling in user preference main view
Commit: a5d7c0fa84d8fe24fc94ac814b9f7502283de7c2
https://github.com/galaxyproject/galaxy/commit/a5d7c0fa84d8fe24fc94ac814b9f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-wrapper.js
M static/maps/mvc/form/form-wrapper.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/form/form-wrapper.js
Log Message:
-----------
Scroll to highlight message
Commit: 4b2eca373e936308b0550b9fabfc6494228b837a
https://github.com/galaxyproject/galaxy/commit/4b2eca373e936308b0550b9fabfc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Remove duplicate roles from selection list
Commit: 5a8adbf8b77dc985353803a724fc4344dcbbdc79
https://github.com/galaxyproject/galaxy/commit/5a8adbf8b77dc985353803a724fc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M doc/source/admin/special_topics/grt.rst
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/runners/util/cli/__init__.py
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/history.py
R scripts/grt.py
R scripts/grt.yml.sample
A scripts/grt/export.py
A scripts/grt/grt.yml.sample
A scripts/grt/upload.py
M test/api/test_tools.py
A test/functional/tools/identifier_source.xml
M test/functional/tools/samples_tool_conf.xml
A test/unit/test_remote_shell.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
M tox.ini
Log Message:
-----------
Merge branch 'remove_duplicates' into admin_grid_roles
Commit: 305f9f94c04579a8414e0034e0ec90311119431b
https://github.com/galaxyproject/galaxy/commit/305f9f94c04579a8414e0034e0ec…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M static/scripts/bundled/admin.bundled.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
Log Message:
-----------
revert static files
Commit: a06ec3e58dc1c53a8bcf515f38c89976eae1a074
https://github.com/galaxyproject/galaxy/commit/a06ec3e58dc1c53a8bcf515f38c8…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
change xml to yml
Commit: a71f64c8da2427b6f5808b9f4e91612fe82efe10
https://github.com/galaxyproject/galaxy/commit/a71f64c8da2427b6f5808b9f4e91…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M config/user_preferences_extra_conf.yml.sample
Log Message:
-----------
fix apollo spelling
Commit: 338fffad0bcaea709cc552dcab5310e4b73ea4c7
https://github.com/galaxyproject/galaxy/commit/338fffad0bcaea709cc552dcab53…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Remove user_preferences_extra_conf.yml sample file from the default list
Commit: eb8f7f0da328b0fd440f67bdf0c6f9c5e366a32d
https://github.com/galaxyproject/galaxy/commit/eb8f7f0da328b0fd440f67bdf0c6…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
remove debug statement
Commit: 20f90254bfae5e2e0579a69fa37b0c45e874d9ce
https://github.com/galaxyproject/galaxy/commit/20f90254bfae5e2e0579a69fa37b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M templates/webapps/tool_shed/repository/common.mako
Log Message:
-----------
Show minimum required galaxy version in tool shed and galaxy installation process
Commit: a77c4587fb9eadfc62da6b8b430154ad18ce1136
https://github.com/galaxyproject/galaxy/commit/a77c4587fb9eadfc62da6b8b4301…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/tool_shed/utility_containers/utility_container_manager.py
Log Message:
-----------
Shorten 'Minimum required Galaxy version' to 'Minimum Galaxy Version'
Commit: 210d3e31ab8bd71569ed6399cfc1894223e4ec36
https://github.com/galaxyproject/galaxy/commit/210d3e31ab8bd71569ed6399cfc1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Refactor to clean up args in one method of galaxy.tools.
Commit: 997e7114be722e56e5633cd10b554d6d1428dfc8
https://github.com/galaxyproject/galaxy/commit/997e7114be722e56e5633cd10b55…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M test/unit/tools_support.py
Log Message:
-----------
More correct tool creation in tools_support.
Now supports creating tool subclasses based on tool source.
Commit: db91b29df96d354c8972f63513ed755b5dd4418d
https://github.com/galaxyproject/galaxy/commit/db91b29df96d354c8972f63513ed…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Have more tests use mock_galaxy's MockApp.
Commit: ecad3996f1f4715db5ff326f9f6ae5067cd2e0fc
https://github.com/galaxyproject/galaxy/commit/ecad3996f1f4715db5ff326f9f6a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/tools/parser/output_objects.py
Log Message:
-----------
Refactor ToolOutputCollectionStructure to allow it be more easily consumed.
Make complex arguments optional.
Commit: e8112210429d710a9eb9702f541cfaed6e219454
https://github.com/galaxyproject/galaxy/commit/e8112210429d710a9eb9702f541c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/tools/parser/output_objects.py
Log Message:
-----------
Improve cohesion of interaction between ToolOutputCollectionStructure and ToolOutputCollection.
Shield more of ToolOutputCollectionStructure internals from ToolOutputCollection.
Commit: 71db6b461da3d3b2e3c6880c9d2bf90bcd44098e
https://github.com/galaxyproject/galaxy/commit/71db6b461da3d3b2e3c6880c9d2b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix lint
Fix
Commit: bf68966accd18af2da1e4fa518d01119f5a696f2
https://github.com/galaxyproject/galaxy/commit/bf68966accd18af2da1e4fa518d0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Fix get_tool returning list when it shouldn't.
Commit: c72aca479729ddee6a8bf8e19431b41e98d39d89
https://github.com/galaxyproject/galaxy/commit/c72aca479729ddee6a8bf8e19431…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Revise admin groups endpoint
Commit: a7c6c69cbf6a6eeffdf53815144e623576c47b13
https://github.com/galaxyproject/galaxy/commit/a7c6c69cbf6a6eeffdf53815144e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix lint
Commit: 097cae67956b972cd609f1155890d122c5bb3742
https://github.com/galaxyproject/galaxy/commit/097cae67956b972cd609f1155890…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Merge branch 'admin_grid_roles' into admin_grid_groups
Commit: 9822dede69c95796c24e87a1c60cd845788095d1
https://github.com/galaxyproject/galaxy/commit/9822dede69c95796c24e87a1c60c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Add client route
Commit: 1bf2d1782fca4c79708261ca98cabe92822e86cb
https://github.com/galaxyproject/galaxy/commit/1bf2d1782fca4c79708261ca98ca…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Use client side formbuilder for rename group form
Commit: 7a58fd113d32659c9ea6e0c4fdb830d5c1ca7a72
https://github.com/galaxyproject/galaxy/commit/7a58fd113d32659c9ea6e0c4fdb8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove self directed operation
Commit: b2d54b377c6c78f016ccb730178afd3f7a70c0b3
https://github.com/galaxyproject/galaxy/commit/b2d54b377c6c78f016ccb730178a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Add async support for group deleting
Commit: afdfbf69ff8d1636c661c5758f52c636f9160220
https://github.com/galaxyproject/galaxy/commit/afdfbf69ff8d1636c661c5758f52…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Add async support for undeleting groups
Commit: 96557cd136730033c3a4b84e506b3cc5831d06af
https://github.com/galaxyproject/galaxy/commit/96557cd136730033c3a4b84e506b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Add async support for purging groups
Commit: fe2d607675acf5e18994957fb8ff4422079987ea
https://github.com/galaxyproject/galaxy/commit/fe2d607675acf5e18994957fb8ff…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Replace list with generator when iterating headers
This should be more memory-friendly. @blankenberg suggested doing this
in #4319.
Commit: 037b7fa75754ae90917d0ee25b1565c9ab29cd03
https://github.com/galaxyproject/galaxy/commit/037b7fa75754ae90917d0ee25b15…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove exposure of async operation handlers, align naming
Commit: 3840c6d61735fa674239be19a10af04d0d3647f9
https://github.com/galaxyproject/galaxy/commit/3840c6d61735fa674239be19a10a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix purge handler for groups
Commit: 1e83a48c4635ba05576cdb8e42bbdf8f971b825a
https://github.com/galaxyproject/galaxy/commit/1e83a48c4635ba05576cdb8e42bb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove exposure of user related operations
Commit: 1795247bd849e3d7d1c034416d27d5c1672039e8
https://github.com/galaxyproject/galaxy/commit/1795247bd849e3d7d1c034416d27…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove new line
Commit: d53a5424967e46d683f7baafe06cb53703e86adf
https://github.com/galaxyproject/galaxy/commit/d53a5424967e46d683f7baafe06c…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/tools/parser/output_objects.py
Log Message:
-----------
Merge pull request #4389 from jmchilton/output_collect_refactor
Refactor ToolOutputCollectionStructure...
Commit: e805db6896352042aa5eb8482febbd75af46b008
https://github.com/galaxyproject/galaxy/commit/e805db6896352042aa5eb8482feb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Use client to build create groups form
Commit: a462afa0b7094a5fa439b0aa3b751e26cc18bd98
https://github.com/galaxyproject/galaxy/commit/a462afa0b7094a5fa439b0aa3b75…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Eliminate second unit test variant of MockApp.
As well as my failed experiment in mocking out sqlalchemy - I think the in-memory database is more useful than mocking out sqlalchemy in retrospect.
Commit: 5605f390fe36c8ab562d049b105db7164b8097c1
https://github.com/galaxyproject/galaxy/commit/5605f390fe36c8ab562d049b105d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Build manage users and roles for groups with client form builder
Commit: c827bb0a867e2fcdf89417bb7ea912641e49cf8a
https://github.com/galaxyproject/galaxy/commit/c827bb0a867e2fcdf89417bb7ea9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/tool_shed/util/admin_util.py
R templates/admin/dataset_security/group/group.mako
R templates/admin/dataset_security/group/group_create.mako
R templates/admin/dataset_security/group/group_rename.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako
Log Message:
-----------
Move unused mako templates to toolshed, adjust paths
Commit: d3b8889c04ef22d740f8b668a8212c728ba5832c
https://github.com/galaxyproject/galaxy/commit/d3b8889c04ef22d740f8b668a821…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/panels/admin-panel.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Fix second role link in admin panel
Commit: dbad2556d05dead2ac0991a7897d95f1eda16087
https://github.com/galaxyproject/galaxy/commit/dbad2556d05dead2ac0991a7897d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/panels/admin-panel.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Merge branch 'admin_grid_roles' into admin_grid_groups
Commit: 4a35bd3532ce3a9e0af84c3a86ee33585e9e0ba3
https://github.com/galaxyproject/galaxy/commit/4a35bd3532ce3a9e0af84c3a86ee…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Merge pull request #4390 from jmchilton/toollist
Fix get_tool returning list when it shouldn't.
Commit: 613f4fb1ced3c9a7e0d1417b8c9c14b681479bdd
https://github.com/galaxyproject/galaxy/commit/613f4fb1ced3c9a7e0d1417b8c9c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Use dict format for admin tool versions grid
Commit: 381bf173d095ce51ba66d9cf19f5827c75c36dc8
https://github.com/galaxyproject/galaxy/commit/381bf173d095ce51ba66d9cf19f5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove message from tool versions
Commit: cdfaebdaa4722226cf121454aa02b455d324d265
https://github.com/galaxyproject/galaxy/commit/cdfaebdaa4722226cf121454aa02…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Switch quotas grid to dict format
Commit: a060690c3afa8f296404eb52e4986202d1d985ca
https://github.com/galaxyproject/galaxy/commit/a060690c3afa8f296404eb52e498…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/util/workflow_util.py
Log Message:
-----------
Get tools with tool_version in more places
Commit: e6c238e234ae4d16d1fd1118c1b7e585ba541645
https://github.com/galaxyproject/galaxy/commit/e6c238e234ae4d16d1fd1118c1b7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/interval.py
Log Message:
-----------
Move iter_headers into try clause (thx @nsoranzo)
Commit: 43702ccacdbfe925d921dac413c02bb7f65b9c4f
https://github.com/galaxyproject/galaxy/commit/43702ccacdbfe925d921dac413c0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
Process the first line when setting metdata for mother.otu files
Commit: 196a2bbcf50c4f9fa41588d8e087e5b5cee9da65
https://github.com/galaxyproject/galaxy/commit/196a2bbcf50c4f9fa41588d8e087…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
A config/user_preferences_extra_conf.yml.sample
M lib/galaxy/config.py
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Merge pull request #3383 from bgruening/extra_user_preferences
Add extension point for user preferences
Commit: f8648b658629d1313029bb1ad707023c44b626df
https://github.com/galaxyproject/galaxy/commit/f8648b658629d1313029bb1ad707…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Add deeptools datatypes to Galaxy
Commit: 0e1b80b28f7558104c9a36bd1d224c60d91c2c70
https://github.com/galaxyproject/galaxy/commit/0e1b80b28f7558104c9a36bd1d22…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/panels/admin-panel.js
M lib/galaxy/actions/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Add async quota grid operations
Commit: ad60f5a8ea4eaf574b4ffa1e51baa5bbe8282d47
https://github.com/galaxyproject/galaxy/commit/ad60f5a8ea4eaf574b4ffa1e51ba…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/actions/admin.py
Log Message:
-----------
Allow empty params
Commit: 83a48f8f336a4c73dd1faabe3c84ce8801fb181d
https://github.com/galaxyproject/galaxy/commit/83a48f8f336a4c73dd1faabe3c84…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/actions/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Build quota renaming form in admin panel using client side form builder
Commit: 0da4768c3535d13c0a141cc30f39e8b86b0c98d1
https://github.com/galaxyproject/galaxy/commit/0da4768c3535d13c0a141cc30f39…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Merge pull request #4388 from mvdbeek/iter_headers
Replace list with generator when iterating headers
Commit: ff197fe915a67c1ad2ba10ed9a6d433a55b45ee1
https://github.com/galaxyproject/galaxy/commit/ff197fe915a67c1ad2ba10ed9a6d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M templates/webapps/tool_shed/repository/common.mako
Log Message:
-----------
Merge pull request #4386 from mvdbeek/display_minimum_required_galaxy_version
Show minimum required galaxy version in tool shed and galaxy installation process
Commit: 9dcc181f72d5f31b3d5feb45f673996714aca913
https://github.com/galaxyproject/galaxy/commit/9dcc181f72d5f31b3d5feb45f673…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix error message handling for quota operations, set default value for payloads to none
Commit: 643f262ea913e8cc0f3bb5e39acf2af80194c71f
https://github.com/galaxyproject/galaxy/commit/643f262ea913e8cc0f3bb5e39acf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/actions/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Use client form builder to render edit quota amount form
Commit: ad2dc168307037070205db27d7bdb09fb82d549f
https://github.com/galaxyproject/galaxy/commit/ad2dc168307037070205db27d7bd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix link to edit quota
Commit: ae181d776fb9a565d7b51c18aa8edcae09018bc3
https://github.com/galaxyproject/galaxy/commit/ae181d776fb9a565d7b51c18aa8e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Provide async support for unsetting default quotas
Commit: bd542000fa9ec420ba0f2e17d2b8f8047eb72f8c
https://github.com/galaxyproject/galaxy/commit/bd542000fa9ec420ba0f2e17d2b8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Build set default quota forms using client form builder
Commit: 17cd7d16c2db988581e26ad59a88a57302a202c9
https://github.com/galaxyproject/galaxy/commit/17cd7d16c2db988581e26ad59a88…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/actions/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Add manage role support for quotas
Commit: 9f580d0630026157f2727651cce2e8f444f78cdc
https://github.com/galaxyproject/galaxy/commit/9f580d0630026157f2727651cce2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Use consistent naming for group and role parameters
Commit: e901a0c867cfa9af3420536c4725cbc001621cf8
https://github.com/galaxyproject/galaxy/commit/e901a0c867cfa9af3420536c4725…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Bugfix for loading subworkflows from workflow descriptions.
Sometimes unrelated workflow steps can be flushed in a half complete state and violate integrity constraints when a subworkflow step causes a flush of during the load of a different step. This fixes that by preloading all subworkflows during workflow import.
This PR doesn't include a test case but one will be included if the CWL branch is merged at a later date (xref https://github.com/common-workflow-language/common-workflow-language/pull/4…)
Commit: cf34d8b75958db007dcaa5368557dda6850d6e95
https://github.com/galaxyproject/galaxy/commit/cf34d8b75958db007dcaa5368557…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Merge pull request #4392 from bgruening/deeptools_datatypes
Add deepTools datatypes to Galaxy
Commit: 7de7f3f63a438a9d2b2b452d61e3118a710826c7
https://github.com/galaxyproject/galaxy/commit/7de7f3f63a438a9d2b2b452d61e3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M test/unit/tools_support.py
Log Message:
-----------
"Fix" import order of tools_support for Travis.
Commit: bc23c26cf4210b46f4d17369902fdaec48a16e98
https://github.com/galaxyproject/galaxy/commit/bc23c26cf4210b46f4d17369902f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/util/workflow_util.py
Log Message:
-----------
Merge pull request #4391 from mvdbeek/more_version_fixes
Get tools with tool_version in more places
Commit: c03b29f4855dcce9677e2fe16779d2eb64b1646d
https://github.com/galaxyproject/galaxy/commit/c03b29f4855dcce9677e2fe16779…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/jobs/command_factory.py
Log Message:
-----------
Revise comment thanks to note from @mvdbeek.
Commit: 11365e9620a5198ca88a35f5a10902744d94a7a3
https://github.com/galaxyproject/galaxy/commit/11365e9620a5198ca88a35f5a109…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/tools/parser/interface.py
M test/unit/tools/test_parsing.py
Log Message:
-----------
Bugfix: __str__ method on tool parsers would throw an Exception.
Commit: d39483bf0a88aa6c62cb69928abc8195e9082db7
https://github.com/galaxyproject/galaxy/commit/d39483bf0a88aa6c62cb69928abc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M test/base/interactor.py
Log Message:
-----------
Revise summarize history errors to display more data and outline collections.
Commit: 67f9e34f530d1d505e12fcca9fef2648025d877e
https://github.com/galaxyproject/galaxy/commit/67f9e34f530d1d505e12fcca9fef…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M test/api/test_tools.py
M test/base/populators.py
Log Message:
-----------
Implement test lib history context.
Commit: b7fe2fa2ecc44bde964be1c44e73e2ea11586bf5
https://github.com/galaxyproject/galaxy/commit/b7fe2fa2ecc44bde964be1c44e73…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M test/base/interactor.py
M test/base/populators.py
Log Message:
-----------
Rework summarizing histories on errors to include all datasets.
```
-------------------- >> begin captured stdout << ---------------------
Problem in history with id adb5f5c93f827949 - summary of datasets below.
--------------------------------------
| 1 - Test Dataset (HID - NAME)
| Dataset State:
| ok
| Dataset Blurb:
| 1 line
| Dataset Info:
| uploaded txt file
| Peek:
| <table cellspacing="0" cellpadding="3"><tr><td>1 2 3</td></tr></table>
| Dataset Job Standard Output:
| *Standard output was empty.*
| Dataset Job Standard Error:
| *Standard error was empty.*
|
--------------------------------------
| 2 - Test Dataset (HID - NAME)
| Dataset State:
| ok
| Dataset Blurb:
| 1 line
| Dataset Info:
| uploaded txt file
| Peek:
| <table cellspacing="0" cellpadding="3"><tr><td>4 5 6</td></tr></table>
| Dataset Job Standard Output:
| *Standard output was empty.*
| Dataset Job Standard Error:
| *Standard error was empty.*
|
--------------------------------------
| 3 - multi_data_param on data 1 and data 2 (HID - NAME)
| Dataset State:
| ok
| Dataset Blurb:
| 2 lines
| Dataset Info:
| *Dataset info is empty.*
| Peek:
| <table cellspacing="0" cellpadding="3"><tr><td>1 2 3</td></tr><tr><td>4 5 6</td></tr></table>
| Dataset Job Standard Output:
| *Standard output was empty.*
| Dataset Job Standard Error:
| *Standard error was empty.*
|
--------------------------------------
| 4 - multi_data_param on data 1 and data 2 (HID - NAME)
| Dataset State:
| ok
| Dataset Blurb:
| 2 lines
| Dataset Info:
| *Dataset info is empty.*
| Peek:
| <table cellspacing="0" cellpadding="3"><tr><td>4 5 6</td></tr><tr><td>1 2 3</td></tr></table>
| Dataset Job Standard Output:
| *Standard output was empty.*
| Dataset Job Standard Error:
| *Standard error was empty.*
|
--------------------------------------
```
Commit: a001145278fb0642325214123da0c5cec6fc6704
https://github.com/galaxyproject/galaxy/commit/a001145278fb0642325214123da0…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M lib/galaxy/jobs/command_factory.py
Log Message:
-----------
Merge pull request #4383 from jmchilton/split_conda
Bugfix: Ensure task splitting handles before job resolution.
Commit: c7d7b6c4695b300739b572b9a94e0de312a0f6ef
https://github.com/galaxyproject/galaxy/commit/c7d7b6c4695b300739b572b9a94e…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M lib/galaxy/tools/parser/interface.py
M test/unit/tools/test_parsing.py
Log Message:
-----------
Merge pull request #4395 from jmchilton/parser_to_str_fix
Bugfix: __str__ method on tool parsers would throw an Exception.
Commit: 7ca5cd6585ef8a69f07cfa8362287a800b48281a
https://github.com/galaxyproject/galaxy/commit/7ca5cd6585ef8a69f07cfa836228…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
Log Message:
-----------
Fix import order and Python3 compatibility for lib/galaxy/web/base/
Commit: 0f84d8bd91722c4bd36d5a736d6ca02a57460cfc
https://github.com/galaxyproject/galaxy/commit/0f84d8bd91722c4bd36d5a736d6c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Add client side form to create new quota
Commit: 5647dfe5dbb22b7d09b1b760e41a2e0cd96cd8c8
https://github.com/galaxyproject/galaxy/commit/5647dfe5dbb22b7d09b1b760e41a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
R templates/admin/quota/quota.mako
R templates/admin/quota/quota_create.mako
R templates/admin/quota/quota_edit.mako
R templates/admin/quota/quota_rename.mako
R templates/admin/quota/quota_set_default.mako
Log Message:
-----------
Remove unused quota makos
Commit: c57c36b51465b1bfaefcf486b9814c32f7f92840
https://github.com/galaxyproject/galaxy/commit/c57c36b51465b1bfaefcf486b981…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove over indent
Commit: 4a77956dc8756300825c3744ccfa3a4646be5775
https://github.com/galaxyproject/galaxy/commit/4a77956dc8756300825c3744ccfa…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Merge branch 'admin_grid_roles' into admin_grid_groups
Commit: 2e53858a2973aa6d4f95c3e8401d9709809d1da3
https://github.com/galaxyproject/galaxy/commit/2e53858a2973aa6d4f95c3e8401d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
Log Message:
-----------
Merge pull request #4403 from nsoranzo/flake8-import-order
Fix import order and Python3 compatibility for lib/galaxy/web/base/
Commit: 8f056c2bbc78040c790255c874b6c321c4ba5b97
https://github.com/galaxyproject/galaxy/commit/8f056c2bbc78040c790255c874b6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M config/datatypes_conf.xml.sample
A config/user_preferences_extra_conf.yml.sample
M doc/source/admin/special_topics/grt.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/util/cli/__init__.py
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
R scripts/grt.py
R scripts/grt.yml.sample
A scripts/grt/export.py
A scripts/grt/grt.yml.sample
A scripts/grt/upload.py
M static/maps/galaxy.js.map
M static/maps/layout/menu.js.map
M static/maps/mvc/user/user-preferences.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/galaxy.js
M static/scripts/layout/menu.js
M static/scripts/mvc/user/user-preferences.js
M templates/galaxy_client_app.mako
M templates/user/login.mako
M templates/user/register.mako
M templates/webapps/galaxy/history/display_structured.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/tool_shed/repository/common.mako
M test/api/test_tools.py
A test/functional/tools/identifier_source.xml
M test/functional/tools/samples_tool_conf.xml
M test/shed_functional/base/twilltestcase.py
A test/unit/test_remote_shell.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' into revise_page
Commit: c01023b5adc402a6a8662e9f319afcd9e4f5fc6e
https://github.com/galaxyproject/galaxy/commit/c01023b5adc402a6a8662e9f319a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix indention
Commit: d32a3a58a50bdbdbe6144a265ef3424a2f011ae2
https://github.com/galaxyproject/galaxy/commit/d32a3a58a50bdbdbe6144a265ef3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M config/datatypes_conf.xml.sample
A config/user_preferences_extra_conf.yml.sample
M lib/galaxy/config.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M templates/webapps/tool_shed/repository/common.mako
M test/unit/tools/test_parsing.py
Log Message:
-----------
Merge branch 'revise_page' into admin_grid_roles
Commit: 06c70d34e2c218b826d813d3dd4e52d077ab94d4
https://github.com/galaxyproject/galaxy/commit/06c70d34e2c218b826d813d3dd4e…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-09 (Wed, 09 Aug 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: cff21d350dc71b1e7b088985eeeb3f27b0fec1d0
https://github.com/galaxyproject/galaxy/commit/cff21d350dc71b1e7b088985eeeb…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/dataset/data.js
A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/grid/grid-model.js
A client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/grid/grid-view.js
R client/galaxy/scripts/mvc/page/page-list.js
M client/galaxy/scripts/mvc/user/user-preferences.js
R client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
A client/package-lock.json
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
A config/plugins/visualizations/unipept/README.md
A config/plugins/visualizations/unipept/config/unipept.xml
A config/plugins/visualizations/unipept/static/style.css
A config/plugins/visualizations/unipept/static/tooltip.css
A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js
A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map
A config/plugins/visualizations/unipept/static/unipept_viz.js
A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png
A config/plugins/visualizations/unipept/templates/unipept.mako
M config/plugins/webhooks/demo/search/static/script.js
M config/tool_conf.xml.main
M config/tool_shed.ini.sample
A config/user_preferences_extra_conf.yml.sample
M doc/source/admin/special_topics/grt.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/util/cli/__init__.py
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/objectstore/__init__.py
A lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/web/base/controller.py
R lib/galaxy/web/base/controllers/__init__.py
R lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/users.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/async.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/tool_shed/metadata/metadata_generator.py
A lib/tool_shed/util/admin_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
R scripts/grt.py
R scripts/grt.yml.sample
A scripts/grt/export.py
A scripts/grt/grt.yml.sample
A scripts/grt/upload.py
M scripts/runtime_stats.py
M static/maps/galaxy.js.map
M static/maps/galaxy.pages.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/dataset/data.js.map
A static/maps/mvc/dataset/dataset-edit-attributes.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/grid/grid-model.js.map
A static/maps/mvc/grid/grid-shared.js.map
M static/maps/mvc/grid/grid-view.js.map
R static/maps/mvc/page/page-list.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/mvc/workflow/workflow.js.map
M static/maps/nls/fr/locale.js.map
M static/maps/nls/ja/locale.js.map
M static/maps/nls/locale.js.map
M static/maps/viz/circster.js.map
M static/maps/viz/phyloviz.js.map
M static/maps/viz/trackster.js.map
M static/maps/viz/trackster/tracks.js.map
M static/maps/viz/visualization.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
M static/scripts/bundled/login.bundled.js.map
M static/scripts/galaxy.js
M static/scripts/galaxy.pages.js
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/dataset/data.js
A static/scripts/mvc/dataset/dataset-edit-attributes.js
M static/scripts/mvc/dataset/dataset-li-edit.js
A static/scripts/mvc/grid/grid-shared.js
M static/scripts/mvc/grid/grid-view.js
R static/scripts/mvc/page/page-list.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/visualization.js
M static/style/blue/base.css
M templates/galaxy_client_app.mako
M templates/user/login.mako
M templates/user/register.mako
R templates/webapps/galaxy/dataset/edit_attributes.mako
M templates/webapps/galaxy/history/display_structured.mako
R templates/webapps/galaxy/history/list_published.mako
M templates/webapps/galaxy/page/editor.mako
R templates/webapps/galaxy/page/select_items_grid.mako
M templates/webapps/galaxy/requests/common/common.mako
R templates/webapps/galaxy/tracks/add_to_viz.mako
R templates/webapps/galaxy/tracks/add_tracks.mako
R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako
R templates/webapps/galaxy/tracks/history_select_grid.mako
R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako
R templates/webapps/galaxy/visualization/list.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/tool_shed/repository/common.mako
M test/api/test_tools.py
A test/functional/tools/identifier_source.xml
M test/functional/tools/samples_tool_conf.xml
M test/shed_functional/base/twilltestcase.py
A test/unit/test_remote_shell.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' into library_tags
Commit: fd0ce1284a9663fab95558fd38ad9477c98d8311
https://github.com/galaxyproject/galaxy/commit/fd0ce1284a9663fab95558fd38ad…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
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
Log Message:
-----------
make client again...
Commit: d52ac533daa8bcfef209f66f8c4e3020d93c09df
https://github.com/galaxyproject/galaxy/commit/d52ac533daa8bcfef209f66f8c4e…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M lib/galaxy/model/migrate/versions/0135_add_library_tags.py
Log Message:
-----------
fix indentation
Commit: 429771820200acd1a0d0b12c85a39ab7fe530195
https://github.com/galaxyproject/galaxy/commit/429771820200acd1a0d0b12c85a3…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0135_add_library_tags.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-foldertoolbar-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-foldertoolbar-view.js
Log Message:
-----------
Merge pull request #4262 from bwlang/library_tags
Library tags
Commit: cfa3220d9f2d257b94795b6f63592459d3011f30
https://github.com/galaxyproject/galaxy/commit/cfa3220d9f2d257b94795b6f6359…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0135_add_library_tags.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Merge branch 'dev' into revise_page
Commit: bdbe3603059b84bb2a91646ebcad003477bb9590
https://github.com/galaxyproject/galaxy/commit/bdbe3603059b84bb2a91646ebcad…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M scripts/grt/export.py
Log Message:
-----------
fix pardir
Commit: f4383bd983ee14d4e85ef610dba4b11266b196ed
https://github.com/galaxyproject/galaxy/commit/f4383bd983ee14d4e85ef610dba4…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M scripts/grt/export.py
Log Message:
-----------
Fun things you find in production
Commit: c5b36128644310e1ac52647df53f226c1457aaeb
https://github.com/galaxyproject/galaxy/commit/c5b36128644310e1ac52647df53f…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M scripts/grt/upload.py
Log Message:
-----------
cleanup url in case
Commit: 847df13fc0ea349ab2103099b696715a6d66b38f
https://github.com/galaxyproject/galaxy/commit/847df13fc0ea349ab2103099b696…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M scripts/grt/upload.py
Log Message:
-----------
this should not have been missed
Commit: 496169719465e18c899b991152a9e327d83e2446
https://github.com/galaxyproject/galaxy/commit/496169719465e18c899b991152a9…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M scripts/grt/upload.py
Log Message:
-----------
fix extension
Commit: a177ccd0268805e0079f39d5d141ae4da39c0a00
https://github.com/galaxyproject/galaxy/commit/a177ccd0268805e0079f39d5d141…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M scripts/grt/upload.py
Log Message:
-----------
not needed
Commit: 5e43fcef3c94e9b3f6d700fc5258067d0547e30d
https://github.com/galaxyproject/galaxy/commit/5e43fcef3c94e9b3f6d700fc5258…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
A client/galaxy/scripts/layout/router.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M static/maps/galaxy.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
A static/maps/layout/router.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
M static/scripts/bundled/login.bundled.js.map
M static/scripts/galaxy.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
A static/scripts/layout/router.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M templates/admin/user/reset_password.mako
M templates/admin/user/user.mako
Log Message:
-----------
Merge pull request #4341 from guerler/revise_page
Admin user grid conversion
Commit: e477cce9b68d90a313d1534c3ad156f9eb8cc6ec
https://github.com/galaxyproject/galaxy/commit/e477cce9b68d90a313d1534c3ad1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M config/datatypes_conf.xml.sample
A config/user_preferences_extra_conf.yml.sample
M doc/source/admin/special_topics/grt.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/util/cli/__init__.py
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0135_add_library_tags.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
R scripts/grt.py
R scripts/grt.yml.sample
A scripts/grt/export.py
A scripts/grt/grt.yml.sample
A scripts/grt/upload.py
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M templates/webapps/tool_shed/repository/common.mako
M test/api/test_tools.py
A test/functional/tools/identifier_source.xml
M test/functional/tools/samples_tool_conf.xml
A test/unit/test_remote_shell.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
M tox.ini
Log Message:
-----------
Merge branch 'revise_page' into revise_grid_forms
Commit: 938bf525f46c8d3c7568d9b2a97edfa958ba900f
https://github.com/galaxyproject/galaxy/commit/938bf525f46c8d3c7568d9b2a97e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0135_add_library_tags.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Merge branch 'revise_grid_forms' into admin_grid_roles
Commit: b8c05ede4dd188dce24c914912f8fa35963d9562
https://github.com/galaxyproject/galaxy/commit/b8c05ede4dd188dce24c914912f8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Log Message:
-----------
Merge branch 'dev' into revise_grid_forms
Commit: 70a64b304eb2b5c9642581061f345e669251eac6
https://github.com/galaxyproject/galaxy/commit/70a64b304eb2b5c9642581061f34…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A config/error_report.xml.sample
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
A lib/galaxy/tools/error_reports/__init__.py
A lib/galaxy/tools/error_reports/sinks/__init__.py
A lib/galaxy/tools/error_reports/sinks/email.py
A lib/galaxy/tools/error_reports/sinks/json.py
A lib/galaxy/tools/error_reports/sinks/sentry.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
A templates/messages.mako
Log Message:
-----------
Refactor bug reporting into plugins
Commit: 9dd27dcc3de5eff03c4a37c34fc810d3f295c85c
https://github.com/galaxyproject/galaxy/commit/9dd27dcc3de5eff03c4a37c34fc8…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/__init__.py
M lib/galaxy/tools/error_reports/sinks/__init__.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
Log Message:
-----------
flake8
Commit: 181a72a6f383aa54c4a053cedba05e345eda2584
https://github.com/galaxyproject/galaxy/commit/181a72a6f383aa54c4a053cedba0…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/sinks/email.py
M lib/galaxy/tools/error_reports/sinks/json.py
M lib/galaxy/tools/error_reports/sinks/sentry.py
Log Message:
-----------
flake8 import
Commit: 437ab325da8b49b9f0e9b796f8515899aa10d035
https://github.com/galaxyproject/galaxy/commit/437ab325da8b49b9f0e9b796f851…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/special_topics/index.rst
Log Message:
-----------
document
Commit: 46b621708aa4b9973c3e6bf6b02417dc3931523c
https://github.com/galaxyproject/galaxy/commit/46b621708aa4b9973c3e6bf6b024…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M doc/source/admin/special_topics/bug_reports.rst
M lib/galaxy/tools/error_reports/sinks/sentry.py
Log Message:
-----------
Allow sentry to be verbose
Commit: d7e400c96ddf51caca3df26e8dc8a75089be2b06
https://github.com/galaxyproject/galaxy/commit/d7e400c96ddf51caca3df26e8dc8…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
R config/error_report.xml.sample
A config/error_report.yml.sample
M lib/galaxy/config.py
Log Message:
-----------
Per @jmchilton comment, rewrite as yml
Commit: f4a823c27a9b533994c593670cf5a13740e5bf7a
https://github.com/galaxyproject/galaxy/commit/f4a823c27a9b533994c593670cf5…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
Log Message:
-----------
add bug reporter
Commit: ed7551e09679b940bd084fd5e5ce5fcf97320ffa
https://github.com/galaxyproject/galaxy/commit/ed7551e09679b940bd084fd5e5ce…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
A client/galaxy/scripts/mvc/job/job-params.js
Log Message:
-----------
redirect to new url
Commit: 2f8347d5bc4bdf52a7d2b10d3e69b55290d104ca
https://github.com/galaxyproject/galaxy/commit/2f8347d5bc4bdf52a7d2b10d3e69…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
add clientside route
Commit: ef6b8cbeea5a0578683df8f013a0739a1e022fe0
https://github.com/galaxyproject/galaxy/commit/ef6b8cbeea5a0578683df8f013a0…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
M templates/show_params.mako
Log Message:
-----------
move css rule to a more generic location
Commit: 98ac18661865e958249f9a21bc847ba558b00893
https://github.com/galaxyproject/galaxy/commit/98ac18661865e958249f9a21bc84…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/sinks/email.py
M lib/galaxy/tools/error_reports/sinks/json.py
M lib/galaxy/tools/error_reports/sinks/sentry.py
Log Message:
-----------
change report code
Commit: 6f8f38170c976b2152ef2e21fc46a47922da4b56
https://github.com/galaxyproject/galaxy/commit/6f8f38170c976b2152ef2e21fc46…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
Log Message:
-----------
refactor into an API
Commit: 838b23358e6d00ce2d65f6a5fde6a413505eaf10
https://github.com/galaxyproject/galaxy/commit/838b23358e6d00ce2d65f6a5fde6…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-error.js
Log Message:
-----------
Handle error report submission
Commit: 64174113bfd8e18b2e87581137a134f8f4520bd7
https://github.com/galaxyproject/galaxy/commit/64174113bfd8e18b2e87581137a1…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-error.js
Log Message:
-----------
refactor a bit
Commit: 73369a2e8dd098d59083c61f67ec140a7c3cd102
https://github.com/galaxyproject/galaxy/commit/73369a2e8dd098d59083c61f67ec…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-error.js
Log Message:
-----------
Add extra parameter to allow multiple messages
Commit: cdb82dd8e64b83e14244b3b46163be1715afcfe2
https://github.com/galaxyproject/galaxy/commit/cdb82dd8e64b83e14244b3b46163…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/__init__.py
M lib/galaxy/webapps/galaxy/api/jobs.py
Log Message:
-----------
Change invocation to pass user information
Commit: 5980bd91bb0f916b576b27386d2b052609610d57
https://github.com/galaxyproject/galaxy/commit/5980bd91bb0f916b576b27386d2b…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/errors.py
Log Message:
-----------
Link in expected places
Commit: fd6c247398133d6f8df26b447328ec64801fcd11
https://github.com/galaxyproject/galaxy/commit/fd6c247398133d6f8df26b447328…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A lib/galaxy/tools/error_reports/sinks/biostars.py
M lib/galaxy/util/biostar.py
Log Message:
-----------
Switch biostars to using HTML submission
Commit: fb78a2118d0e45a11378bbc5e0daf0e351c8b763
https://github.com/galaxyproject/galaxy/commit/fb78a2118d0e45a11378bbc5e0da…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/style/blue/base.css
Log Message:
-----------
merge
Commit: e8a5b48da9ce98c72ac92171be56435ca2b9565f
https://github.com/galaxyproject/galaxy/commit/e8a5b48da9ce98c72ac92171be56…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
R templates/webapps/galaxy/dataset/errors.mako
Log Message:
-----------
Now unused
Commit: 550cb7dfae8706e06a2b7638b078c9b9b134281d
https://github.com/galaxyproject/galaxy/commit/550cb7dfae8706e06a2b7638b078…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/tools/error_reports/__init__.py
A lib/galaxy/tools/error_reports/plugins/__init__.py
A lib/galaxy/tools/error_reports/plugins/biostars.py
A lib/galaxy/tools/error_reports/plugins/email.py
A lib/galaxy/tools/error_reports/plugins/json.py
A lib/galaxy/tools/error_reports/plugins/sentry.py
R lib/galaxy/tools/error_reports/sinks/__init__.py
R lib/galaxy/tools/error_reports/sinks/biostars.py
R lib/galaxy/tools/error_reports/sinks/email.py
R lib/galaxy/tools/error_reports/sinks/json.py
R lib/galaxy/tools/error_reports/sinks/sentry.py
Log Message:
-----------
Requested renames, sink + yml
Commit: fcd94f0483c119a4db0e84e469af3aade0f2847c
https://github.com/galaxyproject/galaxy/commit/fcd94f0483c119a4db0e84e469af…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M config/error_report.yml.sample
M lib/galaxy/app.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/error_reports/__init__.py
M lib/galaxy/webapps/galaxy/api/jobs.py
Log Message:
-----------
more renames
Commit: 7c1c60d82643b100a55edefb6f88d13671defafa
https://github.com/galaxyproject/galaxy/commit/7c1c60d82643b100a55edefb6f88…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A static/maps/mvc/dataset/dataset-error.js.map
A static/maps/mvc/job/job-params.js.map
A static/scripts/mvc/dataset/dataset-error.js
A static/scripts/mvc/job/job-params.js
Log Message:
-----------
forgot static files
Commit: 61a5b7c9e139cfa73fefa048f6ec34a7511b741c
https://github.com/galaxyproject/galaxy/commit/61a5b7c9e139cfa73fefa048f6ec…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
another merge
Commit: a6aedc695336b122c5e552ced771a97b5f62ee52
https://github.com/galaxyproject/galaxy/commit/a6aedc695336b122c5e552ced771…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/biostars.py
Log Message:
-----------
address flaking
Commit: 1e9c31241c419cb53306232856ed7c368d8c6e92
https://github.com/galaxyproject/galaxy/commit/1e9c31241c419cb53306232856ed…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/jobs.py
Log Message:
-----------
remove comment
Commit: 538ef006f36b3e525bb87d18944d596afb5f1639
https://github.com/galaxyproject/galaxy/commit/538ef006f36b3e525bb87d18944d…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/util/plugin_config.py
Log Message:
-----------
Also load yaml sample files. cc @jmchilton, is this ok?
