Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 63f039b66fef6448f10ea639f2be5fb376cca05e
https://github.com/galaxyproject/galaxy/commit/63f039b66fef6448f10ea639f2be…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
remove the default override
since it is wrong and ignores the access permissions
Commit: 9a13a4af7fe44f6482b075bba6cf3fc500226956
https://github.com/galaxyproject/galaxy/commit/9a13a4af7fe44f6482b075bba6cf…
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:
-----------
Merge pull request #5008 from martenson/fix-ldda-access-check
[16.07] history contents api - remove the default flag override
Commit: 4a2814227cd7509ee62a8f5a64190934b4169ae9
https://github.com/galaxyproject/galaxy/commit/4a2814227cd7509ee62a8f5a6419…
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:
-----------
Merge remote-tracking branch 'upstream/release_16.07' into HEAD
Commit: 54b9b09fb2d232b53fa9430606040060d6b21a4e
https://github.com/galaxyproject/galaxy/commit/54b9b09fb2d232b53fa943060604…
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:
-----------
Merge remote-tracking branch 'upstream/release_16.10' into HEAD
Commit: eab30c96522a5a558de4232320c87c1ef102d2d2
https://github.com/galaxyproject/galaxy/commit/eab30c96522a5a558de4232320c8…
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:
-----------
Merge remote-tracking branch 'upstream/release_17.01' into release_17.05
Commit: b25de8b003168ebced8fbc3bfce5274d32cc1ab7
https://github.com/galaxyproject/galaxy/commit/b25de8b003168ebced8fbc3bfce5…
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:
-----------
Merge remote-tracking branch 'upstream/release_17.05' into HEAD
Commit: 39bd5c6a194ac15b155514ea3ea0f06073dd9d5a
https://github.com/galaxyproject/galaxy/commit/39bd5c6a194ac15b155514ea3ea0…
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:
-----------
Merge branch 'release_17.09' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/7c1afa8f16b6...39bd5c6a194a
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: 63f039b66fef6448f10ea639f2be5fb376cca05e
https://github.com/galaxyproject/galaxy/commit/63f039b66fef6448f10ea639f2be…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
remove the default override
since it is wrong and ignores the access permissions
Commit: 9a13a4af7fe44f6482b075bba6cf3fc500226956
https://github.com/galaxyproject/galaxy/commit/9a13a4af7fe44f6482b075bba6cf…
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:
-----------
Merge pull request #5008 from martenson/fix-ldda-access-check
[16.07] history contents api - remove the default flag override
Commit: 4a2814227cd7509ee62a8f5a64190934b4169ae9
https://github.com/galaxyproject/galaxy/commit/4a2814227cd7509ee62a8f5a6419…
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:
-----------
Merge remote-tracking branch 'upstream/release_16.07' into HEAD
Commit: 54b9b09fb2d232b53fa9430606040060d6b21a4e
https://github.com/galaxyproject/galaxy/commit/54b9b09fb2d232b53fa943060604…
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:
-----------
Merge remote-tracking branch 'upstream/release_16.10' into HEAD
Commit: eab30c96522a5a558de4232320c87c1ef102d2d2
https://github.com/galaxyproject/galaxy/commit/eab30c96522a5a558de4232320c8…
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:
-----------
Merge remote-tracking branch 'upstream/release_17.01' into release_17.05
Commit: b25de8b003168ebced8fbc3bfce5274d32cc1ab7
https://github.com/galaxyproject/galaxy/commit/b25de8b003168ebced8fbc3bfce5…
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:
-----------
Merge remote-tracking branch 'upstream/release_17.05' into HEAD
Compare: https://github.com/galaxyproject/galaxy/compare/1a412bfb1b04...b25de8b00316
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: 63f039b66fef6448f10ea639f2be5fb376cca05e
https://github.com/galaxyproject/galaxy/commit/63f039b66fef6448f10ea639f2be…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
remove the default override
since it is wrong and ignores the access permissions
Commit: 9a13a4af7fe44f6482b075bba6cf3fc500226956
https://github.com/galaxyproject/galaxy/commit/9a13a4af7fe44f6482b075bba6cf…
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:
-----------
Merge pull request #5008 from martenson/fix-ldda-access-check
[16.07] history contents api - remove the default flag override
Commit: 4a2814227cd7509ee62a8f5a64190934b4169ae9
https://github.com/galaxyproject/galaxy/commit/4a2814227cd7509ee62a8f5a6419…
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:
-----------
Merge remote-tracking branch 'upstream/release_16.07' into HEAD
Commit: 54b9b09fb2d232b53fa9430606040060d6b21a4e
https://github.com/galaxyproject/galaxy/commit/54b9b09fb2d232b53fa943060604…
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:
-----------
Merge remote-tracking branch 'upstream/release_16.10' into HEAD
Commit: eab30c96522a5a558de4232320c87c1ef102d2d2
https://github.com/galaxyproject/galaxy/commit/eab30c96522a5a558de4232320c8…
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:
-----------
Merge remote-tracking branch 'upstream/release_17.01' into release_17.05
Compare: https://github.com/galaxyproject/galaxy/compare/e5587dcb6489...eab30c96522a
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: 63f039b66fef6448f10ea639f2be5fb376cca05e
https://github.com/galaxyproject/galaxy/commit/63f039b66fef6448f10ea639f2be…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
remove the default override
since it is wrong and ignores the access permissions
Commit: 9a13a4af7fe44f6482b075bba6cf3fc500226956
https://github.com/galaxyproject/galaxy/commit/9a13a4af7fe44f6482b075bba6cf…
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:
-----------
Merge pull request #5008 from martenson/fix-ldda-access-check
[16.07] history contents api - remove the default flag override
Commit: 4a2814227cd7509ee62a8f5a64190934b4169ae9
https://github.com/galaxyproject/galaxy/commit/4a2814227cd7509ee62a8f5a6419…
