- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 085393: Remove input cloning in form section handler
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0853932d42df64f43f8531710947d50a9766d320 https://github.com/galaxyproject/galaxy/commit/0853932d42df64f43f8531710947… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Remove input cloning in form section handler Commit: 009305fb79fe7986e55266993f06047b5bebaf02 https://github.com/galaxyproject/galaxy/commit/009305fb79fe7986e55266993f06… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js Log Message: ----------- Use flat copy for context when traversing input elements Commit: e76397970bd510d10822de3b44d160903c42aedd https://github.com/galaxyproject/galaxy/commit/e76397970bd510d10822de3b44d1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Use flex feature instead of manual size adjustment Commit: 37eb36a60c4749f9cae7e7fe3166dfe56a5ef48f https://github.com/galaxyproject/galaxy/commit/37eb36a60c4749f9cae7e7fe3166… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js Log Message: ----------- Generalize scrolling behavior to highlight errors in tool forms Commit: 51a3a6d5ee6ebe255424a2beb433053801fe60ac https://github.com/galaxyproject/galaxy/commit/51a3a6d5ee6ebe255424a2beb433… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M config/galaxy.yml.sample M config/plugins/webhooks/demo/tour_generator/__init__.py M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/util/workflow_util.py R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M static/style/blue/base.css M test/api/test_tools.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/base/testcase.py R test/base/tool_shed_util.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/twilltestcase.py M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py A test/integration/uses_shed.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_parsing.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge branch 'dev' into workflow_run_performance Commit: 31a3d5eab231302f8bd256bdcb20b1bdb6925d71 https://github.com/galaxyproject/galaxy/commit/31a3d5eab231302f8bd256bdcb20… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-11 (Sun, 11 Mar 2018) Changed paths: M config/job_metrics_conf.xml.sample M lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/upload_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py A lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/data_fetch.py A lib/galaxy/tools/data_fetch.xml M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/special_tools.py M lib/galaxy/util/compression_utils.py A lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py A scripts/api/fetch_to_library.py A scripts/api/fetch_to_library_example.yml A test-data/1.csv A test-data/example-bag.zip A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_libraries.py M test/api/test_tools_upload.py M test/base/driver_util.py M test/base/integration_util.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into workflow_run_performance Commit: 5f73d7fbbd2c71c48f49fca5a0c1c4736a5de5de https://github.com/galaxyproject/galaxy/commit/5f73d7fbbd2c71c48f49fca5a0c1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #5646 from guerler/workflow_run_performance Avoid producing deep-copies of tool input dictionaries Compare: https://github.com/galaxyproject/galaxy/compare/7bcd16d4cc58...5f73d7fbbd2c

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[galaxyproject/galaxy] 73e61f: add security announcement to the rn
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 73e61f5fdc4011d838ff5862ed3713fdca48762e https://github.com/galaxyproject/galaxy/commit/73e61f5fdc4011d838ff5862ed37… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- add security announcement to the rn Commit: 7bcd16d4cc5845a60223212067254f83dabf3f97 https://github.com/galaxyproject/galaxy/commit/7bcd16d4cc5845a6022321206725… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Merge pull request #5685 from martenson/security-rn [18.01] add security announcement to the release notes Compare: https://github.com/galaxyproject/galaxy/compare/a53fb19f1628...7bcd16d4cc58

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[galaxyproject/galaxy] 3e033b: Prefill column selector for datasets which are not...
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3e033bf896918d9e468f2d54dc98e068c3ded6ba https://github.com/galaxyproject/galaxy/commit/3e033bf896918d9e468f2d54dc98… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Prefill column selector for datasets which are not ready yet Commit: 895a858ded2533bf188edba7fa8f4d1cbe1337d4 https://github.com/galaxyproject/galaxy/commit/895a858ded2533bf188edba7fa8f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove explicit loop, use map instead Commit: 7b6321e4a84794471c346d82054d810e274a3e4e https://github.com/galaxyproject/galaxy/commit/7b6321e4a84794471c346d82054d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use list comprehension instead of map Commit: a53fb19f16285caebb3552393cadc570eeb8b22b https://github.com/galaxyproject/galaxy/commit/a53fb19f16285caebb3552393cad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #5680 from guerler/fix_column_selector Populate column selector for datasets which are not ready yet Compare: https://github.com/galaxyproject/galaxy/compare/4558ad64f0bc...a53fb19f1628

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[galaxyproject/galaxy] ee924e: fix the inconsistency between two fixes
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ee924ec173edf4bd7a02b9c1d9b366ff607c1176 https://github.com/galaxyproject/galaxy/commit/ee924ec173edf4bd7a02b9c1d9b3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- fix the inconsistency between two fixes Commit: 4558ad64f0bcd54b99bac0e3f3db12c192b8a3aa https://github.com/galaxyproject/galaxy/commit/4558ad64f0bcd54b99bac0e3f3db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge pull request #5683 from martenson/fix-2-fixes fix the inconsistency between two library fixes Compare: https://github.com/galaxyproject/galaxy/compare/76b305b72a67...4558ad64f0bc

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[galaxyproject/galaxy]
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/tags/v18.01 Home: https://github.com/galaxyproject/galaxy

1 0

[galaxyproject/galaxy] cf4936: Minor cleanup in galaxy.tools.actions
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cf4936b3d480011a4638a393776dd5ec94f11ae4 https://github.com/galaxyproject/galaxy/commit/cf4936b3d480011a4638a393776d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Minor cleanup in galaxy.tools.actions Commit: 513b6a5d65676a2f03d6c4580d16e053d8fe6aaf https://github.com/galaxyproject/galaxy/commit/513b6a5d65676a2f03d6c4580d16… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Fix a few mutable default params in workflow/run_request. Commit: 332d79eb72c4bae90c911707d4db9285556c59b1 https://github.com/galaxyproject/galaxy/commit/332d79eb72c4bae90c911707d4db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix 'uknown' typo in model exceptions Commit: 04404f915c70b90a9d4a56dbeb030748163dce16 https://github.com/galaxyproject/galaxy/commit/04404f915c70b90a9d4a56dbeb03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Support re-execution of immediate PJAs when requing jobs Commit: b685b53d13b9fa91c4abcb631fc3cd5c68d5d9c4 https://github.com/galaxyproject/galaxy/commit/b685b53d13b9fa91c4abcb631fc3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Ship context along with PJA execution when remapping workflow immediate actions Commit: 6a7fb23f11e26b3761cb71128a4c5e0ac605d818 https://github.com/galaxyproject/galaxy/commit/6a7fb23f11e26b3761cb71128a4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Instead of denoting unused var from items(), just use values() Commit: f1dd060d73ccb369aafb1a56e902e4d4faf6dd64 https://github.com/galaxyproject/galaxy/commit/f1dd060d73ccb369aafb1a56e902… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test rename PJA when resuming a failed job Commit: 8dfc1523d31e56a3e632e0d490d08c15722764d5 https://github.com/galaxyproject/galaxy/commit/8dfc1523d31e56a3e632e0d490d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #26 from mvdbeek/workflow-resume-pjas Test rename PJA when resuming a failed job Commit: 040bf5ba77562cc20b822b2068860c2bf6c0399e https://github.com/galaxyproject/galaxy/commit/040bf5ba77562cc20b822b206886… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5678 from dannon/workflow-resume-pjas [18.01] Support re-execution of immediate PJAs when re-queing jobs Commit: 31cb24e4229767425a72d6981bcb359b15792254 https://github.com/galaxyproject/galaxy/commit/31cb24e4229767425a72d6981bcb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tool-genomespace.js.map M static/maps/mvc/ui/ui-select-genomespace.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/onload.js.map M static/maps/ui/loading-indicator.js.map M static/maps/utils/config.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tool-genomespace.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/workflow/workflow.js M static/scripts/onload.js M static/scripts/ui/loading-indicator.js M static/scripts/utils/config.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css Log Message: ----------- add built client with maps for 18.01 tagging Commit: 0182d8d0bec3cf78401434e5c07b012eabcda7e3 https://github.com/galaxyproject/galaxy/commit/0182d8d0bec3cf78401434e5c07b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.01 Commit: 93f778498ac7ec1fb50461147b7173c0301ba91a https://github.com/galaxyproject/galaxy/commit/93f778498ac7ec1fb50461147b71… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py Log Message: ----------- Merge branch 'release_18.01' into dev Commit: 76b305b72a676dbac7b041af225f1884040c4788 https://github.com/galaxyproject/galaxy/commit/76b305b72a676dbac7b041af225f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into dev Compare: https://github.com/galaxyproject/galaxy/compare/7ad5dbab4f0d...76b305b72a67

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[galaxyproject/galaxy] 0182d8: Update version to 18.01
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 0182d8d0bec3cf78401434e5c07b012eabcda7e3 https://github.com/galaxyproject/galaxy/commit/0182d8d0bec3cf78401434e5c07b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.01

