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

[galaxyproject/galaxy] a218b6: Revert "disable 'hg push' to TS repositories"
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a218b6ed2a2ee32b03b2fbbeb22199a6d5adf25e https://github.com/galaxyproject/galaxy/commit/a218b6ed2a2ee32b03b2fbbeb221… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py R test/tool_shed/functional/test_0310_hg_clone.py A test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Revert "disable 'hg push' to TS repositories" Commit: 853fed9b9fffd04cceb8f0af5db5764bfd5bf435 https://github.com/galaxyproject/galaxy/commit/853fed9b9fffd04cceb8f0af5db5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py R test/tool_shed/functional/test_0310_hg_clone.py A test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Merge pull request #2040 from galaxyproject/revert-2033-remove-hg-direct-api Revert "disable 'hg push' to TS repositories" Compare: https://github.com/galaxyproject/galaxy/compare/9a12c14d22ce...853fed9b9fff

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[galaxyproject/galaxy] a218b6: Revert "disable 'hg push' to TS repositories"
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/revert-2033-remove-hg-direct-api Home: https://github.com/galaxyproject/galaxy Commit: a218b6ed2a2ee32b03b2fbbeb22199a6d5adf25e https://github.com/galaxyproject/galaxy/commit/a218b6ed2a2ee32b03b2fbbeb221… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py R test/tool_shed/functional/test_0310_hg_clone.py A test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Revert "disable 'hg push' to TS repositories"

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[galaxyproject/galaxy] 4e45e9: disable 'hg push' to TS repositories
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4e45e993db24c9cadf344c236ec0cd358ff30b0f https://github.com/galaxyproject/galaxy/commit/4e45e993db24c9cadf344c236ec0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- disable 'hg push' to TS repositories deprecated in 15.10 https://docs.galaxyproject.org/en/master/releases/15.10_announce.html#depre… Commit: c866f59915e121adbfaa6d6156857fd1daa05c40 https://github.com/galaxyproject/galaxy/commit/c866f59915e121adbfaa6d615685… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Specify default value when getting disable_push Commit: 0fce175aad0504b6a9e47a41060a3f5b9344bd18 https://github.com/galaxyproject/galaxy/commit/0fce175aad0504b6a9e47a41060a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: A test/tool_shed/functional/test_0310_hg_clone.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Update Tool Shed tests after disabling 'hg push' Commit: 296b21bf8f60ad943e3abe60ded8395ca8595ea1 https://github.com/galaxyproject/galaxy/commit/296b21bf8f60ad943e3abe60ded8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py A test/tool_shed/functional/test_0310_hg_clone.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Merge pull request #13 from nsoranzo/remove-hg-direct-api Fixes for "Remove hg direct api" Commit: 9a12c14d22cea563c986930359c0ccd7c46c5357 https://github.com/galaxyproject/galaxy/commit/9a12c14d22cea563c986930359c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py A test/tool_shed/functional/test_0310_hg_clone.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Merge pull request #2033 from martenson/remove-hg-direct-api disable 'hg push' to TS repositories Compare: https://github.com/galaxyproject/galaxy/compare/3ad68fd68eb0...9a12c14d22ce

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[galaxyproject/galaxy] 9c49f5: Use API to initiate repository installation.
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c49f5720d1a25082d59187d70cc7980ea694ba4 https://github.com/galaxyproject/galaxy/commit/9c49f5720d1a25082d59187d70cc… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Use API to initiate repository installation. Commit: 849cdab31b3f261d690f8479a87909ed60071941 https://github.com/galaxyproject/galaxy/commit/849cdab31b3f261d690f8479a879… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Fix imminent import error in travis. Commit: 3f766f5d97a7614fce956bc166544b2834be234b https://github.com/galaxyproject/galaxy/commit/3f766f5d97a7614fce956bc16654… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Rename API endpoint. Correct url for API endpoint. Commit: cef6ad81f7ef41d01b85803a3639853722bd2b3e https://github.com/galaxyproject/galaxy/commit/cef6ad81f7ef41d01b85803a3639… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Typo. Commit: ea7ad2486add2357d59fac6c17b48c0bccb0c81d https://github.com/galaxyproject/galaxy/commit/ea7ad2486add2357d59fac6c17b4… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Additional cleanup. Commit: 6ce5ac58387a6dc38c0eae5c23f7440781d178a3 https://github.com/galaxyproject/galaxy/commit/6ce5ac58387a6dc38c0eae5c23f7… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add API endpoint to show installation status. This will return a dict of the repository, with the repository_dependencies element containing a list of dicts with the dependency chain descending from that repository. Commit: 992812eb860e58f0c19328bfc6db7ac3e4b26f28 https://github.com/galaxyproject/galaxy/commit/992812eb860e58f0c19328bfc6db… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/categories.py A templates/admin/tool_shed_repository/browse_categories.mako Log Message: ----------- Load toolshed categories with API. Commit: 72e8f73858e5177432b51798cc0e229f81297826 https://github.com/galaxyproject/galaxy/commit/72e8f73858e5177432b51798cc0e… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Update category API endpoint. Optionally show list of repositories in category. Commit: aff62e76c8c8a862166c7e0ac899b2c1a79fea86 https://github.com/galaxyproject/galaxy/commit/aff62e76c8c8a862166c7e0ac899… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add API endpoint to check for updates to installed repositories. Commit: 2dca8f1812a7aaf9f20d3a8baa9f509e7ad8c15a https://github.com/galaxyproject/galaxy/commit/2dca8f1812a7aaf9f20d3a8baa9f… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix the update check API method. Commit: a4bf833e219cc571fd87e6e154530449b44519f3 https://github.com/galaxyproject/galaxy/commit/a4bf833e219cc571fd87e6e15453… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_category.mako A templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Add rudimentary mako files for the new interface. This is only for development purposes, until the UI designer fixes it. Commit: 83a9c6d440a630ea98b307ad67661c7f2314abef https://github.com/galaxyproject/galaxy/commit/83a9c6d440a630ea98b307ad6766… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Add code to initiate repository installation. Commit: 6e58db947878f542ce51c78956e392afe1515a67 https://github.com/galaxyproject/galaxy/commit/6e58db947878f542ce51c78956e3… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Merge in changes from api_install branch. Commit: 099f8eb145cda5064ae587ba171cbd0713cbcaff https://github.com/galaxyproject/galaxy/commit/099f8eb145cda5064ae587ba171c… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/tool_shed/util/common_util.py M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Functional installation of repository. Commit: 2a6712833223507700789440b63eaa6304cbacb5 https://github.com/galaxyproject/galaxy/commit/2a6712833223507700789440b63e… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M client/GruntFile.js M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/grunt-tasks/style.js M client/package.json M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M config/datatypes_conf.xml.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/static/js/ipython.js M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/tool_shed.ini.sample M cron/build_chrom_db.py M doc/source/admin/interactive_environments.rst A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/util/shed_util_common.py M scripts/bootstrap_history.py M static/maps/galaxy-app-base.js.map M static/maps/galaxy.masthead.js.map M static/maps/galaxy.menu.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.masthead.js M static/scripts/galaxy.menu.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css M templates/webapps/galaxy/root/index.mako M test/api/helpers.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/base/api.py M test/base/interactor.py M test/base/twilltestcase.py A test/functional/tools/cheetah_problem_syntax_error.xml A test/functional/tools/cheetah_problem_unbound_var.xml A test/functional/tools/cheetah_problem_unbound_var_input.xml A test/functional/tools/maxseconds.xml A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.yml M test/qunit/package.json M test/unit/tools/test_actions.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: b55ac36a92f9d73406c986fb4b1c637d15065e4d https://github.com/galaxyproject/galaxy/commit/b55ac36a92f9d73406c986fb4b1c… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/webapps/galaxy/admin/index.mako Log Message: ----------- Separate the decoupled and iframed toolshed installations. Commit: 271c8e97f7ddb849f6809a9d8b64a760e88e4efd https://github.com/galaxyproject/galaxy/commit/271c8e97f7ddb849f6809a9d8b64… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/browse_categories.mako M templates/admin/tool_shed_repository/browse_category.mako A templates/webapps/galaxy/admin/toolsheds.mako Log Message: ----------- Some refinements to the beta toolshed browsing. Commit: fb336b92b6b96f805efaf9bc51e8ab9829ebb8dc https://github.com/galaxyproject/galaxy/commit/fb336b92b6b96f805efaf9bc51e8… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh M .gitignore A Makefile M README.rst A client/.docker-build.sh A client/Dockerfile M client/README.md A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/base.js R client/galaxy/scripts/galaxy-app-base.js R client/galaxy/scripts/galaxy.autocom_tagging.js R client/galaxy/scripts/galaxy.base.js R client/galaxy/scripts/galaxy.frame.js A client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.pages.js R client/galaxy/scripts/galaxy.panels.js R client/galaxy/scripts/galaxy.tools.js R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/layout/masthead.js A client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/layout/modal.js A client/galaxy/scripts/layout/page.js A client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/IE/IE7.js R client/galaxy/scripts/libs/IE/IE8.js R client/galaxy/scripts/libs/IE/blank.gif R client/galaxy/scripts/libs/IE/excanvas.js R client/galaxy/scripts/libs/IE/ie7-recalc.js A client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/backbone/backbone.js M client/galaxy/scripts/libs/d3.js A client/galaxy/scripts/mvc/annotation.js R client/galaxy/scripts/mvc/annotations.js R client/galaxy/scripts/mvc/app/app-analysis.js R client/galaxy/scripts/mvc/app/app-login.js R client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-model.js R client/galaxy/scripts/mvc/collection/collection-panel-edit.js R client/galaxy/scripts/mvc/collection/collection-panel.js A client/galaxy/scripts/mvc/collection/collection-view-edit.js A client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js R client/galaxy/scripts/mvc/data.js A client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M 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test/unit/workflows/test_modules.py M test/unit/workflows/test_render.py M test/unit/workflows/test_run_parameters.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: d91fff8f15fdf894b19c67a4328acf8c831c170e https://github.com/galaxyproject/galaxy/commit/d91fff8f15fdf894b19c67a4328a… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M templates/admin/tool_shed_repository/browse_categories.mako M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Add some styling, allow selecting revision to install. Commit: 9206e95144c645bd849043055d2ff5f2413d0144 https://github.com/galaxyproject/galaxy/commit/9206e95144c645bd849043055d2f… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: A .ci/flake8_py3_wrapper.sh A .ci/py3_sources.txt M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/ui.less M lib/galaxy/app.py R lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/output_actions.py A lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A lib/galaxy/tools/special_tools.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/biostar.py A lib/galaxy/util/checkers.py M lib/galaxy/util/dictobj.py M lib/galaxy/util/expressions.