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

[galaxyproject/galaxy] c27d3f: Allow uploading strict BED datatypes.
by GitHub 22 Jul '16

22 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c27d3f296d1d653b96eb2191d203e9a2daa272a6 https://github.com/galaxyproject/galaxy/commit/c27d3f296d1d653b96eb2191d203… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Allow uploading strict BED datatypes. Commit: 47522208c6d7a109d12c8d4dda153fd6bbaf0c1b https://github.com/galaxyproject/galaxy/commit/47522208c6d7a109d12c8d4dda15… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-07-23 (Sat, 23 Jul 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #2648 from blankenberg/bedstrict-up Allow uploading strict BED datatypes. Compare: https://github.com/galaxyproject/galaxy/compare/4da167be7b48...47522208c6d7

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[galaxyproject/galaxy] 897f2f: Merge hubAssembly.py in tracks.py , fix Python3 co...
by GitHub 22 Jul '16

22 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 897f2fe9331e8232a616a6329e0ea23f3237e44e https://github.com/galaxyproject/galaxy/commit/897f2fe9331e8232a616a6329e0e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M .ci/py3_sources.txt R lib/galaxy/datatypes/hubAssembly.py M lib/galaxy/datatypes/tracks.py Log Message: ----------- Merge hubAssembly.py in tracks.py , fix Python3 compatibility Fix unaddressed comments from #2348. Commit: 4da167be7b480c9a0a2050d0bf2b18c9808e548b https://github.com/galaxyproject/galaxy/commit/4da167be7b480c9a0a2050d0bf2b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M .ci/py3_sources.txt R lib/galaxy/datatypes/hubAssembly.py M lib/galaxy/datatypes/tracks.py Log Message: ----------- Merge pull request #2646 from nsoranzo/fixes_for_2348 Merge hubAssembly.py in tracks.py , fix Python3 compatibility Compare: https://github.com/galaxyproject/galaxy/compare/7763aaa39b88...4da167be7b48

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[galaxyproject/galaxy] 193c27: Move execute button and new history form to top of...
by GitHub 22 Jul '16