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[galaxyproject/galaxy] 252118: use a set instead of list
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2521181f5a6d65cfbcee0ed6e876b17cf1e82c9c https://github.com/galaxyproject/galaxy/commit/2521181f5a6d65cfbcee0ed6e876… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- use a set instead of list could be faster per mvdbeek Commit: f8088792e46f1652b4810161357f251340732d97 https://github.com/galaxyproject/galaxy/commit/f8088792e46f1652b4810161357f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Simplify empty set creation Commit: 7ad5dbab4f0df50937feb5c0d1859d8ec86c0735 https://github.com/galaxyproject/galaxy/commit/7ad5dbab4f0df50937feb5c0d185… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge pull request #5681 from martenson/set-from-list library manager - use a set instead of list Compare: https://github.com/galaxyproject/galaxy/compare/ccc5cfc95846...7ad5dbab4f0d

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[galaxyproject/galaxy] 31cb24: add built client with maps for 18.01 tagging
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 31cb24e4229767425a72d6981bcb359b15792254 https://github.com/galaxyproject/galaxy/commit/31cb24e4229767425a72d6981bcb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tool-genomespace.js.map M static/maps/mvc/ui/ui-select-genomespace.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/onload.js.map M static/maps/ui/loading-indicator.js.map M static/maps/utils/config.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tool-genomespace.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/workflow/workflow.js M static/scripts/onload.js M static/scripts/ui/loading-indicator.js M static/scripts/utils/config.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css Log Message: ----------- add built client with maps for 18.01 tagging

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[galaxyproject/galaxy] cf4936: Minor cleanup in galaxy.tools.actions
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: cf4936b3d480011a4638a393776dd5ec94f11ae4 https://github.com/galaxyproject/galaxy/commit/cf4936b3d480011a4638a393776d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Minor cleanup in galaxy.tools.actions Commit: 513b6a5d65676a2f03d6c4580d16e053d8fe6aaf https://github.com/galaxyproject/galaxy/commit/513b6a5d65676a2f03d6c4580d16… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Fix a few mutable default params in workflow/run_request. Commit: 332d79eb72c4bae90c911707d4db9285556c59b1 https://github.com/galaxyproject/galaxy/commit/332d79eb72c4bae90c911707d4db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix 'uknown' typo in model exceptions Commit: 04404f915c70b90a9d4a56dbeb030748163dce16 https://github.com/galaxyproject/galaxy/commit/04404f915c70b90a9d4a56dbeb03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Support re-execution of immediate PJAs when requing jobs Commit: b685b53d13b9fa91c4abcb631fc3cd5c68d5d9c4 https://github.com/galaxyproject/galaxy/commit/b685b53d13b9fa91c4abcb631fc3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Ship context along with PJA execution when remapping workflow immediate actions Commit: 6a7fb23f11e26b3761cb71128a4c5e0ac605d818 https://github.com/galaxyproject/galaxy/commit/6a7fb23f11e26b3761cb71128a4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Instead of denoting unused var from items(), just use values() Commit: f1dd060d73ccb369aafb1a56e902e4d4faf6dd64 https://github.com/galaxyproject/galaxy/commit/f1dd060d73ccb369aafb1a56e902… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test rename PJA when resuming a failed job Commit: 8dfc1523d31e56a3e632e0d490d08c15722764d5 https://github.com/galaxyproject/galaxy/commit/8dfc1523d31e56a3e632e0d490d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #26 from mvdbeek/workflow-resume-pjas Test rename PJA when resuming a failed job Commit: 040bf5ba77562cc20b822b2068860c2bf6c0399e https://github.com/galaxyproject/galaxy/commit/040bf5ba77562cc20b822b206886… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5678 from dannon/workflow-resume-pjas [18.01] Support re-execution of immediate PJAs when re-queing jobs Compare: https://github.com/galaxyproject/galaxy/compare/5cf3d44a6ad5...040bf5ba7756

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[galaxyproject/galaxy] cb5e81: replace incorrect list add syntax
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cb5e81b6a1209ef89dd7edc9bdd870c8953a96a5 https://github.com/galaxyproject/galaxy/commit/cb5e81b6a1209ef89dd7edc9bdd8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- replace incorrect list add syntax Commit: 6b9afb6b360108b194c03ca262a20013b444ece9 https://github.com/galaxyproject/galaxy/commit/6b9afb6b360108b194c03ca262a2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- rmeove overly zealous syntax fix thanks to dannon Commit: 5cf3d44a6ad5f53c3f263ac2a28484686e44ea6a https://github.com/galaxyproject/galaxy/commit/5cf3d44a6ad5f53c3f263ac2a284… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge pull request #5676 from martenson/fix-library-add [18.01] replace incorrect list add syntax Commit: ccc5cfc95846e75fe6b4d48b0e4e1a5886ae9d53 https://github.com/galaxyproject/galaxy/commit/ccc5cfc95846e75fe6b4d48b0e4e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/1cc5f3fe1a06...ccc5cfc95846

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[galaxyproject/galaxy] cb5e81: replace incorrect list add syntax
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: cb5e81b6a1209ef89dd7edc9bdd870c8953a96a5 https://github.com/galaxyproject/galaxy/commit/cb5e81b6a1209ef89dd7edc9bdd8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- replace incorrect list add syntax Commit: 6b9afb6b360108b194c03ca262a20013b444ece9 https://github.com/galaxyproject/galaxy/commit/6b9afb6b360108b194c03ca262a2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- rmeove overly zealous syntax fix thanks to dannon Commit: 5cf3d44a6ad5f53c3f263ac2a28484686e44ea6a https://github.com/galaxyproject/galaxy/commit/5cf3d44a6ad5f53c3f263ac2a284… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge pull request #5676 from martenson/fix-library-add [18.01] replace incorrect list add syntax Compare: https://github.com/galaxyproject/galaxy/compare/1a5f6a349909...5cf3d44a6ad5

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[galaxyproject/galaxy] 1dfaa4: Rebuild client only if there are changes
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1dfaa476c0198f9be9a20c239fcd4c63e9b3966a https://github.com/galaxyproject/galaxy/commit/1dfaa476c0198f9be9a20c239fcd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Rebuild client only if there are changes in the client/ directory since the last build. Commit: 1cc5f3fe1a0635a68135d5591e18b33b0950504e https://github.com/galaxyproject/galaxy/commit/1cc5f3fe1a0635a68135d5591e18… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #5679 from nsoranzo/git_diff_client Rebuild client only if there are changes Compare: https://github.com/galaxyproject/galaxy/compare/4fc638070845...1cc5f3fe1a06

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[galaxyproject/usegalaxy-playbook] b1ea11: Update Test
by GitHub 12 Mar '18

12 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b1ea1153ef06b63a60f3a3ca47ed15b428f7646b https://github.com/galaxyproject/usegalaxy-playbook/commit/b1ea1153ef06b63a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: 09596816c016c696453810fd05893a0d0418d770 https://github.com/galaxyproject/usegalaxy-playbook/commit/09596816c016c696… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/group_vars/all.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/0429dec02a2a...…

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[galaxyproject/usegalaxy-playbook] 0429de: Switch back to dev
by GitHub 12 Mar '18

12 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0429dec02a2ae5c17e2ffb5cda176d38b459fb2b https://github.com/galaxyproject/usegalaxy-playbook/commit/0429dec02a2ae5c1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M env/test/group_vars/all.yml Log Message: ----------- Switch back to dev

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[galaxyproject/galaxy] 70ac42: Disentangle 'view' handling in trackster track ini...
by GitHub 12 Mar '18

