Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 889b5d5e53dc6d613c98c1b975b5c031be3e82ae
https://github.com/galaxyproject/usegalaxy-playbook/commit/889b5d5e53dc6d61…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M env/main/host_vars/login5.stampede.tacc.utexas.edu.yml
M env/test/host_vars/login5.stampede.tacc.utexas.edu.yml
Log Message:
-----------
Disable use of the xsede manager on Stampede because the stats
collection script is asking for a sudo password.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 08eb9859f25dff98edbf2fc4be95012219d389a5
https://github.com/galaxyproject/galaxy/commit/08eb9859f25dff98edbf2fc4be95…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
enhance hdca creation endpoint to accept lddas
by implementing automatic conversion of any such elements
Commit: 5609bfc307cd9a6bdd86cd49128d3c4f8407613b
https://github.com/galaxyproject/galaxy/commit/5609bfc307cd9a6bdd86cd49128d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M test/api/test_libraries.py
M test/base/populators.py
Log Message:
-----------
More API library testing.
Commit: 8a41921b49106276d1e8ed925464e734c07664d8
https://github.com/galaxyproject/galaxy/commit/8a41921b49106276d1e8ed925464…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
Respect permissions when creating HDAs/HDCAs from LDDAs.
Commit: 25e53e13453d594c56cf6f48474d74c7a9a09368
https://github.com/galaxyproject/galaxy/commit/25e53e13453d594c56cf6f48474d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M test/api/test_history_contents.py
Log Message:
-----------
API tests for creating HDCAs from LDDA elements.
Commit: 47737659747955390292723d57381c2d3ca92f63
https://github.com/galaxyproject/galaxy/commit/47737659747955390292723d5738…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
R .ci/flake8_lint_include_list.txt
R .ci/flake8_wrapper_imports.sh
M .ci/jenkins/selenium/run_tests.sh
M .travis.yml
M README.rst
M client/galaxy/scripts/admin.toolshed.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/i18n.js
M client/galaxy/scripts/layout/modal.js
M client/galaxy/scripts/mvc/annotation.js
M client/galaxy/scripts/mvc/collection/collection-li-edit.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/dataset/dataset-list.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/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/hda-li-edit.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
A client/galaxy/scripts/mvc/history/history-item-li.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/job/job-model.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/library/library-util.js
M client/galaxy/scripts/mvc/list/list-view.js
M client/galaxy/scripts/mvc/tag.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/util.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-select.js
M client/galaxy/scripts/mvc/ui/ui-table.js
M client/galaxy/scripts/mvc/ui/ui-thumbnails.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/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/user/user-quotameter.js
M client/galaxy/scripts/mvc/visualization/visualization-model.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
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/ui/autocom_tagging.js
M client/galaxy/scripts/ui/fa-icon-button.js
M client/galaxy/scripts/ui/filter-control.js
M client/galaxy/scripts/ui/mode-button.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.js
M client/galaxy/scripts/ui/search-input.js
M client/galaxy/scripts/utils/ajax-queue.js
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/utils/deferred.js
M client/galaxy/scripts/utils/localization.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/bbi-data-manager.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/visualization.js
M client/galaxy/style/less/trackster.less
M client/yarn.lock
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M doc/source/releases/17.09_announce.rst
A lib/galaxy/actions/library.py
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dataset_collections/registry.py
M lib/galaxy/dataset_collections/types/list.py
M lib/galaxy/dataset_collections/types/paired.py
M lib/galaxy/datatypes/converters/bgzip.py
A lib/galaxy/datatypes/converters/cram_to_bam.py
A lib/galaxy/datatypes/converters/cram_to_bam_converter.xml
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/example.iqtree
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/flake8/Pipfile
M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock
M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile
R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock
R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt
R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/update.sh
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/util/__init__.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
A lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/containers.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/library_datasets.py
M lib/galaxy/managers/pages.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/visualizations.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/openid/providers.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/cache.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_tool.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/lmod.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/error_reports/plugins/biostars.py
M lib/galaxy/tools/error_reports/plugins/email.py
M lib/galaxy/tools/error_reports/plugins/github.py
