September 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 1d1620: Refactor recent toolbox changes for galaxy-lib.
by GitHub 26 Sep '16

26 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1d16200759895b6ede6c38655d085fa7bb0a1e17 https://github.com/galaxyproject/galaxy/commit/1d16200759895b6ede6c38655d08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Refactor recent toolbox changes for galaxy-lib. The abstracttoolbox class is supposed to shield Galaxy from the internals of the toolbox organization and vice versa, so having a reload method that uses Galaxy-specific queueing stuff is less than ideal. The concrete toolbox class is where I have been putting such functionality. In addition to this being the abstract design I prefer, it is definitely needed for galaxy-lib which contains the abstracttoolbox but not the concrete toolbox or the queue worker functionality. xref #2840 Commit: 780473a751ae52868e29b4e34ba2b0894598dc7b https://github.com/galaxyproject/galaxy/commit/780473a751ae52868e29b4e34ba2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #2971 from jmchilton/galaxy-lib-import-fix Refactor recent toolbox changes for galaxy-lib. Compare: https://github.com/galaxyproject/galaxy/compare/7f19ba817c4d...780473a751ae

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[galaxyproject/galaxy] d7ab1c: UI, Modal: re-build dom on render
by GitHub 26 Sep '16

26 Sep '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: d7ab1c5cfbfcdff3ce3e201f6fb0684fdb914096 https://github.com/galaxyproject/galaxy/commit/d7ab1c5cfbfcdff3ce3e201f6fb0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- UI, Modal: re-build dom on render Moves templating to render (and updates dom node attributes after) to reset modal and prevent inline styling and other modifications to the singleton from persisting between calls to show. Commit: 04d62e242412d0eb6e739f3577256d99b1aaa5bf https://github.com/galaxyproject/galaxy/commit/04d62e242412d0eb6e739f357725… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- Merge pull request #2955 from carlfeberhard/fix.modal-resetting [16.07] UI, Modal: re-build dom on render Compare: https://github.com/galaxyproject/galaxy/compare/e667f9f36038...04d62e242412

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[galaxyproject/galaxy] 9c4310: Remove html builders for tool parameters, strip ru...
by GitHub 25 Sep '16