12 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 70ac429f22899684d80190e576b176dbef6be1d7 https://github.com/galaxyproject/galaxy/commit/70ac429f22899684d80190e576b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Disentangle 'view' handling in trackster track initialization. This is a step towards making Trackster work again. Commit: 4112bd51cc59a0a16845fcfeba2b9b8cb3c3925b https://github.com/galaxyproject/galaxy/commit/4112bd51cc59a0a16845fcfeba2b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Fix undefined incomplete_features reference, use correct 'this.view' for tiledtrack Commit: 975e41a0372c85d1caf86c5fde5492e2fa3c4ec9 https://github.com/galaxyproject/galaxy/commit/975e41a0372c85d1caf86c5fde54… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Removal of self reference and unused import in visualization.js Commit: ac872cccf5465a3f3fce197870222168d5b1f550 https://github.com/galaxyproject/galaxy/commit/ac872cccf5465a3f3fce19787022… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Trackster painters overhaul, fixes. Commit: 9c54765e6fb6164816c16ed79628ad37f73a9192 https://github.com/galaxyproject/galaxy/commit/9c54765e6fb6164816c16ed79628… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/slotting.js Log Message: ----------- Scope and minor cleanup in slotting.js Commit: 00f4ffe166716d91fefb6078881d3d79e014c2bb https://github.com/galaxyproject/galaxy/commit/00f4ffe166716d91fefb6078881d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/filters.js Log Message: ----------- Fix undefined var in trackster/filters -- still exists one that I need to fix here, but that'll take some digging. Commit: 2c51bdd5d04f267b5282ee06ed2312e1b3a44d25 https://github.com/galaxyproject/galaxy/commit/2c51bdd5d04f267b5282ee06ed23… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Incremental fixes and work on trackster/tracks.js -- still not painting.... Commit: 4d7539dbeccc2a51bb36a21b8b34733e7345ae8a https://github.com/galaxyproject/galaxy/commit/4d7539dbeccc2a51bb36a21b8b34… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- More trackster/tracks work. More variable scoping issues fixed, function definitions standardized. One callback issue resolved. Commit: 4a7487400aa45a558a87982888c7ce75a234efa1 https://github.com/galaxyproject/galaxy/commit/4a7487400aa45a558a87982888c7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Minor regex fix, drop a debug statement. Commit: 80c7f369148919c93132c08e19e993b290cc4a84 https://github.com/galaxyproject/galaxy/commit/80c7f369148919c93132c08e19e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Fix another regex; var scoping adjustments for trackster. Commit: 43d632d16c2edee3080baa5008269526fc671898 https://github.com/galaxyproject/galaxy/commit/43d632d16c2edee3080baa500826… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Painter fixes, trying to track down initialization bug w/ this.prefs. Commit: 391ac34d5f1bc479b168b6187bd91bc1b21230fe https://github.com/galaxyproject/galaxy/commit/391ac34d5f1bc479b168b6187bd9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- More cleanup in tracks.js, still trying to track down painter initialization bug. Commit: 5d180ba5191f6c427448f836f44c2b3ca15b5d82 https://github.com/galaxyproject/galaxy/commit/5d180ba5191f6c427448f836f44c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Rewrite painters using ES6 classes, for my sanity and future maintenance. Still won't paint, but it's easier to track through the hierarchy now. Commit: 33d17bcbe6b6a7dc85ed35849b7dce95ba04a8fe https://github.com/galaxyproject/galaxy/commit/33d17bcbe6b6a7dc85ed35849b7d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Slight reorg in painters, post-rewrite Commit: 3ac2cabce822ff71ba2fbbb23b1f71ec5428c1e2 https://github.com/galaxyproject/galaxy/commit/3ac2cabce822ff71ba2fbbb23b1f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Spello Commit: 76c8dae70138e113774c43b54c68babfe26b0ed9 https://github.com/galaxyproject/galaxy/commit/76c8dae70138e113774c43b54c68… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- TracksterUI class-ification, minor cleanup. Disentangling globals next. Commit: d7b2e4942fa2e940cce236d0b87c0b48e3c83508 https://github.com/galaxyproject/galaxy/commit/d7b2e4942fa2e940cce236d0b87c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Global var refactoring, removal of some unused stuff. Commit: 9bd112bd9169f6fb782cc9fdd86cbb46824df49a https://github.com/galaxyproject/galaxy/commit/9bd112bd9169f6fb782cc9fdd86c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Trackster refactoring; this pulls apart using a global view. There is a trackster ui, which holds the main view, and should be accessed through it when necessary. Commit: 0e6e468608fd85c3a8bdb41bf329523c821152b0 https://github.com/galaxyproject/galaxy/commit/0e6e468608fd85c3a8bdb41bf329… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Import fixes in main trackster.js Commit: 7c9c9775753d539527ff4d74a2108563fe06a945 https://github.com/galaxyproject/galaxy/commit/7c9c9775753d539527ff4d74a210… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Misc cleanup while trying to debug nonexistent paint vars. Commit: ec8c92604239bdb5b7e92717586bc305fbbf8db3 https://github.com/galaxyproject/galaxy/commit/ec8c92604239bdb5b7e92717586b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Refactoring in feature painter draw. Commit: f0df326e2cdb2c90fb78e0a18dbaadee3d62de17 https://github.com/galaxyproject/galaxy/commit/f0df326e2cdb2c90fb78e0a18dba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Use static getters for default painter preferences, fix 'defailt' ironic typo. Commit: 2270f728c421b81ea14f022beb96203f007180dd https://github.com/galaxyproject/galaxy/commit/2270f728c421b81ea14f022beb96… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Consistent sniffing regardless of in_place. Previously sniffing would happen on the original file (before carriage returns and tabular spaces were converted) if in_place was false and on the converted file if it was true. Commit: 4bca4a056cdf766eec8108db4aaa43ddbfb57c0e https://github.com/galaxyproject/galaxy/commit/4bca4a056cdf766eec8108db4aaa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Config.js fixes; it was trying to import itself and not use it. Commit: f33eee105f02d189cc68914dd72ed0a77f05cfcd https://github.com/galaxyproject/galaxy/commit/f33eee105f02d189cc68914dd72e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Fix config parameter default building in tracks.js; ideally this turns into classes when the multiple inheritance is fixed/refactored, and we can use simple static getter/setter methods. Commit: 2846fa0aa1e92e770e01af15008ed76b93b41b52 https://github.com/galaxyproject/galaxy/commit/2846fa0aa1e92e770e01af15008e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Use target file path when adding missing indexes Previously we would load a TS tool during installation and ask if any of its tool datat tables are missing loc files. If thats the case we copy the sample file and call `handle_found_index_file` for the particular missing *.loc path of this data table. This does not work if the data table already existed (e.g for built-in data tables), but was missing the *.loc file, since we would atempt to load that path. Instead we do now load the path to the loc file that we just copied. Should fix https://github.com/galaxyproject/galaxy/issues/5648. Commit: b655a499f82a73f82f89bc8f962d4f0f0097cabc https://github.com/galaxyproject/galaxy/commit/b655a499f82a73f82f89bc8f962d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- re-add erroneously removed line Commit: b601bcc429b47617e684158a62166575c244fd61 https://github.com/galaxyproject/galaxy/commit/b601bcc429b47617e684158a6216… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M static/style/blue/base.css M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge pull request #5659 from martenson/merge-in-17.09 [18.01] Merge with 17.09 Commit: 206182ea8f1ae437f4a5016fc49f74d5bf68f378 https://github.com/galaxyproject/galaxy/commit/206182ea8f1ae437f4a5016fc49f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Merge pull request #5650 from mvdbeek/missing_index_file_fixes [18.01] Use sample file path when adding missing indexes Commit: cdae68907bdacc4f290f561bff89f3b4525a7b4d https://github.com/galaxyproject/galaxy/commit/cdae68907bdacc4f290f561bff89… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Fix exception if user preference value undefined Fixes the following traceback on main: ``` AttributeError: 'NoneType' object has no attribute 'strip' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/root.py", line 110, in index config.update(self._get_extended_config(trans)) File "galaxy/webapps/galaxy/controllers/root.py", line 57, in _get_extended_config 'toolbox' : app.toolbox.to_dict(trans, in_panel=False), File "galaxy/tools/toolbox/base.py", line 963, in to_dict filter_method = self._build_filter_method(trans) File "galaxy/tools/toolbox/base.py", line 1004, in _build_filter_method filters = self._filter_factory.build_filters(trans) File "galaxy/tools/toolbox/filters/__init__.py", line 37, in build_filters if value.strip(): ``` Commit: 706efdc186177c36871aa47059de64aa0112f1a0 https://github.com/galaxyproject/galaxy/commit/706efdc186177c36871aa47059de… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix exception if email is not specified We render a regular error a few lines lower. Commit: d60b80a537ae4b9d580805014c99d74bb6598896 https://github.com/galaxyproject/galaxy/commit/d60b80a537ae4b9d580805014c99… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Show