December 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 2db85b: Swaps nametags to a div, sets a max-height (intent...
by GitHub 19 Dec '17

19 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2db85b3dd9ede81691ebff7d72d58acfa38524c7 https://github.com/galaxyproject/galaxy/commit/2db85b3dd9ede81691ebff7d72d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/style/less/history.less M static/style/blue/base.css Log Message: ----------- Swaps nametags to a div, sets a max-height (intentionally such that it clips a second line of tags, promoting curiosity to find the scroll Commit: 79465fd13cb2902aa3bb9f284e6e3fc0c86460d1 https://github.com/galaxyproject/galaxy/commit/79465fd13cb2902aa3bb9f284e6e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js Log Message: ----------- Add tooltip with number of nametags. Commit: 067d1c2abe391fe5d3f1794ce8945d9e4ea1b4e7 https://github.com/galaxyproject/galaxy/commit/067d1c2abe391fe5d3f1794ce894… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Constrain nametags in select2 boxes to 5 matching tags. Commit: cb635d22fb2ad93d13fe67bef7865cf3102f7f7f https://github.com/galaxyproject/galaxy/commit/cb635d22fb2ad93d13fe67bef786… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Add an 'extra tags' block in the select interface since we're so limited on space. Commit: 21c18b5a30243c7b107bdc0168115da24e2f7fb3 https://github.com/galaxyproject/galaxy/commit/21c18b5a30243c7b107bdc016811… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js Log Message: ----------- Refactor tag templating, changes order of operations and filtering to improve performance issues noticeable with many tags Commit: ee1655307ddb152f8289f42e3fa67e371fd33288 https://github.com/galaxyproject/galaxy/commit/ee1655307ddb152f8289f42e3fa6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Attempt to fix matched tags counting in select2 (internal state is shared and wonky here). Some cleanup to help see what's going on. Commit: c389a84d71caf5850d101940c132580a17059673 https://github.com/galaxyproject/galaxy/commit/c389a84d71caf5850d101940c132… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Fix select2 tag filtering, counting, indication of extra tags. Commit: 35e1d18c06def858a8ee96986074eb14e2fccb66 https://github.com/galaxyproject/galaxy/commit/35e1d18c06def858a8ee96986074… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- More fat arrow functions and elimination of self in uiselectdefault Commit: 3fcc3c970078f5adc789569a1b80ef47e9c206e2 https://github.com/galaxyproject/galaxy/commit/3fcc3c970078f5adc789569a1b80… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: A .ci/check_py3_compatibility.sh M .ci/first_startup.sh R .ci/py3_sources.txt M .travis.yml M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.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/form/form-repeat.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/library/library-dataset-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-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M 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config/openid_conf.xml.sample M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M contrib/galaxy.fedora-init M contrib/nagios/check_galaxy.py A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/cram_to_bam.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M 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scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/scripts/bundled/admin.bundled.js M 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static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako R templates/common/select_template.mako R templates/common/template_common.mako M templates/display_common.mako R templates/form.mako R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako M templates/user/register.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/populators.py M test/functional/webhooks/phdcomics/helper/__init__.py A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py M test/integration/test_job_resubmission.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py A test/unit/tools/test_tool_validation.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into tag_limit_size Commit: d2d0e4169c93223f645a5e647862a105d9f93d47 https://github.com/galaxyproject/galaxy/commit/d2d0e4169c93223f645a5e647862… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Rebuild client after upstream/dev merge. Commit: 62a3a5c5968c5eeca27fd9e25f05bd718666a70b https://github.com/galaxyproject/galaxy/commit/62a3a5c5968c5eeca27fd9e25f05… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/history.less M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Merge pull request #5155 from dannon/tag_limit_size Dataset hashtag display improvements Compare: https://github.com/galaxyproject/galaxy/compare/be44b9b5eb5c...62a3a5c5968c

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[galaxyproject/galaxy] 7a1d7f: download behaves badly on firefox, preventing righ...
by GitHub 19 Dec '17