Commit: 3e8919c41643352feb6df50d04a71f2291024ef7
https://github.com/galaxyproject/galaxy/commit/3e8919c41643352feb6df50d04a7…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M config/error_report.yml.sample
Log Message:
-----------
correct name to type
Commit: 5563ecc3ffa7d0565be42eea99276d64ec5232dd
https://github.com/galaxyproject/galaxy/commit/5563ecc3ffa7d0565be42eea9927…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/biostars.py
Log Message:
-----------
fix import order
Commit: 00ee109ed4538b6a032489a07807deb7e13c9882
https://github.com/galaxyproject/galaxy/commit/00ee109ed4538b6a032489a07807…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/email.py
Log Message:
-----------
fix css class
Commit: 4c36b5a7a189f9586c061460bfdec7a84b6774c4
https://github.com/galaxyproject/galaxy/commit/4c36b5a7a189f9586c061460bfde…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
not a useful test in this location
Commit: a2b02065ebbfa9759aad5e56db0c251f7ad514bc
https://github.com/galaxyproject/galaxy/commit/a2b02065ebbfa9759aad5e56db0c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/web/framework/webapp.py
R templates/messages.mako
Log Message:
-----------
Remove unneeded messages.mako.
Commit: 41461235b2429ef84c50336021d9921ca6ef8a4a
https://github.com/galaxyproject/galaxy/commit/41461235b2429ef84c50336021d9…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
Log Message:
-----------
rebuild client
Commit: 6d7d4e9e8e55cfcaa504f43e6288c1d39c0ed932
https://github.com/galaxyproject/galaxy/commit/6d7d4e9e8e55cfcaa504f43e6288…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
A client/galaxy/scripts/mvc/job/job-params.js
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
A config/error_report.yml.sample
A doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/special_topics/index.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
A lib/galaxy/tools/error_reports/__init__.py
A lib/galaxy/tools/error_reports/plugins/__init__.py
A lib/galaxy/tools/error_reports/plugins/biostars.py
A lib/galaxy/tools/error_reports/plugins/email.py
A lib/galaxy/tools/error_reports/plugins/json.py
A lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/errors.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
A static/maps/mvc/dataset/dataset-error.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
A static/maps/mvc/job/job-params.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
A static/scripts/mvc/dataset/dataset-error.js
M static/scripts/mvc/dataset/dataset-li-edit.js
A static/scripts/mvc/job/job-params.js
M static/style/blue/base.css
M templates/show_params.mako
R templates/webapps/galaxy/dataset/errors.mako
Log Message:
-----------
Merge pull request #4305 from erasche/bug-report-actions
Refactor bug reporting into plugins / Remove bug report mako
Commit: fcd06a96d61342564febfaf652198bd009c9c76f
https://github.com/galaxyproject/galaxy/commit/fcd06a96d61342564febfaf65219…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M scripts/grt/export.py
M scripts/grt/upload.py
Log Message:
-----------
Merge pull request #4408 from erasche/grt-pardir
Small GRT bugfixes
Commit: e3de5e250d02d105aff4265a0caf13553e3c3ade
https://github.com/galaxyproject/galaxy/commit/e3de5e250d02d105aff4265a0caf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/sort_collection_list.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #4329 from glormph/collection_list_sort
Created alphabetic and numerical sort tool for collection operations
Commit: bcdf2c84f6df020e81c8868b10bcf337e2d72630
https://github.com/galaxyproject/galaxy/commit/bcdf2c84f6df020e81c8868b10bc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/tabular.py
A test-data/test.vcf.gz
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/vcf_bgzip.xml
Log Message:
-----------
Merge pull request #4254 from ffinfo/vcf_gz_datatype
Vcf gz datatype
Commit: 583765c7c087c77c6d1f2756e4233ce97a71240f
https://github.com/galaxyproject/galaxy/commit/583765c7c087c77c6d1f2756e423…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
A client/galaxy/scripts/mvc/job/job-params.js
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
M config/datatypes_conf.xml.sample
A config/error_report.yml.sample
M config/tool_conf.xml.sample
A doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/special_topics/index.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/error_reports/__init__.py
A lib/galaxy/tools/error_reports/plugins/__init__.py
A lib/galaxy/tools/error_reports/plugins/biostars.py
A lib/galaxy/tools/error_reports/plugins/email.py
A lib/galaxy/tools/error_reports/plugins/json.py
A lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/errors.py
A lib/galaxy/tools/sort_collection_list.xml
M lib/galaxy/util/biostar.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M scripts/grt/export.py
M scripts/grt/upload.py
A static/maps/mvc/dataset/dataset-error.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
A static/maps/mvc/job/job-params.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
A static/scripts/mvc/dataset/dataset-error.js
M static/scripts/mvc/dataset/dataset-li-edit.js
A static/scripts/mvc/job/job-params.js
M static/style/blue/base.css
M templates/show_params.mako
R templates/webapps/galaxy/dataset/errors.mako
A test-data/test.vcf.gz
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/vcf_bgzip.xml
Log Message:
-----------
Merge branch 'dev' into revise_grid_forms
Commit: be19b36ecaab43dd9cbf2fd5f80995e7ac9ff507
https://github.com/galaxyproject/galaxy/commit/be19b36ecaab43dd9cbf2fd5f809…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
A client/galaxy/scripts/mvc/job/job-params.js
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
M config/datatypes_conf.xml.sample
A config/error_report.yml.sample
M config/tool_conf.xml.sample
A doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/special_topics/index.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/error_reports/__init__.py
A lib/galaxy/tools/error_reports/plugins/__init__.py
A lib/galaxy/tools/error_reports/plugins/biostars.py
A lib/galaxy/tools/error_reports/plugins/email.py
A lib/galaxy/tools/error_reports/plugins/json.py
A lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/errors.py
A lib/galaxy/tools/sort_collection_list.xml
M lib/galaxy/util/biostar.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M scripts/grt/export.py
M scripts/grt/upload.py
A static/maps/mvc/dataset/dataset-error.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
A static/scripts/mvc/dataset/dataset-error.js
M static/scripts/mvc/dataset/dataset-li-edit.js
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/user/user-preferences.js
M static/style/blue/base.css
M templates/show_params.mako
R templates/webapps/galaxy/dataset/errors.mako
A test-data/test.vcf.gz
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/vcf_bgzip.xml
Log Message:
-----------
Merge branch 'revise_grid_forms' into admin_grid_roles
Commit: b38ccbc10547ded7e3afec262a5819bd3d44613f
https://github.com/galaxyproject/galaxy/commit/b38ccbc10547ded7e3afec262a58…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
A client/galaxy/scripts/mvc/job/job-params.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
M config/datatypes_conf.xml.sample
A config/error_report.yml.sample
M config/tool_conf.xml.sample
A config/user_preferences_extra_conf.yml.sample
A doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/special_topics/index.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0135_add_library_tags.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/upload_common.py
A lib/galaxy/tools/error_reports/__init__.py
A lib/galaxy/tools/error_reports/plugins/__init__.py
A lib/galaxy/tools/error_reports/plugins/biostars.py
A lib/galaxy/tools/error_reports/plugins/email.py
A lib/galaxy/tools/error_reports/plugins/json.py
A lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_objects.py
A lib/galaxy/tools/sort_collection_list.xml
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/users.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/library_common.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M scripts/grt/export.py
M scripts/grt/upload.py
A static/maps/mvc/dataset/dataset-error.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
A static/scripts/mvc/dataset/dataset-error.js
M static/scripts/mvc/dataset/dataset-li-edit.js
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/style/blue/base.css
M templates/show_params.mako
R templates/webapps/galaxy/dataset/errors.mako
M templates/webapps/tool_shed/repository/common.mako
A test-data/test.vcf.gz
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/vcf_bgzip.xml
M test/unit/tools/test_parsing.py
Log Message:
-----------
Merge branch 'admin_grid_roles' into admin_grid_groups
Commit: ad2f39c1e6475c65fcb1e300201c035701640f10
https://github.com/galaxyproject/galaxy/commit/ad2f39c1e6475c65fcb1e300201c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix lint
Commit: 6a7cc34e1b1ade9580e464570fc6b83a488e941f
https://github.com/galaxyproject/galaxy/commit/6a7cc34e1b1ade9580e464570fc6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M run.sh
M run_reports.sh
M run_tool_shed.sh
A scripts/common_startup_functions.sh
Log Message:
-----------
Bring Galaxy, reports, and shed run scripts in sync.
- They now uniformly handle server option processing.
- Reports and Tool Shed now respect many new and important options such as --skip_venv.
- Reports and Tool Shed now do extra checking around Python version that Galaxy does.
In addition to improving the reports and tool shed startup scripts and reducing cognative load with respect to option handling, this is an important pre-condition to us being able us to switch on uwsgi by default for all three services simultaneously without a bunch of copy and pasting.
Commit: 72e5a00ba0ad9c1a8e56ad9544bec23c843d900d
https://github.com/galaxyproject/galaxy/commit/72e5a00ba0ad9c1a8e56ad9544be…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M run_reports.sh
M run_tool_shed.sh
M scripts/common_startup_functions.sh
Log Message:
-----------
Centralize launching server for reports and tool shed.
Initial outline of allowing launch via uwsgi.
Commit: 1bdb99bbd76d0827cd3a7e617d288564584863ea
https://github.com/galaxyproject/galaxy/commit/1bdb99bbd76d0827cd3a7e617d28…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/util/properties.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M scripts/manage_tools.py
Log Message:
-----------
Update galaxy.util.properties to allow YAML.
Commit: 8189a1f1e289e14d362fcb8871b9339c3355e8b2
https://github.com/galaxyproject/galaxy/commit/8189a1f1e289e14d362fcb8871b9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A lib/galaxy/webapps/config_manage.py
A scripts/config_sample_to_kwalify.py
A test/unit/config/1607_root_filters/config/galaxy.ini
A test/unit/config/1607_root_filters/config/tool_shed.ini
A test/unit/config/1607_root_samples/config/galaxy.ini
A test/unit/config/1607_root_samples/config/reports.ini
A test/unit/config/1607_root_samples/config/tool_shed.ini
A test/unit/config/test_config_manage.py
Log Message:
-----------
Scripts to manage configuration infrastructure.
This has been rebased several times and includes a variety of fixes (some thanks to martenson).
Commit: 7973a914e0beef9680475d54947bd953c0b062cd
https://github.com/galaxyproject/galaxy/commit/7973a914e0beef9680475d54947b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A lib/galaxy/webapps/uwsgi_schema.yml
Log Message:
-----------
Add uwsgi_schema.yml.
Commit: 90e899d68fbf21effad1cf309efbd786c54be556
https://github.com/galaxyproject/galaxy/commit/90e899d68fbf21effad1cf309efb…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
R config/tool_shed.ini.sample
A config/tool_shed.yml.sample
M lib/galaxy/webapps/tool_shed/buildapp.py
A lib/galaxy/webapps/tool_shed/config_schema.yml
A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml
M run_tool_shed.sh
Log Message:
-----------
Update tool shed to use newer configuration schema.
- Implement kwalify schema to validate/define the schema.
- Replace ini configuration with YAML (completely backward compatible).
- Rebuild a sample configuration from the schema (config/tool_shed.yml.sample).
Commit: 102566dd5e1c5903726057f1077a1d7fc614b815
https://github.com/galaxyproject/galaxy/commit/102566dd5e1c5903726057f1077a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
R config/reports.ini.sample
A config/reports.yml.sample
M lib/galaxy/webapps/reports/buildapp.py
A lib/galaxy/webapps/reports/config_schema.yml
A lib/galaxy/webapps/reports/uwsgi_schema.yml
M run_reports.sh
Log Message:
-----------
Update Galaxy Reports to use newer configuration schema.
- Implement kwalify schema to validate/define the schema.
- Replace ini configuration with YAML (completely backward compatible).
- Rebuild a sample configuration from the schema (config/reports.yml.sample).
Commit: 50d426ed2b9ae2aff8b243143478ce84c7731816
https://github.com/galaxyproject/galaxy/commit/50d426ed2b9ae2aff8b243143478…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A doc/source/admin/reports.rst
A doc/source/admin/reports_options.rst
Log Message:
-----------
Add reports documentation to ``doc/``.
- Automatically generate RST docs from config schema.
- Describe older functionality as well as new YAML-based configuration.
- Replace https://wiki.galaxyproject.org/Admin/UsageReports.
Commit: 4945f55e4fe28842b58c025b37c4d6c96a07028f
https://github.com/galaxyproject/galaxy/commit/4945f55e4fe28842b58c025b37c4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M Makefile
Log Message:
-----------
Makefile shortcuts for configuration script.
Commit: ef46a60a829e3dae44d935f6f886feef39b873e3
https://github.com/galaxyproject/galaxy/commit/ef46a60a829e3dae44d935f6f886…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Add required dependency on uwsgi.
Required for the new out-of-the-box configuration of tool shed and reports.
Commit: 8191fd492819214b12c0aa28b35e5b6c4ea7bfa1
https://github.com/galaxyproject/galaxy/commit/8191fd492819214b12c0aa28b35e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Add pykwalify as dependency for the new config validation stuff.
xref https://github.com/galaxyproject/starforge/pull/110
Commit: ffe295e96dbd82615c987a2b9ba9bd15ea253826
https://github.com/galaxyproject/galaxy/commit/ffe295e96dbd82615c987a2b9ba9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M test/unit/config/test_config_manage.py
Log Message:
-----------
Fix Python 3 linting problem with test_config_manage.py.
Commit: 1ce93ccfdf7b54ec1efcf08b04c9f28b67ab0615
https://github.com/galaxyproject/galaxy/commit/1ce93ccfdf7b54ec1efcf08b04c9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Pin version of uWSGI to freshly released 2.0.15 available on wheels.galaxyproject.org.
Commit: 539a62f642ada1f2d832f1f88ab339cafe672c1f
https://github.com/galaxyproject/galaxy/commit/539a62f642ada1f2d832f1f88ab3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/util/properties.py
Log Message:
-----------
Fix ORM scripts for #3179.
Commit: 98ca8ce7a68d18533f3bf85097490c5b66e9f876
https://github.com/galaxyproject/galaxy/commit/98ca8ce7a68d18533f3bf8509749…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Update config overhaul branch for introduction of galaxy.web.stack package.
Commit: 23db89ba3ddf54420b40e881bd92edbfeff869c6
https://github.com/galaxyproject/galaxy/commit/23db89ba3ddf54420b40e881bd92…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper_docstrings.sh
A .ci/jenkins/api/run_tests.sh
A .ci/jenkins/framework/run_tests.sh
A .ci/jenkins/integration/run_tests.sh
A .ci/jenkins/selenium/Dockerfile
A .ci/jenkins/selenium/docker-compose.yml
A .ci/jenkins/selenium/galaxy.ini
A .ci/jenkins/selenium/run_galaxy.bash
A .ci/jenkins/selenium/run_tests.sh
A .ci/jenkins/toolshed/run_tests.sh
M .ci/py3_sources.txt
M .gitignore
M .travis.yml
M CITATION
M CONTRIBUTING.md
M CONTRIBUTORS.md
M Makefile
M README.rst
A SECURITY_POLICY.md
A client/galaxy/scripts/admin.toolshed.js
A client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
R client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/apps/login.js
A client/galaxy/scripts/apps/panels/admin-panel.js
A client/galaxy/scripts/apps/panels/history-panel.js
A client/galaxy/scripts/apps/panels/tool-panel.js
R client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
A client/galaxy/scripts/layout/router.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js
M client/galaxy/scripts/mvc/citation/citation-view.js
A client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.js
A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
A client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
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-model.js
A client/galaxy/scripts/mvc/grid/grid-shared.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/hdca-li.js
M client/galaxy/scripts/mvc/history/history-contents.js
A client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/options-menu.js
A client/galaxy/scripts/mvc/job/job-params.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/tag.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
R client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
A client/galaxy/scripts/mvc/toolshed/categories-view.js
A client/galaxy/scripts/mvc/toolshed/repo-queue-view.js
A client/galaxy/scripts/mvc/toolshed/repo-status-view.js
A client/galaxy/scripts/mvc/toolshed/repositories-view.js
A client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
A client/galaxy/scripts/mvc/toolshed/repository-view.js
A client/galaxy/scripts/mvc/toolshed/shed-list-view.js
A client/galaxy/scripts/mvc/toolshed/toolshed-model.js
A client/galaxy/scripts/mvc/toolshed/util.js
A client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.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/ui/ui-slider.js
M client/galaxy/scripts/mvc/ui/ui-table.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
A client/galaxy/scripts/mvc/ui/ui-thumbnails.js
A client/galaxy/scripts/mvc/upload/collection/collection-row.js
A client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-view.js
A client/galaxy/scripts/mvc/user/user-custom-builds.js
A client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/user/user-quotameter.js
A client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
A client/galaxy/scripts/mvc/workflow/workflow-forms.js
A client/galaxy/scripts/mvc/workflow/workflow-icons.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-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
A client/galaxy/scripts/mvc/workflow/workflow.js
A client/galaxy/scripts/nls/de/locale.js
A client/galaxy/scripts/nls/es/locale.js
A client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/nls/zh/locale.js
M client/galaxy/scripts/onload.js
M client/galaxy/scripts/ui/autocom_tagging.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/dataset.less
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
M client/galaxy/style/less/history.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/ui/paired-collection-creator.less
M client/galaxy/style/less/upload.less
M client/galaxy/style/source_material/circle.py
A client/package-lock.json
M client/package.json
M client/webpack.config.js
A config/build_sites.yml.sample
A config/containers_conf.yml.sample
M config/datatypes_conf.xml.sample
M config/dependency_resolvers_conf.xml.sample
A config/error_report.yml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/local_conda_mapping.yml.sample
M config/openid_conf.xml.sample
M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml
A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/plugins/interactive_environments/neo/config/neo.xml
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/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.xml
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
M config/plugins/visualizations/charts/static/client/app.css
M config/plugins/visualizations/charts/static/client/app.js
M config/plugins/visualizations/charts/static/client/views/editor.js
R config/plugins/visualizations/charts/static/client/views/types.js
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js
A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js
A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js
M config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
M config/plugins/visualizations/charts/static/repository/utilities/utils.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
M config/plugins/visualizations/charts/templates/charts.mako
M config/plugins/visualizations/charts/webpack.config.js
M config/plugins/visualizations/csg/templates/csg.mako
M config/plugins/visualizations/graphviz/templates/graphviz.mako
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
A config/plugins/visualizations/unipept/README.md
A config/plugins/visualizations/unipept/config/unipept.xml
A config/plugins/visualizations/unipept/static/style.css
A config/plugins/visualizations/unipept/static/tooltip.css
A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js
A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map
A config/plugins/visualizations/unipept/static/unipept_viz.js
A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png
A config/plugins/visualizations/unipept/templates/unipept.mako
A config/plugins/webhooks/demo/search/config/searchover.yaml
A config/plugins/webhooks/demo/search/static/script.js
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/plugins/webhooks/demo/tour_generator/config/tour_generator.yml
A config/plugins/webhooks/demo/tour_generator/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/static/script.js
A config/plugins/webhooks/demo/tour_generator/static/styles.css
A config/swarm_manager_conf.yml.sample
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
M config/tool_data_table_conf.xml.sample
M config/tool_destinations.yml.sample
M config/tool_shed.ini.sample
A config/user_preferences_extra_conf.yml.sample
M contrib/galaxy.debian-init
M contrib/galaxy_config_merger.py
M contrib/galaxy_supervisor.conf
M contrib/nagios/check_galaxy
M contrib/nagios/check_galaxy.py
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M cron/updateucsc.sh.sample
M display_applications/igv/bigwig.xml
A display_applications/igv/genome_fasta.xml
M doc/Makefile
A doc/fix_schema_rst.sh
M doc/parse_gx_xsd.py
R doc/patch.py
M doc/schema_template.md
A doc/source/admin/authentication.md
R doc/source/admin/chat-0.png
R doc/source/admin/chat-1.png
R doc/source/admin/chat-2.png
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R doc/source/admin/chat-4.png
R doc/source/admin/chat.rst
R doc/source/admin/communication_server.png
R doc/source/admin/communication_server_rooms.png
M doc/source/admin/conda_faq.rst
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/framework_dependencies.rst
R doc/source/admin/grt.rst
M doc/source/admin/index.rst
R doc/source/admin/interactive_environments.png
R doc/source/admin/interactive_environments.rst
R doc/source/admin/interactive_environments.svg
R doc/source/admin/interactive_environments_success.png
R doc/source/admin/mulled_containers.rst
A doc/source/admin/reports.md
A doc/source/admin/special_topics/bug_reports.rst
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A doc/source/admin/special_topics/chat.rst
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A doc/source/admin/special_topics/grafana.png
A doc/source/admin/special_topics/grt.rst
A doc/source/admin/special_topics/images_webhooks/history-menu.png
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A doc/source/admin/special_topics/images_webhooks/masthead_trans_object.png
A doc/source/admin/special_topics/images_webhooks/tool.png
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M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
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M lib/galaxy/datatypes/interval.py
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M lib/galaxy/tools/toolbox/filters/examples.py.sample
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R lib/galaxy/tools/toolbox/lineages/tool_shed.py
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M lib/galaxy/tools/util/galaxyops/__init__.py
M lib/galaxy/tools/util/maf_utilities.py
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M lib/galaxy/tools/verify/asserts/__init__.py
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A lib/galaxy/util/handlers.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/json.py
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M lib/galaxy/util/simplegraph.py
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M lib/galaxy/web/framework/middleware/remoteuser.py
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M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/async.py
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M lib/galaxy/webapps/galaxy/controllers/page.py
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M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/groups.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
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M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py
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M lib/galaxy/workflow/schedulers/core.py
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R lib/galaxy_utils/sequence/__init__.py
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M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
A static/scripts/mvc/grid/grid-shared.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/hdca-li.js
M static/scripts/mvc/history/history-contents.js
A static/scripts/mvc/history/history-list.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/options-menu.js
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/tag.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
A static/scripts/mvc/tool/tool-webhooks.js
M static/scripts/mvc/tool/tools.js
A static/scripts/mvc/toolshed/categories-view.js
A static/scripts/mvc/toolshed/repo-queue-view.js
A static/scripts/mvc/toolshed/repo-status-view.js
A static/scripts/mvc/toolshed/repositories-view.js
A static/scripts/mvc/toolshed/repository-queue-view.js
A static/scripts/mvc/toolshed/repository-view.js
A static/scripts/mvc/toolshed/shed-category-view.js
A static/scripts/mvc/toolshed/shed-list-view.js
A static/scripts/mvc/toolshed/shed-repo-details-view.js
A static/scripts/mvc/toolshed/shed-repo-list-view.js
A static/scripts/mvc/toolshed/sheds-list-view.js
A static/scripts/mvc/toolshed/toolshed-model.js
A static/scripts/mvc/toolshed/util.js
A static/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-options.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/ui/ui-slider.js
M static/scripts/mvc/ui/ui-table.js
M static/scripts/mvc/ui/ui-tabs.js
A static/scripts/mvc/ui/ui-thumbnails.js
A static/scripts/mvc/upload/collection/collection-row.js
A static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-view.js
A static/scripts/mvc/user/change-password.js
A static/scripts/mvc/user/extra-information.js
A static/scripts/mvc/user/manage-user-information.js
A static/scripts/mvc/user/user-custom-builds.js
A static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/user/user-quotameter.js
A static/scripts/mvc/webhooks.js
M static/scripts/mvc/workflow/workflow-canvas.js
A static/scripts/mvc/workflow/workflow-configure-menu.js
A static/scripts/mvc/workflow/workflow-forms.js
A static/scripts/mvc/workflow/workflow-icons.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view-node.js
M static/scripts/mvc/workflow/workflow-view.js
A static/scripts/mvc/workflow/workflow.js
A static/scripts/nls/de/locale.js
A static/scripts/nls/es/locale.js
A static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/nls/zh/locale.js
M static/scripts/onload.js
M static/scripts/ui/autocom_tagging.js
M static/scripts/utils/utils.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/visualization.js
M static/style/blue/base.css
M static/welcome.html.sample
M templates/admin/reload_tool.mako
R templates/admin/tool_shed_repository/browse_toolsheds.mako
M templates/admin/tool_shed_repository/common.mako
R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/admin/user/reset_password.mako
M templates/admin/user/user.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/display_base.mako
M templates/galaxy_client_app.mako
M templates/grid_base.mako
M templates/ind_share_base.mako
M templates/js-app.mako
M templates/sharing_base.mako
M templates/show_params.mako
R templates/user/change_password.mako
R templates/user/communication_settings.mako
R templates/user/dbkeys.mako
R templates/user/edit_address.mako
M templates/user/index.mako
M templates/user/login.mako
M templates/user/logout.mako
R templates/user/new_address.mako
R templates/user/permissions.mako
M templates/user/register.mako
R templates/user/toolbox_filters.mako
R templates/user/username.mako
M templates/webapps/galaxy/admin/center.mako
R templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/galaxy/base_panels.mako
M templates/webapps/galaxy/data_manager/index.mako
M templates/webapps/galaxy/dataset/display.mako
R templates/webapps/galaxy/dataset/edit_attributes.mako
R templates/webapps/galaxy/dataset/errors.mako
R templates/webapps/galaxy/dataset/grid.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/history/display_structured.mako
R templates/webapps/galaxy/history/grid.mako
R templates/webapps/galaxy/history/grid_js.mako
R templates/webapps/galaxy/history/list_published.mako
M templates/webapps/galaxy/history/share.mako
R templates/webapps/galaxy/history/shared_grid.mako
M templates/webapps/galaxy/mobile/form.mako
M templates/webapps/galaxy/mobile/index.mako
M templates/webapps/galaxy/page/editor.mako
R templates/webapps/galaxy/page/index.mako
R templates/webapps/galaxy/page/list_published.mako
R templates/webapps/galaxy/page/select_items_grid.mako
M templates/webapps/galaxy/requests/common/common.mako
M templates/webapps/galaxy/root/tool_runner.mako
R templates/webapps/galaxy/tracks/add_to_viz.mako
R templates/webapps/galaxy/tracks/add_tracks.mako
R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako
R templates/webapps/galaxy/tracks/history_select_grid.mako
R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako
R templates/webapps/galaxy/user/api_keys.mako
M templates/webapps/galaxy/user/list_users.mako
R templates/webapps/galaxy/user/manage_info.mako
R templates/webapps/galaxy/visualization/list.mako
R templates/webapps/galaxy/visualization/list_published.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
R templates/webapps/galaxy/workflow/configure_menu.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/editor.mako
R templates/webapps/galaxy/workflow/editor_generic_form.mako
R templates/webapps/galaxy/workflow/editor_tool_form.mako
R templates/webapps/galaxy/workflow/import.mako
R templates/webapps/galaxy/workflow/index.mako
R templates/webapps/galaxy/workflow/list.mako
R templates/webapps/galaxy/workflow/list_for_run.mako
R templates/webapps/galaxy/workflow/list_published.mako
R templates/webapps/galaxy/workflow/missing_tools.mako
R templates/webapps/galaxy/workflow/myexp_export_content.mako
R templates/webapps/galaxy/workflow/rename.mako
R templates/webapps/galaxy/workflow/run.mako
M templates/webapps/reports/base_panels.mako
M templates/webapps/tool_shed/admin/center.mako
M templates/webapps/tool_shed/base_panels.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/tool_form.mako
A templates/webapps/tool_shed/user/api_keys.mako
A templates/webapps/tool_shed/user/change_password.mako
A templates/webapps/tool_shed/user/index.mako
A templates/webapps/tool_shed/user/username.mako
A test-data/1.fastqsanger.bz2
A test-data/1.fastqsanger.gz
A test-data/5_Ig-like.gff
A test-data/bam_from_sam.bam
A test-data/filter_labels_1.txt
A test-data/new_labels_1.txt
A test-data/new_labels_2.txt
A test-data/new_labels_bad_1.txt
A test-data/new_labels_bad_2.txt
A test-data/sam_with_header.sam
A test-data/simple.xml
A test-data/test.vcf.gz
M test/TESTING.md
R test/api/helpers.py
M test/api/test_api_batch.py
A test/api/test_configuration.py
M test/api/test_dataset_collections.py
M test/api/test_datasets.py
M test/api/test_datatypes.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_history_contents_provenance.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_search.py
M test/api/test_tools.py
M test/api/test_users.py
A test/api/test_visualizations.py
A test/api/test_webhooks.py
R test/api/test_workflow_1.ga
R test/api/test_workflow_2.ga
R test/api/test_workflow_batch.ga
M test/api/test_workflow_extraction.py
R test/api/test_workflow_map_reduce_pause.ga
R test/api/test_workflow_matching_lists.ga
R test/api/test_workflow_missing_tool.ga
R test/api/test_workflow_pause.ga
R test/api/test_workflow_topoambigouity.ga
R test/api/test_workflow_topoambigouity_auto_laidout.ga
R test/api/test_workflow_validation_1.ga
R test/api/test_workflow_with_runtime_input.ga
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M test/api/test_workflows_from_yaml.py
R test/api/workflows_format_2/README.txt
R test/api/workflows_format_2/__init__.py
R test/api/workflows_format_2/converter.py
R test/api/workflows_format_2/interface.py
R test/api/workflows_format_2/main.py
M test/base/api.py
M test/base/api_asserts.py
A test/base/data/test_workflow_1.ga
A test/base/data/test_workflow_2.ga
A test/base/data/test_workflow_batch.ga
A test/base/data/test_workflow_map_reduce_pause.ga
A test/base/data/test_workflow_matching_lists.ga
A test/base/data/test_workflow_missing_tool.ga
A test/base/data/test_workflow_pause.ga
A test/base/data/test_workflow_topoambigouity.ga
A test/base/data/test_workflow_topoambigouity_auto_laidout.ga
A test/base/data/test_workflow_validation_1.ga
A test/base/data/test_workflow_with_runtime_input.ga
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
A test/base/populators.py
M test/base/twilltestcase.py
A test/base/workflows_format_2/README.txt
A test/base/workflows_format_2/__init__.py
A test/base/workflows_format_2/converter.py
A test/base/workflows_format_2/interface.py
A test/base/workflows_format_2/main.py
R test/casperjs/anon-history-tests.js
R test/casperjs/api-batch-tests.js
R test/casperjs/api-configuration-tests.js
R test/casperjs/api-dataset-tests.js
R test/casperjs/api-history-tests.js
R test/casperjs/api-tool-tests.js
R test/casperjs/api-user-tests.js
R test/casperjs/api-visualizations-tests.js
R test/casperjs/hda-state-tests.js
R test/casperjs/history-options-tests.js
R test/casperjs/history-panel-tests.js
R test/casperjs/history-share-tests.js
R test/casperjs/login-tests.js
R test/casperjs/registration-tests.js
R test/casperjs/upload-tests.js
M test/docker/README.md
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/run_test_wrapper.sh
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
M test/functional/tools/checksum.xml
A test/functional/tools/collection_creates_dynamic_nested_fail.xml
A test/functional/tools/collection_creates_list_fail.xml
M test/functional/tools/column_param.xml
A test/functional/tools/compressed_bz2_fastq_conversion.xml
A test/functional/tools/compressed_bz2_fastq_no_conversion.xml
A test/functional/tools/compressed_gz_fastq_conversion.xml
A test/functional/tools/compressed_gz_fastq_no_conversion.xml
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
A test/functional/tools/explicit_conversion.xml
A test/functional/tools/for_tours/filtering.py
A test/functional/tools/for_tours/filtering.xml
A test/functional/tools/for_workflows/mapper2.xml
A test/functional/tools/identifier_multiple_in_conditional.xml
A test/functional/tools/identifier_multiple_in_repeat.xml
A test/functional/tools/identifier_source.xml
A test/functional/tools/implicit_conversion.xml
A test/functional/tools/is_valid_xml.xml
A test/functional/tools/legacy_r.xml
M test/functional/tools/md5sum.xml
A test/functional/tools/mulled_example_conflict.xml
A test/functional/tools/mulled_example_multi_incomplete.xml
A test/functional/tools/mulled_example_multi_versionless.xml
A test/functional/tools/output_format_deprecated_when.xml
A test/functional/tools/paired_collection_map_over_structured_like.xml
A test/functional/tools/param_text_option.xml
A test/functional/tools/python_environment_problem.py
A test/functional/tools/python_environment_problem.xml
A test/functional/tools/sam_to_bam.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/vcf_bgzip.xml
A test/functional/webhooks/history_test1/config/history_test1.yml
A test/functional/webhooks/history_test2/config/history_test2.yml
A test/functional/webhooks/masthead_test/config/masthead_test.yml
A test/functional/webhooks/phdcomics/config/phdcomics.yaml
A test/functional/webhooks/phdcomics/helper/__init__.py
A test/functional/webhooks/phdcomics/static/script.js
A test/functional/webhooks/phdcomics/static/styles.css
A test/functional/webhooks/trans_object/config/trans_object.yaml
A test/functional/webhooks/trans_object/helper/__init__.py
A test/functional/webhooks/xkcd/config/xkcd.yml
A test/functional/webhooks/xkcd/static/script.js
A test/functional/webhooks/xkcd/static/styles.css
R test/functional/workflow.py
A test/galaxy_selenium/__init__.py
A test/galaxy_selenium/cli.py
A test/galaxy_selenium/data.py
A test/galaxy_selenium/driver_factory.py
A test/galaxy_selenium/has_driver.py
A test/galaxy_selenium/navigates_galaxy.py
A test/galaxy_selenium/navigation-data.yml
A test/galaxy_selenium/sizzle.py
A test/integration/resubmission_default_job_conf.xml
A test/integration/resubmission_job_conf.xml
A test/integration/resubmission_job_resource_parameters_conf.xml
A test/integration/resubmission_rules/__init__.py
A test/integration/resubmission_rules/rules.py
A test/integration/resubmission_runners.py
A test/integration/test_config_options_users.py
A test/integration/test_job_resubmission.py
A test/integration/test_maximum_worklfow_invocation_duration.py
M test/integration/test_resolvers.py
A test/integration/test_workflow_handler_configuration.py
A test/integration/workflow_handler_configuration_job_conf.xml
A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml
M test/manual/workflows_scaling.py
M test/qunit/package.json
M test/qunit/test-data/bootstrapped.js
M test/qunit/test-data/paired-collection-creator.data.js
M test/qunit/tests/form_tests.js
M test/qunit/tests/galaxy-app-base.js
M test/qunit/tests/page_tests.js
M test/qunit/tests/ui_tests.html
M test/qunit/tests/ui_tests.js
M test/qunit/tests/workflow_editor_tests.js
A test/selenium_tests/__init__.py
A test/selenium_tests/_workflow_fixtures.py
A test/selenium_tests/framework.py
A test/selenium_tests/test_anon_history.py
A test/selenium_tests/test_collection_builders.py
A test/selenium_tests/test_history_dataset_state.py
A test/selenium_tests/test_history_options.py
A test/selenium_tests/test_history_panel.py
A test/selenium_tests/test_history_sharing.py
A test/selenium_tests/test_login.py
A test/selenium_tests/test_registration.py
A test/selenium_tests/test_stock_tours.py
A test/selenium_tests/test_tool_form.py
A test/selenium_tests/test_uploads.py
A test/selenium_tests/test_workflow_editor.py
A test/selenium_tests/test_workflow_management.py
A test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/twilltestcase.py
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M test/shed_functional/functional/test_1090_repository_dependency_handling.py
M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
M test/shed_functional/functional/test_1150_datatype_converters.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
A test/unit/jobs/conditional_runners_job_conf.xml
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rule_helper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
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M test/unit/shed_unit/test_fabric_util.py
A test/unit/shed_unit/test_installed_repository_manager.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_transactions.py
A test/unit/test_remote_shell.py
M test/unit/test_routes.py
M test/unit/test_sockets.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_select_parameters.py
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M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_external_files.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
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M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
A tool-data/blastdb.loc.sample
A tool-data/blastdb_d.loc.sample
A tool-data/blastdb_p.loc.sample
M tool-data/shared/ucsc/builds.txt.sample
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/evolution/add_scores.xml
M tools/extract/extract_genomic_dna.py
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_fasta.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
R tools/filters/gff/sort_gtf.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
M tools/filters/pasteWrapper.xml
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/trimmer.xml
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wc_gnu.xml
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/genebed_maf_to_fasta.xml
M tools/maf/interval2maf.py
M tools/maf/interval2maf.xml
M tools/maf/interval2maf_pairwise.xml
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/interval_maf_to_merged_fasta.xml
M tools/maf/macros.xml
M tools/maf/maf_by_block_number.py
M tools/maf/maf_by_block_number.xml
M tools/maf/maf_filter.py
M tools/maf/maf_filter.xml
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_size.xml
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_limit_to_species.xml
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_reverse_complement.xml
M tools/maf/maf_split_by_species.py
M tools/maf/maf_split_by_species.xml
M tools/maf/maf_stats.py
M tools/maf/maf_stats.xml
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_thread_for_species.xml
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed.xml
M tools/maf/maf_to_fasta.xml
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/maf_to_interval.xml
M tools/maf/vcf_to_maf_customtrack.py
M tools/maf/vcf_to_maf_customtrack.xml
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.xml
M tools/metag_tools/shrimp_wrapper.xml
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/fastq_gen_conv.xml
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/plotting/bar_chart.xml
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_binned_scores_in_intervals.xml
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/dev' into install_workflow_and_tools
Conflicts:
lib/galaxy/webapps/galaxy/api/workflows.py
Commit: 7dd3ddccafee8f5cc185f1b0dd711056576a92ce
https://github.com/galaxyproject/galaxy/commit/7dd3ddccafee8f5cc185f1b0dd71…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
M test/api/test_workflows.py
Log Message:
-----------
Require admin for new import_tools function in workflows API.
Includes test case.
Commit: 6353704e4b44e9eded6571b467f52a6dd288387d
https://github.com/galaxyproject/galaxy/commit/6353704e4b44e9eded6571b467f5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
M openid/yahoo.xml
Log Message:
-----------
Merge pull request #4039 from VJalili/patch-11
Updated parameters check for OpenID
Commit: e49ba40d771dae0d7056ed089c99f3d53a81b933
https://github.com/galaxyproject/galaxy/commit/e49ba40d771dae0d7056ed089c99…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/parameters/grouping.py
Log Message:
-----------
Generalize allow_library_path_paste to allow_path_paste.
Enable pasting paths in the history upload GUI & general purpose tools API for admin users if enabled.
Commit: f97efa6f90f80ced8bd0c794841e450813238710
https://github.com/galaxyproject/galaxy/commit/f97efa6f90f80ced8bd0c794841e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/parameters/grouping.py
Log Message:
-----------
Remove unused dataset_info in parameters.grouping.
