Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 517f248ac49caca3f0933c4b1f48cd4d74cf89fe https://github.com/galaxyproject/galaxy/commit/517f248ac49caca3f0933c4b1f48c... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/functional/tools/samples_tool_conf.xml M test/functional/tools/tool_provided_metadata_1.xml M test/functional/tools/tool_provided_metadata_2.xml M test/functional/tools/tool_provided_metadata_3.xml A test/functional/tools/tool_provided_metadata_4.xml A test/functional/tools/tool_provided_metadata_5.xml A test/functional/tools/tool_provided_metadata_6.xml M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Overhaul of tool provided job metadata. - Add another test to demonstrate referencing entries in galaxy.json for datasets by dataset path basename instead of ID. - Add a bit more documentation to test tools. - Redo the structure of galaxy.json for profile >= 17.09 tools with two new test tools to demonstrate the new structure - for both output dataset metadata and discovered dataset metadata. - Improved abstractions for interaction between tools and jobs to enable different tool provided metadata collection depending on tool profile version. Commit: 72e361bcf14191dae58af8e3963b89a4e8acd38a https://github.com/galaxyproject/galaxy/commit/72e361bcf14191dae58af8e3963b8... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/collection_creates_dynamic_nested_from_json.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_7.xml Log Message: ----------- Allow discovering datasets directly from galaxy.json... without needing to specify a discovered dataset pattern. If the ``discovered_datasets`` tag includes ``from_tool_provided_metadata="true"`` the datsets listed in galaxy.json will just be used directly without needing to be "discovered" using a dataset pattern. Metadata and such can continue to be specified either in that file or on the discovered_dataset element except things like pattern (which is not used) and sort_by (since the json should describe the order I suppose). Commit: 6563e387a5d001bb6078469b7ad6a13f9bbed8aa https://github.com/galaxyproject/galaxy/commit/6563e387a5d001bb6078469b7ad6a... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py A test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Allow discovering dataset collections in galaxy.json in a nested fashion. Fixes #2658. Commit: 39d4411f8c21b307a86340fc5438ed2193abd766 https://github.com/galaxyproject/galaxy/commit/39d4411f8c21b307a86340fc5438e... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_8.xml Log Message: ----------- Move determining tool provided metadata style to tool parser. Allow override by specifying "provided_metadata_style=" attribute on outputs in tool XML - this should allow newer profile tools to use the older style JSON providing a clear path for upgrades. Commit: a8bec7a275b5bd387daddf6555b6ff382851e8e8 https://github.com/galaxyproject/galaxy/commit/a8bec7a275b5bd387daddf6555b6f... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_9.xml Log Message: ----------- Allow override of provided metadata location. Eliminates that terrible circular dependency between tools and jobs. Commit: 1e1df6786aeb6d02fba1ad84cceb204aa745ea62 https://github.com/galaxyproject/galaxy/commit/1e1df6786aeb6d02fba1ad84cceb2... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Variety of fixes for #4437. Commit: dd89a9c65f7297d4da5f0c0f7b6fea884a9698e6 https://github.com/galaxyproject/galaxy/commit/dd89a9c65f7297d4da5f0c0f7b6fe... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/collection_creates_dynamic_nested_from_json.xml A test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/tool_provided_metadata_1.xml M test/functional/tools/tool_provided_metadata_2.xml M test/functional/tools/tool_provided_metadata_3.xml A test/functional/tools/tool_provided_metadata_4.xml A test/functional/tools/tool_provided_metadata_5.xml A test/functional/tools/tool_provided_metadata_6.xml A test/functional/tools/tool_provided_metadata_7.xml A test/functional/tools/tool_provided_metadata_8.xml A test/functional/tools/tool_provided_metadata_9.xml M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge pull request #4437 from jmchilton/galaxy_json_rev Enhanced tool options for dataset discovery Compare: https://github.com/galaxyproject/galaxy/compare/b459399edebb...dd89a9c65f72