error message if user tries purging datasets without having an associated history. This can be seen by pasting http://<gx_instance>/history/purge_deleted_datasets into an anonymous browser session (be careful to not delete something important ;)). Traceback is: ``` AttributeError: 'NoneType' object has no attribute 'datasets' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/history.py", line 1108, in purge_deleted_datasets for hda in trans.history.datasets: ``` Commit: 17e1786521e458819f2cdb9821fd3e96c18bc3a7 https://github.com/galaxyproject/galaxy/commit/17e1786521e458819f2cdb9821fd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Avoid exception if email is wrong Avoids: ``` AttributeError: 'NoneType' object has no attribute 'active' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/user.py", line 938, in activate if user.active is True: ``` Commit: fe444ab3ef6bf37761859e09a0baf3ec38e7c6c4 https://github.com/galaxyproject/galaxy/commit/fe444ab3ef6bf37761859e09a0ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Show error message if history structure can't be shown Fixes: ``` AttributeError: 'NoneType' object has no attribute 'id' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/history.py", line 494, in display_structured assert (history.user and (history.user.id == trans.user.id) or ``` Commit: 3ce1273d7cc447d9088f9c056649d16c188d509d https://github.com/galaxyproject/galaxy/commit/3ce1273d7cc447d9088f9c056649… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Merge pull request #5662 from mvdbeek/fix_build_filters [18.01] Fix exception if user preference value undefined Commit: 0a95f20f5ba7e41282a29afb21a41290033cfed8 https://github.com/galaxyproject/galaxy/commit/0a95f20f5ba7e41282a29afb21a4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #5663 from mvdbeek/user_activation_fix [18.01] Fix exception if email is not specified or email is wrong Commit: a0fd6307562b38a7ef93291c6450cb92bd0eaf59 https://github.com/galaxyproject/galaxy/commit/a0fd6307562b38a7ef93291c6450… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5665 from mvdbeek/show_error_msg_when_history_structure_cannot_be_shown [18.01] Show error message if history structure can't be shown Commit: 1761d85e7299ddd34565794c43b0c761b44a0bc5 https://github.com/galaxyproject/galaxy/commit/1761d85e7299ddd34565794c43b0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5664 from mvdbeek/show_error_message_if_no_history_associated [18.01] Show error message if user tries purging datasets Commit: 9c9c69ca29fd820263181ab9f92349658aa74d33 https://github.com/galaxyproject/galaxy/commit/9c9c69ca29fd820263181ab9f923… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst Log Message: ----------- iniital work on RN Commit: 0229bf532981394ea3e97fd9f62bcef83789bc25 https://github.com/galaxyproject/galaxy/commit/0229bf532981394ea3e97fd9f62b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- announce removal of planttribe datatypes Commit: fa3ec5f60b9a4b6bed0ee771166c6e49c8fa02d0 https://github.com/galaxyproject/galaxy/commit/fa3ec5f60b9a4b6bed0ee771166c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Merge pull request #5261 from dannon/trackster_fixes [18.01] Trackster fixes. Commit: 63292de10a608d624c3cababad741325386226d9 https://github.com/galaxyproject/galaxy/commit/63292de10a608d624c3cababad74… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- add trackster fix to RN Commit: 02bf18f33b93eac5e6fdd4e163cbed0563196f82 https://github.com/galaxyproject/galaxy/commit/02bf18f33b93eac5e6fdd4e163cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Some initial work on release highlights, still completely broken. Commit: 3515d6040514fdb91b5a8780bb48d0a26ade4ee1 https://github.com/galaxyproject/galaxy/commit/3515d6040514fdb91b5a8780bb48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Another couple sentences of release docs. Commit: e923c61a0726d6d5201e01a017b841d61933f744 https://github.com/galaxyproject/galaxy/commit/e923c61a0726d6d5201e01a017b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- More progress on release notes, still very rough. Commit: cb477ddcf02749e8d949d237ac8945c9bbd13d36 https://github.com/galaxyproject/galaxy/commit/cb477ddcf02749e8d949d237ac89… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Condense many 18.01 release bullets, expand a few. Commit: 1a68096cfa29631beca467acf9bd82c57546d938 https://github.com/galaxyproject/galaxy/commit/1a68096cfa29631beca467acf9bd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Condense many 18.01 release bullets, expand a few - part 2 of 1003. Commit: 1923786a6545bcef1c381baf39bf931b9b9ec8af https://github.com/galaxyproject/galaxy/commit/1923786a6545bcef1c381baf39bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Condense many 18.01 release bullets, expand a few - part 3 of 1003. Commit: b964722acc83d52ae0a107becf02dcee09dae6f4 https://github.com/galaxyproject/galaxy/commit/b964722acc83d52ae0a107becf02… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- More release 18.01 release note tweaks. Commit: 6d4b83990f60f79003f7b6d33446cc9d38eb24a3 https://github.com/galaxyproject/galaxy/commit/6d4b83990f60f79003f7b6d33446… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Spell check 18.01 release notes and small tweaks. Commit: 9e274278f13e970c46f21b26e7e283f262d1c29b https://github.com/galaxyproject/galaxy/commit/9e274278f13e970c46f21b26e7e2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Small language tweaks. Including fixes from :eagle::eyes:. Commit: e68ac4a3c8aeb259b348a6b2f606a207786038fd https://github.com/galaxyproject/galaxy/commit/e68ac4a3c8aeb259b348a6b2f606… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Highlights fixes Commit: 804f815eee221723e1dc35e451783415386d7f6a https://github.com/galaxyproject/galaxy/commit/804f815eee221723e1dc35e45178… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Fix bullet list indentation Commit: 235d6c3269a53191bde7a41e9fda2422df4e28d1 https://github.com/galaxyproject/galaxy/commit/235d6c3269a53191bde7a41e9fda… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Condense some entries Commit: e72e02cc7a98f6c721dbd14a52f5f18f5de33d5f https://github.com/galaxyproject/galaxy/commit/e72e02cc7a98f6c721dbd14a52f5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #5643 from jmchilton/sniff_fix [18.01] Consistent sniffing regardless of in_place. Commit: c5ead795b5f0105b75f56914e7c601aa5983b61b https://github.com/galaxyproject/galaxy/commit/c5ead795b5f0105b75f56914e7c6… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Add #5643 to release notes Commit: df03a59c53250bae402b24e4a6d4a607a32b6cd7 https://github.com/galaxyproject/galaxy/commit/df03a59c53250bae402b24e4a6d4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- move some sections deeper in the document to make the highlights more focused Commit: c034ab3f0b6357628f2b7727e42146b84e9f57b5 https://github.com/galaxyproject/galaxy/commit/c034ab3f0b6357628f2b7727e421… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #5668 from martenson/18.01_release_notes [18.01] Release Notes Commit: 83fa18deb794909afde5e3f21ceeb24fe68335fe https://github.com/galaxyproject/galaxy/commit/83fa18deb794909afde5e3f21cee… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Display error message on IE template fill exception Commit: 2db95b4d1dd8c72fbf20439ac473d8a2b15f5c1a https://github.com/galaxyproject/galaxy/commit/2db95b4d1dd8c72fbf20439ac473… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M doc/source/releases/18.01_announce.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/sniff.py R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Rename datatype extension 'bam_native' to 'unsorted.bam'. We handle other bam types this way and other more specific variants of an extension (e.g. thermo.raw) so this feels like the more consistent thing to do. Commit: 9c0c8ee679571cc037f77b60f03a95760ddca29d https://github.com/galaxyproject/galaxy/commit/9c0c8ee679571cc037f77b60f03a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Mention self.current_pr in release notes. Commit: d632b41b8600604f143d6f6677d83d41ee735abc https://github.com/galaxyproject/galaxy/commit/d632b41b8600604f143d6f6677d8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Fix GIE launch for cases when the published port isn't available immediately (seems to happen with Swarm Mode occasionally) Commit: 4fea3904ab616088ac71a9ac10a3b1656c13f1c0 https://github.com/galaxyproject/galaxy/commit/4fea3904ab616088ac71a9ac10a3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/sniff.py R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5674 from jmchilton/unsorted_bam_rename [18.01] Rename datatype extension 'bam_native' to 'unsorted.bam'. Commit: 1a5f6a3499091182797693bc1bb06a82095bc788 https://github.com/galaxyproject/galaxy/commit/1a5f6a3499091182797693bc1bb0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Merge pull request #5677 from natefoo/docker-swarm-race [18.01] Additional error handling for GIE container launching Commit: 4fc6380708454c15360f0940ee56998c08fc6c8a https://github.com/galaxyproject/galaxy/commit/4fc6380708454c15360f0940ee56… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M config/datatypes_conf.xml.sample A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst M lib/galaxy/containers/docker_model.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/util/tool_util.py R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'origin/release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/dc6b22fc74f4...4fc638070845