Commit: 33acc1f8a337977eb85e9ba570f3404476411edc
https://github.com/galaxyproject/galaxy/commit/33acc1f8a337977eb85e9ba570f3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
A client/galaxy/scripts/mvc/job/job-params.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
M config/datatypes_conf.xml.sample
A config/error_report.yml.sample
M config/tool_conf.xml.sample
A config/user_preferences_extra_conf.yml.sample
A doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/special_topics/index.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0135_add_library_tags.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/upload_common.py
A lib/galaxy/tools/error_reports/__init__.py
A lib/galaxy/tools/error_reports/plugins/__init__.py
A lib/galaxy/tools/error_reports/plugins/biostars.py
A lib/galaxy/tools/error_reports/plugins/email.py
A lib/galaxy/tools/error_reports/plugins/json.py
A lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_objects.py
A lib/galaxy/tools/sort_collection_list.xml
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/users.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/library_common.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M scripts/grt/export.py
M scripts/grt/upload.py
A static/maps/mvc/dataset/dataset-error.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
A static/scripts/mvc/dataset/dataset-error.js
M static/scripts/mvc/dataset/dataset-li-edit.js
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/style/blue/base.css
M templates/show_params.mako
R templates/webapps/galaxy/dataset/errors.mako
M templates/webapps/tool_shed/repository/common.mako
A test-data/test.vcf.gz
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/vcf_bgzip.xml
M test/unit/tools/test_parsing.py
Log Message:
-----------
Merge branch 'admin_grid_groups' into admin_grid_toolversion
Commit: ef2c32ae84706897e70fa41808f46d95f1132ec9
https://github.com/galaxyproject/galaxy/commit/ef2c32ae84706897e70fa41808f4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix lint
Commit: 600b0aad7ce10c1e427513684c4cd7423f5b52aa
https://github.com/galaxyproject/galaxy/commit/600b0aad7ce10c1e427513684c4c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/form/form-view.js
A client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/utils/query-string-parsing.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/util/admin_util.py
M static/maps/mvc/form/form-view.js.map
A static/maps/mvc/form/form-wrapper.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/utils/query-string-parsing.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/form/form-view.js
A static/scripts/mvc/form/form-wrapper.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/utils/query-string-parsing.js
R templates/admin/dataset_security/group/grid.mako
R templates/admin/dataset_security/role/grid.mako
R templates/admin/quota/grid.mako
R templates/admin/tool_shed_repository/grid.mako
R templates/admin/tool_version/grid.mako
R templates/admin/user/grid.mako
R templates/admin/user/reset_password.mako
R templates/admin/user/user.mako
A templates/webapps/tool_shed/admin/user/reset_password.mako
A templates/webapps/tool_shed/admin/user/user.mako
R templates/webapps/tool_shed/repository/grid.mako
Log Message:
-----------
Merge pull request #4377 from guerler/revise_grid_forms
Remove makos of admin user grid forms
Commit: 33c794d273271b14732fb8037c2ea8105a3c688e
https://github.com/galaxyproject/galaxy/commit/33c794d273271b14732fb8037c2e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/utils/query-string-parsing.js
M client/galaxy/style/less/ui.less
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/tool_shed/util/admin_util.py
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-wrapper.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/mvc/ui/ui-list.js.map
M static/maps/mvc/user/user-custom-builds.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/utils/query-string-parsing.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-wrapper.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-list.js
M static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/utils/query-string-parsing.js
M static/style/blue/base.css
R templates/admin/dataset_security/role/role.mako
R templates/admin/dataset_security/role/role_create.mako
R templates/admin/dataset_security/role/role_rename.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako
Log Message:
-----------
Merge pull request #4385 from guerler/admin_grid_roles
Admin grid roles revision
Commit: 10285b8ecbbc6891a4954b5067198df2839a2957
https://github.com/galaxyproject/galaxy/commit/10285b8ecbbc6891a4954b506719…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Tweak Excel format phrasing based on review from @nsoranzo.
Commit: fbde34f8c8e823badd0f565bce4922512448b532
https://github.com/galaxyproject/galaxy/commit/fbde34f8c8e823badd0f565bce49…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Add EDAM format for excel.xls datatype.
Commit: cca00ea5d87fb0baba3ceca715038158cf2ceba0
https://github.com/galaxyproject/galaxy/commit/cca00ea5d87fb0baba3ceca71503…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/parameters/grouping.py
Log Message:
-----------
Merge pull request #4404 from jmchilton/allow_path_paste
Generalize allow_library_path_paste to allow_path_paste.
Commit: c6e45e7b0720376886626393ae355e3398561035
https://github.com/galaxyproject/galaxy/commit/c6e45e7b0720376886626393ae35…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/1.xls
Log Message:
-----------
Merge pull request #4410 from jmchilton/excel97
Add Excel97 Datatype
Commit: 331851b0495d429220450ceb3a540fbba900143a
https://github.com/galaxyproject/galaxy/commit/331851b0495d429220450ceb3a54…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
M Makefile
R config/reports.ini.sample
A config/reports.yml.sample
R config/tool_shed.ini.sample
A config/tool_shed.yml.sample
A doc/source/admin/reports.rst
A doc/source/admin/reports_options.rst
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/util/properties.py
M lib/galaxy/web/framework/webapp.py
A lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/buildapp.py
A lib/galaxy/webapps/reports/config_schema.yml
A lib/galaxy/webapps/reports/uwsgi_schema.yml
M lib/galaxy/webapps/tool_shed/buildapp.py
A lib/galaxy/webapps/tool_shed/config_schema.yml
A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml
A lib/galaxy/webapps/uwsgi_schema.yml
M run.sh
M run_reports.sh
M run_tool_shed.sh
A scripts/common_startup_functions.sh
A scripts/config_sample_to_kwalify.py
M scripts/manage_tools.py
A test/unit/config/1607_root_filters/config/galaxy.ini
A test/unit/config/1607_root_filters/config/tool_shed.ini
A test/unit/config/1607_root_samples/config/galaxy.ini
A test/unit/config/1607_root_samples/config/reports.ini
A test/unit/config/1607_root_samples/config/tool_shed.ini
A test/unit/config/test_config_manage.py
Log Message:
-----------
Merge pull request #3179 from jmchilton/web_config_overhaul_0
Configuration & Server Overhaul - Tool Shed and Reports
Commit: 7a1fbd37e9fb262432daed6eefc4e9c54ceff406
https://github.com/galaxyproject/galaxy/commit/7a1fbd37e9fb262432daed6eefc4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
M lib/galaxy/util/checkers.py
Log Message:
-----------
Fix bug in upload HTML checker.
If a chunk was passed into the check_html function - e.g. it was read from a compressed file - it would search through each character in the string for certain HTML content instead of each line in the string.
Commit: 59aa11864a795861484133dfc85212bf9150cf4a
https://github.com/galaxyproject/galaxy/commit/59aa11864a795861484133dfc852…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/util/checkers.py
M tools/data_source/upload.py
Log Message:
-----------
Add configuration option to disable upload content checking.
Commit: 53b0b25456c170990ad3345021aab16f68e6e185
https://github.com/galaxyproject/galaxy/commit/53b0b25456c170990ad3345021aa…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
M test/base/populators.py
Log Message:
-----------
Better error reporting in test/base/populators.py.
Commit: bee6af1e4117e7ff6f7caac0d9c84253ec1c4882
https://github.com/galaxyproject/galaxy/commit/bee6af1e4117e7ff6f7caac0d9c8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
M test/base/api.py
Log Message:
-----------
Allow API tests to work with admin users (not just admin keys).
Commit: fec1eab82dc6dea2d03711127ed08b3038ad5bf1
https://github.com/galaxyproject/galaxy/commit/fec1eab82dc6dea2d03711127ed0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/parameters/grouping.py
M test/base/populators.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
Log Message:
-----------
Add ability to arbitrarily not decompress files on upload via API.
Commit: fc861cdf38d1d20fd611e8bcb042328eb905b3c4
https://github.com/galaxyproject/galaxy/commit/fc861cdf38d1d20fd611e8bcb042…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #3064 from manabuishii/install_workflow_and_tools
Install tools and workflow
Commit: 06ca789f92ad2f4dfaffc36d3fa0bafb3c74920d
https://github.com/galaxyproject/galaxy/commit/06ca789f92ad2f4dfaffc36d3fa0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
A test-data/1.sam.gz
A test-data/bad.html.gz
A test-data/random-file
M test/functional/tools/sample_datatypes_conf.xml
A test/integration/test_upload_configuration_options.py
Log Message:
-----------
Configuration tests for the last few upload enhancements.
Commit: 5f1b7d5a5060c3c45601b499a953113e0b1b3125
https://github.com/galaxyproject/galaxy/commit/5f1b7d5a5060c3c45601b499a953…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M 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
Log Message:
-----------
Show verison button in workflow editor and trigger on_change
Commit: 25e05b62c7b529b0379e3ff50fc75ccb5b8c28b6
https://github.com/galaxyproject/galaxy/commit/25e05b62c7b529b0379e3ff50fc7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Do postchange action only when modifiying tool versions in the workflow editor
Commit: 5afe490822325d4aa6c9be726183175743dc88f6
https://github.com/galaxyproject/galaxy/commit/5afe490822325d4aa6c9be726183…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Fix qunit test
Commit: 36ce9113f7ccb6372bc2d1f8e92e95a8aafdd066
https://github.com/galaxyproject/galaxy/commit/36ce9113f7ccb6372bc2d1f8e92e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
Log Message:
-----------
Keep spacing consistent (thx @nsoranzo)
Commit: 526e98e372e61747b1e3cd4b86a04603ca08959b
https://github.com/galaxyproject/galaxy/commit/526e98e372e61747b1e3cd4b86a0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Reset outputs when changing tool versions in wf-editor
Commit: db2ea853f699bf6b55b67cf7199ab355196910bc
https://github.com/galaxyproject/galaxy/commit/db2ea853f699bf6b55b67cf7199a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Now thing are mostly working -- input and output connections are correctly altered ... but saving the workflow and reloading occasionally loads the wrong workflow
Commit: ea1f4f866658e77465d1272b4d7f37bb85ee488b
https://github.com/galaxyproject/galaxy/commit/ea1f4f866658e77465d1272b4d7f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
Log Message:
-----------
Fix the occasional loading of the wrong workflow. Turns out that sometimes the tool_version is undefined (i.e) if the exact node had not been manipulated, but config_form.version is always up to date
Commit: bc95f5e81b46a0bee54f6ffdd5c3a6615258af20
https://github.com/galaxyproject/galaxy/commit/bc95f5e81b46a0bee54f6ffdd5c3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Now adding/removing datasets and multiple version switches work fine, but PJA parameters are still problematic
Commit: 92fedc0ae86127d670f3ff8e829d07ee657f30d7
https://github.com/galaxyproject/galaxy/commit/92fedc0ae86127d670f3ff8e829d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M 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
Log Message:
-----------
Fix logic for adding and removing outputs
Commit: 1c286b158a8304380f499709b2f14c958b6fe203
https://github.com/galaxyproject/galaxy/commit/1c286b158a8304380f499709b2f1…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Remove extra newlines
Commit: 2e95026317e2e781163cf8bd4449bfd5ddfb894f
https://github.com/galaxyproject/galaxy/commit/2e95026317e2e781163cf8bd4449…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Remove unused old_version variable
Commit: 31c423a45a4186c41981f71d41a590177bad033d
https://github.com/galaxyproject/galaxy/commit/31c423a45a4186c41981f71d41a5…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Fix typo and remove leftover comment (thanks @nsoranzo)
Commit: df91881c1f4dba06a9fb6a1720db68d059664041
https://github.com/galaxyproject/galaxy/commit/df91881c1f4dba06a9fb6a1720db…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Remove unused workflow outputs
Commit: 73f4141d96ad54c25fdf7a3ffb458f2b1933e14e
https://github.com/galaxyproject/galaxy/commit/73f4141d96ad54c25fdf7a3ffb45…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M static/maps/mvc/tool/tool-form-base.js.map
M 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
M static/scripts/bundled/admin.bundled.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/tool/tool-form-base.js
M 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
Log Message:
-----------
Add static JS
Commit: f849c7e6feafabf905653bd008fde23dc1413a85
https://github.com/galaxyproject/galaxy/commit/f849c7e6feafabf905653bd008fd…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/util/checkers.py
A test-data/1.sam.gz
A test-data/bad.html.gz
A test-data/random-file
M test/base/api.py
M test/base/populators.py
M test/functional/tools/sample_datatypes_conf.xml
A test/integration/test_upload_configuration_options.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge pull request #4417 from jmchilton/upload_enhance
Fixes and enhancements for the upload API
Commit: 8e192dbf4ca2f7c6c0860430a4d8085de7732ab1
https://github.com/galaxyproject/galaxy/commit/8e192dbf4ca2f7c6c0860430a4d8…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M test/api/test_tools.py
M test/base/interactor.py
M test/base/populators.py
Log Message:
-----------
Merge pull request #4397 from jmchilton/api_test_enhancement
Better Error Summaries for API Tests
Commit: e594152de2dd33dbdff2feb8e05f05ad5810ab27
https://github.com/galaxyproject/galaxy/commit/e594152de2dd33dbdff2feb8e05f…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Merge pull request #4394 from jmchilton/subworkflow_loading_fix
Bugfix for loading subworkflows from workflow descriptions.
Commit: 9cbabef17e9afb4953324516d0883976edd51e87
https://github.com/galaxyproject/galaxy/commit/9cbabef17e9afb4953324516d088…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/molecules.py
M static/maps/mvc/library/library-foldertoolbar-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-foldertoolbar-view.js
Log Message:
-----------
Merge branch 'release_17.05' into dev
Conflicts:
static/maps/mvc/library/library-foldertoolbar-view.js.map
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
static/scripts/mvc/library/library-foldertoolbar-view.js
Commit: 4dd503046f59b13e925a76f88862882747dc6ad7
https://github.com/galaxyproject/galaxy/commit/4dd503046f59b13e925a76f88862…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Update conda channel order to sync with Bioconda
Commit: 420e7a4f3408ec064403a4283ba22a134b65ece5
https://github.com/galaxyproject/galaxy/commit/420e7a4f3408ec064403a4283ba2…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Remove _ensure_conda_context() function
and make conda_context argument mandatory in functions/methods.
This should help making sure the correct context (e.g. channels)
is used for all Conda operations.
Also remove unused is_target_available() function.
Commit: cdbac056cb664e4c51f84c41c2519993d0412d74
https://github.com/galaxyproject/galaxy/commit/cdbac056cb664e4c51f84c41c251…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Override channel list on the command line instead of modifying condarc
The way we were modifying condarc in the ensure_channels_configured()
method was broken because we were appending the missing channels at the
end, so the final order may not be the one specified in
conda_ensure_channels .
Also:
- not modifying the user condarc is a much better approach
- overriding the channel list on the command line will make debugging
easier
Commit: eccdc8c248fabef6bc5a988cdb1889c1aa32ca7a
https://github.com/galaxyproject/galaxy/commit/eccdc8c248fabef6bc5a988cdb18…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Removed unreached message line
Commit: fd5f42dc17009cfdfbfc08583549ba608efb166a
https://github.com/galaxyproject/galaxy/commit/fd5f42dc17009cfdfbfc08583549…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M Makefile
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
R config/reports.ini.sample
A config/reports.yml.sample
R config/tool_shed.ini.sample
A config/tool_shed.yml.sample
A doc/source/admin/reports.rst
A doc/source/admin/reports_options.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/1.xls
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/properties.py
M lib/galaxy/web/framework/webapp.py
A lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/reports/buildapp.py
A lib/galaxy/webapps/reports/config_schema.yml
A lib/galaxy/webapps/reports/uwsgi_schema.yml
M lib/galaxy/webapps/tool_shed/buildapp.py
A lib/galaxy/webapps/tool_shed/config_schema.yml
A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml
A lib/galaxy/webapps/uwsgi_schema.yml
M openid/yahoo.xml
M run.sh
M run_reports.sh
M run_tool_shed.sh
A scripts/common_startup_functions.sh
A scripts/config_sample_to_kwalify.py
M scripts/manage_tools.py
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/mvc/library/library-foldertoolbar-view.js
A test-data/1.sam.gz
A test-data/bad.html.gz
A test-data/random-file
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/api.py
M test/base/interactor.py
M test/base/populators.py
M test/functional/tools/sample_datatypes_conf.xml
A test/integration/test_upload_configuration_options.py
A test/unit/config/1607_root_filters/config/galaxy.ini
A test/unit/config/1607_root_filters/config/tool_shed.ini
A test/unit/config/1607_root_samples/config/galaxy.ini
A test/unit/config/1607_root_samples/config/reports.ini
A test/unit/config/1607_root_samples/config/tool_shed.ini
A test/unit/config/test_config_manage.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge branch 'dev' into admin_grid_groups
Commit: 68555f5571b5b872a39a34f8fa6035bfad67ea43
https://github.com/galaxyproject/galaxy/commit/68555f5571b5b872a39a34f8fa60…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
some unicoding
Commit: 8721da8ca2e1f78a018baf4c43d8229327eb477f
https://github.com/galaxyproject/galaxy/commit/8721da8ca2e1f78a018baf4c43d8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Merge pull request #4426 from erasche/local-runner-unicode
some unicoding for local runner
Commit: 44548f8f2fe258051ad2df45b153642586b85e00
https://github.com/galaxyproject/galaxy/commit/44548f8f2fe258051ad2df45b153…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #4409 from nsoranzo/fix_conda_channel_order
Update conda channel order to sync with Bioconda
Commit: 07a30499994b33e27c0b1765df9f32c9bfcea0b2
https://github.com/galaxyproject/galaxy/commit/07a30499994b33e27c0b1765df9f…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Merge branch 'release_17.05' into dev
Conflicts:
lib/galaxy/model/tool_shed_install/__init__.py
Commit: aa7be28960a43802bd476be1d7d996c85134c055
https://github.com/galaxyproject/galaxy/commit/aa7be28960a43802bd476be1d7d9…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/util/checkers.py
M static/maps/mvc/library/library-foldertoolbar-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-foldertoolbar-view.js
A test-data/1.sam.gz
A test-data/bad.html.gz
A test-data/random-file
M test/api/test_tools.py
M test/base/api.py
M test/base/interactor.py
M test/base/populators.py
M test/functional/tools/sample_datatypes_conf.xml
A test/integration/test_upload_configuration_options.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge branch 'dev' into switch_versions_in_workflows
Commit: 27be24963837354af6cac1f429c1bc06e95626e1
https://github.com/galaxyproject/galaxy/commit/27be24963837354af6cac1f429c1…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M 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
M static/maps/mvc/tool/tool-form-base.js.map
M 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
M static/scripts/bundled/admin.bundled.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/tool/tool-form-base.js
M 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
Log Message:
-----------
Merge pull request #4373 from mvdbeek/switch_versions_in_workflows
Allow switching tool versions in workflow editor
Commit: 462b7def5d9b9298d50cea2e62cfbf89bd463d25
https://github.com/galaxyproject/galaxy/commit/462b7def5d9b9298d50cea2e62cf…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Merge pull request #4427 from nsoranzo/merge_release_17.05
Merge release_17.05 into dev
Commit: e72948cb743e50b50a21bf7f778792ba36ec38bd
https://github.com/galaxyproject/galaxy/commit/e72948cb743e50b50a21bf7f7787…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M 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
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/tool/tool-form-base.js.map
M 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
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M 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
Log Message:
-----------
Merge branch 'dev' into admin_grid_groups
Commit: b726c33c80b33ece878343b6208e65f3d983008f
https://github.com/galaxyproject/galaxy/commit/b726c33c80b33ece878343b6208e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M Makefile
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M 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
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
R config/reports.ini.sample
A config/reports.yml.sample
R config/tool_shed.ini.sample
A config/tool_shed.yml.sample
M doc/source/admin/dependency_resolvers.rst
A doc/source/admin/reports.rst
A doc/source/admin/reports_options.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/1.xls
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/properties.py
M lib/galaxy/web/framework/webapp.py
A lib/galaxy/webapps/config_manage.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/user.py
M lib/galaxy/webapps/reports/buildapp.py
A lib/galaxy/webapps/reports/config_schema.yml
A lib/galaxy/webapps/reports/uwsgi_schema.yml
M lib/galaxy/webapps/tool_shed/buildapp.py
A lib/galaxy/webapps/tool_shed/config_schema.yml
A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml
A lib/galaxy/webapps/uwsgi_schema.yml
M lib/galaxy/workflow/modules.py
M openid/yahoo.xml
M run.sh
M run_reports.sh
M run_tool_shed.sh
A scripts/common_startup_functions.sh
A scripts/config_sample_to_kwalify.py
M scripts/manage_tools.py
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M 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
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/library/library-foldertoolbar-view.js
M static/scripts/mvc/tool/tool-form-base.js
M 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
A test-data/1.sam.gz
A test-data/bad.html.gz
A test-data/random-file
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/api.py
M test/base/interactor.py
M test/base/populators.py
M test/functional/tools/sample_datatypes_conf.xml
A test/integration/test_upload_configuration_options.py
A test/unit/config/1607_root_filters/config/galaxy.ini
A test/unit/config/1607_root_filters/config/tool_shed.ini
A test/unit/config/1607_root_samples/config/galaxy.ini
A test/unit/config/1607_root_samples/config/reports.ini
A test/unit/config/1607_root_samples/config/tool_shed.ini
A test/unit/config/test_config_manage.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge branch 'admin_grid_groups' into admin_grid_toolversion
Commit: a078ee025f02732e108cf2d790e18cc826829ac5
https://github.com/galaxyproject/galaxy/commit/a078ee025f02732e108cf2d790e1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Move form augmentation to form handler
Commit: 5cebb086b2849f92ac8da10d7e776e4334c28ff5
https://github.com/galaxyproject/galaxy/commit/5cebb086b2849f92ac8da10d7e77…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/sequence.py
A lib/galaxy/datatypes/test/1.psp
Log Message:
-----------
Add support for the MEME psp format
Commit: 4bddd617fe5df41efcebacdda7a6bb1d280ac2ce
https://github.com/galaxyproject/galaxy/commit/4bddd617fe5df41efcebacdda7a6…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/tool_shed/util/admin_util.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
R templates/admin/dataset_security/group/group.mako
R templates/admin/dataset_security/group/group_create.mako
R templates/admin/dataset_security/group/group_rename.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako
Log Message:
-----------
Merge pull request #4405 from guerler/admin_grid_groups
Admin grid groups revision
Commit: 9dfee375e9782f421832ecc44981a2cbdfc4f183
https://github.com/galaxyproject/galaxy/commit/9dfee375e9782f421832ecc44981…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/form/form-parameters.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Optionally allow to show or hide select all
Commit: a1897bd32a112e68ce09b71fd6ad98e6b97f267b
https://github.com/galaxyproject/galaxy/commit/a1897bd32a112e68ce09b71fd6ad…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Hide select all for role and group selectors
Commit: d6f6a78ab8464bf1a10cbca74632873993744933
https://github.com/galaxyproject/galaxy/commit/d6f6a78ab8464bf1a10cbca74632…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-wrapper.js
M static/maps/mvc/form/form-wrapper.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/form/form-wrapper.js
Log Message:
-----------
Use 'Save' as default title for configuration forms
Commit: 4688eef2a41e79b44e8cb19ad87d5f2fc9a3aaf1
https://github.com/galaxyproject/galaxy/commit/4688eef2a41e79b44e8cb19ad87d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M lib/galaxy/actions/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix user id decoding, fix optional array handling
Commit: 96cad03980b314a7a89a01a5e1d442b2855a22e8
https://github.com/galaxyproject/galaxy/commit/96cad03980b314a7a89a01a5e1d4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix label for default quotas
Commit: 09c4b1037b0034093488ed679628b9f614849a5e
https://github.com/galaxyproject/galaxy/commit/09c4b1037b0034093488ed679628…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M static/maps/mvc/workflow/workflow-node.js.map
M static/maps/mvc/workflow/workflow-terminals.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/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-terminals.js
Log Message:
-----------
Break connection in workflow editor if necessary
When switching tool versions in the workflow editor connections are
maintained by default. If a tool changes the datatype one may end up
with a connection between incompatible input/outputs. Therefore we
update the datatypes and explicitly destroy invalid connections.
Commit: 246489a7aa2b950d7a12bf2610faaaed26d90a55
https://github.com/galaxyproject/galaxy/commit/246489a7aa2b950d7a12bf2610fa…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M lib/galaxy/actions/admin.py
Log Message:
-----------
Fix messages
Commit: f9e889215021f7a99a4ccfe4612431caa963f63c
https://github.com/galaxyproject/galaxy/commit/f9e889215021f7a99a4ccfe46124…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Catch user input error for auto created roles and groups
Commit: bebc5ff56ae41a2660f884a2b04604b2a473dd11
https://github.com/galaxyproject/galaxy/commit/bebc5ff56ae41a2660f884a2b046…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Move decode id to correct location
Commit: f1e13cef05759bc7782248c08d595043d03161fe
https://github.com/galaxyproject/galaxy/commit/f1e13cef05759bc7782248c08d59…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M lib/galaxy/actions/admin.py
Log Message:
-----------
More messages to validate inputs
Commit: 86cdaaf610011b2b0c43f1bd93d36d87907b30e7
https://github.com/galaxyproject/galaxy/commit/86cdaaf610011b2b0c43f1bd93d3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Add validation messages if resource ids are not correct
Commit: 522ca9e5c2ebbf274af26b466c1bab5fb5bc5625
https://github.com/galaxyproject/galaxy/commit/522ca9e5c2ebbf274af26b466c1b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M lib/galaxy/security/__init__.py
Log Message:
-----------
Fix private role validation
Commit: 2073151bf2f6b2c2427c10934b1feea967d010ff
https://github.com/galaxyproject/galaxy/commit/2073151bf2f6b2c2427c10934b1f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Log Message:
-----------
Merge branch 'dev' into admin_grid_toolversion
Commit: abe8117b650bb9ab6575294d2892d33daeb32e4b
https://github.com/galaxyproject/galaxy/commit/abe8117b650bb9ab6575294d2892…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M static/maps/mvc/workflow/workflow-forms.js.map
M static/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Fix
Fix
Commit: 8eb487e7c1383cedd971de8128bb9ba143abaa41
https://github.com/galaxyproject/galaxy/commit/8eb487e7c1383cedd971de8128bb…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M static/maps/mvc/workflow/workflow-node.js.map
M static/maps/mvc/workflow/workflow-terminals.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/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-terminals.js
Log Message:
-----------
Merge pull request #4431 from mvdbeek/break_connections
Break connection in workflow editor if necessary
Commit: 806370123b028eb0728e05fff2f9f9853c5cd6c5
https://github.com/galaxyproject/galaxy/commit/806370123b028eb0728e05fff2f9…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
fix XML error
Commit: 338abee984c6915a3f32f60ff1c448245c030376
https://github.com/galaxyproject/galaxy/commit/338abee984c6915a3f32f60ff1c4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Separate input augmentation helpers from form views, augment inputs for regular form
Commit: b6f0600e98b74a301c2eb787263cd89e5ca487ca
https://github.com/galaxyproject/galaxy/commit/b6f0600e98b74a301c2eb787263c…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Merge pull request #4387 from jmchilton/tool_unit_test_cleanup
Cleanup of Unit Test Code for Loading Tools
Commit: 7af41d472f360c02d41e9113307385141e85ade6
https://github.com/galaxyproject/galaxy/commit/7af41d472f360c02d41e91133073…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Simplify form wrapper calling
Commit: c5a91491c64610ede9421af8b89ddf8389238be3
https://github.com/galaxyproject/galaxy/commit/c5a91491c64610ede9421af8b89d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M lib/galaxy/security/__init__.py
Log Message:
-----------
Merge pull request #4432 from guerler/fix_role_association_check
Fix private role validation
Commit: 7dae650fdbde77336250341832c928f604b41bab
https://github.com/galaxyproject/galaxy/commit/7dae650fdbde77336250341832c9…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/sequence.py
A lib/galaxy/datatypes/test/1.memepsp
R lib/galaxy/datatypes/test/1.psp
Log Message:
-----------
Change Psp to MemePsp and misc fixes per initial review
Commit: 7ef9b4cdafd0e2c6e68cba3729d9bd99645ef15f
https://github.com/galaxyproject/galaxy/commit/7ef9b4cdafd0e2c6e68cba3729d9…
Author: Max Schaefer <max(a)semmle.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/job/job-params.js
Log Message:
-----------
Remove spurious null check.
Commit: 43ddd4732034ca2ee658ccd4ab0ae17d4a1bbe40
https://github.com/galaxyproject/galaxy/commit/43ddd4732034ca2ee658ccd4ab0a…
Author: Max Schaefer <max(a)semmle.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
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-folderrow-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-libraryrow-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repo-status-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/util.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/ui/ui-drilldown.js
M client/galaxy/scripts/mvc/ui/ui-popover.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/upload/upload-view.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/ui/scroll-panel.js
M client/galaxy/scripts/utils/graph.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/toolshed/scripts/mvc/groups/group-list-view.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js
M config/plugins/visualizations/charts/static/client/components/screenshot.js
M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
M config/plugins/webhooks/demo/search/static/script.js
M lib/galaxy/web/proxy/js/lib/proxy.js
M scripts/communication/template/communication.js
Log Message:
-----------
Add missing `var` declarations.
In all these cases, a variable was not declared to be a local using `var` (and hence was implicitly interpreted as a global variable), but all uses of that variable were preceded by a definition within the same function, suggesting that the variable was, in fact, meant to be local, not global.
Commit: 48b835c35cd746c23c185ae69577ab6ae9fc4ee8
https://github.com/galaxyproject/galaxy/commit/48b835c35cd746c23c185ae69577…
Author: Max Schaefer <max(a)semmle.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/viz/circster.js
Log Message:
-----------
Remove an unused variable.
The result of the `_.map` call was never used, so I replaced it with `_.each`.
Commit: 8950d4423ff7d02bcf95b417676b2ef1c311333a
https://github.com/galaxyproject/galaxy/commit/8950d4423ff7d02bcf95b417676b…
Author: Max Schaefer <max(a)semmle.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
Log Message:
-----------
Move two variable definitions to combine them with their declarations.
Commit: 57c6284269c3256529f9c55953279eccb07dfabf
https://github.com/galaxyproject/galaxy/commit/57c6284269c3256529f9c5595327…
Author: Max Schaefer <max(a)semmle.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M static/maps/galaxy.pages.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
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-folderrow-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-libraryrow-view.js.map
M static/maps/mvc/library/library-model.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/toolshed/categories-view.js.map
M static/maps/mvc/toolshed/repo-status-view.js.map
M static/maps/mvc/toolshed/repositories-view.js.map
M static/maps/mvc/toolshed/repository-queue-view.js.map
M static/maps/mvc/toolshed/repository-view.js.map
M static/maps/mvc/toolshed/util.js.map
M static/maps/mvc/toolshed/workflows-view.js.map
M static/maps/mvc/ui/ui-drilldown.js.map
M static/maps/mvc/ui/ui-popover.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/upload/upload-view.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/reports_webapp/run_stats.js.map
M static/maps/ui/scroll-panel.js.map
M static/maps/utils/graph.js.map
M static/maps/utils/uploadbox.js.map
M static/maps/viz/circster.js.map
M static/maps/viz/phyloviz.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/galaxy.pages.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
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-folderrow-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-libraryrow-view.js
M static/scripts/mvc/library/library-model.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repo-status-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/util.js
M static/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/ui/ui-drilldown.js
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/reports_webapp/run_stats.js
M static/scripts/ui/scroll-panel.js
M static/scripts/utils/graph.js
M static/scripts/utils/uploadbox.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
Log Message:
-----------
Run `make client`.
Commit: 3026bf56c9662f47062fbd37904803156a4fe0db
https://github.com/galaxyproject/galaxy/commit/3026bf56c9662f47062fbd379048…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
Remove strange import - no idea from where it originated
Commit: 1b7f25eeaec96ae8b6a5336090dca675076b07bd
https://github.com/galaxyproject/galaxy/commit/1b7f25eeaec96ae8b6a5336090dc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/job/job-params.js
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-folderrow-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-libraryrow-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repo-status-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/util.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/ui/ui-drilldown.js
M client/galaxy/scripts/mvc/ui/ui-popover.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/upload/upload-view.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/ui/scroll-panel.js
M client/galaxy/scripts/utils/graph.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/toolshed/scripts/mvc/groups/group-list-view.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js
M config/plugins/visualizations/charts/static/client/components/screenshot.js
M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
M config/plugins/webhooks/demo/search/static/script.js
M lib/galaxy/web/proxy/js/lib/proxy.js
M scripts/communication/template/communication.js
M static/maps/galaxy.pages.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
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-folderrow-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-libraryrow-view.js.map
M static/maps/mvc/library/library-model.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/toolshed/categories-view.js.map
M static/maps/mvc/toolshed/repo-status-view.js.map
M static/maps/mvc/toolshed/repositories-view.js.map
M static/maps/mvc/toolshed/repository-queue-view.js.map
M static/maps/mvc/toolshed/repository-view.js.map
M static/maps/mvc/toolshed/util.js.map
M static/maps/mvc/toolshed/workflows-view.js.map
M static/maps/mvc/ui/ui-drilldown.js.map
M static/maps/mvc/ui/ui-popover.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/upload/upload-view.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/reports_webapp/run_stats.js.map
M static/maps/ui/scroll-panel.js.map
M static/maps/utils/graph.js.map
M static/maps/utils/uploadbox.js.map
M static/maps/viz/circster.js.map
M static/maps/viz/phyloviz.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/galaxy.pages.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
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-folderrow-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-libraryrow-view.js
M static/scripts/mvc/library/library-model.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repo-status-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/util.js
M static/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/ui/ui-drilldown.js
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/reports_webapp/run_stats.js
M static/scripts/ui/scroll-panel.js
M static/scripts/utils/graph.js
M static/scripts/utils/uploadbox.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
Log Message:
-----------
Merge pull request #4421 from xiemaisi/fix-lgtm-alerts
Fix lgtm alerts
Commit: c72f43dc5fb48e358d65caf6c59876ba0f15324e
https://github.com/galaxyproject/galaxy/commit/c72f43dc5fb48e358d65caf6c598…
Author: Matt Chambers <matt.chambers42(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Avoid adding `(imported from API)` to workflows
This should fail a few tests which I will fix with additional commits. Doing this from GitHub...