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:
-----------
Merge remote-tracking branch 'upstream/release_16.07' into HEAD
Commit: 54b9b09fb2d232b53fa9430606040060d6b21a4e
https://github.com/galaxyproject/galaxy/commit/54b9b09fb2d232b53fa943060604…
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:
-----------
Merge remote-tracking branch 'upstream/release_16.10' into HEAD
Compare: https://github.com/galaxyproject/galaxy/compare/c7b09f870d31...54b9b09fb2d2
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 2cd95c48f6dabfe79ec9a5c440bff8cfc29c68df
https://github.com/galaxyproject/galaxy/commit/2cd95c48f6dabfe79ec9a5c440bf…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
R .ci/flake8_lint_include_list.txt
R .ci/flake8_wrapper_imports.sh
M .travis.yml
M lib/galaxy/app.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/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
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/util/gff_util.py
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/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/splitters/multi.py
M lib/galaxy/managers/citations.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/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/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/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/verify/__init__.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/xml_macros.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/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/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
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/dependencies/attribute_handlers.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/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/utility_containers/__init__.py
M scripts/functional_tests.py
M test/api/test_jobs.py
M test/api/test_page_revisions.py
M test/base/driver_util.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/test_stock_tours.py
M test/shed_functional/base/twilltestcase.py
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_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:
-----------
Fix import order everywhere
- Add flake8-import-order to flake8 Pipfile and remove py27-lint-imports
and py27-lint-imports-include-list tox envs
- Fix most E201 and E202 errors reported by flake8-import-order v0.15,
but pin flake8-import-order to v0.14.3 until
https://github.com/PyCQA/flake8-import-order/issues/123
is fixed
This let us drop 2 jobs on Travis per each job.
Commit: 7c1afa8f16b68fcb8948c760862d4beb68187118
https://github.com/galaxyproject/galaxy/commit/7c1afa8f16b68fcb8948c760862d…
Author: Dannon Baker <dannon.baker(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 .travis.yml
M lib/galaxy/app.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/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
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/util/gff_util.py
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/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/splitters/multi.py
M lib/galaxy/managers/citations.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/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/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/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/verify/__init__.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/xml_macros.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/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/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
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/dependencies/attribute_handlers.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/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/utility_containers/__init__.py
M scripts/functional_tests.py
M test/api/test_jobs.py
M test/api/test_page_revisions.py
M test/base/driver_util.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/test_stock_tours.py
M test/shed_functional/base/twilltestcase.py
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_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 #5005 from nsoranzo/flake8-import-order
Fix import order everywhere
Compare: https://github.com/galaxyproject/galaxy/compare/f86dd647da54...7c1afa8f16b6
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 241a2229f42fb6f64b50a1dd5238f79ec3aa40fa
https://github.com/galaxyproject/galaxy/commit/241a2229f42fb6f64b50a1dd5238…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view.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.js
Log Message:
-----------
Random ES6-ing of files working on in collection_state branch downstream.
A few of these actually bump into things I'm touching, a few of these are just me exploring ES6 and cleaning up the code a bit.
Commit: 53cbbeefca74f64699cad2cc935a5c8a319dfc45
https://github.com/galaxyproject/galaxy/commit/53cbbeefca74f64699cad2cc935a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view.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.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/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
Log Message:
-----------
Rebuild client.
Commit: 61fda75d1f22654417ab66a7896da834d607c28c
https://github.com/galaxyproject/galaxy/commit/61fda75d1f22654417ab66a7896d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view.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.js
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view.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.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/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
Log Message:
-----------
Merge pull request #5001 from jmchilton/es6_collections_2
ES6 refactoring of files touched in collection_state branch.
Compare: https://github.com/galaxyproject/galaxy/compare/049b3550f773...61fda75d1f22