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/topsort.py M lib/galaxy/util/validation.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/workflow/extract.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M scripts/common_startup.sh M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/utils/uploadbox.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M test/qunit/test-app.js A test/qunit/tests/modal_tests.html A test/qunit/tests/modal_tests.js A test/qunit/tests/popover_tests.html A test/qunit/tests/popover_tests.js M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_evaluation.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 4fdfc0f47b430a68a90185ebdacd8aa120f60382 https://github.com/galaxyproject/galaxy/commit/4fdfc0f47b430a68a90185ebdacd… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Update displayed metadata on changeset change. Commit: 7c357d1d56c98480b076bb7d80f9f1adde97e832 https://github.com/galaxyproject/galaxy/commit/7c357d1d56c98480b076bb7d80f9… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/galaxy/web/form_builder.py M lib/tool_shed/util/tool_util.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- More dynamic updating. - Repository dependencies reflect the selected changeset - So do tool dependencies - Tool panel select field shows/hides new tool panel section input field Commit: ba9493aed2ff1402097d9e383772e84dceb3f985 https://github.com/galaxyproject/galaxy/commit/ba9493aed2ff1402097d9e383772… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/browse_category.mako Log Message: ----------- Fill in some gaps in the repository listing. Commit: e7072c0aa268d248872540cd56d1e4c054f1fa42 https://github.com/galaxyproject/galaxy/commit/e7072c0aa268d248872540cd56d1… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/odict.py M lib/galaxy/util/xml_macros.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/common_util.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 68cecc6415054b84016f170c65c79a4460518d76 https://github.com/galaxyproject/galaxy/commit/68cecc6415054b84016f170c65c7… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Fix typo. Commit: bded6cdfd8f5283f0fc319df714687f374027c1f https://github.com/galaxyproject/galaxy/commit/bded6cdfd8f5283f0fc319df7146… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M templates/admin/tool_shed_repository/browse_category.mako Log Message: ----------- Address travis' complaints. Commit: b5a8073d73c15455e89eecc48675cd2fc8bd0622 https://github.com/galaxyproject/galaxy/commit/b5a8073d73c15455e89eecc48675… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Add endpoint for repositories in category, per Martin's suggestion. Commit: 86488d9c71e02a49e102e14acb0e8c1f68802989 https://github.com/galaxyproject/galaxy/commit/86488d9c71e02a49e102e14acb0e… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- s/trans.app/self.app/g Commit: 78d50994bf1b2091cf0244d99a68356cd8fa34e0 https://github.com/galaxyproject/galaxy/commit/78d50994bf1b2091cf0244d99a68… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less R client/galaxy/style/less/masthead.less M client/galaxy/style/less/ui.less M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/jupyter/static/js/jupyter.js A config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/visualizations/charts/templates/charts.mako M config/tool_conf.xml.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/cwl/__init__.py 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test/qunit/tests/masthead_tests.html A test/qunit/tests/masthead_tests.js M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_routes.py A test/unit/tools/test_conda_resolution.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/workflows/test_run_parameters.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: cc8175be8ff5c9affd3eb3051739e0ec9071760b https://github.com/galaxyproject/galaxy/commit/cc8175be8ff5c9affd3eb3051739… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/bower.json M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/onload.js M client/grunt-tasks/install-libs.js M client/webpack.config.js M config/galaxy.ini.sample A config/plugins/tours/core.galaxy_ui.yaml A config/plugins/tours/core.history.yaml M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py A lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/pluginframework.py A lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py A static/maps/galaxy.menu.js.map M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map A static/maps/libs/bootstrap-tour.js.map A static/maps/mvc/tours.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/galaxy.menu.js M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js A static/scripts/libs/bootstrap-tour.js A static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/onload.js A static/style/blue/bootstrap-tour.css M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako A test/api/test_tours.py M test/qunit/tests/workflow_editor_tests.js M test/unit/tools/test_parameter_parsing.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 1c6cffd2926d0201d1c3935e228bdab9ca6f426a https://github.com/galaxyproject/galaxy/commit/1c6cffd2926d0201d1c3935e228b… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/tool_util.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Implemented selecting or creating a tool panel section. Cleaned up UI a little. Commit: a337118d6bea1623410561c5a164713af4fae38c https://github.com/galaxyproject/galaxy/commit/a337118d6bea1623410561c5a164… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Revert per Eric's suggestion. Commit: 25c339a2324f13656a1fc3c112d70849fef235ed https://github.com/galaxyproject/galaxy/commit/25c339a2324f13656a1fc3c112d7… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- One more change to revert. Commit: 3840a6290d048195c3d6fc2748ccefbc96b72b13 https://github.com/galaxyproject/galaxy/commit/3840a6290d048195c3d6fc2748cc… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-07 (Thu, 07 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/project/issues.rst M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py M lib/galaxy/version.py M static/maps/mvc/tool/tool-template.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-template.js M static/style/blue/base.css M test/casperjs/api-tool-tests.js M test/casperjs/modules/historyoptions.js M test/casperjs/modules/user.js M test/casperjs/registration-tests.js M test/casperjs/spaceghost.js Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 6d649c1ec3a537bb383f7d25c0bd2a209f8dcb8d https://github.com/galaxyproject/galaxy/commit/6d649c1ec3a537bb383f7d25c0bd… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-07 (Thu, 07 Jan 2016) Changed paths: M templates/admin/tool_shed_repository/initiate_repository_installation.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Un-break traditional repository installations. Commit: 8b29f3ad0d9d9e2c654bf51f56b3587d7158420e https://github.com/galaxyproject/galaxy/commit/8b29f3ad0d9d9e2c654bf51f56b3… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-07 (Thu, 07 Jan 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py Log Message: ----------- Fix failing tests in jenkins. Commit: d509e8f6028259b8ff055cc67873fcd573fd72de https://github.com/galaxyproject/galaxy/commit/d509e8f6028259b8ff055cc67873… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Additional code and style cleanup. Commit: a156f1db1e28efad2a159caef0951261c50ad41f https://github.com/galaxyproject/galaxy/commit/a156f1db1e28efad2a159caef095… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M .gitignore M .travis.yml M Makefile M lib/galaxy/tours/__init__.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/shed_util_common.py M templates/grid_base.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/embed.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: d51c7d2fd4afc9cb31ae34cd0274f03ee2d6a643 https://github.com/galaxyproject/galaxy/commit/d51c7d2fd4afc9cb31ae34cd0274… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M .gitignore M 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lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/extract.py M lib/pulsar/client/amqp_exchange.py M requirements.txt M run.sh M run_tests.sh M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/common_startup.sh M static/maps/layout/menu.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M 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templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako M test/api/helpers.py M test/api/test_tools.py M test/casperjs/casperjs_runner.py M test/casperjs/modules/user.js M test/functional/test_toolbox.py M test/functional/tools/output_action_change_format.xml M test/qunit/tests/masthead_tests.js M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: e2776530699e2ba4a6a4780dead63300a7575af3 https://github.com/galaxyproject/galaxy/commit/e2776530699e2ba4a6a4780dead6… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Enable selecting a tool panel section on a per-tool basis. Commit: 2483f7673a20997cf8ac764bf06e79f253f9b61c https://github.com/galaxyproject/galaxy/commit/2483f7673a20997cf8ac764bf06e… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Do not attempt to update the tool panel section if it's not separately mapped. Commit: df722f9c7e192fcfe4fa693d5886d38ac4c3a6bc https://github.com/galaxyproject/galaxy/commit/df722f9c7e192fcfe4fa693d5886… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample R config/plugins/visualizations/charts/static/build-app.js M lib/galaxy/config.py M lib/galaxy/web/framework/webapp.py M scripts/binary_compatibility.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/style/blue/base.css A test/qunit/tests/ui_tests.html A test/qunit/tests/ui_tests.js M test/unit/unittest_utils/galaxy_mock.py A test/unit/web/framework/__init__.py A test/unit/web/framework/test_webapp.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 6f72b05bd59708eb3b28b17a165f392f6640bf5a https://github.com/galaxyproject/galaxy/commit/6f72b05bd59708eb3b28b17a165f… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/web/form_builder.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Some tweaks to the repository preview UI. Commit: a3a178a0d332626616e1854ad7829733ecca00e2 https://github.com/galaxyproject/galaxy/commit/a3a178a0d332626616e1854ad782… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-25 (Mon, 25 Jan 2016) Changed paths: M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M 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Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 18bc2f39a3a71d4463f211ad4388eb275cff9f19 https://github.com/galaxyproject/galaxy/commit/18bc2f39a3a71d4463f211ad4388… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/util/metadata_util.py M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Display repository dependencies. Commit: e6247d415c6c5af024e649a09a4d0475cf0ee1da https://github.com/galaxyproject/galaxy/commit/e6247d415c6c5af024e649a09a4d… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/less/tour.less M config/galaxy.ini.sample M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst M doc/source/project/issues.rst A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M lib/galaxy/datatypes/interval.py A lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/special_tools.py M lib/galaxy/webapps/galaxy/controllers/user.py M scripts/bootstrap_history.py M scripts/common_startup.sh R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-view.js M static/style/blue/base.css M test/api/test_workflows.py M test/api/workflows_format_2/converter.py A test/functional/tools/for_workflows/1.bam A test/functional/tools/for_workflows/mapper.xml A test/functional/tools/for_workflows/pileup.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 3d14626aeb276ecdd9b3f873ffae15d74f6a6b00 https://github.com/galaxyproject/galaxy/commit/3d14626aeb276ecdd9b3f873ffae… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py Log Message: ----------- Fix some travis errors. Commit: 8d2e17e6d7e276fb3d36f6d49429660d69b031f9 https://github.com/galaxyproject/galaxy/commit/8d2e17e6d7e276fb3d36f6d49429… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/tool_shed/util/metadata_util.py Log Message: ----------- Fix more travis errors. Commit: 5937e17c1ab40673904f1914211a6ba02c1f081d https://github.com/galaxyproject/galaxy/commit/5937e17c1ab40673904f1914211a… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/web/form_builder.py M lib/tool_shed/util/metadata_util.