Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a279ffb64576258f2f2755f182430e1ccbacbc2 https://github.com/galaxyproject/galaxy/commit/4a279ffb64576258f2f2755f18243... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py Log Message: ----------- Allow inputs section for Format 2 workflow definitions. Arguably a more natural way to define inputs, regardless it allows more CWL-like input definitions for workflows. Commit: b0b26e69019162e335ea5a331ab21009c882f0d1 https://github.com/galaxyproject/galaxy/commit/b0b26e69019162e335ea5a331ab21... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py Log Message: ----------- Allow specifying Format 2 workflow by path. This will allow importing workflow relative resources in subsequent passes at this. Commit: 70a9f213932947758f9882776140727eb6c0e246 https://github.com/galaxyproject/galaxy/commit/70a9f213932947758f98827761407... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py Log Message: ----------- Update workflow format 2 code with infrastructure for nesting runnables. In downstream work this is used for subworkflows and nested tools. Not sure which of these would potentially hit main line Galaxy first so setting this all up in its own commit. Commit: 1bd0a4e9703406223f0e9bfe31df4c801998f400 https://github.com/galaxyproject/galaxy/commit/1bd0a4e9703406223f0e9bfe31df4... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py Log Message: ----------- Refactoring and more testing of format 2 workflow implementation code... ... toward more reusable design. Commit: a597e0e8349f33d4d2c642d2e0a74e3da64b156b https://github.com/galaxyproject/galaxy/commit/a597e0e8349f33d4d2c642d2e0a74... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py Log Message: ----------- Implement workflow outputs for format 2 workflow definitions. Copy CWL style of specifying a outputs specification block at the top-level of the workflow specification and within that use the "source" attribute to specify the output. Reuse the specification used by "$link"s to describe this output - namely <label_or_order_index>[#<output_name=output>]. Commit: 3d0723c812632a276102748ec6a754bbec0b9d9a https://github.com/galaxyproject/galaxy/commit/3d0723c812632a276102748ec6a75... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- JS Model abstractions for dealing workflow outputs. Need to modify how these are represented so I want the logic centralized in the model... also the logic should be centralized in the model. Commit: 7b3fa824b67c0c7f881a514ae5b6598ede62e14c https://github.com/galaxyproject/galaxy/commit/7b3fa824b67c0c7f881a514ae5b65... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/managers/workflows.py M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Update worklfow editor representation of workflow outputs. Modified this for the workflow export representation but this needed to be updated for the workflow editor because they shared some code in the manager. This was going to be needed downstream when I add labels and uuids to workflow outputs anyway. Commit: cee9d4d1b30633689d8dd5fde715aed528e578a1 https://github.com/galaxyproject/galaxy/commit/cee9d4d1b30633689d8dd5fde715a... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-data.js Log Message: ----------- Grunt the workflow JS. Commit: 40e6932a25f71c240e038e4e6dc9be6a19ff8459 https://github.com/galaxyproject/galaxy/commit/40e6932a25f71c240e038e4e6dc9b... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Fix workflow API tests for workflow output changes. Commit: 6126bd0e93e17c2d9cd6512ec068f806cc9da72d https://github.com/galaxyproject/galaxy/commit/6126bd0e93e17c2d9cd6512ec068f... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-data.js M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #1214 from jmchilton/format_2_1 Small enhancements in workflow inputs and outputs Compare: https://github.com/galaxyproject/galaxy/compare/d7f5dbe4ca1b...6126bd0e93e1