mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
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.
This commit is contained in:
Nicola Soranzo
@@ -1,177 +0,0 @@
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client/galaxy/style/source_material/circle.py
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config/
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contrib/
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cron/
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doc/parse_gx_xsd.py
|
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lib/galaxy/actions/
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lib/galaxy/auth/
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lib/galaxy/config.py
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lib/galaxy/containers/
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lib/galaxy/dataset_collections/
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lib/galaxy/datatypes/
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lib/galaxy/dependencies/
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lib/galaxy/eggs/
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lib/galaxy/exceptions/
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lib/galaxy/external_services/__init__.py
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lib/galaxy/external_services/parameters.py
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lib/galaxy/external_services/result_handlers/basic.py
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lib/galaxy/external_services/result_handlers/__init__.py
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lib/galaxy/forms/__init__.py
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lib/galaxy/jobs/actions/
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lib/galaxy/jobs/command_factory.py
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lib/galaxy/jobs/datasets.py
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lib/galaxy/jobs/deferred/
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lib/galaxy/jobs/error_level.py
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lib/galaxy/jobs/handler.py
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lib/galaxy/jobs/__init__.py
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lib/galaxy/jobs/manager.py
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lib/galaxy/jobs/metrics/
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lib/galaxy/jobs/output_checker.py
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lib/galaxy/jobs/rules/
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lib/galaxy/jobs/runners/
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lib/galaxy/jobs/splitters/basic.py
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lib/galaxy/jobs/splitters/__init__.py
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lib/galaxy/jobs/stock_rules.py
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lib/galaxy/jobs/transfer_manager.py
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lib/galaxy/main.py
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lib/galaxy/managers/annotatable.py
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lib/galaxy/managers/api_keys.py
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lib/galaxy/managers/base.py
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lib/galaxy/managers/collections.py
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lib/galaxy/managers/collections_util.py
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lib/galaxy/managers/context.py
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lib/galaxy/managers/deletable.py
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lib/galaxy/managers/__init__.py
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lib/galaxy/managers/jobs.py
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lib/galaxy/managers/lddas.py
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lib/galaxy/managers/libraries.py
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lib/galaxy/managers/secured.py
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lib/galaxy/managers/taggable.py
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lib/galaxy/model/
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lib/galaxy/objectstore/pulsar.py
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lib/galaxy/objectstore/s3_multipart_upload.py
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lib/galaxy/objectstore/s3.py
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lib/galaxy/openid/__init__.py
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lib/galaxy/quota/
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lib/galaxy/sample_tracking/
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lib/galaxy/security/
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lib/galaxy/tags/
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lib/galaxy/tools/
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lib/galaxy/util/
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lib/galaxy/version.py
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lib/galaxy/visualization/data_providers/basic.py
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lib/galaxy/visualization/data_providers/cigar.py
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lib/galaxy/visualization/data_providers/genome.py
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lib/galaxy/visualization/data_providers/__init__.py
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lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
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lib/galaxy/visualization/genome/
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lib/galaxy/visualization/genomes.py
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lib/galaxy/visualization/__init__.py
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lib/galaxy/visualization/plugins/__init__.py
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lib/galaxy/visualization/plugins/plugin.py
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lib/galaxy/visualization/plugins/utils.py
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lib/galaxy/visualization/tracks/
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lib/galaxy/web/base/
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lib/galaxy/web/buildapp.py
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lib/galaxy/web/formatting.py
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lib/galaxy/web/form_builder.py
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lib/galaxy/web/framework/base.py
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lib/galaxy/web/framework/decorators.py
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lib/galaxy/web/framework/helpers/grids.py
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lib/galaxy/web/framework/__init__.py
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lib/galaxy/web/framework/middleware/error.py
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lib/galaxy/web/framework/middleware/__init__.py
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lib/galaxy/web/framework/middleware/request_id.py
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lib/galaxy/web/framework/middleware/sentry.py
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lib/galaxy/web/framework/middleware/static.py
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lib/galaxy/web/framework/middleware/statsd.py
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lib/galaxy/web/framework/middleware/translogger.py
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lib/galaxy/web/framework/middleware/xforwardedhost.py
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lib/galaxy/web/framework/webapp.py
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lib/galaxy/web/__init__.py
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lib/galaxy/web/params.py
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lib/galaxy/web/stack/
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lib/galaxy/webapps/galaxy/api/authenticate.py
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lib/galaxy/webapps/galaxy/api/forms.py
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lib/galaxy/webapps/galaxy/api/genomes.py
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lib/galaxy/webapps/galaxy/api/group_roles.py
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lib/galaxy/webapps/galaxy/api/group_users.py
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lib/galaxy/webapps/galaxy/api/groups.py
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lib/galaxy/webapps/galaxy/api/histories.py
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lib/galaxy/webapps/galaxy/api/__init__.py
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lib/galaxy/webapps/galaxy/api/jobs.py
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lib/galaxy/webapps/galaxy/api/library_contents.py
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lib/galaxy/webapps/galaxy/api/library_datasets.py
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lib/galaxy/webapps/galaxy/api/requests.py
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lib/galaxy/webapps/galaxy/api/request_types.py
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lib/galaxy/webapps/galaxy/api/roles.py
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lib/galaxy/webapps/galaxy/api/samples.py
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lib/galaxy/webapps/galaxy/api/tool_data.py
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lib/galaxy/webapps/galaxy/api/tools.py
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lib/galaxy/webapps/galaxy/api/tours.py
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lib/galaxy/webapps/galaxy/api/users.py
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lib/galaxy/webapps/galaxy/api/workflows.py
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lib/galaxy/webapps/galaxy/buildapp.py
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lib/galaxy/webapps/galaxy/config_watchers.py
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lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
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lib/galaxy/webapps/galaxy/controllers/async.py
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lib/galaxy/webapps/galaxy/controllers/data_manager.py
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lib/galaxy/webapps/galaxy/controllers/dataset.py
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lib/galaxy/webapps/galaxy/controllers/error.py
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lib/galaxy/webapps/galaxy/controllers/external_services.py
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lib/galaxy/webapps/galaxy/controllers/forms.py
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lib/galaxy/webapps/galaxy/controllers/history.py
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lib/galaxy/webapps/galaxy/controllers/__init__.py
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lib/galaxy/webapps/galaxy/controllers/library_common.py
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lib/galaxy/webapps/galaxy/controllers/mobile.py
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lib/galaxy/webapps/galaxy/controllers/page.py
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lib/galaxy/webapps/galaxy/controllers/requests_admin.py
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lib/galaxy/webapps/galaxy/controllers/requests_common.py
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lib/galaxy/webapps/galaxy/controllers/requests.py
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lib/galaxy/webapps/galaxy/controllers/request_type.py
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lib/galaxy/webapps/galaxy/controllers/root.py
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lib/galaxy/webapps/galaxy/controllers/search.py
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lib/galaxy/webapps/galaxy/controllers/tool_runner.py
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lib/galaxy/webapps/galaxy/controllers/userskeys.py
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lib/galaxy/webapps/galaxy/__init__.py
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lib/galaxy/webapps/__init__.py
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lib/galaxy/webapps/reports/buildapp.py
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lib/galaxy/webapps/reports/config.py
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lib/galaxy/webapps/reports/controllers/__init__.py
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lib/galaxy/webapps/reports/controllers/query.py
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lib/galaxy/webapps/reports/controllers/system.py
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lib/galaxy/webapps/reports/controllers/tools.py
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lib/galaxy/webapps/reports/__init__.py
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lib/galaxy/webapps/tool_shed/api/__init__.py
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lib/galaxy/webapps/tool_shed/buildapp.py