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Code cleanup, fixing even more travis errors. Commit: 210d6e6b8e338a246237fde2bb6818b7d08bf065 https://github.com/galaxyproject/galaxy/commit/210d6e6b8e338a246237fde2bb68… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Minor cosmetic cleanup. Commit: aeba386436c3b6741fc3e610a239800149f7bb14 https://github.com/galaxyproject/galaxy/commit/aeba386436c3b6741fc3e610a239… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: eff4462781c5b8c6c5c776abfee6ab2e3bd27c31 https://github.com/galaxyproject/galaxy/commit/eff4462781c5b8c6c5c776abfee6… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Fix installation of selected repository. Commit: 02c15cbd2530989d454ebaedd3fb595332ac1fc5 https://github.com/galaxyproject/galaxy/commit/02c15cbd2530989d454ebaedd3fb… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Remove unused methods and parameters. Commit: b9f9be49559635aec2b7a0690e9c3c58dc77da28 https://github.com/galaxyproject/galaxy/commit/b9f9be49559635aec2b7a0690e9c… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: A .ci/first_startup.sh M .ci/flake8_blacklist.txt M .travis.yml M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M 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Commit: 590115172fe6951ae1c5ac907b0ccc6143d680b2 https://github.com/galaxyproject/galaxy/commit/590115172fe6951ae1c5ac907b0c… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/style/less/library.less M lib/galaxy/webapps/galaxy/api/lda_datasets.py M static/maps/galaxy.library.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-dataset-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: ed5894607dbe1d184d20135a1aa7ba5f9a362c23 https://github.com/galaxyproject/galaxy/commit/ed5894607dbe1d184d20135a1aa7… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Remove duplicate method definition. 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Commit: 7c64277299f576fe84dc1eda86771dc69968fd03 https://github.com/galaxyproject/galaxy/commit/7c64277299f576fe84dc1eda8677… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Somehow the resolution of the merge conflict didn't get committed. Commit: 9f239a011c2aee197a6539799ef568d65991426b https://github.com/galaxyproject/galaxy/commit/9f239a011c2aee197a6539799ef5… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove unused import. Commit: 5d1e86cfb21675b85248a9e58f3bfd3998643fe5 https://github.com/galaxyproject/galaxy/commit/5d1e86cfb21675b85248a9e58f3b… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/browse_categories.mako Log Message: ----------- Add simple search functionality. Commit: dc7f048c4044bcb36582559526c15314461f608d https://github.com/galaxyproject/galaxy/commit/dc7f048c4044bcb36582559526c1… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/interactive_environments.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 63d61b11f7bbd16f06bdcf770b987d798caa1680 https://github.com/galaxyproject/galaxy/commit/63d61b11f7bbd16f06bdcf770b98… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Do not load recursive metadata in the category browser. Commit: 6b5e1af81807d7d20942767cd3ebbe541379820b https://github.com/galaxyproject/galaxy/commit/6b5e1af81807d7d20942767cd3eb… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/py3_sources.txt M .travis.yml M Makefile M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M config/datatypes_conf.xml.sample M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M 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templates/webapps/galaxy/requests/common/view_sample_datasets.mako M templates/webapps/tool_shed/repository/common.mako M test/functional/tools/output_format.xml M test/unit/test_objectstore.py A test/unit/tools/test_history_imp_exp.py M test/unit/unittest_utils/galaxy_mock.py M tox.ini Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 7df463cdd88776a533aa06d9ae96f04e9bf0d58b https://github.com/galaxyproject/galaxy/commit/7df463cdd88776a533aa06d9ae96… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Escape values of extra attributes for select fields. Commit: ad101ded626ee44b24d71884fb6fd257c58f1837 https://github.com/galaxyproject/galaxy/commit/ad101ded626ee44b24d71884fb6f… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Apply modified version of fix from #1798. Commit: 4e3ad3c9845c8ee0546fbaaeb4a70b820ecece5b https://github.com/galaxyproject/galaxy/commit/4e3ad3c9845c8ee0546fbaaeb4a7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/browse_categories.mako M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- offer TS searching while browsing a category fix few usability issues Commit: 1b78b86a5ad64a8e91d2309d545a1a6b7ea33503 https://github.com/galaxyproject/galaxy/commit/1b78b86a5ad64a8e91d2309d545a… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/browse_categories.mako M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Merge pull request #3 from martenson/decouple-polish offer TS searching while browsing a category Commit: 3a5584ab1497d16a5c130641515b798a2c7794f5 https://github.com/galaxyproject/galaxy/commit/3a5584ab1497d16a5c130641515b… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M client/grunt-tasks/style.js M client/package.json M config/galaxy.ini.sample M create_db.sh M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M manage_db.sh M static/maps/mvc/workflow/workflow-view.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/run.mako M test/api/test_tools.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/functional/tools/empty_output.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/strict_shell.xml A test/functional/tools/strict_shell_default_off.xml A test/functional/tools/validation_empty_dataset.xml M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_objectstore.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parsing.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_render.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: f44c3ae85ec195d6f59fa8eaf407d56bac4836a6 https://github.com/galaxyproject/galaxy/commit/f44c3ae85ec195d6f59fa8eaf407… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Update javascript with Carl's suggestions. Commit: 2a91835da47badd9d2b32cbba0c308aa8907901e https://github.com/galaxyproject/galaxy/commit/2a91835da47badd9d2b32cbba0c3… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Do not display the valid tools section if there are none. 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Commit: f60edb952a33ce05538fd10018d59c51dc5f656a https://github.com/galaxyproject/galaxy/commit/f60edb952a33ce05538fd10018d5… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M run_tool_shed.sh M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Show tool panel selector only when needed. Add the virtualenv to run_tool_shed.sh Commit: 96ca49b7d054b413fa2d939e9dcae470933f441e https://github.com/galaxyproject/galaxy/commit/96ca49b7d054b413fa2d939e9dca… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init M doc/source/admin/framework_dependencies.rst M lib/galaxy/app.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M 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static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/tool/tool-form.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/display.mako M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_select_parameters.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: ef960a62f788c432b7891fbbf1f8762dfd3dc9e7 https://github.com/galaxyproject/galaxy/commit/ef960a62f788c432b7891fbbf1f8… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M Makefile M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M 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lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/bootstrap_history.py M scripts/functional_tests.py M scripts/summarize_timings.py M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css M static/style/blue/library.css M templates/base/base_panels.mako M templates/webapps/galaxy/library/common/library_info.mako A test/base/driver_util.py M test/base/twilltestcase.py R test/functional/test_admin_features.py R test/functional/test_data_security.py R test/functional/test_dataset_features.py R test/functional/test_get_data.py R test/functional/test_library_features.py R test/functional/test_library_security.py R test/functional/test_metadata_editing.py R test/functional/test_sample_tracking.py R test/functional/test_tags.py M test/functional/test_toolbox.py R test/functional/test_ucsc_table_browser.py R test/functional/test_user_info.py M test/functional/tools/collection_creates_list.xml A test/functional/tools/for_workflows/create_input_collection.xml A test/functional/tools/for_workflows/split.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/upload_tool_conf.xml M test/functional/workflow.py R test/install_and_test_tool_shed_repositories/__init__.py R test/install_and_test_tool_shed_repositories/base/__init__.py R test/install_and_test_tool_shed_repositories/base/test_db_util.py R test/install_and_test_tool_shed_repositories/base/twilltestcase.py R test/install_and_test_tool_shed_repositories/base/util.py R test/install_and_test_tool_shed_repositories/functional/__init__.py R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py A test/manual/launch_and_run.sh A test/manual/workflow_job_conf.xml M test/manual/workflows_scaling.py M test/qunit/test-app.js A test/qunit/tests/form_tests.html A test/qunit/tests/form_tests.js A test/qunit/tests/page_tests.html A test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.js M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/test_lazy_process.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 3ad68fd68eb023e0a59d55e2489e896b6ce7aad7 https://github.com/galaxyproject/galaxy/commit/3ad68fd68eb023e0a59d55e2489e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M run_tool_shed.sh A templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/initiate_repository_installation.mako A templates/admin/tool_shed_repository/preview_repository.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/toolsheds.mako Log Message: ----------- Merge pull request #1392 from davebx/toolshed_decouple Use the API to install repositories instead of loading the toolshed in an iframe. Compare: https://github.com/galaxyproject/galaxy/compare/565f11f142de...3ad68fd68eb0

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[galaxyproject/galaxy] 5def7e: refactor rest of JS templates;
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5def7ee035645ae155a7c712a068a5a9bc6fdc42 https://github.com/galaxyproject/galaxy/commit/5def7ee035645ae155a7c712a068… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-model.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- refactor rest of JS templates; move all text outside of the fontawesome spans convert console. calls to Galaxy.emit calls Commit: 971b987f0b5d110e51022fcc7d0bfc9fd6c52502 https://github.com/galaxyproject/galaxy/commit/971b987f0b5d110e51022fcc7d0b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js Log Message: ----------- libraries: fetch nondeleted only first to speed up fetch the deleted only when specifically requested Commit: 565f11f142de7cee37faea056f9def237b2d870d https://github.com/galaxyproject/galaxy/commit/565f11f142de7cee37faea056f9d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge branch 'lib-refactor-cleanup' into dev Compare: https://github.com/galaxyproject/galaxy/compare/35767b138012...565f11f142de

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[galaxyproject/galaxy] 516f4f: Fix transiently failing tool shed tests.
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 516f4f017f1635a961d50ea47c36a15053aa9689 https://github.com/galaxyproject/galaxy/commit/516f4f017f1635a961d50ea47c36… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Fix transiently failing tool shed tests. Comments inline - I don't know why but the retry would fix the transient problems acording to the Jenkins tests with the previous exception added to verify this would fix the problem. Commit: 35767b1380121121dddebc6751f072510be8b5cb https://github.com/galaxyproject/galaxy/commit/35767b1380121121dddebc6751f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #2030 from jmchilton/capsule_fix Fix transiently failing tool shed tests. Compare: https://github.com/galaxyproject/galaxy/compare/d15b1030c5ba...35767b138012

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[galaxyproject/galaxy] f27ff0: Fix to 9acbfdf: initial fix borked fa-2x, instead ...