25 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c43103630eb8bceb10021b282b8296218c04729 https://github.com/galaxyproject/galaxy/commit/9c43103630eb8bceb10021b282b8… Author: guerler <aysam.guerler(a)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/cd93da35c11f9374c5ffd03a44cb… Author: guerler <aysam.guerler(a)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/289ac4845ad79cc7ee2079784d31… Author: guerler <aysam.guerler(a)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/9f6a88a28f968a03301e8a516f10… Author: guerler <aysam.guerler(a)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/cd91e3141c7d031b092091ce2234… Author: guerler <aysam.guerler(a)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/b38b9fe2e1663d724651a0c6e1aa… Author: guerler <aysam.guerler(a)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/13f498568c505b24f1b9753aaf15… Author: guerler <aysam.guerler(a)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/d5ca00d6892874dc7da54be0a45d… Author: guerler <aysam.guerler(a)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/143a3ecffcc8da4469245b403369… Author: guerler <aysam.guerler(a)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/adfaa948e9f65c07bf8cf8a67791… Author: guerler <aysam.guerler(a)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/c61933d1b1c0289735945bf97bf8… Author: guerler <aysam.guerler(a)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/979bdd44c60d5aab27e472b19afa… Author: guerler <aysam.guerler(a)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/05923e210c41e0f3a6d14a3bd914… Author: guerler <aysam.guerler(a)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/9863e35368066975fe049adee716… Author: guerler <aysam.guerler(a)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/29cfd1635879987de9d1efc49d70… Author: guerler <aysam.guerler(a)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/474c9a26c495ddddeb6ba7c1966d… Author: guerler <aysam.guerler(a)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/6b40607e7917b98c481c4e47ac31… Author: guerler <aysam.guerler(a)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/0ef6f7826c621235beef70e8e4c3… Author: guerler <aysam.guerler(a)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/057485b6f6a8c545478907d01bd6… Author: guerler <aysam.guerler(a)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/a537daa9ed24fe4a4fd7c9e7c54b… Author: guerler <aysam.guerler(a)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/b2014fe44ce7b5af42956cf74cd6… Author: guerler <aysam.guerler(a)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/2c79755ba2fb752418d7405efdfd… Author: guerler <aysam.guerler(a)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/667d5e83cb6ccb7b46084b73101c… Author: guerler <aysam.guerler(a)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/21b5246c913fbf5ae8361f359e17… Author: guerler <aysam.guerler(a)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/c5d00518fe409d4876c18ceaeeef… Author: guerler <aysam.guerler(a)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/86719ce90e2cb8ee8439b2f4e8a9… Author: guerler <aysam.guerler(a)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/675398c91263eaed37007b76e485… Author: guerler <aysam.guerler(a)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/a0da06d842a6488ee355c0cf37c0… Author: guerler <aysam.guerler(a)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/05b1c988961e9e002e10d4e4cc21… Author: guerler <aysam.guerler(a)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/680e34c1adf87e3f6181bc2d6508… Author: guerler <aysam.guerler(a)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/80b5e5da91cdf65b8f06e75a9a6b… Author: guerler <aysam.guerler(a)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/1ab673a4ed5de36db49e24edae82… Author: guerler <aysam.guerler(a)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/9dc412921e5b5446aa4493aca8c7… Author: guerler <aysam.guerler(a)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/7a736818a6c32615c396a2a18d9e… Author: guerler <aysam.guerler(a)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/42ebe00c060d6fcbc69fd1697399… Author: guerler <aysam.guerler(a)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/2cf7b8ee15856626bff5dfad7350… Author: guerler <aysam.guerler(a)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/e3346e1d273b277445844e38e9e8… Author: guerler <aysam.guerler(a)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/7f19ba817c4d8e7d82380bd6fe8d… Author: John Chilton <jmchilton(a)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

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[galaxyproject/galaxy] e18d4e: UI, datasets: fix optional column form values
by GitHub 25 Sep '16

25 Sep '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: e18d4ed33b8b453229f969f2d05c997b2fa7fe96 https://github.com/galaxyproject/galaxy/commit/e18d4ed33b8b453229f969f2d05c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- UI, datasets: fix optional column form values Updates metadata column checkbox flag from 'true' to '__NOTHING__' to reflect newer form_builder values. Fixes #2175 Commit: e667f9f360388839d723421b884836acb6974e6c https://github.com/galaxyproject/galaxy/commit/e667f9f360388839d723421b8848… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-25 (Sun, 25 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #2960 from carlfeberhard/fix.bed-columns [16.07] UI, datasets: fix optional column form values Compare: https://github.com/galaxyproject/galaxy/compare/26d381c9a5d7...e667f9f36038

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[galaxyproject/usegalaxy-playbook] e703f7: Bridges for Main
by GitHub 23 Sep '16

23 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e703f798aa6e2586d5b3481ef830f4b3d0cf6d83 https://github.com/galaxyproject/usegalaxy-playbook/commit/e703f798aa6e2586… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M files/galaxy/usegalaxy.org/config/job_resource_params_conf.xml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Bridges for Main

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[galaxyproject/galaxy] b83f0a: Fix whoosh indexing.
by GitHub 23 Sep '16

23 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b83f0a10247119ef18bf72688d4e0bb8cfee8e36 https://github.com/galaxyproject/galaxy/commit/b83f0a10247119ef18bf72688d4e… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Fix whoosh indexing. Commit: 2c8a5d9d58c49c662aed4193f71caaf3fafe5651 https://github.com/galaxyproject/galaxy/commit/2c8a5d9d58c49c662aed4193f71c… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Correct import order. Commit: 092a7307c21afa8d66129dca23567b49a540d66a https://github.com/galaxyproject/galaxy/commit/092a7307c21afa8d66129dca2356… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge pull request #2949 from davebx/backport_whoosh [16.07] Fix missing import in whoosh indexing script Commit: 7a604c67d95f51f0afdaa980d01ab4061b4631f0 https://github.com/galaxyproject/galaxy/commit/7a604c67d95f51f0afdaa980d01a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/317fb472c962...7a604c67d95f

