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 client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/shed-list-view.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/scripts/mvc/upload/collection/collection-row.js
M client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-custom-builds.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-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/onload.js
A client/galaxy/scripts/reports/run_stats.js
R client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/filters.js
M client/galaxy/scripts/viz/trackster/tracks.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/object_store_conf.xml.sample
M 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 lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/set_metadata_tool.xml
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/test/1.bam
A lib/galaxy/datatypes/test/1.vcf
A lib/galaxy/datatypes/test/1.vcf.gz
A lib/galaxy/datatypes/test/2.cram
A lib/galaxy/datatypes/test/2.shuffled.bam
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
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/model/__init__.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/objectstore/__init__.py
A lib/galaxy/objectstore/cloud.py
M lib/galaxy/openid/providers.py
M lib/galaxy/security/__init__.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/data/__init__.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/history_query.py
M lib/galaxy/tools/parameters/output_collect.py
A lib/galaxy/tools/repositories.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/permutations.py
A lib/galaxy/util/renamed_temporary_file.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/visualization/genomes.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/form_builder.py
R lib/galaxy/web/framework/formbuilder.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/framework/webapp.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/library_contents.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/api/workflows.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
R lib/galaxy/webapps/reports/controllers/sample_tracking.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/api/tools.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/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.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
M lib/tool_shed/grids/util.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/tool_dependency_util.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/workflow_util.py
R openid/yahoo.xml
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/adminToolshed.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/library.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/masthead.bundled.js
M static/scripts/bundled/viz.bundled.js
M static/scripts/bundled/workflow.bundled.js
M static/scripts/galaxy.pages.js
M static/scripts/layout/generic-nav-view.js
M static/scripts/layout/scratchbook.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/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/dataset/dataset-edit-attributes.js
M static/scripts/mvc/dataset/dataset-error.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/form/form-repeat.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/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-composite.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/toolshed/repo-status-view.js
M static/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/shed-list-view.js
M static/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-genomespace.js
M static/scripts/mvc/upload/collection/collection-row.js
M static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow-canvas.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/onload.js
A static/scripts/reports/run_stats.js
R static/scripts/reports_webapp/run_stats.js
M static/scripts/viz/circster.js
M 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
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
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
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
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
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:
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[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:
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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:
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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