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: f27ff0c7ba829a48f9c0eae443baa36cda92cf98 https://github.com/galaxyproject/galaxy/commit/f27ff0c7ba829a48f9c0eae443ba… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M static/style/blue/base.css Log Message: ----------- Fix to 9acbfdf: initial fix borked fa-2x, instead remove second woff loaded due to fa-icon font-family rule by aliasing that to fa Commit: 7a9d4943cd0571f5adebf850b4e167065289700b https://github.com/galaxyproject/galaxy/commit/7a9d4943cd0571f5adebf850b4e1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Fix tool shed tests for e4a1d5727805168a9fd15aca1cdd21630ada2bbc . Commit: 15c08d80e4a2c027a01dd8dabc16b802be4c18a1 https://github.com/galaxyproject/galaxy/commit/15c08d80e4a2c027a01dd8dabc16… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1791 from carlfeberhard/release_16.01 [16.01] Fix to 9acbfdf: initial fix borked fa-2x, instead remove second woff … Commit: 5546211c0dddb23bbeae34c0cddbd7ad9cebf6b5 https://github.com/galaxyproject/galaxy/commit/5546211c0dddb23bbeae34c0cddb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #1798 from nsoranzo/release_16.01_tool_shed_test_fixes [16.01] Fix tool shed tests for e4a1d5727805168a9fd15aca1cdd21630ada2bbc . Commit: 1aa1d6164a63438b49beb2fd6cc4b80a57bbdb5d https://github.com/galaxyproject/galaxy/commit/1aa1d6164a63438b49beb2fd6cc4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix workflow parameters not rendered when tool parameter wrapped in conditional. Commit: dad1784a087623c990e0b3f05d1c8026f7bd957c https://github.com/galaxyproject/galaxy/commit/dad1784a087623c990e0b3f05d1c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #1799 from mvdbeek/fix_workflow_parameters_conditional [16.01] Fix workflow parameters not rendered when tool parameter wrapped in conditional. Commit: 56076db848459cb1da39b04dc635538ff013d3a9 https://github.com/galaxyproject/galaxy/commit/56076db848459cb1da39b04dc635… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Disable command isolation for Pulsar... ... it builds its own job script - no need to have Galaxy do this isolation on the Galaxy end. The more Pulsar can handle the better. Commit: cb19630bd4e04b21653a2cb9848e888805dfabcc https://github.com/galaxyproject/galaxy/commit/cb19630bd4e04b21653a2cb9848e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Fix unit tests for 56076db848459cb1da39b04dc635538ff013d3a9 Commit: 47c93180708eb138c1fa0393cd18b24d27249359 https://github.com/galaxyproject/galaxy/commit/47c93180708eb138c1fa0393cd18… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-28 (Sun, 28 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #1812 from jmchilton/pulsar_16.01_fixes [16.01] Disable command isolation for Pulsar... Commit: 865f2d49bd04b636552002cd0e4830f2dbad5c75 https://github.com/galaxyproject/galaxy/commit/865f2d49bd04b636552002cd0e48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M create_db.sh M manage_db.sh Log Message: ----------- Fix create/manage db scripts to respect GALAXY_VIRTUAL_ENV. Commit: 5bc55f9fa2fd6af9142df644bf82e830b56f9ce4 https://github.com/galaxyproject/galaxy/commit/5bc55f9fa2fd6af9142df644bf82… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Add js for mako based masthead Commit: 281f5b734610963b437b72837e7b71cebbb3c5bd https://github.com/galaxyproject/galaxy/commit/281f5b734610963b437b72837e7b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M client/galaxy/style/less/ui/icon-btn.less M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/config.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/version.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/shed_util_common.py M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/workflow/workflow-terminals.js M static/style/blue/base.css R templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/common.mako M test/functional/tools/output_format.xml M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Merge branch 'release_16.01' of https://github.com/galaxyproject/galaxy into release_16.01 Commit: fa8beb225004d27da24065f8f633c7917b5be942 https://github.com/galaxyproject/galaxy/commit/fa8beb225004d27da24065f8f633… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge pull request #1823 from martenson/port-masthead-fix [16.01] Port masthead fix Commit: 50bc127a3b55432884ed6350bee3e0ea67beb95f https://github.com/galaxyproject/galaxy/commit/50bc127a3b55432884ed6350bee3… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M create_db.sh M manage_db.sh Log Message: ----------- Merge pull request #1820 from jmchilton/db_script_fixes [16.01] Fix create/manage db scripts to respect GALAXY_VIRTUAL_ENV. Commit: 93494a833ee390811bdc1d13c1ef54b52ed005f2 https://github.com/galaxyproject/galaxy/commit/93494a833ee390811bdc1d13c1ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- This silences logging when display whitelist isn't explicitly defined and the default file doesn't exist. Explicit usage still logs a failure. Commit: 16280c63236621082ce4c3b3d93eb679294cd515 https://github.com/galaxyproject/galaxy/commit/16280c63236621082ce4c3b3d93e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py Log Message: ----------- Only attempt to read/load sanitize_whitelist_file when starting an actual galaxy application. Commit: 7534182d7afd8c997df7d919d0633345ee5c4dfa https://github.com/galaxyproject/galaxy/commit/7534182d7afd8c997df7d919d063… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py Log Message: ----------- Add a default logger prior to full logging configuration. We currently attempt to log at various places in config parsing/etc that fail with 'No handlers could be found for logger ...', and this resolves that. Commit: cf91ab4511897ef5ac4beb8d56219119073073c4 https://github.com/galaxyproject/galaxy/commit/cf91ab4511897ef5ac4beb8d5621… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py Log Message: ----------- Merge pull request #1828 from dannon/cherrypick_logging [16.01] Fix startup logging Commit: f67cbe72d571f87a87e868161650e5965e681881 https://github.com/galaxyproject/galaxy/commit/f67cbe72d571f87a87e868161650… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- revert escaping added in a24e206ff7762d5b86d3dc7240190f043dc532b5 that prevented line endings and spaces to be rendered properly Commit: 0051cab4f35240ff8b85f010b1ae0d66de7273c0 https://github.com/galaxyproject/galaxy/commit/0051cab4f35240ff8b85f010b1ae… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Merge pull request #1830 from martenson/revert-ts-repo-rendering [16.01] revert ts repo long desc escaping Commit: a49401189735daa55e44dec7af6b84a646e8bbc9 https://github.com/galaxyproject/galaxy/commit/a49401189735daa55e44dec7af6b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Improve dataset error log message Commit: 4992684d1fc58d4774e5d6a6c1df9c193218c460 https://github.com/galaxyproject/galaxy/commit/4992684d1fc58d4774e5d6a6c1df… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Hide tools that have been replaced. Commit: dfef64db75c43cd4001a67cf48143e28df3efe60 https://github.com/galaxyproject/galaxy/commit/dfef64db75c43cd4001a67cf4814… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #1836 from natefoo/dataset-error-log [16.01] Improve dataset error log message Commit: de70306407c0682834814c479c91f8b8adc615ce https://github.com/galaxyproject/galaxy/commit/de70306407c0682834814c479c91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Merge pull request #1837 from davebx/release_16.01 [16.01] Hide tools that have been replaced. Commit: 26d5561b4ff48eb770970bee5f2ba49d425e9902 https://github.com/galaxyproject/galaxy/commit/26d5561b4ff48eb770970bee5f2b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M manage_tools.sh M run_reports.sh M run_tool_shed.sh Log Message: ----------- Update more scripts to respect GALAXY_VIRTUAL_ENV. Drop explicit sourcing in run_reports and run_tool_shed since they source common_startup. Commit: e0ce68cc58a6d6eeb306f5c0445563e71bcc1d12 https://github.com/galaxyproject/galaxy/commit/e0ce68cc58a6d6eeb306f5c04455… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix lack of output when discovering large collections... Example log statement collected for each dataset: ``` galaxy.tools.parameters.output_collect DEBUG 2016-03-03 11:47:31,302 (8) Created dynamic collection dataset for path [/home/john/workspace/galaxy/database/job_working_directory/000/8/oe2_ie2.fq] with element identifier [oe2:ie2] for output [list_output]. ``` Commit: 0fbd22c9a30686afe62de1e1f23ff309dd6374a8 https://github.com/galaxyproject/galaxy/commit/0fbd22c9a30686afe62de1e1f23f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #1852 from jmchilton/dataset_collection_log [16.01] Fix lack of log output when discovering large collections... Commit: 97793ab81ab5601466fa89bba7b3250118e95de4 https://github.com/galaxyproject/galaxy/commit/97793ab81ab5601466fa89bba7b3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M manage_tools.sh M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge pull request #1847 from jmchilton/more_virtualenv_fixes [16.01] Update more scripts to respect GALAXY_VIRTUAL_ENV. Commit: e14e8a074c1344ab62dae2254f1e4a250e963b22 https://github.com/galaxyproject/galaxy/commit/e14e8a074c1344ab62dae2254f1e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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/dataset/dataset-li-edit.js Log Message: ----------- Allow rerun of datasets new yet queued by job manager. Commit: 0445fcda51cad08a0b2969140b48948a9e7d759b https://github.com/galaxyproject/galaxy/commit/0445fcda51cad08a0b2969140b48… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add workflow building mode check to collection parameter handling Commit: 8905bafe10845545bedbd1c6b9e758e1b9523b4d https://github.com/galaxyproject/galaxy/commit/8905bafe10845545bedbd1c6b9e7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-06 (Sun, 06 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1859 from guerler/fix_collection_000 [16.01] Add workflow building mode check to collection parameter handling Commit: 0e0c1caec4f14e0a5240763e697bd5d3613db719 https://github.com/galaxyproject/galaxy/commit/0e0c1caec4f14e0a5240763e697b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py Log Message: ----------- Fixing subworkflow migration (0131) to work with mysql Commit: 6442cbc3d4340ea3d03dad01c3ebf2dce05ed6e1 https://github.com/galaxyproject/galaxy/commit/6442cbc3d4340ea3d03dad01c3eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- Fix downgrade attempting to drop parent_workflow_id off the wrong table. Commit: