Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 569ceb4405bef72c420c91c86f4c203f6d7ed29f https://github.com/galaxyproject/galaxy/commit/569ceb4405bef72c420c91c86f4c2... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/configuration.py
Log Message: ----------- Try reloading tool via control_task
Commit: 1223c420cb48ef05db61303ef784ff276716cdc3 https://github.com/galaxyproject/galaxy/commit/1223c420cb48ef05db61303ef784f... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/tools/toolbox/base.py
Log Message: ----------- Explicitly monitor shed_tool_conf for changes
Commit: 1d04755fa39657bb824ca986e41224e77d59d35f https://github.com/galaxyproject/galaxy/commit/1d04755fa39657bb824ca986e4122... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/queue_worker.py
Log Message: ----------- Reference app instead of self when reloading toolbox
Commit: 6e4897dee7d66587d75b445f9211b51f07490241 https://github.com/galaxyproject/galaxy/commit/6e4897dee7d66587d75b445f9211b... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message: ----------- Do not load individual new toolpanel elements (We rely on the tool watcher to reload the toolbox)
Commit: f7693802ce0d2e555cb283a09d0a83740e8664e2 https://github.com/galaxyproject/galaxy/commit/f7693802ce0d2e555cb283a09d0a8... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message: ----------- Remove in-memory removal of tools (rely on toolbox reload)
Commit: 7b259fb10a5f1289ba81ec749a1e86ccf3fb7303 https://github.com/galaxyproject/galaxy/commit/7b259fb10a5f1289ba81ec749a1e8... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/tools/toolbox/base.py
Log Message: ----------- Remove one more unused panel manipulation function
Commit: 128ee9b72a6c7f693a990c65b1c4b34d9be193c5 https://github.com/galaxyproject/galaxy/commit/128ee9b72a6c7f693a990c65b1c4b... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message: ----------- Remove unused variable
Commit: 81bf7b382bc1003c0d1a3b0a019ea7e57d6ecce9 https://github.com/galaxyproject/galaxy/commit/81bf7b382bc1003c0d1a3b0a019ea... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M test/unit/tools/test_watcher.py
Log Message: ----------- Start conf_watcher thread in unit tests
Commit: e340fd4e06f7b8a2063448bad8e2c594af39cdb9 https://github.com/galaxyproject/galaxy/commit/e340fd4e06f7b8a2063448bad8e2c... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M test/unit/tools/test_watcher.py
Log Message: ----------- Wait before triggering a callback in test_watcher.py
Commit: 3206421b91a305d1e38672a1bccd52c732705266 https://github.com/galaxyproject/galaxy/commit/3206421b91a305d1e38672a1bccd5... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M test/unit/tools/test_toolbox.py
Log Message: ----------- Remove update_shed_conf test
We do not update the toolbox in memory, so this test is obsolete
Commit: fe158de11109140b22c408cd6640b547ffd4db30 https://github.com/galaxyproject/galaxy/commit/fe158de11109140b22c408cd6640b... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py
Log Message: ----------- Remove panel_manager tests for deactivated tools
Deactivate tests that rely on deactivating, but not removing entries from tool_conf. For tests that test changes in tool_panel, load a new toolbox after making the changes.
Commit: ad86e2c7840fa9129263fdfb144959c158653874 https://github.com/galaxyproject/galaxy/commit/ad86e2c7840fa9129263fdfb14495... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
Log Message: ----------- Add sleep to allow toolbox to finish loading
Commit: ded1db8b3834bf3de6897b2163a9d208828d259d https://github.com/galaxyproject/galaxy/commit/ded1db8b3834bf3de6897b2163a9d... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
Log Message: ----------- Remove test for deactivated tools and sections
These are tests that verify that deactivated tools were present in the correct tool panel section.
Commit: 693eb5d0c91061fdbe052b41be1e78f4c58f57cb https://github.com/galaxyproject/galaxy/commit/693eb5d0c91061fdbe052b41be1e7... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
Log Message: ----------- Wait 2 seconds after touch shed_tool_conf.xml
The file watcher monitors for changes every second, so 2 seconds should be enough to let tests that check the tool panel after installing new tools pass.