Commit: 9ef13a1c724a2bb326bba3556019448ef69ae8fd
https://github.com/galaxyproject/galaxy/commit/9ef13a1c724a2bb326bba3556019…
Author: Matt Chambers <matt.chambers42(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M test/api/test_search.py
Log Message:
-----------
Remove `(imported from API)` suffix from test
Commit: 03a3d34f1e2326c99798299d53fc6b7026aadb09
https://github.com/galaxyproject/galaxy/commit/03a3d34f1e2326c99798299d53fc…
Author: Matt Chambers <matt.chambers42(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Remove `(imported from API)` suffix from test
Commit: 73d6bd09d30859ca3dfd14debc8f20ed750598a9
https://github.com/galaxyproject/galaxy/commit/73d6bd09d30859ca3dfd14debc8f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Restore build model bypass
Pack
Commit: 1fc4bb1a62d493412f9b28a30c806d10c56474cf
https://github.com/galaxyproject/galaxy/commit/1fc4bb1a62d493412f9b28a30c80…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/job/job-params.js
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-folderrow-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-libraryrow-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repo-status-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/util.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/ui/ui-drilldown.js
M client/galaxy/scripts/mvc/ui/ui-popover.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/upload/upload-view.js
M 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-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/ui/scroll-panel.js
M client/galaxy/scripts/utils/graph.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/toolshed/scripts/mvc/groups/group-list-view.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js
M config/plugins/visualizations/charts/static/client/components/screenshot.js
M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
M config/plugins/webhooks/demo/search/static/script.js
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/web/proxy/js/lib/proxy.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/tool_shed/util/admin_util.py
M scripts/communication/template/communication.js
M static/maps/galaxy.pages.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
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-folderrow-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-libraryrow-view.js.map
M static/maps/mvc/library/library-model.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/toolshed/categories-view.js.map
M static/maps/mvc/toolshed/repo-status-view.js.map
M static/maps/mvc/toolshed/repositories-view.js.map
M static/maps/mvc/toolshed/repository-queue-view.js.map
M static/maps/mvc/toolshed/repository-view.js.map
M static/maps/mvc/toolshed/util.js.map
M static/maps/mvc/toolshed/workflows-view.js.map
M static/maps/mvc/ui/ui-drilldown.js.map
M static/maps/mvc/ui/ui-popover.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/upload/upload-view.js.map
M 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-terminals.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/reports_webapp/run_stats.js.map
M static/maps/ui/scroll-panel.js.map
M static/maps/utils/graph.js.map
M static/maps/utils/uploadbox.js.map
M static/maps/viz/circster.js.map
M static/maps/viz/phyloviz.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/galaxy.pages.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
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-folderrow-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-libraryrow-view.js
M static/scripts/mvc/library/library-model.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repo-status-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/util.js
M static/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/ui/ui-drilldown.js
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-view.js
M 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-terminals.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/reports_webapp/run_stats.js
M static/scripts/ui/scroll-panel.js
M static/scripts/utils/graph.js
M static/scripts/utils/uploadbox.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
R templates/admin/dataset_security/group/group.mako
R templates/admin/dataset_security/group/group_create.mako
R templates/admin/dataset_security/group/group_rename.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Merge branch 'dev' into improve_form_modules
Commit: a0217cb2372bfd83bee833299b3ea956a4d9b5b1
https://github.com/galaxyproject/galaxy/commit/a0217cb2372bfd83bee833299b3e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Attempt to customize build model
Commit: fdcd46918d52c4ee8ab7c2c421fd3e559c9a1fdc
https://github.com/galaxyproject/galaxy/commit/fdcd46918d52c4ee8ab7c2c421fd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove unfilterable columns from group and quota search grids
Commit: 2c4cf686f8fffd17bb7a248571fa7d502f52a046
https://github.com/galaxyproject/galaxy/commit/2c4cf686f8fffd17bb7a248571fa…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/job/job-params.js
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-folderrow-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-libraryrow-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repo-status-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/util.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/ui/ui-drilldown.js
M client/galaxy/scripts/mvc/ui/ui-popover.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/upload/upload-view.js
M 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-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/ui/scroll-panel.js
M client/galaxy/scripts/utils/graph.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/toolshed/scripts/mvc/groups/group-list-view.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js
M config/plugins/visualizations/charts/static/client/components/screenshot.js
M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
M config/plugins/webhooks/demo/search/static/script.js
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/web/proxy/js/lib/proxy.js
M scripts/communication/template/communication.js
M static/maps/galaxy.pages.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
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-folderrow-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-libraryrow-view.js.map
M static/maps/mvc/library/library-model.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/toolshed/categories-view.js.map
M static/maps/mvc/toolshed/repo-status-view.js.map
M static/maps/mvc/toolshed/repositories-view.js.map
M static/maps/mvc/toolshed/repository-queue-view.js.map
M static/maps/mvc/toolshed/repository-view.js.map
M static/maps/mvc/toolshed/util.js.map
M static/maps/mvc/toolshed/workflows-view.js.map
M static/maps/mvc/ui/ui-drilldown.js.map
M static/maps/mvc/ui/ui-popover.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/upload/upload-view.js.map
M 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-terminals.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/reports_webapp/run_stats.js.map
M static/maps/ui/scroll-panel.js.map
M static/maps/utils/graph.js.map
M static/maps/utils/uploadbox.js.map
M static/maps/viz/circster.js.map
M static/maps/viz/phyloviz.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/galaxy.pages.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
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-folderrow-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-libraryrow-view.js
M static/scripts/mvc/library/library-model.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repo-status-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/util.js
M static/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/ui/ui-drilldown.js
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-view.js
M 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-terminals.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/reports_webapp/run_stats.js
M static/scripts/ui/scroll-panel.js
M static/scripts/utils/graph.js
M static/scripts/utils/uploadbox.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Merge branch 'dev' into admin_grid_toolversion
and repack
Commit: 04583346a1970f9bab4f0cd3b9e8693de4fedbf9
https://github.com/galaxyproject/galaxy/commit/04583346a1970f9bab4f0cd3b9e8…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M lib/galaxy/actions/admin.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-wrapper.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/form/form-parameters.js
M static/scripts/mvc/form/form-wrapper.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
R templates/admin/quota/quota.mako
R templates/admin/quota/quota_create.mako
R templates/admin/quota/quota_edit.mako
R templates/admin/quota/quota_rename.mako
R templates/admin/quota/quota_set_default.mako
Log Message:
-----------
Merge pull request #4411 from guerler/admin_grid_toolversion
replace mako templates for tool lineage and quotas grids
Commit: 25bd7178c157f24523333caaf7f5a0a54f264abe
https://github.com/galaxyproject/galaxy/commit/25bd7178c157f24523333caaf7f5…
Author: Matt Chambers <matt.chambers42(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M scripts/api/upload_to_history.py
Log Message:
-----------
Remove print of non-existent attribute 'content'
Commit: 5b64e6d0032f515093a2e2d589839da451081546
https://github.com/galaxyproject/galaxy/commit/5b64e6d0032f515093a2e2d58983…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Decouple model building
Commit: 2b94fa3b890a00bbe170ac1bec68d29e8d19c75a
https://github.com/galaxyproject/galaxy/commit/2b94fa3b890a00bbe170ac1bec68…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Fix MemePsp sniff entry
Commit: 3c4e8927e398e8468b232c2d6a5e49b3206c19b9
https://github.com/galaxyproject/galaxy/commit/3c4e8927e398e8468b232c2d6a5e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Hide initial tool version message
Commit: 8b43348b676161d7d1aa799dd6988040767c7f6f
https://github.com/galaxyproject/galaxy/commit/8b43348b676161d7d1aa799dd698…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Move workflow tool form model rebuilding to workflow forms
Commit: 192c4b1141a5a58b45d42afad93f1565579b31e0
https://github.com/galaxyproject/galaxy/commit/192c4b1141a5a58b45d42afad93f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M static/maps/mvc/workflow/workflow-forms.js.map
M static/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Properly update workflow tool module
Commit: 6d87448b45074b52298c71dfbca562d8c1950343
https://github.com/galaxyproject/galaxy/commit/6d87448b45074b52298c71dfbca5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Add optional initial model caller
Pack
Commit: 409867230cac37572779199d5210210a37663145
https://github.com/galaxyproject/galaxy/commit/409867230cac37572779199d5210…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
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
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
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Remove form dom removal through workflow manager
Commit: 0092600cf384df8888fcb982aadfe1964b4d7a37
https://github.com/galaxyproject/galaxy/commit/0092600cf384df8888fcb982aadf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M lib/galaxy/actions/admin.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-wrapper.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/form/form-parameters.js
M static/scripts/mvc/form/form-wrapper.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
R templates/admin/quota/quota.mako
R templates/admin/quota/quota_create.mako
R templates/admin/quota/quota_edit.mako
R templates/admin/quota/quota_rename.mako
R templates/admin/quota/quota_set_default.mako
Log Message:
-----------
Merge branch 'dev' into improve_form_modules
Commit: d8925d73c5ba7b4e0bcbb36c98d45e45bb3b9e78
https://github.com/galaxyproject/galaxy/commit/d8925d73c5ba7b4e0bcbb36c98d4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Fix message style
Commit: 1b69b9a5fedbd232e76ef684734170e7b06fe3e9
https://github.com/galaxyproject/galaxy/commit/1b69b9a5fedbd232e76ef6847341…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M scripts/api/upload_to_history.py
Log Message:
-----------
Merge pull request #4439 from chambm/patch-2
Remove print of non-existent attribute 'content'
Commit: 008a1d849c4eb86ab52fd032ae611e4844c3cf09
https://github.com/galaxyproject/galaxy/commit/008a1d849c4eb86ab52fd032ae61…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M test/api/test_search.py
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #4434 from chambm/patch-1
Avoid adding `(imported from API)` to workflows
Commit: 5799fbc3d13ae6ec41ef5a17e55faf6f58059ae3
https://github.com/galaxyproject/galaxy/commit/5799fbc3d13ae6ec41ef5a17e55f…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
change file_ext to be inline with memexml and co
Commit: 21b44bf348ae10d170ab96a3b6f30bf9dbbd5a4a
https://github.com/galaxyproject/galaxy/commit/21b44bf348ae10d170ab96a3b6f3…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M client/galaxy/style/source_material/circle.py
M contrib/nagios/check_galaxy.py
M cron/build_chrom_db.py
M lib/galaxy/__init__.py
M lib/galaxy/actions/admin.py
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/builder.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dataset_collections/registry.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/dataset_collections/subcollections.py
M lib/galaxy/dataset_collections/type_description.py
M lib/galaxy/dataset_collections/types/__init__.py
M lib/galaxy/dataset_collections/types/list.py
M lib/galaxy/dataset_collections/types/paired.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/chrominfo.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/coverage.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/chunk.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/exceptions.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/display_applications/util.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/util/generic_util.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/datasets.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/deferred/manual_data_transfer.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/error_level.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/collectl/stats.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/jobs/splitters/basic.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/jobs/stock_rules.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/annotatable.py
M lib/galaxy/managers/api_keys.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/containers.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/deletable.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/lddas.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/pages.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/secured.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/taggable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/visualizations.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/base.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/model/migrate/versions/0002_metadata_file_table.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/0023_page_published_and_deleted_columns.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/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.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/0042_workflow_invocation_fix.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/0054_visualization_dbkey.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.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/0061_tasks.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/0076_fix_form_values_data_corruption.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
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
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
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
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
M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M lib/galaxy/model/migrate/versions/0135_add_library_tags.py
M lib/galaxy/model/orm/engine_factory.py
M lib/galaxy/model/orm/logging_connection_proxy.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/model/search.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/model/tool_shed_install/mapping.py
M lib/galaxy/model/tool_shed_install/migrate/check.py
M lib/galaxy/model/util.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/openid/providers.py
M lib/galaxy/queue_worker.py
M lib/galaxy/quota/__init__.py
M lib/galaxy/sample_tracking/data_transfer.py
M lib/galaxy/sample_tracking/external_service_types.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/sample_tracking/sample.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/data_manager.py
M lib/galaxy/tools/actions/data_source.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cache.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/error_reports/plugins/__init__.py
M lib/galaxy/tools/error_reports/plugins/biostars.py
M lib/galaxy/tools/error_reports/plugins/email.py
M lib/galaxy/tools/error_reports/plugins/json.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/fetcher.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/history_query.py
M lib/galaxy/tools/parameters/input_translation.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/special_tools.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/toolbox/tags.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/util/galaxyops/__init__.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/aliaspickler.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/bunch.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/dbkeys.py
M lib/galaxy/util/dictifiable.py
M lib/galaxy/util/expressions.py
M lib/galaxy/util/handlers.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/image_util.py
M lib/galaxy/util/inflection.py
M lib/galaxy/util/json.py
M lib/galaxy/util/lazy_process.py
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M lib/galaxy/util/log/fluent_log.py
M lib/galaxy/util/multi_byte.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/odict.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/simplegraph.py
M lib/galaxy/util/sleeper.py
M lib/galaxy/util/sockets.py
M lib/galaxy/util/specs.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/template.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/ucsc.py
M lib/galaxy/util/validation.py
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M lib/galaxy/visualization/data_providers/cigar.py
M lib/galaxy/visualization/data_providers/genome.py
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M lib/galaxy/web/framework/middleware/statsd.py
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M lib/galaxy/web/framework/middleware/xforwardedhost.py
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M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/provenance.py
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M lib/galaxy/webapps/galaxy/api/requests.py
M lib/galaxy/webapps/galaxy/api/roles.py
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M lib/galaxy/webapps/galaxy/api/workflows.py
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M lib/galaxy/webapps/galaxy/controllers/error.py
M lib/galaxy/webapps/galaxy/controllers/external_service.py
M lib/galaxy/webapps/galaxy/controllers/external_services.py
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M lib/galaxy/webapps/galaxy/controllers/library.py
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M scripts/tool_shed/api/reset_metadata_on_repositories.py
M scripts/tool_shed/api/tool_shed_repository_revision_update.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/clean_up_tool_dependency_directory.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
M scripts/tools/maf/check_loc_file.py
M scripts/tools/re_escape_output.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M setup.cfg
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_datasets.py
M test/api/test_datatypes.py
M test/api/test_framework.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_history_contents_provenance.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_search.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_tours.py
M test/api/test_users.py
M test/api/test_visualizations.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/api.py
M test/base/api_asserts.py
M test/base/api_util.py
M test/base/driver_util.py
M test/base/instrument.py
M test/base/interactor.py
M test/base/nose_util.py
M test/base/populators.py
M test/base/test_db_util.py
M test/base/tool_shed_util.py
M test/base/twilltestcase.py
M test/casperjs/casperjs_runner.py
M test/casperjs/server_env.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
M test/functional/tools/code_file.py
M test/integration/test_maximum_worklfow_invocation_duration.py
M test/integration/test_resolvers.py
M test/integration/test_upload_configuration_options.py
M test/integration/test_workflow_handler_configuration.py
M test/manual/workflows_scaling.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_login.py
M test/selenium_tests/test_registration.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_0000_basic_repository_features.py
M test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_0020_basic_repository_dependencies.py
M test/shed_functional/functional/test_0030_repository_dependency_revisions.py
M test/shed_functional/functional/test_0040_repository_circular_dependencies.py
M test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py
M test/shed_functional/functional/test_0060_workflows.py
M test/shed_functional/functional/test_0070_invalid_tool.py
M test/shed_functional/functional/test_0080_advanced_circular_dependencies.py
M test/shed_functional/functional/test_0090_tool_search.py
M test/shed_functional/functional/test_0100_complex_repository_dependencies.py
M test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py
M test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py
M test/shed_functional/functional/test_0130_datatype_converters.py
M test/shed_functional/functional/test_0140_tool_help_images.py
M test/shed_functional/functional/test_0150_prior_installation_required.py
M test/shed_functional/functional/test_0160_circular_prior_installation_required.py
M test/shed_functional/functional/test_0170_complex_prior_installation_required.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_0310_hg_api_features.py
M test/shed_functional/functional/test_0400_repository_component_reviews.py
M test/shed_functional/functional/test_0410_repository_component_review_access_control.py
M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py
M test/shed_functional/functional/test_0430_browse_utilities.py
M test/shed_functional/functional/test_0440_deleting_dependency_definitions.py
M test/shed_functional/functional/test_0460_upload_to_repository.py
M test/shed_functional/functional/test_0470_tool_dependency_repository_type.py
M test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py
M test/shed_functional/functional/test_0490_export_import_repositories.py
M test/shed_functional/functional/test_0500_export_repository_simple_dependency.py
M test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py
M test/shed_functional/functional/test_0520_import_export_circular_dependencies.py
M test/shed_functional/functional/test_0530_repository_admin_feature.py
M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py
M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py
M test/shed_functional/functional/test_1000_install_basic_repository.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py
M test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py
M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py
M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
M test/shed_functional/functional/test_1070_invalid_tool.py
M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py
M test/shed_functional/functional/test_1110_install_tool_from_tool_search.py
M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py
M test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py
M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
M test/shed_functional/functional/test_1150_datatype_converters.py
M test/shed_functional/functional/test_1160_tool_help_images.py
M test/shed_functional/functional/test_1170_prior_installation_required.py
M test/shed_functional/functional/test_1180_circular_prior_installation_required.py
M test/shed_functional/functional/test_1190_complex_prior_installation_required.py
M test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
M test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional/test_1400_review_migration_stages.py
M test/shed_functional/functional/test_1410_update_manager.py
M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py
M test/shed_functional/functional/test_1430_repair_installed_repository.py
M test/shed_functional/functional/test_1440_missing_env_sh_files.py
M test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py
M test/shed_functional/functional/test_1460_data_managers.py
M test/shed_functional/functional/test_1470_updating_installed_repositories.py
M test/shed_functional/functional_tests.py
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/datatypes/test_data.py
M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_datasets.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rule_helper.py
M test/unit/jobs/test_rules/10_site.py
M test/unit/jobs/test_runner_local.py
M test/unit/jobs/test_runner_params.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_galaxy_transactions.py
M test/unit/test_routes.py
M test/unit/test_security_helper.py
M test/unit/test_sqlite_utils.py
M test/unit/test_topsort.py
M test/unit/tools/filter_modules/filtermod.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_panel.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_extract_summary.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
M tool_list.py
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/hbvar_filter.py
M tools/data_source/import.py
M tools/data_source/microbial_import.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/plotting/bar_chart.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ.py
M tools/visualization/LAJ_code.py
Log Message:
-----------
Fix all E201 and E202 style errors
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
Commit: a353b2e88fc0693c8b9a60017cbc012448c4f4e0
https://github.com/galaxyproject/galaxy/commit/a353b2e88fc0693c8b9a60017cbc…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M contrib/nagios/check_galaxy.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/deferred/manual_data_transfer.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/error_level.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/lddas.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.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/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/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/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.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/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/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/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.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/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0061_tasks.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/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/0077_create_tool_tag_association_table.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/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.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/0104_update_genome_downloader_job_parameters.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.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/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/orm/logging_connection_proxy.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/model/tool_shed_install/mapping.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/json.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/validation.py
M lib/galaxy/visualization/data_providers/basic.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/registry.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/web/form_builder.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/profile.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/params.py
M lib/galaxy/webapps/galaxy/api/dataset_collections.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/group_roles.py
M lib/galaxy/webapps/galaxy/api/group_users.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/job_files.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/requests.py
M lib/galaxy/webapps/galaxy/api/samples.py
M lib/galaxy/webapps/galaxy/api/tool_data.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/visualizations.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/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/external_service.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library.py
M lib/galaxy/webapps/galaxy/controllers/library_admin.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/request_type.py
M lib/galaxy/webapps/galaxy/controllers/requests.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.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/reports/controllers/history.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/system.py
M lib/galaxy/webapps/reports/controllers/tools.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/groups.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/api/users.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/groups.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py
M lib/galaxy/webapps/tool_shed/search/repo_search.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/render.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/dependencies/tool/tag_attribute_handler.py
M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/galaxy_install/migrate/check.py
M lib/tool_shed/galaxy_install/migrate/common.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/galaxy_install/utility_containers/__init__.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grid_filter_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/admin_util.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/container_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_content_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/review_util.py
M lib/tool_shed/util/search_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_dependency_util.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M scripts/api/install_tool_shed_repositories.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/drmaa_external_runner.py
M scripts/extract_toolbox_sections.py
M scripts/helper.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/microbes/BeautifulSoup.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/tool_shed/api/common.py
M scripts/tool_shed/api/create_categories.py
M scripts/tool_shed/api/create_users.py
M scripts/tool_shed/api/export.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/clean_up_tool_dependency_directory.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
M scripts/transfer.py
M test/api/test_api_batch.py
M test/api/test_workflows.py
M test/base/test_db_util.py
M test/base/tool_shed_util.py
M test/casperjs/casperjs_runner.py
M test/casperjs/server_env.py
M test/functional/test_library_templates.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_0000_basic_repository_features.py
M test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_0020_basic_repository_dependencies.py
M test/shed_functional/functional/test_0030_repository_dependency_revisions.py
M test/shed_functional/functional/test_0040_repository_circular_dependencies.py
M test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py
M test/shed_functional/functional/test_0060_workflows.py
M test/shed_functional/functional/test_0070_invalid_tool.py
M test/shed_functional/functional/test_0080_advanced_circular_dependencies.py
M test/shed_functional/functional/test_0090_tool_search.py
M test/shed_functional/functional/test_0100_complex_repository_dependencies.py
M test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py
M test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py
M test/shed_functional/functional/test_0130_datatype_converters.py
M test/shed_functional/functional/test_0140_tool_help_images.py
M test/shed_functional/functional/test_0150_prior_installation_required.py
M test/shed_functional/functional/test_0160_circular_prior_installation_required.py
M test/shed_functional/functional/test_0170_complex_prior_installation_required.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_0310_hg_api_features.py
M test/shed_functional/functional/test_0400_repository_component_reviews.py
M test/shed_functional/functional/test_0410_repository_component_review_access_control.py
M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py
M test/shed_functional/functional/test_0430_browse_utilities.py
M test/shed_functional/functional/test_0440_deleting_dependency_definitions.py
M test/shed_functional/functional/test_0460_upload_to_repository.py
M test/shed_functional/functional/test_0470_tool_dependency_repository_type.py
M test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py
M test/shed_functional/functional/test_0490_export_import_repositories.py
M test/shed_functional/functional/test_0500_export_repository_simple_dependency.py
M test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py
M test/shed_functional/functional/test_0520_import_export_circular_dependencies.py
M test/shed_functional/functional/test_0530_repository_admin_feature.py
M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py
M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py
M test/shed_functional/functional/test_1000_install_basic_repository.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py
M test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py
M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py
M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
M test/shed_functional/functional/test_1070_invalid_tool.py
M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py
M test/shed_functional/functional/test_1110_install_tool_from_tool_search.py
M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py
M test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py
M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
M test/shed_functional/functional/test_1150_datatype_converters.py
M test/shed_functional/functional/test_1160_tool_help_images.py
M test/shed_functional/functional/test_1170_prior_installation_required.py
M test/shed_functional/functional/test_1180_circular_prior_installation_required.py
M test/shed_functional/functional/test_1190_complex_prior_installation_required.py
M test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
M test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional/test_1400_review_migration_stages.py
M test/shed_functional/functional/test_1410_update_manager.py
M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py
M test/shed_functional/functional/test_1430_repair_installed_repository.py
M test/shed_functional/functional/test_1440_missing_env_sh_files.py
M test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py
M test/shed_functional/functional/test_1460_data_managers.py
M test/shed_functional/functional/test_1470_updating_installed_repositories.py
M test/shed_functional/functional_tests.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_UserManager.py
M tools/data_source/data_source.py
M tools/data_source/upload.py
M tools/filters/axt_to_lav.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Fix E127 errors introduced by previous commit
using:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 .
```
Commit: a8d7b2df8bb0ccf49b2ca7247f2451b6123a5fd8
https://github.com/galaxyproject/galaxy/commit/a8d7b2df8bb0ccf49b2ca7247f24…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/error_level.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/tool_shed_install/mapping.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/controllers/groups.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/webapps/tool_shed/search/tool_search.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/util/admin_util.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M scripts/microbes/BeautifulSoup.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
Log Message:
-----------
Fix more indentation errors
Commit: a85ee599ffc66ce3a5954ad819c864064bff838a
https://github.com/galaxyproject/galaxy/commit/a85ee599ffc66ce3a5954ad819c8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M client/galaxy/style/source_material/circle.py
M contrib/nagios/check_galaxy.py
M cron/build_chrom_db.py
M lib/galaxy/__init__.py
M lib/galaxy/actions/admin.py
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/builder.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dataset_collections/registry.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/dataset_collections/subcollections.py
M lib/galaxy/dataset_collections/type_description.py
M lib/galaxy/dataset_collections/types/__init__.py
M lib/galaxy/dataset_collections/types/list.py
M lib/galaxy/dataset_collections/types/paired.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/chrominfo.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
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M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
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M lib/galaxy/datatypes/dataproviders/exceptions.py
M lib/galaxy/datatypes/dataproviders/external.py
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M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/display_applications/util.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/util/generic_util.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
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M lib/galaxy/jobs/datasets.py
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M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
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M lib/galaxy/jobs/error_level.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/jobs/mapper.py
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M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/collectl/stats.py
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M lib/galaxy/jobs/metrics/instrumenters/collectl.py
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M lib/galaxy/jobs/metrics/instrumenters/uname.py
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M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
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M lib/galaxy/jobs/splitters/multi.py
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M lib/galaxy/jobs/transfer_manager.py
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M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/lddas.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/pages.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/rbac_secured.py
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M lib/galaxy/managers/secured.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/taggable.py
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M lib/galaxy/managers/users.py
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M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
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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
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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
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M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/openid/providers.py
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M lib/galaxy/sample_tracking/request_types.py
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M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/phyloviz/__init__.py
M lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
M lib/galaxy/visualization/data_providers/registry.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/visualization/plugins/utils.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/formbuilder.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/profile.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/request_id.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/middleware/static.py
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/middleware/xforwardedhost.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/params.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/security/__init__.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/__init__.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/annotations.py
M lib/galaxy/webapps/galaxy/api/authenticate.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/dataset_collections.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/extended_metadata.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/forms.py
M lib/galaxy/webapps/galaxy/api/genomes.py
M lib/galaxy/webapps/galaxy/api/group_roles.py
M lib/galaxy/webapps/galaxy/api/group_users.py
M lib/galaxy/webapps/galaxy/api/groups.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/item_tags.py
M lib/galaxy/webapps/galaxy/api/job_files.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/metrics.py
M lib/galaxy/webapps/galaxy/api/page_revisions.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/provenance.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/request_types.py
M lib/galaxy/webapps/galaxy/api/requests.py
M lib/galaxy/webapps/galaxy/api/roles.py
M lib/galaxy/webapps/galaxy/api/samples.py
M lib/galaxy/webapps/galaxy/api/search.py
M lib/galaxy/webapps/galaxy/api/tool_data.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/api/tours.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/config_watchers.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/biostar.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/error.py
M lib/galaxy/webapps/galaxy/controllers/external_service.py
M lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library.py
M lib/galaxy/webapps/galaxy/controllers/library_admin.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/request_type.py
M lib/galaxy/webapps/galaxy/controllers/requests.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.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/reports/config.py
M lib/galaxy/webapps/reports/controllers/history.py
M lib/galaxy/webapps/reports/controllers/home.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/query.py
M lib/galaxy/webapps/reports/controllers/root.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/system.py
M lib/galaxy/webapps/reports/controllers/tools.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/api/authenticate.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/configuration.py
M lib/galaxy/webapps/tool_shed/api/groups.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/api/users.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/groups.py
M lib/galaxy/webapps/tool_shed/controllers/hg.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/webapps/tool_shed/model/migrate/check.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py
M lib/galaxy/webapps/tool_shed/search/repo_search.py
M lib/galaxy/webapps/tool_shed/search/tool_search.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/webapps/tool_shed/util/ratings_util.py
M lib/galaxy/webapps/tool_shed/util/shed_statistics.py
M lib/galaxy/webapps/util.py
M lib/galaxy/work/context.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/render.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/schedulers/__init__.py
M lib/galaxy/workflow/schedulers/core.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/galaxy/workflow/steps.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/log_tempfile.py
M lib/mimeparse.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/dependencies/tool/tag_attribute_handler.py
M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/galaxy_install/migrate/check.py
M lib/tool_shed/galaxy_install/migrate/common.py
M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
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M lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
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M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
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M lib/tool_shed/galaxy_install/utility_containers/__init__.py
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M lib/tool_shed/grids/repository_grid_filter_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/managers/groups.py
M lib/tool_shed/managers/repositories.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
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M lib/tool_shed/repository_types/repository_suite_definition.py
M lib/tool_shed/repository_types/tool_dependency_definition.py
M lib/tool_shed/repository_types/unrestricted.py
M lib/tool_shed/repository_types/util.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/admin_util.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/container_util.py
M lib/tool_shed/util/encoding_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_content_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/review_util.py
M lib/tool_shed/util/search_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_dependency_util.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/web_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/util/xml_util.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M scripts/api/common.py
M scripts/api/copy_hda_to_library_folder.py
M scripts/api/create.py
M scripts/api/data_manager_example_execute.py
M scripts/api/delete.py
M scripts/api/display.py
M scripts/api/example_watch_folder.py
M scripts/api/form_create_from_xml.py
M scripts/api/history_create_history.py
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M scripts/api/import_library_dataset_to_history.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
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M scripts/api/library_create_folder.py
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M test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py
M test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py
M test/shed_functional/functional/test_0130_datatype_converters.py
M test/shed_functional/functional/test_0140_tool_help_images.py
M test/shed_functional/functional/test_0150_prior_installation_required.py
M test/shed_functional/functional/test_0160_circular_prior_installation_required.py
M test/shed_functional/functional/test_0170_complex_prior_installation_required.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_0310_hg_api_features.py
M test/shed_functional/functional/test_0400_repository_component_reviews.py
M test/shed_functional/functional/test_0410_repository_component_review_access_control.py
M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py
M test/shed_functional/functional/test_0430_browse_utilities.py
M test/shed_functional/functional/test_0440_deleting_dependency_definitions.py
M test/shed_functional/functional/test_0460_upload_to_repository.py
M test/shed_functional/functional/test_0470_tool_dependency_repository_type.py
M test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py
M test/shed_functional/functional/test_0490_export_import_repositories.py
M test/shed_functional/functional/test_0500_export_repository_simple_dependency.py
M test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py
M test/shed_functional/functional/test_0520_import_export_circular_dependencies.py
M test/shed_functional/functional/test_0530_repository_admin_feature.py
M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py
M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py
M test/shed_functional/functional/test_1000_install_basic_repository.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py
M test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py
M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py
M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
M test/shed_functional/functional/test_1070_invalid_tool.py
M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py
M test/shed_functional/functional/test_1110_install_tool_from_tool_search.py
M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py
M test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py
M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
M test/shed_functional/functional/test_1150_datatype_converters.py
M test/shed_functional/functional/test_1160_tool_help_images.py
M test/shed_functional/functional/test_1170_prior_installation_required.py
M test/shed_functional/functional/test_1180_circular_prior_installation_required.py
M test/shed_functional/functional/test_1190_complex_prior_installation_required.py
M test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
M test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional/test_1400_review_migration_stages.py
M test/shed_functional/functional/test_1410_update_manager.py
M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py
M test/shed_functional/functional/test_1430_repair_installed_repository.py
M test/shed_functional/functional/test_1440_missing_env_sh_files.py
M test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py
M test/shed_functional/functional/test_1460_data_managers.py
M test/shed_functional/functional/test_1470_updating_installed_repositories.py
M test/shed_functional/functional_tests.py
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/datatypes/test_data.py
M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_datasets.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rule_helper.py
M test/unit/jobs/test_rules/10_site.py
M test/unit/jobs/test_runner_local.py
M test/unit/jobs/test_runner_params.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_galaxy_transactions.py
M test/unit/test_routes.py
M test/unit/test_security_helper.py
M test/unit/test_sqlite_utils.py
M test/unit/test_topsort.py
M test/unit/tools/filter_modules/filtermod.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_panel.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_extract_summary.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
M tool_list.py
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/hbvar_filter.py
M tools/data_source/import.py
M tools/data_source/microbial_import.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/plotting/bar_chart.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ.py
M tools/visualization/LAJ_code.py
Log Message:
-----------
Merge pull request #4440 from nsoranzo/fix_E201_E202
Fix E201 and E202 style errors
Commit: 03df496540a6e2099aa4012fb2d46ec44be9bdbf
https://github.com/galaxyproject/galaxy/commit/03df496540a6e2099aa4012fb2d4…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Fix API tests broken in #4434
Commit: 56c1f25bf385fa3610e447ddc6fad0f063cc2de1
https://github.com/galaxyproject/galaxy/commit/56c1f25bf385fa3610e447ddc6fa…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Fix help text style
Commit: b8f11dfee4efa1d4df47ae3d753af3e9b5c69b82
https://github.com/galaxyproject/galaxy/commit/b8f11dfee4efa1d4df47ae3d753a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Improve error message for unknown module types when encountered.
Commit: 213137028182942b372f2483e3b0bb1e20c79518
https://github.com/galaxyproject/galaxy/commit/213137028182942b372f2483e3b0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Print warning if any input connections are unused during workflow execution.
Commit: 7bf7f3996373f2528ad7ac88037de3a31f227c23
https://github.com/galaxyproject/galaxy/commit/7bf7f3996373f2528ad7ac88037d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Cleanup a couple things in #4396 caught by @nsoranzo.
Commit: 35ab7457b9039e9ac6e076ea16bf86dd828faaed
https://github.com/galaxyproject/galaxy/commit/35ab7457b9039e9ac6e076ea16bf…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #4445 from nsoranzo/followup_on_4434
Fix API tests broken in #4434
Commit: cca1f9e9bcf455b4b655fe9c54707bc34d3c6c32
https://github.com/galaxyproject/galaxy/commit/cca1f9e9bcf455b4b655fe9c5470…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/sequence.py
A lib/galaxy/datatypes/test/1.memepsp
Log Message:
-----------
Merge pull request #4430 from gregvonkuster/psp_format
Add support for the MEME psp format
Commit: df442ea51a05541e83e304432ce4aac678a5b7a9
https://github.com/galaxyproject/galaxy/commit/df442ea51a05541e83e304432ce4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
Fix E201 errors (spaces in parens) in new memepsp datatype
Commit: 7ef099f6a6c97f0d9ac202860d6873c9a7aed66c
https://github.com/galaxyproject/galaxy/commit/7ef099f6a6c97f0d9ac202860d68…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
Merge pull request #4446 from dannon/memepsp_formatting
Fix E201 errors (spaces in parens) in new memepsp datatype
Commit: 5a913700221c3734364d70546abfa1b9342d8c1b
https://github.com/galaxyproject/galaxy/commit/5a913700221c3734364d70546abf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Fix title
Commit: 7bab16ef71c850b3cefab3686beeaee3708e1480
https://github.com/galaxyproject/galaxy/commit/7bab16ef71c850b3cefab3686bee…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-view.js
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/grid/grid-view.js
Log Message:
-----------
Preserve advanced search visibility
Commit: ee4c8e2afac1d16b386c4dc9afa9b0817a0c9325
https://github.com/galaxyproject/galaxy/commit/ee4c8e2afac1d16b386c4dc9afa9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-view.js
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/grid/grid-view.js
Log Message:
-----------
Fix filters
Commit: 114997dca6af7483d3ed3f34fafd0f66e3583afc
https://github.com/galaxyproject/galaxy/commit/114997dca6af7483d3ed3f34fafd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M static/maps/mvc/grid/grid-model.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/grid/grid-model.js
M static/scripts/mvc/grid/grid-view.js
Log Message:
-----------
Prevent search tag duplication
Commit: 0fa287f76a675c49c2702681ac4404f050b77130
https://github.com/galaxyproject/galaxy/commit/0fa287f76a675c49c2702681ac44…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
A .ci/autopep8.sh
M lib/galaxy/actions/admin.py
M lib/galaxy/app.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/chunk.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/exceptions.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/util/drmaa/__init__.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/deletable.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/orm/logging_connection_proxy.py
M lib/galaxy/model/search.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/quota/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/mulled/mulled_search.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/bunch.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/odict.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/simplegraph.py
M lib/galaxy/util/sleeper.py
M lib/galaxy/util/ucsc.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/utils.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/formbuilder.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/request_id.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/middleware/xforwardedhost.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/provenance.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/tool_shed/util/ratings_util.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M test/casperjs/casperjs_runner.py
M test/galaxy_selenium/driver_factory.py
M test/shed_functional/functional/test_0060_workflows.py
M test/shed_functional/functional/test_0400_repository_component_reviews.py
M test/shed_functional/functional/test_0410_repository_component_review_access_control.py
M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
M test/shed_functional/functional/test_1070_invalid_tool.py
M tools/data_source/upload.py
Log Message:
-----------
Add autopep8 script to help rebasing branches after #4440.
Fixes a few more PEP8 issues as part of the autopep8'ing as well.
Commit: 8c225ecf3d928b93aceb318dada1e942a510b8ca
https://github.com/galaxyproject/galaxy/commit/8c225ecf3d928b93aceb318dada1…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Log Message:
-----------
Merge branch 'release_17.05' into dev
Commit: 68e8abc89aba1263f82c643d1bde89da53d70bc9
https://github.com/galaxyproject/galaxy/commit/68e8abc89aba1263f82c643d1bde…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
A .ci/autopep8.sh
M lib/galaxy/actions/admin.py
M lib/galaxy/app.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/chunk.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/exceptions.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/util/drmaa/__init__.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/deletable.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/orm/logging_connection_proxy.py
M lib/galaxy/model/search.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/quota/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/mulled/mulled_search.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/bunch.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/odict.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/simplegraph.py
M lib/galaxy/util/sleeper.py
M lib/galaxy/util/ucsc.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/utils.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/formbuilder.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/request_id.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/middleware/xforwardedhost.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/provenance.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/tool_shed/util/ratings_util.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M test/casperjs/casperjs_runner.py
M test/galaxy_selenium/driver_factory.py
M test/shed_functional/functional/test_0060_workflows.py
M test/shed_functional/functional/test_0400_repository_component_reviews.py
M test/shed_functional/functional/test_0410_repository_component_review_access_control.py
M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
M test/shed_functional/functional/test_1070_invalid_tool.py
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #4447 from jmchilton/autopep8
Add autopep8 script to help rebasing branches after #4440.
Commit: 706741f30b2ee0a1733e49cafa8c0d0e6b78385a
https://github.com/galaxyproject/galaxy/commit/706741f30b2ee0a1733e49cafa8c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M static/maps/mvc/grid/grid-model.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/grid/grid-model.js
M static/scripts/mvc/grid/grid-view.js
Log Message:
-----------
Merge pull request #4449 from guerler/fix_grid_search
Fixes for advanced grid search
Commit: 042386ff8733874fe7004c900fabb16b7798d031
https://github.com/galaxyproject/galaxy/commit/042386ff8733874fe7004c900fab…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-17 (Thu, 17 Aug 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-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M lib/galaxy/webapps/galaxy/api/lda_datasets.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-foldertoolbar-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/scripts/bundled/libs.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-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
Log Message:
-----------
wip on improving libraries
Commit: 61eb0114034703d5ec225c42e3b781b96b02b7f6
https://github.com/galaxyproject/galaxy/commit/61eb0114034703d5ec225c42e3b7…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
Log Message:
-----------
refactor decode_id method to use base manager
Commit: dc834a52c1dfa2bcca61e3cdb74ed9606c752340
https://github.com/galaxyproject/galaxy/commit/dc834a52c1dfa2bcca61e3cdb74e…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/managers/libraries.py
Log Message:
-----------
fix copypasta error
Commit: e17ab411e338043dce2391672322ebc3468d049e
https://github.com/galaxyproject/galaxy/commit/e17ab411e338043dce2391672322…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
A lib/galaxy/managers/library_datasets.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
Log Message:
-----------
refactor show method to use new manager
Commit: cd09d1327a075f83e0c83323da26377ec0336d03
https://github.com/galaxyproject/galaxy/commit/cd09d1327a075f83e0c83323da26…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
Log Message:
-----------
refactor the rest of the module to use new manager
Commit: 25960121310455e2d5b84933fb76cda8daacc1f7
https://github.com/galaxyproject/galaxy/commit/25960121310455e2d5b84933fb76…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
A .ci/autopep8.sh
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/style/source_material/circle.py
M config/datatypes_conf.xml.sample
M contrib/nagios/check_galaxy.py
M cron/build_chrom_db.py
M lib/galaxy/__init__.py
M lib/galaxy/actions/admin.py
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/builder.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dataset_collections/registry.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/dataset_collections/subcollections.py
M lib/galaxy/dataset_collections/type_description.py
M lib/galaxy/dataset_collections/types/__init__.py
M lib/galaxy/dataset_collections/types/list.py
M lib/galaxy/dataset_collections/types/paired.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/chrominfo.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/coverage.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/chunk.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/exceptions.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/display_applications/util.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/1.memepsp
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/util/generic_util.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/datasets.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/deferred/manual_data_transfer.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/error_level.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/collectl/stats.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/jobs/runners/util/drmaa/__init__.py
M lib/galaxy/jobs/splitters/basic.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/jobs/stock_rules.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/annotatable.py
M lib/galaxy/managers/api_keys.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/containers.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/deletable.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/lddas.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/pages.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/secured.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/taggable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/visualizations.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/base.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/model/migrate/versions/0002_metadata_file_table.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/0023_page_published_and_deleted_columns.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/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.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/0042_workflow_invocation_fix.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/0054_visualization_dbkey.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.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
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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
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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
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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/0076_fix_form_values_data_corruption.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
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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
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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
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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
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M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
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M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
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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
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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
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M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
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M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
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M lib/galaxy/sample_tracking/data_transfer.py
M lib/galaxy/sample_tracking/external_service_types.py
M lib/galaxy/sample_tracking/request_types.py
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M lib/galaxy/security/passwords.py
M lib/galaxy/security/validate_user_input.py
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M lib/galaxy/tools/actions/__init__.py
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M lib/galaxy/tools/actions/data_source.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/model_operations.py
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M lib/galaxy/tools/error_reports/plugins/json.py
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M lib/galaxy/tools/imp_exp/export_history.py
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M lib/galaxy/tools/parameters/dataset_matcher.py
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M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/history_query.py
M lib/galaxy/tools/parameters/input_translation.py
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M lib/galaxy/tools/parameters/output_collect.py
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M lib/galaxy/tools/parser/output_objects.py
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M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/toolbox/panel.py
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M lib/galaxy/util/bunch.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/dbkeys.py
M lib/galaxy/util/dictifiable.py
M lib/galaxy/util/expressions.py
M lib/galaxy/util/handlers.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/image_util.py
M lib/galaxy/util/inflection.py
M lib/galaxy/util/json.py
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M lib/galaxy/util/log/fluent_log.py
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M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/odict.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/simplegraph.py
M lib/galaxy/util/sleeper.py
M lib/galaxy/util/sockets.py
M lib/galaxy/util/specs.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/template.py
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M lib/galaxy/util/validation.py
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M lib/galaxy/web/base/interactive_environments.py
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M lib/galaxy/web/framework/middleware/statsd.py
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M lib/galaxy/web/framework/middleware/xforwardedhost.py
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M lib/galaxy/webapps/galaxy/api/group_users.py
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M lib/galaxy/webapps/galaxy/api/pages.py
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M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/plotting/bar_chart.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ.py
M tools/visualization/LAJ_code.py
Log Message:
-----------
Merge branch 'dev' into improve_form_modules
Commit: 50ebc19afd6788125285cbf051f85aec6ac34d00
https://github.com/galaxyproject/galaxy/commit/50ebc19afd6788125285cbf051f8…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
R lib/galaxy/webapps/galaxy/api/lda_datasets.py
A lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-librarytoolbar-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-foldertoolbar-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
Log Message:
-----------
rename lda_datasets to library_datasets
Commit: 517f248ac49caca3f0933c4b1f48cd4d74cf89fe
https://github.com/galaxyproject/galaxy/commit/517f248ac49caca3f0933c4b1f48…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/output_collect.py
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/tool_provided_metadata_1.xml
M test/functional/tools/tool_provided_metadata_2.xml
M test/functional/tools/tool_provided_metadata_3.xml
A test/functional/tools/tool_provided_metadata_4.xml
A test/functional/tools/tool_provided_metadata_5.xml
A test/functional/tools/tool_provided_metadata_6.xml
M test/unit/tools/test_collect_primary_datasets.py
Log Message:
-----------
Overhaul of tool provided job metadata.
- Add another test to demonstrate referencing entries in galaxy.json for datasets by dataset path basename instead of ID.
- Add a bit more documentation to test tools.
- Redo the structure of galaxy.json for profile >= 17.09 tools with two new test tools to demonstrate the new structure - for both output dataset metadata and discovered dataset metadata.
- Improved abstractions for interaction between tools and jobs to enable different tool provided metadata collection depending on tool profile version.
Commit: 72e361bcf14191dae58af8e3963b89a4e8acd38a
https://github.com/galaxyproject/galaxy/commit/72e361bcf14191dae58af8e3963b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/xsd/galaxy.xsd
A test/functional/tools/collection_creates_dynamic_nested_from_json.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/tool_provided_metadata_7.xml
Log Message:
-----------
Allow discovering datasets directly from galaxy.json...
without needing to specify a discovered dataset pattern. If the ``discovered_datasets`` tag includes ``from_tool_provided_metadata="true"`` the datsets listed in galaxy.json will just be used directly without needing to be "discovered" using a dataset pattern. Metadata and such can continue to be specified either in that file or on the discovered_dataset element except things like pattern (which is not used) and sort_by (since the json should describe the order I suppose).
Commit: 6563e387a5d001bb6078469b7ad6a13f9bbed8aa
https://github.com/galaxyproject/galaxy/commit/6563e387a5d001bb6078469b7ad6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/tools/parameters/output_collect.py
A test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Allow discovering dataset collections in galaxy.json in a nested fashion.
Fixes #2658.
Commit: 39d4411f8c21b307a86340fc5438ed2193abd766
https://github.com/galaxyproject/galaxy/commit/39d4411f8c21b307a86340fc5438…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/xsd/galaxy.xsd
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/tool_provided_metadata_8.xml
Log Message:
-----------
Move determining tool provided metadata style to tool parser.
Allow override by specifying "provided_metadata_style=" attribute on outputs in tool XML - this should allow newer profile tools to use the older style JSON providing a clear path for upgrades.
Commit: a8bec7a275b5bd387daddf6555b6ff382851e8e8
https://github.com/galaxyproject/galaxy/commit/a8bec7a275b5bd387daddf6555b6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/xsd/galaxy.xsd
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/tool_provided_metadata_9.xml
Log Message:
-----------
Allow override of provided metadata location.
Eliminates that terrible circular dependency between tools and jobs.
Commit: 1e1df6786aeb6d02fba1ad84cceb204aa745ea62
https://github.com/galaxyproject/galaxy/commit/1e1df6786aeb6d02fba1ad84cceb…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Variety of fixes for #4437.
Commit: 2489499fb656acc61dc9275931dafcdad381d25c
https://github.com/galaxyproject/galaxy/commit/2489499fb656acc61dc9275931da…
Author: xgaia <xgaia(a)gmx.com>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
possibility to don't uppercase env variables
Commit: cff9292f07d1318ce789bcfdab7dbf3e67c8d162
https://github.com/galaxyproject/galaxy/commit/cff9292f07d1318ce789bcfdab7d…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/pastescript/serve.py
Log Message:
-----------
Uniform indentation of multiline if conditionals
Use 8-spaces indentation for the conditional continuation lines of an
`if`-statement where the conditional part spans multiple lines.
According to PEP-8, using 4-spaces "can produce a visual conflict with
the indented suite of code nested inside the `if`-statement", but the PEP
"takes no explicit position".
There were only 2 places in the whole codebase where 8 spaces were not
used, this will make it uniform.