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[galaxyproject/galaxy] 70ac42: Disentangle 'view' handling in trackster track ini...
by GitHub 12 Mar '18

12 Mar '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 70ac429f22899684d80190e576b176dbef6be1d7 https://github.com/galaxyproject/galaxy/commit/70ac429f22899684d80190e576b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Disentangle 'view' handling in trackster track initialization. This is a step towards making Trackster work again. Commit: 4112bd51cc59a0a16845fcfeba2b9b8cb3c3925b https://github.com/galaxyproject/galaxy/commit/4112bd51cc59a0a16845fcfeba2b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Fix undefined incomplete_features reference, use correct 'this.view' for tiledtrack Commit: 975e41a0372c85d1caf86c5fde5492e2fa3c4ec9 https://github.com/galaxyproject/galaxy/commit/975e41a0372c85d1caf86c5fde54… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Removal of self reference and unused import in visualization.js Commit: ac872cccf5465a3f3fce197870222168d5b1f550 https://github.com/galaxyproject/galaxy/commit/ac872cccf5465a3f3fce19787022… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Trackster painters overhaul, fixes. Commit: 9c54765e6fb6164816c16ed79628ad37f73a9192 https://github.com/galaxyproject/galaxy/commit/9c54765e6fb6164816c16ed79628… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/slotting.js Log Message: ----------- Scope and minor cleanup in slotting.js Commit: 00f4ffe166716d91fefb6078881d3d79e014c2bb https://github.com/galaxyproject/galaxy/commit/00f4ffe166716d91fefb6078881d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/filters.js Log Message: ----------- Fix undefined var in trackster/filters -- still exists one that I need to fix here, but that'll take some digging. Commit: 2c51bdd5d04f267b5282ee06ed2312e1b3a44d25 https://github.com/galaxyproject/galaxy/commit/2c51bdd5d04f267b5282ee06ed23… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Incremental fixes and work on trackster/tracks.js -- still not painting.... Commit: 4d7539dbeccc2a51bb36a21b8b34733e7345ae8a https://github.com/galaxyproject/galaxy/commit/4d7539dbeccc2a51bb36a21b8b34… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- More trackster/tracks work. More variable scoping issues fixed, function definitions standardized. One callback issue resolved. Commit: 4a7487400aa45a558a87982888c7ce75a234efa1 https://github.com/galaxyproject/galaxy/commit/4a7487400aa45a558a87982888c7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Minor regex fix, drop a debug statement. Commit: 80c7f369148919c93132c08e19e993b290cc4a84 https://github.com/galaxyproject/galaxy/commit/80c7f369148919c93132c08e19e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Fix another regex; var scoping adjustments for trackster. Commit: 43d632d16c2edee3080baa5008269526fc671898 https://github.com/galaxyproject/galaxy/commit/43d632d16c2edee3080baa500826… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Painter fixes, trying to track down initialization bug w/ this.prefs. Commit: 391ac34d5f1bc479b168b6187bd91bc1b21230fe https://github.com/galaxyproject/galaxy/commit/391ac34d5f1bc479b168b6187bd9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- More cleanup in tracks.js, still trying to track down painter initialization bug. Commit: 5d180ba5191f6c427448f836f44c2b3ca15b5d82 https://github.com/galaxyproject/galaxy/commit/5d180ba5191f6c427448f836f44c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Rewrite painters using ES6 classes, for my sanity and future maintenance. Still won't paint, but it's easier to track through the hierarchy now. Commit: 33d17bcbe6b6a7dc85ed35849b7dce95ba04a8fe https://github.com/galaxyproject/galaxy/commit/33d17bcbe6b6a7dc85ed35849b7d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Slight reorg in painters, post-rewrite Commit: 3ac2cabce822ff71ba2fbbb23b1f71ec5428c1e2 https://github.com/galaxyproject/galaxy/commit/3ac2cabce822ff71ba2fbbb23b1f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Spello Commit: 76c8dae70138e113774c43b54c68babfe26b0ed9 https://github.com/galaxyproject/galaxy/commit/76c8dae70138e113774c43b54c68… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- TracksterUI class-ification, minor cleanup. Disentangling globals next. Commit: d7b2e4942fa2e940cce236d0b87c0b48e3c83508 https://github.com/galaxyproject/galaxy/commit/d7b2e4942fa2e940cce236d0b87c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Global var refactoring, removal of some unused stuff. Commit: 9bd112bd9169f6fb782cc9fdd86cbb46824df49a https://github.com/galaxyproject/galaxy/commit/9bd112bd9169f6fb782cc9fdd86c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Trackster refactoring; this pulls apart using a global view. There is a trackster ui, which holds the main view, and should be accessed through it when necessary. Commit: 0e6e468608fd85c3a8bdb41bf329523c821152b0 https://github.com/galaxyproject/galaxy/commit/0e6e468608fd85c3a8bdb41bf329… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Import fixes in main trackster.js Commit: 166fe7eada87d242be506a8d1369df019acd20b1 https://github.com/galaxyproject/galaxy/commit/166fe7eada87d242be506a8d1369… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Conda fixes for 18.01 - stdout redirection. Broken in #5397 I think. Commit: 7c9c9775753d539527ff4d74a2108563fe06a945 https://github.com/galaxyproject/galaxy/commit/7c9c9775753d539527ff4d74a210… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Misc cleanup while trying to debug nonexistent paint vars. Commit: 6b782ad16d010d6da7808ac7deaecef3ec301b73 https://github.com/galaxyproject/galaxy/commit/6b782ad16d010d6da7808ac7deae… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Changed GenomeSpace token handling to use manual OpenID association only Commit: 7254d55e8b192ff4387ef6a276e202db5821ca60 https://github.com/galaxyproject/galaxy/commit/7254d55e8b192ff4387ef6a276e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove href from grid sorting links Commit: 7ffabb1df3f6feb11a3746c2f27bc762b1af29c7 https://github.com/galaxyproject/galaxy/commit/7ffabb1df3f6feb11a3746c2f27b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove unused variable Commit: bd69278f0bcc67afc1eb827a8a7bc80ae7766072 https://github.com/galaxyproject/galaxy/commit/bd69278f0bcc67afc1eb827a8a7b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M test/functional/tools/multi_output_recurse.xml Log Message: ----------- Add a testcase for optional output discovery This test correctly fails with: ``` galaxy.jobs.runners.local ERROR 2018-03-02 17:55:32,396 Job wrapper finish method failed Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/local.py", line 152, in queue_job self._finish_or_resubmit_job(job_state, stdout, stderr, exit_code) File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/__init__.py", line 432, in _finish_or_resubmit_job job_state.job_wrapper.finish(stdout, stderr, exit_code, check_output_detected_state=check_output_detected_state) File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/__init__.py", line 1381, in finish 'primary': self.tool.collect_primary_datasets(out_data, self.get_tool_provided_job_metadata(), tool_working_directory, input_ext, input_dbkey) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 1614, in collect_primary_datasets return output_collect.collect_primary_datasets(self, output, tool_provided_metadata, job_working_directory, input_ext, input_dbkey=input_dbkey) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 372, in collect_primary_datasets for discovered_file in discover_files(name, tool_provided_metadata, dataset_collectors, job_working_directory, outdata): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 490, in discover_files for (match, collector) in walk_over_file_collectors(extra_file_collectors, job_working_directory, matchable): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 507, in walk_over_file_collectors for match in walk_over_extra_files(extra_file_collector.directory, extra_file_collector, job_working_directory, matchable): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 519, in walk_over_extra_files for filename in os.listdir(directory): OSError: [Errno 2] No such file or directory: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp5Tz0m9/tmpfUHHl6/tmpVBcnfI/database/job_working_directory_LJioiW/000/2/working/i_do_not_exist' ``` Commit: d21d7d9d2e10d9c09bdbadbf328fd3eef84630e6 https://github.com/galaxyproject/galaxy/commit/d21d7d9d2e10d9c09bdbadbf328f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix output discovery when directory doesn't exist This broke in 8b76a5a698fd3bc13d4acc38194221def9ed5163. Checking if `directory` is a directory is what we had done previously. Commit: 10cf046ea8604a367b734b7d1b58e623705ed11c https://github.com/galaxyproject/galaxy/commit/10cf046ea8604a367b734b7d1b58… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- replace syntax that is too new Commit: 69bbcda0b3577edcb7042cdf26f4373ea1ed5f67 https://github.com/galaxyproject/galaxy/commit/69bbcda0b3577edcb7042cdf26f4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M static/maps/mvc/ui/ui-select-genomespace.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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-genomespace.js M static/style/blue/base.css Log Message: ----------- build client Commit: e01f9fa1b89e6a5fd12f9ef98ddb005959e1b761 https://github.com/galaxyproject/galaxy/commit/e01f9fa1b89e6a5fd12f9ef98ddb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #5634 from guerler/fix_async_grid_links [18.01] Remove href from grid sorting links Commit: 7ed81e18101c33a1e83bb5e72851698910a118e9 https://github.com/galaxyproject/galaxy/commit/7ed81e18101c33a1e83bb5e72851… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M test/functional/tools/multi_output_recurse.xml Log Message: ----------- Move `optional` tag to the output data element Thx @nsoranzo! Commit: da867852ae6437c02c64287521dde0b8aa1e8109 https://github.com/galaxyproject/galaxy/commit/da867852ae6437c02c64287521dd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M test/functional/tools/multi_output_recurse.xml Log Message: ----------- Drop optional="true" altogther Commit: d77845268a9243535e2b77383bc4ed3d433e2e7a https://github.com/galaxyproject/galaxy/commit/d77845268a9243535e2b77383bc4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-04 (Sun, 04 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/functional/tools/multi_output_recurse.xml Log Message: ----------- Merge pull request #5635 from mvdbeek/fix_optional_output_discovery [18.01] Fix output discovery if dir doesn't exist Commit: a6593d4cafe966062460e33eaac1c5a28566c109 https://github.com/galaxyproject/galaxy/commit/a6593d4cafe966062460e33eaac1… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M tools/stats/gsummary.py Log Message: ----------- python3 fix strings can not be written to byte mode file handlers. writing resulted in: TypeError: a bytes-like object is required, not 'str' Alternative would be to make string byte. Commit: 28724ab795ac5dfcc5fa5b9a9a88fb0b64fc7752 https://github.com/galaxyproject/galaxy/commit/28724ab795ac5dfcc5fa5b9a9a88… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Merge pull request #5639 from nsoranzo/release_17.09_backport_5043 [17.09] Backport of #5043 Commit: ec8c92604239bdb5b7e92717586bc305fbbf8db3 https://github.com/galaxyproject/galaxy/commit/ec8c92604239bdb5b7e92717586b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Refactoring in feature painter draw. Commit: ff9bc843fab96ab95b7a5ae69c71a99185977b96 https://github.com/galaxyproject/galaxy/commit/ff9bc843fab96ab95b7a5ae69c71… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-05 (Mon, 05 Mar 2018) Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: f0df326e2cdb2c90fb78e0a18dbaadee3d62de17 https://github.com/galaxyproject/galaxy/commit/f0df326e2cdb2c90fb78e0a18dba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Use static getters for default painter preferences, fix 'defailt' ironic typo. Commit: f8d44c2b69516f9464aad4acfc2bbf68ce3ede08 https://github.com/galaxyproject/galaxy/commit/f8d44c2b69516f9464aad4acfc2b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-genomespace.