19 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7a1d7fcaf4672c0a3ad382b07362b969180797d2 https://github.com/galaxyproject/galaxy/commit/7a1d7fcaf4672c0a3ad382b07362… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- download behaves badly on firefox, preventing right clicking to copy the url here Commit: 0ab21a2f4ed195711d0a55fa369dbc2fc09b123a https://github.com/galaxyproject/galaxy/commit/0ab21a2f4ed195711d0a55fa369d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- We preventdefault on this anyway, so the void(0) doesn't do anything. This allows right click copy on primary dataset regardless of whether or not there are extra meta files. Commit: ab084ffd4b9a797d3ccee35ffcdc1953970b88a0 https://github.com/galaxyproject/galaxy/commit/ab084ffd4b9a797d3ccee35ffcdc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Convert download blob to template literals instead of array concats. Commit: d3d6e723539618bea80a9f18b1895cc82aee280b https://github.com/galaxyproject/galaxy/commit/d3d6e723539618bea80a9f18b189… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Use the local var for urls.download Commit: ca8ec7395860f82a3622a5c21821a9341a3e1267 https://github.com/galaxyproject/galaxy/commit/ca8ec7395860f82a3622a5c21821… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: A .ci/check_py3_compatibility.sh M .ci/first_startup.sh R .ci/py3_sources.txt M .travis.yml M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-list.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/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/job_conf.xml.sample_advanced M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M contrib/galaxy.fedora-init M contrib/nagios/check_galaxy.py M doc/source/admin/production.md M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/workflows.py M lib/galaxy/openid/providers.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/util/biostar.py M lib/galaxy/util/permutations.py M lib/galaxy/util/script.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.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/history.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.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 R scripts/api/form_create_from_xml.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py R scripts/api/sequencer_configuration_create.py M scripts/build_universe_config.py M scripts/data_libraries/build_lucene_index.py M scripts/galaxy-main M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.pages.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js R static/scripts/libs/vue.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/user/user-preferences.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js M static/scripts/viz/trackster.js M static/scripts/viz/visualization.js R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/repository_review/grid.mako M test/api/test_tools_upload.py M test/base/driver_util.py M test/base/populators.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_tool_form.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into download_fixes Commit: d93a2b437972d08c3df38f2c8020b04fb659f696 https://github.com/galaxyproject/galaxy/commit/d93a2b437972d08c3df38f2c8020… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Client-format. Commit: 202305687abcf887541d6d16fc71e96f9afb63d9 https://github.com/galaxyproject/galaxy/commit/202305687abcf887541d6d16fc71… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Rebuild client again. Commit: be44b9b5eb5c87eb79e561c2ebceba75106bf5b3 https://github.com/galaxyproject/galaxy/commit/be44b9b5eb5c87eb79e561c2ebce… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Merge pull request #5125 from dannon/download_fixes Download fixes Compare: https://github.com/galaxyproject/galaxy/compare/1880230e5fdf...be44b9b5eb5c

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[galaxyproject/galaxy] 13c470: related to #4937 - add option to check file permis...
by GitHub 19 Dec '17

19 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 13c4701f947d5f993f74bf9a37aeed9a2766a58b https://github.com/galaxyproject/galaxy/commit/13c4701f947d5f993f74bf9a37ae… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/util/path/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- related to #4937 - add option to check file permissions for the user library imports Commit: b17e7ecffa924bab244128cf91b5bb5c2931c55b https://github.com/galaxyproject/galaxy/commit/b17e7ecffa924bab244128cf91b5… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/util/path/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- fix linting errors Commit: a5c705e6741cb27d305c2eda2b55d457a8cb0a28 https://github.com/galaxyproject/galaxy/commit/a5c705e6741cb27d305c2eda2b55… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- right import order? Commit: 3294eba7c02bebecd61f181584cb5a9e8200cf98 https://github.com/galaxyproject/galaxy/commit/3294eba7c02bebecd61f181584cb… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- fix flake8 errors Commit: 1880230e5fdfffe89f10806debe422d1e3471afe https://github.com/galaxyproject/galaxy/commit/1880230e5fdfffe89f10806debe4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/util/path/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Merge pull request #5154 from scholtalbers/feature/add_permission_check_to_user_lib_import add option to check file permissions for the user library imports Compare: https://github.com/galaxyproject/galaxy/compare/6bf5d663b4f3...1880230e5fdf