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[galaxyproject/galaxy] b83f0a: Fix whoosh indexing.
by GitHub 23 Sep '16

23 Sep '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: b83f0a10247119ef18bf72688d4e0bb8cfee8e36 https://github.com/galaxyproject/galaxy/commit/b83f0a10247119ef18bf72688d4e… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Fix whoosh indexing. Commit: 2c8a5d9d58c49c662aed4193f71caaf3fafe5651 https://github.com/galaxyproject/galaxy/commit/2c8a5d9d58c49c662aed4193f71c… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Correct import order. Commit: 092a7307c21afa8d66129dca23567b49a540d66a https://github.com/galaxyproject/galaxy/commit/092a7307c21afa8d66129dca2356… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge pull request #2949 from davebx/backport_whoosh [16.07] Fix missing import in whoosh indexing script Compare: https://github.com/galaxyproject/galaxy/compare/3b3e2e3358aa...092a7307c21a

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[galaxyproject/galaxy] c0e8a7: [16.07] Fix tool dependencies handling in Tool She...
by GitHub 23 Sep '16

23 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c0e8a7608351679b8ebdb71207339384161d6616 https://github.com/galaxyproject/galaxy/commit/c0e8a7608351679b8ebdb7120733… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: 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 Log Message: ----------- [16.07] Fix tool dependencies handling in Tool Shed model (#2950) * Fix the cause of toolshed test 1400 failing. * Fix handling of repositories without tool dependencies. * Fix tool dependency retrieval. In some cases, a process might attempt to fetch tool dependencies for revision 1:7334f6d0ac17, but the repository has been updated, and tool dependency metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves that issue. * Correct the logic that returns an empty string for an empty dict. * Fix getting latest revision with tool dependencies. * Use self.app instead of trans.app Commit: 9b3c061addb4f3e61d72465cf492396b9e07464e https://github.com/galaxyproject/galaxy/commit/9b3c061addb4f3e61d72465cf492… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: 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 Log Message: ----------- [16.07] Fix tool dependencies handling in Tool Shed model (#2950) * Fix the cause of toolshed test 1400 failing. * Fix handling of repositories without tool dependencies. * Fix tool dependency retrieval. In some cases, a process might attempt to fetch tool dependencies for revision 1:7334f6d0ac17, but the repository has been updated, and tool dependency metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves that issue. * Correct the logic that returns an empty string for an empty dict. * Fix getting latest revision with tool dependencies. * Use self.app instead of trans.app Conflicts: lib/galaxy/webapps/tool_shed/controllers/repository.py Commit: a78b8bcd2aa02abf787f0974fe567ab4f70f41a1 https://github.com/galaxyproject/galaxy/commit/a78b8bcd2aa02abf787f0974fe56… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04 Commit: c06f8c29968971c6c1e0dfc6847b3baf755f3a96 https://github.com/galaxyproject/galaxy/commit/c06f8c29968971c6c1e0dfc6847b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- correct the method call Commit: 5e7ee28e0d6937fa53f39b350e04357b554ce9ae https://github.com/galaxyproject/galaxy/commit/5e7ee28e0d6937fa53f39b350e04… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- bump freebayes in test (since it was updated) Commit: 45e6949eeae88c0d3c4c3f6341ddc5695d329bb2 https://github.com/galaxyproject/galaxy/commit/45e6949eeae88c0d3c4c3f6341dd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: 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 test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge pull request #2959 from martenson/release_16.04 [16.04] backport of model tool dependencies fix Commit: 3b3e2e3358aa73a5374345686581310d37349ff9 https://github.com/galaxyproject/galaxy/commit/3b3e2e3358aa73a5374345686581… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Conflicts: lib/galaxy/webapps/tool_shed/controllers/repository.py lib/galaxy/webapps/tool_shed/model/__init__.py Commit: 317fb472c96296c6de4d094b7236b9c3f25610da https://github.com/galaxyproject/galaxy/commit/317fb472c96296c6de4d094b7236… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: 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 test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/51a6d849342f...317fb472c962