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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-genomespace.js M static/style/blue/base.css M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge pull request #5631 from martenson/genomespace [17.09] Changed GenomeSpace token handling to use manual OpenID association only Commit: 4850ca5c839cb80bff202c86b7d9a4d04c318dcb https://github.com/galaxyproject/galaxy/commit/4850ca5c839cb80bff202c86b7d9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #5620 from jmchilton/conda_fixes_1801 [18.01] Conda fix for commands using stdout redirection. Commit: 2270f728c421b81ea14f022beb96203f007180dd https://github.com/galaxyproject/galaxy/commit/2270f728c421b81ea14f022beb96… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Consistent sniffing regardless of in_place. Previously sniffing would happen on the original file (before carriage returns and tabular spaces were converted) if in_place was false and on the converted file if it was true. Commit: 4bca4a056cdf766eec8108db4aaa43ddbfb57c0e https://github.com/galaxyproject/galaxy/commit/4bca4a056cdf766eec8108db4aaa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Config.js fixes; it was trying to import itself and not use it. Commit: f33eee105f02d189cc68914dd72ed0a77f05cfcd https://github.com/galaxyproject/galaxy/commit/f33eee105f02d189cc68914dd72e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Fix config parameter default building in tracks.js; ideally this turns into classes when the multiple inheritance is fixed/refactored, and we can use simple static getter/setter methods. Commit: 90b700be42da9f7f6fa69bae6f8d71776badd351 https://github.com/galaxyproject/galaxy/commit/90b700be42da9f7f6fa69bae6f8d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Do not sniff BamInputSorted Only aligners should produce this datatype. If an alignment is not explicitly coordinate or queryname sorted it should be BamNative. Also addresses https://github.com/galaxyproject/galaxy/pull/5628#issuecomment-370874329, though I think the sniff order should be dependent on the order with which datatypes are loaded. Commit: 9e6f3f57a0b27ad3b64cd4e3ea2cb51f10a3b8e7 https://github.com/galaxyproject/galaxy/commit/9e6f3f57a0b27ad3b64cd4e3ea2c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5644 from mvdbeek/disable_sniffer_qname_input_sorted [18.01] Do not sniff BamInputSorted Commit: 2846fa0aa1e92e770e01af15008ed76b93b41b52 https://github.com/galaxyproject/galaxy/commit/2846fa0aa1e92e770e01af15008e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Use target file path when adding missing indexes Previously we would load a TS tool during installation and ask if any of its tool datat tables are missing loc files. If thats the case we copy the sample file and call `handle_found_index_file` for the particular missing *.loc path of this data table. This does not work if the data table already existed (e.g for built-in data tables), but was missing the *.loc file, since we would atempt to load that path. Instead we do now load the path to the loc file that we just copied. Should fix https://github.com/galaxyproject/galaxy/issues/5648. Commit: 10f8c3bc82b3a87dfa4125aa6eca9eb9071d3609 https://github.com/galaxyproject/galaxy/commit/10f8c3bc82b3a87dfa4125aa6eca… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M static/style/blue/base.css M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge branch 'release_17.09' into release_18.01 dropped all static content from merge except of styles Commit: b655a499f82a73f82f89bc8f962d4f0f0097cabc https://github.com/galaxyproject/galaxy/commit/b655a499f82a73f82f89bc8f962d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- re-add erroneously removed line Commit: b601bcc429b47617e684158a62166575c244fd61 https://github.com/galaxyproject/galaxy/commit/b601bcc429b47617e684158a6216… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M static/style/blue/base.css M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge pull request #5659 from martenson/merge-in-17.09 [18.01] Merge with 17.09 Commit: 206182ea8f1ae437f4a5016fc49f74d5bf68f378 https://github.com/galaxyproject/galaxy/commit/206182ea8f1ae437f4a5016fc49f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Merge pull request #5650 from mvdbeek/missing_index_file_fixes [18.01] Use sample file path when adding missing indexes Commit: cdae68907bdacc4f290f561bff89f3b4525a7b4d https://github.com/galaxyproject/galaxy/commit/cdae68907bdacc4f290f561bff89… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Fix exception if user preference value undefined Fixes the following traceback on main: ``` AttributeError: 'NoneType' object has no attribute 'strip' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/root.py", line 110, in index config.update(self._get_extended_config(trans)) File "galaxy/webapps/galaxy/controllers/root.py", line 57, in _get_extended_config 'toolbox' : app.toolbox.to_dict(trans, in_panel=False), File "galaxy/tools/toolbox/base.py", line 963, in to_dict filter_method = self._build_filter_method(trans) File "galaxy/tools/toolbox/base.py", line 1004, in _build_filter_method filters = self._filter_factory.build_filters(trans) File "galaxy/tools/toolbox/filters/__init__.py", line 37, in build_filters if value.strip(): ``` Commit: 706efdc186177c36871aa47059de64aa0112f1a0 https://github.com/galaxyproject/galaxy/commit/706efdc186177c36871aa47059de… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix exception if email is not specified We render a regular error a few lines lower. Commit: d60b80a537ae4b9d580805014c99d74bb6598896 https://github.com/galaxyproject/galaxy/commit/d60b80a537ae4b9d580805014c99… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Show error message if user tries purging datasets without having an associated history. This can be seen by pasting http://<gx_instance>/history/purge_deleted_datasets into an anonymous browser session (be careful to not delete something important ;)). Traceback is: ``` AttributeError: 'NoneType' object has no attribute 'datasets' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/history.py", line 1108, in purge_deleted_datasets for hda in trans.history.datasets: ``` Commit: 17e1786521e458819f2cdb9821fd3e96c18bc3a7 https://github.com/galaxyproject/galaxy/commit/17e1786521e458819f2cdb9821fd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Avoid exception if email is wrong Avoids: ``` AttributeError: 'NoneType' object has no attribute 'active' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/user.py", line 938, in activate if user.active is True: ``` Commit: fe444ab3ef6bf37761859e09a0baf3ec38e7c6c4 https://github.com/galaxyproject/galaxy/commit/fe444ab3ef6bf37761859e09a0ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Show error message if history structure can't be shown Fixes: ``` AttributeError: 'NoneType' object has no attribute 'id' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/history.py", line 494, in display_structured assert (history.user and (history.user.id == trans.user.id) or ``` Commit: 3ce1273d7cc447d9088f9c056649d16c188d509d https://github.com/galaxyproject/galaxy/commit/3ce1273d7cc447d9088f9c056649… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Merge pull request #5662 from mvdbeek/fix_build_filters [18.01] Fix exception if user preference value undefined Commit: 0a95f20f5ba7e41282a29afb21a41290033cfed8 https://github.com/galaxyproject/galaxy/commit/0a95f20f5ba7e41282a29afb21a4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #5663 from mvdbeek/user_activation_fix [18.01] Fix exception if email is not specified or email is wrong Commit: a0fd6307562b38a7ef93291c6450cb92bd0eaf59 https://github.com/galaxyproject/galaxy/commit/a0fd6307562b38a7ef93291c6450… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5665 from mvdbeek/show_error_msg_when_history_structure_cannot_be_shown [18.01] Show error message if history structure can't be shown Commit: 1761d85e7299ddd34565794c43b0c761b44a0bc5 https://github.com/galaxyproject/galaxy/commit/1761d85e7299ddd34565794c43b0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5664 from mvdbeek/show_error_message_if_no_history_associated [18.01] Show error message if user tries purging datasets Commit: 9c9c69ca29fd820263181ab9f92349658aa74d33 https://github.com/galaxyproject/galaxy/commit/9c9c69ca29fd820263181ab9f923… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst Log Message: ----------- iniital work on RN Commit: 0229bf532981394ea3e97fd9f62bcef83789bc25 https://github.com/galaxyproject/galaxy/commit/0229bf532981394ea3e97fd9f62b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- announce removal of planttribe datatypes Commit: fa3ec5f60b9a4b6bed0ee771166c6e49c8fa02d0 https://github.com/galaxyproject/galaxy/commit/fa3ec5f60b9a4b6bed0ee771166c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Merge pull request #5261 from dannon/trackster_fixes [18.01] Trackster fixes. Commit: 63292de10a608d624c3cababad741325386226d9 https://github.com/galaxyproject/galaxy/commit/63292de10a608d624c3cababad74… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- add trackster fix to RN Commit: 02bf18f33b93eac5e6fdd4e163cbed0563196f82 https://github.com/galaxyproject/galaxy/commit/02bf18f33b93eac5e6fdd4e163cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Some initial work on release highlights, still completely broken. Commit: 3515d6040514fdb91b5a8780bb48d0a26ade4ee1 https://github.com/galaxyproject/galaxy/commit/3515d6040514fdb91b5a8780bb48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Another couple sentences of release docs. Commit: e923c61a0726d6d5201e01a017b841d61933f744 https://github.com/galaxyproject/galaxy/commit/e923c61a0726d6d5201e01a017b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- More progress on release notes, still very rough. Commit: cb477ddcf02749e8d949d237ac8945c9bbd13d36 https://github.com/galaxyproject/galaxy/commit/cb477ddcf02749e8d949d237ac89… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Condense many 18.01 release bullets, expand a few. Commit: 1a68096cfa29631beca467acf9bd82c57546d938 https://github.com/galaxyproject/galaxy/commit/1a68096cfa29631beca467acf9bd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Condense many 18.01 release bullets, expand a few - part 2 of 1003. Commit: 1923786a6545bcef1c381baf39bf931b9b9ec8af https://github.com/galaxyproject/galaxy/commit/1923786a6545bcef1c381baf39bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Condense many 18.01 release bullets, expand a few - part 3 of 1003. Commit: b964722acc83d52ae0a107becf02dcee09dae6f4 https://github.com/galaxyproject/galaxy/commit/b964722acc83d52ae0a107becf02… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- More release 18.01 release note tweaks. Commit: 6d4b83990f60f79003f7b6d33446cc9d38eb24a3 https://github.com/galaxyproject/galaxy/commit/6d4b83990f60f79003f7b6d33446… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Spell check 18.01 release notes and small tweaks. Commit: 9e274278f13e970c46f21b26e7e283f262d1c29b https://github.com/galaxyproject/galaxy/commit/9e274278f13e970c46f21b26e7e2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Small language tweaks. Including fixes from :eagle::eyes:. Commit: e68ac4a3c8aeb259b348a6b2f606a207786038fd https://github.com/galaxyproject/galaxy/commit/e68ac4a3c8aeb259b348a6b2f606… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Highlights fixes Commit: 804f815eee221723e1dc35e451783415386d7f6a https://github.com/galaxyproject/galaxy/commit/804f815eee221723e1dc35e45178… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Fix bullet list indentation Commit: 235d6c3269a53191bde7a41e9fda2422df4e28d1 https://github.com/galaxyproject/galaxy/commit/235d6c3269a53191bde7a41e9fda… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Condense some entries Commit: e72e02cc7a98f6c721dbd14a52f5f18f5de33d5f https://github.com/galaxyproject/galaxy/commit/e72e02cc7a98f6c721dbd14a52f5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #5643 from jmchilton/sniff_fix [18.01] Consistent sniffing regardless of in_place. Commit: c5ead795b5f0105b75f56914e7c601aa5983b61b https://github.com/galaxyproject/galaxy/commit/c5ead795b5f0105b75f56914e7c6… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Add #5643 to release notes Commit: df03a59c53250bae402b24e4a6d4a607a32b6cd7 https://github.com/galaxyproject/galaxy/commit/df03a59c53250bae402b24e4a6d4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- move some sections deeper in the document to make the highlights more focused Commit: c034ab3f0b6357628f2b7727e42146b84e9f57b5 https://github.com/galaxyproject/galaxy/commit/c034ab3f0b6357628f2b7727e421… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #5668 from martenson/18.01_release_notes [18.01] Release Notes Commit: 83fa18deb794909afde5e3f21ceeb24fe68335fe https://github.com/galaxyproject/galaxy/commit/83fa18deb794909afde5e3f21cee… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Display error message on IE template fill exception Commit: 2db95b4d1dd8c72fbf20439ac473d8a2b15f5c1a https://github.com/galaxyproject/galaxy/commit/2db95b4d1dd8c72fbf20439ac473… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M doc/source/releases/18.01_announce.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/sniff.py R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Rename datatype extension 'bam_native' to 'unsorted.bam'. We handle other bam types this way and other more specific variants of an extension (e.g. thermo.raw) so this feels like the more consistent thing to do. Commit: 9c0c8ee679571cc037f77b60f03a95760ddca29d https://github.com/galaxyproject/galaxy/commit/9c0c8ee679571cc037f77b60f03a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Mention self.current_pr in release notes. Commit: d632b41b8600604f143d6f6677d83d41ee735abc https://github.com/galaxyproject/galaxy/commit/d632b41b8600604f143d6f6677d8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Fix GIE launch for cases when the published port isn't available immediately (seems to happen with Swarm Mode occasionally) Commit: 4fea3904ab616088ac71a9ac10a3b1656c13f1c0 https://github.com/galaxyproject/galaxy/commit/4fea3904ab616088ac71a9ac10a3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/sniff.py R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5674 from jmchilton/unsorted_bam_rename [18.01] Rename datatype extension 'bam_native' to 'unsorted.bam'. Commit: 1a5f6a3499091182797693bc1bb06a82095bc788 https://github.com/galaxyproject/galaxy/commit/1a5f6a3499091182797693bc1bb0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Merge pull request #5677 from natefoo/docker-swarm-race [18.01] Additional error handling for GIE container launching Commit: e12e773eddca7f2ebb342534c40672a3800a129c https://github.com/galaxyproject/galaxy/commit/e12e773eddca7f2ebb342534c406… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst M lib/galaxy/containers/docker_model.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/util/tool_util.py M static/style/blue/base.css M test/functional/tools/multi_output_recurse.xml R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M tools/data_source/upload.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge remote-tracking branch 'origin/release_18.01' into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/56b8ecd3d503...e12e773eddca

