Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c43103630eb8bceb10021b282b8296218c04729 https://github.com/galaxyproject/galaxy/commit/9c43103630eb8bceb10021b282b82... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/basic.py M templates/webapps/galaxy/workflow/run.mako

Log Message: ----------- Remove html builders for tool parameters, strip run workflow mako

Commit: cd93da35c11f9374c5ffd03a44cbf33876dffb29 https://github.com/galaxyproject/galaxy/commit/cd93da35c11f9374c5ffd03a44cbf... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py R templates/webapps/galaxy/workflow/run_complete.mako

Log Message: ----------- Remove old run controller

Commit: 289ac4845ad79cc7ee2079784d31182d3df23027 https://github.com/galaxyproject/galaxy/commit/289ac4845ad79cc7ee2079784d311... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/basic.py

Log Message: ----------- Remove unused checked list state for booleans

Commit: 9f6a88a28f968a03301e8a516f10a5322bc77f4e https://github.com/galaxyproject/galaxy/commit/9f6a88a28f968a03301e8a516f10a... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/basic.py

Log Message: ----------- Remove unused to_dict parameters

Commit: cd91e3141c7d031b092091ce22345d87b8aa76d2 https://github.com/galaxyproject/galaxy/commit/cd91e3141c7d031b092091ce22345... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/basic.py

Log Message: ----------- Rename regex parameter, fix spacing

Commit: b38b9fe2e1663d724651a0c6e1aa78e87acaa43d https://github.com/galaxyproject/galaxy/commit/b38b9fe2e1663d724651a0c6e1aa7... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/basic.py

Log Message: ----------- Remove comment

Commit: 13f498568c505b24f1b9753aaf158be324542219 https://github.com/galaxyproject/galaxy/commit/13f498568c505b24f1b9753aaf158... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/basic.py

Log Message: ----------- Remove unused repeat handling

Commit: d5ca00d6892874dc7da54be0a45da3cea4acb878 https://github.com/galaxyproject/galaxy/commit/d5ca00d6892874dc7da54be0a45da... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/basic.py

Log Message: ----------- Adjust first half of test cases in basic paramter handling

Commit: 143a3ecffcc8da4469245b40336901f944b531e0 https://github.com/galaxyproject/galaxy/commit/143a3ecffcc8da4469245b4033690... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/basic.py

Log Message: ----------- Fix test cases

Commit: adfaa948e9f65c07bf8cf8a67791bb3dd0e30bc6 https://github.com/galaxyproject/galaxy/commit/adfaa948e9f65c07bf8cf8a67791b... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Remove unused imports

Commit: c61933d1b1c0289735945bf97bf8b1f4bf5e5fc8 https://github.com/galaxyproject/galaxy/commit/c61933d1b1c0289735945bf97bf8b... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/unittest_utils/galaxy_mock.py

Log Message: ----------- Fix dataset parameter tests

Commit: 979bdd44c60d5aab27e472b19afa8dd704ee195a https://github.com/galaxyproject/galaxy/commit/979bdd44c60d5aab27e472b19afa8... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/basic.py

Log Message: ----------- Fix drilldown tests

Commit: 05923e210c41e0f3a6d14a3bd914356c042f4670 https://github.com/galaxyproject/galaxy/commit/05923e210c41e0f3a6d14a3bd9143... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/basic.py

Log Message: ----------- Undo name change for workflow regex

Commit: 9863e35368066975fe049adee716c5cabad4c60f https://github.com/galaxyproject/galaxy/commit/9863e35368066975fe049adee716c... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M test/unit/tools/test_data_parameters.py

Log Message: ----------- Attempt to remove value_mapper parsing

Commit: 29cfd1635879987de9d1efc49d704894454a3ddf https://github.com/galaxyproject/galaxy/commit/29cfd1635879987de9d1efc49d704... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M test/unit/tools/test_parameter_parsing.py

Log Message: ----------- Fix test_parameter_parsing

Commit: 474c9a26c495ddddeb6ba7c1966de6ae32cedea7 https://github.com/galaxyproject/galaxy/commit/474c9a26c495ddddeb6ba7c1966de... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M templates/webapps/tool_shed/repository/tool_form.mako M test/unit/tools/test_data_parameters.py

Log Message: ----------- Fix toolshed tool form preview, import order

Commit: 6b40607e7917b98c481c4e47ac31d31698ce2660 https://github.com/galaxyproject/galaxy/commit/6b40607e7917b98c481c4e47ac31d... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/basic.py

Log Message: ----------- Remove debug output

Commit: 0ef6f7826c621235beef70e8e4c3352d2ab2e2b6 https://github.com/galaxyproject/galaxy/commit/0ef6f7826c621235beef70e8e4c33... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M templates/webapps/galaxy/workflow/run.mako

Log Message: ----------- Move controller build endpoint to api

Commit: 057485b6f6a8c545478907d01bd6ceadfea0d1f6 https://github.com/galaxyproject/galaxy/commit/057485b6f6a8c545478907d01bd6c... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py

Log Message: ----------- Import exception, fix parameter names

Commit: a537daa9ed24fe4a4fd7c9e7c54ba30f6de6e156 https://github.com/galaxyproject/galaxy/commit/a537daa9ed24fe4a4fd7c9e7c54ba... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/tool/tool-form-composite.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/tool/tool-form-composite.js M templates/webapps/galaxy/workflow/run.mako

Log Message: ----------- Move run form model builder to workflow data manager

Commit: b2014fe44ce7b5af42956cf74cd6e75c51a8df0f https://github.com/galaxyproject/galaxy/commit/b2014fe44ce7b5af42956cf74cd6e... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Disable target history specification for run workflow form