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[galaxyproject/galaxy] 9b3c06: [16.07] Fix tool dependencies handling in Tool She...
by GitHub 23 Sep '16

23 Sep '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 9b3c061addb4f3e61d72465cf492396b9e07464e https://github.com/galaxyproject/galaxy/commit/9b3c061addb4f3e61d72465cf492… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: 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 Log Message: ----------- [16.07] Fix tool dependencies handling in Tool Shed model (#2950) * Fix the cause of toolshed test 1400 failing. * Fix handling of repositories without tool dependencies. * Fix tool dependency retrieval. In some cases, a process might attempt to fetch tool dependencies for revision 1:7334f6d0ac17, but the repository has been updated, and tool dependency metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves that issue. * Correct the logic that returns an empty string for an empty dict. * Fix getting latest revision with tool dependencies. * Use self.app instead of trans.app Conflicts: lib/galaxy/webapps/tool_shed/controllers/repository.py Commit: a78b8bcd2aa02abf787f0974fe567ab4f70f41a1 https://github.com/galaxyproject/galaxy/commit/a78b8bcd2aa02abf787f0974fe56… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04 Commit: c06f8c29968971c6c1e0dfc6847b3baf755f3a96 https://github.com/galaxyproject/galaxy/commit/c06f8c29968971c6c1e0dfc6847b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- correct the method call Commit: 5e7ee28e0d6937fa53f39b350e04357b554ce9ae https://github.com/galaxyproject/galaxy/commit/5e7ee28e0d6937fa53f39b350e04… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- bump freebayes in test (since it was updated) Commit: 45e6949eeae88c0d3c4c3f6341ddc5695d329bb2 https://github.com/galaxyproject/galaxy/commit/45e6949eeae88c0d3c4c3f6341dd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: 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 test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge pull request #2959 from martenson/release_16.04 [16.04] backport of model tool dependencies fix Commit: 3b3e2e3358aa73a5374345686581310d37349ff9 https://github.com/galaxyproject/galaxy/commit/3b3e2e3358aa73a5374345686581… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Conflicts: lib/galaxy/webapps/tool_shed/controllers/repository.py lib/galaxy/webapps/tool_shed/model/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/c0e8a7608351...3b3e2e3358aa

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[galaxyproject/usegalaxy-playbook] ec1b31: Update common_roles submodule
by GitHub 23 Sep '16

23 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ec1b31676d89956bd03dfcb2fa71f4df141b8f75 https://github.com/galaxyproject/usegalaxy-playbook/commit/ec1b31676d89956b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M common_roles Log Message: ----------- Update common_roles submodule Commit: 59ede2e8437717be6deff9364be8dbb9269f0f7b https://github.com/galaxyproject/usegalaxy-playbook/commit/59ede2e8437717be… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: A files/pulsar/common/config/bridges_dependency_resolvers_conf.xml A files/pulsar/test.galaxyproject.org/config/bridges_dependency_resolvers_con… A files/pulsar/usegalaxy.org/config/bridges_dependency_resolvers_conf.xml M pulsar.yml M stage/host_vars/br005.bridges.psc.edu.yml Log Message: ----------- Install dependency_resolvers_conf.xml for Bridges Commit: 1f4f64897137d68d12c576c0b6cbdae28f11cb1a https://github.com/galaxyproject/usegalaxy-playbook/commit/1f4f64897137d68d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: A production/host_vars/br005.bridges.psc.edu.yml M production/inventory A production/secret_host_vars/br005.bridges.psc.edu.yml Log Message: ----------- Main Pulsar on Bridges Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/158bf29be216...…

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