M lib/galaxy/tools/error_reports/plugins/influxdb.py
M lib/galaxy/tools/error_reports/plugins/json.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/locations/__init__.py
M lib/galaxy/tools/locations/dockstore.py
M lib/galaxy/tools/locations/http.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/properties.py
A lib/galaxy/util/script.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/phyloviz/__init__.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
M lib/galaxy/visualization/data_providers/registry.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/formbuilder.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/graphite.py
M lib/galaxy/web/framework/middleware/profile.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/security/__init__.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/annotations.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/dataset_collections.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/extended_metadata.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/forms.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/item_tags.py
M lib/galaxy/webapps/galaxy/api/job_files.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/api/metrics.py
M lib/galaxy/webapps/galaxy/api/page_revisions.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/provenance.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/search.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/webhooks.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/biostar.py
M lib/galaxy/webapps/galaxy/controllers/library.py
R lib/galaxy/webapps/galaxy/controllers/library_admin.py
R lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/tag.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/app.py
M lib/galaxy/webapps/reports/controllers/history.py
M lib/galaxy/webapps/reports/controllers/home.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/root.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/api/authenticate.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/configuration.py
M lib/galaxy/webapps/tool_shed/api/groups.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/api/users.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/controllers/admin.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/controllers/user.py
M lib/galaxy/webapps/tool_shed/search/tool_search.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/schedulers/core.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/repository_types/registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/utility_containers/__init__.py
M run_tests.sh
M scripts/functional_tests.py
M scripts/manage_tool_dependencies.py
M static/maps/admin.toolshed.js.map
M static/maps/galaxy.interactive_environments.js.map
M static/maps/galaxy.library.js.map
M static/maps/galaxy.pages.js.map
M static/maps/i18n.js.map
M static/maps/layout/modal.js.map
M static/maps/mvc/annotation.js.map
M static/maps/mvc/collection/collection-li-edit.js.map
M static/maps/mvc/collection/collection-li.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/dataset/dataset-list.js.map
M static/maps/mvc/dataset/dataset-model.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/grid/grid-shared.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/hda-li-edit.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li-edit.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/hdca-model.js.map
M static/maps/mvc/history/history-content-model.js.map
M static/maps/mvc/history/history-contents.js.map
A static/maps/mvc/history/history-item-li.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/job/job-model.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/maps/mvc/library/library-libraryrow-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/mvc/library/library-model.js.map
M static/maps/mvc/library/library-util.js.map
M static/maps/mvc/list/list-view.js.map
M static/maps/mvc/tag.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/toolshed/util.js.map
M static/maps/mvc/toolshed/workflows-view.js.map
M static/maps/mvc/ui/ui-list.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-popover.js.map
M static/maps/mvc/ui/ui-select.js.map
M static/maps/mvc/ui/ui-table.js.map
M static/maps/mvc/ui/ui-thumbnails.js.map
M static/maps/mvc/upload/collection/collection-row.js.map
M static/maps/mvc/upload/collection/collection-view.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/mvc/user/user-model.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/user/user-quotameter.js.map
M static/maps/mvc/visualization/visualization-model.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/mvc/workflow/workflow.js.map
M static/maps/nls/ja/locale.js.map
M static/maps/reports_webapp/run_stats.js.map
M static/maps/ui/autocom_tagging.js.map
M static/maps/ui/fa-icon-button.js.map
M static/maps/ui/filter-control.js.map
M static/maps/ui/mode-button.js.map
M static/maps/ui/pagination.js.map
M static/maps/ui/peek-column-selector.js.map
M static/maps/ui/search-input.js.map
M static/maps/utils/ajax-queue.js.map
M static/maps/utils/config.js.map
M static/maps/utils/deferred.js.map
M static/maps/utils/localization.js.map
M static/maps/utils/utils.js.map
M static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/circster.js.map
M static/maps/viz/phyloviz.js.map
M static/maps/viz/sweepster.js.map
M static/maps/viz/trackster.js.map
M static/maps/viz/trackster/filters.js.map
M static/maps/viz/visualization.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-content-model.js