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[galaxyproject/galaxy] 09f51f: Upload optimization - eliminate second call to che...
by GitHub 18 Dec '17

18 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09f51f59af9290cd4c93345c6e0f682d32af052e https://github.com/galaxyproject/galaxy/commit/09f51f59af9290cd4c93345c6e0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Upload optimization - eliminate second call to check_binary in upload.py. Commit: cafac19f65020ef29cd8d73d226c43e901318616 https://github.com/galaxyproject/galaxy/commit/cafac19f65020ef29cd8d73d226c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Upload refactor - make link_data_only a bool. Since it is a bool. Commit: 2528ef33cdd4f7b5b07c9de6e6adc5a35a7851b3 https://github.com/galaxyproject/galaxy/commit/2528ef33cdd4f7b5b07c9de6e6ad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Upload refactor - supply reasonable defaults to sniff methods making it easier to use. Commit: 7e1bff7d69b0bc25056c6e2b18ccd2a689654c0e https://github.com/galaxyproject/galaxy/commit/7e1bff7d69b0bc25056c6e2b18cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Upload refactor - change upload.py to use exceptions. Make decomposing and reuse of this easier downstream and feels cleaner to me. Commit: 6bf5d663b4f3cc448b25df50f486dfb383fbd267 https://github.com/galaxyproject/galaxy/commit/6bf5d663b4f3cc448b25df50f486… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M lib/galaxy/datatypes/sniff.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5229 from jmchilton/upload_refactor Refactor upload.py toward reuse Compare: https://github.com/galaxyproject/galaxy/compare/21dc271bf014...6bf5d663b4f3

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[galaxyproject/galaxy] 1253ef: Adds k8s support for CPU and memory resource setti...
by GitHub 18 Dec '17

18 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1253eff2f5737183dbd702382534e920b32b2270 https://github.com/galaxyproject/galaxy/commit/1253eff2f5737183dbd702382534… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Adds k8s support for CPU and memory resource settings. Commit: 3145509b7a870d3ff06a2ad6037d5c5ce20eb559 https://github.com/galaxyproject/galaxy/commit/3145509b7a870d3ff06a2ad6037d… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Avoids cleaning up container name when destination id is not str, probably applicable for dynamic destinations. Commit: ca2e121fa67443797436189387e7ff6733cfc6b9 https://github.com/galaxyproject/galaxy/commit/ca2e121fa67443797436189387e7… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Minor code formatting for tox tests Commit: 7654935f031afdd852df3a800f2f012a89bdb08f https://github.com/galaxyproject/galaxy/commit/7654935f031afdd852df3a800f2f… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- k8s runner: Adds ability to detect OOMKilled jobs and signals it for resubmission. Commit: ac477fc0216c9c22af659eb9f1de7622c9207779 https://github.com/galaxyproject/galaxy/commit/ac477fc0216c9c22af659eb9f1de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Rework k8s resource request parameters. xref https://github.com/galaxyproject/galaxy/pull/4751#issuecomment-341196780 Commit: ec6011c23815355cdc35acc3246f473d9b2a98d9 https://github.com/galaxyproject/galaxy/commit/ec6011c23815355cdc35acc3246f… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #19 from jmchilton/feature/k8s-resources-requests-limits Rework k8s resource request parameters and docs Commit: 21dc271bf014889de3c4b2a3c1124c55811e4e22 https://github.com/galaxyproject/galaxy/commit/21dc271bf014889de3c4b2a3c112… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #4751 from phnmnl/feature/k8s-resources-requests-limits Kubernetes resources requests/limits support Compare: https://github.com/galaxyproject/galaxy/compare/6fc9296d5359...21dc271bf014