22 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 193c27e3dbc21ca539d9634b29618f86ab1c84b6 https://github.com/galaxyproject/galaxy/commit/193c27e3dbc21ca539d9634b2961… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-buttons.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-buttons.js M test/qunit/tests/ui_tests.js Log Message: ----------- Move execute button and new history form to top of workflow execution form Commit: 7b49080dc1ea410842ffb16825f86c69a95e0989 https://github.com/galaxyproject/galaxy/commit/7b49080dc1ea410842ffb16825f8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/mvc/ui/ui-buttons.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/ui/ui-buttons.js M test/qunit/tests/ui_tests.js Log Message: ----------- Adjust/fix button link variation, add test cases Commit: 842a98106257e21e9609370af7a55e31fdc99a6a https://github.com/galaxyproject/galaxy/commit/842a98106257e21e9609370af7a5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/mvc/ui/ui-buttons.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/ui/ui-buttons.js M test/qunit/tests/ui_tests.js Log Message: ----------- Adjust check state button and add test cases Commit: 80d20900efb6c319a6373bd6adb63ba547cafd16 https://github.com/galaxyproject/galaxy/commit/80d20900efb6c319a6373bd6adb6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-buttons.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/ui/ui-buttons.js M static/style/blue/base.css M test/qunit/tests/ui_tests.js Log Message: ----------- Adjust icon button, add test cases Commit: 9e82e59baff3ae23fe356aa6ad145324dcd30bf9 https://github.com/galaxyproject/galaxy/commit/9e82e59baff3ae23fe356aa6ad14… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-buttons.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/ui/ui-buttons.js M static/style/blue/base.css Log Message: ----------- Adjust menu button Commit: 361f89e8717738809fe2eecc08954809f271a049 https://github.com/galaxyproject/galaxy/commit/361f89e8717738809fe2eecc0895… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/mvc/ui/ui-buttons.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/ui/ui-buttons.js Log Message: ----------- Remove unused download attribute from button menu options Fix spacing Commit: 4781aafb472e7299e5a2204661584c4aeb52b98d https://github.com/galaxyproject/galaxy/commit/4781aafb472e7299e5a220466158… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-view.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/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Adjust upload button, unify model and option attributes Commit: 31a8dbf670bed9666d5c4afeaf7c4fb2c55d70ce https://github.com/galaxyproject/galaxy/commit/31a8dbf670bed9666d5c4afeaf7c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-buttons.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/ui/ui-buttons.js M static/style/blue/base.css Log Message: ----------- Fix margin handling Commit: 072b28b091c66316d7eedb3482800f1aa2bc77e4 https://github.com/galaxyproject/galaxy/commit/072b28b091c66316d7eedb348280… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix workflow wait label for workflow submission Commit: 01d14a0435d52666df69b21844e60a24b83fa25f https://github.com/galaxyproject/galaxy/commit/01d14a0435d52666df69b21844e6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Reduce distance between icon and title Commit: 35ef492e21b6e6a70fe52b4d089f67c137909925 https://github.com/galaxyproject/galaxy/commit/35ef492e21b6e6a70fe52b4d089f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M config/job_conf.xml.sample_advanced M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/library/datasets.js M config/plugins/visualizations/charts/static/library/jobs.js M config/plugins/visualizations/charts/static/library/storage.js R config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/models/chart.js M config/plugins/visualizations/charts/static/models/config.js R config/plugins/visualizations/charts/static/models/group.js R config/plugins/visualizations/charts/static/models/groups.js M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css M config/plugins/visualizations/charts/static/views/editor.js R config/plugins/visualizations/charts/static/views/group.js A config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewer.js M config/plugins/visualizations/charts/static/views/viewport.js A config/tool_destinations.yml.sample A doc/source/admin/grt.rst M doc/source/admin/index.rst M doc/source/admin/interactive_environments.rst M doc/source/dev/index.rst A doc/source/dev/interactive_environments.rst M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/web/framework/base.py A scripts/grt.py A scripts/grt.yml.sample M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-tabs.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/form/form-data.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-tabs.js M static/style/blue/base.css A test/functional/tools/output_filter_exception_1.xml M test/functional/tools/samples_tool_conf.xml A test/unit/jobs/dynamic_tool_destination/__init__.py A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml A test/unit/jobs/dynamic_tool_destination/data/test.empty A test/unit/jobs/dynamic_tool_destination/data/test.fasta A test/unit/jobs/dynamic_tool_destination/data/test1.full A test/unit/jobs/dynamic_tool_destination/data/test3.full A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml A test/unit/jobs/dynamic_tool_destination/data/test_users.yml A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- Merge branch 'dev' into move_workflow_run Commit: 45038d1399bf9e619ee815dad587f8ec3b3c4815 https://github.com/galaxyproject/galaxy/commit/45038d1399bf9e619ee815dad587… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M config/tool_data_table_conf.xml.sample M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M test/qunit/tests/ui_tests.js Log Message: ----------- Merge branch 'dev' into move_workflow_run Commit: 881af45dfedc8415f0a444e958be4c1c1eeeeb68 https://github.com/galaxyproject/galaxy/commit/881af45dfedc8415f0a444e958be… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Fix upload dialog test cases Commit: 7763aaa39b882e6fd9076055266b271abbf69829 https://github.com/galaxyproject/galaxy/commit/7763aaa39b882e6fd9076055266b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-view.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-buttons.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Merge pull request #2643 from guerler/move_workflow_run Move workflow run and history options to top, add loading indicator Compare: https://github.com/galaxyproject/galaxy/compare/40fde4ecf6e4...7763aaa39b88

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[galaxyproject/galaxy] 0a9d03: Add the composite datatype
by GitHub 22 Jul '16