M static/scripts/mvc/history/history-contents.js
A static/scripts/mvc/history/history-item-li.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/reports_webapp/run_stats.js
M static/scripts/utils/ajax-queue.js
M static/scripts/viz/circster.js
M static/scripts/viz/trackster.js
M static/style/blue/trackster.css
R templates/admin/library/grid.mako
R templates/admin/library/new_library.mako
M templates/admin/tool_shed_repository/repository_actions_menu.mako
M templates/admin/tool_shed_repository/view_tool_metadata.mako
M templates/show_params.mako
M templates/webapps/galaxy/admin/center.mako
R templates/webapps/galaxy/library/common/browse_library.mako
R templates/webapps/galaxy/library/common/browse_library_opt.mako
R templates/webapps/galaxy/library/common/common.mako
R templates/webapps/galaxy/library/common/folder_info.mako
R templates/webapps/galaxy/library/common/folder_permissions.mako
R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako
R templates/webapps/galaxy/library/common/ldda_edit_info.mako
R templates/webapps/galaxy/library/common/ldda_info.mako
R templates/webapps/galaxy/library/common/ldda_permissions.mako
R templates/webapps/galaxy/library/common/library_dataset_info.mako
R templates/webapps/galaxy/library/common/library_dataset_permissions.mako
R templates/webapps/galaxy/library/common/library_dataset_search_results.mako
R templates/webapps/galaxy/library/common/library_info.mako
R templates/webapps/galaxy/library/common/library_item_info.mako
R templates/webapps/galaxy/library/common/library_permissions.mako
R templates/webapps/galaxy/library/common/move_library_item.mako
R templates/webapps/galaxy/library/common/new_folder.mako
R templates/webapps/galaxy/library/common/upload.mako
R templates/webapps/galaxy/library/grid.mako
R templates/webapps/galaxy/library/index.mako
M templates/webapps/reports/run_stats.mako
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_page_revisions.py
M test/base/driver_util.py
M test/base/populators.py
M test/base/testcase.py
M test/functional/test_toolbox.py
M test/galaxy_selenium/components.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/navigates_galaxy.py
M test/manual/workflows_scaling.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_history_dataset_state.py
M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_jupyter.py
M test/selenium_tests/test_library_contents.py
M test/selenium_tests/test_library_landing.py
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_saved_histories.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_management.py
M test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/twilltestcase.py
M test/unit/config/1607_root_filters/config/galaxy.ini
M test/unit/config/1607_root_samples/config/galaxy.ini
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_installed_repository_manager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_objectstore.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
M test/unit/tools_support.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/phenotype_association/senatag.py
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/dev' into lib-to-colllection
Commit: 87987b4c949b881ba59c17caa5fd8559c89eef6a
https://github.com/galaxyproject/galaxy/commit/87987b4c949b881ba59c17caa5fd…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
R .ci/flake8_lint_include_list.txt
R .ci/flake8_wrapper_imports.sh
M .ci/jenkins/selenium/run_tests.sh
M .travis.yml
M README.rst
M client/galaxy/scripts/admin.toolshed.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/i18n.js
M client/galaxy/scripts/layout/modal.js
M client/galaxy/scripts/mvc/annotation.js
M client/galaxy/scripts/mvc/collection/collection-li-edit.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/dataset/dataset-list.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/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/hda-li-edit.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
A client/galaxy/scripts/mvc/history/history-item-li.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/job/job-model.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/library/library-util.js
M client/galaxy/scripts/mvc/list/list-view.js
M client/galaxy/scripts/mvc/tag.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/util.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-select.js
M client/galaxy/scripts/mvc/ui/ui-table.js
M client/galaxy/scripts/mvc/ui/ui-thumbnails.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/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/user/user-quotameter.js
M client/galaxy/scripts/mvc/visualization/visualization-model.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
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/ui/autocom_tagging.js
M client/galaxy/scripts/ui/fa-icon-button.js
M client/galaxy/scripts/ui/filter-control.js
M client/galaxy/scripts/ui/mode-button.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.js
M client/galaxy/scripts/ui/search-input.js
M client/galaxy/scripts/utils/ajax-queue.js
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/utils/deferred.js
M client/galaxy/scripts/utils/localization.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/bbi-data-manager.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/visualization.js
M client/galaxy/style/less/trackster.less
M client/yarn.lock
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M doc/source/releases/17.09_announce.rst
A lib/galaxy/actions/library.py