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lib/galaxy/webapps/tool_shed/config.py
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lib/galaxy/webapps/tool_shed/controllers/groups.py
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lib/galaxy/webapps/tool_shed/controllers/__init__.py
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lib/galaxy/webapps/tool_shed/controllers/repository.py
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lib/galaxy/webapps/tool_shed/controllers/user.py
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lib/galaxy/webapps/tool_shed/framework/__init__.py
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lib/galaxy/webapps/tool_shed/framework/middleware/__init__.py
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lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py
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lib/galaxy/webapps/tool_shed/__init__.py
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lib/galaxy/webapps/tool_shed/model/__init__.py
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lib/galaxy/webapps/tool_shed/model/mapping.py
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lib/galaxy/webapps/tool_shed/model/migrate/
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lib/galaxy/webapps/tool_shed/search/__init__.py
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lib/galaxy/webapps/tool_shed/search/repo_search.py
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lib/galaxy/webapps/tool_shed/security/
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lib/galaxy/webapps/tool_shed/util/__init__.py
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lib/galaxy/webapps/tool_shed/util/ratings_util.py
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lib/galaxy/webapps/tool_shed/util/shed_statistics.py
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lib/galaxy/webapps/util.py
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lib/galaxy/webhooks/
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lib/galaxy/work/
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lib/galaxy/workflow/
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lib/galaxy_ext/
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lib/log_tempfile.py
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lib/mimeparse.py
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lib/psyco_full.py
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lib/tool_shed/
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scripts/
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test/
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tool_list.py
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tools/
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@@ -1,5 +0,0 @@
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#!/bin/bash
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set -e
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flake8 `paste .ci/flake8_lint_include_list.txt`
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@@ -9,15 +9,12 @@ env:
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- TOX_ENV=py27-unit
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- TOX_ENV=qunit
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- TOX_ENV=first_startup
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- TOX_ENV=py27-lint-imports
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- TOX_ENV=py27-lint-imports-include-list
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- TOX_ENV=validate-test-tools
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- TOX_ENV=py27-lint-docstring-include-list
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- TOX_ENV=check-python-dependencies
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matrix:
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allow_failures:
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- env: TOX_ENV=py27-lint-imports
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- env: TOX_ENV=check-python-dependencies
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addons:
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+17
-16
@@ -1,39 +1,40 @@
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from __future__ import absolute_import
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import logging
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import signal
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import sys
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import time
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from galaxy import config, jobs
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import galaxy.model
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import galaxy.security
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import galaxy.queues
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from galaxy.managers.collections import DatasetCollectionManager
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import galaxy.quota
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import galaxy.security
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from galaxy import config, jobs
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from galaxy.jobs import metrics as job_metrics
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from galaxy.managers.collections import DatasetCollectionManager
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from galaxy.managers.tags import GalaxyTagManager
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from galaxy.visualization.genomes import Genomes
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from galaxy.visualization.data_providers.registry import DataProviderRegistry
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from galaxy.visualization.plugins.registry import VisualizationsRegistry
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from galaxy.tools.special_tools import load_lib_tools
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from galaxy.tours import ToursRegistry
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from galaxy.webapps.galaxy.config_watchers import ConfigWatchers
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from galaxy.webhooks import WebhooksRegistry
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from galaxy.sample_tracking import external_service_types
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from galaxy.openid.providers import OpenIDProviders
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from galaxy.tools.data_manager.manager import DataManagers
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from galaxy.queue_worker import GalaxyQueueWorker
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from galaxy.sample_tracking import external_service_types
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from galaxy.tools.cache import (
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ToolCache,
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ToolShedRepositoryCache
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)
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from galaxy.jobs import metrics as job_metrics
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from galaxy.tools.data_manager.manager import DataManagers
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from galaxy.tools.error_reports import ErrorReports
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from galaxy.web.proxy import ProxyManager
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from galaxy.web.stack import application_stack_instance
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from galaxy.queue_worker import GalaxyQueueWorker
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from galaxy.tools.special_tools import load_lib_tools
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from galaxy.tours import ToursRegistry
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from galaxy.util import (
|
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ExecutionTimer,
|
||||
heartbeat
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)
|
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from galaxy.visualization.data_providers.registry import DataProviderRegistry
|
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from galaxy.visualization.genomes import Genomes
|
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from galaxy.visualization.plugins.registry import VisualizationsRegistry
|
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from galaxy.web.proxy import ProxyManager
|
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from galaxy.web.stack import application_stack_instance
|
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from galaxy.webapps.galaxy.config_watchers import ConfigWatchers
|
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from galaxy.webhooks import WebhooksRegistry
|
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from tool_shed.galaxy_install import update_repository_manager
|
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|
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|
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|
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@@ -16,7 +16,6 @@ import sys
|
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import tempfile
|
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import threading
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import time
|
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|
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from datetime import timedelta
|
||||
|
||||
from six import string_types
|
||||
|
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@@ -1,6 +1,5 @@
|
||||
from galaxy import exceptions
|
||||
from galaxy.util import bunch
|
||||
|
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from .structure import (
|
||||
get_structure,
|
||||
leaf
|
||||
|
||||
@@ -1,5 +1,4 @@
|
||||
from galaxy import model
|
||||
|
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from .types import (
|
||||
list,
|
||||
paired
|
||||
|
||||
@@ -1,5 +1,4 @@
|
||||
from galaxy.model import DatasetCollectionElement
|
||||
|
||||
from ..types import BaseDatasetCollectionType
|
||||
|
||||
|
||||
|
||||
@@ -1,5 +1,4 @@
|
||||
from galaxy.model import DatasetCollectionElement, HistoryDatasetAssociation
|
||||
|
||||
from ..types import BaseDatasetCollectionType
|
||||
|
||||
FORWARD_IDENTIFIER = "forward"
|
||||
|
||||
@@ -16,16 +16,19 @@ import six
|
||||
|
||||
from galaxy import util
|
||||
from galaxy.datatypes.metadata import MetadataElement # import directly to maintain ease of use in Datatype class definitions
|
||||
from galaxy.util import compression_utils
|
||||
from galaxy.util import FILENAME_VALID_CHARS
|
||||
from galaxy.util import inflector
|
||||
from galaxy.util import unicodify
|
||||
from galaxy.util import (
|
||||
compression_utils,
|
||||
FILENAME_VALID_CHARS,
|
||||
inflector,
|
||||
unicodify
|
||||
)
|
||||
from galaxy.util.bunch import Bunch
|
||||
from galaxy.util.odict import odict
|
||||
from galaxy.util.sanitize_html import sanitize_html
|
||||
|
||||
from . import dataproviders
|
||||
from . import metadata
|
||||
from . import (
|
||||
dataproviders,
|
||||
metadata
|
||||
)
|
||||
|
||||
XSS_VULNERABLE_MIME_TYPES = [
|
||||
'image/svg+xml', # Unfiltered by Galaxy and may contain JS that would be executed by some browsers.
|
||||
|
||||
@@ -14,7 +14,6 @@ from bx import (
|
||||
)
|
||||
|
||||
from galaxy.util import sqlite
|
||||
|
||||
from . import (
|
||||
base,
|
||||
column,
|
||||
|
||||
@@ -12,7 +12,6 @@ from galaxy.util import (
|
||||
from galaxy.util.odict import odict
|
||||
from galaxy.util.template import fill_template
|
||||
from galaxy.web import url_for
|
||||
|
||||
from .parameters import (
|
||||
DEFAULT_DATASET_NAME,
|
||||
DisplayApplicationDataParameter,
|
||||
|
||||
@@ -4,7 +4,6 @@ Graph content classes.
|
||||
import logging
|
||||
|
||||
from galaxy.util import simplegraph
|
||||
|
||||
from . import (
|
||||
data,
|
||||
dataproviders,
|
||||
|
||||
@@ -20,7 +20,6 @@ from galaxy.datatypes.sniff import (
|
||||
from galaxy.datatypes.tabular import Tabular
|
||||
from galaxy.datatypes.util.gff_util import parse_gff3_attributes, parse_gff_attributes
|
||||
from galaxy.web import url_for
|
||||
|
||||
from . import (
|
||||
data,
|
||||
dataproviders
|
||||
|
||||
@@ -13,7 +13,6 @@ from xml.etree.ElementTree import Element
|
||||
import yaml
|
||||
|
||||
import galaxy.util
|
||||
|
||||
from . import (
|
||||
binary,
|
||||
coverage,
|
||||
|
||||
@@ -30,9 +30,7 @@ from galaxy.util.checkers import (
|
||||
is_bz2,
|
||||
is_gzip
|
||||
)
|
||||
|
||||
from galaxy.util.image_util import check_image_type
|
||||
|
||||
from . import data
|
||||
|
||||
if sys.version_info > (3,):
|
||||
|
||||
@@ -23,7 +23,6 @@ from galaxy.datatypes.sniff import (
|
||||
iter_headers
|
||||
)
|
||||
from galaxy.util import compression_utils
|
||||
|
||||
from . import dataproviders
|
||||
|
||||
if sys.version_info > (3,):
|
||||
|
||||
@@ -4,7 +4,6 @@ Datatype classes for tracks/track views within galaxy.