b23c354f91f9d1a572f488a4d49f25b8681e58ba https://github.com/galaxyproject/galaxy/commit/b23c354f91f9d1a572f488a4d49f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- Replace testing keynames with real ones. Commit: ad6273307da4b971ea4354d9ad33cb08ca912577 https://github.com/galaxyproject/galaxy/commit/ad6273307da4b971ea4354d9ad33… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- We can't flip storedworkflow back to non-nullable in a downgrade step here, so don't try. Just leave it alone. Commit: 0c34d5bd3ff414d6beb669e106306066f663d75f https://github.com/galaxyproject/galaxy/commit/0c34d5bd3ff414d6beb669e10630… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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/dataset/dataset-li-edit.js Log Message: ----------- Merge pull request #1858 from jmchilton/rerun_new_datasets [16.01] Allow rerun of datasets new yet queued by job manager. Commit: 0f97b50e9ca8ca8b54e8d30769cd3fe46204f27c https://github.com/galaxyproject/galaxy/commit/0f97b50e9ca8ca8b54e8d30769cd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- Different logic for mysql (just don't worry about keys, due to the agony -- access to the database is entirely procedural and due to this we'd likely see any issues breaking these fk constraints in postgres before mysql (if ever) anyway. Commit: 29c78e984e52ac08b1b36a03e39b65c6edbe6200 https://github.com/galaxyproject/galaxy/commit/29c78e984e52ac08b1b36a03e39b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Fix virtualenv broken with #1847. Commit: 5824bc04af9270afbebcb2c8f9b6b3bea371b788 https://github.com/galaxyproject/galaxy/commit/5824bc04af9270afbebcb2c8f9b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Fix duplicate print statement reported by @dannon... https://github.com/galaxyproject/galaxy/pull/1890#issuecomment-193873380 Commit: 50f1089c72ff46397e525d4aa99dc80569081509 https://github.com/galaxyproject/galaxy/commit/50f1089c72ff46397e525d4aa99d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Slight tweaks to our tabix usage. This fixes trackster without more divergence in our version of pysam. Commit: c6f3e9b5b28268cba1ef8d7be5f1bed90b6ecc00 https://github.com/galaxyproject/galaxy/commit/c6f3e9b5b28268cba1ef8d7be5f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Slight cleanup, remove outdated comment regarding tabixfile.close() Commit: f0b7a34dd3ea5b3b10494c7e186fb10fda30441f https://github.com/galaxyproject/galaxy/commit/f0b7a34dd3ea5b3b10494c7e186f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Apply patch from Fabien Mareuil to resolve json serialization of Decimal error; for more see http://dev.list.galaxyproject.org/quota-api-error-td4669081.html Commit: a351c75687921bb8d2487577c5c4c0a64bee5e5f https://github.com/galaxyproject/galaxy/commit/a351c75687921bb8d2487577c5c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Extra documentation for @mvdbeek Commit: 438661e8945c1bb317f75dabe3db429ea779255d https://github.com/galaxyproject/galaxy/commit/438661e8945c1bb317f75dabe3db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Another fix for virtualenv fixes. Commit: 62b5f207566eb9666df58f1ab107d3e7b1f0c736 https://github.com/galaxyproject/galaxy/commit/62b5f207566eb9666df58f1ab107… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Remove unnecessary encoding in remote_files. This allows paths and filenames like Ăfile.txt Commit: 0c225bec2e9af0c941ccc943d9ad010f2893a6e0 https://github.com/galaxyproject/galaxy/commit/0c225bec2e9af0c941ccc943d9ad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Update library_info.mako escaping. This allows use of non-ascii characters like 'This is Ă data library' Commit: afb4e9c8f40da5331412c2a8f83ece814fb54b05 https://github.com/galaxyproject/galaxy/commit/afb4e9c8f40da5331412c2a8f83e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #1897 from dannon/pysam_compat [16.01] Slight tweaks to our tabix usage. Commit: 3abd2c213ae508bd3547d08729c96bbff4a5b740 https://github.com/galaxyproject/galaxy/commit/3abd2c213ae508bd3547d08729c9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Merge pull request #1898 from dannon/quota_api_fix_fabien [16.01] Quota API issue with serialization to JSON of Decimal Commit: b3e9398c3affa964fdc8cf090eb5c149f7a6bf47 https://github.com/galaxyproject/galaxy/commit/b3e9398c3affa964fdc8cf090eb5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Replace get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision with get_repository_for_dependency_relationship Commit: d6e38c7d482eae65fc135cd65a13b7f215220cd5 https://github.com/galaxyproject/galaxy/commit/d6e38c7d482eae65fc135cd65a13… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- remove unused import Commit: 5a50a4691c11edb9366f2e0d3eeb68aaaabb9c80 https://github.com/galaxyproject/galaxy/commit/5a50a4691c11edb9366f2e0d3eeb… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Merge pull request #1909 from mvdbeek/backport_repository_for_dependency_relationship [16.01] Backport PR #1868 Commit: 90fcd8c668865ce109b3fbc011319a9794e9e47f https://github.com/galaxyproject/galaxy/commit/90fcd8c668865ce109b3fbc01131… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-14 (Mon, 14 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Handle sections in view workflow Fixes 1723 Commit: 65a5b08c7129462a310fc741fb64e7f883bd8b0f https://github.com/galaxyproject/galaxy/commit/65a5b08c7129462a310fc741fb64… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge pull request #1916 from erasche/fix-1723-back [16.01] Handle sections in view workflow Commit: 18473a187e019421933746abb31f8b226e828b80 https://github.com/galaxyproject/galaxy/commit/18473a187e019421933746abb31f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Ensure chrom, start, end as bytestring in BamDataProvider Commit: 9a343efe8b7dd393842e0f971e59d575f2286de2 https://github.com/galaxyproject/galaxy/commit/9a343efe8b7dd393842e0f971e59… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #1930 from mvdbeek/more_bytestring_for_pysam [16.01] Ensure chrom, start, end as bytestring in BamDataProvider Commit: 00a7c3af057c0689a53748802740bc2002df375c https://github.com/galaxyproject/galaxy/commit/00a7c3af057c0689a53748802740… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge pull request #1890 from jmchilton/fix_virtualenvs [16.01] Fix virtual env handling broken with #1847. Commit: f277f99aed411fede7d1cb91d3177469922a58ae https://github.com/galaxyproject/galaxy/commit/f277f99aed411fede7d1cb91d317… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Fix handling of time in fluent logger. Commit: 87bcb5f5a1b6801e948b2cc0f5dc676c7faca682 https://github.com/galaxyproject/galaxy/commit/87bcb5f5a1b6801e948b2cc0f5dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Fix in a different way not requiring signature change; still not thrilled about overlapping kwarg names w/ stdlib module names. Commit: c8e48bfaccb5d10552df4200e616a9eee49206b0 https://github.com/galaxyproject/galaxy/commit/c8e48bfaccb5d10552df4200e616… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add fluentd configuration to galaxy.ini.sample Commit: 98c65dcee08338ea80a7e34251f8fa4ed6bd8dd5 https://github.com/galaxyproject/galaxy/commit/98c65dcee08338ea80a7e34251f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py Log Message: ----------- Swap back to the first fix, update metrics api to use new signature. Commit: 4ef186812f1d3f16b36080654ee043065237d0c5 https://github.com/galaxyproject/galaxy/commit/4ef186812f1d3f16b36080654ee0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Encode user_login as utf8 prior to directory manipulation. Commit: e3e49a477d96ec5fc4623646e7ea240090f80ae2 https://github.com/galaxyproject/galaxy/commit/e3e49a477d96ec5fc4623646e7ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- extreme casting to 1) make this code actually work with python 2, and 3) work should the web framework ever be functional in python3 Commit: 19bf334c7763c2418408083b9a7369386e50ad66 https://github.com/galaxyproject/galaxy/commit/19bf334c7763c2418408083b9a73… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py Log Message: ----------- Merge pull request #1945 from dannon/fluent_logging_fix [16.01] Fix handling of time in fluent logger Commit: bd0439d9b724bb72c1fab4c27a4c72814abef0b9 https://github.com/galaxyproject/galaxy/commit/bd0439d9b724bb72c1fab4c27a4c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Fix tool access rights and forwarding Commit: 054fdf76f09faf35662adf0f4a8a6f6428abab4f https://github.com/galaxyproject/galaxy/commit/054fdf76f09faf35662adf0f4a8a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Parse user when filtering tools Commit: 9e9dfdfd55b2b8d2377f8ef4e288a1fa482105b9 https://github.com/galaxyproject/galaxy/commit/9e9dfdfd55b2b8d2377f8ef4e288… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix workflow scheduler log message. Commit: 5f5f0af5cd5e21c64810d29202e149915226c34a https://github.com/galaxyproject/galaxy/commit/5f5f0af5cd5e21c64810d29202e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #1955 from jmchilton/fix_wf_log_message [16.01] Fix workflow scheduler log message. Commit: 2efd9c2687d2ca818520249cdb3484e781659069 https://github.com/galaxyproject/galaxy/commit/2efd9c2687d2ca818520249cdb34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix #1721. TODO: write test... Commit: 377ccbe23b717f9c8cb0d571de9f0d6da08a1ee8 https://github.com/galaxyproject/galaxy/commit/377ccbe23b717f9c8cb0d571de9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1967 from jmchilton/fix_optional_numeric_params [16.01] Fix #1721. Commit: 566f556b076db164ce73750f33c9824fe0285530 https://github.com/galaxyproject/galaxy/commit/566f556b076db164ce73750f33c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #1952 from guerler/fix_tool_access_000 [16.01] Fix tool access rights and forwarding Commit: 30750c32e4817de18aecba8bc4f523f4369e7292 https://github.com/galaxyproject/galaxy/commit/30750c32e4817de18aecba8bc4f5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py Log Message: ----------- Merge pull request #1880 from dannon/fix_migration_0131_mysql [16.01] Fixes to subworkflow migration 0131 Commit: 58346169dfbe89f845a3f2317bde514c3e65f79f https://github.com/galaxyproject/galaxy/commit/58346169dfbe89f845a3f2317bde… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Fix dom duplication Commit: fa1414759e604073bc45fe3f2b15dc9f21c72c4c https://github.com/galaxyproject/galaxy/commit/fa1414759e604073bc45fe3f2b15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1976 from guerler/fix_ui_000 [16.01] Fix dom duplication Commit: 