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dataset_collections/registry.py
M lib/galaxy/dataset_collections/types/list.py
M lib/galaxy/dataset_collections/types/paired.py
M lib/galaxy/datatypes/converters/bgzip.py
A lib/galaxy/datatypes/converters/cram_to_bam.py
A lib/galaxy/datatypes/converters/cram_to_bam_converter.xml
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/example.iqtree
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/flake8/Pipfile
M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock
M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile
R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock
R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt
R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/update.sh
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/util/__init__.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
A lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/containers.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/library_datasets.py
M lib/galaxy/managers/pages.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/visualizations.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/openid/providers.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/cache.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_tool.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/lmod.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/error_reports/plugins/biostars.py
M lib/galaxy/tools/error_reports/plugins/email.py
M lib/galaxy/tools/error_reports/plugins/github.py
M lib/galaxy/tools/error_reports/plugins/influxdb.py
M lib/galaxy/tools/error_reports/plugins/json.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/locations/__init__.py
M lib/galaxy/tools/locations/dockstore.py
M lib/galaxy/tools/locations/http.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/properties.py
A lib/galaxy/util/script.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/phyloviz/__init__.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
M lib/galaxy/visualization/data_providers/registry.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/formbuilder.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/graphite.py
M lib/galaxy/web/framework/middleware/profile.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/security/__init__.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/annotations.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/dataset_collections.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/extended_metadata.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/forms.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/item_tags.py
M lib/galaxy/webapps/galaxy/api/job_files.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/api/metrics.py
M lib/galaxy/webapps/galaxy/api/page_revisions.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/provenance.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/search.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/webhooks.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/biostar.py
M lib/galaxy/webapps/galaxy/controllers/library.py
R lib/galaxy/webapps/galaxy/controllers/library_admin.py
R lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/tag.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/app.py
M lib/galaxy/webapps/reports/controllers/history.py
M lib/galaxy/webapps/reports/controllers/home.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/root.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/api/authenticate.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/configuration.py
M lib/galaxy/webapps/tool_shed/api/groups.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/api/users.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/controllers/admin.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/controllers/user.py
M lib/galaxy/webapps/tool_shed/search/tool_search.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/schedulers/core.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/repository_types/registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/utility_containers/__init__.py
M run_tests.sh
M scripts/functional_tests.py
M scripts/manage_tool_dependencies.py
M static/maps/admin.toolshed.js.map
M static/maps/galaxy.interactive_environments.js.map
M static/maps/galaxy.library.js.map
M static/maps/galaxy.pages.js.map
M static/maps/i18n.js.map
M static/maps/layout/modal.js.map
M static/maps/mvc/annotation.js.map
M static/maps/mvc/collection/collection-li-edit.js.map
M static/maps/mvc/collection/collection-li.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/dataset/dataset-list.js.map
M static/maps/mvc/dataset/dataset-model.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/grid/grid-shared.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/hda-li-edit.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li-edit.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/hdca-model.js.map
M static/maps/mvc/history/history-content-model.js.map
M static/maps/mvc/history/history-contents.js.map
A static/maps/mvc/history/history-item-li.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/job/job-model.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/maps/mvc/library/library-libraryrow-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/mvc/library/library-model.js.map
M static/maps/mvc/library/library-util.js.map
M static/maps/mvc/list/list-view.js.map
M static/maps/mvc/tag.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/toolshed/util.js.map