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[galaxyproject/galaxy] 83fa18: Display error message on IE template fill exceptio...
by GitHub 12 Mar '18

12 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 83fa18deb794909afde5e3f21ceeb24fe68335fe https://github.com/galaxyproject/galaxy/commit/83fa18deb794909afde5e3f21cee… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Display error message on IE template fill exception Commit: d632b41b8600604f143d6f6677d83d41ee735abc https://github.com/galaxyproject/galaxy/commit/d632b41b8600604f143d6f6677d8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Fix GIE launch for cases when the published port isn't available immediately (seems to happen with Swarm Mode occasionally) Commit: 1a5f6a3499091182797693bc1bb06a82095bc788 https://github.com/galaxyproject/galaxy/commit/1a5f6a3499091182797693bc1bb0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Merge pull request #5677 from natefoo/docker-swarm-race [18.01] Additional error handling for GIE container launching Compare: https://github.com/galaxyproject/galaxy/compare/4fea3904ab61...1a5f6a349909

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[galaxyproject/galaxy] 2db95b: Rename datatype extension 'bam_native' to 'unsorte...
by GitHub 12 Mar '18

12 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 2db95b4d1dd8c72fbf20439ac473d8a2b15f5c1a https://github.com/galaxyproject/galaxy/commit/2db95b4d1dd8c72fbf20439ac473… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M doc/source/releases/18.01_announce.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/sniff.py R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Rename datatype extension 'bam_native' to 'unsorted.bam'. We handle other bam types this way and other more specific variants of an extension (e.g. thermo.raw) so this feels like the more consistent thing to do. Commit: 9c0c8ee679571cc037f77b60f03a95760ddca29d https://github.com/galaxyproject/galaxy/commit/9c0c8ee679571cc037f77b60f03a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Mention self.current_pr in release notes. Commit: 4fea3904ab616088ac71a9ac10a3b1656c13f1c0 https://github.com/galaxyproject/galaxy/commit/4fea3904ab616088ac71a9ac10a3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/sniff.py R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5674 from jmchilton/unsorted_bam_rename [18.01] Rename datatype extension 'bam_native' to 'unsorted.bam'. Compare: https://github.com/galaxyproject/galaxy/compare/c034ab3f0b63...4fea3904ab61

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[galaxyproject/usegalaxy-playbook] 9c74b6: Fix for update_galaxy.sh when using a specific rep...
by GitHub 12 Mar '18

12 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9c74b667c3436a2fa0d0132d0f54b13cce78bbd5 https://github.com/galaxyproject/usegalaxy-playbook/commit/9c74b667c3436a2f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M roles/usegalaxy_cvmfs/files/update_galaxy.sh Log Message: ----------- Fix for update_galaxy.sh when using a specific repo

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[galaxyproject/usegalaxy-playbook] 0cd616: Run a branch of mine on Test for testing
by GitHub 12 Mar '18

12 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0cd616a93bfbb3feb0fe8c418bd8904c4564a9db https://github.com/galaxyproject/usegalaxy-playbook/commit/0cd616a93bfbb3fe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M env/test/group_vars/all.yml Log Message: ----------- Run a branch of mine on Test for testing

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[galaxyproject/galaxy] 9c9c69: iniital work on RN
by GitHub 12 Mar '18