|
||||
import logging
|
||||
|
||||
from galaxy.datatypes.text import Html
|
||||
|
||||
from . import binary
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -5,7 +5,6 @@ import copy
|
||||
|
||||
from bx.intervals.io import GenomicInterval, GenomicIntervalReader, MissingFieldError, NiceReaderWrapper, ParseError
|
||||
from bx.tabular.io import Comment, Header
|
||||
|
||||
from six import Iterator
|
||||
|
||||
from galaxy.util.odict import odict
|
||||
|
||||
@@ -11,4 +11,5 @@ name = "pypi"
|
||||
|
||||
[packages]
|
||||
|
||||
"flake8" = "*"
|
||||
"flake8" = "*"
|
||||
"flake8-import-order" = "==0.14.3"
|
||||
|
||||
+27
-6
@@ -1,7 +1,7 @@
|
||||
{
|
||||
"_meta": {
|
||||
"hash": {
|
||||
"sha256": "23a9dc7e33425cf99801df781bf42cfb2ee9a72cfc8bbf725e1008ae543a821f"
|
||||
"sha256": "fd536e5360456866463f669e38bd7977303b59f1995671fcc2508dfdc744fd6b"
|
||||
},
|
||||
"host-environment-markers": {
|
||||
"implementation_name": "cpython",
|
||||
@@ -9,12 +9,12 @@
|
||||
"os_name": "posix",
|
||||
"platform_machine": "x86_64",
|
||||
"platform_python_implementation": "CPython",
|
||||
"platform_release": "16.7.0",
|
||||
"platform_system": "Darwin",
|
||||
"platform_version": "Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64",
|
||||
"python_full_version": "2.7.12",
|
||||
"platform_release": "3.13.0-133-generic",
|
||||
"platform_system": "Linux",
|
||||
"platform_version": "#182-Ubuntu SMP Tue Sep 19 15:49:21 UTC 2017",
|
||||
"python_full_version": "2.7.6",
|
||||
"python_version": "2.7",
|
||||
"sys_platform": "darwin"
|
||||
"sys_platform": "linux2"
|
||||
},
|
||||
"pipfile-spec": 6,
|
||||
"requires": {},
|
||||
@@ -27,6 +27,13 @@
|
||||
]
|
||||
},
|
||||
"default": {
|
||||
"asttokens": {
|
||||
"hashes": [
|
||||
"sha256:af77320626fbe29b8f5c6c43f82d5012a145a1dadbd2de286ea9398c640c072b",
|
||||
"sha256:3d630eb1532e6877bc01c0a933570693783b7c97ece3260bd3ad964aaf7d566b"
|
||||
],
|
||||
"version": "==1.1.7"
|
||||
},
|
||||
"configparser": {
|
||||
"hashes": [
|
||||
"sha256:5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a"
|
||||
@@ -51,6 +58,13 @@
|
||||
],
|
||||
"version": "==3.5.0"
|
||||
},
|
||||
"flake8-import-order": {
|
||||
"hashes": [
|
||||
"sha256:26c052d93d8b2d17c5e31bdcf0cdcb513c0b039d2671905dc9ddb5bcec8f72e1",
|
||||
"sha256:a025f6d691e6ca3a749ebcb9dea8ee3aa341407d767dda1c263060f80f6b377e"
|
||||
],
|
||||
"version": "==0.14.3"
|
||||
},
|
||||
"mccabe": {
|
||||
"hashes": [
|
||||
"sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42",
|
||||
@@ -71,6 +85,13 @@
|
||||
"sha256:8d616a382f243dbf19b54743f280b80198be0bca3a5396f1d2e1fca6223e8805"
|
||||
],
|
||||
"version": "==1.6.0"
|
||||
},
|
||||
"six": {
|
||||
"hashes": [
|
||||
"sha256:832dc0e10feb1aa2c68dcc57dbb658f1c7e65b9b61af69048abc87a2db00a0eb",
|
||||
"sha256:70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9"
|
||||
],
|
||||
"version": "==1.11.0"
|
||||
}
|
||||
},
|
||||
"develop": {}
|
||||
|
||||
@@ -1,6 +1,9 @@
|
||||
mccabe==0.6.1 --hash=sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42 --hash=sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f
|
||||
pycodestyle==2.3.1 --hash=sha256:6c4245ade1edfad79c3446fadfc96b0de2759662dc29d07d80a6f27ad1ca6ba9 --hash=sha256:682256a5b318149ca0d2a9185d365d8864a768a28db66a84a2ea946bcc426766
|
||||
asttokens==1.1.7 --hash=sha256:af77320626fbe29b8f5c6c43f82d5012a145a1dadbd2de286ea9398c640c072b --hash=sha256:3d630eb1532e6877bc01c0a933570693783b7c97ece3260bd3ad964aaf7d566b
|
||||
pyflakes==1.6.0 --hash=sha256:08bd6a50edf8cffa9fa09a463063c425ecaaf10d1eb0335a7e8b1401aef89e6f --hash=sha256:8d616a382f243dbf19b54743f280b80198be0bca3a5396f1d2e1fca6223e8805
|
||||
enum34==1.1.6; python_version < '3.4' --hash=sha256:6bd0f6ad48ec2aa117d3d141940d484deccda84d4fcd884f5c3d93c23ecd8c79 --hash=sha256:644837f692e5f550741432dd3f223bbb9852018674981b1664e5dc339387588a --hash=sha256:8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1 --hash=sha256:2d81cbbe0e73112bdfe6ef8576f2238f2ba27dd0d55752a776c41d38b7da2850
|
||||
flake8-import-order==0.14.3 --hash=sha256:26c052d93d8b2d17c5e31bdcf0cdcb513c0b039d2671905dc9ddb5bcec8f72e1 --hash=sha256:a025f6d691e6ca3a749ebcb9dea8ee3aa341407d767dda1c263060f80f6b377e
|
||||
six==1.11.0 --hash=sha256:832dc0e10feb1aa2c68dcc57dbb658f1c7e65b9b61af69048abc87a2db00a0eb --hash=sha256:70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9
|
||||
mccabe==0.6.1 --hash=sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42 --hash=sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f
|
||||
pycodestyle==2.3.1 --hash=sha256:6c4245ade1edfad79c3446fadfc96b0de2759662dc29d07d80a6f27ad1ca6ba9 --hash=sha256:682256a5b318149ca0d2a9185d365d8864a768a28db66a84a2ea946bcc426766
|
||||
flake8==3.5.0 --hash=sha256:c7841163e2b576d435799169b78703ad6ac1bbb0f199994fc05f700b2a90ea37 --hash=sha256:7253265f7abd8b313e3892944044a365e3f4ac3fcdcfb4298f55ee9ddf188ba0
|
||||
configparser==3.5.0; python_version < '3.2' --hash=sha256:5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a
|
||||
|
||||
@@ -1,6 +1,9 @@
|
||||
mccabe==0.6.1
|
||||
pycodestyle==2.3.1
|
||||
asttokens==1.1.7
|
||||
pyflakes==1.6.0
|
||||
enum34==1.1.6; python_version < '3.4'
|
||||
flake8-import-order==0.14.3
|
||||
six==1.11.0
|
||||
mccabe==0.6.1
|
||||
pycodestyle==2.3.1
|
||||
flake8==3.5.0
|
||||
configparser==3.5.0; python_version < '3.2'
|
||||
|
||||
@@ -1,15 +0,0 @@
|
||||
[[source]]
|
||||
|
||||
url = "https://pypi.python.org/simple"
|
||||
verify_ssl = true
|
||||
name = "pypi"
|
||||
|
||||
|
||||
[dev-packages]
|
||||
|
||||
|
||||
|
||||
[packages]
|
||||
|
||||
"flake8" = "*"
|
||||
"flake8-import-order" = "*"
|
||||
@@ -1,98 +0,0 @@
|
||||
{
|
||||
"_meta": {
|
||||
"hash": {
|
||||
"sha256": "68f35c8c353b79ccfd80ad884f83009e2b196c6fe761fa91b01f3d3c6804bb93"
|
||||
},
|
||||
"host-environment-markers": {
|
||||
"implementation_name": "cpython",
|
||||
"implementation_version": "0",
|
||||
"os_name": "posix",
|
||||
"platform_machine": "x86_64",
|
||||
"platform_python_implementation": "CPython",
|
||||
"platform_release": "16.7.0",
|