133f77413e9fb933ec1964d279408c1fb8846db4 https://github.com/galaxyproject/galaxy/commit/133f77413e9fb933ec1964d27940… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Fix 'Resend verification' link in inactive user message box which would display as [Object object] Commit: fef166545c36df5c7ba73924c7b0ea4e1d44ec82 https://github.com/galaxyproject/galaxy/commit/fef166545c36df5c7ba73924c7b0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Layout: Fix optional panel rendering and associated inline css Commit: dd476fc42c57b5e17d8e1e342d7a597b986b6b3e https://github.com/galaxyproject/galaxy/commit/dd476fc42c57b5e17d8e1e342d7a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1978 from carlfeberhard/release_16.01 [16.01] Fixes to page.js Commit: 79d16f71f9064c1f35a0bf4c7de1191872398428 https://github.com/galaxyproject/galaxy/commit/79d16f71f9064c1f35a0bf4c7de1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/masthead.js M static/scripts/layout/page.js Log Message: ----------- Fix scratchbook Commit: 9eb1db82ca4bbae598d0070de8da78172ca90fa9 https://github.com/galaxyproject/galaxy/commit/9eb1db82ca4bbae598d0070de8da… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Do not convert spaces to tabs when importing datasets into a library. Reported (with fix provided) by Fabien Mareuil in http://dev.list.galaxyproject.org/automatic-adding-of-a-tab-in-a-fastq-head… Commit: cf16b1d692d0e96f3d0aa4d2cf0f9f52c8dd7bb3 https://github.com/galaxyproject/galaxy/commit/cf16b1d692d0e96f3d0aa4d2cf0f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1985 from nsoranzo/release_16.01_lda_fixes [16.01] Do not convert spaces to tabs when importing datasets into a library. Commit: 8e41fda58a6b8def4f261121269c321e5dd8ff34 https://github.com/galaxyproject/galaxy/commit/8e41fda58a6b8def4f261121269c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/masthead.js M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1984 from guerler/fix_scratchbook_000 [16.01] Fix scratchbook Commit: 21e71a9b46b9f4cd90b8fe5023981460775e4b59 https://github.com/galaxyproject/galaxy/commit/21e71a9b46b9f4cd90b8fe502398… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Merge pull request #1905 from dannon/library_errors [16.01] Encoding in libraries Commit: b51bdd06b189baccab235def65d15a69c761ac28 https://github.com/galaxyproject/galaxy/commit/b51bdd06b189baccab235def65d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Basepanels don't have Galaxy object, causing failures in views like published tracks, etc., when resource urls are generated incorrectly Commit: dede9459b019ceb1212f4f152b4108632f892384 https://github.com/galaxyproject/galaxy/commit/dede9459b019ceb1212f4f152b41… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Merge pull request #2003 from dannon/trackster_debugging [16.01] Fix shared viz (and other base_panels.mako displays) early URL generation. Commit: dc49a9cbc1b24fb4abd1c5b98eba433218a3042d https://github.com/galaxyproject/galaxy/commit/dc49a9cbc1b24fb4abd1c5b98eba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Fix unbound error that is possible if using tool bursting. Commit: 8accc56132ff5863ff4d0e3127d9aa5c8fc419d4 https://github.com/galaxyproject/galaxy/commit/8accc56132ff5863ff4d0e3127d9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #2009 from jmchilton/execute_params_fix [16.01] Fix unbound error that is possible if using tool bursting. Commit: 7d1b525682c9dd0786b7ccca23c3b0695b3c0751 https://github.com/galaxyproject/galaxy/commit/7d1b525682c9dd0786b7ccca23c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/webapps/galaxy/api/datasets.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- The response from dataproviders here can return data===null in addition to being simply undefined. This corrects the logic shortcutting and prevents errors like 'Cannot read property 'min' of null' Commit: 425f0daa2d9030a36c2af5b144a4d563542153a2 https://github.com/galaxyproject/galaxy/commit/425f0daa2d9030a36c2af5b144a4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/webapps/galaxy/api/datasets.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Merge pull request #2014 from dannon/trackster_dataprovider_fix [16.01] Fix trackster erroring when fetching data from regions or datasets with no content. Commit: 4f2661a1e9b3179b8df7ff773b71d15aa756dd8d https://github.com/galaxyproject/galaxy/commit/4f2661a1e9b3179b8df7ff773b71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix PJA creation in tool bursting threads. Potentially fixes #1657. Commit: 948a4aa55bf9409a69b7af75b9987d60f09890f3 https://github.com/galaxyproject/galaxy/commit/948a4aa55bf9409a69b7af75b998… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2013 from jmchilton/fix_1657_stable [16.01] Fix PJA creation in tool bursting threads. Commit: e6d3529b4c85708bb0b1fbea32e8ce36921e60e1 https://github.com/galaxyproject/galaxy/commit/e6d3529b4c85708bb0b1fbea32e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- [16.01] Fix for running jobs when metadata tool is not in toolbox. Happens when -installed or -migrated are passed into run_tests.sh because of the way the tool shed hacks up Galaxy's tool config. Commit: 68ca4b9237a5c44a88377c32cecc9014013c32cc https://github.com/galaxyproject/galaxy/commit/68ca4b9237a5c44a88377c32cecc… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #2024 from jmchilton/metadata_tool_fix [16.01] Fix for running jobs when metadata tool is not in toolbox. Commit: 7b2a2b1ef1154699d064482ffc41b4d3b6efdabb https://github.com/galaxyproject/galaxy/commit/7b2a2b1ef1154699d064482ffc41… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/unit/test_lazy_process.py Log Message: ----------- [16.01] More robust test_lazy_process. Hopefully this will fix a transiently failing test (I've only seen in fail on OS X). Commit: 7c94ac8d93b8c7fd2dd2f18d3939fa23a1589ad9 https://github.com/galaxyproject/galaxy/commit/7c94ac8d93b8c7fd2dd2f18d3939… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/unit/test_lazy_process.py Log Message: ----------- Merge pull request #2032 from jmchilton/lazy_process_test_fix [16.01] More robust test_lazy_process. Compare: https://github.com/galaxyproject/galaxy/compare/5677c2ee4fce...7c94ac8d93b8

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[galaxyproject/galaxy] 7d1b52: The response from dataproviders here can return da...
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7d1b525682c9dd0786b7ccca23c3b0695b3c0751 https://github.com/galaxyproject/galaxy/commit/7d1b525682c9dd0786b7ccca23c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/webapps/galaxy/api/datasets.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- The response from dataproviders here can return data===null in addition to being simply undefined. This corrects the logic shortcutting and prevents errors like 'Cannot read property 'min' of null' Commit: 425f0daa2d9030a36c2af5b144a4d563542153a2 https://github.com/galaxyproject/galaxy/commit/425f0daa2d9030a36c2af5b144a4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/webapps/galaxy/api/datasets.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Merge pull request #2014 from dannon/trackster_dataprovider_fix [16.01] Fix trackster erroring when fetching data from regions or datasets with no content. Commit: 4f2661a1e9b3179b8df7ff773b71d15aa756dd8d https://github.com/galaxyproject/galaxy/commit/4f2661a1e9b3179b8df7ff773b71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix PJA creation in tool bursting threads. Potentially fixes #1657. Commit: 948a4aa55bf9409a69b7af75b9987d60f09890f3 https://github.com/galaxyproject/galaxy/commit/948a4aa55bf9409a69b7af75b998… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2013 from jmchilton/fix_1657_stable [16.01] Fix PJA creation in tool bursting threads. Commit: e6d3529b4c85708bb0b1fbea32e8ce36921e60e1 https://github.com/galaxyproject/galaxy/commit/e6d3529b4c85708bb0b1fbea32e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- [16.01] Fix for running jobs when metadata tool is not in toolbox. Happens when -installed or -migrated are passed into run_tests.sh because of the way the tool shed hacks up Galaxy's tool config. Commit: 68ca4b9237a5c44a88377c32cecc9014013c32cc https://github.com/galaxyproject/galaxy/commit/68ca4b9237a5c44a88377c32cecc… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #2024 from jmchilton/metadata_tool_fix [16.01] Fix for running jobs when metadata tool is not in toolbox. Commit: 7b2a2b1ef1154699d064482ffc41b4d3b6efdabb https://github.com/galaxyproject/galaxy/commit/7b2a2b1ef1154699d064482ffc41… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/unit/test_lazy_process.py Log Message: ----------- [16.01] More robust test_lazy_process. Hopefully this will fix a transiently failing test (I've only seen in fail on OS X). Commit: 7c94ac8d93b8c7fd2dd2f18d3939fa23a1589ad9 https://github.com/galaxyproject/galaxy/commit/7c94ac8d93b8c7fd2dd2f18d3939… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/unit/test_lazy_process.py Log Message: ----------- Merge pull request #2032 from jmchilton/lazy_process_test_fix [16.01] More robust test_lazy_process. Commit: d15b1030c5bad75f41e46bdc38d860ebb35bd4fe https://github.com/galaxyproject/galaxy/commit/d15b1030c5bad75f41e46bdc38d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/workflow/modules.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js M test/unit/test_lazy_process.py Log Message: ----------- Merge, rebuild. Compare: https://github.com/galaxyproject/galaxy/compare/d693aaf624ce...d15b1030c5ba

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[galaxyproject/galaxy] 7b2a2b: [16.01] More robust test_lazy_process.
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 7b2a2b1ef1154699d064482ffc41b4d3b6efdabb https://github.com/galaxyproject/galaxy/commit/7b2a2b1ef1154699d064482ffc41… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/unit/test_lazy_process.py Log Message: ----------- [16.01] More robust test_lazy_process. Hopefully this will fix a transiently failing test (I've only seen in fail on OS X). Commit: 7c94ac8d93b8c7fd2dd2f18d3939fa23a1589ad9 https://github.com/galaxyproject/galaxy/commit/7c94ac8d93b8c7fd2dd2f18d3939… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/unit/test_lazy_process.py Log Message: ----------- Merge pull request #2032 from jmchilton/lazy_process_test_fix [16.01] More robust test_lazy_process. Compare: https://github.com/galaxyproject/galaxy/compare/68ca4b9237a5...7c94ac8d93b8

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[galaxyproject/galaxy] 3cb2bb: Start work on synchronizing functional test driver...
