diff --git a/.ci/flake8_lint_include_list.txt b/.ci/flake8_lint_include_list.txt deleted file mode 100644 index 7f2cb903132..00000000000 --- a/.ci/flake8_lint_include_list.txt +++ /dev/null @@ -1,177 +0,0 @@ -client/galaxy/style/source_material/circle.py -config/ -contrib/ -cron/ -doc/parse_gx_xsd.py -lib/galaxy/actions/ -lib/galaxy/auth/ -lib/galaxy/config.py -lib/galaxy/containers/ -lib/galaxy/dataset_collections/ -lib/galaxy/datatypes/ -lib/galaxy/dependencies/ -lib/galaxy/eggs/ -lib/galaxy/exceptions/ -lib/galaxy/external_services/__init__.py -lib/galaxy/external_services/parameters.py -lib/galaxy/external_services/result_handlers/basic.py -lib/galaxy/external_services/result_handlers/__init__.py -lib/galaxy/forms/__init__.py -lib/galaxy/jobs/actions/ -lib/galaxy/jobs/command_factory.py -lib/galaxy/jobs/datasets.py -lib/galaxy/jobs/deferred/ -lib/galaxy/jobs/error_level.py -lib/galaxy/jobs/handler.py -lib/galaxy/jobs/__init__.py -lib/galaxy/jobs/manager.py -lib/galaxy/jobs/metrics/ -lib/galaxy/jobs/output_checker.py -lib/galaxy/jobs/rules/ -lib/galaxy/jobs/runners/ -lib/galaxy/jobs/splitters/basic.py -lib/galaxy/jobs/splitters/__init__.py -lib/galaxy/jobs/stock_rules.py -lib/galaxy/jobs/transfer_manager.py -lib/galaxy/main.py -lib/galaxy/managers/annotatable.py -lib/galaxy/managers/api_keys.py -lib/galaxy/managers/base.py -lib/galaxy/managers/collections.py -lib/galaxy/managers/collections_util.py -lib/galaxy/managers/context.py -lib/galaxy/managers/deletable.py -lib/galaxy/managers/__init__.py -lib/galaxy/managers/jobs.py -lib/galaxy/managers/lddas.py -lib/galaxy/managers/libraries.py -lib/galaxy/managers/secured.py -lib/galaxy/managers/taggable.py -lib/galaxy/model/ -lib/galaxy/objectstore/pulsar.py -lib/galaxy/objectstore/s3_multipart_upload.py -lib/galaxy/objectstore/s3.py -lib/galaxy/openid/__init__.py -lib/galaxy/quota/ -lib/galaxy/sample_tracking/ -lib/galaxy/security/ -lib/galaxy/tags/ -lib/galaxy/tools/ -lib/galaxy/util/ -lib/galaxy/version.py -lib/galaxy/visualization/data_providers/basic.py -lib/galaxy/visualization/data_providers/cigar.py -lib/galaxy/visualization/data_providers/genome.py -lib/galaxy/visualization/data_providers/__init__.py -lib/galaxy/visualization/data_providers/phyloviz/baseparser.py -lib/galaxy/visualization/genome/ -lib/galaxy/visualization/genomes.py -lib/galaxy/visualization/__init__.py -lib/galaxy/visualization/plugins/__init__.py -lib/galaxy/visualization/plugins/plugin.py -lib/galaxy/visualization/plugins/utils.py -lib/galaxy/visualization/tracks/ -lib/galaxy/web/base/ -lib/galaxy/web/buildapp.py -lib/galaxy/web/formatting.py -lib/galaxy/web/form_builder.py -lib/galaxy/web/framework/base.py -lib/galaxy/web/framework/decorators.py -lib/galaxy/web/framework/helpers/grids.py -lib/galaxy/web/framework/__init__.py -lib/galaxy/web/framework/middleware/error.py -lib/galaxy/web/framework/middleware/__init__.py -lib/galaxy/web/framework/middleware/request_id.py -lib/galaxy/web/framework/middleware/sentry.py -lib/galaxy/web/framework/middleware/static.py -lib/galaxy/web/framework/middleware/statsd.py -lib/galaxy/web/framework/middleware/translogger.py -lib/galaxy/web/framework/middleware/xforwardedhost.py -lib/galaxy/web/framework/webapp.py -lib/galaxy/web/__init__.py -lib/galaxy/web/params.py -lib/galaxy/web/stack/ -lib/galaxy/webapps/galaxy/api/authenticate.py -lib/galaxy/webapps/galaxy/api/forms.py -lib/galaxy/webapps/galaxy/api/genomes.py -lib/galaxy/webapps/galaxy/api/group_roles.py -lib/galaxy/webapps/galaxy/api/group_users.py -lib/galaxy/webapps/galaxy/api/groups.py -lib/galaxy/webapps/galaxy/api/histories.py -lib/galaxy/webapps/galaxy/api/__init__.py -lib/galaxy/webapps/galaxy/api/jobs.py -lib/galaxy/webapps/galaxy/api/library_contents.py -lib/galaxy/webapps/galaxy/api/library_datasets.py -lib/galaxy/webapps/galaxy/api/requests.py -lib/galaxy/webapps/galaxy/api/request_types.py -lib/galaxy/webapps/galaxy/api/roles.py -lib/galaxy/webapps/galaxy/api/samples.py -lib/galaxy/webapps/galaxy/api/tool_data.py -lib/galaxy/webapps/galaxy/api/tools.py -lib/galaxy/webapps/galaxy/api/tours.py -lib/galaxy/webapps/galaxy/api/users.py -lib/galaxy/webapps/galaxy/api/workflows.py -lib/galaxy/webapps/galaxy/buildapp.py -lib/galaxy/webapps/galaxy/config_watchers.py -lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py -lib/galaxy/webapps/galaxy/controllers/async.py -lib/galaxy/webapps/galaxy/controllers/data_manager.py -lib/galaxy/webapps/galaxy/controllers/dataset.py -lib/galaxy/webapps/galaxy/controllers/error.py -lib/galaxy/webapps/galaxy/controllers/external_services.py -lib/galaxy/webapps/galaxy/controllers/forms.py -lib/galaxy/webapps/galaxy/controllers/history.py -lib/galaxy/webapps/galaxy/controllers/__init__.py -lib/galaxy/webapps/galaxy/controllers/library_common.py -lib/galaxy/webapps/galaxy/controllers/mobile.py -lib/galaxy/webapps/galaxy/controllers/page.py -lib/galaxy/webapps/galaxy/controllers/requests_admin.py -lib/galaxy/webapps/galaxy/controllers/requests_common.py -lib/galaxy/webapps/galaxy/controllers/requests.py -lib/galaxy/webapps/galaxy/controllers/request_type.py -lib/galaxy/webapps/galaxy/controllers/root.py -lib/galaxy/webapps/galaxy/controllers/search.py -lib/galaxy/webapps/galaxy/controllers/tool_runner.py -lib/galaxy/webapps/galaxy/controllers/userskeys.py -lib/galaxy/webapps/galaxy/__init__.py -lib/galaxy/webapps/__init__.py -lib/galaxy/webapps/reports/buildapp.py -lib/galaxy/webapps/reports/config.py -lib/galaxy/webapps/reports/controllers/__init__.py -lib/galaxy/webapps/reports/controllers/query.py -lib/galaxy/webapps/reports/controllers/system.py -lib/galaxy/webapps/reports/controllers/tools.py -lib/galaxy/webapps/reports/__init__.py -lib/galaxy/webapps/tool_shed/api/__init__.py -lib/galaxy/webapps/tool_shed/buildapp.py -lib/galaxy/webapps/tool_shed/config.py -lib/galaxy/webapps/tool_shed/controllers/groups.py -lib/galaxy/webapps/tool_shed/controllers/__init__.py -lib/galaxy/webapps/tool_shed/controllers/repository.py -lib/galaxy/webapps/tool_shed/controllers/user.py -lib/galaxy/webapps/tool_shed/framework/__init__.py -lib/galaxy/webapps/tool_shed/framework/middleware/__init__.py -lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py -lib/galaxy/webapps/tool_shed/__init__.py -lib/galaxy/webapps/tool_shed/model/__init__.py -lib/galaxy/webapps/tool_shed/model/mapping.py -lib/galaxy/webapps/tool_shed/model/migrate/ -lib/galaxy/webapps/tool_shed/search/__init__.py -lib/galaxy/webapps/tool_shed/search/repo_search.py -lib/galaxy/webapps/tool_shed/security/ -lib/galaxy/webapps/tool_shed/util/__init__.py -lib/galaxy/webapps/tool_shed/util/ratings_util.py -lib/galaxy/webapps/tool_shed/util/shed_statistics.py -lib/galaxy/webapps/util.py -lib/galaxy/webhooks/ -lib/galaxy/work/ -lib/galaxy/workflow/ -lib/galaxy_ext/ -lib/log_tempfile.py -lib/mimeparse.py -lib/psyco_full.py -lib/tool_shed/ -scripts/ -test/ -tool_list.py -tools/ diff --git a/.ci/flake8_wrapper_imports.sh b/.ci/flake8_wrapper_imports.sh deleted file mode 100755 index 22afed26991..00000000000 --- a/.ci/flake8_wrapper_imports.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -set -e - -flake8 `paste .ci/flake8_lint_include_list.txt` diff --git a/.travis.yml b/.travis.yml index 62f6f251405..08db9472ce1 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,15 +9,12 @@ env: - TOX_ENV=py27-unit - TOX_ENV=qunit - TOX_ENV=first_startup - - TOX_ENV=py27-lint-imports - - TOX_ENV=py27-lint-imports-include-list - TOX_ENV=validate-test-tools - TOX_ENV=py27-lint-docstring-include-list - TOX_ENV=check-python-dependencies matrix: allow_failures: - - env: TOX_ENV=py27-lint-imports - env: TOX_ENV=check-python-dependencies addons: diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py index 6fbcca2124a..f076a5a4bf1 100644 --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -1,39 +1,40 @@ from __future__ import absolute_import + import logging import signal import sys import time -from galaxy import config, jobs import galaxy.model -import galaxy.security import galaxy.queues -from galaxy.managers.collections import DatasetCollectionManager import galaxy.quota +import galaxy.security +from galaxy import config, jobs +from galaxy.jobs import metrics as job_metrics +from galaxy.managers.collections import DatasetCollectionManager from galaxy.managers.tags import GalaxyTagManager -from galaxy.visualization.genomes import Genomes -from galaxy.visualization.data_providers.registry import DataProviderRegistry -from galaxy.visualization.plugins.registry import VisualizationsRegistry -from galaxy.tools.special_tools import load_lib_tools -from galaxy.tours import ToursRegistry -from galaxy.webapps.galaxy.config_watchers import ConfigWatchers -from galaxy.webhooks import WebhooksRegistry -from galaxy.sample_tracking import external_service_types from galaxy.openid.providers import OpenIDProviders -from galaxy.tools.data_manager.manager import DataManagers +from galaxy.queue_worker import GalaxyQueueWorker +from galaxy.sample_tracking import external_service_types from galaxy.tools.cache import ( ToolCache, ToolShedRepositoryCache ) -from galaxy.jobs import metrics as job_metrics +from galaxy.tools.data_manager.manager import DataManagers from galaxy.tools.error_reports import ErrorReports -from galaxy.web.proxy import ProxyManager -from galaxy.web.stack import application_stack_instance -from galaxy.queue_worker import GalaxyQueueWorker +from galaxy.tools.special_tools import load_lib_tools +from galaxy.tours import ToursRegistry from galaxy.util import ( ExecutionTimer, heartbeat ) +from galaxy.visualization.data_providers.registry import DataProviderRegistry +from galaxy.visualization.genomes import Genomes +from galaxy.visualization.plugins.registry import VisualizationsRegistry +from galaxy.web.proxy import ProxyManager +from galaxy.web.stack import application_stack_instance +from galaxy.webapps.galaxy.config_watchers import ConfigWatchers +from galaxy.webhooks import WebhooksRegistry from tool_shed.galaxy_install import update_repository_manager diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index 7ae7a6fb08c..13305fb4d83 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -16,7 +16,6 @@ import sys import tempfile import threading import time - from datetime import timedelta from six import string_types diff --git a/lib/galaxy/dataset_collections/matching.py b/lib/galaxy/dataset_collections/matching.py index 739ef4cc5e4..b8720ccf80b 100644 --- a/lib/galaxy/dataset_collections/matching.py +++ b/lib/galaxy/dataset_collections/matching.py @@ -1,6 +1,5 @@ from galaxy import exceptions from galaxy.util import bunch - from .structure import ( get_structure, leaf diff --git a/lib/galaxy/dataset_collections/registry.py b/lib/galaxy/dataset_collections/registry.py index 43acdc18203..a95e47309ee 100644 --- a/lib/galaxy/dataset_collections/registry.py +++ b/lib/galaxy/dataset_collections/registry.py @@ -1,5 +1,4 @@ from galaxy import model - from .types import ( list, paired diff --git a/lib/galaxy/dataset_collections/types/list.py b/lib/galaxy/dataset_collections/types/list.py index 570a48c4084..7297f051469 100644 --- a/lib/galaxy/dataset_collections/types/list.py +++ b/lib/galaxy/dataset_collections/types/list.py @@ -1,5 +1,4 @@ from galaxy.model import DatasetCollectionElement - from ..types import BaseDatasetCollectionType diff --git a/lib/galaxy/dataset_collections/types/paired.py b/lib/galaxy/dataset_collections/types/paired.py index 36763d91566..d1623491050 100644 --- a/lib/galaxy/dataset_collections/types/paired.py +++ b/lib/galaxy/dataset_collections/types/paired.py @@ -1,5 +1,4 @@ from galaxy.model import DatasetCollectionElement, HistoryDatasetAssociation - from ..types import BaseDatasetCollectionType FORWARD_IDENTIFIER = "forward" diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py index 54723f4cd51..1ae1b583f17 100644 --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -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. diff --git a/lib/galaxy/datatypes/dataproviders/dataset.py b/lib/galaxy/datatypes/dataproviders/dataset.py index 4d8a5b76823..76666fa5ab0 100644 --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -14,7 +14,6 @@ from bx import ( ) from galaxy.util import sqlite - from . import ( base, column, diff --git a/lib/galaxy/datatypes/display_applications/application.py b/lib/galaxy/datatypes/display_applications/application.py index d9e6bbd9bbe..e0bc7484148 100644 --- a/lib/galaxy/datatypes/display_applications/application.py +++ b/lib/galaxy/datatypes/display_applications/application.py @@ -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, diff --git a/lib/galaxy/datatypes/graph.py b/lib/galaxy/datatypes/graph.py index 6e7ca5e9afe..cb50fb81d29 100644 --- a/lib/galaxy/datatypes/graph.py +++ b/lib/galaxy/datatypes/graph.py @@ -4,7 +4,6 @@ Graph content classes. import logging from galaxy.util import simplegraph - from . import ( data, dataproviders, diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py index dea3850b946..762a82c8926 100644 --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -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 diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py index f11b8498719..4fd441e5863 100644 --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -13,7 +13,6 @@ from xml.etree.ElementTree import Element import yaml import galaxy.util - from . import ( binary, coverage, diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py index a2083fab2b5..ec47b34235d 100644 --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -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,): diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py index 7858d28a638..731ec358464 100644 --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -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,): diff --git a/lib/galaxy/datatypes/tracks.py b/lib/galaxy/datatypes/tracks.py index dbb9e04eb11..14eae7fe1ce 100644 --- a/lib/galaxy/datatypes/tracks.py +++ b/lib/galaxy/datatypes/tracks.py @@ -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__) diff --git a/lib/galaxy/datatypes/util/gff_util.py b/lib/galaxy/datatypes/util/gff_util.py index 248a5d9842d..6efb6d356df 100644 --- a/lib/galaxy/datatypes/util/gff_util.py +++ b/lib/galaxy/datatypes/util/gff_util.py @@ -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 diff --git a/lib/galaxy/dependencies/pipfiles/flake8/Pipfile b/lib/galaxy/dependencies/pipfiles/flake8/Pipfile index 1799cac56fd..9e79c4171e0 100644 --- a/lib/galaxy/dependencies/pipfiles/flake8/Pipfile +++ b/lib/galaxy/dependencies/pipfiles/flake8/Pipfile @@ -11,4 +11,5 @@ name = "pypi" [packages] -"flake8" = "*" \ No newline at end of file +"flake8" = "*" +"flake8-import-order" = "==0.14.3" diff --git a/lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock b/lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock index f45726344c0..0ecbedcedce 100644 --- a/lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock +++ b/lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock @@ -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": {} diff --git a/lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt b/lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt index 12e76601cc6..8f30621d703 100644 --- a/lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt +++ b/lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt @@ -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 diff --git a/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt index 23f41e35bc4..cf027df14a4 100644 --- a/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt @@ -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' diff --git a/lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile b/lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile deleted file mode 100644 index 479069f0784..00000000000 --- a/lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile +++ /dev/null @@ -1,15 +0,0 @@ -[[source]] - -url = "https://pypi.python.org/simple" -verify_ssl = true -name = "pypi" - - -[dev-packages] - - - -[packages] - -"flake8" = "*" -"flake8-import-order" = "*" \ No newline at end of file diff --git a/lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock b/lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock deleted file mode 100644 index 68ba705251c..00000000000 --- a/lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock +++ /dev/null @@ -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": {} -} diff --git a/lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt b/lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt deleted file mode 100644 index 5d83a41360a..00000000000 --- a/lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt +++ /dev/null @@ -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 diff --git a/lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt deleted file mode 100644 index 87440c4ac28..00000000000 --- a/lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt +++ /dev/null @@ -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' diff --git a/lib/galaxy/dependencies/pipfiles/update.sh b/lib/galaxy/dependencies/pipfiles/update.sh index e47b1fd232e..1005cd98f38 100755 --- a/lib/galaxy/dependencies/pipfiles/update.sh +++ b/lib/galaxy/dependencies/pipfiles/update.sh @@ -31,8 +31,7 @@ done THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)" ENVS="develop -flake8 -flake8_imports" +flake8" for env in $ENVS do diff --git a/lib/galaxy/external_services/actions.py b/lib/galaxy/external_services/actions.py index 13dc83703d3..d39c3a05d36 100644 --- a/lib/galaxy/external_services/actions.py +++ b/lib/galaxy/external_services/actions.py @@ -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__) diff --git a/lib/galaxy/external_services/service.py b/lib/galaxy/external_services/service.py index 569864db742..5b5a15cf3b2 100644 --- a/lib/galaxy/external_services/service.py +++ b/lib/galaxy/external_services/service.py @@ -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__) diff --git a/lib/galaxy/forms/forms.py b/lib/galaxy/forms/forms.py index 60bba718e11..a79178ad865 100644 --- a/lib/galaxy/forms/forms.py +++ b/lib/galaxy/forms/forms.py @@ -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()]) diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index c9d64a418de..34365d1ac37 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -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 diff --git a/lib/galaxy/jobs/dynamic_tool_destination.py b/lib/galaxy/jobs/dynamic_tool_destination.py index 34117d57903..d7dbca87534 100755 --- a/lib/galaxy/jobs/dynamic_tool_destination.py +++ b/lib/galaxy/jobs/dynamic_tool_destination.py @@ -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__) diff --git a/lib/galaxy/jobs/mapper.py b/lib/galaxy/jobs/mapper.py index 7a2cbe6284b..c9f8f0da874 100644 --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -1,5 +1,5 @@ -import logging import inspect +import logging import os import sys diff --git a/lib/galaxy/jobs/metrics/__init__.py b/lib/galaxy/jobs/metrics/__init__.py index ac6c932e4db..14413a8ab1d 100644 --- a/lib/galaxy/jobs/metrics/__init__.py +++ b/lib/galaxy/jobs/metrics/__init__.py @@ -16,7 +16,6 @@ import os from galaxy import util from galaxy.util import plugin_config - from ..metrics import formatting log = logging.getLogger(__name__) diff --git a/lib/galaxy/jobs/metrics/collectl/processes.py b/lib/galaxy/jobs/metrics/collectl/processes.py index c3c4fdcddc3..a3198eff217 100644 --- a/lib/galaxy/jobs/metrics/collectl/processes.py +++ b/lib/galaxy/jobs/metrics/collectl/processes.py @@ -8,7 +8,6 @@ import sys import tempfile from galaxy import util - from ..collectl import stats if sys.version_info > (3,): diff --git a/lib/galaxy/jobs/metrics/instrumenters/collectl.py b/lib/galaxy/jobs/metrics/instrumenters/collectl.py index 4a12b69464f..f7ea2957915 100644 --- a/lib/galaxy/jobs/metrics/instrumenters/collectl.py +++ b/lib/galaxy/jobs/metrics/instrumenters/collectl.py @@ -4,7 +4,6 @@ import os import shutil from galaxy import util - from ..collectl import ( cli, processes, diff --git a/lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py b/lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py index b54d13df059..eb96aa82bec 100644 --- a/lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py +++ b/lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py @@ -3,7 +3,6 @@ import logging import re from galaxy import util - from ..instrumenters import InstrumentPlugin from ...metrics import formatting diff --git a/lib/galaxy/jobs/metrics/instrumenters/meminfo.py b/lib/galaxy/jobs/metrics/instrumenters/meminfo.py index 984e57f57fd..fdebe125e52 100644 --- a/lib/galaxy/jobs/metrics/instrumenters/meminfo.py +++ b/lib/galaxy/jobs/metrics/instrumenters/meminfo.py @@ -3,7 +3,6 @@ import re import sys from galaxy import util - from ..instrumenters import InstrumentPlugin from ...metrics import formatting diff --git a/lib/galaxy/jobs/rule_helper.py b/lib/galaxy/jobs/rule_helper.py index 2a76715bb6f..3261d636703 100644 --- a/lib/galaxy/jobs/rule_helper.py +++ b/lib/galaxy/jobs/rule_helper.py @@ -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"] diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py index b29e6e57f7d..7435e8e5c9a 100644 --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -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__) diff --git a/lib/galaxy/jobs/runners/chronos.py b/lib/galaxy/jobs/runners/chronos.py index 0a04fe89b59..e7450bd222b 100644 --- a/lib/galaxy/jobs/runners/chronos.py +++ b/lib/galaxy/jobs/runners/chronos.py @@ -1,6 +1,8 @@ from __future__ import absolute_import + import functools import logging + from galaxy import model from galaxy.jobs.runners import AsynchronousJobRunner, AsynchronousJobState diff --git a/lib/galaxy/jobs/runners/cli.py b/lib/galaxy/jobs/runners/cli.py index 107dea18907..b697cc6bc5f 100644 --- a/lib/galaxy/jobs/runners/cli.py +++ b/lib/galaxy/jobs/runners/cli.py @@ -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__) diff --git a/lib/galaxy/jobs/runners/local.py b/lib/galaxy/jobs/runners/local.py index 58c60dd341c..dc9bdfac309 100644 --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -16,7 +16,6 @@ from galaxy.util import ( DATABASE_MAX_STRING_SIZE, shrink_stream_by_size ) - from ..runners import ( BaseJobRunner, JobState diff --git a/lib/galaxy/jobs/runners/state_handlers/resubmit.py b/lib/galaxy/jobs/runners/state_handlers/resubmit.py index 6ded2f6eb4f..392d8fbe27f 100644 --- a/lib/galaxy/jobs/runners/state_handlers/resubmit.py +++ b/lib/galaxy/jobs/runners/state_handlers/resubmit.py @@ -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', diff --git a/lib/galaxy/jobs/runners/util/__init__.py b/lib/galaxy/jobs/runners/util/__init__.py index c0bd4daf6a9..6f204e8d814 100644 --- a/lib/galaxy/jobs/runners/util/__init__.py +++ b/lib/galaxy/jobs/runners/util/__init__.py @@ -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') diff --git a/lib/galaxy/jobs/splitters/multi.py b/lib/galaxy/jobs/splitters/multi.py index 3a60663c667..35e761262c0 100644 --- a/lib/galaxy/jobs/splitters/multi.py +++ b/lib/galaxy/jobs/splitters/multi.py @@ -1,7 +1,7 @@ -import os -import logging -import shutil import inspect +import logging +import os +import shutil from galaxy import model, util diff --git a/lib/galaxy/managers/citations.py b/lib/galaxy/managers/citations.py index 5ff70e7c666..19a33b0d0ef 100644 --- a/lib/galaxy/managers/citations.py +++ b/lib/galaxy/managers/citations.py @@ -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__) diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py index 727a3c3683b..0de6e1574b6 100644 --- a/lib/galaxy/managers/configuration.py +++ b/lib/galaxy/managers/configuration.py @@ -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__) diff --git a/lib/galaxy/managers/containers.py b/lib/galaxy/managers/containers.py index a2da3c9982d..a86a64da02f 100644 --- a/lib/galaxy/managers/containers.py +++ b/lib/galaxy/managers/containers.py @@ -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__) diff --git a/lib/galaxy/managers/datasets.py b/lib/galaxy/managers/datasets.py index 82b5d831f4e..c7cd192593f 100644 --- a/lib/galaxy/managers/datasets.py +++ b/lib/galaxy/managers/datasets.py @@ -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__) diff --git a/lib/galaxy/managers/folders.py b/lib/galaxy/managers/folders.py index 506518b0b2e..fe253277789 100644 --- a/lib/galaxy/managers/folders.py +++ b/lib/galaxy/managers/folders.py @@ -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__) diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py index feb132d3f76..d17b5424e61 100644 --- a/lib/galaxy/managers/hdas.py +++ b/lib/galaxy/managers/hdas.py @@ -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__) diff --git a/lib/galaxy/managers/hdcas.py b/lib/galaxy/managers/hdcas.py index a6f1ac8159b..e6591c61f4d 100644 --- a/lib/galaxy/managers/hdcas.py +++ b/lib/galaxy/managers/hdcas.py @@ -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__) diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py index ec2b92d07f4..a7765dff8dd 100644 --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -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__) diff --git a/lib/galaxy/managers/history_contents.py b/lib/galaxy/managers/history_contents.py index fc38bb98edf..c495de58fa8 100644 --- a/lib/galaxy/managers/history_contents.py +++ b/lib/galaxy/managers/history_contents.py @@ -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__) diff --git a/lib/galaxy/managers/library_datasets.py b/lib/galaxy/managers/library_datasets.py index 115f3cb66e8..5db80efce67 100644 --- a/lib/galaxy/managers/library_datasets.py +++ b/lib/galaxy/managers/library_datasets.py @@ -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 diff --git a/lib/galaxy/managers/pages.py b/lib/galaxy/managers/pages.py index 3dbee544483..79eba905883 100644 --- a/lib/galaxy/managers/pages.py +++ b/lib/galaxy/managers/pages.py @@ -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__) diff --git a/lib/galaxy/managers/ratable.py b/lib/galaxy/managers/ratable.py index 1686c44658b..c7d52a31bb5 100644 --- a/lib/galaxy/managers/ratable.py +++ b/lib/galaxy/managers/ratable.py @@ -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__) diff --git a/lib/galaxy/managers/rbac_secured.py b/lib/galaxy/managers/rbac_secured.py index 45d92ff57c5..e8bae4d6afa 100644 --- a/lib/galaxy/managers/rbac_secured.py +++ b/lib/galaxy/managers/rbac_secured.py @@ -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__) diff --git a/lib/galaxy/managers/roles.py b/lib/galaxy/managers/roles.py index 5200e9935cf..0c6b3e58562 100644 --- a/lib/galaxy/managers/roles.py +++ b/lib/galaxy/managers/roles.py @@ -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__) diff --git a/lib/galaxy/managers/sharable.py b/lib/galaxy/managers/sharable.py index 8a857b761d2..96708da3aeb 100644 --- a/lib/galaxy/managers/sharable.py +++ b/lib/galaxy/managers/sharable.py @@ -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__) diff --git a/lib/galaxy/managers/tags.py b/lib/galaxy/managers/tags.py index 74cb04f2596..b3d3b0743f9 100644 --- a/lib/galaxy/managers/tags.py +++ b/lib/galaxy/managers/tags.py @@ -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__) diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py index a1b4009f4c5..030258f7595 100644 --- a/lib/galaxy/managers/users.py +++ b/lib/galaxy/managers/users.py @@ -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__) diff --git a/lib/galaxy/managers/visualizations.py b/lib/galaxy/managers/visualizations.py index cf99f515e14..f3f4a679850 100644 --- a/lib/galaxy/managers/visualizations.py +++ b/lib/galaxy/managers/visualizations.py @@ -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__) diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py index 0c1e1982b7e..8c9b98b5047 100644 --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -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__) diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 259c77461f9..147090a6171 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -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 diff --git a/lib/galaxy/model/migrate/check.py b/lib/galaxy/model/migrate/check.py index fb963393a71..7655774214e 100644 --- a/lib/galaxy/model/migrate/check.py +++ b/lib/galaxy/model/migrate/check.py @@ -3,7 +3,6 @@ import os.path import sys from migrate.versioning import repository, schema - from sqlalchemy import ( create_engine, MetaData, diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py index 2e340cd361d..270722a9143 100644 --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -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." diff --git a/lib/galaxy/objectstore/azure_blob.py b/lib/galaxy/objectstore/azure_blob.py index 02f08b6efbe..a2cc6462c61 100644 --- a/lib/galaxy/objectstore/azure_blob.py +++ b/lib/galaxy/objectstore/azure_blob.py @@ -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.") diff --git a/lib/galaxy/objectstore/pithos.py b/lib/galaxy/objectstore/pithos.py index 31a1508eed5..8398ff64ac8 100644 --- a/lib/galaxy/objectstore/pithos.py +++ b/lib/galaxy/objectstore/pithos.py @@ -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 " diff --git a/lib/galaxy/objectstore/rods.py b/lib/galaxy/objectstore/rods.py index f5718f8c743..65114037c16 100644 --- a/lib/galaxy/objectstore/rods.py +++ b/lib/galaxy/objectstore/rods.py @@ -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') diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py index ad312fa872a..e56b7d6e084 100644 --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -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 diff --git a/lib/galaxy/objectstore/s3_multipart_upload.py b/lib/galaxy/objectstore/s3_multipart_upload.py index 704d9441725..f564c1f8524 100644 --- a/lib/galaxy/objectstore/s3_multipart_upload.py +++ b/lib/galaxy/objectstore/s3_multipart_upload.py @@ -11,7 +11,6 @@ import glob import multiprocessing import os import subprocess - from multiprocessing.pool import IMapIterator try: diff --git a/lib/galaxy/openid/providers.py b/lib/galaxy/openid/providers.py index 8c1ae0d7ff5..5885167a095 100644 --- a/lib/galaxy/openid/providers.py +++ b/lib/galaxy/openid/providers.py @@ -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 diff --git a/lib/galaxy/queue_worker.py b/lib/galaxy/queue_worker.py index 9881d8136e6..0691b984d8b 100644 --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -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__) diff --git a/lib/galaxy/queues.py b/lib/galaxy/queues.py index 238900fcdc8..333ac281eb3 100644 --- a/lib/galaxy/queues.py +++ b/lib/galaxy/queues.py @@ -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') diff --git a/lib/galaxy/sample_tracking/request_types.py b/lib/galaxy/sample_tracking/request_types.py index dd05dd34786..14a54400128 100644 --- a/lib/galaxy/sample_tracking/request_types.py +++ b/lib/galaxy/sample_tracking/request_types.py @@ -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()]) diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 1c607ada3ad..f29e2dbf95f 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -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, diff --git a/lib/galaxy/tools/actions/metadata.py b/lib/galaxy/tools/actions/metadata.py index e58ead289ae..6e97706dc66 100644 --- a/lib/galaxy/tools/actions/metadata.py +++ b/lib/galaxy/tools/actions/metadata.py @@ -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__) diff --git a/lib/galaxy/tools/actions/upload.py b/lib/galaxy/tools/actions/upload.py index 089205c41a2..70bf8152c44 100644 --- a/lib/galaxy/tools/actions/upload.py +++ b/lib/galaxy/tools/actions/upload.py @@ -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__) diff --git a/lib/galaxy/tools/cwl/parser.py b/lib/galaxy/tools/cwl/parser.py index cb9a78d8e27..1c8a957c9a3 100644 --- a/lib/galaxy/tools/cwl/parser.py +++ b/lib/galaxy/tools/cwl/parser.py @@ -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__) diff --git a/lib/galaxy/tools/cwl/schema.py b/lib/galaxy/tools/cwl/schema.py index 6b3e1e49ccd..0ca2c30d85a 100644 --- a/lib/galaxy/tools/cwl/schema.py +++ b/lib/galaxy/tools/cwl/schema.py @@ -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 diff --git a/lib/galaxy/tools/deps/__init__.py b/lib/galaxy/tools/deps/__init__.py index 1c173aa1333..b344268c9b4 100644 --- a/lib/galaxy/tools/deps/__init__.py +++ b/lib/galaxy/tools/deps/__init__.py @@ -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 diff --git a/lib/galaxy/tools/deps/conda_util.py b/lib/galaxy/tools/deps/conda_util.py index 4ed629d2c30..4209e201198 100644 --- a/lib/galaxy/tools/deps/conda_util.py +++ b/lib/galaxy/tools/deps/conda_util.py @@ -6,7 +6,6 @@ import os import re import shutil import tempfile - from distutils.version import LooseVersion from sys import platform as _platform diff --git a/lib/galaxy/tools/deps/containers.py b/lib/galaxy/tools/deps/containers.py index f3ca14c8552..ab00a1b0b1e 100644 --- a/lib/galaxy/tools/deps/containers.py +++ b/lib/galaxy/tools/deps/containers.py @@ -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, diff --git a/lib/galaxy/tools/deps/mulled/mulled_build.py b/lib/galaxy/tools/deps/mulled/mulled_build.py index 381afbe2718..aa1c5d3e4c4 100644 --- a/lib/galaxy/tools/deps/mulled/mulled_build.py +++ b/lib/galaxy/tools/deps/mulled/mulled_build.py @@ -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, diff --git a/lib/galaxy/tools/deps/mulled/mulled_build_tool.py b/lib/galaxy/tools/deps/mulled/mulled_build_tool.py index 58de0eba9cd..a46cb06da57 100644 --- a/lib/galaxy/tools/deps/mulled/mulled_build_tool.py +++ b/lib/galaxy/tools/deps/mulled/mulled_build_tool.py @@ -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, diff --git a/lib/galaxy/tools/deps/mulled/util.py b/lib/galaxy/tools/deps/mulled/util.py index 46ede34a55d..f0a1409e15c 100644 --- a/lib/galaxy/tools/deps/mulled/util.py +++ b/lib/galaxy/tools/deps/mulled/util.py @@ -3,7 +3,6 @@ from __future__ import print_function import collections import hashlib - from distutils.version import LooseVersion try: diff --git a/lib/galaxy/tools/deps/resolvers/__init__.py b/lib/galaxy/tools/deps/resolvers/__init__.py index d7760f8b7d2..a732ec1d761 100644 --- a/lib/galaxy/tools/deps/resolvers/__init__.py +++ b/lib/galaxy/tools/deps/resolvers/__init__.py @@ -10,7 +10,6 @@ import yaml from galaxy.util import listify from galaxy.util.dictifiable import Dictifiable - from ..requirements import ToolRequirement diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py index 7f0b72c5ab2..1992b348ac6 100644 --- a/lib/galaxy/tools/deps/resolvers/conda.py +++ b/lib/galaxy/tools/deps/resolvers/conda.py @@ -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, diff --git a/lib/galaxy/tools/deps/resolvers/galaxy_packages.py b/lib/galaxy/tools/deps/resolvers/galaxy_packages.py index f3d5dea2f5b..edd7a18ae04 100644 --- a/lib/galaxy/tools/deps/resolvers/galaxy_packages.py +++ b/lib/galaxy/tools/deps/resolvers/galaxy_packages.py @@ -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, diff --git a/lib/galaxy/tools/error_reports/plugins/biostars.py b/lib/galaxy/tools/error_reports/plugins/biostars.py index 5bc071a5a2d..d063209c2b8 100644 --- a/lib/galaxy/tools/error_reports/plugins/biostars.py +++ b/lib/galaxy/tools/error_reports/plugins/biostars.py @@ -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__) diff --git a/lib/galaxy/tools/error_reports/plugins/email.py b/lib/galaxy/tools/error_reports/plugins/email.py index bbf61db5629..6d231e8281b 100644 --- a/lib/galaxy/tools/error_reports/plugins/email.py +++ b/lib/galaxy/tools/error_reports/plugins/email.py @@ -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__) diff --git a/lib/galaxy/tools/error_reports/plugins/github.py b/lib/galaxy/tools/error_reports/plugins/github.py index 080880a30ee..baa756e1aa8 100644 --- a/lib/galaxy/tools/error_reports/plugins/github.py +++ b/lib/galaxy/tools/error_reports/plugins/github.py @@ -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__) diff --git a/lib/galaxy/tools/error_reports/plugins/influxdb.py b/lib/galaxy/tools/error_reports/plugins/influxdb.py index a2fa8f22346..77553c5db75 100644 --- a/lib/galaxy/tools/error_reports/plugins/influxdb.py +++ b/lib/galaxy/tools/error_reports/plugins/influxdb.py @@ -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__) diff --git a/lib/galaxy/tools/error_reports/plugins/json.py b/lib/galaxy/tools/error_reports/plugins/json.py index 2bfa5c4453f..c1ce581216c 100644 --- a/lib/galaxy/tools/error_reports/plugins/json.py +++ b/lib/galaxy/tools/error_reports/plugins/json.py @@ -7,7 +7,6 @@ import os import tempfile from galaxy.util import string_as_bool - from ..plugins import ErrorPlugin log = logging.getLogger(__name__) diff --git a/lib/galaxy/tools/error_reports/plugins/sentry.py b/lib/galaxy/tools/error_reports/plugins/sentry.py index 5d485382c76..5c8fcec5694 100644 --- a/lib/galaxy/tools/error_reports/plugins/sentry.py +++ b/lib/galaxy/tools/error_reports/plugins/sentry.py @@ -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__) diff --git a/lib/galaxy/tools/lint.py b/lib/galaxy/tools/lint.py index f2e04e24c83..5957c58dd4a 100644 --- a/lib/galaxy/tools/lint.py +++ b/lib/galaxy/tools/lint.py @@ -4,7 +4,6 @@ from __future__ import print_function import inspect from galaxy.util import submodules - from .parser import get_tool_source diff --git a/lib/galaxy/tools/linters/inputs.py b/lib/galaxy/tools/linters/inputs.py index 2f85cfca09b..ffcc5c974d5 100644 --- a/lib/galaxy/tools/linters/inputs.py +++ b/lib/galaxy/tools/linters/inputs.py @@ -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 diff --git a/lib/galaxy/tools/locations/__init__.py b/lib/galaxy/tools/locations/__init__.py index 91b7a6f9f87..3fe9cff73ef 100644 --- a/lib/galaxy/tools/locations/__init__.py +++ b/lib/galaxy/tools/locations/__init__.py @@ -1,6 +1,5 @@ import os import tempfile - from abc import ( ABCMeta, abstractmethod, diff --git a/lib/galaxy/tools/locations/dockstore.py b/lib/galaxy/tools/locations/dockstore.py index 3eb96e55e24..a156780f136 100644 --- a/lib/galaxy/tools/locations/dockstore.py +++ b/lib/galaxy/tools/locations/dockstore.py @@ -3,7 +3,6 @@ try: except ImportError: requests = None import yaml - from six.moves.urllib.parse import quote from ..locations import ( diff --git a/lib/galaxy/tools/locations/http.py b/lib/galaxy/tools/locations/http.py index d03ef3854da..699df9200d2 100644 --- a/lib/galaxy/tools/locations/http.py +++ b/lib/galaxy/tools/locations/http.py @@ -1,5 +1,4 @@ from galaxy.util import download_to_file - from ..locations import ( ToolLocationResolver, ) diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py index c0343ff2c47..0d0d90e1d77 100644 --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -9,7 +9,6 @@ from json import dumps from galaxy.util.expressions import ExpressionContext from galaxy.util.json import json_fix from galaxy.util.json import safe_loads - from .basic import DataCollectionToolParameter, DataToolParameter, RuntimeValue, SelectToolParameter from .grouping import Conditional, Repeat, Section, UploadDataset diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 74f74e03a90..76faccdee44 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -23,7 +23,6 @@ from galaxy.util.bunch import Bunch from galaxy.util.dictifiable import Dictifiable from galaxy.util.expressions import ExpressionContext from galaxy.web import url_for - from . import validation from .dataset_matcher import ( DatasetCollectionMatcher, diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py index 514f02b1feb..86d30d0a0c2 100644 --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -14,7 +14,6 @@ from galaxy.model import ( User ) from galaxy.util import string_as_bool - from . import validation log = logging.getLogger(__name__) diff --git a/lib/galaxy/tools/parameters/output_collect.py b/lib/galaxy/tools/parameters/output_collect.py index cefa90132e9..c24babea7c4 100644 --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -6,7 +6,6 @@ import logging import operator import os import re - from collections import namedtuple from galaxy import util diff --git a/lib/galaxy/tools/parser/cwl.py b/lib/galaxy/tools/parser/cwl.py index 2c9a1444cc0..251862c8bab 100644 --- a/lib/galaxy/tools/parser/cwl.py +++ b/lib/galaxy/tools/parser/cwl.py @@ -4,11 +4,12 @@ import os from galaxy.tools.cwl import tool_proxy from galaxy.tools.deps import requirements from galaxy.util.odict import odict - -from .interface import PageSource -from .interface import PagesSource -from .interface import ToolSource -from .interface import ToolStdioExitCode +from .interface import ( + PageSource, + PagesSource, + ToolSource, + ToolStdioExitCode +) from .output_actions import ToolOutputActionGroup from .output_objects import ToolOutput from .yaml import YamlInputSource diff --git a/lib/galaxy/tools/parser/factory.py b/lib/galaxy/tools/parser/factory.py index 52a11ad7b57..28c3e877257 100644 --- a/lib/galaxy/tools/parser/factory.py +++ b/lib/galaxy/tools/parser/factory.py @@ -7,12 +7,10 @@ import yaml from galaxy.tools.loader import load_tool_with_refereces from galaxy.util.odict import odict - from .cwl import CwlToolSource from .interface import InputSource from .xml import XmlInputSource, XmlToolSource from .yaml import YamlToolSource - from ..fetcher import ToolLocationFetcher log = logging.getLogger(__name__) diff --git a/lib/galaxy/tools/parser/xml.py b/lib/galaxy/tools/parser/xml.py index a38a45190a2..266839a7151 100644 --- a/lib/galaxy/tools/parser/xml.py +++ b/lib/galaxy/tools/parser/xml.py @@ -3,13 +3,11 @@ import re import sys import traceback import uuid - from math import isinf from galaxy.tools.deps import requirements from galaxy.util import string_as_bool, xml_text, xml_to_string from galaxy.util.odict import odict - from .interface import ( InputSource, PageSource, diff --git a/lib/galaxy/tools/parser/yaml.py b/lib/galaxy/tools/parser/yaml.py index c50e4efab8b..71a593e3cf6 100644 --- a/lib/galaxy/tools/parser/yaml.py +++ b/lib/galaxy/tools/parser/yaml.py @@ -1,7 +1,5 @@ - from galaxy.tools.deps import requirements from galaxy.util.odict import odict - from .interface import InputSource from .interface import PageSource from .interface import PagesSource diff --git a/lib/galaxy/tools/toolbox/__init__.py b/lib/galaxy/tools/toolbox/__init__.py index 604c4e49231..b4774ed8709 100644 --- a/lib/galaxy/tools/toolbox/__init__.py +++ b/lib/galaxy/tools/toolbox/__init__.py @@ -1,7 +1,6 @@ """API for this module containing functionality related to the toolbox.""" from .base import AbstractToolBox, BaseGalaxyToolBox - from .panel import panel_item_types, ToolSection, ToolSectionLabel __all__ = ( diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py index 52452ed41c9..49de5c2a04b 100644 --- a/lib/galaxy/tools/toolbox/base.py +++ b/lib/galaxy/tools/toolbox/base.py @@ -10,8 +10,6 @@ from six import iteritems from six.moves.urllib.parse import urlparse from galaxy.exceptions import MessageException, ObjectNotFound -# Next two are extra tool dependency not used by AbstractToolBox but by -# BaseGalaxyToolBox. from galaxy.tools.deps import build_dependency_manager from galaxy.tools.loader_directory import looks_like_a_tool from galaxy.util import ( @@ -23,7 +21,6 @@ from galaxy.util import ( from galaxy.util.bunch import Bunch from galaxy.util.dictifiable import Dictifiable from galaxy.util.odict import odict - from .filters import FilterFactory from .integrated_panel import ManagesIntegratedToolPanelMixin from .lineages import LineageMap diff --git a/lib/galaxy/tools/toolbox/filters/__init__.py b/lib/galaxy/tools/toolbox/filters/__init__.py index 5d36d24c19b..ae9422c624a 100644 --- a/lib/galaxy/tools/toolbox/filters/__init__.py +++ b/lib/galaxy/tools/toolbox/filters/__init__.py @@ -1,6 +1,5 @@ import logging import sys - from copy import deepcopy from galaxy.util import listify diff --git a/lib/galaxy/tools/toolbox/lineages/factory.py b/lib/galaxy/tools/toolbox/lineages/factory.py index 0893f9471b7..ffaa108dab9 100644 --- a/lib/galaxy/tools/toolbox/lineages/factory.py +++ b/lib/galaxy/tools/toolbox/lineages/factory.py @@ -1,5 +1,4 @@ from galaxy.util.tool_version import remove_version_from_guid - from .interface import ToolLineage diff --git a/lib/galaxy/tools/toolbox/lineages/interface.py b/lib/galaxy/tools/toolbox/lineages/interface.py index 44018a9070c..3605b3ebf8b 100644 --- a/lib/galaxy/tools/toolbox/lineages/interface.py +++ b/lib/galaxy/tools/toolbox/lineages/interface.py @@ -1,5 +1,4 @@ import threading - from distutils.version import LooseVersion from galaxy.util.tool_version import remove_version_from_guid diff --git a/lib/galaxy/tools/toolbox/panel.py b/lib/galaxy/tools/toolbox/panel.py index d07a6fcb59d..0f8deb55f6f 100644 --- a/lib/galaxy/tools/toolbox/panel.py +++ b/lib/galaxy/tools/toolbox/panel.py @@ -5,7 +5,6 @@ from six import iteritems from galaxy.util import bunch from galaxy.util.dictifiable import Dictifiable from galaxy.util.odict import odict - from .parser import ensure_tool_conf_item diff --git a/lib/galaxy/tools/verify/__init__.py b/lib/galaxy/tools/verify/__init__.py index 8e80fc69f95..c2f873dfa45 100644 --- a/lib/galaxy/tools/verify/__init__.py +++ b/lib/galaxy/tools/verify/__init__.py @@ -15,7 +15,6 @@ except ImportError: pysam = None from galaxy.util.compression_utils import get_fileobj - from .asserts import verify_assertions from .test_data import TestDataResolver diff --git a/lib/galaxy/tools/verify/test_data.py b/lib/galaxy/tools/verify/test_data.py index 01459a217c3..9bacf3f640c 100644 --- a/lib/galaxy/tools/verify/test_data.py +++ b/lib/galaxy/tools/verify/test_data.py @@ -4,7 +4,6 @@ import hashlib import os import re import subprocess - from string import Template from galaxy.util import asbool diff --git a/lib/galaxy/tours/__init__.py b/lib/galaxy/tours/__init__.py index 6dc82da82c3..8c214ac81c1 100644 --- a/lib/galaxy/tours/__init__.py +++ b/lib/galaxy/tours/__init__.py @@ -1,10 +1,10 @@ """ This module manages loading/etc of Galaxy interactive tours. """ - -import os -import yaml import logging +import os + +import yaml from galaxy import util diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py index 24ee2cd9011..49835e48990 100644 --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -21,18 +21,18 @@ import sys import tempfile import threading import time -try: - import grp -except ImportError: - # For Pulsar on Windows (which does not use the function that uses grp) - grp = None - from datetime import datetime from hashlib import md5 from os.path import relpath from xml.etree import ElementInclude, ElementTree from xml.etree.ElementTree import ParseError +try: + import grp +except ImportError: + # For Pulsar on Windows (which does not use the function that uses grp) + grp = None + from six import binary_type, iteritems, string_types, text_type from six.moves import email_mime_multipart, email_mime_text, xrange, zip from six.moves.urllib import ( diff --git a/lib/galaxy/util/biostar.py b/lib/galaxy/util/biostar.py index dd5a783ee7f..c0f8df585ca 100644 --- a/lib/galaxy/util/biostar.py +++ b/lib/galaxy/util/biostar.py @@ -7,14 +7,12 @@ import hmac import logging import re import urlparse - from unicodedata import normalize from six import text_type from galaxy.tools.errors import ErrorReporter from galaxy.web.base.controller import url_for - from . import smart_str log = logging.getLogger(__name__) diff --git a/lib/galaxy/util/object_wrapper.py b/lib/galaxy/util/object_wrapper.py index 63f448bbbfb..b136548d462 100644 --- a/lib/galaxy/util/object_wrapper.py +++ b/lib/galaxy/util/object_wrapper.py @@ -9,6 +9,19 @@ import logging import string import sys from numbers import Number +from types import ( + BuiltinFunctionType, + BuiltinMethodType, + CodeType, + FrameType, + FunctionType, + GeneratorType, + GetSetDescriptorType, + MemberDescriptorType, + MethodType, + ModuleType, + TracebackType, +) try: from types import NoneType @@ -45,20 +58,6 @@ except ImportError: BufferType = SliceType DictProxyType = SliceType -from types import ( - BuiltinFunctionType, - BuiltinMethodType, - CodeType, - FrameType, - FunctionType, - GeneratorType, - GetSetDescriptorType, - MemberDescriptorType, - MethodType, - ModuleType, - TracebackType, -) - from six.moves import ( copyreg as copy_reg, UserDict diff --git a/lib/galaxy/util/pastescript/loadwsgi.py b/lib/galaxy/util/pastescript/loadwsgi.py index ed7f15cded3..8d773283fcf 100644 --- a/lib/galaxy/util/pastescript/loadwsgi.py +++ b/lib/galaxy/util/pastescript/loadwsgi.py @@ -9,7 +9,6 @@ import re import sys import pkg_resources - from six import iteritems from six.moves.urllib.parse import unquote diff --git a/lib/galaxy/util/properties.py b/lib/galaxy/util/properties.py index 8c22e0aaf59..23890219c0f 100644 --- a/lib/galaxy/util/properties.py +++ b/lib/galaxy/util/properties.py @@ -7,7 +7,6 @@ import os.path import sys import yaml - from six import iteritems from six.moves.configparser import ConfigParser diff --git a/lib/galaxy/util/submodules.py b/lib/galaxy/util/submodules.py index 7add15263a0..65c0644b5a5 100644 --- a/lib/galaxy/util/submodules.py +++ b/lib/galaxy/util/submodules.py @@ -1,7 +1,6 @@ from __future__ import absolute_import import logging - from os import listdir log = logging.getLogger(__name__) diff --git a/lib/galaxy/util/xml_macros.py b/lib/galaxy/util/xml_macros.py index 0667c8c6550..c3d437b9894 100644 --- a/lib/galaxy/util/xml_macros.py +++ b/lib/galaxy/util/xml_macros.py @@ -1,5 +1,4 @@ import os - from copy import deepcopy from xml.etree import ElementInclude, ElementTree diff --git a/lib/galaxy/visualization/data_providers/phyloviz/__init__.py b/lib/galaxy/visualization/data_providers/phyloviz/__init__.py index d7644ff23fc..718e2a5ec54 100644 --- a/lib/galaxy/visualization/data_providers/phyloviz/__init__.py +++ b/lib/galaxy/visualization/data_providers/phyloviz/__init__.py @@ -2,8 +2,8 @@ """ Data providers code for PhyloViz """ from galaxy.visualization.data_providers.basic import BaseDataProvider -from galaxy.visualization.data_providers.phyloviz.nexusparser import Nexus_Parser from galaxy.visualization.data_providers.phyloviz.newickparser import Newick_Parser +from galaxy.visualization.data_providers.phyloviz.nexusparser import Nexus_Parser from galaxy.visualization.data_providers.phyloviz.phyloxmlparser import Phyloxml_Parser diff --git a/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py b/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py index c3d2a9d1086..2066cacd730 100644 --- a/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py +++ b/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py @@ -1,6 +1,6 @@ +import re from .baseparser import Base_Parser, PhyloTree -import re class Newick_Parser(Base_Parser): diff --git a/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py b/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py index 8ef67f649d4..bf07b7eaefd 100644 --- a/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py +++ b/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py @@ -1,7 +1,7 @@ -from __future__ import with_statement -from newickparser import Newick_Parser import re +from .newickparser import Newick_Parser + MAX_READLINES = 200000 diff --git a/lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py b/lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py index 817cca6a566..522d4ccd9cb 100644 --- a/lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py +++ b/lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py @@ -1,6 +1,11 @@ -from baseparser import Base_Parser, PhyloTree, Node from xml.etree import ElementTree +from .baseparser import ( + Base_Parser, + Node, + PhyloTree +) + class Phyloxml_Parser(Base_Parser): """Parses a phyloxml file into a json file that will be passed to PhyloViz for display""" diff --git a/lib/galaxy/visualization/data_providers/registry.py b/lib/galaxy/visualization/data_providers/registry.py index 519dd3b2f9e..dc336c6dd88 