||||
"platform_system": "Darwin",
|
||||
"platform_version": "Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64",
|
||||
"python_full_version": "2.7.12",
|
||||
"python_version": "2.7",
|
||||
"sys_platform": "darwin"
|
||||
},
|
||||
"pipfile-spec": 6,
|
||||
"requires": {},
|
||||
"sources": [
|
||||
{
|
||||
"name": "pypi",
|
||||
"url": "https://pypi.python.org/simple",
|
||||
"verify_ssl": true
|
||||
}
|
||||
]
|
||||
},
|
||||
"default": {
|
||||
"asttokens": {
|
||||
"hashes": [
|
||||
"sha256:37d32633cdeaebfd171f548aa0e77cc863b0692a1e96dc93d49c997a8d655a1a",
|
||||
"sha256:97f568e6eaf9a133850bd5370193ef10a459fc9fff0c8954e986a30b44415a88"
|
||||
],
|
||||
"version": "==1.1.6"
|
||||
},
|
||||
"configparser": {
|
||||
"hashes": [
|
||||
"sha256:5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a"
|
||||
],
|
||||
"markers": "python_version < '3.2'",
|
||||
"version": "==3.5.0"
|
||||
},
|
||||
"enum34": {
|
||||
"hashes": [
|
||||
"sha256:6bd0f6ad48ec2aa117d3d141940d484deccda84d4fcd884f5c3d93c23ecd8c79",
|
||||
"sha256:644837f692e5f550741432dd3f223bbb9852018674981b1664e5dc339387588a",
|
||||
"sha256:8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1",
|
||||
"sha256:2d81cbbe0e73112bdfe6ef8576f2238f2ba27dd0d55752a776c41d38b7da2850"
|
||||
],
|
||||
"markers": "python_version < '3.4'",
|
||||
"version": "==1.1.6"
|
||||
},
|
||||
"flake8": {
|
||||
"hashes": [
|
||||
"sha256:c7841163e2b576d435799169b78703ad6ac1bbb0f199994fc05f700b2a90ea37",
|
||||
"sha256:7253265f7abd8b313e3892944044a365e3f4ac3fcdcfb4298f55ee9ddf188ba0"
|
||||
],
|
||||
"version": "==3.5.0"
|
||||
},
|
||||
"flake8-import-order": {
|
||||
"hashes": [
|
||||
"sha256:26c052d93d8b2d17c5e31bdcf0cdcb513c0b039d2671905dc9ddb5bcec8f72e1",
|
||||
"sha256:a025f6d691e6ca3a749ebcb9dea8ee3aa341407d767dda1c263060f80f6b377e"
|
||||
],
|
||||
"version": "==0.14.3"
|
||||
},
|
||||
"mccabe": {
|
||||
"hashes": [
|
||||
"sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42",
|
||||
"sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f"
|
||||
],
|
||||
"version": "==0.6.1"
|
||||
},
|
||||
"pycodestyle": {
|
||||
"hashes": [
|
||||
"sha256:6c4245ade1edfad79c3446fadfc96b0de2759662dc29d07d80a6f27ad1ca6ba9",
|
||||
"sha256:682256a5b318149ca0d2a9185d365d8864a768a28db66a84a2ea946bcc426766"
|
||||
],
|
||||
"version": "==2.3.1"
|
||||
},
|
||||
"pyflakes": {
|
||||
"hashes": [
|
||||
"sha256:08bd6a50edf8cffa9fa09a463063c425ecaaf10d1eb0335a7e8b1401aef89e6f",
|
||||
"sha256:8d616a382f243dbf19b54743f280b80198be0bca3a5396f1d2e1fca6223e8805"
|
||||
],
|
||||
"version": "==1.6.0"
|
||||
},
|
||||
"six": {
|
||||
"hashes": [
|
||||
"sha256:832dc0e10feb1aa2c68dcc57dbb658f1c7e65b9b61af69048abc87a2db00a0eb",
|
||||
"sha256:70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9"
|
||||
],
|
||||
"version": "==1.11.0"
|
||||
}
|
||||
},
|
||||
"develop": {}
|
||||
}
|
||||
@@ -1,9 +0,0 @@
|
||||
asttokens==1.1.6 --hash=sha256:37d32633cdeaebfd171f548aa0e77cc863b0692a1e96dc93d49c997a8d655a1a --hash=sha256:97f568e6eaf9a133850bd5370193ef10a459fc9fff0c8954e986a30b44415a88
|
||||
pyflakes==1.6.0 --hash=sha256:08bd6a50edf8cffa9fa09a463063c425ecaaf10d1eb0335a7e8b1401aef89e6f --hash=sha256:8d616a382f243dbf19b54743f280b80198be0bca3a5396f1d2e1fca6223e8805
|
||||
enum34==1.1.6; python_version < '3.4' --hash=sha256:6bd0f6ad48ec2aa117d3d141940d484deccda84d4fcd884f5c3d93c23ecd8c79 --hash=sha256:644837f692e5f550741432dd3f223bbb9852018674981b1664e5dc339387588a --hash=sha256:8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1 --hash=sha256:2d81cbbe0e73112bdfe6ef8576f2238f2ba27dd0d55752a776c41d38b7da2850
|
||||
flake8-import-order==0.14.3 --hash=sha256:26c052d93d8b2d17c5e31bdcf0cdcb513c0b039d2671905dc9ddb5bcec8f72e1 --hash=sha256:a025f6d691e6ca3a749ebcb9dea8ee3aa341407d767dda1c263060f80f6b377e
|
||||
six==1.11.0 --hash=sha256:832dc0e10feb1aa2c68dcc57dbb658f1c7e65b9b61af69048abc87a2db00a0eb --hash=sha256:70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9
|
||||
mccabe==0.6.1 --hash=sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42 --hash=sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f
|
||||
pycodestyle==2.3.1 --hash=sha256:6c4245ade1edfad79c3446fadfc96b0de2759662dc29d07d80a6f27ad1ca6ba9 --hash=sha256:682256a5b318149ca0d2a9185d365d8864a768a28db66a84a2ea946bcc426766
|
||||
flake8==3.5.0 --hash=sha256:c7841163e2b576d435799169b78703ad6ac1bbb0f199994fc05f700b2a90ea37 --hash=sha256:7253265f7abd8b313e3892944044a365e3f4ac3fcdcfb4298f55ee9ddf188ba0
|
||||
configparser==3.5.0; python_version < '3.2' --hash=sha256:5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a
|
||||
@@ -1,9 +0,0 @@
|
||||
asttokens==1.1.6
|
||||
pyflakes==1.6.0
|
||||
enum34==1.1.6; python_version < '3.4'
|
||||
flake8-import-order==0.14.3
|
||||
six==1.11.0
|
||||
mccabe==0.6.1
|
||||
pycodestyle==2.3.1
|
||||
flake8==3.5.0
|
||||
configparser==3.5.0; python_version < '3.2'
|
||||
@@ -31,8 +31,7 @@ done
|
||||
|
||||
THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
|
||||
ENVS="develop
|
||||
flake8
|
||||
flake8_imports"
|
||||
flake8"
|
||||
|
||||
for env in $ENVS
|
||||
do
|
||||
|
||||
@@ -1,9 +1,11 @@
|
||||
# Contains actions that are used in External Services
|
||||
import logging
|
||||
|
||||
import requests
|
||||
from galaxy.web import url_for
|
||||
|
||||
from galaxy.util.template import fill_template
|
||||
from result_handlers.basic import ExternalServiceActionResultHandler
|
||||
from galaxy.web import url_for
|
||||
from .result_handlers.basic import ExternalServiceActionResultHandler
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
@@ -1,8 +1,9 @@
|
||||
# Contains objects for accessing external services applications
|
||||
import logging
|
||||
from parameters import ExternalServiceParameter
|
||||
from actions import ExternalServiceAction
|
||||
|
||||
from galaxy.util.bunch import Bunch
|
||||
from .actions import ExternalServiceAction
|
||||
from .parameters import ExternalServiceParameter
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
@@ -3,8 +3,11 @@ FormDefinition and field factories
|
||||
"""