Commit: 2c79755ba2fb752418d7405efdfdcd46bf14d8a4 https://github.com/galaxyproject/galaxy/commit/2c79755ba2fb752418d7405efdfdc... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Fix stored/workflow handling

Commit: 667d5e83cb6ccb7b46084b73101cb85cc81dd9fa https://github.com/galaxyproject/galaxy/commit/667d5e83cb6ccb7b46084b73101cb... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M templates/webapps/tool_shed/repository/tool_form.mako

Log Message: ----------- Fix value parsing

Commit: 21b5246c913fbf5ae8361f359e17252718f1f87d https://github.com/galaxyproject/galaxy/commit/21b5246c913fbf5ae8361f359e172... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Remove unused data manager

Commit: c5d00518fe409d4876c18ceaeeef2ad5b6829385 https://github.com/galaxyproject/galaxy/commit/c5d00518fe409d4876c18ceaeeef2... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Fix error messages

Commit: 86719ce90e2cb8ee8439b2f4e8a947cc239e1957 https://github.com/galaxyproject/galaxy/commit/86719ce90e2cb8ee8439b2f4e8a94... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Remove redundant imports

Commit: 675398c91263eaed37007b76e4856a6d81f888a3 https://github.com/galaxyproject/galaxy/commit/675398c91263eaed37007b76e4856... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Use message exception to parse errors

Commit: a0da06d842a6488ee355c0cf37c06f7ffb8ee837 https://github.com/galaxyproject/galaxy/commit/a0da06d842a6488ee355c0cf37c06... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Revise comment

Commit: 05b1c988961e9e002e10d4e4cc21f49ff4ab958a https://github.com/galaxyproject/galaxy/commit/05b1c988961e9e002e10d4e4cc21f... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js

Log Message: ----------- Add basic step version changes notification

Commit: 680e34c1adf87e3f6181bc2d6508f3f5ab84c903 https://github.com/galaxyproject/galaxy/commit/680e34c1adf87e3f6181bc2d6508f... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css

Log Message: ----------- Fix form preview height style

Commit: 80b5e5da91cdf65b8f06e75a9a6b2c202b94d409 https://github.com/galaxyproject/galaxy/commit/80b5e5da91cdf65b8f06e75a9a6b2... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-portlet.js M static/style/blue/base.css

Log Message: ----------- Remove unused portlet footer

Commit: 1ab673a4ed5de36db49e24edae821d226040d183 https://github.com/galaxyproject/galaxy/commit/1ab673a4ed5de36db49e24edae821... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js

Log Message: ----------- Fix padding distance

Commit: 9dc412921e5b5446aa4493aca8c7c0105f7d0725 https://github.com/galaxyproject/galaxy/commit/9dc412921e5b5446aa4493aca8c7c... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css

Log Message: ----------- Fix bottom margin

Commit: 7a736818a6c32615c396a2a18d9ebd884ddccebb https://github.com/galaxyproject/galaxy/commit/7a736818a6c32615c396a2a18d9eb... Author: guerler aysam.guerler@gmail.com Date: 2016-09-21 (Wed, 21 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M test/qunit/tests/form_tests.js

Log Message: ----------- Avoid inheritance in tool-form view

Avoid inheritance for workflow editor form

Fix test cases

Commit: 42ebe00c060d6fcbc69fd16973995c33aba48207 https://github.com/galaxyproject/galaxy/commit/42ebe00c060d6fcbc69fd16973995... Author: guerler aysam.guerler@gmail.com Date: 2016-09-23 (Fri, 23 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js

Log Message: ----------- Add listener to properly clean up deferred form building processes

Commit: 2cf7b8ee15856626bff5dfad735023a43ace978b https://github.com/galaxyproject/galaxy/commit/2cf7b8ee15856626bff5dfad73502... Author: guerler aysam.guerler@gmail.com Date: 2016-09-23 (Fri, 23 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/utils/utils.js M static/maps/mvc/tool/tool-form-base.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/tool/tool-form-base.js M static/scripts/utils/utils.js

Log Message: ----------- Fix status handling for ajax requests

Commit: e3346e1d273b277445844e38e9e8d29873b4d619 https://github.com/galaxyproject/galaxy/commit/e3346e1d273b277445844e38e9e8d... Author: guerler aysam.guerler@gmail.com Date: 2016-09-23 (Fri, 23 Sep 2016)

Changed paths: M .gitignore M Makefile A doc/parse_gx_xsd.py A doc/schema_template.md M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py M scripts/bootstrap_history.py M scripts/tool_shed/build_ts_whoosh_index.py M templates/webapps/galaxy/dataset/copy_view.mako M test/shed_functional/functional/test_1400_review_migration_stages.py

Log Message: ----------- Merge branch 'dev' into strip_run_form_mako

Commit: 7f19ba817c4d8e7d82380bd6fe8d03a7247488f3 https://github.com/galaxyproject/galaxy/commit/7f19ba817c4d8e7d82380bd6fe8d0... Author: John Chilton jmchilton@gmail.com Date: 2016-09-25 (Sun, 25 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-portlet.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/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/run.mako R templates/webapps/galaxy/workflow/run_complete.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/qunit/tests/form_tests.js M test/unit/tools/test_data_parameters.py M test/unit/tools/test_parameter_parsing.py M test/unit/unittest_utils/galaxy_mock.py

Log Message: ----------- Merge pull request #2935 from guerler/strip_run_form_mako

Strip workflow run mako

Compare: https://github.com/galaxyproject/galaxy/compare/cbb957028f0c...7f19ba817c4d