Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0da66ee8dcf5fef52b11558228c1eb95479cbce9
https://github.com/galaxyproject/galaxy/commit/0da66ee8dcf5fef52b11558228c1…
Author: John Chilton <jmchilton(a)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/a9d4783f2c3d22e7d830fc88d30b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-03 (Sun, 03 Jan 2016)
Changed paths:
M lib/galaxy/tools/loader_directory.py
Log Message:
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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/2054f538be010ab6d47e0de1da64…
Author: John Chilton <jmchilton(a)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/db845fa1875bcb08aa2129830f1d…
Author: John Chilton <jmchilton(a)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/fcc83d4e09d4603c5fbd831e9e19…
Author: John Chilton <jmchilton(a)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:
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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/b68991c4caa44aefeaba752748ae…
Author: John Chilton <jmchilton(a)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/864cc32892a1b4bf91b5d2fe70f7…
Author: John Chilton <jmchilton(a)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/4086dd61dafe562ec01a8b1fce68…
Author: John Chilton <jmchilton(a)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/8027228639a771e4c62131ab15ba…
Author: John Chilton <jmchilton(a)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:
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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/eddfec36fdf6d19bae398d09ee16…
Author: John Chilton <jmchilton(a)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:
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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/ce24ec6821bdb87f14f3047eef18…
Author: John Chilton <jmchilton(a)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/523e2b40063d2abb7662a163f014…
Author: John Chilton <jmchilton(a)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/73defd48ce70241d7cc163aaadfe…
Author: Martin Cech <cech.marten(a)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
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f597b08b878f478b9beee32c59b5e4218458c4fe
https://github.com/galaxyproject/galaxy/commit/f597b08b878f478b9beee32c59b5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-30 (Wed, 30 Dec 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Refactor ToolBox functionality.
This moves in two directions toward a better design. It moves some Galaxy tool specific logic out of the AbstractToolBox (which should just be worried about panels, etc... IMO) and it moves more galaxy-lib functionality (dependency resolution) into a galaxy-lib module (galaxy.tools.toolbox). It does this by creating a BaseGalaxyToolBox that can reason about which files look like tools and what dependency resoution should be - without dependening on Galaxy models, job running, etc... that is in galaxy.tools.__init__.
Commit: 204aa96206a7fdaff69d22fde6387a9956c1a0bc
https://github.com/galaxyproject/galaxy/commit/204aa96206a7fdaff69d22fde638…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-30 (Wed, 30 Dec 2015)
Changed paths:
M lib/galaxy/tools/deps/__init__.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/modules.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
A lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/toolbox/base.py
A lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/unit/test_routes.py
Log Message:
-----------
API-ify tool dependency resolution.
Commit: b167a741a444c3988447b0d63a1ba3dc5e4e62f5
https://github.com/galaxyproject/galaxy/commit/b167a741a444c3988447b0d63a1b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-30 (Wed, 30 Dec 2015)
Changed paths:
M lib/galaxy/tools/deps/__init__.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/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/webapps/galaxy/api/tool_dependencies.py
Log Message:
-----------
Include information about whether matches are dependencies are exact.
Commit: 71a876840a6c9acf11bd2ac7706ec21b32d2fb88
https://github.com/galaxyproject/galaxy/commit/71a876840a6c9acf11bd2ac7706e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-30 (Wed, 30 Dec 2015)
Changed paths:
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/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/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
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Implement concept of listable dependency resolvers.
DependencyResolver classes which can enumerate the requirements then can resolve "exactly" should mix in ListableDependencyResolver and implement list_dependencies.
The galaxy package resolver can easily be enumerated but its subclasses like the tool shed dependency resolver couldn't, so I have separated that class into a base class that there others can inherit and an actual resolver that implements ListableDependencyResolver.
Rebase into listable.
Commit: 29f20cf09c18e24e898517bf685418ec1db4cd11
https://github.com/galaxyproject/galaxy/commit/29f20cf09c18e24e898517bf6854…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-30 (Wed, 30 Dec 2015)
Changed paths:
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Implement concept of installable dependency resolvers.
DependencyResolver classes which can install "simple" dependences should mix in the new InstallableDependencyResolver and implement install_dependency.
Currently this is only the conda dependency resolver, one can easily imagine doing the same for the brew dependency resolver and potentially doing it for some variant of the unlinked dependency resolvers.
Commit: 868a7dfe0e03503adaf6646e10d8184d18b66a34
https://github.com/galaxyproject/galaxy/commit/868a7dfe0e03503adaf6646e10d8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-02 (Sat, 02 Jan 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M test/unit/tools/test_conda_resolution.py
Log Message:
-----------
Modify unmodified conda behavior.
- Add configuration option for overriding condarc location used by conda resolve commands.
- Default location of condarc to be in tool_dependency_dir.
- Delay updating the condarc to ensure channels until this would actually be needed (during package installation).
- Add configuration flag to allow Galaxy to *NOT* check the PATH for conda.
- Update unit test that verifies conda's installation to never use conda on PATH, since a precondition of this test is that certain packages haven't been installed previously.
- Change default behavior to not check the PATH for conda, everything else here I feel pretty good about - this I'm ambivalent about - it will reduce error reports and problems with network filesystems, but doesn't seem to be good Unix best practice.
Points 2 and 3 above should address this issue: https://github.com/galaxyproject/ansible-galaxy-extras/pull/33#issuecomment…
This commit also addresses most of #1406.
Commit: ef9e1876a2d4dd02718784f2b9f1045f2f9d0b59
https://github.com/galaxyproject/galaxy/commit/ef9e1876a2d4dd02718784f2b9f1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-03 (Sun, 03 Jan 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
Log Message:
-----------
Fixup dependency module and API comments.
Thanks to suggestions by @bgruening.
Commit: 4650d77bd988b90b6652cc108f83bf6d86cae271
https://github.com/galaxyproject/galaxy/commit/4650d77bd988b90b6652cc108f83…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-03 (Sun, 03 Jan 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Fix listing conda requirements if conda hasn't been installed.
Fix problem discovered by @bgruening.
Commit: 5ca71d6f292ff122d35c25d0dfd7c0e14d5366e2
https://github.com/galaxyproject/galaxy/commit/5ca71d6f292ff122d35c25d0dfd7…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-01-03 (Sun, 03 Jan 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.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/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
A lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
A lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/unit/test_routes.py
M test/unit/tools/test_conda_resolution.py
Log Message:
-----------
Merge pull request #1409 from jmchilton/dep_resolution_api
Evolving from dependency resolution to dependency management.
Compare: https://github.com/galaxyproject/galaxy/compare/0aa1c5133e02...5ca71d6f292f