|
||||
# TODO: A FormDefinitionField is closely linked to a form_builder result.
|
||||
# Can this functionality be further abstracted and merged with form_builder?
|
||||
from galaxy.model import (
|
||||
FormDefinition,
|
||||
FormDefinitionCurrent
|
||||
)
|
||||
from galaxy.util import string_as_bool
|
||||
from galaxy.model import FormDefinitionCurrent, FormDefinition
|
||||
|
||||
FORM_TYPES = dict([(f_type.lower(), f_descript) for f_type, f_descript in FormDefinition.types.items()])
|
||||
|
||||
|
||||
@@ -32,7 +32,6 @@ from galaxy.util.bunch import Bunch
|
||||
from galaxy.util.expressions import ExpressionContext
|
||||
from galaxy.util.handlers import ConfiguresHandlers
|
||||
from galaxy.util.xml_macros import load
|
||||
|
||||
from .datasets import (DatasetPath, NullDatasetPathRewriter,
|
||||
OutputsToWorkingDirectoryPathRewriter, TaskPathRewriter)
|
||||
from .output_checker import check_output
|
||||
|
||||
@@ -1,18 +1,17 @@
|
||||
from __future__ import print_function
|
||||
|
||||
__version__ = '1.0.0'
|
||||
import argparse
|
||||
import collections
|
||||
import copy
|
||||
import logging
|
||||
import os
|
||||
import re
|
||||
import sys
|
||||
from functools import reduce
|
||||
|
||||
from yaml import load
|
||||
|
||||
import argparse
|
||||
import logging
|
||||
import os
|
||||
import sys
|
||||
import copy
|
||||
import collections
|
||||
import re
|
||||
from functools import reduce
|
||||
|
||||
__version__ = '1.0.0'
|
||||
|
||||
# log to galaxy's logger
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
import logging
|
||||
import inspect
|
||||
import logging
|
||||
import os
|
||||
import sys
|
||||
|
||||
|
||||
@@ -16,7 +16,6 @@ import os
|
||||
|
||||
from galaxy import util
|
||||
from galaxy.util import plugin_config
|
||||
|
||||
from ..metrics import formatting
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -8,7 +8,6 @@ import sys
|
||||
import tempfile
|
||||
|
||||
from galaxy import util
|
||||
|
||||
from ..collectl import stats
|
||||
|
||||
if sys.version_info > (3,):
|
||||
|
||||
@@ -4,7 +4,6 @@ import os
|
||||
import shutil
|
||||
|
||||
from galaxy import util
|
||||
|
||||
from ..collectl import (
|
||||
cli,
|
||||
processes,
|
||||
|
||||
@@ -3,7 +3,6 @@ import logging
|
||||
import re
|
||||
|
||||
from galaxy import util
|
||||
|
||||
from ..instrumenters import InstrumentPlugin
|
||||
from ...metrics import formatting
|
||||
|
||||
|
||||
@@ -3,7 +3,6 @@ import re
|
||||
import sys
|
||||
|
||||
from galaxy import util
|
||||
|
||||
from ..instrumenters import InstrumentPlugin
|
||||
from ...metrics import formatting
|
||||
|
||||
|
||||
@@ -1,13 +1,15 @@
|
||||
from datetime import datetime
|
||||
import hashlib
|
||||
import logging
|
||||
import random
|
||||
from datetime import datetime
|
||||
|
||||
from sqlalchemy import func
|
||||
|
||||
from galaxy import model
|
||||
from galaxy import util
|
||||
from galaxy import (
|
||||
model,
|
||||
util
|
||||
)
|
||||
|
||||
import logging
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
VALID_JOB_HASH_STRATEGIES = ["job", "user", "history", "workflow_invocation"]
|
||||
|
||||
@@ -30,7 +30,6 @@ from galaxy.util import (
|
||||
)
|
||||
from galaxy.util.bunch import Bunch
|
||||
from galaxy.util.monitors import Monitors
|
||||
|
||||
from .state_handler_factory import build_state_handlers
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -1,6 +1,8 @@
|
||||
from __future__ import absolute_import
|
||||
|
||||
import functools
|
||||
import logging
|
||||
|
||||
from galaxy import model
|
||||
from galaxy.jobs.runners import AsynchronousJobRunner, AsynchronousJobState
|
||||
|
||||
|
||||
@@ -12,7 +12,6 @@ from galaxy.jobs.runners import (
|
||||
AsynchronousJobState
|
||||
)
|
||||
from galaxy.util import asbool
|
||||
|
||||
from .util.cli import CliInterface, split_params
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -16,7 +16,6 @@ from galaxy.util import (
|
||||
DATABASE_MAX_STRING_SIZE,
|
||||
shrink_stream_by_size
|
||||
)
|
||||
|
||||
from ..runners import (
|
||||
BaseJobRunner,
|
||||
JobState
|
||||
|
||||
@@ -1,17 +1,14 @@
|
||||
import logging
|
||||
|
||||
from datetime import datetime
|
||||
|
||||
from galaxy import model
|
||||
from galaxy.jobs.runners import JobState
|
||||
from ._safe_eval import safe_eval
|
||||
|
||||
__all__ = ('failure', )
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
from galaxy import model
|
||||
from galaxy.jobs.runners import JobState
|
||||
|
||||
from ._safe_eval import safe_eval
|
||||
|
||||
|
||||
MESSAGES = dict(
|
||||
walltime_reached='it reached the walltime',
|
||||
memory_limit_reached='it exceeded the amount of allocated memory',
|
||||
|
||||
@@ -4,7 +4,6 @@ processes and interfacing with job managers. This module should contain
|
||||
functionality shared between Galaxy and the Pulsar.
|
||||
"""
|
||||
from galaxy.util.bunch import Bunch
|
||||
|
||||
from .kill import kill_pid
|
||||
|
||||
__all__ = ('kill_pid', 'Bunch')
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
import os
|
||||
import logging
|
||||
import shutil
|
||||
import inspect
|
||||
import logging
|
||||
import os
|
||||
import shutil
|
||||
|
||||
from galaxy import model, util
|
||||
|
||||
|
||||
@@ -1,11 +1,11 @@
|
||||
import functools
|
||||
import logging
|
||||
import os
|
||||
import requests
|
||||
|
||||
import requests
|
||||
from beaker.cache import CacheManager
|
||||
from beaker.util import parse_cache_config_options
|
||||
|
||||
import logging
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -7,11 +7,11 @@ Used by both the API and bootstrapped data.
|
||||
# TODO: this is a bit of an odd duck. It uses the serializer structure from managers
|
||||
# but doesn't have a model like them. It might be better in config.py or a
|
||||
# totally new area, but I'm leaving it in managers for now for class consistency.
|
||||
|
||||
from galaxy.web.framework.base import server_starttime
|
||||
from galaxy.managers import base
|
||||
|
||||
import logging
|
||||
|
||||
from galaxy.managers import base
|
||||
from galaxy.web.framework.base import server_starttime
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -6,14 +6,13 @@ and other (nested) containers.
|
||||
"""
|
||||
# Histories should be DatasetCollections.
|
||||
# Libraries should be DatasetCollections.
|
||||
|
||||
import logging
|
||||
import operator
|
||||
|
||||
from galaxy import model
|
||||
import galaxy.exceptions
|
||||
import galaxy.util
|
||||
from galaxy import model
|
||||
|
||||
import logging
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -2,21 +2,25 @@
|
||||
Manager and Serializer for Datasets.
|
||||
"""
|
||||
import glob
|
||||
import logging
|
||||
import os
|
||||
|
||||
from six import string_types
|
||||
|
||||
from galaxy import model
|
||||
from galaxy import exceptions
|
||||
import galaxy.datatypes.metadata
|
||||
from galaxy import (
|
||||
exceptions,
|
||||
model
|
||||
)
|
||||
from galaxy.managers import (
|
||||
base,
|
||||
deletable,
|
||||
rbac_secured,
|
||||
roles,
|
||||
secured,
|
||||
users
|
||||
)
|
||||
|
||||
from galaxy.managers import base
|
||||
from galaxy.managers import secured
|
||||
from galaxy.managers import deletable
|
||||
from galaxy.managers import roles
|
||||
from galaxy.managers import rbac_secured
|
||||
from galaxy.managers import users
|
||||
|
||||
import logging
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -1,17 +1,23 @@
|
||||
"""
|
||||
Manager and Serializer for Library Folders.
|
||||
"""
|
||||
|
||||
from galaxy.exceptions import ItemAccessibilityException
|
||||
from galaxy.exceptions import InconsistentDatabase
|
||||
from galaxy.exceptions import RequestParameterInvalidException
|
||||
from galaxy.exceptions import InternalServerError
|
||||
from galaxy.exceptions import AuthenticationRequired
|
||||
from galaxy.exceptions import InsufficientPermissionsException
|
||||
from galaxy.exceptions import MalformedId
|
||||
from sqlalchemy.orm.exc import MultipleResultsFound
|
||||
from sqlalchemy.orm.exc import NoResultFound
|
||||
import logging
|
||||
|
||||
from sqlalchemy.orm.exc import (
|
||||
MultipleResultsFound,
|
||||
NoResultFound
|
||||
)
|
||||
|
||||
from galaxy.exceptions import (
|
||||
AuthenticationRequired,
|
||||
InconsistentDatabase,
|
||||
InsufficientPermissionsException,
|
||||
InternalServerError,
|
||||
ItemAccessibilityException,
|
||||
MalformedId,
|
||||
RequestParameterInvalidException
|
||||
)
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
+15
-12
@@ -4,20 +4,23 @@ Manager and Serializer for HDAs.
|
||||
HistoryDatasetAssociations (HDAs) are datasets contained or created in a
|
||||
history.