Commit: d2d1f857bbc2b7528e2e17cc8fcfdaad7d79fa75
https://github.com/galaxyproject/galaxy/commit/d2d1f857bbc2b7528e2e17cc8fcf…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M lib/galaxy/util/pastescript/serve.py
Log Message:
-----------
Fix import order and Python3 compatibility for lib/galaxy/util/pastescript/serve.py
Commit: 784e6f5fd360f8374045b256171303f5f795264e
https://github.com/galaxyproject/galaxy/commit/784e6f5fd360f8374045b2561713…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Merge pull request #4396 from jmchilton/workflow_warnings
Slightly improve workflow warnings/errors logging.
Commit: 4e75635d629f654f7b9d203fa6b6c1bc61495aa6
https://github.com/galaxyproject/galaxy/commit/4e75635d629f654f7b9d203fa6b6…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/tools/execute.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/users.py
M scripts/communication/communication_server.py
M scripts/secret_decoder_ring.py
Log Message:
-----------
Use log.warning() instead of deprecated warn()
Commit: e32ad2864f6b4ea05a347602b19202b94ae0ea81
https://github.com/galaxyproject/galaxy/commit/e32ad2864f6b4ea05a347602b192…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M lib/galaxy/containers/__init__.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/cleanup_datasets.py
Log Message:
-----------
Remove container config log message from cleanup scripts logs
Commit: bd88524a109e6695a68f57e55ace64c21f907089
https://github.com/galaxyproject/galaxy/commit/bd88524a109e6695a68f57e55ace…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/containers/__init__.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/users.py
M scripts/communication/communication_server.py
M scripts/secret_decoder_ring.py
Log Message:
-----------
Fix import order and Python3 compatibility
Commit: b459399edebbeada2be6254a8567de85b43dabc4
https://github.com/galaxyproject/galaxy/commit/b459399edebbeada2be6254a8567…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
Merge pull request #4454 from xgaia/interactive_environment
Interactive Environment: possibility to don't uppercase env variables
Commit: 8d132b2bca0dab22f7e028773dd31aa553cae668
https://github.com/galaxyproject/galaxy/commit/8d132b2bca0dab22f7e028773dd3…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
More detailed sentry reports
Commit: dd89a9c65f7297d4da5f0c0f7b6fea884a9698e6
https://github.com/galaxyproject/galaxy/commit/dd89a9c65f7297d4da5f0c0f7b6f…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/xsd/galaxy.xsd
A test/functional/tools/collection_creates_dynamic_nested_from_json.xml
A test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/tool_provided_metadata_1.xml
M test/functional/tools/tool_provided_metadata_2.xml
M test/functional/tools/tool_provided_metadata_3.xml
A test/functional/tools/tool_provided_metadata_4.xml
A test/functional/tools/tool_provided_metadata_5.xml
A test/functional/tools/tool_provided_metadata_6.xml
A test/functional/tools/tool_provided_metadata_7.xml
A test/functional/tools/tool_provided_metadata_8.xml
A test/functional/tools/tool_provided_metadata_9.xml
M test/unit/tools/test_collect_primary_datasets.py
Log Message:
-----------
Merge pull request #4437 from jmchilton/galaxy_json_rev
Enhanced tool options for dataset discovery
Commit: e987b9b9e48bfa2f5ee69c013f991eb8bec70a2d
https://github.com/galaxyproject/galaxy/commit/e987b9b9e48bfa2f5ee69c013f99…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
swap id to username
Commit: 30562c09c54e112f141a91635e91aa942ff4ece7
https://github.com/galaxyproject/galaxy/commit/30562c09c54e112f141a91635e91…
Author: xgaia <xgaia(a)gmx.com>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
don't uppercase envoverride
Commit: e4924942825c6ea2d472d8ccff45222f165fa6bf
https://github.com/galaxyproject/galaxy/commit/e4924942825c6ea2d472d8ccff45…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/config.py
M lib/galaxy/containers/__init__.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/tools/execute.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/users.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/communication/communication_server.py
M scripts/secret_decoder_ring.py
Log Message:
-----------
Merge pull request #4456 from nsoranzo/logging_fixes
Logging fixes
Commit: 9c6fd670cf201b9b3fed67cd5f100d75a24cb5f6
https://github.com/galaxyproject/galaxy/commit/9c6fd670cf201b9b3fed67cd5f10…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/pastescript/serve.py
Log Message:
-----------
Merge pull request #4455 from nsoranzo/multiline_if_conditionals
Uniform indentation of multiline if conditionals
Commit: cd22de114c2098ecbf2ab2108f3526abe70f00e6
https://github.com/galaxyproject/galaxy/commit/cd22de114c2098ecbf2ab2108f35…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
Merge pull request #4457 from erasche/sentry-extra-info
More detailed sentry reports
Commit: d883fc162e4d0a6606b9e4408337e5c564fd1840
https://github.com/galaxyproject/galaxy/commit/d883fc162e4d0a6606b9e4408337…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
add ommitted conflict resolution
Commit: 7f50a8a29f53c7fa86e5b0c7a57d2d898c6c4650
https://github.com/galaxyproject/galaxy/commit/7f50a8a29f53c7fa86e5b0c7a57d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M 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
M client/galaxy/style/less/ui.less
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
M 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
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/form/form-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
M 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/style/blue/base.css
Log Message:
-----------
Merge pull request #4438 from guerler/improve_form_modules
Augment form module separation
Commit: dd27c1edccb06b54ef5d503749ce51f79abcfcf0
https://github.com/galaxyproject/galaxy/commit/dd27c1edccb06b54ef5d503749ce…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
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
Log Message:
-----------
Client rebuild, @guerler and I were trying to figure out what changed in the recently merged #4438 but don't see anything obvious.
Commit: 263018326895c3f6e36288dcdeb242a056580892
https://github.com/galaxyproject/galaxy/commit/263018326895c3f6e36288dcdeb2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
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
Log Message:
-----------
Merge pull request #4464 from dannon/rebuild_000
Client rebuild, @guerler and I were trying to figure out what changed…
Commit: 1342c2bd706b353038871a73992ae1a19878a694
https://github.com/galaxyproject/galaxy/commit/1342c2bd706b353038871a73992a…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
A client/galaxy/scripts/mvc/tool/tool-genomespace.js
A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/web/form_builder.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_file_browser.py
R tools/genomespace/genomespace_file_browser_dev.xml
R tools/genomespace/genomespace_file_browser_prod.xml
R tools/genomespace/genomespace_file_browser_test.xml
M tools/genomespace/genomespace_importer.py
M tools/genomespace/genomespace_importer.xml
Log Message:
-----------
Integrated File Browsing and Workflow support for GenomeSpace
Commit: e39901ef0695d6e7828d81ce3d1a9a230fda1569
https://github.com/galaxyproject/galaxy/commit/e39901ef0695d6e7828d81ce3d1a…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M client/galaxy/style/less/ui.less
M lib/galaxy/dependencies/pinned-requirements.txt
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.py
M tools/genomespace/genomespace_importer.xml
Log Message:
-----------
Moved back some code to wrapper and added back data type sniffing.
Commit: ad1b61344557b53af10fae91011ec4a7be5d4a67
https://github.com/galaxyproject/galaxy/commit/ad1b61344557b53af10fae91011e…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
M tools/genomespace/genomespace_importer.py
M tools/genomespace/genomespace_importer.xml
A tools/genomespace/genomespace_push.xml
Log Message:
-----------
Added support for pushing multiple files from GenomeSpace to Galaxy.
Commit: b04ccbe55b33ffca1aa09668885bceea61951dfe
https://github.com/galaxyproject/galaxy/commit/b04ccbe55b33ffca1aa09668885b…
Author: slugger70 <slugger70(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M tools/genomespace/genomespace_importer.xml
Log Message:
-----------
Fixed genomespace_importer.xml command block
Commit: cb1b086324b1625d4f5ac0087e00971f3048afd4
https://github.com/galaxyproject/galaxy/commit/cb1b086324b1625d4f5ac0087e00…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Fixed pylint errors
Commit: 46c04dcbd4eb47a2f3a2ff559c9ba4e280621750
https://github.com/galaxyproject/galaxy/commit/46c04dcbd4eb47a2f3a2ff559c9b…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Fix incorrect reference when determining file type through file ext
Commit: 678d575a7ae2cf7056564b525971396dc16d9b39
https://github.com/galaxyproject/galaxy/commit/678d575a7ae2cf7056564b525971…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Improved recognition of compressed files
Commit: ae6ae8ffe2c1558513737b5fab77840a22cea0a8
https://github.com/galaxyproject/galaxy/commit/ae6ae8ffe2c1558513737b5fab77…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-genomespace.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
Log Message:
-----------
Added new config setting for GenomeSpace UI URL
Commit: 517fd23fc8cd84c5277ccadc33222fa913230cc8
https://github.com/galaxyproject/galaxy/commit/517fd23fc8cd84c5277ccadc3322…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M tools/genomespace/genomespace_exporter.xml
Log Message:
-----------
Fixed typo in exporter help text
Commit: b73e21b584dc13716460f550ed80108634adca37
https://github.com/galaxyproject/galaxy/commit/b73e21b584dc13716460f550ed80…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/web/form_builder.py
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Formatting and linting fixes for GenomeSpace tool
Commit: b995e551d408bd192322de530db89ddd08d35db2
https://github.com/galaxyproject/galaxy/commit/b995e551d408bd192322de530db8…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
Log Message:
-----------
Fixed alignment of buttons in Genomespace Importer
Commit: 46dc4a252cf6144672053864b16e52a85c810e34
https://github.com/galaxyproject/galaxy/commit/46dc4a252cf6144672053864b16e…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.xml
M tools/genomespace/genomespace_push.xml
Log Message:
-----------
Fixed template formatting according to review comments
Commit: 3e8bf3c4e72ca035f98142b3dc153de0a8e9d6a1
https://github.com/galaxyproject/galaxy/commit/3e8bf3c4e72ca035f98142b3dc15…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.py
M tools/genomespace/genomespace_push.xml
Log Message:
-----------
Moved genomespace token to environment variable
Commit: 52b26f45a2bd3bcb0155553bf6e3e765d3bd4b2c
https://github.com/galaxyproject/galaxy/commit/52b26f45a2bd3bcb0155553bf6e3…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M tools/genomespace/genomespace_importer.xml
Log Message:
-----------
Registered genomespace_importer as a tool needing Galaxy's python env
Commit: 32401978234c46aeef80bc0ee144a478820468dc
https://github.com/galaxyproject/galaxy/commit/32401978234c46aeef80bc0ee144…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M static/maps/mvc/form/form-parameters.js.map
A static/maps/mvc/tool/tool-genomespace.js.map
A static/maps/mvc/ui/ui-select-genomespace.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/form/form-parameters.js
A static/scripts/mvc/tool/tool-genomespace.js
A static/scripts/mvc/ui/ui-select-genomespace.js
M static/style/blue/base.css
Log Message:
-----------
Rebuilt galaxy client files
Commit: ac5be429e70a8533aae3583fed9cd29cb17fc13f
https://github.com/galaxyproject/galaxy/commit/ac5be429e70a8533aae3583fed9c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
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-foldertoolbar-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/maps/mvc/library/library-librarytoolbar-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-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
Log Message:
-----------
repack
Commit: f5ac8ce30d369c3661a8e1e4ea8424a540a41f66
https://github.com/galaxyproject/galaxy/commit/f5ac8ce30d369c3661a8e1e4ea84…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
add mz5 datatype
Commit: fd51a61d014c4d3affe146b69fc3ed097037d2a1
https://github.com/galaxyproject/galaxy/commit/fd51a61d014c4d3affe146b69fc3…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-18 (Fri, 18 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
A client/galaxy/scripts/mvc/tool/tool-genomespace.js
A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
M config/galaxy.ini.sample
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
M lib/galaxy/config.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/managers/configuration.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/web/form_builder.py
M static/maps/mvc/form/form-parameters.js.map
A static/maps/mvc/tool/tool-genomespace.js.map
A static/maps/mvc/ui/ui-select-genomespace.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/form/form-parameters.js
A static/scripts/mvc/tool/tool-genomespace.js
A static/scripts/mvc/ui/ui-select-genomespace.js
M static/style/blue/base.css
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_file_browser.py
R tools/genomespace/genomespace_file_browser_dev.xml
R tools/genomespace/genomespace_file_browser_prod.xml
R tools/genomespace/genomespace_file_browser_test.xml
M tools/genomespace/genomespace_importer.py
M tools/genomespace/genomespace_importer.xml
A tools/genomespace/genomespace_push.xml
Log Message:
-----------
Merge pull request #1814 from gvlproject/genomespace_workflows
Galaxy Workflow support for GenomeSpace
Commit: 912da2f3b93e7ae655725b6619febf0dbbcc4455
https://github.com/galaxyproject/galaxy/commit/912da2f3b93e7ae655725b6619fe…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M test/api/test_workflows.py
Log Message:
-----------
Fix checking WorkflowInvocation for published workflows
Commit: 413233eec3ce9b3f930db8e40413856831dfc0cb
https://github.com/galaxyproject/galaxy/commit/413233eec3ce9b3f930db8e40413…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Correctly raise Exception if invocation not found
Commit: 0a4203ed92acb795a2f32c5ca095146b388a2ec2
https://github.com/galaxyproject/galaxy/commit/0a4203ed92acb795a2f32c5ca095…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Fix test to use invocation_id instead of history_id
Commit: 80e264d35ffbf9eecacf37918fab7f7dbfa27cc7
https://github.com/galaxyproject/galaxy/commit/80e264d35ffbf9eecacf37918fab…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-19 (Sat, 19 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Check ownership of invocation, instead of stored_workflow
Commit: 2d16470132b86fb04bd67665bbdaf20e55874170
https://github.com/galaxyproject/galaxy/commit/2d16470132b86fb04bd67665bbda…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-20 (Sun, 20 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Allow admin user to view workflow invocation (thx @nsoranzo)
Commit: cff306b86bc6368b4489805b96f92da04761c013
https://github.com/galaxyproject/galaxy/commit/cff306b86bc6368b4489805b96f9…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-20 (Sun, 20 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Only skip check_security checks if check_ownership and check_accessible are false
Commit: 64f8e74adeb5f46e781fb3cf54294097c6301880
https://github.com/galaxyproject/galaxy/commit/64f8e74adeb5f46e781fb3cf5429…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-20 (Sun, 20 Aug 2017)
Changed paths:
M test/unit/workflows/workflow_support.py
Log Message:
-----------
Fix subworkflow tests
Commit: 0e46888eed5412a85439f82907f58f540d9963d9
https://github.com/galaxyproject/galaxy/commit/0e46888eed5412a85439f82907f5…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-20 (Sun, 20 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Show up to 15 histories by default in saved histories menu
Commit: a9d5c7c59c6b1bf2b656ec58d6ae3cea5a94d6ca
https://github.com/galaxyproject/galaxy/commit/a9d5c7c59c6b1bf2b656ec58d6ae…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-20 (Sun, 20 Aug 2017)
Changed paths:
M templates/tagging_common.mako
Log Message:
-----------
Show tag if < 3 tags on history
Commit: 2346c0aa7e66580792b4cd2d0bd48656421c5352
https://github.com/galaxyproject/galaxy/commit/2346c0aa7e66580792b4cd2d0bd4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-20 (Sun, 20 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
M templates/tagging_common.mako
Log Message:
-----------
Merge pull request #4467 from mvdbeek/saved_history_tags
More items per page in saved history and directly show tags
Commit: e3b3457b1fbeac31e1837be18f96a2e4d795902f
https://github.com/galaxyproject/galaxy/commit/e3b3457b1fbeac31e1837be18f96…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-21 (Mon, 21 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M test/api/test_workflows.py
M test/unit/workflows/workflow_support.py
Log Message:
-----------
Merge pull request #4465 from mvdbeek/workflow_invocation_security_check
Fix checking WorkflowInvocation for published workflows
Commit: 092ad6d67fe63a8b8895c003e2ad6ce54a612878
https://github.com/galaxyproject/galaxy/commit/092ad6d67fe63a8b8895c003e2ad…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-21 (Mon, 21 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/quotas.py
Log Message:
-----------
Fix quota function name
Commit: ae48774f54f317c2417b7677f1ef6cfde662a5f4
https://github.com/galaxyproject/galaxy/commit/ae48774f54f317c2417b7677f1ef…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-21 (Mon, 21 Aug 2017)
Changed paths:
M lib/galaxy/webapps/reports/config.py
Log Message:
-----------
needed for sentry functionality in reports webapp
Commit: 63d1d428a1d98f3f607381c84e501030481eadbf
https://github.com/galaxyproject/galaxy/commit/63d1d428a1d98f3f607381c84e50…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-08-21 (Mon, 21 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/quotas.py
Log Message:
-----------
Merge pull request #4469 from guerler/fix_quota_api
Fix quota function name
Commit: da5b72a030d8d07c663566527fc64560e067eb54
https://github.com/galaxyproject/galaxy/commit/da5b72a030d8d07c663566527fc6…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-22 (Tue, 22 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py
R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml
R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py
R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml
A lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml
A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml
A lib/galaxy/datatypes/test/1.bcf
A lib/galaxy/datatypes/test/1.bcf_uncompressed
Log Message:
-----------
Alias `bcf_bgzip` datatype to `bcf`. Add `bcf_uncompressed` and converters
Since https://bitbucket.org/galaxy/galaxy-central/pull-requests/353
(only) compressed BCF files have been sniffed as `bcf`, so the `bcf_bgzip`
datatype (introduced 2 years later in
https://github.com/galaxyproject/galaxy/pull/1148 ) is an unused duplicate.
This adds also a distinct `bcf_uncompressed` datatype (and converters) for
the rare cases when it may be useful.
Commit: 8dc0e697d3f8841270f6d934d19b271cf23b219e
https://github.com/galaxyproject/galaxy/commit/8dc0e697d3f8841270f6d934d19b…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-22 (Tue, 22 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/tabular.py
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Fix `vcf_bgzip` datatype
In https://github.com/galaxyproject/galaxy/pull/4254 `vcf_bgzip` was made
a proper datatype with the introduction of the `VcfGz` class, but was
still described as a subclass in `datatypes_conf.xml` .
Also fix `file_ext` attribute in `BaseVcf` and subclasses.
Commit: a63af63b41e81a104dc177cb13dc2f6f3b4e9e6d
https://github.com/galaxyproject/galaxy/commit/a63af63b41e81a104dc177cb13dc…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-22 (Tue, 22 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/set_metadata_tool.xml
Log Message:
-----------
Add requirement for bcftools to set_metadata tool
The `bcftools` binary is used by the `set_meta()` method of the `Bcf`
datatype class. Having a `<requirement>` for it in the set_metadata tool
makes it possible to use conda to resolve the dependency instead of
forcing the admin to install `bcftools` on the PATH of the Galaxy user.
This will also fix errors like
https://travis-ci.org/galaxyproject/tools-iuc/jobs/266923024#L1994
when running
```
planemo test --conda_dependency_resolution --conda_auto_install
```
Commit: d3ae7351f734b4e841c91495c1e41c77fe4e01b1
https://github.com/galaxyproject/galaxy/commit/d3ae7351f734b4e841c91495c1e4…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-22 (Tue, 22 Aug 2017)
Changed paths:
M lib/galaxy/tools/verify/__init__.py
Log Message:
-----------
Use pysam instead of samtools binary
This will make it possible to remove the requirement of having `samtools`
installed when testing tools, e.g. in the tools-iuc TravisCI setup:
https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml#L59
Commit: eefc268eae2961186a84dc396921326549ea4822
https://github.com/galaxyproject/galaxy/commit/eefc268eae2961186a84dc396921…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-08-23 (Wed, 23 Aug 2017)
Changed paths:
A test/selenium_tests/test_published_history_grid.py
Log Message:
-----------
add the first test: history grid
Commit: 946d64b8f7dc08b92ebb03f34a91cab8aa7ecfbb
https://github.com/galaxyproject/galaxy/commit/946d64b8f7dc08b92ebb03f34a91…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-23 (Wed, 23 Aug 2017)
Changed paths:
A lib/galaxy/tools/deps/resolvers/lmod.py
Log Message:
-----------
LMOD Dependency resolver - Initial commit (lib lmod.py)
Initial commit of a prototype dependency resolver based on the LMOD environment modules system.
Commit: 4d143479d5998531cc4803af11579e12d160c87b
https://github.com/galaxyproject/galaxy/commit/4d143479d5998531cc4803af1157…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-23 (Wed, 23 Aug 2017)
Changed paths:
M config/dependency_resolvers_conf.xml.sample
Log Message:
-----------
Update of the dependency_resolvers_conf.xml.sample file
Addition of the LMOD Dependency resolver to the appropriate sample configuration file (dependency_resolvers_conf.xml.sample). Comment lines have also been added to describe the possible attributes of the resolver as well as their default values.
Commit: e84284c477182b3c03e785b79f93dd88d63e6ebd
https://github.com/galaxyproject/galaxy/commit/e84284c477182b3c03e785b79f93…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-23 (Wed, 23 Aug 2017)
Changed paths:
M config/dependency_resolvers_conf.xml.sample
A config/lmod_modules_mapping.yml.sample
M lib/galaxy/tools/deps/resolvers/lmod.py
Log Message:
-----------
LMOD Dependency resolver - Default mapping file
If a lmod_modules_mapping.yml file exists in the config folder then it will be taken into consideration automatically to map Galaxy requirements to LMOD modules.
Commit: a6632f31338911176052db99257aa8f825286008
https://github.com/galaxyproject/galaxy/commit/a6632f31338911176052db99257a…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-23 (Wed, 23 Aug 2017)
Changed paths:
M client/galaxy/style/less/dataset.less
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/style/blue/base.css
Log Message:
-----------
replace exclamation with a clock icon
Commit: 27bd71332a66195f66536825d6da05ed505330f1
https://github.com/galaxyproject/galaxy/commit/27bd71332a66195f66536825d6da…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-23 (Wed, 23 Aug 2017)
Changed paths:
M client/galaxy/style/less/dataset.less
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/style/blue/base.css
Log Message:
-----------
Merge pull request #4485 from martenson/remove-exclamation
replace exclamation with a clock icon
Commit: 89c811b790d7ef3508f361195ca4333903e5b955
https://github.com/galaxyproject/galaxy/commit/89c811b790d7ef3508f361195ca4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-23 (Wed, 23 Aug 2017)
Changed paths:
M templates/webapps/galaxy/dataset/copy_view.mako
Log Message:
-----------
Move 'Copy History Items' to the bottom of the second column in the old copy histories page.
Commit: b664f26aa0d7a3ad151f236ba569efecb09a5526
https://github.com/galaxyproject/galaxy/commit/b664f26aa0d7a3ad151f236ba569…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-08-23 (Wed, 23 Aug 2017)
Changed paths:
M test/selenium_tests/test_published_history_grid.py
Log Message:
-----------
add standard search test
Commit: a83438159c2aa8d92b9c9f53ec64f9188ec94a8f
https://github.com/galaxyproject/galaxy/commit/a83438159c2aa8d92b9c9f53ec64…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-08-23 (Wed, 23 Aug 2017)
Changed paths:
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
Merge pull request #4458 from xgaia/interactive_environment
don't uppercase envoverride
Commit: 0e1cbc09f8a604c1b45127faf30170ba1b67bb1b
https://github.com/galaxyproject/galaxy/commit/0e1cbc09f8a604c1b45127faf301…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-08-23 (Wed, 23 Aug 2017)
Changed paths:
M test/selenium_tests/test_published_history_grid.py
Log Message:
-----------
add 'sort by name/owner' tests
Commit: fed3206a87e4ae4ede380c90cfa3409220847cf7
https://github.com/galaxyproject/galaxy/commit/fed3206a87e4ae4ede380c90cfa3…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/lmod.py
Log Message:
-----------
Fix errors reported by the initial Travis tests
Fix incorrect numbers of blank lines.
Fix deprecated syntax.
Commit: 09887529765ba88adb70e739d1b9d8896cb86229
https://github.com/galaxyproject/galaxy/commit/09887529765ba88adb70e739d1b9…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/lmod.py
Log Message:
-----------
Syntax fix in the shell_commands method
The built command now reflect more directly the command that is really executed by the the LMOD "module" bash function when a user execute "module load package_name/package_version".
Commit: 574e697a4d66a53f298f37f4987d31db96ff8e14
https://github.com/galaxyproject/galaxy/commit/574e697a4d66a53f298f37f4987d…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M config/dependency_resolvers_conf.xml.sample
Log Message:
-----------
Dependency_resolvers_conf.xml - More explanations
Some more explanations about the versionless mode have been added.
Commit: db5efdaa7cbc197eaf6a777d4d390de24b212e88
https://github.com/galaxyproject/galaxy/commit/db5efdaa7cbc197eaf6a777d4d39…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/lmod.py
Log Message:
-----------
Clearer comment lines in the has_module method
A comment of the has_module method of the AvailModuleChecker class has been modified to be clearer and more explicit.
Commit: eda36ffb99a1abec8f878c0b7ae194938781c8d6
https://github.com/galaxyproject/galaxy/commit/eda36ffb99a1abec8f878c0b7ae1…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M test/unit/tools/test_tool_deps.py
Log Message:
-----------
LMOD Dependency resolver - Unit tests added
The unit/tools/tests_tool_deps.py script has been updated to includ unit tests for the LMOD dependency resolver.
Commit: bbec357bbd744b9e0d760e8d0903adfa43d1b7e2
https://github.com/galaxyproject/galaxy/commit/bbec357bbd744b9e0d760e8d0903…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M test/unit/tools/test_tool_deps.py
Log Message:
-----------
Fix the import order error raised by Travis
The order of the import statements in the test_tool_deps script was incorrect (as stated by travis). That should no longer be the case.
Commit: 9822f5f2a91fae7e3420a06c58f2621a2cf084ac
https://github.com/galaxyproject/galaxy/commit/9822f5f2a91fae7e3420a06c58f2…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M test/unit/tools/test_tool_deps.py
Log Message:
-----------
Fix attempt for the modulepath issue in unit tests
On a computer where LMOD is not installed, the MODULEPATH variable is not defined and the modulepath attributes of the LMOD dependency resolver must be used.
Commit: 001d94ae4ea0af1ed16c809a6e8e26c356549396
https://github.com/galaxyproject/galaxy/commit/001d94ae4ea0af1ed16c809a6e8e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M lib/galaxy/tools/verify/__init__.py
Log Message:
-----------
Merge pull request #4479 from nsoranzo/use_pysam_in_verify
Use pysam instead of samtools binary
Commit: 5d04c593b637146c69eed1b6909a74c67ab4de1a
https://github.com/galaxyproject/galaxy/commit/5d04c593b637146c69eed1b6909a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Removes unused comma from subworkflow populator
Commit: 5ae1446970ec43e578ab400f529bd753cd81d052
https://github.com/galaxyproject/galaxy/commit/5ae1446970ec43e578ab400f529b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Merge pull request #4492 from guerler/fix_subworkflow_comma
Remove unused comma from subworkflow populator
Commit: b80ee79b4302bd208ce5aa1fb86fb58e2b89a0c7
https://github.com/galaxyproject/galaxy/commit/b80ee79b4302bd208ce5aa1fb86f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
R lib/galaxy/webapps/galaxy/controllers/mobile.py
R templates/webapps/galaxy/mobile/dataset/detail.mako
R templates/webapps/galaxy/mobile/dataset/peek.mako
R templates/webapps/galaxy/mobile/form.mako
R templates/webapps/galaxy/mobile/history/detail.mako
R templates/webapps/galaxy/mobile/history/list.mako
R templates/webapps/galaxy/mobile/index.mako
R templates/webapps/galaxy/mobile/manage_library.mako
R templates/webapps/galaxy/mobile/settings.mako
Log Message:
-----------
Remove /mobile and associated templates. It has been deactivated for almost three years now.
Commit: e542c47872881964c9c5fd0220904caee16f868a
https://github.com/galaxyproject/galaxy/commit/e542c47872881964c9c5fd022090…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
R client/galaxy/style/less/iphone.less
M client/grunt-tasks/style.js
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
R static/style/blue/iphone.css
Log Message:
-----------
Remove ancient 'iphone' styling that is unused (and missing assets)
Commit: 4c14de6955a6c2fef489fd9603aec4e88df65539
https://github.com/galaxyproject/galaxy/commit/4c14de6955a6c2fef489fd9603ae…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M client/bower.json
R client/galaxy/scripts/libs/jquery/jqtouch.js
M client/grunt-tasks/install-libs.js
R static/jqtouch/img/backButton.png
R static/jqtouch/img/back_button.png
R static/jqtouch/img/back_button_clicked.png
R static/jqtouch/img/bg_row.gif
R static/jqtouch/img/bg_row_select.gif
R static/jqtouch/img/blueButton.png
R static/jqtouch/img/button.png
R static/jqtouch/img/button_clicked.png
R static/jqtouch/img/cancel.png
R static/jqtouch/img/chevron.png
R static/jqtouch/img/chevron_select.png
R static/jqtouch/img/grayButton.png
R static/jqtouch/img/header.gif
R static/jqtouch/img/listGroup.png
R static/jqtouch/img/loading.gif
R static/jqtouch/img/pinstripes.png
R static/jqtouch/img/selection.png
R static/jqtouch/img/thumb.png
R static/jqtouch/img/toggle.png
R static/jqtouch/img/toggleOn.png
R static/jqtouch/img/toolButton.png
R static/jqtouch/img/toolbar.gif
R static/jqtouch/img/toolbar.png
R static/jqtouch/img/whiteButton.png
R static/jqtouch/jqtouch.css
Log Message:
-----------
strip jqtouch
Commit: 1426225a78d0adc7a024d33f314bdfa613eabe5d
https://github.com/galaxyproject/galaxy/commit/1426225a78d0adc7a024d33f314b…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M client/bower.json
R client/galaxy/scripts/libs/jquery/jqtouch.js
R client/galaxy/style/less/iphone.less
M client/grunt-tasks/install-libs.js
M client/grunt-tasks/style.js
R lib/galaxy/webapps/galaxy/controllers/mobile.py
R static/jqtouch/img/backButton.png
R static/jqtouch/img/back_button.png
R static/jqtouch/img/back_button_clicked.png
R static/jqtouch/img/bg_row.gif
R static/jqtouch/img/bg_row_select.gif
R static/jqtouch/img/blueButton.png
R static/jqtouch/img/button.png
R static/jqtouch/img/button_clicked.png
R static/jqtouch/img/cancel.png
R static/jqtouch/img/chevron.png
R static/jqtouch/img/chevron_select.png
R static/jqtouch/img/grayButton.png
R static/jqtouch/img/header.gif
R static/jqtouch/img/listGroup.png
R static/jqtouch/img/loading.gif
R static/jqtouch/img/pinstripes.png
R static/jqtouch/img/selection.png
R static/jqtouch/img/thumb.png
R static/jqtouch/img/toggle.png
R static/jqtouch/img/toggleOn.png
R static/jqtouch/img/toolButton.png
R static/jqtouch/img/toolbar.gif
R static/jqtouch/img/toolbar.png
R static/jqtouch/img/whiteButton.png
R static/jqtouch/jqtouch.css
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
R static/style/blue/iphone.css
R templates/webapps/galaxy/mobile/dataset/detail.mako
R templates/webapps/galaxy/mobile/dataset/peek.mako
R templates/webapps/galaxy/mobile/form.mako
R templates/webapps/galaxy/mobile/history/detail.mako
R templates/webapps/galaxy/mobile/history/list.mako
R templates/webapps/galaxy/mobile/index.mako
R templates/webapps/galaxy/mobile/manage_library.mako
R templates/webapps/galaxy/mobile/settings.mako
Log Message:
-----------
Merge pull request #4494 from dannon/no_mobile
Remove /mobile and associated templates
Commit: c89233c7cbbe263d3670fd5d4066a83f537ee173
https://github.com/galaxyproject/galaxy/commit/c89233c7cbbe263d3670fd5d4066…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py
R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml
R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py
R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml
A lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml
A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml
M lib/galaxy/datatypes/set_metadata_tool.xml
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/1.bcf
A lib/galaxy/datatypes/test/1.bcf_uncompressed
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Merge pull request #4477 from nsoranzo/vcf_bcf_fixes
Fixes for VCF/BCF datatypes
Commit: 0e467b73bcb1c6493bda6997bb133c19b72a275d
https://github.com/galaxyproject/galaxy/commit/0e467b73bcb1c6493bda6997bb13…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M lib/galaxy/webapps/reports/config.py
Log Message:
-----------
Fixes for reports sentry dsn (lint and missing import).
Commit: f09b5c5b9de02d66fbca836bbe5a19a8f1e66dfb
https://github.com/galaxyproject/galaxy/commit/f09b5c5b9de02d66fbca836bbe5a…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-08-25 (Fri, 25 Aug 2017)
Changed paths:
M lib/galaxy/webapps/reports/config.py
Log Message:
-----------
Merge pull request #19 from dannon/reports-sentry-dsn
Fixes for reports sentry dsn (lint and missing import).
Commit: df0507e494208018ff19c71d17afb9f5c4b3b6ce
https://github.com/galaxyproject/galaxy/commit/df0507e494208018ff19c71d17af…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-25 (Fri, 25 Aug 2017)
Changed paths:
M lib/galaxy/webapps/reports/config.py
Log Message:
-----------
Merge pull request #4471 from erasche/reports-sentry-dsn
needed for sentry functionality in reports webapp
Commit: a904df604ef6962628916635d42068ece1368d01
https://github.com/galaxyproject/galaxy/commit/a904df604ef6962628916635d420…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-25 (Fri, 25 Aug 2017)
Changed paths:
M lib/tool_shed/galaxy_install/installed_repository_manager.py
Log Message:
-----------
Only parse once
Commit: cbe6970a4cf5c5a3b7bb55c97d7190fef4019388
https://github.com/galaxyproject/galaxy/commit/cbe6970a4cf5c5a3b7bb55c97d71…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-25 (Fri, 25 Aug 2017)
Changed paths:
M lib/tool_shed/galaxy_install/installed_repository_manager.py
Log Message:
-----------
per @nsoranzo, only log error message when it is there
Commit: 2ff4292cd6171fc128e91ddbb66f5124368c25ee
https://github.com/galaxyproject/galaxy/commit/2ff4292cd6171fc128e91ddbb66f…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-25 (Fri, 25 Aug 2017)
Changed paths:
M client/galaxy/style/less/base.less
M client/galaxy/style/less/galaxy_bootstrap/variables.less
Log Message:
-----------
move to somewhere it can be overridden
Commit: 68f9c6905ef56ce9b82e2889a48b4185370e83b4
https://github.com/galaxyproject/galaxy/commit/68f9c6905ef56ce9b82e2889a48b…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-25 (Fri, 25 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/style/less/base.less
Log Message:
-----------
Large click target for tools
Commit: cd6cc88ac19b5d7c218e31fb14c74382d2439a1f
https://github.com/galaxyproject/galaxy/commit/cd6cc88ac19b5d7c218e31fb14c7…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-25 (Fri, 25 Aug 2017)
Changed paths:
M client/galaxy/style/less/galaxy_variables.less
A client/galaxy/style/less/theme/plain.less
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tools.js
Log Message:
-----------
Plain theme
Commit: 0010f6c0d8ab7ad128ba4bfefd406dccc9bc5e9f
https://github.com/galaxyproject/galaxy/commit/0010f6c0d8ab7ad128ba4bfefd40…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-08-25 (Fri, 25 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Merge pull request #4466 from bgruening/mz5
add mz5 datatype
Commit: 97ee0f1fcdd7d059d5c37e1bb25a8c3389559698
https://github.com/galaxyproject/galaxy/commit/97ee0f1fcdd7d059d5c37e1bb25a…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-25 (Fri, 25 Aug 2017)
Changed paths:
M static/style/blue/base.css
Log Message:
-----------
rebuild style
Commit: 426aa310fd21f320767b575dcd209ae63ad88b24
https://github.com/galaxyproject/galaxy/commit/426aa310fd21f320767b575dcd20…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-08-25 (Fri, 25 Aug 2017)
Changed paths:
M templates/webapps/galaxy/dataset/copy_view.mako
Log Message:
-----------
Merge pull request #4486 from dannon/copy_history_minor_improvement
Minor copy datasets dialog improvement.
Commit: 72195e14baa5e5f3131f2364858e71c4e4fb960c
https://github.com/galaxyproject/galaxy/commit/72195e14baa5e5f3131f2364858e…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-08-25 (Fri, 25 Aug 2017)
Changed paths:
M test/selenium_tests/test_published_history_grid.py
Log Message:
-----------
[WIP]: add advanced search tests
Commit: 2403916c7b6a29810e74cb3485d3634ef904dde6
https://github.com/galaxyproject/galaxy/commit/2403916c7b6a29810e74cb3485d3…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-08-26 (Sat, 26 Aug 2017)
Changed paths:
M test/selenium_tests/test_published_history_grid.py
Log Message:
-----------
test clicking tags
Commit: 2f547b09737d6711e44de7d9c7600384aa97038e
https://github.com/galaxyproject/galaxy/commit/2f547b09737d6711e44de7d9c760…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-08-26 (Sat, 26 Aug 2017)
Changed paths:
M test/selenium_tests/test_published_history_grid.py
Log Message:
-----------
small improvements
Commit: da1518db48265617cb2e2a00f9b738058c648f4b
https://github.com/galaxyproject/galaxy/commit/da1518db48265617cb2e2a00f9b7…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-08-26 (Sat, 26 Aug 2017)
Changed paths:
M test/selenium_tests/test_published_history_grid.py
Log Message:
-----------
set annotations
Commit: 2dda34a00240a9af990a23c14cd73abb87db4268
https://github.com/galaxyproject/galaxy/commit/2dda34a00240a9af990a23c14cd7…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-08-26 (Sat, 26 Aug 2017)
Changed paths:
A test/selenium_tests/test_published_histories_grid.py
R test/selenium_tests/test_published_history_grid.py
Log Message:
-----------
rename the file
Commit: a0bd78034defb11adf2140f7c6dd90e63bc7da43
https://github.com/galaxyproject/galaxy/commit/a0bd78034defb11adf2140f7c6dd…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-27 (Sun, 27 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Optimize loading of StoredWorkflow attributes
WorkflowsManager.get_stored_workflow is used when exporting or editing
workflows. In these cases we iterate over the related workflow objects
steps as well as the related tags and annotation objects. Each iteration
will emit a new SQL statement. Joinedloading these relations here speeds
up the workflow run form and the editor. With sqlite as backend this
speeds up exporting a workflow for the workflow editor by about 5X.
Commit: 62204de0aeb4a833e43e5a1f81657293853ffb03
https://github.com/galaxyproject/galaxy/commit/62204de0aeb4a833e43e5a1f8165…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-27 (Sun, 27 Aug 2017)
Changed paths:
M lib/galaxy/model/item_attrs.py
Log Message:
-----------
Use pre-existing annotations object if possible
This avoids additional requests to the database.
