Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 199fe7e0fccbeeb55501bad54f8ae4e44e7c100c https://github.com/galaxyproject/galaxy/commit/199fe7e0fccbeeb55501bad54f8ae... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Allow saving workflows with input parameters Commit: 638b1b7581d38b9044e17937f308c82fd36663ee https://github.com/galaxyproject/galaxy/commit/638b1b7581d38b9044e17937f308c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Allow inserting input parameter into workflow Commit: c09d1bc150775909f0e2a8f1c48ad0b2b70afea0 https://github.com/galaxyproject/galaxy/commit/c09d1bc150775909f0e2a8f1c48ad... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.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-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- WIP: add StepParameter inputs to workflow editor In the current state when a text, integer, float, boolean or boolean parameter is set as "Set at Runtime" a new connectable input appears for the tool node, to which a Parameter can be properly dragged and connected. This still needs a little more separation from data inputs/outputs, and the new connection isn't persisted in a meaningful way. Commit: 99c270fd77367a813af6202465d5453be78ac4eb https://github.com/galaxyproject/galaxy/commit/99c270fd77367a813af6202465d54... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix rebuilding parameter node Commit: b0d64a8f09e6dc3d29c069edcb2abe77ee9c3662 https://github.com/galaxyproject/galaxy/commit/b0d64a8f09e6dc3d29c069edcb2ab... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix selecting the correct item from select list select lists don't take a `value` argument. Commit: c624cc4bce8b7b2bea9eaf61ecbf8bea485c4640 https://github.com/galaxyproject/galaxy/commit/c624cc4bce8b7b2bea9eaf61ecbf8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix getting correct type Commit: 83a25c90e66b52890fcd8ad9288059d87b4f4932 https://github.com/galaxyproject/galaxy/commit/83a25c90e66b52890fcd8ad928805... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Fix restoring saved non-data connections in workflow editor Commit: 4e3004bb250f86b8c16a1c94c8599f497488e732 https://github.com/galaxyproject/galaxy/commit/4e3004bb250f86b8c16a1c94c8599... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Fix node.addOuputParameter Commit: e135fac159e80549ce611a40f4c66598f51632d2 https://github.com/galaxyproject/galaxy/commit/e135fac159e80549ce611a40f4c66... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Don't render data inputs on parameter_input node Commit: 0340dcb18a99d9d7984eb7566b3826290fe90025 https://github.com/galaxyproject/galaxy/commit/0340dcb18a99d9d7984eb7566b382... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- More defensive runtime check Commit: 5a5b4abb5bd4b1b142601a94b4498556c4f14946 https://github.com/galaxyproject/galaxy/commit/5a5b4abb5bd4b1b142601a94b4498... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Allow loading in test-data workfows Commit: 4812586156b4cf01fe8ee1cb743306cc91ba2c84 https://github.com/galaxyproject/galaxy/commit/4812586156b4cf01fe8ee1cb74330... Author: John Chilton <jmchilton@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-data.js Log Message: ----------- Add label to input parameters without labels. Commit: dbe4033abe74035082b510c862c7729212367341 https://github.com/galaxyproject/galaxy/commit/dbe4033abe74035082b510c862c77... Author: John Chilton <jmchilton@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-icons.js Log Message: ----------- Give parameter inputs a workflow icon. Commit: 00b8776db521cab884a107f8b66441690f644f88 https://github.com/galaxyproject/galaxy/commit/00b8776db521cab884a107f8b6644... Author: John Chilton <jmchilton@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Convert raw parameters from map into formal parameters when invoking wfs. Commit: d74b959419a667b2ff3192c9fde07a2cddc5e90d https://github.com/galaxyproject/galaxy/commit/d74b959419a667b2ff3192c9fde07... Author: John Chilton <jmchilton@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Revert non-data connection handling, send connections unfiltered to editor. Commit: 85d777dbe704ccdbf71898853e542c1c2df05303 https://github.com/galaxyproject/galaxy/commit/85d777dbe704ccdbf71898853e542... Author: John Chilton <jmchilton@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py Log Message: ----------- Separate RuntimeValue into RuntimeValue and ConnectedValue. Use ConnectedValue values to determine what non-data parameters to display connections for. Commit: dd8d74f364770a1272555a3753f5d1e1288315e1 https://github.com/galaxyproject/galaxy/commit/dd8d74f364770a1272555a3753f5d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Unify data/non-data input/output handling for workflow editor. Don't treat data and non-data inputs/outputs different at the API boundary or at the workflow-manager.js level. Keep differences at the level of walking inputs/outputs in the workflow module on the backend and at the terminal definition (models and views) level on the frontend. Make the code and interfaces more consistent in my opinion and is more compatible with future directions I'd like to take things with mix-mode inputs/outputs for CWL. Commit: 5a99ebd5af9d68f028b86d295846a1c4cefccfb4 https://github.com/galaxyproject/galaxy/commit/5a99ebd5af9d68f028b86d295846a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Remove filtering of connections for workflow editor. Things not matching should be handled there. Commit: 29950be83f8240acba05685b4a057b38d803b445 https://github.com/galaxyproject/galaxy/commit/29950be83f8240acba05685b4a057... Author: John Chilton <jmchilton@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Workflow editor testing for step parameters/connections. - Fixes and refactoring for existing input tests (toward reuse). - Add simple test for non-data input. Commit: f12e548872b0087b4ba8b5828bc80b6aa10207e4 https://github.com/galaxyproject/galaxy/commit/f12e548872b0087b4ba8b5828bc80... Author: John Chilton <jmchilton@gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/workflow/run.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_workflow_run.py Log Message: ----------- Step parameter workflow run test case and fix. Commit: e98f63caf2d2adfd7857ff9fcba6df0b5923b668 https://github.com/galaxyproject/galaxy/commit/e98f63caf2d2adfd7857ff9fcba6d... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-11-10 (Sat, 10 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.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-terminals.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.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/galaxy_selenium/navigation.yml M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #6925 from jmchilton/workflow_step_parameters_3 Add workflow step parameters to workflow editor (try 3) Compare: https://github.com/galaxyproject/galaxy/compare/b57c25622b74...e98f63caf2d2 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.