|
||||
"""
|
||||
|
||||
import os
|
||||
import gettext
|
||||
|
||||
from galaxy import model
|
||||
from galaxy import exceptions
|
||||
from galaxy import datatypes
|
||||
from galaxy.managers import datasets
|
||||
from galaxy.managers import secured
|
||||
from galaxy.managers import taggable
|
||||
from galaxy.managers import annotatable
|
||||
from galaxy.managers import users
|
||||
|
||||
import logging
|
||||
import os
|
||||
|
||||
from galaxy import (
|
||||
datatypes,
|
||||
exceptions,
|
||||
model
|
||||
)
|
||||
from galaxy.managers import (
|
||||
annotatable,
|
||||
datasets,
|
||||
secured,
|
||||
taggable,
|
||||
users
|
||||
)
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -4,18 +4,18 @@ Manager and Serializer for HDCAs.
|
||||
HistoryDatasetCollectionAssociations (HDCAs) are datasets contained or created in a
|
||||
history.
|
||||
"""
|
||||
import logging
|
||||
|
||||
from galaxy import model
|
||||
from galaxy.managers import (
|
||||
annotatable,
|
||||
base,
|
||||
deletable,
|
||||
hdas,
|
||||
secured,
|
||||
taggable
|
||||
)
|
||||
|
||||
from galaxy.managers import base
|
||||
from galaxy.managers import secured
|
||||
from galaxy.managers import deletable
|
||||
from galaxy.managers import taggable
|
||||
from galaxy.managers import annotatable
|
||||
|
||||
from galaxy.managers import hdas
|
||||
|
||||
import logging
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -4,19 +4,24 @@ Manager and Serializer for histories.
|
||||
Histories are containers for datasets or dataset collections
|
||||
created (or copied) by users over the course of an analysis.
|
||||
"""
|
||||
|
||||
from sqlalchemy import desc, asc
|
||||
|
||||
from galaxy import model
|
||||
from galaxy import exceptions as glx_exceptions
|
||||
from galaxy.managers import sharable
|
||||
from galaxy.managers import deletable
|
||||
from galaxy.managers import hdas
|
||||
# from galaxy.managers import hdcas
|
||||
from galaxy.managers import history_contents
|
||||
|
||||
|
||||
import logging
|
||||
|
||||
from sqlalchemy import (
|
||||
asc,
|
||||
desc
|
||||
)
|
||||
|
||||
from galaxy import (
|
||||
exceptions as glx_exceptions,
|
||||
model
|
||||
)
|
||||
from galaxy.managers import (
|
||||
deletable,
|
||||
hdas,
|
||||
history_contents,
|
||||
sharable
|
||||
)
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -2,25 +2,34 @@
|
||||
Heterogenous lists/contents are difficult to query properly since unions are
|
||||
not easily made.
|
||||
"""
|
||||
|
||||
from sqlalchemy import literal
|
||||
from sqlalchemy import sql
|
||||
from sqlalchemy import asc, desc
|
||||
from sqlalchemy import true, false
|
||||
from sqlalchemy import func
|
||||
from sqlalchemy.orm import eagerload
|
||||
from sqlalchemy.orm import undefer
|
||||
|
||||
from galaxy import model
|
||||
from galaxy import exceptions as glx_exceptions
|
||||
|
||||
from galaxy.managers import base
|
||||
from galaxy.managers import deletable
|
||||
from galaxy.managers import containers
|
||||
from galaxy.managers import hdas
|
||||
from galaxy.managers import hdcas
|
||||
|
||||
import logging
|
||||
|
||||
from sqlalchemy import (
|
||||
asc,
|
||||
desc,
|
||||
false,
|
||||
func,
|
||||
literal,
|
||||
sql,
|
||||
true
|
||||
)
|
||||
from sqlalchemy.orm import (
|
||||
eagerload,
|
||||
undefer
|
||||
)
|
||||
|
||||
from galaxy import (
|
||||
exceptions as glx_exceptions,
|
||||
model
|
||||
)
|
||||
from galaxy.managers import (
|
||||
base,
|
||||
containers,
|
||||
deletable,
|
||||
hdas,
|
||||
hdcas
|
||||
)
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -2,11 +2,12 @@
|
||||
import logging
|
||||
|
||||
from galaxy import util
|
||||
|
||||
from galaxy.exceptions import InternalServerError
|
||||
from galaxy.exceptions import InsufficientPermissionsException
|
||||
from galaxy.exceptions import ObjectNotFound
|
||||
from galaxy.exceptions import RequestParameterInvalidException
|
||||
from galaxy.exceptions import (
|
||||
InsufficientPermissionsException,
|
||||
InternalServerError,
|
||||
ObjectNotFound,
|
||||
RequestParameterInvalidException
|
||||
)
|
||||
from galaxy.managers import tags
|
||||
from galaxy.util import validation
|
||||
|
||||
|
||||
@@ -5,11 +5,11 @@ Pages are markup created and saved by users that can contain Galaxy objects
|
||||
(such as datasets) and are often used to describe or present an analysis
|
||||
from within Galaxy.
|
||||
"""
|
||||
import logging
|
||||
|
||||
from galaxy import model
|
||||
from galaxy.managers import sharable
|
||||
|
||||
import logging
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -1,11 +1,12 @@
|
||||
"""
|
||||
Mixins for Ratable model managers and serializers.
|
||||
"""
|
||||
import logging
|
||||
|
||||
from sqlalchemy.sql.expression import func
|
||||
|
||||
from . import base
|
||||
|
||||
import logging
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -1,9 +1,12 @@
|
||||
from galaxy import security
|
||||
import logging
|
||||
|
||||
import galaxy.exceptions
|
||||
from galaxy import model
|
||||
from galaxy import (
|
||||
model,
|
||||
security
|
||||
)
|
||||
from galaxy.managers import users
|
||||
|
||||
import logging
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
"""
|
||||
Manager and Serializer for Roles.
|
||||
"""
|
||||
import logging
|
||||
|
||||
from sqlalchemy.orm import exc as sqlalchemy_exceptions
|
||||
|
||||
@@ -8,7 +9,6 @@ import galaxy.exceptions
|
||||
from galaxy import model
|
||||
from galaxy.managers import base
|
||||
|
||||
import logging
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -9,19 +9,21 @@ A sharable Galaxy object:
|
||||
can be published effectively making it available to all other Users
|
||||
can be rated
|
||||
"""
|
||||
import logging
|
||||
import re
|
||||
|
||||
from sqlalchemy import true
|
||||
import re
|
||||
|
||||
from galaxy import exceptions
|
||||
from galaxy.managers import (
|
||||
annotatable,
|
||||
base,
|
||||
ratable,
|
||||
secured,
|
||||
taggable,
|
||||
users
|
||||
)
|
||||
|
||||
from galaxy.managers import base
|
||||
from galaxy.managers import secured
|
||||
from galaxy.managers import taggable
|
||||
from galaxy.managers import annotatable
|
||||
from galaxy.managers import ratable
|
||||
from galaxy.managers import users
|
||||
|
||||
import logging
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -1,12 +1,13 @@
|
||||
import logging
|
||||
import re
|
||||
import galaxy.model
|
||||
|
||||
from galaxy.util import unicodify
|
||||
from six import string_types
|
||||
from sqlalchemy.sql import select
|
||||
from sqlalchemy.sql.expression import func
|
||||
|
||||
import galaxy.model
|
||||
from galaxy.util import unicodify
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -1,19 +1,22 @@
|
||||
"""
|
||||
Manager and Serializer for Users.
|
||||
"""
|
||||
import logging
|
||||
|
||||
import sqlalchemy
|
||||
|
||||
from galaxy import model
|
||||
from galaxy import exceptions
|
||||
from galaxy import util
|
||||
|
||||
from galaxy.managers import base
|
||||
from galaxy.managers import deletable
|
||||
from galaxy.managers import api_keys
|
||||
from galaxy import (
|
||||
exceptions,
|
||||
model,
|
||||
util
|
||||
)
|
||||
from galaxy.managers import (
|
||||
api_keys,
|
||||
base,
|
||||
deletable
|
||||
)
|
||||
from galaxy.security import validate_user_input
|
||||
|
||||
import logging
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -4,11 +4,11 @@ Manager and Serializers for Visualizations.
|
||||
Visualizations are saved configurations/variables used to
|
||||
reproduce a specific view in a Galaxy visualization.