Commit: db04f295d34e8ca03b151f462e7ffd1d613a1321
https://github.com/galaxyproject/galaxy/commit/db04f295d34e8ca03b151f462e7f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-27 (Sun, 27 Aug 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Do not provide a history in workflow_building_mode
Commit: cb1392fd2d707587859bcbbb3e1744fb472ebf22
https://github.com/galaxyproject/galaxy/commit/cb1392fd2d707587859bcbbb3e17…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-27 (Sun, 27 Aug 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
Log Message:
-----------
Use WorkflowManager to get StoredWorkflow in workflow web controller
Commit: 83bb7b108e90086ae0f421d63107c3870dea5d73
https://github.com/galaxyproject/galaxy/commit/83bb7b108e90086ae0f421d63107…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-27 (Sun, 27 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Avoid ToolShedRepository attributes where possible
Commit: d5eee194252270ebf4be008c6cf0492d5c6c3340
https://github.com/galaxyproject/galaxy/commit/d5eee194252270ebf4be008c6cf0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-27 (Sun, 27 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Use workflow_building_modes.ENABLED instead of True
Commit: e4f4dc91eebe7d5e4fbf8667bff52079498d88ea
https://github.com/galaxyproject/galaxy/commit/e4f4dc91eebe7d5e4fbf8667bff5…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-27 (Sun, 27 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
Log Message:
-----------
Cache edam_data and edam_formats
Commit: 17246225d962f4d1494b4b718440f42631fd6210
https://github.com/galaxyproject/galaxy/commit/17246225d962f4d1494b4b718440…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-27 (Sun, 27 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Use joinedload for latest_workflow.steps when building workflow editor config
Commit: 1a1232e11dd31b96284d2842292d13f9b67ee22e
https://github.com/galaxyproject/galaxy/commit/1a1232e11dd31b96284d2842292d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-27 (Sun, 27 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Use get_item_annotation_str instead of get_item_annotation_obj
Commit: e6155367e61d8b4e66883992db6af88444f346a0
https://github.com/galaxyproject/galaxy/commit/e6155367e61d8b4e66883992db6a…
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: 773029bd364037943a810506a79cebca85f2a260
https://github.com/galaxyproject/galaxy/commit/773029bd364037943a810506a79c…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M test/selenium_tests/test_published_histories_grid.py
Log Message:
-----------
fix flake8 issues
Commit: e130b55b04c8bc7c30b85ac7e2688890b890c71c
https://github.com/galaxyproject/galaxy/commit/e130b55b04c8bc7c30b85ac7e268…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M lib/tool_shed/util/xml_util.py
Log Message:
-----------
log error if does not exist
Commit: 0159162c9e7b3463b2f667fec820d3ae83bfd3dc
https://github.com/galaxyproject/galaxy/commit/0159162c9e7b3463b2f667fec820…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M lib/tool_shed/galaxy_install/installed_repository_manager.py
Log Message:
-----------
Merge branch 'parse-once' of github.com:erasche/galaxy into parse-once
Commit: 4b9b14979a7137f4aca90e1e1e7869e88ae1bb6e
https://github.com/galaxyproject/galaxy/commit/4b9b14979a7137f4aca90e1e1e78…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/galaxy_bootstrap/variables.less
M client/galaxy/style/less/galaxy_variables.less
A client/galaxy/style/less/theme/plain.less
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tools.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #4470 from erasche/retheme
Nicer tool click targets for base + "plain" theme
Commit: f159df391ea4eeaac01779426cfad00e38b5f907
https://github.com/galaxyproject/galaxy/commit/f159df391ea4eeaac01779426cfa…
Author: Martin Cech <marten(a)bx.psu.edu>
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:
-----------
Merge pull request #4501 from erasche/2017-08-security
2017-08 Security Patch
Commit: 9337c9fdc118f7c4883a6c7b4cada483b09461c7
https://github.com/galaxyproject/galaxy/commit/9337c9fdc118f7c4883a6c7b4cad…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M lib/galaxy/datatypes/data.py
M lib/galaxy/workflow/modules.py
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 branch 'release_17.05' into merge-release1705
Commit: 8aefa9d49535b7592bd7398541f9cbeaba9146ce
https://github.com/galaxyproject/galaxy/commit/8aefa9d49535b7592bd7398541f9…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/ui/ui-select-content.js
Log Message:
-----------
repack client
Commit: 15b1a41df83940961d8f516e4023cd410b38964b
https://github.com/galaxyproject/galaxy/commit/15b1a41df83940961d8f516e4023…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M lib/galaxy/datatypes/data.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/ui/ui-select-content.js
Log Message:
-----------
Merge pull request #4506 from martenson/merge-release1705
Merge release_17.05 to dev
Commit: 6613df5b7a826e8147b2a46c8e87391b230f4315
https://github.com/galaxyproject/galaxy/commit/6613df5b7a826e8147b2a46c8e87…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M lib/galaxy/managers/library_datasets.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
add methods for vlidating and updating ld's attributes
Commit: a394faf3be18eceae72ca68dae67596123c89ff6
https://github.com/galaxyproject/galaxy/commit/a394faf3be18eceae72ca68dae67…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/library_datasets.py
Log Message:
-----------
fix refactoring error
Commit: c060bbb5fa54c7062a8daf8df7192d793e354e6e
https://github.com/galaxyproject/galaxy/commit/c060bbb5fa54c7062a8daf8df719…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M lib/galaxy/managers/library_datasets.py
Log Message:
-----------
fix wrongly called exceptions
Commit: 2ede34659b688089ed549ea24416f7610be0a698
https://github.com/galaxyproject/galaxy/commit/2ede34659b688089ed549ea24416…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
Fix bad merge of security patch from 17.05 into dev.
Commit: d56fcf6777d93c83db5ebbc4af7968cb9889e524
https://github.com/galaxyproject/galaxy/commit/d56fcf6777d93c83db5ebbc4af79…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
Merge pull request #4508 from jmchilton/dev_merge_fix
Fix bad merge of security patch from 17.05 into dev.
Commit: 5ab28634cabc1df2aa14e9db303247e41b9ea311
https://github.com/galaxyproject/galaxy/commit/5ab28634cabc1df2aa14e9db3032…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-29 (Tue, 29 Aug 2017)
Changed paths:
M test/api/test_jobs.py
Log Message:
-----------
Prevent transient job state test failures from failing the build.
A precondition to the real meat of the test is failing to be met sometimes in production - this failure is indicating a problem with the test and not with Galaxy. I previously tried to address this with https://github.com/galaxyproject/galaxy/pull/3988 but that didn't work. Now if the trainsient ok occurs the test will be skipped. Most of the time it won't skip and the rest of the test will execute and ensure there aren't regressions in behaviors related to cleaning up datasets after job completion. I'm placing the skips a couple different places so hopefully we can get a stack trace at somepoint - knowing where the code is when the job state is changing from running to ok will help puzzle out what is handing for the two minutes the job is running in the test framework.
Commit: 6deff3f9e518a1c7b51cea584ced1e4755ba9254
https://github.com/galaxyproject/galaxy/commit/6deff3f9e518a1c7b51cea584ced…
Author: Frederic Sapet <frederic.sapet(a)biogemma.com>
Date: 2017-08-29 (Tue, 29 Aug 2017)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
Log Message:
-----------
import of history works even if we use symlink in database directory
Commit: 82687795413520b5a23e86b17bc3198df3803e39
https://github.com/galaxyproject/galaxy/commit/82687795413520b5a23e86b17bc3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-29 (Tue, 29 Aug 2017)
Changed paths:
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
Log Message:
-----------
Allow paramiko runner to recover from ssh timeout
Commit: d76e304d9bec3d09867c2c264af3f73eabcd17dc
https://github.com/galaxyproject/galaxy/commit/d76e304d9bec3d09867c2c264af3…
Author: Frederic Sapet <frederic.sapet(a)biogemma.com>
Date: 2017-08-29 (Tue, 29 Aug 2017)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
Log Message:
-----------
remove the redundant call to os.path.abspath(), which is called internally by os.path.realpath()
Commit: a464fe9db6ab993e282feb1ba9ec4eea78ada376
https://github.com/galaxyproject/galaxy/commit/a464fe9db6ab993e282feb1ba9ec…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-29 (Tue, 29 Aug 2017)
Changed paths:
M test/selenium_tests/test_published_histories_grid.py
Log Message:
-----------
Rework published histories selenium test a bit.
- Wait for elements to be clickable before clicking them.
- Allow individual tests to be run on their own and out of order.
- Use randomly generated emails - the tests still can't really be applied to an external Galaxy test server but this gets us closer.
Commit: 2faa56eefe7a8b029ed62b9b4402894c2a26248f
https://github.com/galaxyproject/galaxy/commit/2faa56eefe7a8b029ed62b9b4402…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-29 (Tue, 29 Aug 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Rework if statement to be more explicit
Commit: b096155637e922ab87bab9b86c606e08ef82fea1
https://github.com/galaxyproject/galaxy/commit/b096155637e922ab87bab9b86c60…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-29 (Tue, 29 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M lib/galaxy/managers/library_datasets.py
M static/maps/mvc/library/library-dataset-view.js.map
M static/scripts/mvc/library/library-dataset-view.js
Log Message:
-----------
add functionality to the UI for updating library dataset
Commit: b75f793ea4c58786747da3a9571ba3bd938cd181
https://github.com/galaxyproject/galaxy/commit/b75f793ea4c58786747da3a9571b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-29 (Tue, 29 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M lib/galaxy/tools/__init__.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Load tools with collection type source attributes into the workflow editor.
Should allow using filter failed and merge collection tools within workflows.
Commit: ba8a7f0e3a540c99b3d8e7be3ea67008e2e76ff2
https://github.com/galaxyproject/galaxy/commit/ba8a7f0e3a540c99b3d8e7be3ea6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-29 (Tue, 29 Aug 2017)
Changed paths:
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/maps/mvc/workflow/workflow-view-terminals.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/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view-terminals.js
Log Message:
-----------
Pack client.
Commit: 2d9ae75cae83969b3a708c0921ca33841ad08ef5
https://github.com/galaxyproject/galaxy/commit/2d9ae75cae83969b3a708c0921ca…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-29 (Tue, 29 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
Fix another bad merge issue?
Commit: 80c9763757a626355a70e360fd9aedffd8f8dac3
https://github.com/galaxyproject/galaxy/commit/80c9763757a626355a70e360fd9a…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
add biom2 datatype
Commit: 86902068268903292d1caf003a2274e0a5438f7d
https://github.com/galaxyproject/galaxy/commit/86902068268903292d1caf003a22…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom
Log Message:
-----------
add test biom2 file
Commit: b9fb935be594db1224c524bfd03c22b8b90f4bea
https://github.com/galaxyproject/galaxy/commit/b9fb935be594db1224c524bfd03c…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/text.py
Log Message:
-----------
add edam format to biom1 datatype
Commit: 8314867ecb57b58caceb4843c021f300dc39472e
https://github.com/galaxyproject/galaxy/commit/8314867ecb57b58caceb4843c021…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
fix sniffer order
Commit: 6feb3e22d19c2cb162adc0b5d80655540305a805
https://github.com/galaxyproject/galaxy/commit/6feb3e22d19c2cb162adc0b5d806…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
order matters
Commit: 07ef9b4f4b2a38259ae55f382ebee36e43743a9d
https://github.com/galaxyproject/galaxy/commit/07ef9b4f4b2a38259ae55f382ebe…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
use h5py to parse hdf5 header
Commit: ca1ebf97c02e7261fc36352206834de5ab74a0fd
https://github.com/galaxyproject/galaxy/commit/ca1ebf97c02e7261fc3635220683…
Author: Saskia Hiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
set metadata
Commit: ac61072452cd345d45e87d3548e6564858589029
https://github.com/galaxyproject/galaxy/commit/ac61072452cd345d45e87d3548e6…
Author: Saskia Hiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
add h5py requirement
for extracting metadata from biom2/hdf5 datatypes
Commit: 92e25158410238bfbc80a931fedb80a55b570e2d
https://github.com/galaxyproject/galaxy/commit/92e25158410238bfbc80a931fedb…
Author: Saskia Hiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
fix import order
Commit: 4119caf9b7fbd1fc9c374403e7f7836b8d9397c1
https://github.com/galaxyproject/galaxy/commit/4119caf9b7fbd1fc9c374403e7f7…
Author: Saskia Hiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
remove unused variable
Commit: 062c88a3cce66df350dc0da7aed14542fe6ad65b
https://github.com/galaxyproject/galaxy/commit/062c88a3cce66df350dc0da7aed1…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
A lib/galaxy/datatypes/converters/biom1_to_biom2.xml
A lib/galaxy/datatypes/converters/biom2_to_biom1.xml
Log Message:
-----------
add converters
Commit: a3b316031c5aa1565d7255eab5aa92ff4a749f4d
https://github.com/galaxyproject/galaxy/commit/a3b316031c5aa1565d7255eab5aa…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
simplify
Commit: 995f2cee4a2914c157420467829ff647a2e8c7d6
https://github.com/galaxyproject/galaxy/commit/995f2cee4a2914c157420467829f…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/sniff.py
Log Message:
-----------
add guess_ext test
Commit: 21eac0d445cbf8523cd48402d0992dc7ff1720c6
https://github.com/galaxyproject/galaxy/commit/21eac0d445cbf8523cd48402d099…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
Merge pull request #4515 from jmchilton/another_merge_issue
Fix subdirectory listing for extra files
Commit: f3b8a121b7d9d5535381aa8cae7887bd978f9678
https://github.com/galaxyproject/galaxy/commit/f3b8a121b7d9d5535381aa8cae78…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
A test/selenium_tests/test_published_histories_grid.py
Log Message:
-----------
Merge pull request #4502 from anatskiy/published_history_test
Published History Grid tests
Commit: 95aacc010e730ce24e2e10557bac8395c538d2af
https://github.com/galaxyproject/galaxy/commit/95aacc010e730ce24e2e10557bac…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
add metadata to peek
Commit: 907e931fa8f62856fa846d2b9a9bc6392f26952a
https://github.com/galaxyproject/galaxy/commit/907e931fa8f62856fa846d2b9a9b…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
don't cast to string
Commit: e8de89afd56b5e125e1e879855d7168a7d2c79b5
https://github.com/galaxyproject/galaxy/commit/e8de89afd56b5e125e1e879855d7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Display d3 hierarchy files in uploader
Commit: 3ac0c7ced7224e63bc55cde9fad3679b390d9628
https://github.com/galaxyproject/galaxy/commit/3ac0c7ced7224e63bc55cde9fad3…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-30 (Wed, 30 Aug 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:
-----------
improve UX of importing from history to folder
fixes #4151
Commit: 48bb43b8b04b1bdcfb636277c9a595c6a8cbbbb6
https://github.com/galaxyproject/galaxy/commit/48bb43b8b04b1bdcfb636277c9a5…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/managers/library_datasets.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
Log Message:
-----------
fix travis issues - whitespace, imports
Commit: 43fd81df59c1862c745813e3b340e93976ef1e2b
https://github.com/galaxyproject/galaxy/commit/43fd81df59c1862c745813e3b340…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M test/galaxy_selenium/driver_factory.py
M test/selenium_tests/framework.py
Log Message:
-----------
More logging for selenium tests.
Dumb the browser log and the driver log out as JSON to the test error directory for that test.
Commit: f35fed29356d1f55af803f2f24cd2e54634cc8a6
https://github.com/galaxyproject/galaxy/commit/f35fed29356d1f55af803f2f24cd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M test/galaxy_selenium/sizzle.py
A test/selenium_tests/test_sizzle_loading.py
Log Message:
-----------
Improve setting up Sizzle for Selenium tests.
Something releated to AMD broke our way of injecting Sizzle into Galaxy for Selenium tests. This is a much better way that seems to work - just use jQuery ($) as Sizzle if it is available. Avoids an external dependency and another page fetch per test as well as fixing the problem.
Add a test case that just tests the sizzle stuff works on its own. It will be a clear indiciation what is broken if there are related regressions in the future.
Commit: f79eba25b532e42e38fec5f6df25229ea6085a03
https://github.com/galaxyproject/galaxy/commit/f79eba25b532e42e38fec5f6df25…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/managers/library_datasets.py
M test/api/test_libraries.py
Log Message:
-----------
fix small regressions and add tests for the new API
Commit: 2f9cd0ee491cc99af4a64416e21ce95e6e7dbb33
https://github.com/galaxyproject/galaxy/commit/2f9cd0ee491cc99af4a64416e21c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M test/api/test_jobs.py
Log Message:
-----------
Merge pull request #4510 from jmchilton/job_test_fix
Prevent transient job state test failures from failing the build.
Commit: bd13cadbddbbd991460095ad94d9c974cc2a40c9
https://github.com/galaxyproject/galaxy/commit/bd13cadbddbbd991460095ad94d9…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Merge pull request #4522 from guerler/d3_hierarchy_in_uploader
Display d3 hierarchy datatype in upload interface
Commit: 4071fb65c3a8ee83dad2d45fa33c76a787ed3842
https://github.com/galaxyproject/galaxy/commit/4071fb65c3a8ee83dad2d45fa33c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-30 (Wed, 30 Aug 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:
-----------
allow linking, posix and spaces conversions
closes #2977
Commit: 65185f5e435a733c0f6b4639ac91f607b12eb844
https://github.com/galaxyproject/galaxy/commit/65185f5e435a733c0f6b4639ac91…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/library_datasets.py
Log Message:
-----------
lint imports
Commit: 5142509f131591b978ecadebbaefc1bb6f608f47
https://github.com/galaxyproject/galaxy/commit/5142509f131591b978ecadebbaef…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Make a couple workflow invocation tests more robust.
Less random sleeping, wait for actual invocation. I think this is likely the cause this transient failure (https://jenkins.galaxyproject.org/job/docker-api/8215/testReport/junit/api.…) picking up the input as the last dataset in the history instead of the output - I bet the workflow just hadn't been invoked yet.
Commit: a85d65c6a2ce3fd0a166e130f8a89dc198c3e0c7
https://github.com/galaxyproject/galaxy/commit/a85d65c6a2ce3fd0a166e130f8a8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M test/selenium_tests/test_workflow_run.py
Log Message:
-----------
Another fix for Selenium worklow tests.
This time for the workflow upgrade message test, mirrors the fix in #4524 - the content we are searching for in on this page is no longer in the iframe.
Commit: 01d16358efa5a71f7030c48c302129cca515e6c6
https://github.com/galaxyproject/galaxy/commit/01d16358efa5a71f7030c48c3021…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M static/maps/mvc/workflow/workflow-terminals.js.map
Log Message:
-----------
Adjust JS styling for workflow-terminal.js.
Commit: 326477d957bda9c32f63497b5fc911e8c2a9731d
https://github.com/galaxyproject/galaxy/commit/326477d957bda9c32f63497b5fc9…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M config/error_report.yml.sample
M doc/source/admin/special_topics/bug_reports.rst
A lib/galaxy/tools/error_reports/plugins/influxdb.py
Log Message:
-----------
implement influxdb error reporter
Commit: f67fa22dd9bd05d72df859065a3e126af0161d62
https://github.com/galaxyproject/galaxy/commit/f67fa22dd9bd05d72df859065a3e…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/influxdb.py
M lib/galaxy/tools/error_reports/plugins/json.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
also add destination id everywhere
Commit: 823eb1d4ec84f17f92e4bbf2a12194b2bc0ea9d0
https://github.com/galaxyproject/galaxy/commit/823eb1d4ec84f17f92e4bbf2a121…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #4530 from jmchilton/api_test_fixes
More robust workflow invocation testing.
Commit: d09ced249d729b5c0a2098a9d5e81472c91f62b6
https://github.com/galaxyproject/galaxy/commit/d09ced249d729b5c0a2098a9d5e8…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M test/galaxy_selenium/driver_factory.py
M test/galaxy_selenium/sizzle.py
M test/selenium_tests/framework.py
A test/selenium_tests/test_sizzle_loading.py
Log Message:
-----------
Merge pull request #4523 from jmchilton/selenium_fixes_15
Selenium test fixes and improvements.
Commit: 49f2438622075f3e9cbe9097ad31b177c97f532a
https://github.com/galaxyproject/galaxy/commit/49f2438622075f3e9cbe9097ad31…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M lib/galaxy/tools/__init__.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/maps/mvc/workflow/workflow-view-terminals.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/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view-terminals.js
Log Message:
-----------
Merge pull request #4514 from jmchilton/collection_operations
Load tools with collection type source attributes into the workflow editor
Commit: cd1c38c527e54b8f7b0817eda5ac9aa0c68dc349
https://github.com/galaxyproject/galaxy/commit/cd1c38c527e54b8f7b0817eda5ac…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M test/base/populators.py
Log Message:
-----------
Break up populator methods for greater composibility and reuse.
All of these changes are needed for various downstream enhancements I'm working on for things like CWL support and extra file testing - but I think they should all be okay refactorings on their own.
Commit: 5a7a15d161bececf0a3cd93714e15768b329d95f
https://github.com/galaxyproject/galaxy/commit/5a7a15d161bececf0a3cd93714e1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
M test/api/test_tools.py
M test/base/interactor.py
M test/base/populators.py
M test/functional/tools/composite.xml
M test/functional/tools/composite_output.xml
M test/functional/tools/composite_output_tests.xml
M test/functional/tools/metadata.xml
M tools/sr_assembly/velvetg.xml
Log Message:
-----------
Test and clarifications for composite uploads.
- Add an API test for datatype-defined composite uploads - including exercising newline conversion and the space_to_tab parameter.
- Add a test decorator skip_without_datatype to mirror skip_without_tool for this test, improve both decorators.
- The ftype parameter in the composite test tools does nothing - drop it and drop it from the XSD spec.
- Slightly improve the documentation for these composite_data elements in the XSD.
Commit: cfefeebdd713552c9e0776b932fca59fe65961a3
https://github.com/galaxyproject/galaxy/commit/cfefeebdd713552c9e0776b932fc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M test/api/test_histories.py
Log Message:
-----------
Refactor history import/export tests to allow collection testing (not yet implemented).
xref #4345, #4532
Commit: 7db1a3fb3e6f61540f1354a899fce1c55e834775
https://github.com/galaxyproject/galaxy/commit/7db1a3fb3e6f61540f1354a899fc…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M config/error_report.yml.sample
M doc/source/admin/special_topics/bug_reports.rst
A lib/galaxy/tools/error_reports/plugins/influxdb.py
M lib/galaxy/tools/error_reports/plugins/json.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
Merge pull request #4533 from erasche/influxdb-error-reporter
Implement influxdb error reporter
Commit: de624b48b14f491841921363e4ef7d1ba72db3f3
https://github.com/galaxyproject/galaxy/commit/de624b48b14f491841921363e4ef…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/linters/help.py
M lib/galaxy/util/__init__.py
Log Message:
-----------
Sync non-CWL galaxy-lib changes.
Covers https://github.com/galaxyproject/galaxy-lib/pull/71 and https://github.com/galaxyproject/galaxy-lib/pull/69.
Commit: 9fb78b1010f8e106d34bf0b44888265b980521fd
https://github.com/galaxyproject/galaxy/commit/9fb78b1010f8e106d34bf0b44888…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M test/selenium_tests/test_workflow_run.py
Log Message:
-----------
Merge pull request #4531 from jmchilton/selenium_fixes_17
Another fix for Selenium worklow tests.
Commit: 354ce19677bae15d5cf976386ca988586a0c3eff
https://github.com/galaxyproject/galaxy/commit/354ce19677bae15d5cf976386ca9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_workflow_run.py
Log Message:
-----------
Fix workflow run Selenium test and make it more robust.
This test went from transiently broken to always broken during this release cycle. This PR makes two changes to try to fix both of those conditions. It correct the frame and button Selector for the new workflow run UX for the newer error and this allows explicitly refreshing the browser when waiting for datasets to appear to deal with the transient problems.
Commit: edd3b07c3dcace5263dafafef72b8564c8b7ce06
https://github.com/galaxyproject/galaxy/commit/edd3b07c3dcace5263dafafef72b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M test/galaxy_selenium/driver_factory.py
Log Message:
-----------
Fix "all" vs. "ALL" in Selenium logging configuration.
The previous value broke all the tests on Jenkins.
Commit: dd9c757a15e929be2ab6d138fb181f0ed543c156
https://github.com/galaxyproject/galaxy/commit/dd9c757a15e929be2ab6d138fb18…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Merge pull request #4500 from mvdbeek/workflow_loading_speedup
Workflow loading speedup
Commit: f5b29b82d29548a05da911b03d1b3e0dce5dc6e7
https://github.com/galaxyproject/galaxy/commit/f5b29b82d29548a05da911b03d1b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/tag.js
A client/galaxy/scripts/mvc/workflow/workflow-model.js
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
WIP - show/add/remove workflow tags
Commit: 5e667a7d54eba623bbf6cb42865507e063bdb4a5
https://github.com/galaxyproject/galaxy/commit/5e667a7d54eba623bbf6cb428655…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/tag.js
M client/galaxy/scripts/mvc/workflow/workflow-model.js
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Allow editing tags in workflow overview page
Commit: b57b2de7dac8c2fb36e4f3a626d6d33c57da6064
https://github.com/galaxyproject/galaxy/commit/b57b2de7dac8c2fb36e4f3a626d6…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Allow exporting and importing workflow tags
Commit: e1b5a459dcfd183327d8ea1d3485fb5f509b6d82
https://github.com/galaxyproject/galaxy/commit/e1b5a459dcfd183327d8ea1d3485…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Allow updating workflows from partial information
The workflow overview page gets workflow information from the
/api/workflows, which returns a reduced amount of information, most
notably the steps are not being returned. This commit skips updating the
actual workflow steps if the steps are not included in the workflow
payload. We can now update name, tags and whether a workflow should be
shown in the tool panel. We also return owner and number of steps in the
response to importing workflows.
Commit: e2d1fabf58f813c2d722849ad9bf5d1d46517665
https://github.com/galaxyproject/galaxy/commit/e2d1fabf58f813c2d722849ad9bf…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-model.js
Log Message:
-----------
Remove unncessary boilerplate from workflow model
Commit: 17be825cdf3714d2f335ba20ad2b6f51ad10c622
https://github.com/galaxyproject/galaxy/commit/17be825cdf3714d2f335ba20ad2b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Allow renaming, downloading, dropping workflow files to import
Commit: 5dfe36deceb6d4e38a82c0130a011956c29c06df
https://github.com/galaxyproject/galaxy/commit/5dfe36deceb6d4e38a82c0130a01…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Only access tags if workflow exists
Commit: 060952fa88dd84af04bc1e879e67726596cbc7ff
https://github.com/galaxyproject/galaxy/commit/060952fa88dd84af04bc1e879e67…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Allow downloading .ga workflows via the UI
Commit: 1a4effa70e9ad8088e19ae334753b7a898d286aa
https://github.com/galaxyproject/galaxy/commit/1a4effa70e9ad8088e19ae334753…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Remove downloading workflows through controller
Commit: 1015b510f81723b927866546390d179abef796f9
https://github.com/galaxyproject/galaxy/commit/1015b510f81723b927866546390d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Properly raise Exception if tool not found
Commit: 70c889435892ebfd1fb88edaab187cb84ba1dccf
https://github.com/galaxyproject/galaxy/commit/70c889435892ebfd1fb88edaab18…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-model.js
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Copy workflows without reloading page
Commit: 1dcfe56bb9f1c81567efe68f5ebe4c2f4c6bfb7f
https://github.com/galaxyproject/galaxy/commit/1dcfe56bb9f1c81567efe68f5ebe…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/tag.js
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Merge WorkflowTagsEditor with TagsEditor
Commit: f1f412ff298a3d859da1f4fe8b7640d722827a1f
https://github.com/galaxyproject/galaxy/commit/f1f412ff298a3d859da1f4fe8b76…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Make tag_editor local variable
Commit: 911c969631a1dcfb7eee2f2499f81d662b617800
https://github.com/galaxyproject/galaxy/commit/911c969631a1dcfb7eee2f2499f8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Fix logic for determining whether username should be mentioned
Commit: e54b1d1c379f56f2b45ef129a9863be77c379ae7
https://github.com/galaxyproject/galaxy/commit/e54b1d1c379f56f2b45ef129a986…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Fix adjusting dropdown menu
Commit: 0aa4e5463d410df448f484c13174b0e8d6ba87f8
https://github.com/galaxyproject/galaxy/commit/0aa4e5463d410df448f484c13174…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Use toastr for informing user about success/failure
Commit: 61ac1d77a4679938c98e43f54bea9e52073ae32e
https://github.com/galaxyproject/galaxy/commit/61ac1d77a4679938c98e43f54bea…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/style/less/base.less
Log Message:
-----------
Highlight workflow dropzone
Commit: 09f66a6394303a70b279a34c8f63458b059febc5
https://github.com/galaxyproject/galaxy/commit/09f66a6394303a70b279a34c8f63…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Remove unused $el_wf_link variable
Commit: 1de485d3f70165ca1860fbc388a30f40d1a21888
https://github.com/galaxyproject/galaxy/commit/1de485d3f70165ca1860fbc388a3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
camelCase functions and variables
Commit: bbaf59a05a7ff6bb048f93fe1eb192157301d6db
https://github.com/galaxyproject/galaxy/commit/bbaf59a05a7ff6bb048f93fe1eb1…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Display errors to user
Commit: 2968e0e588e35da24caecd0cc4223f694332673b
https://github.com/galaxyproject/galaxy/commit/2968e0e588e35da24caecd0cc422…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Show toast at the top-right (which is the default setting)
Commit: 268a895d2b787d9c77a5b87d04ec772382615a8b
https://github.com/galaxyproject/galaxy/commit/268a895d2b787d9c77a5b87d04ec…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-model.js
Log Message:
-----------
Describe workflow model and collection (thx @martenson)
Commit: aa49c0053a278d40dcc0affaf894b0e60b3d3949
https://github.com/galaxyproject/galaxy/commit/aa49c0053a278d40dcc0affaf894…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-model.js
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Move fetching out of WorkflowCollection
thx for the hint @martenson.
Commit: 9a331363cb51733b446aa44eca71f3439152d4ab
https://github.com/galaxyproject/galaxy/commit/9a331363cb51733b446aa44eca71…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Improve error reporting to user
Commit: ede8c200f944a9cc21d894654fb6ec0027747333
https://github.com/galaxyproject/galaxy/commit/ede8c200f944a9cc21d894654fb6…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M static/maps/mvc/tag.js.map
A static/maps/mvc/workflow/workflow-model.js.map
M static/maps/mvc/workflow/workflow.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/tag.js
A static/scripts/mvc/workflow/workflow-model.js
M static/scripts/mvc/workflow/workflow.js
M static/style/blue/base.css
Log Message:
-----------
Add static JS
Commit: d0df3886fa7acaa3d5f63360e2af78aab2deaaaa
https://github.com/galaxyproject/galaxy/commit/d0df3886fa7acaa3d5f63360e2af…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_workflow_management.py
Log Message:
-----------
More workflow index page Selenium tests.
- Fix rename test for recent change to using alert.
- Test basic adding a tag.
- Outline of a test for downloading workflows.
- Add test for publishing display on index.
- Add test for using the search box on the workflow index page.
Commit: 259e12d760c721badf9a6f65da90a9bb5bcb0983
https://github.com/galaxyproject/galaxy/commit/259e12d760c721badf9a6f65da90…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M test/base/api.py
A test/base/testcase.py
M test/base/twilltestcase.py
M test/functional/test_toolbox.py
M test/selenium_tests/framework.py
Log Message:
-----------
Continue separation of FunctionalTestCase from TwillTestCase.
Move non-twill stuff out into its own module including FunctionalTestCase.
Commit: 6e17ff57ea62320e8764b390e50135d95aaa242d
https://github.com/galaxyproject/galaxy/commit/6e17ff57ea62320e8764b390e501…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
R test/functional/test_library_templates.py
Log Message:
-----------
Remove test/functional/test_library_templates.py.
Hasn't been run in forever and it seems like we are deprecating these features.
Commit: 6d7c8b3136e24ff3e752efecb14f57574cd53174
https://github.com/galaxyproject/galaxy/commit/6d7c8b3136e24ff3e752efecb14f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M test/base/tool_shed_util.py
Log Message:
-----------
Cleanup sys.path hacking in test/base/tool_shed_util.py.
Commit: 7343463daca00ef60836e99faecdf90f85c9fd2a
https://github.com/galaxyproject/galaxy/commit/7343463daca00ef60836e99faecd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M test/base/driver_util.py
R test/base/test_db_util.py
R test/functional/database_contexts.py
M test/shed_functional/base/test_db_util.py
Log Message:
-----------
Rework hack to inject database contexts into Tool Shed tests.
Rather than depend on something in ``functional`` test module from ``base.driver_util``, just set these global hacks up in ``driver_util`` itself. This eliminates a dependency of ``functional`` on ``base`` - ideally ``base`` would not depend on any other test modules.
Commit: aba726a89f69fe1dbd4b4147e725c7ce0a7a3a33
https://github.com/galaxyproject/galaxy/commit/aba726a89f69fe1dbd4b4147e725…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
R test/base/twilltestcase.py
M test/functional/test_toolbox.py
A test/functional/twilltestcase.py
M test/shed_functional/base/twilltestcase.py
Log Message:
-----------
Move twilltestcase from ``base`` to ``functional`` module.
This way nothing in ``base`` has any dependencies on Twill anymore.
Commit: 558e22a49cbd9a1622a6b7db77ad6f66f17b5229
https://github.com/galaxyproject/galaxy/commit/558e22a49cbd9a1622a6b7db77ad…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/linters/help.py
M lib/galaxy/util/__init__.py
Log Message:
-----------
Merge pull request #4535 from jmchilton/galaxy-lib
Sync non-CWL galaxy-lib changes.
Commit: 47efd8089c5b1dfc67af7cf3887ce5b8b907e057
https://github.com/galaxyproject/galaxy/commit/47efd8089c5b1dfc67af7cf3887c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/tag.js
A client/galaxy/scripts/mvc/workflow/workflow-model.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/style/less/base.less
M lib/galaxy/managers/workflows.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/tag.js.map
A static/maps/mvc/workflow/workflow-model.js.map
M static/maps/mvc/workflow/workflow.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/tag.js
A static/scripts/mvc/workflow/workflow-model.js
M static/scripts/mvc/workflow/workflow.js
M static/style/blue/base.css
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_workflow_management.py
Log Message:
-----------
Merge pull request #4476 from mvdbeek/workflow_view_tags
Show tags, import by drag-and-drop and avoid refreshed in workflow page
Commit: 5358db58231482312850351d3d1dded25797dec8
https://github.com/galaxyproject/galaxy/commit/5358db58231482312850351d3d1d…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M test/base/tool_shed_util.py
Log Message:
-----------
fix lint order
Commit: 14497719ba6d3a9727563d15dbeacf2b537551f3
https://github.com/galaxyproject/galaxy/commit/14497719ba6d3a9727563d15dbea…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
M tools/data_source/upload.py
Log Message:
-----------
Prevent in-place editing if purge_source is false
When importing files from the FTP folder the admin can choose to prevent
purging of imported files. In this case the source file should not be
modified in-place by galaxy.
This also modifies relevant bare `except:` statements and modifies
the meaning of `in_place` in upload.py from no external chown script to
do not edit files in place if we keep the source file.
This fixes https://github.com/galaxyproject/galaxy/issues/4527.
Commit: 62ef8b52aedb9b9b34403db83703083a0cddbaf9
https://github.com/galaxyproject/galaxy/commit/62ef8b52aedb9b9b34403db83703…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M tools/data_source/upload.py
Log Message:
-----------
Fix sniffing for non-binary files
Commit: 06db29413e838fd88a2ec84ede347f097be161e2
https://github.com/galaxyproject/galaxy/commit/06db29413e838fd88a2ec84ede34…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M tools/data_source/upload.py
Log Message:
-----------
Move instead of copying converted datasets when possible
shutil.move tries to move files by renaming them. If that fails with
OSError (due to permission or cross-filesystem rename) it falls back to
copying files followed by removing them
(https://github.com/python/cpython/blob/2.7/Lib/shutil.py#L279) By
using shutil.move and catching permission problems we avoid an
unnecessary copy if source and destination are on the same filesystem.
Also avoids shutil.move if the upload tool is run as real-user which
should fix https://github.com/galaxyproject/galaxy/issues/4300.
Commit: 471707bd7dfa048a412aad9cdcc1d0b4aea70bc7
https://github.com/galaxyproject/galaxy/commit/471707bd7dfa048a412aad9cdcc1…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
Log Message:
-----------
Build converters_by_datatype only once per registry lifetime
Commit: ea9f5f7eb2536765a175f7e411f8d64cb8c34cad
https://github.com/galaxyproject/galaxy/commit/ea9f5f7eb2536765a175f7e411f8…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M test/galaxy_selenium/driver_factory.py
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_workflow_run.py
Log Message:
-----------
Merge pull request #4524 from jmchilton/selenium_fixes_16
Fix workflow run Selenium test and make it more robust.
Commit: d1a2007275f128fea051ead55fb47d2c2686abf5
https://github.com/galaxyproject/galaxy/commit/d1a2007275f128fea051ead55fb4…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M lib/galaxy/work/context.py
Log Message:
-----------
Cache user roles during WorkRequestContext lifetime
This speeds up building the tool module by a factor of 5.
Commit: 2d8b242e697a08775879fc873578b5f244d4d5cb
https://github.com/galaxyproject/galaxy/commit/2d8b242e697a08775879fc873578…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
Log Message:
-----------
Fix caching of `get_converters_by_datatype` result
Commit: ae7e1f97f0b71f90968abd09dd2f88387d0dc2e4
https://github.com/galaxyproject/galaxy/commit/ae7e1f97f0b71f90968abd09dd2f…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/work/context.py
Log Message:
-----------
Merge pull request #4541 from mvdbeek/build_module_speedup
Speedup toolform building
Commit: a1e79b13e1471f73a9ef192c0b7762ec6322fa93
https://github.com/galaxyproject/galaxy/commit/a1e79b13e1471f73a9ef192c0b77…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
A test/selenium_tests/test_saved_histories.py
Log Message:
-----------
add the first test
Commit: 634f7dcd3917eef17994a29c1f63f91c4b22a4b9
https://github.com/galaxyproject/galaxy/commit/634f7dcd3917eef17994a29c1f63…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
A doc/source/dev/finding_and_improving_slow_code.rst
Log Message:
-----------
Add a small howto on profiling galaxy code
Commit: 2e5bbad353ca76f25bff9588fea2958cd6d5596a
https://github.com/galaxyproject/galaxy/commit/2e5bbad353ca76f25bff9588fea2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M doc/source/dev/finding_and_improving_slow_code.rst
Log Message:
-----------
Clarify the last section
Commit: b2ceef5b6c258b0d6bc90240549299dbcc3d6ee4
https://github.com/galaxyproject/galaxy/commit/b2ceef5b6c258b0d6bc902405492…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M test/base/api.py
M test/base/driver_util.py
R test/base/test_db_util.py
A test/base/testcase.py
M test/base/tool_shed_util.py
R test/base/twilltestcase.py
R test/functional/database_contexts.py
R test/functional/test_library_templates.py
M test/functional/test_toolbox.py
A test/functional/twilltestcase.py
M test/selenium_tests/framework.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/base/twilltestcase.py
Log Message:
-----------
Merge pull request #4536 from jmchilton/test_refactoring
Refactor test modules toward cleaner dependencies
Commit: f6fa7c39f104d390f4a7df62d0b227ab1823c838
https://github.com/galaxyproject/galaxy/commit/f6fa7c39f104d390f4a7df62d0b2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
A doc/source/dev/finding_and_improving_slow_code.rst
Log Message:
-----------
Merge pull request #4542 from mvdbeek/build_module_speedup
Add a small howto on profiling galaxy code
Commit: 8f1303217eea29e4973cbbbd13c4b3f8b47f8d5c
https://github.com/galaxyproject/galaxy/commit/8f1303217eea29e4973cbbbd13c4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/util/xml_util.py
Log Message:
-----------
Merge pull request #4495 from erasche/parse-once
41% reduction in freiburg galaxy startup time
Commit: 3d9809a50d942e51c8afc7dd4cbae8e775b33147
https://github.com/galaxyproject/galaxy/commit/3d9809a50d942e51c8afc7dd4cba…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-04 (Mon, 04 Sep 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
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-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M lib/galaxy/managers/libraries.py
A lib/galaxy/managers/library_datasets.py
M lib/galaxy/managers/workflows.py
R lib/galaxy/webapps/galaxy/api/lda_datasets.py
A lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/buildapp.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-foldertoolbar-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.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-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M test/api/test_libraries.py
Log Message:
-----------
Merge pull request #4512 from martenson/improving-datalibraries
A round of data libraries improvements.
Commit: 9556c467e3a4c9947939f8444873530b53b39c20
https://github.com/galaxyproject/galaxy/commit/9556c467e3a4c9947939f8444873…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-04 (Mon, 04 Sep 2017)
Changed paths:
M lib/galaxy/work/context.py
Log Message:
-----------
Check user roles only once if user has no roles
The previous implementation in #4541 would check user roles multiple
times if a user has no roles.
Noticed by @nsoranzo, many thanks!
Commit: 003344ac2f0e6ebd13d78aa8222b958f93bfcf93
https://github.com/galaxyproject/galaxy/commit/003344ac2f0e6ebd13d78aa8222b…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-09-04 (Mon, 04 Sep 2017)
Changed paths:
M lib/galaxy/work/context.py
Log Message:
-----------
Merge pull request #4546 from mvdbeek/tool_form_followup
Check user roles only once if user has no roles
Commit: 9b4cd096e1e9cbbd86aafb384e5b7773abf585ab
https://github.com/galaxyproject/galaxy/commit/9b4cd096e1e9cbbd86aafb384e5b…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-04 (Mon, 04 Sep 2017)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
M test/api/test_tools.py
M test/base/interactor.py
M test/base/populators.py
M test/functional/tools/composite.xml
M test/functional/tools/composite_output.xml
M test/functional/tools/composite_output_tests.xml
M test/functional/tools/metadata.xml
M tools/sr_assembly/velvetg.xml
Log Message:
-----------
Merge pull request #4505 from jmchilton/composite_upload_refine
Tests and clarifications for composite uploads.
Commit: 4d3452c09e67be62812a13ea7ad803f62ce76fbb
https://github.com/galaxyproject/galaxy/commit/4d3452c09e67be62812a13ea7ad8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-04 (Mon, 04 Sep 2017)
Changed paths:
M .ci/jenkins/selenium/docker-compose.yml
Log Message:
-----------
Update the default testing Selenium Chrome Docker target.