100644 --- a/lib/galaxy/visualization/data_providers/registry.py +++ b/lib/galaxy/visualization/data_providers/registry.py @@ -1,13 +1,20 @@ from six import string_types -from galaxy.visualization.data_providers.basic import ColumnDataProvider -from galaxy.visualization.data_providers import genome -from galaxy.model import NoConverterException -from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider -from galaxy.datatypes.tabular import Tabular, Vcf -from galaxy.datatypes.interval import Interval, ENCODEPeak, ChromatinInteractions, Gtf, Gff, Bed -from galaxy.datatypes.xml import Phyloxml from galaxy.datatypes.data import Newick, Nexus +from galaxy.datatypes.interval import ( + Bed, + ChromatinInteractions, + ENCODEPeak, + Gff, + Gtf, + Interval +) +from galaxy.datatypes.tabular import Tabular, Vcf +from galaxy.datatypes.xml import Phyloxml +from galaxy.model import NoConverterException +from galaxy.visualization.data_providers import genome +from galaxy.visualization.data_providers.basic import ColumnDataProvider +from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider class DataProviderRegistry(object): diff --git a/lib/galaxy/visualization/plugins/config_parser.py b/lib/galaxy/visualization/plugins/config_parser.py index 1c32035411f..9ba2e37de48 100644 --- a/lib/galaxy/visualization/plugins/config_parser.py +++ b/lib/galaxy/visualization/plugins/config_parser.py @@ -1,9 +1,10 @@ +import logging + from six import string_types import galaxy.model from galaxy import util -import logging log = logging.getLogger(__name__) diff --git a/lib/galaxy/visualization/plugins/registry.py b/lib/galaxy/visualization/plugins/registry.py index 6d815986ebb..e9093538b6b 100644 --- a/lib/galaxy/visualization/plugins/registry.py +++ b/lib/galaxy/visualization/plugins/registry.py @@ -8,14 +8,18 @@ import logging import os import weakref -from galaxy.util import config_directories_from_setting -from galaxy.util import odict -from galaxy.util import parse_xml -from galaxy.web import url_for from galaxy.exceptions import ObjectNotFound -from galaxy.visualization.plugins import config_parser -from galaxy.visualization.plugins import plugin as vis_plugins -from galaxy.visualization.plugins import utils as vis_utils +from galaxy.util import ( + config_directories_from_setting, + odict, + parse_xml +) +from galaxy.visualization.plugins import ( + config_parser, + plugin as vis_plugins, + utils as vis_utils +) +from galaxy.web import url_for log = logging.getLogger(__name__) diff --git a/lib/galaxy/visualization/plugins/resource_parser.py b/lib/galaxy/visualization/plugins/resource_parser.py index 1bb0743ad58..1ac6b65464a 100644 --- a/lib/galaxy/visualization/plugins/resource_parser.py +++ b/lib/galaxy/visualization/plugins/resource_parser.py @@ -8,9 +8,11 @@ import weakref import galaxy.exceptions import galaxy.util +from galaxy.managers import ( + hdas as hda_manager, + visualizations as visualization_manager +) from galaxy.util import bunch -from galaxy.managers import visualizations as visualization_manager -from galaxy.managers import hdas as hda_manager log = logging.getLogger(__name__) diff --git a/lib/galaxy/web/form_builder.py b/lib/galaxy/web/form_builder.py index c138e00c747..b4a04140d24 100644 --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -4,8 +4,8 @@ Classes for generating HTML forms from __future__ import print_function import logging - from cgi import escape + from six import string_types from galaxy.util import restore_text, unicodify diff --git a/lib/galaxy/web/framework/formbuilder.py b/lib/galaxy/web/framework/formbuilder.py index 33c14c47fc7..1603e3bf4a8 100644 --- a/lib/galaxy/web/framework/formbuilder.py +++ b/lib/galaxy/web/framework/formbuilder.py @@ -1,6 +1,7 @@ +import logging + from galaxy.util import bunch -import logging log = logging.getLogger(__name__) diff --git a/lib/galaxy/web/framework/helpers/__init__.py b/lib/galaxy/web/framework/helpers/__init__.py index b54ade34301..d2901d4a126 100644 --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -1,17 +1,21 @@ """ Galaxy web framework helpers """ - -from ..base import server_starttime from datetime import datetime, timedelta -from galaxy.util import hash_util -from galaxy.util import unicodify -from galaxy.util.json import safe_dumps as dumps # Used by mako templates # noqa: F401 -from webhelpers import date -from webhelpers.html.tags import stylesheet_link, javascript_link - from routes import url_for +from webhelpers import date +from webhelpers.html.tags import ( + javascript_link, + stylesheet_link +) + +from galaxy.util import ( + hash_util, + unicodify +) +from galaxy.util.json import safe_dumps as dumps # Used by mako templates # noqa: F401 +from ..base import server_starttime def time_ago(x): diff --git a/lib/galaxy/web/framework/middleware/batch.py b/lib/galaxy/web/framework/middleware/batch.py index 9d666c08d81..2cd21e2f780 100644 --- a/lib/galaxy/web/framework/middleware/batch.py +++ b/lib/galaxy/web/framework/middleware/batch.py @@ -20,14 +20,14 @@ API tasks. IOW, this ain't about batching jobs. ..warning: this endpoint is experimental is likely to change. """ import io -from urlparse import urlparse import json -import re - -from paste import httpexceptions -import routes - import logging +import re +from urlparse import urlparse + +import routes +from paste import httpexceptions + log = logging.getLogger(__name__) diff --git a/lib/galaxy/web/framework/middleware/graphite.py b/lib/galaxy/web/framework/middleware/graphite.py index 73283ee551c..cdc5fa9b2e5 100644 --- a/lib/galaxy/web/framework/middleware/graphite.py +++ b/lib/galaxy/web/framework/middleware/graphite.py @@ -3,8 +3,9 @@ Middleware for sending request statistics to graphite """ from __future__ import absolute_import -import time import logging +import time + log = logging.getLogger(__name__) try: diff --git a/lib/galaxy/web/framework/middleware/profile.py b/lib/galaxy/web/framework/middleware/profile.py index b5cf31c94a7..53e79d51030 100644 --- a/lib/galaxy/web/framework/middleware/profile.py +++ b/lib/galaxy/web/framework/middleware/profile.py @@ -2,11 +2,10 @@ Middleware that profiles the request with cProfile and displays profiling information at the bottom of each page. """ - -import threading import cgi import cProfile import pstats +import threading from paste import response diff --git a/lib/galaxy/web/framework/middleware/remoteuser.py b/lib/galaxy/web/framework/middleware/remoteuser.py index c635f9d2d7a..43e5368840d 100644 --- a/lib/galaxy/web/framework/middleware/remoteuser.py +++ b/lib/galaxy/web/framework/middleware/remoteuser.py @@ -1,10 +1,11 @@ """ Middleware for handling $REMOTE_USER if use_remote_user is enabled. """ - -import socket -from galaxy.util import safe_str_cmp import logging +import socket + +from galaxy.util import safe_str_cmp + log = logging.getLogger(__name__) errorpage = """ diff --git a/lib/galaxy/web/framework/openid_manager.py b/lib/galaxy/web/framework/openid_manager.py index 22b8b6d1c4e..03a2a0f55f0 100644 --- a/lib/galaxy/web/framework/openid_manager.py +++ b/lib/galaxy/web/framework/openid_manager.py @@ -2,15 +2,15 @@ Manage the OpenID consumer and related data stores. """ +import logging import os import pickle -import logging try: from openid import oidutil - from openid.store import filestore from openid.consumer import consumer from openid.extensions import sreg + from openid.store import filestore except ImportError: oidutil = None diff --git a/lib/galaxy/web/proxy/__init__.py b/lib/galaxy/web/proxy/__init__.py index 581050a3d5e..2ab6e1f6d40 100644 --- a/lib/galaxy/web/proxy/__init__.py +++ b/lib/galaxy/web/proxy/__init__.py @@ -1,17 +1,19 @@ +import json import logging import os -import json +import time from collections import namedtuple -from galaxy.util.filelock import FileLock -from galaxy.util import sockets -from galaxy.util.lazy_process import LazyProcess, NoOpLazyProcess -from galaxy.util import sqlite -from galaxy.util import unique_id -import time - import requests +from galaxy.util import ( + sockets, + sqlite, + unique_id +) +from galaxy.util.filelock import FileLock +from galaxy.util.lazy_process import LazyProcess, NoOpLazyProcess + log = logging.getLogger(__name__) diff --git a/lib/galaxy/web/security/__init__.py b/lib/galaxy/web/security/__init__.py index cb50d37bcb5..a7962e0229d 100644 --- a/lib/galaxy/web/security/__init__.py +++ b/lib/galaxy/web/security/__init__.py @@ -1,14 +1,13 @@ import collections +import logging import os import os.path -import logging from Crypto.Cipher import Blowfish -from Crypto.Util.randpool import RandomPool from Crypto.Util import number +from Crypto.Util.randpool import RandomPool import galaxy.exceptions - from galaxy.util import smart_str log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/config_manage.py b/lib/galaxy/webapps/config_manage.py index 685b5abcf56..695500a9cff 100644 --- a/lib/galaxy/webapps/config_manage.py +++ b/lib/galaxy/webapps/config_manage.py @@ -2,21 +2,22 @@ from __future__ import absolute_import from __future__ import print_function import argparse -from collections import namedtuple -from collections import OrderedDict import copy import os import shutil import string import sys import tempfile +from collections import ( + namedtuple, + OrderedDict +) from textwrap import TextWrapper import requests import six -from six import StringIO - import yaml +from six import StringIO try: from pykwalify.core import Core @@ -26,8 +27,8 @@ except ImportError: if __name__ == '__main__': sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir))) -from galaxy.util.properties import nice_config_parser from galaxy.util import safe_makedirs +from galaxy.util.properties import nice_config_parser DESCRIPTION = "Convert configuration files." diff --git a/lib/galaxy/webapps/galaxy/api/annotations.py b/lib/galaxy/webapps/galaxy/api/annotations.py index 66851e0ad06..50ea8f0931c 100644 --- a/lib/galaxy/webapps/galaxy/api/annotations.py +++ b/lib/galaxy/webapps/galaxy/api/annotations.py @@ -1,18 +1,20 @@ """ API operations on annotations. """ - -from galaxy.web.base.controller import BaseAPIController -from galaxy.web.base.controller import UsesStoredWorkflowMixin -from galaxy.model.item_attrs import UsesAnnotations - -from galaxy import managers - -from galaxy import exceptions -from galaxy.web import _future_expose_api as expose_api -from galaxy.util import sanitize_html - import logging + +from galaxy import ( + exceptions, + managers +) +from galaxy.model.item_attrs import UsesAnnotations +from galaxy.util import sanitize_html +from galaxy.web import _future_expose_api as expose_api +from galaxy.web.base.controller import ( + BaseAPIController, + UsesStoredWorkflowMixin +) + log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/configuration.py b/lib/galaxy/webapps/galaxy/api/configuration.py index a6e498b94d4..63843062b99 100644 --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -2,19 +2,19 @@ API operations allowing clients to determine Galaxy instance's capabilities and configuration settings. """ - -from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless -from galaxy.web import _future_expose_api as expose_api -from galaxy.web import _future_expose_api as expose_api_anonymous -from galaxy.web import require_admin -from galaxy.web.base.controller import BaseAPIController -from galaxy.managers import configuration, users -from galaxy.queue_worker import send_control_task - import json +import logging import os -import logging +from galaxy.managers import configuration, users +from galaxy.queue_worker import send_control_task +from galaxy.web import ( + _future_expose_api as expose_api, + _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless, + require_admin +) +from galaxy.web.base.controller import BaseAPIController + log = logging.getLogger(__name__) @@ -26,7 +26,7 @@ class ConfigurationController(BaseAPIController): self.admin_config_serializer = configuration.AdminConfigSerializer(app) self.user_manager = users.UserManager(app) - @expose_api_anonymous + @expose_api def whoami(self, trans, **kwd): """ GET /api/whoami diff --git a/lib/galaxy/webapps/galaxy/api/dataset_collections.py b/lib/galaxy/webapps/galaxy/api/dataset_collections.py index 5aeec294f69..37badbcaffc 100644 --- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py +++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py @@ -1,12 +1,13 @@ -from galaxy.web import _future_expose_api as expose_api - -from galaxy.web.base.controller import BaseAPIController -from galaxy.web.base.controller import UsesLibraryMixinItems +from logging import getLogger from galaxy import managers from galaxy.managers.collections_util import api_payload_to_create_params, dictify_dataset_collection_instance +from galaxy.web import _future_expose_api as expose_api +from galaxy.web.base.controller import ( + BaseAPIController, + UsesLibraryMixinItems +) -from logging import getLogger log = getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py index 81e6889337c..f4e03132947 