|
||||
"""
|
||||
import logging
|
||||
|
||||
from galaxy import model
|
||||
from galaxy.managers import sharable
|
||||
|
||||
import logging
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -1,31 +1,43 @@
|
||||
from __future__ import absolute_import
|
||||
|
||||
from six import string_types
|
||||
|
||||
from collections import namedtuple
|
||||
import logging
|
||||
import json
|
||||
import logging
|
||||
import uuid
|
||||
from collections import namedtuple
|
||||
|
||||
from six import string_types
|
||||
from sqlalchemy import and_
|
||||
from sqlalchemy.orm import joinedload, subqueryload
|
||||
|
||||
from galaxy import model
|
||||
from galaxy import util
|
||||
from galaxy import exceptions
|
||||
from galaxy.model.item_attrs import UsesAnnotations
|
||||
from galaxy.util.json import safe_loads
|
||||
from galaxy.workflow import modules
|
||||
from .base import decode_id
|
||||
|
||||
# For WorkflowContentManager
|
||||
from galaxy.util.sanitize_html import sanitize_html
|
||||
from galaxy.workflow.steps import attach_ordered_steps
|
||||
from galaxy.workflow.modules import module_factory, is_tool_module_type, ToolModule, WorkflowModuleInjector
|
||||
from galaxy.tools.parameters.basic import DataToolParameter, DataCollectionToolParameter, RuntimeValue, workflow_building_modes
|
||||
from galaxy.tools.parameters import visit_input_values, params_to_incoming
|
||||
from galaxy import (
|
||||
exceptions,
|
||||
model,
|
||||
util
|
||||
)
|
||||
from galaxy.jobs.actions.post import ActionBox
|
||||
from galaxy.model.item_attrs import UsesAnnotations
|
||||
from galaxy.tools.parameters import (
|
||||
params_to_incoming,
|
||||
visit_input_values
|
||||
)
|
||||
from galaxy.tools.parameters.basic import (
|
||||
DataCollectionToolParameter,
|
||||
DataToolParameter,
|
||||
RuntimeValue,
|
||||
workflow_building_modes
|
||||
)
|
||||
from galaxy.util.json import safe_loads
|
||||
from galaxy.util.sanitize_html import sanitize_html
|
||||
from galaxy.web import url_for
|
||||
from galaxy.workflow import modules
|
||||
from galaxy.workflow.modules import (
|
||||
is_tool_module_type,
|
||||
module_factory,
|
||||
ToolModule,
|
||||
WorkflowModuleInjector
|
||||
)
|
||||
from galaxy.workflow.steps import attach_ordered_steps
|
||||
from .base import decode_id
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
@@ -28,7 +28,6 @@ import galaxy.model.metadata
|
||||
import galaxy.model.orm.now
|
||||
import galaxy.security.passwords
|
||||
import galaxy.util
|
||||
|
||||
from galaxy.managers import tags
|
||||
from galaxy.model.item_attrs import UsesAnnotations
|
||||
from galaxy.model.util import pgcalc
|
||||
|
||||
@@ -3,7 +3,6 @@ import os.path
|
||||
import sys
|
||||
|
||||
from migrate.versioning import repository, schema
|
||||
|
||||
from sqlalchemy import (
|
||||
create_engine,
|
||||
MetaData,
|
||||
|
||||
@@ -10,7 +10,6 @@ import os
|
||||
import random
|
||||
import shutil
|
||||
import threading
|
||||
|
||||
from xml.etree import ElementTree
|
||||
|
||||
try:
|
||||
@@ -24,11 +23,11 @@ from galaxy.util import (
|
||||
force_symlink,
|
||||
umask_fix_perms,
|
||||
)
|
||||
from galaxy.util.odict import odict
|
||||
from galaxy.util.path import (
|
||||
safe_makedirs,
|
||||
safe_relpath,
|
||||
)
|
||||
from galaxy.util.odict import odict
|
||||
from galaxy.util.sleeper import Sleeper
|
||||
|
||||
NO_SESSION_ERROR_MESSAGE = "Attempted to 'create' object store entity in configuration with no database session present."
|
||||
|
||||
@@ -7,15 +7,8 @@ import os
|
||||
import shutil
|
||||
import threading
|
||||
import time
|
||||
|
||||
from datetime import datetime
|
||||
|
||||
from galaxy.exceptions import ObjectInvalid, ObjectNotFound
|
||||
from galaxy.util import directory_hash_id, umask_fix_perms
|
||||
from galaxy.util.path import safe_relpath
|
||||
from galaxy.util.sleeper import Sleeper
|
||||
from ..objectstore import convert_bytes, ObjectStore
|
||||
|
||||
try:
|
||||
from azure.common import AzureHttpError
|
||||
from azure.storage import CloudStorageAccount
|
||||
@@ -24,6 +17,21 @@ try:
|
||||
except ImportError:
|
||||
BlockBlobService = None
|
||||
|
||||
from galaxy.exceptions import (
|
||||
ObjectInvalid,
|
||||
ObjectNotFound
|
||||
)
|
||||
from galaxy.util import (
|
||||
directory_hash_id,
|
||||
umask_fix_perms
|
||||
)
|
||||
from galaxy.util.path import safe_relpath
|
||||
from galaxy.util.sleeper import Sleeper
|
||||
from ..objectstore import (
|
||||
convert_bytes,
|
||||
ObjectStore
|
||||
)
|
||||
|
||||
NO_BLOBSERVICE_ERROR_MESSAGE = ("ObjectStore configured, but no azure.storage.blob dependency available."
|
||||
"Please install and properly configure azure.storage.blob or modify Object Store configuration.")
|
||||
|
||||
|
||||
@@ -5,7 +5,22 @@
|
||||
import logging
|
||||
import os
|
||||
import shutil
|
||||
from galaxy.exceptions import ObjectInvalid, ObjectNotFound
|
||||
|
||||
try:
|
||||
from kamaki.clients import (
|
||||
astakos,
|
||||
Client as KamakiClient,
|
||||
ClientError,
|
||||
pithos,
|
||||
utils
|
||||
)
|
||||
except ImportError:
|
||||
KamakiClient = None
|
||||
|
||||
from galaxy.exceptions import (
|
||||
ObjectInvalid,
|
||||
ObjectNotFound
|
||||
)
|
||||
from galaxy.util import (
|
||||
directory_hash_id,
|
||||
umask_fix_perms,
|
||||
@@ -13,12 +28,6 @@ from galaxy.util import (
|
||||
from galaxy.util.path import safe_relpath
|
||||
from ..objectstore import ObjectStore
|
||||
|
||||
try:
|
||||
from kamaki.clients import (
|
||||
astakos, pithos, utils, ClientError, Client as KamakiClient)
|
||||
except ImportError:
|
||||
KamakiClient = None
|
||||
|
||||
NO_KAMAKI_ERROR_MESSAGE = (
|
||||
"ObjectStore configured, but no kamaki.clients dependency available."
|
||||
"Please install and properly configure kamaki.clients or modify Object "
|
||||
|
||||
@@ -7,21 +7,26 @@ The module is named rods to avoid conflicting with the PyRods module, irods
|
||||
import logging
|
||||
import os
|
||||
import time
|
||||
|
||||
from posixpath import basename as path_basename
|
||||
from posixpath import dirname as path_dirname
|
||||
from posixpath import join as path_join
|
||||
|
||||
from galaxy.exceptions import ObjectInvalid, ObjectNotFound
|
||||
from galaxy.util.path import safe_relpath
|
||||
|
||||
from ..objectstore import DiskObjectStore, local_extra_dirs
|
||||
from posixpath import (
|
||||
basename as path_basename,
|
||||
dirname as path_dirname,
|
||||
join as path_join
|
||||
)
|
||||
|
||||
try:
|
||||
import irods
|
||||
except ImportError:
|
||||
irods = None
|
||||
|
||||
from galaxy.exceptions import (
|
||||
ObjectInvalid,
|
||||
ObjectNotFound
|
||||
)
|
||||
from galaxy.util.path import safe_relpath
|
||||
from ..objectstore import (
|
||||
DiskObjectStore,
|
||||
local_extra_dirs
|
||||
)
|
||||
|
||||
IRODS_IMPORT_MESSAGE = ('The Python irods package is required to use this '
|
||||
'feature, please install it')
|
||||
|
||||
@@ -28,7 +28,6 @@ from galaxy.util import (
|
||||
)
|
||||
from galaxy.util.path import safe_relpath
|
||||
from galaxy.util.sleeper import Sleeper
|
||||
|
||||
from .s3_multipart_upload import multipart_upload
|
||||
from ..objectstore import convert_bytes, ObjectStore
|
||||
|
||||
|
||||
@@ -11,7 +11,6 @@ import glob
|
||||
import multiprocessing
|
||||
import os
|
||||
import subprocess
|
||||
|
||||
from multiprocessing.pool import IMapIterator
|
||||
|
||||
try:
|
||||
|
||||
@@ -1,9 +1,9 @@
|
||||
"""
|
||||
Contains OpenID provider functionality
|
||||
"""
|
||||
|
||||
import os
|
||||
import logging
|
||||
import os
|
||||
|
||||
from galaxy.util import parse_xml, string_as_bool
|
||||
from galaxy.util.odict import odict
|
||||
|
||||
|
||||
@@ -6,13 +6,13 @@ reloading the toolbox, etc., across multiple processes.