Some recent changes was incompatible with some bug in the older version (possibly this bug https://bugs.chromium.org/p/chromedriver/issues/detail?id=1552) the result is a huge number of failures in Jenkins as some persistent session error occurs. For example the older (https://jenkins.galaxyproject.org/job/selenium/209/testReport/) but with me hacking the Jenkins job to make this change only two tests fail (https://jenkins.galaxyproject.org/job/selenium/210/testReport/)
Commit: ebcb4aa623dce9f92b904bf1f2ad58f59f07dbaf
https://github.com/galaxyproject/galaxy/commit/ebcb4aa623dce9f92b904bf1f2ad…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-04 (Mon, 04 Sep 2017)
Changed paths:
M test/selenium_tests/test_published_histories_grid.py
Log Message:
-----------
Possible fix for a transient failure in the published histories grid tests.
See failure here (https://jenkins.galaxyproject.org/job/selenium/210/testReport/selenium_test…)
Uses technique to retry atomic assertions that may not be immediately true but will settle as the DOM is updated in response to changes to be true (added in https://github.com/galaxyproject/galaxy/commit/d0df3886fa7acaa3d5f63360e2af…)
Commit: a91c03d4403ad57336ce5cc235b22cf4be5ebd6d
https://github.com/galaxyproject/galaxy/commit/a91c03d4403ad57336ce5cc235b2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-04 (Mon, 04 Sep 2017)
Changed paths:
M test/selenium_tests/test_workflow_editor.py
Log Message:
-----------
Remove Selenium test that is broken because Galaxy is broken.
See (https://github.com/galaxyproject/galaxy/issues/4548) for more information on the underlying issue.
Commit: 686cb48c716912212effc3d584d194ead54f216e
https://github.com/galaxyproject/galaxy/commit/686cb48c716912212effc3d584d1…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Alternative fix for workflow editor hang with missing tools
Commit: 33defd130772a0c7a3b63594aad27307e108ead9
https://github.com/galaxyproject/galaxy/commit/33defd130772a0c7a3b63594aad2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Revert "Properly raise Exception if tool not found"
This reverts commit 1015b510f81723b927866546390d179abef796f9.
Commit: 09c96dace2f6eb84ae33c856183fcf25175b65bf
https://github.com/galaxyproject/galaxy/commit/09c96dace2f6eb84ae33c856183f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Fix extra-space (thx @nsoranzo)
Commit: 40c9ca5ee9e3ab6eee8396218a8467a311225d37
https://github.com/galaxyproject/galaxy/commit/40c9ca5ee9e3ab6eee8396218a84…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Log warning for missing tools when building workflow modules
Commit: af9173d7cfa85156babca323e1a93d98f53acffd
https://github.com/galaxyproject/galaxy/commit/af9173d7cfa85156babca323e1a9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Merge pull request #4552 from mvdbeek/fix_missing_tools_wf_editor_alternative
Fix missing tools wf editor alternative
Commit: bff6b58a1ba356f904af7ec17735a88be4b348de
https://github.com/galaxyproject/galaxy/commit/bff6b58a1ba356f904af7ec17735…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Allow exporting workflows when tool is uninstalled
Commit: 6e6845b4987ab2de5608e216b1f537ad9b1f0fd5
https://github.com/galaxyproject/galaxy/commit/6e6845b4987ab2de5608e216b1f5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M test/api/test_histories.py
Log Message:
-----------
Merge pull request #4534 from jmchilton/collection_import_export_test_case
Refactor history import/export tests to allow collection testing.
Commit: 96cf1b94f14b7c92c767943fa4595e638eb322e3
https://github.com/galaxyproject/galaxy/commit/96cf1b94f14b7c92c767943fa459…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
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-of-pairs-collection-creator.js
Log Message:
-----------
Lower threshold for auto-matching dataset pairs in the collection builder.
Thanks to @mvdbeek for originally testing this and verifying it works.
Fixes #4349.
Commit: 1e3bd2d4e831331b8e3b314bac287288fa4533fc
https://github.com/galaxyproject/galaxy/commit/1e3bd2d4e831331b8e3b314bac28…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M config/dependency_resolvers_conf.xml.sample
A config/lmod_modules_mapping.yml.sample
A lib/galaxy/tools/deps/resolvers/lmod.py
M test/unit/tools/test_tool_deps.py
Log Message:
-----------
Merge pull request #4489 from arbernard/LMOD_Dependency_resolver
New Dependency resolver for the LMOD environment modules system
Commit: 63392a61071b89d699f26f06d036d7b42a235ff7
https://github.com/galaxyproject/galaxy/commit/63392a61071b89d699f26f06d036…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
fix copypasta
Commit: a13bd06f48eb1eda43c034e3fe0a3d9363d8cda4
https://github.com/galaxyproject/galaxy/commit/a13bd06f48eb1eda43c034e3fe0a…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
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-of-pairs-collection-creator.js
Log Message:
-----------
Merge pull request #4555 from jmchilton/lower_matching_threshold
Lower threshold for auto-matching dataset pairs in the collection builder
Commit: 932a3aa3be3327938b619b6c7f97d837264a12a6
https://github.com/galaxyproject/galaxy/commit/932a3aa3be3327938b619b6c7f97…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Make chronos dependency conditional.
Fixes #4085.
Commit: c6715819006256e429bf4e589dd456835b8d349c
https://github.com/galaxyproject/galaxy/commit/c6715819006256e429bf4e589dd4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Prevent unbound variable error history controller.
Fixes #4423 I suppose - thanks @erasche.
Commit: 338b0c994cf8f249ac2f4cd7dce2ced811e3a58a
https://github.com/galaxyproject/galaxy/commit/338b0c994cf8f249ac2f4cd7dce2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
Log Message:
-----------
Merge pull request #4511 from FredericBGA/import_history_and_symlink
import of history works even if we use symlink in database directory
Commit: 46c85ffa986ec2211bbda7be4f90ab579d3fff69
https://github.com/galaxyproject/galaxy/commit/46c85ffa986ec2211bbda7be4f90…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/compression_utils.py
M lib/tool_shed/util/commit_util.py
M tools/data_source/upload.py
Log Message:
-----------
Allow working with pbzip2 compressed files
This adds supprt for uploading and uncompressing pbzip2 compressed
files by exchanging the bz2 module with bz2file (recommended as workaround in
https://docs.python.org/2/library/bz2.html) The problem was reported by
@alpapan in #4538 and this commit should fix #4538.
Depends on https://github.com/galaxyproject/starforge/pull/147 for the
bz2file wheel.
Commit: 65b86e3eb0152f872a4d30b3be6741972f2fe7f7
https://github.com/galaxyproject/galaxy/commit/65b86e3eb0152f872a4d30b3be67…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Merge pull request #4553 from mvdbeek/allow_exporting_workflow_with_uninstalled_tools
Allow exporting workflows when tool is uninstalled
Commit: b12d29d14b64ce9aa267f1e1a9dd7a452ecf6270
https://github.com/galaxyproject/galaxy/commit/b12d29d14b64ce9aa267f1e1a9dd…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/managers/library_datasets.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
Log Message:
-----------
improve docs and access checks
thanks @nsoranzo
Commit: 4de0ec59f396868c5b56fb139929672c5ac8c3cd
https://github.com/galaxyproject/galaxy/commit/4de0ec59f396868c5b56fb139929…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Add bz2file to list of requirements
Commit: 87b798d40a5acb78ddf428d82639f2d5a7f40098
https://github.com/galaxyproject/galaxy/commit/87b798d40a5acb78ddf428d82639…
Author: jvolkening <jdv(a)base2bio.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
FAST5 archive support
Commit: 235bdca1eb942605eadedf719190de54559fde3a
https://github.com/galaxyproject/galaxy/commit/235bdca1eb942605eadedf719190…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Merge pull request #4556 from jmchilton/conditional_chronos
Make chronos dependency conditional.
Commit: cccf79ac5f1d4ef8dcd6d66585b5cc7966847bca
https://github.com/galaxyproject/galaxy/commit/cccf79ac5f1d4ef8dcd6d66585b5…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/util/checkers.py
M lib/galaxy/util/compression_utils.py
M lib/tool_shed/util/commit_util.py
M tools/data_source/upload.py
Log Message:
-----------
Make bz2file dependency conditional on python being below version 3.3
Commit: 3962ba94d756defce37b49375d77e221890904d7
https://github.com/galaxyproject/galaxy/commit/3962ba94d756defce37b49375d77…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M .ci/jenkins/selenium/docker-compose.yml
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_workflow_editor.py
Log Message:
-----------
Merge pull request #4549 from jmchilton/selenium_fixes_18
Assorted Selenium test fixes
Commit: 2541928855159504caf049dd58ffca9570b8bde1
https://github.com/galaxyproject/galaxy/commit/2541928855159504caf049dd58ff…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M test/selenium_tests/test_workflow_editor.py
Log Message:
-----------
Revert "Remove Selenium test that is broken because Galaxy is broken."
This reverts commit a91c03d4403ad57336ce5cc235b22cf4be5ebd6d.
Commit: b734581495f4bf39da16013ce8ae5536d0cc4437
https://github.com/galaxyproject/galaxy/commit/b734581495f4bf39da16013ce8ae…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M test/selenium_tests/test_workflow_editor.py
Log Message:
-----------
Merge pull request #4561 from mvdbeek/reintroduce_missing_tool_test
Revert "Remove Selenium test that is broken because Galaxy is broken."
Commit: 7db47e7e3c012d34fd27cfb7aadfca17469b2480
https://github.com/galaxyproject/galaxy/commit/7db47e7e3c012d34fd27cfb7aadf…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Merge pull request #4557 from jmchilton/shared_histories_unbound
Prevent unbound variable error history controller.
Commit: 8c4716e71d600711021041fc31bc8b02972c24c4
https://github.com/galaxyproject/galaxy/commit/8c4716e71d600711021041fc31bc…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Use environment markers to select bz2file when python is < 3.3
Commit: f78eca89126f8f35062541d201af4a85c602808e
https://github.com/galaxyproject/galaxy/commit/f78eca89126f8f35062541d201af…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M lib/galaxy/managers/library_datasets.py
Log Message:
-----------
remove unused import
Commit: 580811d7405f4566bfb8cb62e3bff5c7cc0e80a7
https://github.com/galaxyproject/galaxy/commit/580811d7405f4566bfb8cb62e3bf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M test/selenium_tests/test_published_histories_grid.py
Log Message:
-----------
Potential fix for transiently failing Selenium published histories test.
The the [latest Selenium test execution](https://jenkins.galaxyproject.org/job/selenium/212/testReport/) most of the published histories tests failed. It looks like this is because of the three histories that were supposed to be published, only 2 were actually published. My best guess for what happeend was that the click of the button to publish the history occurred but the next Selenium command happened so quickly that the page had not gotten a chance to respond to the click. This tweaked approach to publishing histories ensures we stay on the page until the "unpublish" link appears - this will either fix the problem or rule this theory out as the explanation.
Commit: 29622bba69422389f7bae7dfa2b6f7c9a6542acb
https://github.com/galaxyproject/galaxy/commit/29622bba69422389f7bae7dfa2b6…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
add history rename test
Commit: 3aacbdffd63c4e6a0570b3144082edffdcad175a
https://github.com/galaxyproject/galaxy/commit/3aacbdffd63c4e6a0570b3144082…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 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:
-----------
Merge pull request #4547 from martenson/library-import-conversions
allow linking, posix and spaces conversions in datalib imports
Commit: 486f436e76b0d3c67514a0d676a85002e5b82f1e
https://github.com/galaxyproject/galaxy/commit/486f436e76b0d3c67514a0d676a8…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/util/checkers.py
M lib/galaxy/util/compression_utils.py
M lib/tool_shed/util/commit_util.py
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #4559 from mvdbeek/use_bzip2file
Allow working with pbzip2 compressed files
Commit: 49eadb682ac5b2662dbe603cea4f0ba68cf59eec
https://github.com/galaxyproject/galaxy/commit/49eadb682ac5b2662dbe603cea4f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_workflow_management.py
Log Message:
-----------
Increase the robustness of Selenium workflow management tests.
Next Selenium build encountered a few different problems with importing workflows from URL:
- https://jenkins.galaxyproject.org/job/selenium/213/artifact/213-test-errors…
- https://jenkins.galaxyproject.org/job/selenium/213/artifact/213-test-errors…
- https://jenkins.galaxyproject.org/job/selenium/213/artifact/213-test-errors…
On full test retry, only one of these actually caused a test error but we shouldn't have to depend on the test re-running stuff.
Commit: 37802abee2b545a2524ef10b8ebaa628a03681fa
https://github.com/galaxyproject/galaxy/commit/37802abee2b545a2524ef10b8eba…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
M lib/galaxy/managers/library_datasets.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
Log Message:
-----------
Merge pull request #4560 from martenson/improving-datalibraries
improve docs and access checks in datalibs manager/api
Commit: c57b993b456d226da3896633a576013b977eab1b
https://github.com/galaxyproject/galaxy/commit/c57b993b456d226da3896633a576…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
quick fix
Commit: 7824fdab6b0001570001b60bc76e3a77da402877
https://github.com/galaxyproject/galaxy/commit/7824fdab6b0001570001b60bc76e…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
add delete/undelete test
Commit: a95566b36c18667cca73286f463b89fabeb8fbf8
https://github.com/galaxyproject/galaxy/commit/a95566b36c18667cca73286f463b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
M test/selenium_tests/test_published_histories_grid.py
Log Message:
-----------
Merge pull request #4562 from jmchilton/selenium_fixes_19
Potential fix for transiently failing Selenium published histories test.
Commit: eb799267ee35da3b5b9dbef8a58ed8107aeb16ae
https://github.com/galaxyproject/galaxy/commit/eb799267ee35da3b5b9dbef8a58e…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Log Message:
-----------
Merge branch 'release_17.05' into dev
Commit: 095c1045b6605756934ef9524907d6cb73c4baf9
https://github.com/galaxyproject/galaxy/commit/095c1045b6605756934ef9524907…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
M scripts/tool_shed/build_ts_whoosh_index.py
Log Message:
-----------
add logging to ts index building
Commit: e8ee2741f9093496aa68c2afe435aa9fc7dd8fcc
https://github.com/galaxyproject/galaxy/commit/e8ee2741f9093496aa68c2afe435…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
M scripts/tool_shed/build_ts_whoosh_index.py
Log Message:
-----------
Merge pull request #4567 from martenson/index-refresh-logging
add logging to ts index building
Commit: 30b97f1f1ea9987f967e9774f65ed2e3d8450a3b
https://github.com/galaxyproject/galaxy/commit/30b97f1f1ea9987f967e9774f65e…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-06 (Wed, 06 Sep 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:
-----------
refactor callback hell to use promises
Commit: cf09a25fdc742998d5bd71deca32527a947c6812
https://github.com/galaxyproject/galaxy/commit/cf09a25fdc742998d5bd71deca32…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-06 (Wed, 06 Sep 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 import of collections to datalibs
I swear I fixed this before
Commit: 8f7d2374cac0fcf44b2f878490d912e9bb98a8ec
https://github.com/galaxyproject/galaxy/commit/8f7d2374cac0fcf44b2f878490d9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_workflow_management.py
Log Message:
-----------
Merge pull request #4564 from jmchilton/selenium_fixes_20
Increase the robustness of Selenium workflow management tests.
Commit: 20b935639670d171eadb96b3406d00174d978ae6
https://github.com/galaxyproject/galaxy/commit/20b935639670d171eadb96b3406d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-06 (Wed, 06 Sep 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:
-----------
Merge pull request #4568 from martenson/fix-collection-import
Fix datalib collection import
Commit: 9e6cb13e314d451cba7e0eaf841f05410ac19750
https://github.com/galaxyproject/galaxy/commit/9e6cb13e314d451cba7e0eaf841f…
Author: jvolkening <jdv(a)base2bio.com>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
A .ci/autopep8.sh
M .ci/flake8_blacklist.txt
M .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper_docstrings.sh
M .ci/jenkins/selenium/docker-compose.yml
M .ci/jenkins/selenium/run_tests.sh
M .ci/py3_sources.txt
M .gitignore
M .travis.yml
M CITATION
M CONTRIBUTING.md
M CONTRIBUTORS.md
M Makefile
M README.rst
A SECURITY_POLICY.md
M client/bower.json
A client/galaxy/scripts/admin.toolshed.js
A client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
R client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/apps/login.js
A client/galaxy/scripts/apps/panels/admin-panel.js
A client/galaxy/scripts/apps/panels/history-panel.js
A client/galaxy/scripts/apps/panels/tool-panel.js
R client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
A client/galaxy/scripts/layout/router.js
M client/galaxy/scripts/layout/scratchbook.js
R client/galaxy/scripts/libs/jquery/jqtouch.js
M client/galaxy/scripts/mvc/citation/citation-view.js
A client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
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M static/scripts/mvc/library/library-libraryrow-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/library/library-model.js
M static/scripts/mvc/tag.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
A static/scripts/mvc/tool/tool-genomespace.js
M static/scripts/mvc/tool/tools.js
A static/scripts/mvc/toolshed/categories-view.js
A static/scripts/mvc/toolshed/repo-queue-view.js
A static/scripts/mvc/toolshed/repo-status-view.js
A static/scripts/mvc/toolshed/repositories-view.js
A static/scripts/mvc/toolshed/repository-queue-view.js
A static/scripts/mvc/toolshed/repository-view.js
A static/scripts/mvc/toolshed/shed-category-view.js
A static/scripts/mvc/toolshed/shed-list-view.js
A static/scripts/mvc/toolshed/shed-repo-details-view.js
A static/scripts/mvc/toolshed/shed-repo-list-view.js
A static/scripts/mvc/toolshed/sheds-list-view.js
A static/scripts/mvc/toolshed/toolshed-model.js
A static/scripts/mvc/toolshed/util.js
A static/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-drilldown.js
M static/scripts/mvc/ui/ui-list.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-options.js
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
A static/scripts/mvc/ui/ui-select-genomespace.js
M static/scripts/mvc/ui/ui-slider.js
M static/scripts/mvc/ui/ui-table.js
A static/scripts/mvc/upload/collection/collection-row.js
A static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-view.js
A static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/user/user-quotameter.js
M static/scripts/mvc/webhooks.js
A static/scripts/mvc/workflow/workflow-configure-menu.js
A static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-manager.js
A static/scripts/mvc/workflow/workflow-model.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view-terminals.js
M static/scripts/mvc/workflow/workflow-view.js
A static/scripts/mvc/workflow/workflow.js
A static/scripts/nls/de/locale.js
A static/scripts/nls/es/locale.js
A static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/nls/zh/locale.js
M static/scripts/onload.js
M static/scripts/reports_webapp/run_stats.js
M static/scripts/ui/scroll-panel.js
M static/scripts/utils/graph.js
M static/scripts/utils/query-string-parsing.js
M static/scripts/utils/uploadbox.js
M static/scripts/utils/utils.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/visualization.js
M static/style/blue/base.css
R static/style/blue/iphone.css
M static/welcome.html.sample
R templates/admin/dataset_security/group/grid.mako
R templates/admin/dataset_security/group/group.mako
R templates/admin/dataset_security/group/group_create.mako
R templates/admin/dataset_security/group/group_rename.mako
R templates/admin/dataset_security/role/grid.mako
R templates/admin/dataset_security/role/role.mako
R templates/admin/dataset_security/role/role_create.mako
R templates/admin/dataset_security/role/role_rename.mako
R templates/admin/quota/grid.mako
R templates/admin/quota/quota.mako
R templates/admin/quota/quota_create.mako
R templates/admin/quota/quota_edit.mako
R templates/admin/quota/quota_rename.mako
R templates/admin/quota/quota_set_default.mako
M templates/admin/reload_tool.mako
R templates/admin/tool_shed_repository/browse_toolsheds.mako
R templates/admin/tool_shed_repository/grid.mako
R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
R templates/admin/tool_version/grid.mako
R templates/admin/user/grid.mako
R templates/admin/user/reset_password.mako
R templates/admin/user/user.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/display_base.mako
M templates/galaxy_client_app.mako
M templates/grid_base.mako
M templates/js-app.mako
M templates/sharing_base.mako
M templates/show_params.mako
M templates/tagging_common.mako
R templates/user/dbkeys.mako
M templates/user/index.mako
M templates/user/login.mako
M templates/user/logout.mako
M templates/user/register.mako
M templates/webapps/galaxy/admin/center.mako
R templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/galaxy/base_panels.mako
M templates/webapps/galaxy/data_manager/index.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/dataset/display.mako
R templates/webapps/galaxy/dataset/edit_attributes.mako
R templates/webapps/galaxy/dataset/errors.mako
R templates/webapps/galaxy/dataset/grid.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/history/display_structured.mako
R templates/webapps/galaxy/history/grid.mako
R templates/webapps/galaxy/history/grid_js.mako
R templates/webapps/galaxy/history/list_published.mako
R templates/webapps/galaxy/history/shared_grid.mako
R templates/webapps/galaxy/mobile/dataset/detail.mako
R templates/webapps/galaxy/mobile/dataset/peek.mako
R templates/webapps/galaxy/mobile/form.mako
R templates/webapps/galaxy/mobile/history/detail.mako
R templates/webapps/galaxy/mobile/history/list.mako
R templates/webapps/galaxy/mobile/index.mako
R templates/webapps/galaxy/mobile/manage_library.mako
R templates/webapps/galaxy/mobile/settings.mako
M templates/webapps/galaxy/page/editor.mako
R templates/webapps/galaxy/page/index.mako
R templates/webapps/galaxy/page/list_published.mako
R templates/webapps/galaxy/page/select_items_grid.mako
M templates/webapps/galaxy/requests/common/common.mako
M templates/webapps/galaxy/root/tool_runner.mako
R templates/webapps/galaxy/tracks/add_to_viz.mako
R templates/webapps/galaxy/tracks/add_tracks.mako
R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako
R templates/webapps/galaxy/tracks/history_select_grid.mako
R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako
R templates/webapps/galaxy/visualization/list.mako
R templates/webapps/galaxy/visualization/list_published.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
R templates/webapps/galaxy/workflow/configure_menu.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/editor.mako
R templates/webapps/galaxy/workflow/import.mako
R templates/webapps/galaxy/workflow/list.mako
R templates/webapps/galaxy/workflow/list_for_run.mako
R templates/webapps/galaxy/workflow/list_published.mako
R templates/webapps/galaxy/workflow/run.mako
M templates/webapps/reports/base_panels.mako
M templates/webapps/tool_shed/admin/center.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako
A templates/webapps/tool_shed/admin/user/reset_password.mako
A templates/webapps/tool_shed/admin/user/user.mako
M templates/webapps/tool_shed/base_panels.mako
M templates/webapps/tool_shed/repository/common.mako
R templates/webapps/tool_shed/repository/grid.mako
M templates/webapps/tool_shed/repository/tool_form.mako
A test-data/1.sam.gz
A test-data/5_Ig-like.gff
A test-data/bad.html.gz
A test-data/filter_labels_1.txt
A test-data/new_labels_1.txt
A test-data/new_labels_2.txt
A test-data/new_labels_bad_1.txt
A test-data/new_labels_bad_2.txt
A test-data/random-file
A test-data/test.vcf.gz
M test/TESTING.md
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_datasets.py
M test/api/test_datatypes.py
M test/api/test_framework.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_history_contents_provenance.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_search.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_tours.py
M test/api/test_users.py
M test/api/test_visualizations.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
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M test/base/api_asserts.py
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M test/base/instrument.py
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M test/base/nose_util.py
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R test/base/test_db_util.py
A test/base/testcase.py
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R test/base/twilltestcase.py
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M test/casperjs/server_env.py
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R test/functional/database_contexts.py
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M test/functional/test_toolbox.py
M test/functional/tools/code_file.py
A test/functional/tools/collection_creates_dynamic_nested_fail.xml
A test/functional/tools/collection_creates_dynamic_nested_from_json.xml
A test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml
A test/functional/tools/collection_creates_list_fail.xml
M test/functional/tools/composite.xml
M test/functional/tools/composite_output.xml
M test/functional/tools/composite_output_tests.xml
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
A test/functional/tools/identifier_multiple_in_conditional.xml
A test/functional/tools/identifier_multiple_in_repeat.xml
A test/functional/tools/identifier_source.xml
M test/functional/tools/metadata.xml
A test/functional/tools/mulled_example_multi_incomplete.xml
A test/functional/tools/mulled_example_multi_versionless.xml
A test/functional/tools/output_format_deprecated_when.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/tool_provided_metadata_1.xml
M test/functional/tools/tool_provided_metadata_2.xml
M test/functional/tools/tool_provided_metadata_3.xml
A test/functional/tools/tool_provided_metadata_4.xml
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A test/functional/tools/tool_provided_metadata_6.xml
A test/functional/tools/tool_provided_metadata_7.xml
A test/functional/tools/tool_provided_metadata_8.xml
A test/functional/tools/tool_provided_metadata_9.xml
A test/functional/tools/vcf_bgzip.xml
A test/functional/twilltestcase.py
M test/functional/webhooks/phdcomics/helper/__init__.py
M test/functional/webhooks/trans_object/config/trans_object.yaml
M test/functional/webhooks/trans_object/helper/__init__.py
M test/galaxy_selenium/driver_factory.py
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation-data.yml
M test/galaxy_selenium/sizzle.py
A test/integration/test_config_options_users.py
A test/integration/test_maximum_worklfow_invocation_duration.py
M test/integration/test_resolvers.py
A test/integration/test_upload_configuration_options.py
A test/integration/test_workflow_handler_configuration.py
A test/integration/workflow_handler_configuration_job_conf.xml
A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml
M test/manual/workflows_scaling.py
M test/qunit/package.json
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M test/qunit/test-data/paired-collection-creator.data.js
M test/qunit/tests/form_tests.js
M test/qunit/tests/galaxy-app-base.js
M test/qunit/tests/page_tests.js
M test/qunit/tests/ui_tests.html
M test/qunit/tests/ui_tests.js
M test/selenium_tests/framework.py
A test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_login.py
A test/selenium_tests/test_published_histories_grid.py
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A test/selenium_tests/test_sizzle_loading.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/selenium_tests/test_workflow_management.py
M test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/test_db_util.py
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M test/shed_functional/functional/test_0040_repository_circular_dependencies.py
M test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py
M test/shed_functional/functional/test_0060_workflows.py
M test/shed_functional/functional/test_0070_invalid_tool.py
M test/shed_functional/functional/test_0080_advanced_circular_dependencies.py
M test/shed_functional/functional/test_0090_tool_search.py
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M test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py
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M test/shed_functional/functional/test_0140_tool_help_images.py
M test/shed_functional/functional/test_0150_prior_installation_required.py
M test/shed_functional/functional/test_0160_circular_prior_installation_required.py
M test/shed_functional/functional/test_0170_complex_prior_installation_required.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_0310_hg_api_features.py
M test/shed_functional/functional/test_0400_repository_component_reviews.py
M test/shed_functional/functional/test_0410_repository_component_review_access_control.py
M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py
M test/shed_functional/functional/test_0430_browse_utilities.py
M test/shed_functional/functional/test_0440_deleting_dependency_definitions.py
M test/shed_functional/functional/test_0460_upload_to_repository.py
M test/shed_functional/functional/test_0470_tool_dependency_repository_type.py
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M test/shed_functional/functional/test_0490_export_import_repositories.py
M test/shed_functional/functional/test_0500_export_repository_simple_dependency.py
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M test/shed_functional/functional/test_0520_import_export_circular_dependencies.py
M test/shed_functional/functional/test_0530_repository_admin_feature.py
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M test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py
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M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
M tool_list.py
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/hbvar_filter.py
M tools/data_source/import.py
M tools/data_source/microbial_import.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/trimmer.xml
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/wc_gnu.xml
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_file_browser.py
R tools/genomespace/genomespace_file_browser_dev.xml
R tools/genomespace/genomespace_file_browser_prod.xml
R tools/genomespace/genomespace_file_browser_test.xml
M tools/genomespace/genomespace_importer.py
M tools/genomespace/genomespace_importer.xml
A tools/genomespace/genomespace_push.xml
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/plotting/bar_chart.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg.xml
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into fast5
Commit: d887cb17f0e330bed43d80073801568165746454
https://github.com/galaxyproject/galaxy/commit/d887cb17f0e330bed43d80073801…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
A test-data/joiner_header_in1.tab
A test-data/joiner_header_in2.tab
A test-data/joiner_out1.bed
A test-data/joiner_out2.bed
A test-data/joiner_out3.bed
A test-data/joiner_out4.bed
A test-data/joiner_out5.tab
A test-data/joiner_out6.tab
A test-data/joiner_out7.tab
M tools/filters/join.py
M tools/filters/joiner.xml
Log Message:
-----------
Merge join_header into dev.
Commit: 696a1eda3ca5695f9c0631c3f2f357c83b4a8995
https://github.com/galaxyproject/galaxy/commit/696a1eda3ca5695f9c0631c3f2f3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
A test-data/joiner_header_in1.tab
A test-data/joiner_header_in2.tab
A test-data/joiner_out1.bed
A test-data/joiner_out2.bed
A test-data/joiner_out3.bed
A test-data/joiner_out4.bed
A test-data/joiner_out5.tab
A test-data/joiner_out6.tab
A test-data/joiner_out7.tab
M tools/filters/join.py
M tools/filters/joiner.xml
Log Message:
-----------
Merge integration branch of 'header_join' into dev
Commit: bca6dfefb6946aa5497819a5d80c74f3d2a7210f
https://github.com/galaxyproject/galaxy/commit/bca6dfefb6946aa5497819a5d80c…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
add history switch test
Commit: da42c16ae7014723012dccdc17c0d39a32ab5713
https://github.com/galaxyproject/galaxy/commit/da42c16ae7014723012dccdc17c0…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
add history view test
Commit: ff769da9287ddc7f6ad598799a9773d6a2d77c30
https://github.com/galaxyproject/galaxy/commit/ff769da9287ddc7f6ad598799a97…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
add history publish test
Commit: 29ed1bec66ddfb5b1a8559a0a6a8f34aeb928c14
https://github.com/galaxyproject/galaxy/commit/29ed1bec66ddfb5b1a8559a0a6a8…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
add multiple histories delete/undelete test
Commit: 2fc60430a187cc4a95e2d935b89b65f52acd86b8
https://github.com/galaxyproject/galaxy/commit/2fc60430a187cc4a95e2d935b89b…
Author: jvolkening <jdv(a)base2bio.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
fix formatting to make tox happy
Commit: 5dedd397718166723cdc0bb054565b69e7435d23
https://github.com/galaxyproject/galaxy/commit/5dedd397718166723cdc0bb05456…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
add sort by name test
Commit: e6ebc9e022dd184109374f7f30dec3505b9a2c6e
https://github.com/galaxyproject/galaxy/commit/e6ebc9e022dd184109374f7f30de…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
add standard search test
Commit: 90f0dfc8bcf04309873e8cd8771840c2c7e9fa8d
https://github.com/galaxyproject/galaxy/commit/90f0dfc8bcf04309873e8cd87718…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
add advanced search test
Commit: 57ff68edd0627a58c1bdce645d666ad3243df8d2
https://github.com/galaxyproject/galaxy/commit/57ff68edd0627a58c1bdce645d66…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #4539 from mvdbeek/purge_source
Prevent in-place editing of uploaded files if files are imported from the FTP folder
Commit: 74f7181eafa93eec8fb2bd21ccab5c1373e73c07
https://github.com/galaxyproject/galaxy/commit/74f7181eafa93eec8fb2bd21ccab…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
Log Message:
-----------
Merge pull request #4503 from mvdbeek/paramiko_long_running
Allow paramiko cli to recover from ssh timeout
Commit: 316eb330bb21b4bd54c340b389217de9f91f0097
https://github.com/galaxyproject/galaxy/commit/316eb330bb21b4bd54c340b38921…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
add permanently delete history test
Commit: e50e7239b58ef80f62c537096bdf642198aaa9cb
https://github.com/galaxyproject/galaxy/commit/e50e7239b58ef80f62c537096bdf…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
Log Message:
-----------
Implement IP address whitelisting
Commit: 569bd6bedf17b1b1f73c964345dd41b3d29cf104
https://github.com/galaxyproject/galaxy/commit/569bd6bedf17b1b1f73c964345dd…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M client/galaxy/scripts/utils/uploadbox.js
M static/maps/utils/uploadbox.js.map
M static/scripts/utils/uploadbox.js
Log Message:
-----------
Show a more useful error when one is available
Commit: d1892fc4446474b14da33b6862002a7d54fd9fd2
https://github.com/galaxyproject/galaxy/commit/d1892fc4446474b14da33b686200…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/tools/actions/upload_common.py
Log Message:
-----------
the library prefers unicode stuff
Commit: 36758478d590664615f7fe8e32ef9f7879eb2284
https://github.com/galaxyproject/galaxy/commit/36758478d590664615f7fe8e32ef…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
Log Message:
-----------
non-URL things get passed to this function
Commit: b620536dc25af3b68a28aade5682b6b7a92af15d
https://github.com/galaxyproject/galaxy/commit/b620536dc25af3b68a28aade5682…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
rebuild client
Commit: cb416390781e546ce77b94f56cca73e48faed070
https://github.com/galaxyproject/galaxy/commit/cb416390781e546ce77b94f56cca…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
flake8
Commit: e8ea1104a7ec1775350d881d3f5eed9fb420b38e
https://github.com/galaxyproject/galaxy/commit/e8ea1104a7ec1775350d881d3f5e…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M test/integration/test_upload_configuration_options.py
Log Message:
-----------
add a test expecting failure
Commit: 618d89b972258db5d2dafcb127ed3a6b473402ae
https://github.com/galaxyproject/galaxy/commit/618d89b972258db5d2dafcb127ed…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
lint-import-order
Commit: 4e2cd5fea628884d1dddd305e28f3ec81b509982
https://github.com/galaxyproject/galaxy/commit/4e2cd5fea628884d1dddd305e28f…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M static/maps/mvc/library/library-foldertoolbar-view.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/library/library-foldertoolbar-view.js
Log Message:
-----------
rebuild client
Commit: 2aeb4590d1c9c7bb86bb21b42d6fe20ffc8d59f8
https://github.com/galaxyproject/galaxy/commit/2aeb4590d1c9c7bb86bb21b42d6f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M client/galaxy/scripts/utils/uploadbox.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/utils/uploadbox.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/library/library-foldertoolbar-view.js
M static/scripts/utils/uploadbox.js
M test/integration/test_upload_configuration_options.py
Log Message:
-----------
Merge pull request #4289 from erasche/local-network
Local network access restrictions
Commit: 8f3c65c59efe623c325f54e2407c383688ffeedb
https://github.com/galaxyproject/galaxy/commit/8f3c65c59efe623c325f54e2407c…
Author: Saskia Hiltemann <shiltemann(a)users.noreply.github.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
use version 2.7.1 of h5py
Commit: d4cf4bff4f249c5e100fde8a31315c92acbe4fc8
https://github.com/galaxyproject/galaxy/commit/d4cf4bff4f249c5e100fde8a3131…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
PEP8 fix
Commit: 2615094597ff6bdb0b03e496ea075c2a16f561b9
https://github.com/galaxyproject/galaxy/commit/2615094597ff6bdb0b03e496ea07…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
Revert "remove unused variable"
This reverts commit 4119caf9b7fbd1fc9c374403e7f7836b8d9397c1.
Commit: f07c6a98431f1a4c2a2d81f99d3b54a23f0a901e
https://github.com/galaxyproject/galaxy/commit/f07c6a98431f1a4c2a2d81f99d3b…
Author: jvolkening <jdv(a)base2bio.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
optimized sniffing, subclassed different tarball types
Commit: 65b2fe8a4aa48ec0fefa36b4f30aeab1627ff33d
https://github.com/galaxyproject/galaxy/commit/65b2fe8a4aa48ec0fefa36b4f30a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/maps/mvc/history/options-menu.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/history/options-menu.js
Log Message:
-----------
Fix delete option in history menu.
Commit: 31043698d0a8a20294c9964d93a0e726b0ff91ca
https://github.com/galaxyproject/galaxy/commit/31043698d0a8a20294c9964d93a0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/maps/mvc/history/options-menu.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/history/options-menu.js
Log Message:
-----------
Fix purge option in history menu. Now delete&purge use modern models/handling.
Commit: 297d2353ce594b3325d029fb72c3ffd825c07f57
https://github.com/galaxyproject/galaxy/commit/297d2353ce594b3325d029fb72c3…
Author: jvolkening <jdv(a)base2bio.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/test/test.fast5.tar
A lib/galaxy/datatypes/test/test.fast5.tar.bz2
A lib/galaxy/datatypes/test/test.fast5.tar.gz
Log Message:
-----------
add datatype tests
Commit: b3f0f36c89a09056e6a49e4e5c65779a676fc1c5
https://github.com/galaxyproject/galaxy/commit/b3f0f36c89a09056e6a49e4e5c65…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/maps/mvc/history/options-menu.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/history/options-menu.js
Log Message:
-----------
Merge pull request #4574 from dannon/history_options_fixes
Fix delete option in history menu
Commit: a8df8729b8670e23c4f77616cd775aed98463ca7
https://github.com/galaxyproject/galaxy/commit/a8df8729b8670e23c4f77616cd77…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/converters/biom1_to_biom2.xml
A lib/galaxy/datatypes/converters/biom2_to_biom1.xml
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Merge pull request #4519 from shiltemann/biom2_datatype
add biom2 datatype
Commit: 46b799dfbb56a25df10b3e85368db372ce97f8be
https://github.com/galaxyproject/galaxy/commit/46b799dfbb56a25df10b3e85368d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_login.py
Log Message:
-----------
Make submitting logins for Selenium tests a bit more robust.
There are a few different transiently failing tests on Jenkins that seem to fail because the test thinks Galaxy is logged in but it is not. So now after we click the login button in Selenium - we will wait for to see the "Register or Login" button turn into the "User" button.
This is a similar problem and fix to what was done in #4562 - which seemed to help.
Commit: 5e179df2a852aa956ce3bd48d4c365d646c2d035
https://github.com/galaxyproject/galaxy/commit/5e179df2a852aa956ce3bd48d4c3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M test/selenium_tests/test_published_histories_grid.py
Log Message:
-----------
Fix logic error in new published histories sort by owner test.
I switched to randomly generated usernames without actually ensure the random usernames would be generated in the same lexiographic order - that wasn't super bright of me. That sort by owner test should pass as frequently as the other tests in that test case class now.
Commit: f623613a392ca21b23b5278530f95257e8d2f365
https://github.com/galaxyproject/galaxy/commit/f623613a392ca21b23b5278530f9…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M test/selenium_tests/test_published_histories_grid.py
Log Message:
-----------
Merge pull request #4577 from jmchilton/selenium_fixes_22
Fix logic error in new published histories sort by owner test.
Commit: 508fdb9d2b4766668e3d1b962216db7e4e7b3e48
https://github.com/galaxyproject/galaxy/commit/508fdb9d2b4766668e3d1b962216…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml
A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js
A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
Log Message:
-----------
Merge pull request #3330 from bgruening/hicbrowser
HiCBrowser as Galaxy IE
Commit: 49258a7df8bb0f8c489c06dc2a77c27b2244b5f9
https://github.com/galaxyproject/galaxy/commit/49258a7df8bb0f8c489c06dc2a77…
Author: jvolkening <jdv(a)base2bio.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
fixed sniff order and misc linting errors
Commit: 08b5a47c396d38d288d54806edb87e9e717b799d
https://github.com/galaxyproject/galaxy/commit/08b5a47c396d38d288d54806edb8…
Author: jvolkening <jdv(a)base2bio.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/utils/uploadbox.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml
A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js
A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/converters/biom1_to_biom2.xml
A lib/galaxy/datatypes/converters/biom2_to_biom1.xml
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/utils/uploadbox.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/history/options-menu.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/utils/uploadbox.js
A test-data/joiner_header_in1.tab
A test-data/joiner_header_in2.tab
A test-data/joiner_out1.bed
A test-data/joiner_out2.bed
A test-data/joiner_out3.bed
A test-data/joiner_out4.bed
A test-data/joiner_out5.tab
A test-data/joiner_out6.tab
A test-data/joiner_out7.tab
M test/integration/test_upload_configuration_options.py
M test/selenium_tests/test_published_histories_grid.py
M tools/data_source/upload.py
M tools/filters/join.py
M tools/filters/joiner.xml
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into fast5
Commit: 82267855ed3bc6d3f8911acf6e7e388023f6693d
https://github.com/galaxyproject/galaxy/commit/82267855ed3bc6d3f8911acf6e7e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M static/maps/layout/page.js.map
M static/maps/mvc/workflow/workflow.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/layout/page.js
M static/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Support for applying window title on display() of views.