22 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0a9d038a5d75560bc27e1f20d833e435b2f90e6e https://github.com/galaxyproject/galaxy/commit/0a9d038a5d75560bc27e1f20d833… Author: remiarenco <remimarenco(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M config/datatypes_conf.xml.sample A display_applications/ucsc/huba.xml A lib/galaxy/datatypes/hubAssembly.py Log Message: ----------- Add the composite datatype Commit: 4002e4ed1dbf6bbdad89e2e2420295e37c6789f0 https://github.com/galaxyproject/galaxy/commit/4002e4ed1dbf6bbdad89e2e24202… Author: remiarenco <remimarenco(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/hubAssembly.py Log Message: ----------- Pass pylint and better xml formatting Commit: e0ffb2d8d021248019c3a9a9d9e18ca0cdd9cf26 https://github.com/galaxyproject/galaxy/commit/e0ffb2d8d021248019c3a9a9d9e1… Author: remiarenco <remimarenco(a)gmail.com> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M config/datatypes_conf.xml.sample R display_applications/ucsc/huba.xml A display_applications/ucsc/trackhub.xml M lib/galaxy/datatypes/tracks.py Log Message: ----------- Following advices: renamed the extension to 'trackhub', renamed the huba.xml to trackhub.xml, changed iteritems to items, removed hubAssembly.py to port it into tracks.py Commit: 873a5d9f725cf574550b88805c543ebb33ee3ffc https://github.com/galaxyproject/galaxy/commit/873a5d9f725cf574550b88805c54… Author: remiarenco <remimarenco(a)gmail.com> Date: 2016-05-14 (Sat, 14 May 2016) Changed paths: M lib/galaxy/datatypes/tracks.py Log Message: ----------- Fix the uppercase in the extension (did not seem to affect the loading of the datatype/its use in Galaxy Commit: 1f6d3bc47069b054c86687bf00a8cad2afdd43bd https://github.com/galaxyproject/galaxy/commit/1f6d3bc47069b054c86687bf00a8… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Update datatypes_conf.xml.sample Typo in the extension Commit: 7cf435438817672854d524f8359c92675c36b046 https://github.com/galaxyproject/galaxy/commit/7cf435438817672854d524f8359c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M lib/galaxy/datatypes/hubAssembly.py M lib/galaxy/datatypes/tracks.py Log Message: ----------- Remove blank lines in file. Commit: 50fa525a440b0d3dc76a97053c58fead86b4bc2f https://github.com/galaxyproject/galaxy/commit/50fa525a440b0d3dc76a97053c58… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M lib/galaxy/datatypes/hubAssembly.py M lib/galaxy/datatypes/tracks.py Log Message: ----------- Merge pull request #1 from dannon/huba_datatype Remove blank lines in file. Commit: e66cf8358940e9bf298de4e3416b952d44987c65 https://github.com/galaxyproject/galaxy/commit/e66cf8358940e9bf298de4e3416b… Author: remimarenco <remi.marenco(a)gmail.com> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M lib/galaxy/datatypes/tracks.py Log Message: ----------- Remove the support of Galaxy version <= 16.01 Commit: 611ade3552d2cfe665156a64214e7a1e58d14683 https://github.com/galaxyproject/galaxy/commit/611ade3552d2cfe665156a64214e… Author: remimarenco <remi.marenco(a)gmail.com> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M display_applications/ucsc/trackhub.xml Log Message: ----------- Remove the strip_https attribute because we don't need it anymore Commit: 40fde4ecf6e4e8b2951c6fd2738205450144a07b https://github.com/galaxyproject/galaxy/commit/40fde4ecf6e4e8b2951c6fd27382… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M config/datatypes_conf.xml.sample A display_applications/ucsc/trackhub.xml A lib/galaxy/datatypes/hubAssembly.py M lib/galaxy/datatypes/tracks.py Log Message: ----------- Merge pull request #2348 from remimarenco/huba_datatype Add the trackhub composite datatype Compare: https://github.com/galaxyproject/galaxy/compare/1839e8144231...40fde4ecf6e4

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[galaxyproject/galaxy] 43523d: Fix flushing so mapped output collections created ...
by GitHub 22 Jul '16

22 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 43523dac98c6a7dda819caa7835349c11adf0a6c https://github.com/galaxyproject/galaxy/commit/43523dac98c6a7dda819caa78353… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Fix flushing so mapped output collections created uniformly. Commit: 9ede8e556be1f6038361b579c1457068e50e951a https://github.com/galaxyproject/galaxy/commit/9ede8e556be1f6038361b579c145… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Fix duplicated entries when using collections in history extract. This would "sometimes" correctly pick the first job to represent a collection creation step but in many cases not. Explicitly grab the "first". Commit: 1839e8144231abfcdd9a158ce221badcfd2c1d66 https://github.com/galaxyproject/galaxy/commit/1839e8144231abfcdd9a158ce221… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/workflow/extract.py Log Message: ----------- Merge pull request #2625 from jmchilton/history_extract_fixes_2 Fixes for workflow extraction of mapping collection jobs. Compare: https://github.com/galaxyproject/galaxy/compare/a8c1dfc16163...1839e8144231

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[galaxyproject/galaxy] f947fb: Remove dependency of select2 to regular select fie...
by GitHub 22 Jul '16