|
||||
import logging
|
||||
import threading
|
||||
|
||||
import galaxy.queues
|
||||
from galaxy import util
|
||||
|
||||
from kombu import Connection
|
||||
from kombu.mixins import ConsumerMixin
|
||||
from kombu.pools import producers
|
||||
|
||||
import galaxy.queues
|
||||
from galaxy import util
|
||||
|
||||
logging.getLogger('kombu').setLevel(logging.WARNING)
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
@@ -4,7 +4,11 @@ All message queues used by Galaxy
|
||||
|
||||
"""
|
||||
|
||||
from kombu import Exchange, Queue, Connection
|
||||
from kombu import (
|
||||
Connection,
|
||||
Exchange,
|
||||
Queue
|
||||
)
|
||||
|
||||
ALL_CONTROL = "control.*"
|
||||
galaxy_exchange = Exchange('galaxy_core_exchange', type='topic')
|
||||
|
||||
@@ -2,7 +2,6 @@
|
||||
RequestType
|
||||
"""
|
||||
from galaxy.model import RequestType
|
||||
|
||||
from .sample import sample_state_factory
|
||||
|
||||
RENAME_DATASET_OPTIONS = dict([(f_type.lower(), f_descript) for f_type, f_descript in RequestType.rename_dataset_options.items()])
|
||||
|
||||
@@ -20,7 +20,6 @@ from six.moves.urllib.parse import unquote_plus
|
||||
|
||||
import tool_shed.util.repository_util as repository_util
|
||||
import tool_shed.util.shed_util_common
|
||||
|
||||
from galaxy import (
|
||||
exceptions,
|
||||
model
|
||||
@@ -85,7 +84,6 @@ from galaxy.web import url_for
|
||||
from galaxy.web.form_builder import SelectField
|
||||
from galaxy.work.context import WorkRequestContext
|
||||
from tool_shed.util import common_util
|
||||
|
||||
from .execute import execute as execute_job
|
||||
from .loader import (
|
||||
imported_macro_paths,
|
||||
|
||||
@@ -5,7 +5,6 @@ from json import dumps
|
||||
from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper
|
||||
from galaxy.jobs.datasets import DatasetPath
|
||||
from galaxy.util.odict import odict
|
||||
|
||||
from . import ToolAction
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -2,7 +2,6 @@ import logging
|
||||
|
||||
from galaxy.tools.actions import upload_common
|
||||
from galaxy.util import ExecutionTimer
|
||||
|
||||
from . import ToolAction
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -15,12 +15,10 @@ import six
|
||||
from galaxy.util import safe_makedirs
|
||||
from galaxy.util.bunch import Bunch
|
||||
from galaxy.util.odict import odict
|
||||
|
||||
from .cwltool_deps import (
|
||||
ensure_cwltool_available,
|
||||
process,
|
||||
)
|
||||
|
||||
from .schema import non_strict_schema_loader, schema_loader
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -1,6 +1,5 @@
|
||||
"""Abstraction around cwltool and related libraries for loading a CWL artifact."""
|
||||
import os
|
||||
|
||||
from collections import namedtuple
|
||||
|
||||
from six.moves.urllib.parse import urldefrag
|
||||
|
||||
@@ -6,7 +6,6 @@ import json
|
||||
import logging
|
||||
import os.path
|
||||
import shutil
|
||||
|
||||
from collections import OrderedDict
|
||||
|
||||
from galaxy.util import (
|
||||
@@ -14,7 +13,6 @@ from galaxy.util import (
|
||||
plugin_config
|
||||
)
|
||||
from galaxy.util.oset import OrderedSet
|
||||
|
||||
from .requirements import (
|
||||
ToolRequirement,
|
||||
ToolRequirements
|
||||
|
||||
@@ -6,7 +6,6 @@ import os
|
||||
import re
|
||||
import shutil
|
||||
import tempfile
|
||||
|
||||
from distutils.version import LooseVersion
|
||||
from sys import platform as _platform
|
||||
|
||||
|
||||
@@ -1,7 +1,6 @@
|
||||
import logging
|
||||
import os
|
||||
import string
|
||||
|
||||
from abc import (
|
||||
ABCMeta,
|
||||
abstractmethod
|
||||
@@ -12,7 +11,6 @@ import six
|
||||
from galaxy.util import asbool
|
||||
from galaxy.util import in_directory
|
||||
from galaxy.util import plugin_config
|
||||
|
||||
from .container_resolvers.explicit import ExplicitContainerResolver
|
||||
from .container_resolvers.mulled import (
|
||||
BuildMulledDockerContainerResolver,
|
||||
|
||||
@@ -24,9 +24,7 @@ except ImportError:
|
||||
yaml = None
|
||||
|
||||
from galaxy.tools.deps import commands, installable
|
||||
|
||||
from galaxy.util import safe_makedirs
|
||||
|
||||
from ._cli import arg_parser
|
||||
from .util import (
|
||||
build_target,
|
||||
|
||||
@@ -10,7 +10,6 @@ Build mulled images for requirements defined in a tool:
|
||||
"""
|
||||
|
||||
from galaxy.tools.parser import get_tool_source
|
||||
|
||||
from ._cli import arg_parser
|
||||
from .mulled_build import (
|
||||
add_build_arguments,
|
||||
|
||||
@@ -3,7 +3,6 @@ from __future__ import print_function
|
||||
|
||||
import collections
|
||||
import hashlib
|
||||
|
||||
from distutils.version import LooseVersion
|
||||
|
||||
try:
|
||||
|
||||
@@ -10,7 +10,6 @@ import yaml
|
||||
|
||||
from galaxy.util import listify
|
||||
from galaxy.util.dictifiable import Dictifiable
|
||||
|
||||
from ..requirements import ToolRequirement
|
||||
|
||||
|
||||
|
||||
@@ -9,7 +9,6 @@ import re
|
||||
|
||||
import galaxy.tools.deps.installable
|
||||
import galaxy.tools.deps.requirements
|
||||
|
||||
from ..conda_util import (
|
||||
build_isolated_environment,
|
||||
cleanup_failed_install,
|
||||
|
||||
@@ -1,5 +1,4 @@
|
||||
import logging
|
||||
|
||||
from os import listdir
|
||||
from os.path import (
|
||||
basename,
|
||||
@@ -11,7 +10,6 @@ from os.path import (
|
||||
)
|
||||
|
||||
from .resolver_mixins import UsesToolDependencyDirMixin
|
||||
|
||||
from ..resolvers import (
|
||||
Dependency,
|
||||
DependencyResolver,
|
||||
|
||||
@@ -6,7 +6,6 @@ import logging
|
||||
from galaxy.util import biostar
|
||||
from galaxy.util import string_as_bool
|
||||
from galaxy.web.base.controller import url_for
|
||||
|
||||
from ..plugins import ErrorPlugin
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -5,7 +5,6 @@ import logging
|
||||
|
||||
from galaxy.tools.errors import EmailErrorReporter
|
||||
from galaxy.util import string_as_bool
|
||||
|
||||
from ..plugins import ErrorPlugin
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -5,8 +5,6 @@ import logging
|
||||
|
||||
from galaxy.tools.errors import EmailErrorReporter
|
||||
from galaxy.util import string_as_bool, unicodify
|
||||
|
||||
|
||||
from ..plugins import ErrorPlugin
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -4,16 +4,15 @@ from __future__ import absolute_import
|
||||
import datetime
|
||||
import logging
|
||||
|
||||
from galaxy.util import unicodify
|
||||
|
||||
from ..plugins import ErrorPlugin
|
||||
|
||||
try:
|
||||
import influxdb
|
||||
except ImportError:
|
||||
# This middleware will never be used without influxdb.
|
||||
influxdb = None
|
||||
|
||||
from galaxy.util import unicodify
|
||||
from ..plugins import ErrorPlugin
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -7,7 +7,6 @@ import os
|
||||
import tempfile
|
||||
|
||||
from galaxy.util import string_as_bool
|
||||
|
||||
from ..plugins import ErrorPlugin
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -3,7 +3,6 @@ import logging
|
||||
|
||||
from galaxy import web
|
||||
from galaxy.util import string_as_bool, unicodify
|
||||
|
||||
from ..plugins import ErrorPlugin
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -4,7 +4,6 @@ from __future__ import print_function
|
||||
import inspect
|
||||
|
||||
from galaxy.util import submodules
|
||||
|
||||
from .parser import get_tool_source
|
||||
|
||||
|
||||
|
||||
@@ -1,6 +1,5 @@
|
||||
"""This module contains a linting functions for tool inputs."""
|
||||
from galaxy.util import string_as_bool
|
||||
|
||||
from ..lint_util import is_datasource
|
||||
|
||||
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user