100644 --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -1,24 +1,29 @@ """ API operations on the contents of a history dataset. """ +import logging + from six import string_types -from galaxy import model -from galaxy import exceptions as galaxy_exceptions -from galaxy import web -from galaxy.web.framework.helpers import is_true -from galaxy import util - -from galaxy.visualization.data_providers.genome import FeatureLocationIndexDataProvider -from galaxy.visualization.data_providers.genome import SamDataProvider -from galaxy.visualization.data_providers.genome import BamDataProvider +from galaxy import ( + exceptions as galaxy_exceptions, + managers, + model, + util, + web +) from galaxy.datatypes import dataproviders +from galaxy.visualization.data_providers.genome import ( + BamDataProvider, + FeatureLocationIndexDataProvider, + SamDataProvider +) +from galaxy.web.base.controller import ( + BaseAPIController, + UsesVisualizationMixin +) +from galaxy.web.framework.helpers import is_true -from galaxy.web.base.controller import BaseAPIController -from galaxy.web.base.controller import UsesVisualizationMixin -from galaxy import managers - -import logging log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/datatypes.py b/lib/galaxy/webapps/galaxy/api/datatypes.py index 0087f77c10b..2bb8ab6c849 100644 --- a/lib/galaxy/webapps/galaxy/api/datatypes.py +++ b/lib/galaxy/webapps/galaxy/api/datatypes.py @@ -1,14 +1,14 @@ """ API operations allowing clients to determine datatype supported by Galaxy. """ - -from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless -from galaxy import exceptions -from galaxy.web.base.controller import BaseAPIController -from galaxy.util import asbool -from galaxy.datatypes.data import Data - import logging + +from galaxy import exceptions +from galaxy.datatypes.data import Data +from galaxy.util import asbool +from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless +from galaxy.web.base.controller import BaseAPIController + log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/extended_metadata.py b/lib/galaxy/webapps/galaxy/api/extended_metadata.py index b9c5e43772d..784d01cadf5 100644 --- a/lib/galaxy/webapps/galaxy/api/extended_metadata.py +++ b/lib/galaxy/webapps/galaxy/api/extended_metadata.py @@ -2,10 +2,18 @@ API operations on annotations. """ import logging -from galaxy import web -from galaxy import managers -from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixinItems, UsesStoredWorkflowMixin, UsesExtendedMetadataMixin, HTTPNotImplemented +from galaxy import ( + managers, + web +) +from galaxy.web.base.controller import ( + BaseAPIController, + HTTPNotImplemented, + UsesExtendedMetadataMixin, + UsesLibraryMixinItems, + UsesStoredWorkflowMixin +) log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/folder_contents.py b/lib/galaxy/webapps/galaxy/api/folder_contents.py index 63ff60d4564..22bcbbb3c82 100644 --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -1,15 +1,20 @@ """ API operations on the contents of a library folder. """ -from galaxy import util -from galaxy import exceptions -from galaxy import managers +import logging + +from galaxy import ( + exceptions, + managers, + util +) from galaxy.managers import folders -from galaxy.web import _future_expose_api as expose_api -from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from galaxy.web import ( + _future_expose_api as expose_api, + _future_expose_api_anonymous as expose_api_anonymous +) from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems -import logging log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/folders.py b/lib/galaxy/webapps/galaxy/api/folders.py index e638d7119be..e7ad9849a44 100644 --- a/lib/galaxy/webapps/galaxy/api/folders.py +++ b/lib/galaxy/webapps/galaxy/api/folders.py @@ -1,13 +1,16 @@ """ API operations on library folders. """ -from galaxy import util -from galaxy import exceptions +import logging + +from galaxy import ( + exceptions, + util +) from galaxy.managers import folders, roles from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems -import logging log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/forms.py b/lib/galaxy/webapps/galaxy/api/forms.py index bd44665a150..67fd98c4dd4 100644 --- a/lib/galaxy/webapps/galaxy/api/forms.py +++ b/lib/galaxy/webapps/galaxy/api/forms.py @@ -2,7 +2,6 @@ API operations on FormDefinition objects. """ import logging - from xml.etree.ElementTree import XML from galaxy import web diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py index b496ac385ea..feec3990daa 100644 --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -1,36 +1,41 @@ """ API operations on the contents of a history. """ +import logging import os import re -from galaxy import exceptions -from galaxy import util -from galaxy.util.streamball import StreamBall -from galaxy.util.json import safe_dumps - -from galaxy.web import _future_expose_api as expose_api -from galaxy.web import _future_expose_api_raw as expose_api_raw -from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous -from galaxy.web import _future_expose_api_raw_anonymous as expose_api_raw_anonymous - -from galaxy.web.base.controller import BaseAPIController -from galaxy.web.base.controller import UsesLibraryMixin -from galaxy.web.base.controller import UsesLibraryMixinItems -from galaxy.web.base.controller import UsesTagsMixin - -from galaxy.managers import histories -from galaxy.managers import history_contents -from galaxy.managers import hdas -from galaxy.managers import hdcas -from galaxy.managers import folders +from galaxy import ( + exceptions, + util +) +from galaxy.managers import ( + folders, + hdas, + hdcas, + histories, + history_contents +) from galaxy.managers.collections_util import ( api_payload_to_create_params, dictify_dataset_collection_instance, get_hda_and_element_identifiers ) +from galaxy.util.json import safe_dumps +from galaxy.util.streamball import StreamBall +from galaxy.web import ( + _future_expose_api as expose_api, + _future_expose_api_anonymous as expose_api_anonymous, + _future_expose_api_raw as expose_api_raw, + _future_expose_api_raw_anonymous as expose_api_raw_anonymous +) +from galaxy.web.base.controller import ( + BaseAPIController, + UsesLibraryMixin, + UsesLibraryMixinItems, + UsesTagsMixin +) -import logging log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/item_tags.py b/lib/galaxy/webapps/galaxy/api/item_tags.py index 995f0d3823e..e27c47d4997 100644 --- a/lib/galaxy/webapps/galaxy/api/item_tags.py +++ b/lib/galaxy/webapps/galaxy/api/item_tags.py @@ -1,13 +1,15 @@ """ API operations related to tagging items. """ -from galaxy.web.base.controller import BaseAPIController -from galaxy.web.base.controller import UsesTagsMixin - -from galaxy.web import _future_expose_api as expose_api -from galaxy import exceptions - import logging + +from galaxy import exceptions +from galaxy.web import _future_expose_api as expose_api +from galaxy.web.base.controller import ( + BaseAPIController, + UsesTagsMixin +) + log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/job_files.py b/lib/galaxy/webapps/galaxy/api/job_files.py index 9a9137f4ed2..7e5c8c07115 100644 --- a/lib/galaxy/webapps/galaxy/api/job_files.py +++ b/lib/galaxy/webapps/galaxy/api/job_files.py @@ -1,18 +1,21 @@ """ API for asynchronous job running mechanisms can use to fetch or put files related to running and queued jobs. """ +import logging import os import shutil -from galaxy import exceptions -from galaxy import util -from galaxy import model +from galaxy import ( + exceptions, + model, + util +) +from galaxy.web import ( + _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless, + _future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless +) from galaxy.web.base.controller import BaseAPIController -from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless -from galaxy.web import _future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless - -import logging log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/libraries.py b/lib/galaxy/webapps/galaxy/api/libraries.py index f9d461fe129..7300b9962e3 100644 --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -1,14 +1,23 @@ """ API operations on a data library. """ -from galaxy import util -from galaxy import exceptions -from galaxy.managers import libraries, folders, roles -from galaxy.web import _future_expose_api as expose_api -from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +import logging + +from galaxy import ( + exceptions, + util +) +from galaxy.managers import ( + folders, + libraries, + roles +) +from galaxy.web import ( + _future_expose_api as expose_api, + _future_expose_api_anonymous as expose_api_anonymous +) from galaxy.web.base.controller import BaseAPIController -import logging log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/library_contents.py b/lib/galaxy/webapps/galaxy/api/library_contents.py index 7e7a9582f5f..70f51b5a88d 100644 --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -2,10 +2,12 @@ API operations on the contents of a data library. """ import logging + from sqlalchemy.orm.exc import ( MultipleResultsFound, NoResultFound, ) + from galaxy import ( exceptions, managers, diff --git a/lib/galaxy/webapps/galaxy/api/metrics.py b/lib/galaxy/webapps/galaxy/api/metrics.py index 270b4b064cf..472d1e3e7f0 100644 --- a/lib/galaxy/webapps/galaxy/api/metrics.py +++ b/lib/galaxy/webapps/galaxy/api/metrics.py @@ -5,12 +5,11 @@ API operations for for querying and recording user metrics from some client # TODO: facade or adapter to fluentd import datetime +import logging from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous - from galaxy.web.base.controller import BaseAPIController -import logging log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/page_revisions.py b/lib/galaxy/webapps/galaxy/api/page_revisions.py index 83fe08607fe..31e8969eed5 100644 --- a/lib/galaxy/webapps/galaxy/api/page_revisions.py +++ b/lib/galaxy/webapps/galaxy/api/page_revisions.py @@ -2,11 +2,16 @@ API for updating Galaxy Pages """ import logging -from galaxy.web import _future_expose_api as expose_api -from galaxy.web.base.controller import SharableItemSecurityMixin, BaseAPIController, SharableMixin + from galaxy import exceptions from galaxy.model.item_attrs import UsesAnnotations from galaxy.util.sanitize_html import sanitize_html +from galaxy.web import _future_expose_api as expose_api +from galaxy.web.base.controller import ( + BaseAPIController, + SharableItemSecurityMixin, + SharableMixin +) log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/pages.py b/lib/galaxy/webapps/galaxy/api/pages.py index fc3b9befa1e..baf046cf86a 100644 --- a/lib/galaxy/webapps/galaxy/api/pages.py +++ b/lib/galaxy/webapps/galaxy/api/pages.py @@ -2,11 +2,16 @@ API for updating Galaxy Pages """ import logging -from galaxy.web import _future_expose_api as expose_api -from galaxy.web.base.controller import SharableItemSecurityMixin, BaseAPIController, SharableMixin + from galaxy import exceptions from galaxy.model.item_attrs import UsesAnnotations from galaxy.util.sanitize_html import sanitize_html +from galaxy.web import _future_expose_api as expose_api +from galaxy.web.base.controller import ( + BaseAPIController, + SharableItemSecurityMixin, + SharableMixin +) log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/provenance.py b/lib/galaxy/webapps/galaxy/api/provenance.py index f3d0c5f1542..731e50dd6c8 100644 --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -2,10 +2,17 @@ API operations provenance """ import logging -from galaxy import web + +from paste.httpexceptions import ( + HTTPBadRequest, + HTTPNotImplemented +) + +from galaxy import ( + managers, + web +) from galaxy.web.base.controller import BaseAPIController -from paste.httpexceptions import HTTPNotImplemented, HTTPBadRequest -from galaxy import managers log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/quotas.py b/lib/galaxy/webapps/galaxy/api/quotas.py index 4ba16de6133..68b78ffeb7c 100644 --- a/lib/galaxy/webapps/galaxy/api/quotas.py +++ b/lib/galaxy/webapps/galaxy/api/quotas.py @@ -4,12 +4,22 @@ API operations on Quota objects. import logging from paste.httpexceptions import HTTPBadRequest -from sqlalchemy import false, true +from sqlalchemy import ( + false, + true +) -from galaxy import web, util +from galaxy import ( + util, + web +) from galaxy.actions.admin import AdminActions from galaxy.exceptions import ActionInputError -from galaxy.web.base.controller import BaseAPIController, UsesQuotaMixin, url_for +from galaxy.web.base.controller import ( + BaseAPIController, + url_for, + UsesQuotaMixin +) from galaxy.web.params import QuotaParamParser log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py index 7360f8ec12d..347bdc6e2a8 100644 --- a/lib/galaxy/webapps/galaxy/api/remote_files.py +++ b/lib/galaxy/webapps/galaxy/api/remote_files.py @@ -1,16 +1,17 @@ """ API operations on remote files. """ +import hashlib +import logging import os import time -import hashlib -from galaxy