22 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f947fb604e28992b445d82d60df063e53553622e https://github.com/galaxyproject/galaxy/commit/f947fb604e28992b445d82d60df0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-default.js M test/qunit/tests/ui_tests.js Log Message: ----------- Remove dependency of select2 to regular select fields Commit: 67c3ec899d510c2956a876236e9a4e8d67f2c0dc https://github.com/galaxyproject/galaxy/commit/67c3ec899d510c2956a876236e9a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-default.js M test/qunit/tests/ui_tests.js Log Message: ----------- Reinsert classic multiple select field box Commit: 4fac8884b6e3ac85b91e078a8dab3f4750cd5505 https://github.com/galaxyproject/galaxy/commit/4fac8884b6e3ac85b91e078a8dab… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-select-default.js M test/qunit/tests/ui_tests.js Log Message: ----------- Preserve selection order, allow empty string as valid selection Commit: b4ee77d28279f3fdfc5e81ea34bf822477c30522 https://github.com/galaxyproject/galaxy/commit/b4ee77d28279f3fdfc5e81ea34bf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M test/qunit/tests/ui_tests.js Log Message: ----------- Adjust content selector tests Commit: a030aaf6ee31bcea782940a819611e6ac8a96c23 https://github.com/galaxyproject/galaxy/commit/a030aaf6ee31bcea782940a81961… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Repack scripts Commit: 8ae831aa9e669265c1b67dd3b630241d303cfc3b https://github.com/galaxyproject/galaxy/commit/8ae831aa9e669265c1b67dd3b630… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Add query feature to select2 options list Commit: 8e933f6e92e1276da7617b2a22ec69cb5164c549 https://github.com/galaxyproject/galaxy/commit/8e933f6e92e1276da7617b2a22ec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-default.js Log Message: ----------- Add select2 pagination Commit: 4a289ce4a083163e4027d61ff312b502f587fd31 https://github.com/galaxyproject/galaxy/commit/4a289ce4a083163e4027d61ff312… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.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/ui/ui-select-content.js Log Message: ----------- Add pagination criteria to content selector Commit: cc81cdb9465c742b4f089b31081a5e9eb8c64ad6 https://github.com/galaxyproject/galaxy/commit/cc81cdb9465c742b4f089b31081a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Hide select all button optionally Commit: f239a0a927c0635f6ade3a39d7a42650dd2d890e https://github.com/galaxyproject/galaxy/commit/f239a0a927c0635f6ade3a39d7a4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Add search word filtering Commit: 0372bdb4add3f44eef28febabf5658f7e2bbebd7 https://github.com/galaxyproject/galaxy/commit/0372bdb4add3f44eef28febabf56… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-default.js Log Message: ----------- Optimize logic for first value and button all selection Commit: 576e09fe63baaa1c5f7f90967d32f0b957d474e3 https://github.com/galaxyproject/galaxy/commit/576e09fe63baaa1c5f7f90967d32… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M test/qunit/tests/ui_tests.js Log Message: ----------- Merge branch 'select_performance' into dev Commit: a8c1dfc16163ab1fd6ef1096ce4cd9a636fdab36 https://github.com/galaxyproject/galaxy/commit/a8c1dfc16163ab1fd6ef1096ce4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-default.js Log Message: ----------- Rebuild client, borked merge of #2615. Compare: https://github.com/galaxyproject/galaxy/compare/09278b2afbda...a8c1dfc16163

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[galaxyproject/galaxy] 92948b: Overload select wrapper`s concat function
by GitHub 22 Jul '16

22 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 92948b5b0fc062ce904c5987c1d48d3831730a9a https://github.com/galaxyproject/galaxy/commit/92948b5b0fc062ce904c5987c1d4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Overload select wrapper`s concat function Commit: e4a35f943b42401c92646d8f6b7b1c1fd515a9c1 https://github.com/galaxyproject/galaxy/commit/e4a35f943b42401c92646d8f6b7b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py Log Message: ----------- Paste handles encoding automatically when thrown unicode, but uwsgi does not. This was resulting in unencoded (unicode) workflow drawings (svg) not appearing at all when the gen_image was invoked. Also took the opportunity to add a correct header for a standalone svg document. Commit: 68a64182c14af9f4cc10915c466177292d24ebfc https://github.com/galaxyproject/galaxy/commit/68a64182c14af9f4cc10915c4661… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py Log Message: ----------- Merge pull request #2628 from dannon/workflow_svg_uwsgi_fix [16.04] Workflow SVG generation fix Commit: 1de7beca98d0bc8b11b9dca46a4984ac1cee9428 https://github.com/galaxyproject/galaxy/commit/1de7beca98d0bc8b11b9dca46a49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #2623 from guerler/fix_select_value_concat [16.04] Overload select wrapper`s concat function Commit: 09278b2afbdacbf871df6e8560ba8739206b9dda https://github.com/galaxyproject/galaxy/commit/09278b2afbdacbf871df6e8560ba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0808015c9a42...09278b2afbda