Commit: 2fb4045abd61b9ccb1afb4e5e422ad6e73167db8 https://github.com/galaxyproject/galaxy/commit/2fb4045abd61b9ccb1afb4e5e422a... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py
Log Message: ----------- Also reload data managers upon touching data_manager.conf
Commit: f6fc5ed44299f2d1a9ac1c966d43281fd9515bf0 https://github.com/galaxyproject/galaxy/commit/f6fc5ed44299f2d1a9ac1c966d432... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py
Log Message: ----------- Shut down old data manager watchers
Commit: abd4fa611a3f1d4d089a03aef48ecb43383bb101 https://github.com/galaxyproject/galaxy/commit/abd4fa611a3f1d4d089a03aef48ec... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py
Log Message: ----------- Implement hashing for tool conf watcher
If modification time of watched files changes, only trigger event if hashes differ as well
Commit: 49ab74827cd0905cd0fa62eee7a5643b43ad41d9 https://github.com/galaxyproject/galaxy/commit/49ab74827cd0905cd0fa62eee7a56... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/tools/toolbox/watcher.py
Log Message: ----------- Log who's triggering a reload
Commit: a2669c565ae7c25bcd20c9831a470bbc0731597c https://github.com/galaxyproject/galaxy/commit/a2669c565ae7c25bcd20c9831a470... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message: ----------- Add back integrated_tool_panel saving
Commit: 6fc46a8c46549bc43fca00cfbd2e32b07db158d5 https://github.com/galaxyproject/galaxy/commit/6fc46a8c46549bc43fca00cfbd2e3... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/base.py
Log Message: ----------- Directly reload toolbox or data manager when watcher triggers reload
Commit: 054fbd05cb2ca3918f0dd2819cc71e5485ef4580 https://github.com/galaxyproject/galaxy/commit/054fbd05cb2ca3918f0dd2819cc71... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/tool_shed/metadata/metadata_generator.py
Log Message: ----------- Use the tool_data_tables.tool_data_path, to avoid persisting the temporary in-memory path to the data table
Commit: 612eea85e6e2322d277f4210005d2efbddaae3e1 https://github.com/galaxyproject/galaxy/commit/612eea85e6e2322d277f4210005d2... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py
Log Message: ----------- Fix reload thread for uwsgi workers.
and fix typos
Commit: 1bc84e0b4f5a77d018126656fc2808ed66c4712e https://github.com/galaxyproject/galaxy/commit/1bc84e0b4f5a77d018126656fc280... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/watcher.py
Log Message: ----------- Do not call start() method of watchter
as this happens when it starts watching a file.
Commit: b8695b36280f195242215c56cffad9aff5a7fad4 https://github.com/galaxyproject/galaxy/commit/b8695b36280f195242215c56cffad... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/tools/toolbox/watcher.py
Log Message: ----------- One last attempt to revive launched thread
Commit: 9e36a15e22f92fd3913a1dbed0700bcae91b61e7 https://github.com/galaxyproject/galaxy/commit/9e36a15e22f92fd3913a1dbed0700... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py
Log Message: ----------- Transplant tool conf watcher thread
Commit: 95c0e3cbf78e45f7786cab918835004dc67c156d https://github.com/galaxyproject/galaxy/commit/95c0e3cbf78e45f7786cab9188350... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py
Log Message: ----------- Also reload conf_watchers for data managers
Commit: c0cef19eb7a68e61ac30d9eb55b6bef14705648d https://github.com/galaxyproject/galaxy/commit/c0cef19eb7a68e61ac30d9eb55b6b... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/queue_worker.py
Log Message: ----------- Reload data managers after reloading the toolbox
Commit: 3d42be5f234d837ff5fa3792c53d138d3e28fcac https://github.com/galaxyproject/galaxy/commit/3d42be5f234d837ff5fa3792c53d1... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths: M lib/galaxy/tools/toolbox/watcher.py
Log Message: ----------- Trigger event with lock
Commit: 271959d1345077baa064c60fe79ff00a6ed0b021 https://github.com/galaxyproject/galaxy/commit/271959d1345077baa064c60fe79ff... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/tool_shed/metadata/metadata_generator.py M test/unit/tools/test_watcher.py
Log Message: ----------- Reload data table managers and data tables
... before reloading data managers. Data managers need to have access to the data tables, so that they can process the results. Do not explicitly start watcher thread for shed_data_manager_conf changes.