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3cb2bb1c359a7dd9f66e07e04490262b753e83e6 https://github.com/galaxyproject/galaxy/commit/3cb2bb1c359a7dd9f66e07e04490… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py A test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Start work on synchronizing functional test drivers. - Tweak paths in same way. - Don't write tool shed temp files to GALAXY_ROOT - respect /tmp. - Build identical loggers. Commit: 9d1a54e88c9ce55e9473cfd823c2d1ebe5cd7b8e https://github.com/galaxyproject/galaxy/commit/9d1a54e88c9ce55e9473cfd823c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/tool_shed/functional_tests.py Log Message: ----------- Synchronize main() handling between functional test driver scripts. Commit: 3369dfafa0ed12886d1adea7ea2155fc3ebe31aa https://github.com/galaxyproject/galaxy/commit/3369dfafa0ed12886d1adea7ea21… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Synchronize a bunch of test launch and nose configure stuff. Commit: 55297b75e10a49ffe081087e5a7d5a1140af38ff https://github.com/galaxyproject/galaxy/commit/55297b75e10a49ffe081087e5a7d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Sync code for retrieving prepopulated databases. Commit: 173d98484bc50cec7f755d85c46ae941b1e5bc50 https://github.com/galaxyproject/galaxy/commit/173d98484bc50cec7f755d85c46a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/tool_shed/functional_tests.py Log Message: ----------- Eliminate always True variable to simplify test driver logic. For now, always serve static content with these tests. Commit: d60fe9f5aa3bb264d2a1873aaa383ee9657487ad https://github.com/galaxyproject/galaxy/commit/d60fe9f5aa3bb264d2a1873aaa38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Synchronize static configuration stuff. Commit: b7c75f20a5bfb625d01c85d1821d11ff50fb5949 https://github.com/galaxyproject/galaxy/commit/b7c75f20a5bfb625d01c85d1821d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Eliminate duplication in waiting for HTTP servers in test drivers. Commit: 103098c7e421043b79b3629c8c6f61b1ee792fb1 https://github.com/galaxyproject/galaxy/commit/103098c7e421043b79b3629c8c6f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- De-duplicate and simplify launching a webapp for functional tests. Commit: d0ee53f8017ef4fde97efb05ee82b4f95d037b62 https://github.com/galaxyproject/galaxy/commit/d0ee53f8017ef4fde97efb05ee82… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- Simplify ignore_files logic in scripts/functional_tests.py. These details are taken care of by run_tests.sh. Commit: 34f154d92e162bcb56e4ffa9524bdaae4cb4f140 https://github.com/galaxyproject/galaxy/commit/34f154d92e162bcb56e4ffa9524b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py A test/functional/tools/upload_tool_conf.xml Log Message: ----------- Rework upload tool. Commit: 8c857694f3792520950cbdf6a2dcd5df4e7f332c https://github.com/galaxyproject/galaxy/commit/8c857694f3792520950cbdf6a2dc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Synchronize locale handling for test drivers. Commit: e0a9d6b67fd9a7063b292a7f2ede04ae70c470fc https://github.com/galaxyproject/galaxy/commit/e0a9d6b67fd9a7063b292a7f2ede… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- De-duplicate code for setting up Galaxy database. Commit: 887edb647b5175c9e24a3e432a0ef38fe84ed02c https://github.com/galaxyproject/galaxy/commit/887edb647b5175c9e24a3e432a0e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/tool_shed/functional_tests.py Log Message: ----------- Remove no longer valid sample references in scripts/functional_tests.py. Commit: fe39f5bf553dd3b2a41b5bfaf960b9a175e8d904 https://github.com/galaxyproject/galaxy/commit/fe39f5bf553dd3b2a41b5bfaf960… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/base/driver_util.py Log Message: ----------- Revise test driver logging so log is available in driver_util. Commit: db37011d700d3ba174033dc68808a9882525268d https://github.com/galaxyproject/galaxy/commit/db37011d700d3ba174033dc68808… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- De-duplicate code for cleaning up test directories. Commit: 91a71068979ca19763ca18cde73d350a37546ec4 https://github.com/galaxyproject/galaxy/commit/91a71068979ca19763ca18cde73d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/tool_shed/functional_tests.py Log Message: ----------- Remove unused proxy port stuff in test drivers. Commit: ce9a55207fe5f467a71e03fb3f364fc08ed4f943 https://github.com/galaxyproject/galaxy/commit/ce9a55207fe5f467a71e03fb3f36… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/tool_shed/functional_tests.py Log Message: ----------- Remove unused or un-useful code from tool shed test driver. Commit: 97070b4b532b2fd8f11276d8056dc036a4155d50 https://github.com/galaxyproject/galaxy/commit/97070b4b532b2fd8f11276d8056d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Move tool shed test data handling into driver_util. Commit: fd46a1f987fe6c9fa95b62e9b21bc00273c36fe9 https://github.com/galaxyproject/galaxy/commit/fd46a1f987fe6c9fa95b62e9b21b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Move tool_conf logic for drivers into driver_util. - Don't generate a tool_conf for upload in tool shed tests - just use the fixed one setup for framework tools. - Move every mention of that directory and files into constants in driver_util. Commit: 9804eb56bf6d4ba4df0ec787501366d1dab8102e https://github.com/galaxyproject/galaxy/commit/9804eb56bf6d4ba4df0ec7875013… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- De-duplicate test driver logic for install database connection. Commit: 72716750d1f6ba1b91781144d12c6fd90ce51bca https://github.com/galaxyproject/galaxy/commit/72716750d1f6ba1b91781144d12c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- Simplify GALAXY_TEST_SAVE logic... ... script/functional_tests.py was just pulling it out of the environ and sticking it back in - made no sense. Commit: 75f0cb470c69d05ad69ff4e4d96d83ff036940cd https://github.com/galaxyproject/galaxy/commit/75f0cb470c69d05ad69ff4e4d96d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/tool_shed/functional_tests.py Log Message: ----------- Eliminate ability to set Galaxy tool path for tool shed tests... Makes sense in Galaxy tests but not for tool shed tests, I see no reason for this extension point. If it is needed GALAXY_CONFIG_TOOL_PATH will work instead of TOOL_SHED_TEST_TOOL_PATH. Commit: 16c0ae216aa5414b4a9d19c53b47a9d94fc6e3af https://github.com/galaxyproject/galaxy/commit/16c0ae216aa5414b4a9d19c53b47… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- De-duplicate XXX_TEST_DBPATH logic. Commit: c2b260539b58291c6a207f1d779ac8465302c831 https://github.com/galaxyproject/galaxy/commit/c2b260539b58291c6a207f1d779a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M run_tests.sh Log Message: ----------- Start list of environment variables used for testing. Commit: e86fa83e863b7da20ba1cc1b2ce96bec6dd76896 https://github.com/galaxyproject/galaxy/commit/e86fa83e863b7da20ba1cc1b2ce9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Begin work on test driver function for setting up Galaxy config. Commit: a18cbd5930cc21a3997cdc0d69fcf4f0ba53ea55 https://github.com/galaxyproject/galaxy/commit/a18cbd5930cc21a3997cdc0d69fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- De-duplicate test driver - move more Galaxy config into common method. Commit: ec3f0506c9ee791b8c2e3ba22eb158e14375a267 https://github.com/galaxyproject/galaxy/commit/ec3f0506c9ee791b8c2e3ba22eb1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/tool_shed/functional_tests.py Log Message: ----------- Remove unused config variable from test drivers. Commit: e309c7f6ebaf7b29a00902af9fb71fd69fac4070 https://github.com/galaxyproject/galaxy/commit/e309c7f6ebaf7b29a00902af9fb7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Make XXX_TEST_DBPATH and XXX_TEST_DB_TEMPLATE generic and shared with shed. Now the variable TOOL_SHED_TEST_DB_TEMPLATE works as one might expect like GALAXY_TEST_DB_TEMPLATE. Commit: 7eab64eed0e06872d3eb209f68f1f32667dda65e https://github.com/galaxyproject/galaxy/commit/7eab64eed0e06872d3eb209f68f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/tool_shed/functional_tests.py Log Message: ----------- Remove unused shed tool dependency logic in tool shed tests. Commit: dcbdcbe081bdeebdc8e2539007d210db267dcb37 https://github.com/galaxyproject/galaxy/commit/dcbdcbe081bdeebdc8e2539007d2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Unify tool dependency dir handling between test driver scripts. Commit: 5af770972d47fcabf7d2c062fa9b4f1739ec146a https://github.com/galaxyproject/galaxy/commit/5af770972d47fcabf7d2c062fa9b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/tool_shed/functional_tests.py Log Message: ----------- Fix naming and comment best practices for test driver scripts. Commit: 6b278478d30f03298ac9cc8a5ebeaf6c2f1bd04f https://github.com/galaxyproject/galaxy/commit/6b278478d30f03298ac9cc8a5ebe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Move tool_path logic into setup_galaxy_config. Commit: 18c366c6d064147a118ab8397a1c2cbc3b0ec4d0 https://github.com/galaxyproject/galaxy/commit/18c366c6d064147a118ab8397a1c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/tool_shed/functional_tests.py Log Message: ----------- Remove now unused variable and documentation. Commit: 88ce7a2fa4ac7a5c44e08ca4dcea9fcfe257f406 https://github.com/galaxyproject/galaxy/commit/88ce7a2fa4ac7a5c44e08ca4dcea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/tool_shed/functional_tests.py Log Message: ----------- Remove unused branch for tool shed test driver code. Commit: d03651f4ef7c5e5540d3a23c84b38e840900b500 https://github.com/galaxyproject/galaxy/commit/d03651f4ef7c5e5540d3a23c84b3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Move more shared galaxy configuration into driver_util. Commit: e7b5293534d6cf9a704b9d295271abffda0f3c5d https://github.com/galaxyproject/galaxy/commit/e7b5293534d6cf9a704b9d295271… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Refactor toolbox hacks used by installed and migration tool tests out... into driver_util. This greatly simplifies the code structure of scripts/functional_tests.py's main method. Add description of GALAXY_TEST_SHED_TOOL_CONF and some documentation to all of this. Commit: 651b91248b350de951c95e5c2bd8edd6e517b9d2 https://github.com/galaxyproject/galaxy/commit/651b91248b350de951c95e5c2bd8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- Restructure