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[galaxyproject/galaxy] ab1549: Set allow_duplicate_entries="False" for built-in T...
by GitHub 22 Jul '16

22 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab15495b8ee4c630b7e45575cdddc2e5a6a4bd97 https://github.com/galaxyproject/galaxy/commit/ab15495b8ee4c630b7e45575cddd… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Set allow_duplicate_entries="False" for built-in Tool Data Tables. Commit: 59dd11c8bc6746c23af759e2005bc5793713a939 https://github.com/galaxyproject/galaxy/commit/59dd11c8bc6746c23af759e2005b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Fix duplicate allow_duplicate_entries Commit: 0808015c9a4255f097a1f18a28c65ae6396ff7f7 https://github.com/galaxyproject/galaxy/commit/0808015c9a4255f097a1f18a28c6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Merge pull request #2644 from blankenberg/dm-no-dupe Set allow_duplicate_entries="False" for built-in Tool Data Tables. Compare: https://github.com/galaxyproject/galaxy/compare/8dbf987e10cb...0808015c9a42

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[galaxyproject/galaxy] f2941c: Add Galactic Radio Telescope script
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f2941c47aad24b301377792843a60428099e73c9 https://github.com/galaxyproject/galaxy/commit/f2941c47aad24b301377792843a6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: A scripts/grt.py Log Message: ----------- Add Galactic Radio Telescope script Commit: d032a1a4aa26b0d365418e9fb846c5fbedd3d4d1 https://github.com/galaxyproject/galaxy/commit/d032a1a4aa26b0d365418e9fb846… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-04 (Sat, 04 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Linting Commit: 6344ff40fdd843f6d6f02a9ae6956854f85ea474 https://github.com/galaxyproject/galaxy/commit/6344ff40fdd843f6d6f02a9ae695… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-04 (Sat, 04 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Make time length an option Commit: b1a07c0cfbf30968987755b3df84d9059176542d https://github.com/galaxyproject/galaxy/commit/b1a07c0cfbf30968987755b3df84… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-04 (Sat, 04 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Submit more metadata Commit: bf8f8e2d08a1d5db5831aa0f26dc584fa631ca36 https://github.com/galaxyproject/galaxy/commit/bf8f8e2d08a1d5db5831aa0f26dc… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-04 (Sat, 04 Jun 2016) Changed paths: A doc/source/admin/grt.rst M doc/source/admin/index.rst Log Message: ----------- Document GRT Commit: 9e596cdf5fbd4e63f7811d7d82929ee2d03fc79b https://github.com/galaxyproject/galaxy/commit/9e596cdf5fbd4e63f7811d7d8292… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-04 (Sat, 04 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- E303 Commit: 012101692c9cac152f8f2a48dc6c8983375a5823 https://github.com/galaxyproject/galaxy/commit/012101692c9cac152f8f2a48dc6c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Ignore metadata setting Commit: d1d8642756a062ee6df554dc9bdc3840d6fc828b https://github.com/galaxyproject/galaxy/commit/d1d8642756a062ee6df554dc9bdc… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Change metric captured Commit: 722695a01b8531560ee5f5cb12c2b235dff53308 https://github.com/galaxyproject/galaxy/commit/722695a01b8531560ee5f5cb12c2… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Added in last_job_id_sent and removed days options so no duplicates will be sent. Commit: bb3f026bfa14d7ae77b2b50dcdaf080fa6917875 https://github.com/galaxyproject/galaxy/commit/bb3f026bfa14d7ae77b2b50dcdaf… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Removed call to args.days Commit: 473b7eadc1feb6f6ca3b216080b319174f8f1229 https://github.com/galaxyproject/galaxy/commit/473b7eadc1feb6f6ca3b216080b3… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: A scripts/grt.ini.sample M scripts/grt.py Log Message: ----------- Added in tool_blacklist Commit: c2239b1d9bed06552571de862ec2ecb2bb3b46aa https://github.com/galaxyproject/galaxy/commit/c2239b1d9bed06552571de862ec2… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.ini.sample M scripts/grt.py Log Message: ----------- Moved almost all cmd line