M static/maps/mvc/toolshed/workflows-view.js.map
M static/maps/mvc/ui/ui-list.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-popover.js.map
M static/maps/mvc/ui/ui-select.js.map
M static/maps/mvc/ui/ui-table.js.map
M static/maps/mvc/ui/ui-thumbnails.js.map
M static/maps/mvc/upload/collection/collection-row.js.map
M static/maps/mvc/upload/collection/collection-view.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/mvc/user/user-model.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/user/user-quotameter.js.map
M static/maps/mvc/visualization/visualization-model.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/mvc/workflow/workflow.js.map
M static/maps/nls/ja/locale.js.map
M static/maps/reports_webapp/run_stats.js.map
M static/maps/ui/autocom_tagging.js.map
M static/maps/ui/fa-icon-button.js.map
M static/maps/ui/filter-control.js.map
M static/maps/ui/mode-button.js.map
M static/maps/ui/pagination.js.map
M static/maps/ui/peek-column-selector.js.map
M static/maps/ui/search-input.js.map
M static/maps/utils/ajax-queue.js.map
M static/maps/utils/config.js.map
M static/maps/utils/deferred.js.map
M static/maps/utils/localization.js.map
M static/maps/utils/utils.js.map
M static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/circster.js.map
M static/maps/viz/phyloviz.js.map
M static/maps/viz/sweepster.js.map
M static/maps/viz/trackster.js.map
M static/maps/viz/trackster/filters.js.map
M static/maps/viz/visualization.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-content-model.js
M static/scripts/mvc/history/history-contents.js
A static/scripts/mvc/history/history-item-li.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/reports_webapp/run_stats.js
M static/scripts/utils/ajax-queue.js
M static/scripts/viz/circster.js
M static/scripts/viz/trackster.js
M static/style/blue/trackster.css
R templates/admin/library/grid.mako
R templates/admin/library/new_library.mako
M templates/admin/tool_shed_repository/repository_actions_menu.mako
M templates/admin/tool_shed_repository/view_tool_metadata.mako
M templates/show_params.mako
M templates/webapps/galaxy/admin/center.mako
R templates/webapps/galaxy/library/common/browse_library.mako
R templates/webapps/galaxy/library/common/browse_library_opt.mako
R templates/webapps/galaxy/library/common/common.mako
R templates/webapps/galaxy/library/common/folder_info.mako
R templates/webapps/galaxy/library/common/folder_permissions.mako
R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako
R templates/webapps/galaxy/library/common/ldda_edit_info.mako
R templates/webapps/galaxy/library/common/ldda_info.mako
R templates/webapps/galaxy/library/common/ldda_permissions.mako
R templates/webapps/galaxy/library/common/library_dataset_info.mako
R templates/webapps/galaxy/library/common/library_dataset_permissions.mako
R templates/webapps/galaxy/library/common/library_dataset_search_results.mako
R templates/webapps/galaxy/library/common/library_info.mako
R templates/webapps/galaxy/library/common/library_item_info.mako
R templates/webapps/galaxy/library/common/library_permissions.mako
R templates/webapps/galaxy/library/common/move_library_item.mako
R templates/webapps/galaxy/library/common/new_folder.mako
R templates/webapps/galaxy/library/common/upload.mako
R templates/webapps/galaxy/library/grid.mako
R templates/webapps/galaxy/library/index.mako
M templates/webapps/reports/run_stats.mako
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_page_revisions.py
M test/base/driver_util.py
M test/base/populators.py
M test/base/testcase.py
M test/functional/test_toolbox.py
M test/galaxy_selenium/components.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/navigates_galaxy.py
M test/manual/workflows_scaling.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_history_dataset_state.py
M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_jupyter.py
M test/selenium_tests/test_library_contents.py
M test/selenium_tests/test_library_landing.py
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_saved_histories.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_management.py
M test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/twilltestcase.py
M test/unit/config/1607_root_filters/config/galaxy.ini
M test/unit/config/1607_root_samples/config/galaxy.ini
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_installed_repository_manager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_objectstore.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
M test/unit/tools_support.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/phenotype_association/senatag.py
M tox.ini
Log Message:
-----------
Merge pull request #25 from jmchilton/lib-to-colllection
Merge with dev and add more tests.
Commit: abe1b240c33c0a2031a56fc52b8bcd5ec34ae27d
https://github.com/galaxyproject/galaxy/commit/abe1b240c33c0a2031a56fc52b8b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M test/api/test_libraries.py
Log Message:
-----------
Fix broken library test I recently added.
Commit: 38c620c62bd7f9cce5c3a792563d88ec5120e3e0
https://github.com/galaxyproject/galaxy/commit/38c620c62bd7f9cce5c3a792563d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
M test/api/test_history_contents.py
M test/api/test_libraries.py
M test/base/populators.py
Log Message:
-----------
Merge pull request #4998 from martenson/lib-to-colllection
enhance hdca creation API endpoint to accept lddas
Compare: https://github.com/galaxyproject/galaxy/compare/f44cbd5d8210...38c620c62bd7