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[galaxyproject/galaxy] 0cf38e: Force window jquery access for charts.mako. This ...
by GitHub 17 Dec '17

17 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0cf38e5d52c9eb9120dcc0e6971355402c95128a https://github.com/galaxyproject/galaxy/commit/0cf38e5d52c9eb9120dcc0e69713… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Force window jquery access for charts.mako. This isn't great, but charts *and* the rest of the viz framework are being refactored into bundles that will avoid this hackery. Commit: 6fc9296d5359afecdfff8c3a3b5af9bace14ac6b https://github.com/galaxyproject/galaxy/commit/6fc9296d5359afecdfff8c3a3b5a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-17 (Sun, 17 Dec 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Merge pull request #5210 from dannon/fix_charts_jquery_usage Force window jquery access for charts Compare: https://github.com/galaxyproject/galaxy/compare/02b6ff3492ef...6fc9296d5359

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[galaxyproject/galaxy] f9969e: Remove API scripts for axed APIs.
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f9969ee97acfb985c82c98946f08f522c232e654 https://github.com/galaxyproject/galaxy/commit/f9969ee97acfb985c82c98946f08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: R scripts/api/form_create_from_xml.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py R scripts/api/sequencer_configuration_create.py Log Message: ----------- Remove API scripts for axed APIs. Commit: 02b6ff3492efca986e34c769cc5a4869167332fb https://github.com/galaxyproject/galaxy/commit/02b6ff3492efca986e34c769cc5a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: R scripts/api/form_create_from_xml.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py R scripts/api/sequencer_configuration_create.py Log Message: ----------- Merge pull request #5230 from jmchilton/axed_api_scripts Remove API scripts for axed API (requests, samples...) Compare: https://github.com/galaxyproject/galaxy/compare/94dae3b7de18...02b6ff3492ef

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[galaxyproject/galaxy] d5e39c: Python3: fix list.sort() and sorted() to use `key`...
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5e39c873e9aed6a2b0822b0f7187aa8a73430be https://github.com/galaxyproject/galaxy/commit/d5e39c873e9aed6a2b0822b0f718… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/users.py Log Message: ----------- Python3: fix list.sort() and sorted() to use `key` parameter instead of `cmp` xref. https://github.com/galaxyproject/galaxy/issues/1715 xref. https://github.com/galaxyproject/galaxy/issues/5216 Commit: 94dae3b7de180303427d4bfd0b1cbd4ee183469c https://github.com/galaxyproject/galaxy/commit/94dae3b7de180303427d4bfd0b1c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/users.py Log Message: ----------- Merge pull request #5225 from nsoranzo/fix_sort_sorted Python3: fix list.sort() and sorted() to use `key` parameter instead of `cmp` Compare: https://github.com/galaxyproject/galaxy/compare/6d3eadedbd70...94dae3b7de18