import exceptions -from galaxy.web import _future_expose_api as expose_api -from galaxy.util import jstree, unicodify -from galaxy.web.base.controller import BaseAPIController from operator import itemgetter -import logging +from galaxy import exceptions +from galaxy.util import jstree, unicodify +from galaxy.web import _future_expose_api as expose_api +from galaxy.web.base.controller import BaseAPIController + log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/search.py b/lib/galaxy/webapps/galaxy/api/search.py index e19501cc824..b1d5ae580df 100644 --- a/lib/galaxy/webapps/galaxy/api/search.py +++ b/lib/galaxy/webapps/galaxy/api/search.py @@ -2,10 +2,14 @@ API for searching Galaxy Datasets """ import logging + from galaxy import web -from galaxy.web.base.controller import SharableItemSecurityMixin, BaseAPIController -from galaxy.model.search import GalaxySearchEngine from galaxy.exceptions import ItemAccessibilityException +from galaxy.model.search import GalaxySearchEngine +from galaxy.web.base.controller import ( + BaseAPIController, + SharableItemSecurityMixin +) log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/tool_dependencies.py b/lib/galaxy/webapps/galaxy/api/tool_dependencies.py index 17f52c880bd..3c511bd5b9c 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_dependencies.py +++ b/lib/galaxy/webapps/galaxy/api/tool_dependencies.py @@ -1,15 +1,15 @@ """ API operations allowing clients to manage tool dependencies. """ - -from galaxy.web import _future_expose_api as expose_api -from galaxy.web import require_admin -from galaxy.web.base.controller import BaseAPIController +import logging from galaxy.tools.deps import views +from galaxy.web import ( + _future_expose_api as expose_api, + require_admin +) +from galaxy.web.base.controller import BaseAPIController - -import logging log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py index a9047c4fba6..5ffbdcfe1b2 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -3,28 +3,32 @@ import logging import re from time import strftime -from paste.httpexceptions import HTTPBadRequest, HTTPForbidden - +from paste.httpexceptions import ( + HTTPBadRequest, + HTTPForbidden +) from sqlalchemy import and_ -import tool_shed.util.shed_util_common as suc -from galaxy import util -from galaxy import web -from galaxy import exceptions +import tool_shed.util.shed_util_common as suc +from galaxy import ( + exceptions, + util, + web +) from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController - from tool_shed.galaxy_install.install_manager import InstallRepositoryManager from tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager -from tool_shed.util import common_util -from tool_shed.util import encoding_util -from tool_shed.util import hg_util -from tool_shed.util import repository_util -from tool_shed.util import tool_util -from tool_shed.util import workflow_util - +from tool_shed.util import ( + common_util, + encoding_util, + hg_util, + repository_util, + tool_util, + workflow_util +) log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/toolshed.py b/lib/galaxy/webapps/galaxy/api/toolshed.py index e0dbd459f97..48bc75f6ad1 100644 --- a/lib/galaxy/webapps/galaxy/api/toolshed.py +++ b/lib/galaxy/webapps/galaxy/api/toolshed.py @@ -1,18 +1,23 @@ import json import logging import re -from six.moves.urllib.parse import quote as urlquote -from six.moves.urllib.parse import unquote as urlunquote -from galaxy import util -from galaxy import web +from six.moves.urllib.parse import ( + quote as urlquote, + unquote as urlunquote +) +from galaxy import ( + util, + web +) from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController - -from tool_shed.util import common_util -from tool_shed.util import repository_util -from tool_shed.util import tool_util +from tool_shed.util import ( + common_util, + repository_util, + tool_util +) log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/visualizations.py b/lib/galaxy/webapps/galaxy/api/visualizations.py index d125c802171..dd28fc79af9 100644 --- a/lib/galaxy/webapps/galaxy/api/visualizations.py +++ b/lib/galaxy/webapps/galaxy/api/visualizations.py @@ -4,19 +4,24 @@ Visualizations resource control over the API. NOTE!: this is a work in progress and functionality and data structures may change often. """ -from six import string_types - -from galaxy.web.base.controller import BaseAPIController -from galaxy.web.base.controller import UsesVisualizationMixin -from galaxy.web.base.controller import SharableMixin -from galaxy.model.item_attrs import UsesAnnotations - -from galaxy.web import _future_expose_api as expose_api -from galaxy import web -from galaxy import util -from galaxy import exceptions import json import logging + +from six import string_types + +from galaxy import ( + exceptions, + util, + web +) +from galaxy.model.item_attrs import UsesAnnotations +from galaxy.web import _future_expose_api as expose_api +from galaxy.web.base.controller import ( + BaseAPIController, + SharableMixin, + UsesVisualizationMixin +) + log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/webhooks.py b/lib/galaxy/webapps/galaxy/api/webhooks.py index 98e3ad1a1d2..8b543e77754 100644 --- a/lib/galaxy/webapps/galaxy/api/webhooks.py +++ b/lib/galaxy/webapps/galaxy/api/webhooks.py @@ -1,15 +1,14 @@ """ API Controller providing Galaxy Webhooks """ +import imp +import logging +import random from galaxy.web import _future_expose_api_anonymous_and_sessionless as \ expose_api_anonymous_and_sessionless from galaxy.web.base.controller import BaseAPIController -import logging -import random -import imp - log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py index ebf18f32da9..11063366c0d 100644 --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -31,7 +31,6 @@ from galaxy.workflow.extract import extract_workflow from galaxy.workflow.modules import module_factory from galaxy.workflow.run import invoke, queue_invoke from galaxy.workflow.run_request import build_workflow_run_configs - from tool_shed.galaxy_install.install_manager import InstallRepositoryManager log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py index ab3ac554cd3..c73f93d4cf9 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -2,28 +2,37 @@ import imp import logging import os from datetime import datetime, timedelta -import six from string import punctuation as PUNCTUATION + +import six from sqlalchemy import and_, false, func, or_ import galaxy.queue_worker -from galaxy import util -from galaxy import model -from galaxy import web +from galaxy import ( + model, + util, + web +) from galaxy.actions.admin import AdminActions from galaxy.exceptions import ActionInputError, MessageException from galaxy.model import tool_shed_install as install_model -from galaxy.util import nice_size, sanitize_text, url_get +from galaxy.tools import global_tool_errors +from galaxy.util import ( + nice_size, + sanitize_text, + url_get +) from galaxy.util.odict import odict from galaxy.web import url_for from galaxy.web.base import controller from galaxy.web.base.controller import UsesQuotaMixin from galaxy.web.framework.helpers import grids, time_ago from galaxy.web.params import QuotaParamParser -from galaxy.tools import global_tool_errors -from tool_shed.util import common_util -from tool_shed.util import encoding_util -from tool_shed.util import repository_util +from tool_shed.util import ( + common_util, + encoding_util, + repository_util +) from tool_shed.util.web_util import escape diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py index 84eefa457bf..cce33191d5d 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -34,7 +34,6 @@ from tool_shed.util import ( workflow_util ) from tool_shed.util.web_util import escape - from .admin import AdminGalaxy log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/biostar.py b/lib/galaxy/webapps/galaxy/controllers/biostar.py index 1708384bcf1..dbad55edb9e 100644 --- a/lib/galaxy/webapps/galaxy/controllers/biostar.py +++ b/lib/galaxy/webapps/galaxy/controllers/biostar.py @@ -1,9 +1,12 @@ """ Controller for integration with the Biostar application """ - -from galaxy.web.base.controller import BaseUIController, error, web from galaxy.util import biostar +from galaxy.web.base.controller import ( + BaseUIController, + error, + web +) class BiostarController(BaseUIController): diff --git a/lib/galaxy/webapps/galaxy/controllers/library.py b/lib/galaxy/webapps/galaxy/controllers/library.py index 240d5d9cff5..25664717719 100644 --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -1,4 +1,5 @@ import logging + from galaxy import web from galaxy.web.base.controller import BaseUIController diff --git a/lib/galaxy/webapps/galaxy/controllers/tag.py b/lib/galaxy/webapps/galaxy/controllers/tag.py index aa48a3a0c3a..6b4947319b5 100644 --- a/lib/galaxy/webapps/galaxy/controllers/tag.py +++ b/lib/galaxy/webapps/galaxy/controllers/tag.py @@ -2,6 +2,7 @@ Tags Controller: handles tagging/untagging of entities and provides autocomplete support. """ +import logging from six import text_type from sqlalchemy.sql import select @@ -10,7 +11,6 @@ from sqlalchemy.sql.expression import and_, func from galaxy import web from galaxy.web.base.controller import BaseUIController, UsesTagsMixin -import logging log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py index 8076aa8b7e3..a2be9a422b4 100644 --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -9,21 +9,33 @@ import urllib from datetime import datetime, timedelta from markupsafe import escape -from sqlalchemy import and_, or_, func, true -from galaxy import model -from galaxy import util -from galaxy import web +from sqlalchemy import ( + and_, + func, + or_, + true +) + +from galaxy import ( + model, + util, + web +) from galaxy.queue_worker import send_local_control_task -from galaxy.security.validate_user_input import (transform_publicname, - validate_email, - validate_password, - validate_publicname) +from galaxy.security.validate_user_input import ( + transform_publicname, + validate_email, + validate_password, + validate_publicname +) from galaxy.util import biostar, hash_util from galaxy.web import url_for -from galaxy.web.base.controller import (BaseUIController, - CreatesApiKeysMixin, - CreatesUsersMixin, - UsesFormDefinitionsMixin) +from galaxy.web.base.controller import ( + BaseUIController, + CreatesApiKeysMixin, + CreatesUsersMixin, + UsesFormDefinitionsMixin +) from galaxy.web.form_builder import CheckboxField from galaxy.web.framework.helpers import grids, time_ago diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py index 80aad9cb67c..524bfcb0e93 100644 --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -1,10 +1,15 @@ from __future__ import absolute_import import logging +import os from json import loads +import yaml from markupsafe import escape -from paste.httpexceptions import HTTPNotFound, HTTPBadRequest +from paste.httpexceptions import ( + HTTPBadRequest, + HTTPNotFound +) from six import string_types from sqlalchemy import and_, desc, false, or_, true @@ -19,12 +24,13 @@ from galaxy.visualization.genomes import decode_dbkey from galaxy.visualization.genomes import GenomeRegion from galaxy.visualization.plugins import registry from galaxy.web import error -from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesVisualizationMixin +from galaxy.web.base.controller import ( + BaseUIController, + SharableMixin, + UsesVisualizationMixin +) from galaxy.web.framework.helpers import grids, time_ago -import os -import yaml - log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py index 3541cab94c4..78abd6af8f9 100644 --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -6,33 +6,52 @@ import json import logging import os import sgmllib -import requests +import requests +from markupsafe import escape from sqlalchemy import and_ from sqlalchemy.orm import joinedload from sqlalchemy.sql import expression -from markupsafe import escape -from tool_shed.util import encoding_util - -from galaxy import model -from galaxy import util -from galaxy import web +from galaxy import ( + model, + util, + web +) from galaxy.managers import workflows from galaxy.model.item_attrs import UsesItemRatings from galaxy.model.mapping import desc from galaxy.tools.parameters.basic import workflow_building_modes -from galaxy.util import unicodify, FILENAME_VALID_CHARS +from galaxy.util import ( + FILENAME_VALID_CHARS, + unicodify +) from galaxy.util.sanitize_html import sanitize_html from galaxy.web import error, url_for -from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin +from galaxy.web.base.controller import ( + BaseUIController, + SharableMixin, + UsesStoredWorkflowMixin +) from galaxy.web.framework.formbuilder import form -from galaxy.web.framework.helpers import grids, time_ago, to_unicode -from galaxy.workflow.extract import extract_workflow -from galaxy.workflow.extract import summarize -from galaxy.workflow.modules import module_factory -from galaxy.workflow.modules import WorkflowModuleInjector -from galaxy.workflow.render import