Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8a4c63738897a7324e31683076f4e77253ef3408
https://github.com/galaxyproject/galaxy/commit/8a4c63738897a7324e31683076f4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-18 (Mon, 18 Sep 2017)
Changed paths:
M lib/galaxy/managers/libraries.py
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
optimize the process of identifying public libraries
this aims to speed up the library loading considerably
Commit: c5d29be0a2c2c2d16be13d0fa528ad01e5022e1d
https://github.com/galaxyproject/galaxy/commit/c5d29be0a2c2c2d16be13d0fa528…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-19 (Tue, 19 Sep 2017)
Changed paths:
M lib/galaxy/managers/libraries.py
Log Message:
-----------
avoid mutable default, improve docs
switch to set comprehension
Commit: 7d394f202d84200e9b4a3c63ce42bf7baf53ccc8
https://github.com/galaxyproject/galaxy/commit/7d394f202d84200e9b4a3c63ce42…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-19 (Tue, 19 Sep 2017)
Changed paths:
M lib/galaxy/managers/libraries.py
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
Merge pull request #4640 from martenson/datalibs-optimize-access-checks
optimize the process of identifying public libraries
Compare: https://github.com/galaxyproject/galaxy/compare/3f51e7dc1ef9...7d394f202d84
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 87bb576c39dadadbf119167dee581a6801a54cea
https://github.com/galaxyproject/galaxy/commit/87bb576c39dadadbf119167dee58…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-19 (Tue, 19 Sep 2017)
Changed paths:
M test/selenium_tests/framework.py
M test/selenium_tests/test_custom_builds.py
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
Improved state handling for @anatskiy-style Selenium tests.
These tests aren't idealized unittest.TestCase because they initialize class level data in instance level methods. While this isn't ideal, it is seems an entirely fair workaround given that SeleniumTestCase setups up the Selenium connection itself in an instance method - so class-level initializers would not be able to setup Galaxy data. Since I think we will continue using this pattern then, probably best to formalize it a bit and improve error handling.
This provides a formal super class for these test cases that provides a uniform method for setting up the class level data and tracks whether this is successful or not. This serves a couple purposes beyond simple uniformity. First, it tracks if the state has actually been setup or not and will skip subsequent tests if it hasn't. Some of these tests aren't passing very consistently on Jenkins and so we get a bunch of extra noise for tests that are attempting to run without their preconditions met - this will fix that and make the original errors much more clear. Moving the "hacky" part of this into the framework itself also means the tests themselves don't have to repeat hacks like seeing if variables are set with ``getattr`` and such - I always prefer one framework hack to a dozen application hacks.
Commit: 3f51e7dc1ef99a68aa8694cfe6858a70e9482e50
https://github.com/galaxyproject/galaxy/commit/3f51e7dc1ef99a68aa8694cfe685…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-19 (Tue, 19 Sep 2017)
Changed paths:
M test/selenium_tests/framework.py
M test/selenium_tests/test_custom_builds.py
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_saved_histories.py
Log Message:
-----------
Merge pull request #4647 from jmchilton/selenium_fixes_28
Improved state handling for @anatskiy-style Selenium tests.
Compare: https://github.com/galaxyproject/galaxy/compare/844f083c7b8c...3f51e7dc1ef9
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
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: 260a8346197e4a8997f7033f1d99be7acdf302c6
https://github.com/galaxyproject/galaxy/commit/260a8346197e4a8997f7033f1d99…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-18 (Mon, 18 Sep 2017)
Changed paths:
M .travis.yml
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/history/history-model.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-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/galaxy/scripts/mvc/user/user-custom-builds.js
M client/toolshed/scripts/mvc/groups/group-detail-view.js
M client/toolshed/scripts/mvc/groups/group-list-view.js
M create_db.sh
M extract_dataset_parts.sh
M lib/galaxy/jobs/__init__.py
M lib/galaxy/model/__init__.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webhooks/__init__.py
M manage_db.sh
M manage_tools.sh
M static/maps/mvc/base/controlled-fetch-collection.js.map
M static/maps/mvc/history/history-model.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-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/maps/mvc/user/user-custom-builds.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/base/controlled-fetch-collection.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-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/user/user-custom-builds.js
M static/toolshed/scripts/mvc/groups/group-detail-view.js
M static/toolshed/scripts/mvc/groups/group-list-view.js
M templates/webapps/galaxy/admin/sanitize_whitelist.mako
Log Message:
-----------
Merge branch 'dev' into custom_builds_tests
Commit: db67d254ed02f628254464f8b60d2043b871f282
https://github.com/galaxyproject/galaxy/commit/db67d254ed02f628254464f8b60d…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-18 (Mon, 18 Sep 2017)
Changed paths:
M test/selenium_tests/test_custom_builds.py
Log Message:
-----------
don't test the uploading of fasta files
Commit: e01b57da58d55763870ad7943a3c04b0e6a34c5b
https://github.com/galaxyproject/galaxy/commit/e01b57da58d55763870ad7943a3c…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-09-18 (Mon, 18 Sep 2017)
Changed paths:
M test/selenium_tests/test_custom_builds.py
Log Message:
-----------
small improvement
Commit: 844f083c7b8c9d29d95a4bca3817db3f918273a4
https://github.com/galaxyproject/galaxy/commit/844f083c7b8c9d29d95a4bca3817…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-19 (Tue, 19 Sep 2017)
Changed paths:
A test/selenium_tests/test_custom_builds.py
Log Message:
-----------
Merge pull request #4641 from anatskiy/custom_builds_tests
Custom Builds tests
Compare: https://github.com/galaxyproject/galaxy/compare/a17ae7b90cda...844f083c7b8c
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
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: 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: 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: 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: 706434da41e70922f3d723b8cc390f3d0e5d984a
https://github.com/galaxyproject/galaxy/commit/706434da41e70922f3d723b8cc39…
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
M test/integration/test_resolvers.py
Log Message:
-----------
Append temp dirs to test_driver list of temp dirs
Thanks for the hint @jmchilton.
Commit: 642aaa811bb99a0ef3b532eac3fd5d245972994a
https://github.com/galaxyproject/galaxy/commit/642aaa811bb99a0ef3b532eac3fd…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-16 (Sat, 16 Sep 2017)
Changed paths:
M test/base/driver_util.py
Log Message:
-----------
Do cleanup if skip_cleanup is not set
Commit: a17ae7b90cda7c6c71875f0a7b332410dab15a43
https://github.com/galaxyproject/galaxy/commit/a17ae7b90cda7c6c71875f0a7b33…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-19 (Tue, 19 Sep 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/dev-requirements.txt
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/config_watchers.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/tools/tool_validator.py
M test/base/driver_util.py
A test/integration/test_data_manager_table_reload.py
M test/integration/test_resolvers.py
A test/integration/tool_sheds_conf.xml
Log Message:
-----------
Merge pull request #4617 from mvdbeek/data_manager_watch_new_tables
Allow adding new data tables without restart
Compare: https://github.com/galaxyproject/galaxy/compare/d9a805536840...a17ae7b90cda