parameters to config file. Commit: 5cd9423677ef34e417059ae0be474872fc215909 https://github.com/galaxyproject/galaxy/commit/5cd9423677ef34e417059ae0be47… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.ini.sample M scripts/grt.py Log Message: ----------- Added grt_url to grt.ini.sample and removed default from argparse Commit: db4abace58711cef08e5a48d2d06f07f17c6d0c5 https://github.com/galaxyproject/galaxy/commit/db4abace58711cef08e5a48d2d06… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Flake8 fixes Commit: 0c24b1c408defa1c0d43754521a698a16a029bbf https://github.com/galaxyproject/galaxy/commit/0c24b1c408defa1c0d43754521a6… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Fixed remaining flake8 issues Commit: 0383d47037b1e18a60e882ff6bf8e4b905ec32b2 https://github.com/galaxyproject/galaxy/commit/0383d47037b1e18a60e882ff6bf8… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Added in params reporting with initial sanitization Commit: 2fc3ffffff39acbbfca0bdd265fd61f5b80a40f6 https://github.com/galaxyproject/galaxy/commit/2fc3ffffff39acbbfca0bdd265fd… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Removed unused copy import Commit: 417d43fb3ed5996657b568e1d2f9b6c728594b9b https://github.com/galaxyproject/galaxy/commit/417d43fb3ed5996657b568e1d2f9… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M scripts/grt.ini.sample Log Message: ----------- Added upload1 to tool blacklist Commit: 0280daebef16e83894812a813d673e576f571806 https://github.com/galaxyproject/galaxy/commit/0280daebef16e83894812a813d67… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: R scripts/grt.ini.sample M scripts/grt.py A scripts/grt.yml.sample Log Message: ----------- grt.ini.sample is a YAML file, git it a YAML extension. Commit: 6432eae251c1a85e0c22b17d80af731a5b8a9752 https://github.com/galaxyproject/galaxy/commit/6432eae251c1a85e0c22b17d80af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M scripts/grt.py Log Message: ----------- Give grt a top-level docstring. Commit: a93874fe7b6939c32b907a6f8fdd1cc0da6ce519 https://github.com/galaxyproject/galaxy/commit/a93874fe7b6939c32b907a6f8fdd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M scripts/grt.py Log Message: ----------- Define a main() function for grt client. This is purely stylistic - but I prefer to structure code to allow testing even if there are no actual test cases yet. For more information see discussion here - http://stackoverflow.com/questions/4041238/why-use-def-main. Commit: 1f292824a161d8d62767b47424b255146edb89d4 https://github.com/galaxyproject/galaxy/commit/1f292824a161d8d62767b47424b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M scripts/grt.py Log Message: ----------- Fix some obvious Python 2isms in grt client... ... and one instance of bare exception. Commit: bbe1d7bed036499d9a60b7db9daa9a93ee9bc4ef https://github.com/galaxyproject/galaxy/commit/bbe1d7bed036499d9a60b7db9daa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M scripts/grt.py Log Message: ----------- Remove custom Galaxy config parsing in grt.py. Use existing abstractions - so things like environment variable based configuration will work. Commit: 76628c720318c43665ef0067663738d4927f291f https://github.com/galaxyproject/galaxy/commit/76628c720318c43665ef00676637… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M scripts/grt.py Log Message: ----------- Refactor grt.py method names to be clear public interface is only main(). Commit: 212f7f0d9de67afb446989ae91cae79843358360 https://github.com/galaxyproject/galaxy/commit/212f7f0d9de67afb446989ae91ca… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: R scripts/grt.ini.sample M scripts/grt.py A scripts/grt.yml.sample Log Message: ----------- Merge pull request #16 from jmchilton/grt Touch up grt.py. Commit: 8dbf987e10cb946c96b7ec82c996892d443f61ab https://github.com/galaxyproject/galaxy/commit/8dbf987e10cb946c96b7ec82c996… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: A doc/source/admin/grt.rst M doc/source/admin/index.rst A scripts/grt.py A scripts/grt.yml.sample Log Message: ----------- Merge pull request #2455 from erasche/grt Galactic Radio Telescope Compare: https://github.com/galaxyproject/galaxy/compare/5ff6d7ad194f...8dbf987e10cb

