Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: dd5e3c6c68077268d3d551857e508d914ed1d3f9
https://github.com/galaxyproject/galaxy/commit/dd5e3c6c68077268d3d551857e50…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-12-17 (Mon, 17 Dec 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Move error stack controller endpoint to tools api
Commit: 3665ef056d377960edd92b558fcf903f9280a204
https://github.com/galaxyproject/galaxy/commit/3665ef056d377960edd92b558fcf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-12-17 (Mon, 17 Dec 2018)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
A client/galaxy/scripts/components/admin/AdminServices.js
A client/galaxy/scripts/components/admin/ErrorStack.vue
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Add error stack vue component and client side routes
Commit: 8eceb76ee1e36ae14403ccfbaf082ed6395451b6
https://github.com/galaxyproject/galaxy/commit/8eceb76ee1e36ae14403ccfbaf08…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-12-17 (Mon, 17 Dec 2018)
Changed paths:
R templates/admin/tool_errors.mako
Log Message:
-----------
Remove legacy tool error mako file
Commit: 481243c3ed0a31ebde7a4ed85592e7068e5e4b45
https://github.com/galaxyproject/galaxy/commit/481243c3ed0a31ebde7a4ed85592…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-12-17 (Mon, 17 Dec 2018)
Changed paths:
M client/galaxy/scripts/components/admin/ErrorStack.vue
Log Message:
-----------
Remove unused attribute
Commit: 462303043d47437486fb0d6df5b65d43f8235790
https://github.com/galaxyproject/galaxy/commit/462303043d47437486fb0d6df5b6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-12-17 (Mon, 17 Dec 2018)
Changed paths:
M client/galaxy/scripts/components/admin/ErrorStack.vue
Log Message:
-----------
Remove unused tag in vue component
Commit: 8a439cfb0f81e2ca8a7ab8c2526452c27a875046
https://github.com/galaxyproject/galaxy/commit/8a439cfb0f81e2ca8a7ab8c25264…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-12-17 (Mon, 17 Dec 2018)
Changed paths:
M client/galaxy/scripts/components/admin/ErrorStack.vue
Log Message:
-----------
Allow sorting by file name in error log table
Commit: 30d5baf90978f79b57fbd7f8008a76c05fe5c11d
https://github.com/galaxyproject/galaxy/commit/30d5baf90978f79b57fbd7f8008a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-12-17 (Mon, 17 Dec 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tools.py
Log Message:
-----------
Fix comment section of error stack api endpoint
Commit: bc695f898c3f7098cc6cef1acb68bcbec2c77f0b
https://github.com/galaxyproject/galaxy/commit/bc695f898c3f7098cc6cef1acb68…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-12-19 (Wed, 19 Dec 2018)
Changed paths:
M client/galaxy/scripts/components/admin/ErrorStack.vue
Log Message:
-----------
Use bootstrap vue message alerts
Commit: d53e33cf9f814700d14743d8addd4e059b380ebd
https://github.com/galaxyproject/galaxy/commit/d53e33cf9f814700d14743d8addd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-12-21 (Fri, 21 Dec 2018)
Changed paths:
M client/galaxy/scripts/app/singleton.js
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/extended.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/components/GalaxyLoader.vue
M client/galaxy/scripts/components/admin/AdminServices.js
A client/galaxy/scripts/components/admin/DisplayApplications.vue
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-view.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/history/hdca-li.js
M client/galaxy/scripts/mvc/history/history-item-li.js
M client/galaxy/scripts/mvc/list/list-item.js
M client/galaxy/scripts/mvc/list/list-view.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/utils/utils.js
M config/datatypes_conf.xml.sample
M config/tool_conf.xml.sample
M doc/source/dev/build_a_job_runner.rst
M lib/galaxy/datatypes/binary.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/filter_from_file.xml
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/verify/__init__.py
A lib/galaxy/webapps/galaxy/api/display_applications.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
R templates/webapps/galaxy/admin/view_display_applications.mako
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/tool_provided_metadata_10.xml
A test/functional/tools/tool_provided_metadata_11.xml
A test/functional/tools/tool_provided_metadata_12.xml
M test/selenium_tests/test_admin_app.py
Log Message:
-----------
Merge branch 'dev' into admin_error_log
Commit: d385be993a4939f5741c54296a041ab994731f50
https://github.com/galaxyproject/galaxy/commit/d385be993a4939f5741c54296a04…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-12-21 (Fri, 21 Dec 2018)
Changed paths:
M client/galaxy/scripts/components/admin/ErrorStack.vue
Log Message:
-----------
Fix consistency of parameter naming to in error stack component
Commit: 65419bd3763dcfc78d92808a6a323ed10ee014ef
https://github.com/galaxyproject/galaxy/commit/65419bd3763dcfc78d92808a6a32…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-01-02 (Wed, 02 Jan 2019)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/components/admin/AdminServices.js
A client/galaxy/scripts/components/admin/ErrorStack.vue
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
R templates/admin/tool_errors.mako
Log Message:
-----------
Merge pull request #7124 from guerler/admin_error_log
Adds a vue component to display tool errors in the admin panel
Compare: https://github.com/galaxyproject/galaxy/compare/a8944f5a039a...65419bd3763d
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0d28c65c3d1ce504850a3ba94b99099abb68cd92
https://github.com/galaxyproject/galaxy/commit/0d28c65c3d1ce504850a3ba94b99…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-12-31 (Mon, 31 Dec 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/api/test_tools.py
Log Message:
-----------
Allow anonymous downloading of test-data files
Commit: 6791f3b99905ac0db0a8e2c23f38a4bce8b1d3c8
https://github.com/galaxyproject/galaxy/commit/6791f3b99905ac0db0a8e2c23f38…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-12-31 (Mon, 31 Dec 2018)
Changed paths:
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/webapps/galaxy/api/tools.py
M test/api/test_tools.py
Log Message:
-----------
Also allow downloading test-data directories
This is (apparently ...) used by tools that create/test
directories in the extra_files_path.
