Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b11002bef32d83b058e3495f96695c8dc12cb91b https://github.com/galaxyproject/galaxy/commit/b11002bef32d83b058e3495f96695... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M test/api/workflows_format_2/converter.py Log Message: ----------- Don't iterate over unused key. Thanks to @bgruening. Commit: 2aa7f04364e10e46c655de636925883a43698694 https://github.com/galaxyproject/galaxy/commit/2aa7f04364e10e46c655de6369258... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M test/api/workflows_format_2/converter.py Log Message: ----------- Replace __rip_value with dict.pop. Thanks @bgruening. Commit: 98249058e85d8133748519ac59ebed96a28a77ac https://github.com/galaxyproject/galaxy/commit/98249058e85d8133748519ac59ebe... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Cleanup error message. Thanks @bgruening. Commit: f17a6c996a060f68bc8a250effa23f60b96b44a7 https://github.com/galaxyproject/galaxy/commit/f17a6c996a060f68bc8a250effa23... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/web/base/controller.py Log Message: ----------- Synchronize decoding ids across base controller and manager base. To ensure we have the same kind of exception thrown in both cases. Commit: f6d26c9ee6f148fd033d1b070c2dbe8c69b08fa8 https://github.com/galaxyproject/galaxy/commit/f6d26c9ee6f148fd033d1b070c2db... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M test/unit/workflows/test_modules.py Log Message: ----------- Small refactor making workflow views and modules tad more generic. - Reduce duplication between initializing generic modules and tool modules. - Switch tool_id to content_id as variable names throughout the client. - Rename get_tool_id to get_content_id on workflow modules. - Add some minimal documentation to the workflow module about get_content_id. Downstream in the subworkflow commit I switch the over-the-wire communication to use content_id instead of tool_id also and use content_ids to refer to workflow ids in subworkflow moduls. Commit: 73bfbf016347f764a0747ad7c6d138c74b6f519d https://github.com/galaxyproject/galaxy/commit/73bfbf016347f764a0747ad7c6d13... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Refactor some workflow API code into workflows manager. This allows for reuse outside of the API controller, such as loading subworkflows downstream. Commit: f92220a74f216d937dc5b147472261d154779512 https://github.com/galaxyproject/galaxy/commit/f92220a74f216d937dc5b14747226... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Allow workflow outputs on non-tool steps. Commit: d18c75ceb875632f9e68a74ebeb88389262d6fa8 https://github.com/galaxyproject/galaxy/commit/d18c75ceb875632f9e68a74ebeb88... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako Log Message: ----------- Bring gneric and tool module styles into alignment in workflow editor. Commit: d7ac52f6bb61fe360198f91310a3e22076183d7b https://github.com/galaxyproject/galaxy/commit/d7ac52f6bb61fe360198f91310a3e... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add icons to existing workflow steps in workflow editor. Tools have an icon there. Commit: e3161b4671e9fb19a47c7f341e3fb46617111a9e https://github.com/galaxyproject/galaxy/commit/e3161b4671e9fb19a47c7f341e3fb... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-06 (Sun, 06 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-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.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-node.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-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Add support for workflow step labels in editor. - If a step has a label, display it in the step editor side panel title. - Allow clicking the title to change the label. - Display the label (if set) as the workflow node box title. - Add icon to workflow node since the title might not be related to type anymore. - Enforce unique labels accross the workflow in the editor. - Qunit test cases for some of this behavior and other recent changes. Commit: ef0b6cc459a40227db2e63ee709e9dd5d8fd37c6 https://github.com/galaxyproject/galaxy/commit/ef0b6cc459a40227db2e63ee709e9... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-manager.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-view.js Log Message: ----------- show notifications as Toasts and not like JS alerts (bleh) Commit: 4a9dad9f14b94df14b52f41466c9e66dbbfb0556 https://github.com/galaxyproject/galaxy/commit/4a9dad9f14b94df14b52f41466c9e... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-manager.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-view.js Log Message: ----------- Merge pull request #12 from martenson/labels_toastr show notifications as Toasts and not like JS alerts (bleh) Commit: 3f8950628c3e31d9e2abe0b4f4a360c035133b8e https://github.com/galaxyproject/galaxy/commit/3f8950628c3e31d9e2abe0b4f4a36... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako Log Message: ----------- Workflow label UI refinement. - Escape workflow labels in mako. - Handle unlabelling steps properly (restore original node name to node and editor form titles). Commit: fe1c9dd2931fb8efccb98fb1646c3e1063b0ab52 https://github.com/galaxyproject/galaxy/commit/fe1c9dd2931fb8efccb98fb1646c3... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-12-08 (Tue, 08 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-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/base.py M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.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-node.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-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/api/workflows_format_2/converter.py M test/qunit/tests/workflow_editor_tests.js M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #1251 from jmchilton/workflow_labels_2 Workflow Editor UI for Step Labels Compare: https://github.com/galaxyproject/galaxy/compare/0e5d42f3d67e...fe1c9dd2931f