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[galaxyproject/galaxy] 930c37: Style fixes
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 930c37ffb10bf36d2e95cee34da35997cdf59d8d https://github.com/galaxyproject/galaxy/commit/930c37ffb10bf36d2e95cee34da3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/library/datasets.js M config/plugins/visualizations/charts/static/library/jobs.js M config/plugins/visualizations/charts/static/library/storage.js M config/plugins/visualizations/charts/static/models/chart.js M config/plugins/visualizations/charts/static/models/config.js M config/plugins/visualizations/charts/static/models/group.js M config/plugins/visualizations/charts/static/models/groups.js M config/plugins/visualizations/charts/static/views/viewer.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Style fixes Commit: 4dd33fecb7b7643e7a4e14440a56187b790219a0 https://github.com/galaxyproject/galaxy/commit/4dd33fecb7b7643e7a4e14440a56… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Align editor view style Commit: 0861bb5b946bef5f5b7bb3d6c40670ec4eb1661d https://github.com/galaxyproject/galaxy/commit/0861bb5b946bef5f5b7bb3d6c406… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Fix spacing Commit: b6914479fba31057c064fcdcfc48060760d15400 https://github.com/galaxyproject/galaxy/commit/b6914479fba31057c064fcdcfc48… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/group.js Log Message: ----------- Align group view coding style Commit: 58a237eb4597cd709f8dbd0dcf6143f0adebc7f7 https://github.com/galaxyproject/galaxy/commit/58a237eb4597cd709f8dbd0dcf61… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/group.js Log Message: ----------- Adjust group view coding styles Commit: d38a4a4f6b193aa4aae84d200cdf77916aee9038 https://github.com/galaxyproject/galaxy/commit/d38a4a4f6b193aa4aae84d200cdf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Align remaining view code styles Commit: c6e9a56a46e97c7991eb3b67084c60d0d839f81e https://github.com/galaxyproject/galaxy/commit/c6e9a56a46e97c7991eb3b67084c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/models/chart.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/group.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Adjust viewport styles Commit: ad9f8b139d77575281900997039cc3bba3d00eb5 https://github.com/galaxyproject/galaxy/commit/ad9f8b139d77575281900997039c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.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/form/form-parameters.js M static/scripts/mvc/form/form-section.js Log Message: ----------- Decouple change handler for input parameters Commit: a8da228c8fddcff29c73c0900574e74290166359 https://github.com/galaxyproject/galaxy/commit/a8da228c8fddcff29c73c0900574… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-select-default.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/form/form-parameters.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Use common parameter factory for charts Commit: 0486ea4cc6aee83ea3d57f5fff0bf75b562410e2 https://github.com/galaxyproject/galaxy/commit/0486ea4cc6aee83ea3d57f5fff0b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/library/ui-table-form.js Log Message: ----------- Fadein additional options Commit: ef029042fd30c46b02e423b00f80cfb8dbf38e49 https://github.com/galaxyproject/galaxy/commit/ef029042fd30c46b02e423b00f80… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: R config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/views/settings.js Log Message: ----------- Combine ui-table-form and settings view Commit: 08b8cd6f00aed9554256ecf2c7eafd2e4f99ce99 https://github.com/galaxyproject/galaxy/commit/08b8cd6f00aed9554256ecf2c7ea… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/settings.js Log Message: ----------- Remove unused rendering options for settings view Commit: ce131d8b51dec8bb99571a524dc4c4f045e675d7 https://github.com/galaxyproject/galaxy/commit/ce131d8b51dec8bb99571a524dc4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css Log Message: ----------- Fix font size change caused by report styles Commit: 39c544c7742c9cc7853a9bbeac1d43c564b43e7b https://github.com/galaxyproject/galaxy/commit/39c544c7742c9cc7853a9bbeac1d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed 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Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Revise to 3-tab mode Commit: 645727c7a520a25b2459155604ff05eb533de4dd https://github.com/galaxyproject/galaxy/commit/645727c7a520a25b2459155604ff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Fix margin Commit: 539eeef5123f4adac296806ac4faf6931b24bb3c https://github.com/galaxyproject/galaxy/commit/539eeef5123f4adac296806ac4fa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Use large margin Commit: 916d2d01f788f32f126dd31ad4cf8fca1f99af85 https://github.com/galaxyproject/galaxy/commit/916d2d01f788f32f126dd31ad4cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M config/plugins/visualizations/charts/static/views/editor.js M static/maps/mvc/ui/ui-tabs.