12 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 9c9c69ca29fd820263181ab9f92349658aa74d33 https://github.com/galaxyproject/galaxy/commit/9c9c69ca29fd820263181ab9f923… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst Log Message: ----------- iniital work on RN Commit: 0229bf532981394ea3e97fd9f62bcef83789bc25 https://github.com/galaxyproject/galaxy/commit/0229bf532981394ea3e97fd9f62b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- announce removal of planttribe datatypes Commit: 63292de10a608d624c3cababad741325386226d9 https://github.com/galaxyproject/galaxy/commit/63292de10a608d624c3cababad74… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- add trackster fix to RN Commit: 02bf18f33b93eac5e6fdd4e163cbed0563196f82 https://github.com/galaxyproject/galaxy/commit/02bf18f33b93eac5e6fdd4e163cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Some initial work on release highlights, still completely broken. Commit: 3515d6040514fdb91b5a8780bb48d0a26ade4ee1 https://github.com/galaxyproject/galaxy/commit/3515d6040514fdb91b5a8780bb48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Another couple sentences of release docs. Commit: e923c61a0726d6d5201e01a017b841d61933f744 https://github.com/galaxyproject/galaxy/commit/e923c61a0726d6d5201e01a017b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- More progress on release notes, still very rough. Commit: cb477ddcf02749e8d949d237ac8945c9bbd13d36 https://github.com/galaxyproject/galaxy/commit/cb477ddcf02749e8d949d237ac89… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Condense many 18.01 release bullets, expand a few. Commit: 1a68096cfa29631beca467acf9bd82c57546d938 https://github.com/galaxyproject/galaxy/commit/1a68096cfa29631beca467acf9bd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Condense many 18.01 release bullets, expand a few - part 2 of 1003. Commit: 1923786a6545bcef1c381baf39bf931b9b9ec8af https://github.com/galaxyproject/galaxy/commit/1923786a6545bcef1c381baf39bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Condense many 18.01 release bullets, expand a few - part 3 of 1003. Commit: b964722acc83d52ae0a107becf02dcee09dae6f4 https://github.com/galaxyproject/galaxy/commit/b964722acc83d52ae0a107becf02… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- More release 18.01 release note tweaks. Commit: 6d4b83990f60f79003f7b6d33446cc9d38eb24a3 https://github.com/galaxyproject/galaxy/commit/6d4b83990f60f79003f7b6d33446… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Spell check 18.01 release notes and small tweaks. Commit: 9e274278f13e970c46f21b26e7e283f262d1c29b https://github.com/galaxyproject/galaxy/commit/9e274278f13e970c46f21b26e7e2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Small language tweaks. Including fixes from :eagle::eyes:. Commit: e68ac4a3c8aeb259b348a6b2f606a207786038fd https://github.com/galaxyproject/galaxy/commit/e68ac4a3c8aeb259b348a6b2f606… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Highlights fixes Commit: 804f815eee221723e1dc35e451783415386d7f6a https://github.com/galaxyproject/galaxy/commit/804f815eee221723e1dc35e45178… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Fix bullet list indentation Commit: 235d6c3269a53191bde7a41e9fda2422df4e28d1 https://github.com/galaxyproject/galaxy/commit/235d6c3269a53191bde7a41e9fda… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Condense some entries Commit: c5ead795b5f0105b75f56914e7c601aa5983b61b https://github.com/galaxyproject/galaxy/commit/c5ead795b5f0105b75f56914e7c6… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Add #5643 to release notes Commit: df03a59c53250bae402b24e4a6d4a607a32b6cd7 https://github.com/galaxyproject/galaxy/commit/df03a59c53250bae402b24e4a6d4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- move some sections deeper in the document to make the highlights more focused Commit: c034ab3f0b6357628f2b7727e42146b84e9f57b5 https://github.com/galaxyproject/galaxy/commit/c034ab3f0b6357628f2b7727e421… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #5668 from martenson/18.01_release_notes [18.01] Release Notes Compare: https://github.com/galaxyproject/galaxy/compare/e72e02cc7a98...c034ab3f0b63

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[galaxyproject/galaxy] f715ae: Fix tool test job data collection broken in #5628.
by GitHub 12 Mar '18

12 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f715ae5b65868a557da280e064cfea657ff53c80 https://github.com/galaxyproject/galaxy/commit/f715ae5b65868a557da280e064cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M test/functional/test_toolbox.py Log Message: ----------- Fix tool test job data collection broken in #5628. Commit: 0ce9e257ee78cd0a8be42c394a5d55b7826937e6 https://github.com/galaxyproject/galaxy/commit/0ce9e257ee78cd0a8be42c394a5d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/verify/script.py Log Message: ----------- Improvements to tool test driver script. - Run all tests for a tool by default. - Gather a couple more things into output JSON needed to emulate what Planemo produces by combining JSON and XUnit produces from nose. - Add --verbose flag, default to quiter testing. - Add --append flag to gather multiple test runs together into a single test JSON file that can be converted to HTML, XUnit, or Markdown with Planemo (https://github.com/galaxyproject/planemo/pull/799) Commit: aa699eba783de4b9c57e55dbf284925d8c1fd3df https://github.com/galaxyproject/galaxy/commit/aa699eba783de4b9c57e55dbf284… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Cleanup logic around register_job_data callback in tool test interactor code. Suggested by @nsoranzo. Commit: f13f7e240591e3a9d55b8a6c9081a2ae53be0bb2 https://github.com/galaxyproject/galaxy/commit/f13f7e240591e3a9d55b8a6c9081… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/tools/verify/script.py Log Message: ----------- Switch around Python expression for @nsoranzo. Commit: dc6b22fc74f434398749ef364c02428510359218 https://github.com/galaxyproject/galaxy/commit/dc6b22fc74f434398749ef364c02… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/verify/script.py M test/functional/test_toolbox.py Log Message: ----------- Merge pull request #5667 from jmchilton/tool_test_fixes Tool Testing Fix and Enhancements Compare: https://github.com/galaxyproject/galaxy/compare/c5df43cd000a...dc6b22fc74f4

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[galaxyproject/galaxy] f6b2cc: add basic cgroup metric collection
by GitHub 09 Mar '18

09 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6b2cc65b900e67300efb573f3b124d82836a80a https://github.com/galaxyproject/galaxy/commit/f6b2cc65b900e67300efb573f3b1… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M config/job_metrics_conf.xml.sample A lib/galaxy/jobs/metrics/instrumenters/cgroup.py Log Message: ----------- add basic cgroup metric collection Commit: 899ea47c9af999d9d8bf177eadbf4992193521f7 https://github.com/galaxyproject/galaxy/commit/899ea47c9af999d9d8bf177eadbf… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/cgroup.py Log Message: ----------- fix cgroup metric collector when no cgroup is available Commit: 7c40725f3fd77f881bc1be167dde760d89eec421 https://github.com/galaxyproject/galaxy/commit/7c40725f3fd77f881bc1be167dde… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M config/job_metrics_conf.xml.sample Log Message: ----------- fix broken xml in job_metrics.xml Commit: 7bf04bc88d0015e022d45e5c2b755e55a9e49e66 https://github.com/galaxyproject/galaxy/commit/7bf04bc88d0015e022d45e5c2b75… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/cgroup.py Log Message: ----------- only need to check if /proc/36642/cgroup exists, not if its executable... Commit: 47caac3f5ca61051e84414dbb63bdeab88a53b36 https://github.com/galaxyproject/galaxy/commit/47caac3f5ca61051e84414dbb63b… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/cgroup.py Log Message: ----------- actually..also need to explicitly check if cgget is available.. Commit: c5df43cd000a1891ca6911d1ca85ed646c5b21fa https://github.com/galaxyproject/galaxy/commit/c5df43cd000a1891ca6911d1ca85… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/job_metrics_conf.xml.sample A lib/galaxy/jobs/metrics/instrumenters/cgroup.py Log Message: ----------- Merge pull request #5610 from scholtalbers/feature/cgroup_metrics Add basic cgroup metric collection Compare: https://github.com/galaxyproject/galaxy/compare/21959113e7a0...c5df43cd000a

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[galaxyproject/galaxy] 2270f7: Consistent sniffing regardless of in_place.
by GitHub 09 Mar '18

09 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 2270f728c421b81ea14f022beb96203f007180dd https://github.com/galaxyproject/galaxy/commit/2270f728c421b81ea14f022beb96… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Consistent sniffing regardless of in_place. Previously sniffing would happen on the original file (before carriage returns and tabular spaces were converted) if in_place was false and on the converted file if it was true. Commit: e72e02cc7a98f6c721dbd14a52f5f18f5de33d5f https://github.com/galaxyproject/galaxy/commit/e72e02cc7a98f6c721dbd14a52f5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #5643 from jmchilton/sniff_fix [18.01] Consistent sniffing regardless of in_place. Compare: https://github.com/galaxyproject/galaxy/compare/fa3ec5f60b9a...e72e02cc7a98

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