Commit: e30ff62b0e1069d4316e15660d130df87e6c6217
https://github.com/galaxyproject/galaxy/commit/e30ff62b0e1069d4316e15660d13…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-12-31 (Mon, 31 Dec 2018)
Changed paths:
M lib/galaxy/util/streamball.py
M lib/galaxy/webapps/galaxy/api/tools.py
Log Message:
-----------
Move stream_archive to galaxy.util.streamball
Commit: 5490a6db7c5fa5db431c64b51998f923110106a6
https://github.com/galaxyproject/galaxy/commit/5490a6db7c5fa5db431c64b51998…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-12-31 (Mon, 31 Dec 2018)
Changed paths:
M test/functional/tools/composite_output_tests.xml
Log Message:
-----------
Add `extra_files type="directory"` test
Commit: 95f866d77c4adbe2055b28f37808b709658a9903
https://github.com/galaxyproject/galaxy/commit/95f866d77c4adbe2055b28f37808…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-12-31 (Mon, 31 Dec 2018)
Changed paths:
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/interactor.py
Log Message:
-----------
Make type="directory" remote compatible
We download an archive containing the specified directory
for tests.
Commit: f1acff02ded73df1014316f276b7e89d9decec37
https://github.com/galaxyproject/galaxy/commit/f1acff02ded73df1014316f276b7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-12-31 (Mon, 31 Dec 2018)
Changed paths:
M test/functional/tools/composite_output_tests.xml
Log Message:
-----------
Quote remaining parametera
Commit: 4877bfafa6cd5b8af419c9dad0615bcd39e9559e
https://github.com/galaxyproject/galaxy/commit/4877bfafa6cd5b8af419c9dad061…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2019-01-01 (Tue, 01 Jan 2019)
Changed paths:
M test/api/test_tools.py
Log Message:
-----------
Test that test-data paths outside of test-data folder cannot be downloaded
Commit: e87e1561e336bb187ac5e40f55a107614bc38686
https://github.com/galaxyproject/galaxy/commit/e87e1561e336bb187ac5e40f55a1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-01-02 (Wed, 02 Jan 2019)
Changed paths:
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/util/streamball.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/api/test_tools.py
M test/functional/tools/composite_output_tests.xml
Log Message:
-----------
Merge pull request #7160 from mvdbeek/unprivileged_remote_tool_tests
Unprivileged remote tool tests
Compare: https://github.com/galaxyproject/galaxy/compare/6869883309bb...e87e1561e336
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d3cdf43563c1f3eacfae7cb5f887589a81f2acc6
https://github.com/galaxyproject/galaxy/commit/d3cdf43563c1f3eacfae7cb5f887…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-12-13 (Thu, 13 Dec 2018)
Changed paths:
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/cloud.py
M lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/s3.py
M test/unit/test_objectstore.py
Log Message:
-----------
Add to_dict() to ObjectStores.
Dictify an object store configuration back to its to config_dict description.
Commit: 9c08b416dbdbac16106f7dbd5b7eaf805d2ec996
https://github.com/galaxyproject/galaxy/commit/9c08b416dbdbac16106f7dbd5b7e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-01-01 (Tue, 01 Jan 2019)
Changed paths:
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/cloud.py
M lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/s3.py
M test/unit/test_objectstore.py
Log Message:
-----------
Merge pull request #7110 from jmchilton/os_to_dict
Add to_dict() to ObjectStores.
Compare: https://github.com/galaxyproject/galaxy/compare/4c741ef00ef0...9c08b416dbdb
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.