Commit: f92d496bd9ae42387e5017e2ef84a032de6e49ea https://github.com/galaxyproject/galaxy/commit/f92d496bd9ae42387e5017e2ef84a... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths: M lib/galaxy/tools/toolbox/base.py
Log Message: ----------- Remove debugging statements and mention uwsgi/threads in line
Commit: 7afb25d5fbf8bcb37d4c9fc7e25b20b8d8373011 https://github.com/galaxyproject/galaxy/commit/7afb25d5fbf8bcb37d4c9fc7e25b2... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py
Log Message: ----------- Wait for shed_data_manager_conf watcher to pick up changes
Commit: a19f67f8be85c4d5b459082ea9343cbda0a298b3 https://github.com/galaxyproject/galaxy/commit/a19f67f8be85c4d5b459082ea9343... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py
Log Message: ----------- Try locking load_item
Commit: 426ea3b726a085f1a89033ed875584468db7b321 https://github.com/galaxyproject/galaxy/commit/426ea3b726a085f1a89033ed87558... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message: ----------- Keep a count of reloads
Commit: c4aa171ae4bc16667b082122ef14dfc0f08891c8 https://github.com/galaxyproject/galaxy/commit/c4aa171ae4bc16667b082122ef14d... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message: ----------- Always wait for reload action to be finished
Commit: 7f893f39f6d1087afe50af9d9a61da77fcbe14db https://github.com/galaxyproject/galaxy/commit/7f893f39f6d1087afe50af9d9a61d... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths: M lib/galaxy/queue_worker.py M test/unit/tools_support.py
Log Message: ----------- Mock the Lock; fix linting problems
Commit: c1d66d1fbc7281cb2cd5b050e8516818093d3e6a https://github.com/galaxyproject/galaxy/commit/c1d66d1fbc7281cb2cd5b050e8516... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths: M test/unit/tools_support.py
Log Message: ----------- One more linting fix
Commit: 4adc872e5864d9a8262948a56a4552fbafe68390 https://github.com/galaxyproject/galaxy/commit/4adc872e5864d9a8262948a56a455... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths: M test/unit/tools_support.py
Log Message: ----------- Fix indentation
Commit: 99acb36da32ec2d2d4d7d1ce7cdc4da426e51645 https://github.com/galaxyproject/galaxy/commit/99acb36da32ec2d2d4d7d1ce7cdc4... Author: John Chilton jmchilton@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths: M test/unit/tools_support.py
Log Message: ----------- Add server_name to unit test app's config.
Required for messaging stuff.
Commit: 9f7c749638340fb63ac00a417a9e328875296885 https://github.com/galaxyproject/galaxy/commit/9f7c749638340fb63ac00a417a9e3... Author: John Chilton jmchilton@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M test/unit/tools_support.py
Log Message: ----------- Fix test case for tool manager.
Commit: 9a9a1f9becf185db5a778f1436913bc6942b2ac3 https://github.com/galaxyproject/galaxy/commit/9a9a1f9becf185db5a778f1436913... Author: John Chilton jmchilton@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message: ----------- Lint for last commit.
Commit: 4479bcebbe6984c06d0b5b9411d6d9e8bc2f22ca https://github.com/galaxyproject/galaxy/commit/4479bcebbe6984c06d0b5b9411d6d... Author: John Chilton jmchilton@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M doc/source/admin/conda_faq.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py R lib/galaxy/tools/toolbox/requirements.py A lib/galaxy/util/filelock.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py R lib/galaxy/web/proxy/filelock.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.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/visualization.py M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js R templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_toolsheds.mako R templates/admin/tool_shed_repository/preview_repository.mako M templates/webapps/galaxy/workflow/display.mako
Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into reload_toolbox_across_handlers
Commit: 53d387d771b3bb95cd17cf0c74ec90099122f376 https://github.com/galaxyproject/galaxy/commit/53d387d771b3bb95cd17cf0c74ec9... Author: John Chilton jmchilton@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths: M lib/galaxy/config.py
Log Message: ----------- Another linting fix.
Commit: fed59596a37176b388d74346cd7fce6bba224c8e https://github.com/galaxyproject/galaxy/commit/fed59596a37176b388d74346cd7fc... Author: John Chilton jmchilton@gmail.com Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths: M lib/galaxy/config.py
Log Message: ----------- Fix the infinite loop.
Thanks @mvdbeek!
Commit: 61fb26181c7dfaefa821f616171a281928153b70 https://github.com/galaxyproject/galaxy/commit/61fb26181c7dfaefa821f616171a2... Author: John Chilton jmchilton@gmail.com Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py
Log Message: ----------- Merge pull request #2840 from mvdbeek/reload_toolbox_across_handlers
Allow reloading tools without restarting galaxy, simplify tool panel handling for tool shed installed tools
Compare: https://github.com/galaxyproject/galaxy/compare/afefb9dd831f...61fb26181c7d