Commit: 9a66adb4fe7a3be6e07baaec6cef8f553d6b486d
https://github.com/galaxyproject/galaxy/commit/9a66adb4fe7a3be6e07baaec6cef…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Standard (for now) paren spacing.
Commit: 0a54a313b77b7c47cf57d5f7365cd37231b879ea
https://github.com/galaxyproject/galaxy/commit/0a54a313b77b7c47cf57d5f7365c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/style/less/library.less
M static/maps/mvc/library/library-foldertoolbar-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-foldertoolbar-view.js
M static/style/blue/base.css
M static/style/blue/library.css
Log Message:
-----------
remove unneeded property, fix import from history targets
some refactoring
Commit: 5b87754ab77dbba1aab632345517e404bc421295
https://github.com/galaxyproject/galaxy/commit/5b87754ab77dbba1aab632345517…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
refactor traversing to use latest() instead
Commit: 84de84294c95110f0ee3059ad8a5e9924daf6a9d
https://github.com/galaxyproject/galaxy/commit/84de84294c95110f0ee3059ad8a5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/history/history-list.js.map
M static/maps/mvc/tours.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-list.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
History List, Tours, and User Preferences titles
Commit: 6b2277e37dd0520de26442701407badcf792cfab
https://github.com/galaxyproject/galaxy/commit/6b2277e37dd0520de26442701407…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Automatically append 'Galaxy | ' to title instead of requiring it for all view titles.
Commit: 2cb8a28f7be2ff8b7076ef04a6d575d276e3bca6
https://github.com/galaxyproject/galaxy/commit/2cb8a28f7be2ff8b7076ef04a6d5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M static/maps/layout/page.js.map
M static/maps/mvc/history/history-list.js.map
M static/maps/mvc/tours.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow.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/layout/page.js
M static/scripts/mvc/history/history-list.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Rebuild.
Commit: 9a0506c5c0832c93dcd7844ea9de92b619c00773
https://github.com/galaxyproject/galaxy/commit/9a0506c5c0832c93dcd7844ea9de…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
Include Galaxy brand in titles.
Commit: 8adbf03f565b1d60fb42ca986d184387e19e94af
https://github.com/galaxyproject/galaxy/commit/8adbf03f565b1d60fb42ca986d18…
Author: chambm <matt.chambers42(a)gmail.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-view-edit.js
Log Message:
-----------
Add show/hide deleted/hidden links when history is filtered by find box; addresses #4103
Commit: 91eb849500faec57bebb35228a5a2e2638be70aa
https://github.com/galaxyproject/galaxy/commit/91eb849500faec57bebb35228a5a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
Use 'Galaxy / Brand' consistent styling instead of 'Galaxy | Brand'
Commit: 2259c7d41380f6a2aa23ea1bc13169d1d7a5fb54
https://github.com/galaxyproject/galaxy/commit/2259c7d41380f6a2aa23ea1bc131…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_history_panel.py
Log Message:
-----------
Retry failed clicks more aggressively for Selenium tests.
Would have prevented from this (https://jenkins.galaxyproject.org/job/selenium/238/testReport/junit/seleniu…) failure in retrospect. Also refactor that common pattern into a helper and use throughout. Add missing @selenium_test decorator on that test also - it would have retried if this had been there and we would have a screenshot.
Commit: 28fd37be40f09ac7054043eed7ef5fdbc10333ef
https://github.com/galaxyproject/galaxy/commit/28fd37be40f09ac7054043eed7ef…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_login.py
Log Message:
-----------
Merge pull request #4576 from jmchilton/selenium_fixes_21
Make submitting logins for Selenium tests a bit more robust.
Commit: 935f25aa32b3a22a53de02d5bfe4b5f7de819a0b
https://github.com/galaxyproject/galaxy/commit/935f25aa32b3a22a53de02d5bfe4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-shared.js
M static/maps/mvc/grid/grid-shared.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/grid/grid-shared.js
Log Message:
-----------
Titles for abstract grids w/ plural set.
Commit: f83188e7f3c19a5686a623d9bb30f683cd04ff27
https://github.com/galaxyproject/galaxy/commit/f83188e7f3c19a5686a623d9bb30…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-view.js
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/grid/grid-view.js
Log Message:
-----------
Normal grid title propagation.
Commit: 97264e3de8d9ea8cd0b4cec9bbe91b1b3d81636d
https://github.com/galaxyproject/galaxy/commit/97264e3de8d9ea8cd0b4cec9bbe9…
Author: chambm <matt.chambers42(a)gmail.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-view-edit.js
Log Message:
-----------
Try to start personal CI build
Commit: 900699037da5db8528a51a2f0dd7bc287e346301
https://github.com/galaxyproject/galaxy/commit/900699037da5db8528a51a2f0dd7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-09 (Sat, 09 Sep 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_history_panel.py
Log Message:
-----------
Retry failed clicks more aggressively for Selenium tests.
Would have prevented from this (https://jenkins.galaxyproject.org/job/selenium/238/testReport/junit/seleniu…) failure in retrospect. Also refactor that common pattern into a helper and use throughout. Add missing @selenium_test decorator on that test also - it would have retried if this had been there and we would have a screenshot.
Commit: b9cff7ad91f4e157fc2f65e28d00969a4434c09a
https://github.com/galaxyproject/galaxy/commit/b9cff7ad91f4e157fc2f65e28d00…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-09 (Sat, 09 Sep 2017)
Changed paths:
M test/selenium_tests/test_published_histories_grid.py
Log Message:
-----------
Fix another issue with sorting by owner for published histories Selenium test.
Locally this never happens, but remotely sometimes when sorting by owner the histories are sorted by owner but not in the same order as the test was asserting. I would assume this is likely a postgres vs. sqlite difference - perhaps the former doesn't sort the rows by the order they were created within equal sort classifications (i.e. same owner) but the latter does. I've fixed this - the test should not have been asserting such a strong condition I don't think.
Commit: 928ad294936c4f6ca4ebc007963578527886af02
https://github.com/galaxyproject/galaxy/commit/928ad294936c4f6ca4ebc0079635…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-09 (Sat, 09 Sep 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
Localize displayed titles.
Commit: a2ef2cc4b95b1a5fd6f5be9d6ceb6cd1c8ed0e7d
https://github.com/galaxyproject/galaxy/commit/a2ef2cc4b95b1a5fd6f5be9d6ceb…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-09-10 (Sun, 10 Sep 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_history_panel.py
Log Message:
-----------
Merge pull request #4582 from jmchilton/selenium_fixes_23
Retry failed clicks more aggressively for Selenium tests.
Commit: a21f05d9a8aa457c7b73398caf946b5428ee24a9
https://github.com/galaxyproject/galaxy/commit/a21f05d9a8aa457c7b73398caf94…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-09-10 (Sun, 10 Sep 2017)
Changed paths:
M test/selenium_tests/test_published_histories_grid.py
Log Message:
-----------
Merge pull request #4586 from jmchilton/selenium_fixes_24
Fix another issue with sorting by owner for published histories Selenium test.
Commit: ca59aaeda017d605f05f6a22b8c6dc09a6f3be3c
https://github.com/galaxyproject/galaxy/commit/ca59aaeda017d605f05f6a22b8c6…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-10 (Sun, 10 Sep 2017)
Changed paths:
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
add the tags test
Commit: d78e60186b6138efe45c1b4107254e624d7424f2
https://github.com/galaxyproject/galaxy/commit/d78e60186b6138efe45c1b410725…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-10 (Sun, 10 Sep 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/jenkins/selenium/docker-compose.yml
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/history/options-menu.js
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-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/utils/uploadbox.js
M config/datatypes_conf.xml.sample
M config/dependency_resolvers_conf.xml.sample
M config/galaxy.ini.sample
A config/lmod_modules_mapping.yml.sample
A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml
A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js
A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
A doc/source/dev/finding_and_improving_slow_code.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/converters/biom1_to_biom2.xml
A lib/galaxy/datatypes/converters/biom2_to_biom1.xml
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/managers/libraries.py
A lib/galaxy/managers/library_datasets.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
A lib/galaxy/tools/deps/resolvers/lmod.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/checkers.py
M lib/galaxy/util/compression_utils.py
R lib/galaxy/webapps/galaxy/api/lda_datasets.py
A lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/work/context.py
M lib/galaxy/workflow/modules.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/xml_util.py
M scripts/tool_shed/build_ts_whoosh_index.py
M static/maps/mvc/history/options-menu.js.map
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-foldertoolbar-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/utils/uploadbox.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-of-pairs-collection-creator.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folder-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-librarytoolbar-view.js
M static/scripts/utils/uploadbox.js
A test-data/joiner_header_in1.tab
A test-data/joiner_header_in2.tab
A test-data/joiner_out1.bed
A test-data/joiner_out2.bed
A test-data/joiner_out3.bed
A test-data/joiner_out4.bed
A test-data/joiner_out5.tab
A test-data/joiner_out6.tab
A test-data/joiner_out7.tab
M test/api/test_histories.py
M test/api/test_libraries.py
M test/api/test_tools.py
M test/base/api.py
M test/base/driver_util.py
M test/base/interactor.py
M test/base/populators.py
R test/base/test_db_util.py
A test/base/testcase.py
M test/base/tool_shed_util.py
R test/base/twilltestcase.py
R test/functional/database_contexts.py
R test/functional/test_library_templates.py
M test/functional/test_toolbox.py
M test/functional/tools/composite.xml
M test/functional/tools/composite_output.xml
M test/functional/tools/composite_output_tests.xml
M test/functional/tools/metadata.xml
A test/functional/twilltestcase.py
M test/galaxy_selenium/navigates_galaxy.py
M test/integration/test_upload_configuration_options.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_history_panel.py
M test/selenium_tests/test_login.py
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_workflow_management.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/base/twilltestcase.py
M test/unit/tools/test_tool_deps.py
M tools/data_source/upload.py
M tools/filters/join.py
M tools/filters/joiner.xml
M tools/sr_assembly/velvetg.xml
Log Message:
-----------
Merge branch 'dev' into saved_histories_tests
Commit: 8533c717879f7505b8f293c1ba945f3db63addcb
https://github.com/galaxyproject/galaxy/commit/8533c717879f7505b8f293c1ba94…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-10 (Sun, 10 Sep 2017)
Changed paths:
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
use the wait_for_and_click_selector function
Commit: b61ca47c99da6661dee64d6612f8aa30daa464f8
https://github.com/galaxyproject/galaxy/commit/b61ca47c99da6661dee64d6612f8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-10 (Sun, 10 Sep 2017)
Changed paths:
M test/selenium_tests/test_history_sharing.py
Log Message:
-----------
Make history sharing tests more robust and informative.
- Be sure when sharing a history with a user we wait to actually see that user's e-mail address appear in the history's sharing list after submission.
- Print something for the failed history sharing assertions (I'm pretty sure they are 403 errors because some aspect of the sharing or login didn't work - but might as well verify).
Commit: e2730ca7143f71758d6cd18f129c566447423302
https://github.com/galaxyproject/galaxy/commit/e2730ca7143f71758d6cd18f129c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-10 (Sun, 10 Sep 2017)
Changed paths:
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_history_panel.py
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
Reduce duplication, increase robustness in Selenium history tests.
- set_tags() appeared in both published and saved history tests, refactored into navigates_galaxy with function name history_panel_add_tags
- is_displayed() appeared in both published and saved history tests, refactored into has_driver as selector_is_displayed
- Introduced history_panel_rename to reduce duplication across history panel tests and newer published and saved history tests.
- Removed custom history click option helper in saved and published history tests and just used the variant in navigates_galaxy.
- use wait_for_and_click a couple more places...
Commit: 1e832733db6c6d3e7e191886d836f05708a84440
https://github.com/galaxyproject/galaxy/commit/1e832733db6c6d3e7e191886d836…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-10 (Sun, 10 Sep 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
Improve error reporting in Selenium tests when ``wait_for_logged_in`` fails.
Previously just a notification about waiting for ``a.loggedin-only`` failed would show up. This doesn't indicate if the login failed completely or the masthead just failed to update. I suspect the login failed completely, but just in case I've updated the error handling to actually ping the API and check and print a better error message with this information.
New messages look like:
```
TimeoutException: Message: Failed waiting for masthead to update for login, but user API response indicates [test0ol61vs8fo] is logged in. This seems to be a bug in Galaxy. API response was [{u'username': u'test0ol61vs8fo', u'quota_percent': None, u'preferences': {}, u'total_disk_usage': 0.0, u'deleted': False, u'id': u'adb5f5c93f827949', u'nice_total_disk_usage': u'0 bytes', u'quota': None, u'email': u'test0ol61vs8fo(a)test.test', u'is_admin': False, u'tags_used': [], u'purged': False}].Timeout waiting on CSS selector [a.loggedin-only-x] to become visible.
```
and
```
TimeoutException: Message: Failed waiting for masthead to update for login, API indicates no user is logged in - there is a problem with this test. API response was [{u'quota_percent': None, u'nice_total_disk_usage': u'0 bytes', u'total_disk_usage': 0}]. Timeout waiting on CSS selector [a.loggedin-only] to become visible.
```
Commit: dcbe30515f02c3a9f7332f2f3a043132c6cf1fe5
https://github.com/galaxyproject/galaxy/commit/dcbe30515f02c3a9f7332f2f3a04…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-10 (Sun, 10 Sep 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
More robust rename for histories.
I think the wait_for_and_click_selector method will prevent errors like this one https://jenkins.galaxyproject.org/job/selenium/249/testReport/selenium_test….
Commit: 6b14dda216d103da518a906f4eda018eb58bafbe
https://github.com/galaxyproject/galaxy/commit/6b14dda216d103da518a906f4eda…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M static/maps/layout/page.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/layout/page.js
M static/scripts/mvc/grid/grid-view.js
Log Message:
-----------
Grids do a late initialization and the title isn't available until this happens (after display()), so provide a way to allow views to set title late if necessary.
Commit: dcc18134e79bcae7fb055162ba9f8d5f74e66b65
https://github.com/galaxyproject/galaxy/commit/dcc18134e79bcae7fb055162ba9f…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
generate random history names
Commit: 59d0e297f7217faed3d7c6d30e88678f1eaef600
https://github.com/galaxyproject/galaxy/commit/59d0e297f7217faed3d7c6d30e88…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
When title isn't set, revert to the default -- otherwise display()'d contents without titles show up with the previous and incorrect titles.
Commit: 2c40efb6c236220ccaffd7893fafa1b8969f1ad2
https://github.com/galaxyproject/galaxy/commit/2c40efb6c236220ccaffd7893faf…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/utils/utils.js
M static/maps/layout/page.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/layout/page.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/utils/utils.js
Log Message:
-----------
Minor refactor, use a single Utils.setWindowTitle() method.
Commit: a5dbf29e13e1d558ac1c6798e7952963b0599e6e
https://github.com/galaxyproject/galaxy/commit/a5dbf29e13e1d558ac1c6798e795…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Use standard naming for Utils import.
Commit: 51464551647635e5a1859b3d42ddf281a4f89ad8
https://github.com/galaxyproject/galaxy/commit/51464551647635e5a1859b3d42dd…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
generate random history names for the published history grid tests
Commit: 1359965a992f3a5f3a33276e6d1e1ea6afca0bd8
https://github.com/galaxyproject/galaxy/commit/1359965a992f3a5f3a33276e6d1e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
Merge pull request #4589 from jmchilton/selenium_fixes_26
Improve error reporting in Selenium tests when ``wait_for_logged_in`` fails.
Commit: 31f2168c3d7f321927a20f21baaddcbfec496389
https://github.com/galaxyproject/galaxy/commit/31f2168c3d7f321927a20f21baad…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_history_panel.py
M test/selenium_tests/test_published_histories_grid.py
A test/selenium_tests/test_saved_histories.py
Log Message:
-----------
Merge pull request #4587 from anatskiy/saved_histories_tests
Add Selenium tests for the Saved Histories
Commit: a190903bd031ff78f286977cdb7eaca04884de4c
https://github.com/galaxyproject/galaxy/commit/a190903bd031ff78f286977cdb7e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M test/selenium_tests/test_history_sharing.py
Log Message:
-----------
Merge pull request #4588 from jmchilton/selenium_fixes_25
Make history sharing Selenium tests more robust and informative.
Commit: 79a37830bb75ccd4d8c18236f7938a50a83f87c2
https://github.com/galaxyproject/galaxy/commit/79a37830bb75ccd4d8c18236f793…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_workflow_editor.py
Log Message:
-----------
Small improvements to workflow editor Selenium tests.
I saw a failed test earlier that would have been fixed by a switch to wait_for_and_click in workflow_editor_click_options. This makes that switch and moves some of these workflow editor helper functions into navigates_galaxy.py for reuse by other test cases and by library users.
Commit: 1aadd7866f6b94460a5703a8aa35949f7632adcf
https://github.com/galaxyproject/galaxy/commit/1aadd7866f6b94460a5703a8aa35…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js
Log Message:
-----------
Make client.
Commit: fd1926767996a161cd2fc8bd184e6835fd688765
https://github.com/galaxyproject/galaxy/commit/fd1926767996a161cd2fc8bd184e…
Author: Matt Chambers <matt.chambers42(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js
Log Message:
-----------
Merge pull request #2 from dannon/chambmdev
Make client
Commit: ecb4e06799fb61c4577e1a52276359149670cdf7
https://github.com/galaxyproject/galaxy/commit/ecb4e06799fb61c4577e1a522763…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M client/galaxy/scripts/utils/utils.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/utils/utils.js
Log Message:
-----------
We apparently always use '|' in the title, even though masthead uses '/'. It does look better.
Commit: ae1c68c7dbb9214def95e97a2f6714c68e23927b
https://github.com/galaxyproject/galaxy/commit/ae1c68c7dbb9214def95e97a2f67…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Set title on base admin page.
Commit: ff5b430319196a61e2a593b04a4bc60859062e3c
https://github.com/galaxyproject/galaxy/commit/ff5b430319196a61e2a593b04a4b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Workflow editor title fix (not new-style, to keep it simple and use the approach consistent with the .mako layout used.
Commit: 74a486084bcb5d0aef50bebe499b9b39b8a68a74
https://github.com/galaxyproject/galaxy/commit/74a486084bcb5d0aef50bebe499b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/style/less/library.less
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-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-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/style/blue/base.css
M static/style/blue/library.css
Log Message:
-----------
Merge pull request #4579 from martenson/fix-reload-error
datalibs: fix two bugs, refactor
Commit: c71d3035ab7bbcdfb682a39e4e9e3cb49417289d
https://github.com/galaxyproject/galaxy/commit/c71d3035ab7bbcdfb682a39e4e9e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/style/less/library.less
A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml
A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js
A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/style/blue/base.css
M static/style/blue/library.css
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_history_panel.py
M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_login.py
M test/selenium_tests/test_published_histories_grid.py
A test/selenium_tests/test_saved_histories.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into titles_in_views
Commit: 5da62ca264826bca0318a08f10d9d5e0ab6a3cc8
https://github.com/galaxyproject/galaxy/commit/5da62ca264826bca0318a08f10d9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M lib/galaxy/workflow/run.py
M test/api/test_workflows.py
Log Message:
-----------
Cancel workflow invocations when histories are deleted.
With test case, rebased with spelling fixes thanks to @nsoranzo.
xref #3555 (third point)
Commit: 7efe561867b7c5a3a16e873c215889c58d225277
https://github.com/galaxyproject/galaxy/commit/7efe561867b7c5a3a16e873c2158…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Rework invocation state tracking in API tests.
At the insistence of @nsoranzo, be more explicit about waiting for workflow test in API tests. While I was in there I also setup new abstractions for waiting on state and updated various workflow cancelling tests to use test_history context for better error reporting.
Commit: e1cdb740cb431104439dbbd63c2f1c0472d2c16b
https://github.com/galaxyproject/galaxy/commit/e1cdb740cb431104439dbbd63c2f…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-09-12 (Tue, 12 Sep 2017)
Changed paths:
M lib/galaxy/workflow/run.py
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #4580 from jmchilton/deleted_history
Cancel workflow invocations when histories are deleted.
Commit: 7e2727bc0a74868198e7e457f99df3d1e39f1ddb
https://github.com/galaxyproject/galaxy/commit/7e2727bc0a74868198e7e457f99d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-12 (Tue, 12 Sep 2017)
Changed paths:
M config/datatypes_conf.xml.sample
R lib/galaxy/datatypes/converters/bam_to_bai.xml
Log Message:
-----------
Remove bam to bai converter
This converter served no real purpose (you can download bam index files
by clicking on the floppy icon, and we never had a bai datatype).
Commit: c5a08186b7ff8090b5ec7191ed149c3e13c9aa90
https://github.com/galaxyproject/galaxy/commit/c5a08186b7ff8090b5ec7191ed14…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-12 (Tue, 12 Sep 2017)
Changed paths:
M lib/galaxy/jobs/runners/cli.py
Log Message:
-----------
Retry job submissions in ShellJobRunner
If I submit a large amount of jobs in a very short time I sometimes see
```
galaxy.jobs.runners.cli ERROR 2017-09-11 05:03:02,404 (17633) submission
failed (stderr): qsub: submit error (Invalid credential)
```
in my logs for a minor subset of jobs (2 out of 120 in the last instance
that this happened).
In this case waiting a little while and trying again solves the problem.
By default we will try submitting the job 3 times, and sleep 10 seconds
before trying again.
Commit: c0e2db2d98ead7f9d532ad0f5106d644019d5265
https://github.com/galaxyproject/galaxy/commit/c0e2db2d98ead7f9d532ad0f5106…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-09-12 (Tue, 12 Sep 2017)
Changed paths:
M config/datatypes_conf.xml.sample
R lib/galaxy/datatypes/converters/bam_to_bai.xml
Log Message:
-----------
Merge pull request #4598 from mvdbeek/remove_bai_converter
Remove bam to bai converter
Commit: 36a3a6b3d9c0b00c26ae861649983a441f725ae8
https://github.com/galaxyproject/galaxy/commit/36a3a6b3d9c0b00c26ae86164998…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-09-12 (Tue, 12 Sep 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/test/test.fast5.tar
A lib/galaxy/datatypes/test/test.fast5.tar.bz2
A lib/galaxy/datatypes/test/test.fast5.tar.gz
Log Message:
-----------
Merge pull request #4569 from jvolkening/fast5
fast5_archive datatype
Commit: 2e160935d9ceb3ca8441e3b51107594b9539573d
https://github.com/galaxyproject/galaxy/commit/2e160935d9ceb3ca8441e3b51107…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-12 (Tue, 12 Sep 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/utils/utils.js
M static/maps/layout/page.js.map
M static/maps/mvc/grid/grid-shared.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/history-list.js.map
M static/maps/mvc/tours.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/layout/page.js
M static/scripts/mvc/grid/grid-shared.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/history-list.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/utils/utils.js
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Merge pull request #4578 from dannon/titles_in_views
Delegate displaying of page titles to Layout.display()
Commit: 9468bef057f6372f75ceaee832457386c79e39cc
https://github.com/galaxyproject/galaxy/commit/9468bef057f6372f75ceaee83245…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-12 (Tue, 12 Sep 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_workflow_editor.py
Log Message:
-----------
Merge pull request #4592 from jmchilton/workflow_click_fix
Small improvements to workflow editor Selenium tests.
Commit: b3b71343c101ce7ca39ced3308bd2540dcccc59c
https://github.com/galaxyproject/galaxy/commit/b3b71343c101ce7ca39ced3308bd…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-12 (Tue, 12 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/tools/evaluation.py
Log Message:
-----------
Write out registry once per job
Commit: 51f2ecf857dbbdd0e2fd3c78d7f515a87b0ff7e5
https://github.com/galaxyproject/galaxy/commit/51f2ecf857dbbdd0e2fd3c78d7f5…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-12 (Tue, 12 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
Log Message:
-----------
Use a string template to write registry xml
Commit: 49884cdfa3d9cc06192d204c3cc0d727449987d5
https://github.com/galaxyproject/galaxy/commit/49884cdfa3d9cc06192d204c3cc0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-12 (Tue, 12 Sep 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/tools/actions/metadata.py
Log Message:
-----------
Remove references to integrated_datatypes_config
Commit: 26c7abb130bade73b64284956f0077f35067095f
https://github.com/galaxyproject/galaxy/commit/26c7abb130bade73b64284956f00…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-12 (Tue, 12 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-view-edit.js
M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js
Log Message:
-----------
Merge remote-tracking branch 'chambm/dev' into dev
Commit: 194b249e1d53a480a38910d51e24e267d3164a46
https://github.com/galaxyproject/galaxy/commit/194b249e1d53a480a38910d51e24…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-12 (Tue, 12 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
Log Message:
-----------
Fix import order
Commit: 60dd7306d04c47aa4a9b2efed149cb3c4d259a10
https://github.com/galaxyproject/galaxy/commit/60dd7306d04c47aa4a9b2efed149…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/model/metadata.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/pulsar.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/grids/repository_grids.py
Log Message:
-----------
Remove unreachable statements
Commit: 61e05670c26cb75b9a76e3660e049a6f9383a644
https://github.com/galaxyproject/galaxy/commit/61e05670c26cb75b9a76e3660e04…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
Log Message:
-----------
now unused imports
Commit: e33b35def3453d6158bf6ed4109c3ec2dbffbc37
https://github.com/galaxyproject/galaxy/commit/e33b35def3453d6158bf6ed4109c…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/model/metadata.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/pulsar.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/grids/repository_grids.py
Log Message:
-----------
Merge pull request #4603 from erasche/dead-code
Remove unreachable statements
Commit: ecd8b90e44decbef60db4359bf4837ef5b12ed1f
https://github.com/galaxyproject/galaxy/commit/ecd8b90e44decbef60db4359bf48…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
M lib/galaxy/jobs/runners/cli.py
Log Message:
-----------
Decrease log-level for resubmission msg
and specifiy log level directly in if/else clause. Thx @erasche.
Commit: 11d4380d2b40b4e18806f6b2d1e07f4a6eec1f8b
https://github.com/galaxyproject/galaxy/commit/11d4380d2b40b4e18806f6b2d1e0…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
M lib/galaxy/jobs/runners/cli.py
Log Message:
-----------
Merge pull request #4599 from mvdbeek/make_qsub_submissions_more_robust
Retry job submissions in ShellJobRunner
Commit: 38add849710c4e7bb8d350dfae2d7b86b7c8b50b
https://github.com/galaxyproject/galaxy/commit/38add849710c4e7bb8d350dfae2d…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/toolshed/scripts/mvc/groups/group-list-view.js
M static/maps/mvc/library/library-librarylist-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-librarylist-view.js
Log Message:
-----------
remove unused cruft
Commit: 2daf4317f1f22a683ae29f44e566ad9c2bf4883e
https://github.com/galaxyproject/galaxy/commit/2daf4317f1f22a683ae29f44e566…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M static/maps/mvc/library/library-librarylist-view.js.map
M static/scripts/mvc/library/library-librarylist-view.js
Log Message:
-----------
show the first page of search results
insted of the current selected (would hide short resutls)
Commit: bf8940071372d0244314795723a24118b3c622bf
https://github.com/galaxyproject/galaxy/commit/bf8940071372d0244314795723a2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M static/maps/mvc/library/library-librarylist-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-librarylist-view.js
Log Message:
-----------
remove unused requirements
thanks @anuprulez
Commit: 191d11c4a096df44e3e469328197358d6200dd20
https://github.com/galaxyproject/galaxy/commit/191d11c4a096df44e3e469328197…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
M lib/galaxy_ext/metadata/set_metadata.py
Log Message:
-----------
Python 3 fixes for set_metadata.py
Commit: cdca22b33e84053df4c6aa6eae7b2d9f5157d9a7
https://github.com/galaxyproject/galaxy/commit/cdca22b33e84053df4c6aa6eae7b…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
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
Log Message:
-----------
rebuild client
Commit: e7696027e489c0438fda83293b0efb04a494e465
https://github.com/galaxyproject/galaxy/commit/e7696027e489c0438fda83293b0e…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-13 (Wed, 13 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-library-view.js
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-library-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
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-library-view.js
Log Message:
-----------
remove cruft
Commit: 1f69ae5d5bc58a31963a91df2e74807c5746d76b
https://github.com/galaxyproject/galaxy/commit/1f69ae5d5bc58a31963a91df2e74…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/maps/mvc/library/library-dataset-view.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
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
refactor few functionas and rename variables
Commit: d63601eacf2ae5de703a24efb470255ee8baf535
https://github.com/galaxyproject/galaxy/commit/d63601eacf2ae5de703a24efb470…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-13 (Wed, 13 Sep 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 the bug with accessing length instead of the variable itself
Commit: ba3ffd82d3a56d9ae66e462d0fe82979e5e70a66
https://github.com/galaxyproject/galaxy/commit/ba3ffd82d3a56d9ae66e462d0fe8…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
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
Log Message:
-----------
rebuild client
Commit: b442113e76fde691577bf14bfd0717fcca166539
https://github.com/galaxyproject/galaxy/commit/b442113e76fde691577bf14bfd07…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
M lib/galaxy_ext/metadata/set_metadata.py
Log Message:
-----------
Don't use + on iterators.
Commit: 52436aa4f93d13a5d2345deaed7a8f0a343a0074
https://github.com/galaxyproject/galaxy/commit/52436aa4f93d13a5d2345deaed7a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/evaluation.py
Log Message:
-----------
Merge pull request #4600 from mvdbeek/datatypes_registroy_in_working_directory
Write datatypes registry xml to working directory
Commit: 4f93f88f0a2df07c5a8c3fa7c62fd4bda40fb3c1
https://github.com/galaxyproject/galaxy/commit/4f93f88f0a2df07c5a8c3fa7c62f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-13 (Wed, 13 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:
-----------
Allow fetchMore to actually specify a 0 offset when intentional. This should fix the mysterious missing history in multiview bug.
Commit: 1502e0067552b72b87853834d3f857a409ead379
https://github.com/galaxyproject/galaxy/commit/1502e0067552b72b87853834d3f8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/history/history-model.js
M static/maps/mvc/base/controlled-fetch-collection.js.map
M static/maps/mvc/history/history-model.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:
-----------
Some cruft fixing and configuring of Galaxy.debug output instead of commented out console.logs -- should help immensely for troubleshooting
Commit: a6acf116cd50aec61fbf9d670145e30f2273a5fc
https://github.com/galaxyproject/galaxy/commit/a6acf116cd50aec61fbf9d670145…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-13 (Wed, 13 Sep 2017)
Changed paths:
M lib/galaxy_ext/metadata/set_metadata.py
Log Message:
-----------
Merge pull request #4607 from natefoo/py3-set-meta
Python 3 fixes for set_metadata.py
Commit: a9bfb04caa41129ffb524b1caf880f1ce90544b5
https://github.com/galaxyproject/galaxy/commit/a9bfb04caa41129ffb524b1caf88…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-09-14 (Thu, 14 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-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
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-foldertoolbar-view.js.map
M static/maps/mvc/library/library-library-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-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
Log Message:
-----------
Merge pull request #4595 from martenson/datalib-various-fixes
Datalibs various fixes
Commit: cdb95d6045739175e440e68e643e0f4cebadfe50
https://github.com/galaxyproject/galaxy/commit/cdb95d6045739175e440e68e643e…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/toolshed/scripts/mvc/groups/group-list-view.js
M static/maps/mvc/library/library-librarylist-view.js.map
M static/scripts/mvc/library/library-librarylist-view.js
Log Message:
-----------
Merge pull request #4594 from martenson/fix-search-pagination
Fix datalib search pagination
Commit: 62e73a37d3736063113f2118b3e997449e54c75e
https://github.com/galaxyproject/galaxy/commit/62e73a37d3736063113f2118b3e9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-14 (Thu, 14 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-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-list-view.js
M lib/galaxy/app.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy_ext/metadata/set_metadata.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-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-dataset-view.js
M static/scripts/mvc/library/library-folder-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
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into fix_missing_histories
Commit: 95969267c226193152e62b537824e6567144c1db
https://github.com/galaxyproject/galaxy/commit/95969267c226193152e62b537824…
Author: Marius van den Beek <m.vandenbeek(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/galaxy/scripts/mvc/history/history-model.js
M static/maps/mvc/base/controlled-fetch-collection.js.map
M static/maps/mvc/history/history-model.js.map
M static/scripts/bundled/admin.bundled.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 #4610 from dannon/fix_missing_histories
Multiview missing histories fix
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: 2c128b097a07057f4d5a6f9c622eab0f5dabcf3b
https://github.com/galaxyproject/galaxy/commit/2c128b097a07057f4d5a6f9c622e…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
A test/selenium_tests/test_custom_builds.py
Log Message:
-----------
add custom builds tests
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: 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: 8b9e91310fd98c9e21bc3511df940b0cba5720b7
https://github.com/galaxyproject/galaxy/commit/8b9e91310fd98c9e21bc3511df94…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
Merge branch 'release_17.05' into dev
Commit: 3f38e81cb7bb2246cc3c79dd10dc5992685f1337
https://github.com/galaxyproject/galaxy/commit/3f38e81cb7bb2246cc3c79dd10dc…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/webapps/galaxy/config_watchers.py
A test/integration/test_data_manager_table_reload.py
Log Message:
-----------
Update tables to watch when installing new data manager
Commit: 843d2e420011cde58e3742cacc58d3c6f1ab6255
https://github.com/galaxyproject/galaxy/commit/843d2e420011cde58e3742cacc58…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Assign correct guids to DM tools after TS install
Commit: d6ae9127ebb7c654ea93f98b1de18ccb92705713
https://github.com/galaxyproject/galaxy/commit/d6ae9127ebb7c654ea93f98b1de1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix group creation label in admin panel
Commit: d247d698a29e3e24816068624061411be97d6ad1
https://github.com/galaxyproject/galaxy/commit/d247d698a29e3e24816068624061…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-14 (Thu, 14 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix auto create checkbox name
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
Commit: c677621481abf7823f2d77a506c8aa6908070022
https://github.com/galaxyproject/galaxy/commit/c677621481abf7823f2d77a506c8…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Merge pull request #4619 from guerler/fix_group_label
Fix group creation label in admin panel and checkbox name
Commit: d06fb09f4bb93906ef36faf0c947eb5625c457e9
https://github.com/galaxyproject/galaxy/commit/d06fb09f4bb93906ef36faf0c947…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/tool_shed/tools/tool_validator.py
A test/integration/tool_sheds_conf.xml
Log Message:
-----------
Make DynamicOptions use updated tool_data_tables
Otherwise a restart would be necessary after adding items to a data
table.
Commit: 2e6654b18bd2a38f39d202e35ee5d24562122b3a
https://github.com/galaxyproject/galaxy/commit/2e6654b18bd2a38f39d202e35ee5…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/tools/parameters/dynamic_options.py
M test/integration/test_data_manager_table_reload.py
Log Message:
-----------
Linting fixes
Commit: a4c4d826dca64b2d85bd8c38cccf9cf6f7762008
https://github.com/galaxyproject/galaxy/commit/a4c4d826dca64b2d85bd8c38cccf…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
Log Message:
-----------
Make watchdog a conditional dependency
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
Commit: 4b403008270bf26e29f037ae902526641dea8e3e
https://github.com/galaxyproject/galaxy/commit/4b403008270bf26e29f037ae9025…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/config.py
M lib/tool_shed/tool_shed_registry.py
Log Message:
-----------
Remove unused root_dir argument
Commit: 2d844a86e7b1534c4211d4a3de7de6e367b5fd44
https://github.com/galaxyproject/galaxy/commit/2d844a86e7b1534c4211d4a3de7d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/dependencies/dev-requirements.txt
Log Message:
-----------
Add watchdog to dev-requirements so it is available for integration tests
Commit: ac084495978a8e5b607d90cf45dfb36c853aaf79
https://github.com/galaxyproject/galaxy/commit/ac084495978a8e5b607d90cf45df…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M templates/webapps/galaxy/admin/sanitize_whitelist.mako
Log Message:
-----------
Swap sanitize whitelist form to use a post.
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: 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
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.
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: 69af37f653569117371413bfadd06e5428486526
https://github.com/galaxyproject/galaxy/commit/69af37f653569117371413bfadd0…
Author: Vahid <VJalili(a)users.noreply.github.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/objectstore/__init__.py
Log Message:
-----------
Typo fix
Commit: fe88dab79b0b47245c079ebc372563392c917f30
https://github.com/galaxyproject/galaxy/commit/fe88dab79b0b47245c079ebc3725…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/objectstore/__init__.py
Log Message:
-----------
Merge pull request #4628 from VJalili/patch-3
Typo fix
Commit: 2c77d386def0dc21b8aa40d5d7cf5f8934c16a74
https://github.com/galaxyproject/galaxy/commit/2c77d386def0dc21b8aa40d5d7cf…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/tools/evaluation.py
Log Message:
-----------
Write out registry once per job
Commit: 860f0ab6ba6c45c98b5c9f3f002096cc9ef0c7b6
https://github.com/galaxyproject/galaxy/commit/860f0ab6ba6c45c98b5c9f3f0020…
Author: Vahid <VJalili(a)users.noreply.github.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Some function description updates
Commit: e3e26ae202369876eb1523562b2582f2a15495cb
https://github.com/galaxyproject/galaxy/commit/e3e26ae202369876eb1523562b25…
Author: Vahid <VJalili(a)users.noreply.github.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Updated a comment
Commit: 3cca06a153253f65f752d1f80aae2fd2e3cf221e
https://github.com/galaxyproject/galaxy/commit/3cca06a153253f65f752d1f80aae…
Author: Vahid <VJalili(a)users.noreply.github.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
updated a comment.
Commit: 604fdde4248dc2d7f261e63449ab5530463058a3
https://github.com/galaxyproject/galaxy/commit/604fdde4248dc2d7f261e63449ab…
Author: Vahid <VJalili(a)users.noreply.github.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
typo
Commit: 2897992ab56b69164a916ec400a2ed92b9c72d20
https://github.com/galaxyproject/galaxy/commit/2897992ab56b69164a916ec400a2…
Author: Vahid <VJalili(a)users.noreply.github.com>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Refactored a dataset variable to hda
Commit: ea7b27443715730597e273b315dce875910738ce
https://github.com/galaxyproject/galaxy/commit/ea7b27443715730597e273b315dc…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/model/__init__.py
Log Message:
-----------
Merge pull request #4629 from VJalili/patch-3
Updated function description and fix some typos
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
Commit: 0624a043a73f1a16fc36621b1c61a5cf52c67ba4
https://github.com/galaxyproject/galaxy/commit/0624a043a73f1a16fc36621b1c61…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M .travis.yml
Log Message:
-----------
remove macos testing
Commit: 432d7f44053a7c7d1fde1504e3f382edf2a539ec
https://github.com/galaxyproject/galaxy/commit/432d7f44053a7c7d1fde1504e3f3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-16 (Sat, 16 Sep 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Restore correct metadata path in setup_external_metdata
This is a change I shouldn't have touched in
https://github.com/galaxyproject/galaxy/pull/4600
Commit: 9d3af63660461c8738782f0a3903e8112e1e5c93
https://github.com/galaxyproject/galaxy/commit/9d3af63660461c8738782f0a3903…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-16 (Sat, 16 Sep 2017)
Changed paths:
M test/integration/test_data_manager_table_reload.py
Log Message:
-----------
Skip DataManagerIntegrationTestCase when watchdog unavailable
Commit: e03ee53f3c398fe429ba1fe8693782a06b20cd73
https://github.com/galaxyproject/galaxy/commit/e03ee53f3c398fe429ba1fe86937…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-16 (Sat, 16 Sep 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/tools/actions/metadata.py
Log Message:
-----------
Remove references to integrated_datatypes_config
Commit: 22b0542d0bb7a2f88b1503b53a8950d236be0f25
https://github.com/galaxyproject/galaxy/commit/22b0542d0bb7a2f88b1503b53a89…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-16 (Sat, 16 Sep 2017)
Changed paths:
M .travis.yml
Log Message:
-----------
Merge pull request #4631 from martenson/disable-macos-travis
disable MacOS CI on travis
Commit: 6dbd47e661971969c734a46938a06c42b85eea8f
https://github.com/galaxyproject/galaxy/commit/6dbd47e661971969c734a46938a0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-16 (Sat, 16 Sep 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Merge pull request #4632 from mvdbeek/fix_unintended_change
[BUG] Restore tool provided metadata path in setup_external_metdata
Commit: 4c9cc67a8f107887f341b1e386b2ac994acc2ba5