Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0da66ee8dcf5fef52b11558228c1eb95479cbce9 https://github.com/galaxyproject/galaxy/commit/0da66ee8dcf5fef52b11558228c1e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Small improvements to load_directory for downstream extension. Commit: a9d4783f2c3d22e7d830fc88d30b6112e2d43fc0 https://github.com/galaxyproject/galaxy/commit/a9d4783f2c3d22e7d830fc88d30b6... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Add CWL suppoort to tool checking and parsing. To be clear, this provides none of the infrastructure for running the tools. This is just so that planemo and future tool registry efforts can have a unified interface for accessing and reasoning about tools using the same methods Galaxy does. Commit: 2054f538be010ab6d47e0de1da646268ca6d6ff4 https://github.com/galaxyproject/galaxy/commit/2054f538be010ab6d47e0de1da646... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: A lib/galaxy/tools/cwl/__init__.py A lib/galaxy/tools/cwl/cwltool_deps.py A lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/representation.py A lib/galaxy/tools/cwl/runtime_actions.py A lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py Log Message: ----------- Infrastructure for parsing CWL tools. Commit: db845fa1875bcb08aa2129830f1d405d1d894cfb https://github.com/galaxyproject/galaxy/commit/db845fa1875bcb08aa2129830f1d4... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Refactor loader_directory to support beta formats in other ways. Commit: fcc83d4e09d4603c5fbd831e9e1933916bf00827 https://github.com/galaxyproject/galaxy/commit/fcc83d4e09d4603c5fbd831e9e193... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/tools/toolbox/parser.py Log Message: ----------- Introduce ToolBox parser. Abstract simpler ToolBox interactions to separate XML representation from handling. Doesn't cover tool shed operations since the tool shed explicitly writes XML. Commit: b68991c4caa44aefeaba752748ae62db98a446fd https://github.com/galaxyproject/galaxy/commit/b68991c4caa44aefeaba752748ae6... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/parser.py M test/unit/tools/test_toolbox.py Log Message: ----------- Allow loading tool confs written in YAML and JSON. Because lets say someone was writing a programatic way to manage elements in a tool conf, that hypothetical person probably shouldn't be writing XML. Commit: 864cc32892a1b4bf91b5d2fe70f7e64eec736393 https://github.com/galaxyproject/galaxy/commit/864cc32892a1b4bf91b5d2fe70f7e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/toolbox/cache.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M templates/admin/reload_tool.mako Log Message: ----------- Allow toolbox reloading via app, UI, and API. Introduce an app ToolCache to help ensure this operation remains speedy. Commit: 4086dd61dafe562ec01a8b1fce687a539aedbcfe https://github.com/galaxyproject/galaxy/commit/4086dd61dafe562ec01a8b1fce687... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M test/unit/tools/test_watcher.py Log Message: ----------- Implement toolbox monitoring. - Add monitor tag on toolbox root elements to force Galaxy to watch the toolbox for changes. - Refactoring and test improvements for existing tool monitoring code. - Implement toolbox shutdown process to ensure different watchers don't compete with each other. - Set the default tool conf to be monitored. Commit: 8027228639a771e4c62131ab15ba4ffbb656498a https://github.com/galaxyproject/galaxy/commit/8027228639a771e4c62131ab15ba4... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/tool_util.py Log Message: ----------- Revise tool caching for tool shed tool loading... The tool shed appears to load the same tool in the toolbox multiple times with different settings. Get around this by not using the cache when loading tools from a few tool shed components later in this process. Commit: eddfec36fdf6d19bae398d09ee16952136d2b379 https://github.com/galaxyproject/galaxy/commit/eddfec36fdf6d19bae398d09ee169... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Refactor package_tool for better separation of concerns. The tool should know how to package itself, it shouldn't be the responsiblity of the toolbox. Update the code to reflect this and use more pythonic exception handling. Commit: ce24ec6821bdb87f14f3047eef186c246de2d5ed https://github.com/galaxyproject/galaxy/commit/ce24ec6821bdb87f14f3047eef186... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M templates/admin/reload_tool.mako Log Message: ----------- Remove alert from toolbox reload. Commit: 523e2b40063d2abb7662a163f0144902541bed18 https://github.com/galaxyproject/galaxy/commit/523e2b40063d2abb7662a163f0144... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Fix shutdown of tool watcher if never activated. Caused a harmless, but distracting stacktrace to be printed on toolbox reload as pointed out by @bgruening https://github.com/galaxyproject/galaxy/pull/1398#issuecomment-168499678. Commit: 73defd48ce70241d7cc163aaadfef6fcd6830231 https://github.com/galaxyproject/galaxy/commit/73defd48ce70241d7cc163aaadfef... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/cwl/__init__.py A lib/galaxy/tools/cwl/cwltool_deps.py A lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/representation.py A lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/tool_util.py M templates/admin/reload_tool.mako M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py Log Message: ----------- Merge pull request #1398 from jmchilton/toolbox_overhaul ToolBox Overhaul Compare: https://github.com/galaxyproject/galaxy/compare/5ca71d6f292f...73defd48ce70