Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d41caa53cf24aca29bb90e32b420558558461d9c https://github.com/galaxyproject/galaxy/commit/d41caa53cf24aca29bb90e32b4205... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py Log Message: ----------- Database migration enabling subworkflow and input parameter modules. Commit: 45962f32344a00162f5d04b94096c8a570f2adf1 https://github.com/galaxyproject/galaxy/commit/45962f32344a00162f5d04b94096c... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Input parameter workflow module (experimental). - Implement a input parameter module that mirrors data and collection input modules but has a type that can currently be one of text, integer, float, color, and boolean. - Allow connections between these and tool step inputs. - Extend model to support this. - Add new input types for format 2 workflow definitions for various types that all map to this kind of step. Typed inputs such as this match well with CWL workflow inputs. Someday I imagine these will be superior to just marking a tool input "Specify at Runtime" for all the same reasons input steps are superior to leaving inputs unattached. Commit: 157939aa8f46b7599f48011d9f1e2c40c9f6cd47 https://github.com/galaxyproject/galaxy/commit/157939aa8f46b7599f48011d9f1e2... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js 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-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-workflow.js.map 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-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/tool/tool-form-workflow.js 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 static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Implement nested workflows. Details: - Add a new workflow module describing subworkflows. - Add workflow list to editor side panel - with options to link in a subworkflow module or copy the target workflow into the workflow being editted node for node. - Update workflow, workflow step, and workflow invocation models to track subworkflow connections and execution. - Extend workflow outputs with concepts of labels (and UUIDs while I'm there) to match workflow inputs. This allow us to have something to label outputs with in the workflow editor and to reference in the format 2 workflow description language. - Extend workflow editor UI to allow labeling workflow outputs (and enforce that these are unique across a workflow). - Extend workflow invocation and progress tracking to allow invoking a subworkflow as part of another workflow invocation. - Extend workflow import and export code to allow a nested representation of workflows. - Update format 2 workflow description to allow testing nested workflows. Most relevant new and modified test cases can be run using the following commands: ``` ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_run_subworkflow_simple ./run_tests.sh -api test/api/test_workflows_from_yaml.py:WorkflowsFromYamlApiTestCase.test_subworkflow_simple ./run_tests.sh -api test/api/test_workflows_from_yaml.py:WorkflowsFromYamlApiTestCase.test_outputs nosetests test/unit/test_galaxy_mapping.py nosetests test/unit/workflows/test_workflow_progress.py ``` Commit: f88ad8d4e35b51a5f88b0d29b71755f576fc1f7a https://github.com/galaxyproject/galaxy/commit/f88ad8d4e35b51a5f88b0d29b7175... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Fix Change type label in editor form Commit: 48eec81f48f92d7b5e7a42a9cf4be453f9f14fa5 https://github.com/galaxyproject/galaxy/commit/48eec81f48f92d7b5e7a42a9cf4be... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Allow specifying workflow outputs on subworkflow nodes. Commit: f10b968075e37b650f46811f6f83286c6aaefccd https://github.com/galaxyproject/galaxy/commit/f10b968075e37b650f46811f6f832... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Build section dom in js Commit: b4bfde4089a5f1893ddd839fa4a2c34c71378ae2 https://github.com/galaxyproject/galaxy/commit/b4bfde4089a5f1893ddd839fa4a2c... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js 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-view-data.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix attribute Commit: 530ceb13befdc0850efb9db47c5389c3218338b3 https://github.com/galaxyproject/galaxy/commit/530ceb13befdc0850efb9db47c538... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Fix for failing qunit test. Commit: 12014cc2252d710b617953dbfcc804fc9b3f0a67 https://github.com/galaxyproject/galaxy/commit/12014cc2252d710b617953dbfcc80... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Show correct subworkflow name Commit: 2ff3bf0c0c66946557f21f0bafa55768b7a8cd63 https://github.com/galaxyproject/galaxy/commit/2ff3bf0c0c66946557f21f0bafa55... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix label change handling Commit: c9016f9553784b3a83f448c787fa8b90e11a2599 https://github.com/galaxyproject/galaxy/commit/c9016f9553784b3a83f448c787fa8... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #15 from guerler/fix_subworkflows_005 Fix subworkflows 005 Commit: 41da9b0f88727759d1d2453a90b548858d10ffa7 https://github.com/galaxyproject/galaxy/commit/41da9b0f88727759d1d2453a90b54... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js 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-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-workflow.js.map 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-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-workflow.js 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 static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/qunit/tests/workflow_editor_tests.js M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #1306 from common-workflow-language/subworkflows New Workflow Modules - Input Parameters and Subworkflows Compare: https://github.com/galaxyproject/galaxy/compare/1ec67c864b3a...41da9b0f8872