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[galaxyproject/galaxy] e8a128: [17.09] Deployer doc fixes.
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e8a1280f78e1fa19e2173f922f2221ea28279964 https://github.com/galaxyproject/galaxy/commit/e8a1280f78e1fa19e2173f922f22… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- [17.09] Deployer doc fixes. Commit: 42c572f34469ec39a55588504a97f1466c59f332 https://github.com/galaxyproject/galaxy/commit/42c572f34469ec39a55588504a97… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- Merge pull request #5147 from jmchilton/1709_docs_fixes [17.09] Small deployer doc fixes. Commit: 710177f3983d5e66b11c329f699079f67667329c https://github.com/galaxyproject/galaxy/commit/710177f3983d5e66b11c329f6990… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/api/test_tools.py Log Message: ----------- Add API tests for history uploads from URL Commit: a1f399c451715424dcd8d1bc9d9ec804e44de24d https://github.com/galaxyproject/galaxy/commit/a1f399c451715424dcd8d1bc9d9e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Read in stderr form galaxy.json before checking whether stderr and exit code combination should result in a failed job. This should fix https://github.com/galaxyproject/galaxy/issues/5214. Commit: 3d2adcd1f310b94d0d6f6e37e71d1ee74da2fb3d https://github.com/galaxyproject/galaxy/commit/3d2adcd1f310b94d0d6f6e37e71d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Restrict reading tool provided metadata to tools that actually provide metadata Commit: 62a3ff3562c5b9c534794c2d0bb6320de7747135 https://github.com/galaxyproject/galaxy/commit/62a3ff3562c5b9c534794c2d0bb6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Do not assert dataset state in test_gzipped_html_content_blocked_by_default test Commit: 9ee2a7d4577a715137edcf33fd2b0a474a7a8b8d https://github.com/galaxyproject/galaxy/commit/9ee2a7d4577a715137edcf33fd2b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Adjust stderr collection to (Legacy-)ToolProvidedMetadata Commit: b39772011a717dc7c70f1e05dd581b427e33a521 https://github.com/galaxyproject/galaxy/commit/b39772011a717dc7c70f1e05dd58… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M test/base/populators.py Log Message: ----------- Optionally allow dataset populators to fail Commit: 121285b40be5d7233af33b40045a9c2ffb5a9c46 https://github.com/galaxyproject/galaxy/commit/121285b40be5d7233af33b40045a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M tools/data_source/upload.py Log Message: ----------- Let ToolProvidedMetadata interface more directly decide if it has failed outputs. I like this better for three reasons: - Since usually it is scripts producing this JSON - we have the most control at that point for determining the failure and we don't have to deal with an artificial dependency between the tool's stdio and the output. - At some point we could potentially allow some datasets to be ok now even though the job fails. - It is a cleaner interface at the Python level between job finish and output collection IMO (no need for isinstance checking). Commit: d52802d7962c3006b7fe91f43a9d21721187f27c https://github.com/galaxyproject/galaxy/commit/d52802d7962c3006b7fe91f43a9d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #6 from jmchilton/fail_if_galaxy_json_tools_write_to_stderr Let ToolProvidedMetadata interface more directly decide if it has failed outputs. Commit: 3f6c45578e2c4e99fa725054c829e03a9c409a1b https://github.com/galaxyproject/galaxy/commit/3f6c45578e2c4e99fa725054c829… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix dataset spelling (thx @nsoranzo) Commit: 44635eae1dc1aeb511f3cf9c6006aff4219de841 https://github.com/galaxyproject/galaxy/commit/44635eae1dc1aeb511f3cf9c6006… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5217 from mvdbeek/fail_if_galaxy_json_tools_write_to_stderr [17.09] Fail job if tools that use galaxy.json write to stderr Commit: 90ba35a9a49f583a1fe2a173c1239be86d71125a https://github.com/galaxyproject/galaxy/commit/90ba35a9a49f583a1fe2a173c123… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools_upload.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_17.09' into merge_1709 Commit: 6d3eadedbd7093fc19553d7812152293960f3f14 https://github.com/galaxyproject/galaxy/commit/6d3eadedbd7093fc19553d781215… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools_upload.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5227 from jmchilton/merge_1709 Merge 17.09. Compare: https://github.com/galaxyproject/galaxy/compare/717b5bbce9c5...6d3eadedbd70

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[galaxyproject/galaxy] 3b9d28: Add check_py3_compatibility Travis job
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3b9d2881618ca47f2135e3d226262ff736994260 https://github.com/galaxyproject/galaxy/commit/3b9d2881618ca47f2135e3d22626… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M .ci/check_py3_compatibility.sh M .travis.yml M tox.ini Log Message: ----------- Add check_py3_compatibility Travis job Commit: 717b5bbce9c552de5d28d783bc8620c9396f269c https://github.com/galaxyproject/galaxy/commit/717b5bbce9c552de5d28d783bc86… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M .ci/check_py3_compatibility.sh M .travis.yml M tox.ini Log Message: ----------- Merge pull request #5228 from nsoranzo/add_check_py3_compatibility_travis_job Add check_py3_compatibility Travis job Compare: https://github.com/galaxyproject/galaxy/compare/7e7dc249ab93...717b5bbce9c5

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