scripts/functional_test.py's main() to reflect recent simplifications. Commit: be0107b6204b5b47b9c6e8ea3196a893d4409c05 https://github.com/galaxyproject/galaxy/commit/be0107b6204b5b47b9c6e8ea3196… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- Simplify test tool_data_table_config logic. Added with https://github.com/galaxyproject/galaxy/commit/246ea04cc7ee1d0d470a514302bf…. Commit: 528b74ca1e470499d53719ccbeb8acd78002ee33 https://github.com/galaxyproject/galaxy/commit/528b74ca1e470499d53719ccbeb8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- Remove unused test job conf stuff. Not that this wouldn't be useful - it would be but it wasn't wired up to do anything currently. Commit: fe460008faf33a673185672ee2f34b26b8878ea5 https://github.com/galaxyproject/galaxy/commit/fe460008faf33a673185672ee2f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- More work on syncrhonized test database configuration... for test drivers. Commit: 2729699bf69c7b4ca6750fbc628f4eb147c12717 https://github.com/galaxyproject/galaxy/commit/2729699bf69c7b4ca6750fbc628f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Further unification of how to setup Galaxy databases for testing. Reuse setup_galaxy_config for this task. Commit: ec0a12384994774522380165302934531ca12901 https://github.com/galaxyproject/galaxy/commit/ec0a123849947745223801653029… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/tool_shed/functional_tests.py Log Message: ----------- Unify and simplify how Galaxy is launched across test drivers. Commit: ecbb7326658ee4f400be865cfc7d3a4baf199b39 https://github.com/galaxyproject/galaxy/commit/ecbb7326658ee4f400be865cfc7d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Move construction of test driver app objects into driver_util. This de-duplicates some of the Galaxy stuff and makes the tool shed stuff look very uniform. Commit: ee537a119b381b78ce1d58769970c0302fe5b684 https://github.com/galaxyproject/galaxy/commit/ee537a119b381b78ce1d58769970… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- Restructure to simplify the main() in scripts/functional_tests.py. Previously this was entering a conditional on the same condition twice. This simplifies this to just do that once and makes the galaxy and tool shed driver code look more similar with respect to launching a Galaxy webapp. Commit: 0f362294000b005073c8167ac553c88403316951 https://github.com/galaxyproject/galaxy/commit/0f362294000b005073c8167ac553… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Unify and simplify configuration and launch of test web servers. - Sync up the logic for reading and setting GALAXY_TEST_HOST, GALAXY_TEST_PORT, TOOL_SHED_TEST_HOST, and TOOL_SHED_TEST_PORT. - Setup one high level method for taking a Galaxy-style "app" and creating a webapp from a factory method and then launching a paste server for that entity respecting the above variables. Commit: 671b6933dd602e47ba8d99ba8e39e0419dde51f3 https://github.com/galaxyproject/galaxy/commit/671b6933dd602e47ba8d99ba8e39… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- De-duplicate test driver logic for closing apps and stopping severs... Commit: 33d312b906ac4c50554fb1bff1e0dc39bdaea077 https://github.com/galaxyproject/galaxy/commit/33d312b906ac4c50554fb1bff1e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- [16.01] Fix for running jobs when metadata tool is not in toolbox. Happens when -installed or -migrated are passed into run_tests.sh because of the way the tool shed hacks up Galaxy's tool config. Commit: 3c47105732febe5ca69a6ba20df875177fb7a31a https://github.com/galaxyproject/galaxy/commit/3c47105732febe5ca69a6ba20df8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Fix shed tool test file shed_tools_dict handling. Instead of writing it below GALAXY_ROOT (which it shouldn't do at all) - add to the temp directory managed for the test so that special clean up logic isn't required for it. The global switch GALAXY_TEST_NO_CLEANUP can be used to recover the state of this file if needed now also. Commit: d657855b7f075bbcc1b2c7aa7f2e7b679ff1a6dd https://github.com/galaxyproject/galaxy/commit/d657855b7f075bbcc1b2c7aa7f2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/config.py M scripts/functional_tests.py Log Message: ----------- Remove unused test_conf variable. Commit: 65806641c1aa0260923f0733bff7b1f81304d3a3 https://github.com/galaxyproject/galaxy/commit/65806641c1aa0260923f0733bff7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Simplify(?) tool data table config logic at lest in scripts/functional_tests.py. Commit: 5b826a0839f6545ee94b3c3cd3ff710e5b8747f3 https://github.com/galaxyproject/galaxy/commit/5b826a0839f6545ee94b3c3cd3ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Move more galaxy config logic into driver_util. This time for galaxy master API key. Commit: e356c80c02e23ff42d0c3ba0b94575865793168c https://github.com/galaxyproject/galaxy/commit/e356c80c02e23ff42d0c3ba0b945… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Move enable_tool_shed_check test driver logic into driver_util. Commit: 1b80e6e8d1e4e2ecddaac4b37337e7cfd7016d57 https://github.com/galaxyproject/galaxy/commit/1b80e6e8d1e4e2ecddaac4b37337… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Move another galaxy config (clean up job) into driver_util. Commit: 3c72c2129bd5a92e4fe0722e50e5f6d31c5d3737 https://github.com/galaxyproject/galaxy/commit/3c72c2129bd5a92e4fe0722e50e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Move data_manager_config_file setup into driver_util. Seems it doesn't hurt tool shed tests to configure this. Commit: 362194b2c023dc54cd220038a529ae411e6a2ea3 https://github.com/galaxyproject/galaxy/commit/362194b2c023dc54cd220038a529… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Cleanup logic for GALAXY_TEST_TMP_DIR add docs. Commit: 3546bdf22b0defd8236e184331a041bb3f4f8840 https://github.com/galaxyproject/galaxy/commit/3546bdf22b0defd8236e184331a0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- Cleanup Galaxy tempdir handling in driver util. Commit: a8033a543baa7f919e0d7c061baa62263c7f633e https://github.com/galaxyproject/galaxy/commit/a8033a543baa7f919e0d7c061baa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Move galaxy test data manager setup logic into driver_util. Commit: f3c757ff1c5349ef683a092cc8b758b93cf84614 https://github.com/galaxyproject/galaxy/commit/f3c757ff1c5349ef683a092cc8b7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Move more galaxy config into driver_util... Handle logging and enabling of beta formats consistently across driver scripts. Commit: e1aa0b3acc83ef219752cad75b262b71cd232199 https://github.com/galaxyproject/galaxy/commit/e1aa0b3acc83ef219752cad75b26… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Simplify/unify tool conf handling logic across two driver util... Commit: 586fa6801b9d7cec1db1ceaf5488f66dadfbc183 https://github.com/galaxyproject/galaxy/commit/586fa6801b9d7cec1db1ceaf5488… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Move yet more logic into driver_util to reduce driver method for scripts/functional_tests.py. Commit: 93cfdff9103dc4216893ed494e22bdc2d870ff22 https://github.com/galaxyproject/galaxy/commit/93cfdff9103dc4216893ed494e22… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Eliminate last custom config value setup in scripts/functional_tests.py... ... outside of driver_util. So now we can just use the driver_util config object. Commit: 8fdecbb3bf5c6ba02393531117c3e2160e5ea22b https://github.com/galaxyproject/galaxy/commit/8fdecbb3bf5c6ba02393531117c3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- Another simplifcation to method structure in scripts/functional_tests.py. Commit: fc1861c4d9ab8b7ecae5b959c3e59f33146e6802 https://github.com/galaxyproject/galaxy/commit/fc1861c4d9ab8b7ecae5b959c3e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py Log Message: ----------- Move "with framework test tools" logic out of nose driver and into run_tests. Commit: 915b7edcb7b0120d4690c3fa59b97e7dbdcb4a2a https://github.com/galaxyproject/galaxy/commit/915b7edcb7b0120d4690c3fa59b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py M test/functional/workflow.py Log Message: ----------- Unify and simplify script driver argument processing. Commit: eac6c10ec93a6f5a610a9d07d1e7601049f4f7cf https://github.com/galaxyproject/galaxy/commit/eac6c10ec93a6f5a610a9d07d1e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py M test/base/twilltestcase.py Log Message: ----------- Allow running Galaxy tests on an existing external instance. Commit: 8538c0ed774c89416c80e8688723238386a90736 https://github.com/galaxyproject/galaxy/commit/8538c0ed774c89416c80e8688723… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Add comment describing metadata_tool hack. Commit: 6faef4df2ec5a1b189594bf528debd521e869d96 https://github.com/galaxyproject/galaxy/commit/6faef4df2ec5a1b189594bf528de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Introduce a TestDriver class to reduce duplication between test drivers. Classes allow de-duplicating logic and state organization in a different way than methods. Use a common setup, run, tear down paradigm for these tests. Commit: 05a2f441261c176dfe2cc802d4743aad6652a9ea https://github.com/galaxyproject/galaxy/commit/05a2f441261c176dfe2cc802d474… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Separate different style Galaxy testing behaviors into classes. Commit: b8ecf36f2ae52af1cda3eac64f53400e56e895db https://github.com/galaxyproject/galaxy/commit/b8ecf36f2ae52af1cda3eac64f53… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M run_tests.sh Log Message: ----------- Improve testing environment variable and CLI documentation. Document many more variables and improve documentation of what is there. Include fixes recommended by @nsoranzo. Commit: d693aaf624ce1ca1f501e3ed98fe2ad74ca0836d https://github.com/galaxyproject/galaxy/commit/d693aaf624ce1ca1f501e3ed98fe… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/webapps/tool_shed/config.py M run_tests.sh M scripts/functional_tests.py A test/base/driver_util.py M test/base/twilltestcase.py A test/functional/tools/upload_tool_conf.xml M test/functional/workflow.py M test/tool_shed/functional_tests.py Log Message: ----------- Merge pull request #2016 from jmchilton/test_driver_cleanup Functional Test Drivers Overhaul Compare: https://github.com/galaxyproject/galaxy/compare/2687002a27ad...d693aaf624ce

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