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/ui/ui-tabs.js Log Message: ----------- Refactor ui-tabs view Commit: b59cf74589e98c0666e1202750611a610e49826a https://github.com/galaxyproject/galaxy/commit/b59cf74589e98c0666e120275061… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M config/plugins/visualizations/charts/static/views/editor.js M static/maps/mvc/ui/ui-tabs.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/ui/ui-tabs.js Log Message: ----------- 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static/maps/mvc/ui/ui-tabs.js.map M static/scripts/mvc/ui/ui-tabs.js Log Message: ----------- Insert tab icons Commit: 3ca50a6b237b77cda3f7dba9acd6c151b4893b80 https://github.com/galaxyproject/galaxy/commit/3ca50a6b237b77cda3f7dba9acd6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M config/plugins/visualizations/charts/static/views/editor.js M static/maps/mvc/ui/ui-tabs.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/ui/ui-tabs.js Log Message: ----------- Insert tab icons Commit: e10d63cee00018ebf176976b6af4899634e87103 https://github.com/galaxyproject/galaxy/commit/e10d63cee00018ebf176976b6af4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/groups.js Log Message: ----------- Fix margin within data group repeat blocks Commit: 3d8840b86d5640ba74c80a1b9104eb768d6717f6 https://github.com/galaxyproject/galaxy/commit/3d8840b86d5640ba74c80a1b9104… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/views/groups.js M static/maps/mvc/form/form-repeat.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/form/form-repeat.js M static/style/blue/base.css Log Message: ----------- Revise group repeat block background and border colors Commit: 3ae19661f929de5278008d6cb9a07dde00ad7a80 https://github.com/galaxyproject/galaxy/commit/3ae19661f929de5278008d6cb9a0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-tabs.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/ui/ui-tabs.js M static/style/blue/base.css Log Message: ----------- Use classes instead of fixed ids to tag ui-tab dom elements Commit: 13b599158d2cbe80b8e1ddbff8ecdc1d14d3a4d0 https://github.com/galaxyproject/galaxy/commit/13b599158d2cbe80b8e1ddbff8ec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Allow displaying same message multiple times Commit: c2c6318061e1ad25513930ffc63f362fd36c5593 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config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/groups.js Log Message: ----------- Refactor individual model files, auto add first data series Commit: e25057c0d12e4570d53f4cb5eeed213e081b850a https://github.com/galaxyproject/galaxy/commit/e25057c0d12e4570d53f4cb5eeed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/library/storage.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/groups.js M static/maps/mvc/form/form-data.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/form/form-data.js M static/style/blue/base.css Log Message: ----------- Use regular form view for groups Commit: 6ebc19aa2e4978d4bf151f5f994c54e37fa5dd25 https://github.com/galaxyproject/galaxy/commit/6ebc19aa2e4978d4bf151f5f994c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css Log Message: ----------- Fix status margin Commit: fdf7a917c440087d206890e08b39608131ace241 https://github.com/galaxyproject/galaxy/commit/fdf7a917c440087d206890e08b39… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/models/config.js Log Message: ----------- Limit query size Commit: 2ee278a20fbedd6391c015b85689d834150a3a39 https://github.com/galaxyproject/galaxy/commit/2ee278a20fbedd6391c015b85689… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/groups.js Log Message: ----------- Add semicolon Commit: f25e177fa55e456e0fd739f772e2a9dbc69304a0 https://github.com/galaxyproject/galaxy/commit/f25e177fa55e456e0fd739f772e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/viewport.js M static/maps/mvc/form/form-view.js.map M static/scripts/mvc/form/form-view.js Log Message: ----------- Series color Commit: 9e3a9212754da8407bf93a9078e5f61116660f38 https://github.com/galaxyproject/galaxy/commit/9e3a9212754da8407bf93a9078e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M 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test/unit/jobs/dynamic_tool_destination/data/test_users.yml A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_conda_resolution.py M tools/stats/gsummary.xml Log Message: ----------- Merge branch 'dev' into charts_revision_000 Commit: 5ff6d7ad194f9e5145facef5c6baf2736e52c330 https://github.com/galaxyproject/galaxy/commit/5ff6d7ad194f9e5145facef5c6ba… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M 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