Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7b8f6751720a2caaa5b13f7089d1aa1c98fbedf6 https://github.com/galaxyproject/galaxy/commit/7b8f6751720a2caaa5b13f7089d1a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M lib/galaxy/managers/configuration.py M static/maps/layout/masthead.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/masthead.js M templates/webapps/galaxy/galaxy.masthead.mako M test/qunit/tests/masthead_tests.js Log Message: ----------- Place logo into config, add masthead test cases Commit: 580895af1d642a52559e0bfa1788808a7c790b05 https://github.com/galaxyproject/galaxy/commit/580895af1d642a52559e0bfa17888... Author: guerler <aysam.guerler@gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M static/maps/mvc/workflow/workflow-view-node.js.map M static/scripts/mvc/workflow/workflow-view-node.js Log Message: ----------- Revision Commit: 7ea4668ff732f22c0d686ed35fd6ff1a0c431736 https://github.com/galaxyproject/galaxy/commit/7ea4668ff732f22c0d686ed35fd6f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/utils/utils.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/modules.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js 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/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/utils/utils.js M test/qunit/tests/masthead_tests.js Log Message: ----------- Remove former populate_state Commit: 032ecd1e6edc8075de5b3ad0c7a815b46099a1de https://github.com/galaxyproject/galaxy/commit/032ecd1e6edc8075de5b3ad0c7a81... Author: guerler <aysam.guerler@gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Remove former update state Commit: 25c6eda06e75353c904f4e42864b72a30e35df62 https://github.com/galaxyproject/galaxy/commit/25c6eda06e75353c904f4e42864b7... Author: guerler <aysam.guerler@gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove regular tool handling from editor_form_post Commit: 89759a00c15e567e6e01ba47d28237d62605aaaa https://github.com/galaxyproject/galaxy/commit/89759a00c15e567e6e01ba47d2823... Author: guerler <aysam.guerler@gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Remove DummyDataset Commit: 6ffa104cb3931a60a484a4a42808e57a64dfbdd6 https://github.com/galaxyproject/galaxy/commit/6ffa104cb3931a60a484a4a42808e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/form_builder.py M lib/galaxy/workflow/modules.py Log Message: ----------- Use visit inputs to set runtime config, remove conflicting booleans Commit: 9423283e83f756f79dd6167c39c47a38557075a0 https://github.com/galaxyproject/galaxy/commit/9423283e83f756f79dd6167c39c47... Author: guerler <aysam.guerler@gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix ftp handling Commit: 664ae0c8dfa61fac9147675d6da2a32128ea7136 https://github.com/galaxyproject/galaxy/commit/664ae0c8dfa61fac9147675d6da2a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/modules.py M lib/tool_shed/util/workflow_util.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M test/api/test_tools.py M test/unit/tools/test_execution.py Log Message: ----------- Attempt to strip legacy collection handling, fixes Commit: 5a8246878473b988a163606d21bbd6b5ab0edaf4 https://github.com/galaxyproject/galaxy/commit/5a8246878473b988a163606d21bbd... Author: guerler <aysam.guerler@gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use regular dataset matching for selected values Commit: 5041c80d85ba5686f3d5f815349263ed4f8f0150 https://github.com/galaxyproject/galaxy/commit/5041c80d85ba5686f3d5f81534926... Author: guerler <aysam.guerler@gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Fix optional column parameter handling and accept_default tag Commit: 5ff028a9d0636e1e7f0e4bab02d40c98666a4ed8 https://github.com/galaxyproject/galaxy/commit/5ff028a9d0636e1e7f0e4bab02d40... Author: John Chilton <jmchilton@gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/utils/utils.js M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/tool_shed/util/workflow_util.py M static/maps/layout/masthead.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js 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/layout/masthead.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/utils/utils.js M templates/webapps/galaxy/galaxy.masthead.mako M test/api/test_tools.py M test/qunit/tests/masthead_tests.js M test/unit/tools/test_column_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Merge pull request #1711 from guerler/revise_states_000 Revise tool parameter handling, remove redundancies Compare: https://github.com/galaxyproject/galaxy/compare/a0537762f286...5ff028a9d063