WorkflowCanvas, STANDALONE_SVG_TEMPLATE +from galaxy.web.framework.helpers import ( + grids, + time_ago, + to_unicode +) +from galaxy.workflow.extract import ( + extract_workflow, + summarize +) +from galaxy.workflow.modules import ( + module_factory, + WorkflowModuleInjector +) +from galaxy.workflow.render import ( + STANDALONE_SVG_TEMPLATE, + WorkflowCanvas +) +from tool_shed.util import encoding_util log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/reports/app.py b/lib/galaxy/webapps/reports/app.py index 109f3eceec1..27318ae99cd 100644 --- a/lib/galaxy/webapps/reports/app.py +++ b/lib/galaxy/webapps/reports/app.py @@ -1,11 +1,12 @@ -import config +import logging import sys import time import galaxy.model from galaxy.web import security from galaxy.web.stack import application_stack_instance -import logging +from . import config + log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/reports/controllers/history.py b/lib/galaxy/webapps/reports/controllers/history.py index a4a4d75b5b4..1eb8f41c156 100644 --- a/lib/galaxy/webapps/reports/controllers/history.py +++ b/lib/galaxy/webapps/reports/controllers/history.py @@ -1,14 +1,14 @@ -import galaxy.model import collections import logging + import sqlalchemy as sa - -from galaxy import util -from galaxy.web.base.controller import BaseUIController, web - from markupsafe import escape from sqlalchemy import and_ +import galaxy.model +from galaxy import util +from galaxy.web.base.controller import BaseUIController, web + log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/reports/controllers/home.py b/lib/galaxy/webapps/reports/controllers/home.py index ab120c7ba81..bdba42cdcb4 100644 --- a/lib/galaxy/webapps/reports/controllers/home.py +++ b/lib/galaxy/webapps/reports/controllers/home.py @@ -1,11 +1,13 @@ -from datetime import datetime, timedelta -from galaxy.web.base.controller import BaseUIController, web -from galaxy import model import calendar +import logging +from datetime import datetime, timedelta + import sqlalchemy as sa + +from galaxy import model +from galaxy.web.base.controller import BaseUIController, web from galaxy.webapps.reports.controllers.query import ReportQueryBuilder -import logging log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index 73dba30fc1b..73804c3fa16 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -1,19 +1,23 @@ from __future__ import print_function + import calendar import logging +import re from collections import namedtuple -from datetime import datetime, date, timedelta +from datetime import ( + date, + datetime, + timedelta +) +from math import ceil, floor import sqlalchemy as sa -from sqlalchemy import and_, not_, or_ - from markupsafe import escape +from sqlalchemy import and_, not_, or_ from galaxy import model, util from galaxy.web.base.controller import BaseUIController, web from galaxy.web.framework.helpers import grids -import re -from math import ceil, floor from galaxy.webapps.reports.controllers.query import ReportQueryBuilder log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/reports/controllers/root.py b/lib/galaxy/webapps/reports/controllers/root.py index 3a4c8df1d7d..26f87ddc792 100644 --- a/lib/galaxy/webapps/reports/controllers/root.py +++ b/lib/galaxy/webapps/reports/controllers/root.py @@ -1,5 +1,10 @@ -from galaxy.web.base.controller import BaseUIController, web import logging + +from galaxy.web.base.controller import ( + BaseUIController, + web +) + log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/reports/controllers/sample_tracking.py b/lib/galaxy/webapps/reports/controllers/sample_tracking.py index 1c95026c21f..b608a47c534 100644 --- a/lib/galaxy/webapps/reports/controllers/sample_tracking.py +++ b/lib/galaxy/webapps/reports/controllers/sample_tracking.py @@ -3,8 +3,8 @@ import logging from datetime import date, timedelta import sqlalchemy as sa -from sqlalchemy import and_ from markupsafe import escape +from sqlalchemy import and_ from galaxy import model, util from galaxy.web.base.controller import BaseUIController, web diff --git a/lib/galaxy/webapps/reports/controllers/users.py b/lib/galaxy/webapps/reports/controllers/users.py index 3d9e6b4f2d1..a01ebd94923 100644 --- a/lib/galaxy/webapps/reports/controllers/users.py +++ b/lib/galaxy/webapps/reports/controllers/users.py @@ -1,18 +1,22 @@ import calendar import logging import operator -import galaxy.model -import sqlalchemy as sa +from datetime import ( + date, + datetime, + timedelta +) +import sqlalchemy as sa +from markupsafe import escape +from sqlalchemy import false + +import galaxy.model from galaxy import util from galaxy.web.base.controller import BaseUIController, web from galaxy.webapps.reports.controllers.jobs import sorter from galaxy.webapps.reports.controllers.query import ReportQueryBuilder -from datetime import datetime, date, timedelta -from markupsafe import escape -from sqlalchemy import false - log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/reports/controllers/workflows.py b/lib/galaxy/webapps/reports/controllers/workflows.py index 8e1d7f3bee2..fe6e06dfac0 100644 --- a/lib/galaxy/webapps/reports/controllers/workflows.py +++ b/lib/galaxy/webapps/reports/controllers/workflows.py @@ -1,19 +1,29 @@ import calendar -from datetime import datetime, date, timedelta import logging +import re from collections import namedtuple +from datetime import ( + date, + datetime, + timedelta +) +from math import ( + ceil, + floor +) + import sqlalchemy as sa -from sqlalchemy import and_ from markupsafe import escape +from sqlalchemy import and_ from galaxy import model, util -from math import floor from galaxy.web.base.controller import BaseUIController, web from galaxy.web.framework.helpers import grids -import re -from math import ceil +from galaxy.webapps.reports.controllers.jobs import ( + get_spark_time, + sorter +) from galaxy.webapps.reports.controllers.query import ReportQueryBuilder -from galaxy.webapps.reports.controllers.jobs import sorter, get_spark_time log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/api/authenticate.py b/lib/galaxy/webapps/tool_shed/api/authenticate.py index 2ca4905d343..e203c0e48ef 100644 --- a/lib/galaxy/webapps/tool_shed/api/authenticate.py +++ b/lib/galaxy/webapps/tool_shed/api/authenticate.py @@ -11,8 +11,8 @@ Returns: """ import logging -from galaxy.webapps.galaxy.api.authenticate import AuthenticationController from galaxy.web import _future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless +from galaxy.webapps.galaxy.api.authenticate import AuthenticationController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/api/categories.py b/lib/galaxy/webapps/tool_shed/api/categories.py index b2e02d32a11..e8928eb9bda 100644 --- a/lib/galaxy/webapps/tool_shed/api/categories.py +++ b/lib/galaxy/webapps/tool_shed/api/categories.py @@ -1,14 +1,18 @@ import logging -from galaxy import util -from galaxy import web -from galaxy import exceptions -from galaxy.web import require_admin as require_admin -from galaxy.web import _future_expose_api as expose_api -from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless +import tool_shed.util.shed_util_common as suc +from galaxy import ( + exceptions, + util, + web +) +from galaxy.web import ( + _future_expose_api as expose_api, + _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless, + require_admin as require_admin +) from galaxy.web.base.controller import BaseAPIController from tool_shed.util import repository_util -import tool_shed.util.shed_util_common as suc log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/api/configuration.py b/lib/galaxy/webapps/tool_shed/api/configuration.py index 9d7f66d80ab..61cf7274497 100644 --- a/lib/galaxy/webapps/tool_shed/api/configuration.py +++ b/lib/galaxy/webapps/tool_shed/api/configuration.py @@ -2,11 +2,11 @@ API operations allowing clients to determine Tool Shed instance's capabilities and configuration settings. """ +import logging from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless from galaxy.web.base.controller import BaseAPIController -import logging log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/api/groups.py b/lib/galaxy/webapps/tool_shed/api/groups.py index d1c8eca145e..c34eb787aaf 100644 --- a/lib/galaxy/webapps/tool_shed/api/groups.py +++ b/lib/galaxy/webapps/tool_shed/api/groups.py @@ -1,13 +1,20 @@ import logging -from galaxy import util -from galaxy import web + +from galaxy import ( + util, + web +) +from galaxy.exceptions import ( + AdminRequiredException, + ObjectNotFound, + RequestParameterMissingException +) from galaxy.util import pretty_print_time_interval -from galaxy.exceptions import RequestParameterMissingException -from galaxy.exceptions import AdminRequiredException -from galaxy.exceptions import ObjectNotFound -from galaxy.web import require_admin as require_admin -from galaxy.web import _future_expose_api as expose_api -from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless +from galaxy.web import ( + _future_expose_api as expose_api, + _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless, + require_admin as require_admin +) from galaxy.web.base.controller import BaseAPIController from tool_shed.managers import groups diff --git a/lib/galaxy/webapps/tool_shed/api/repositories.py b/lib/galaxy/webapps/tool_shed/api/repositories.py index 6af9046438f..916a02795a8 100644 --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -1,42 +1,52 @@ import json import logging import os -import tarfile import StringIO +import tarfile from cgi import FieldStorage from collections import namedtuple from time import strftime from sqlalchemy import and_, false -from galaxy import util -from galaxy import web +from galaxy import ( + util, + web +) +from galaxy.exceptions import ( + ActionInputError, + ConfigDoesNotAllowException, + InsufficientPermissionsException, + MalformedId, + ObjectNotFound, + RequestParameterInvalidException, + RequestParameterMissingException +) from galaxy.util import checkers -from galaxy.exceptions import ActionInputError -from galaxy.exceptions import ConfigDoesNotAllowException -from galaxy.exceptions import InsufficientPermissionsException -from galaxy.exceptions import MalformedId -from galaxy.exceptions import ObjectNotFound -from galaxy.exceptions import RequestParameterInvalidException -from galaxy.exceptions import RequestParameterMissingException -from galaxy.web import _future_expose_api as expose_api -from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless -from galaxy.web import _future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless -from galaxy.web.base.controller import BaseAPIController -from galaxy.web.base.controller import HTTPBadRequest +from galaxy.web import ( + _future_expose_api as expose_api, + _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless, + _future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless +) +from galaxy.web.base.controller import ( + BaseAPIController, + HTTPBadRequest +) from galaxy.webapps.tool_shed.search.repo_search import RepoSearch from tool_shed.capsule import capsule_manager from tool_shed.dependencies import attribute_handlers from tool_shed.metadata import repository_metadata_manager from tool_shed.repository_types import util as rt_util -from tool_shed.util import basic_util -from tool_shed.util import commit_util -from tool_shed.util import encoding_util -from tool_shed.util import hg_util -from tool_shed.util import metadata_util -from tool_shed.util import repository_content_util -from tool_shed.util import repository_util -from tool_shed.util import tool_util +from tool_shed.util import ( + basic_util, + commit_util, + encoding_util, + hg_util, + metadata_util, + repository_content_util, + repository_util, + tool_util +) log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/api/tools.py b/lib/galaxy/webapps/tool_shed/api/tools.py index eb9f97ff39a..b049e4b771c 100644 --- a/lib/galaxy/webapps/tool_shed/api/tools.py +++ b/lib/galaxy/webapps/tool_shed/api/tools.py @@ -1,22 +1,29 @@ import json import logging from collections import namedtuple -from galaxy import web -from galaxy import util + +from galaxy import ( + util, + web +) +from galaxy.exceptions import ( + ConfigDoesNotAllowException, + NotImplemented, + RequestParameterInvalidException +) from galaxy.tools.parameters import params_to_strings from galaxy.web import _future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless from galaxy.web.base.controller import BaseAPIController from galaxy.webapps.tool_shed.search.tool_search import ToolSearch -from galaxy.exceptions import NotImplemented -from galaxy.exceptions import RequestParameterInvalidException -from galaxy.exceptions import ConfigDoesNotAllowException from tool_shed.dependencies.repository import relation_builder from tool_shed.tools import tool_validator +from tool_shed.util import ( + common_util, + metadata_util, + repository_util, + shed_util_common as suc +) from tool_shed.utility_containers import ToolShedUtilityContainerManager -from tool_shed.util import common_util -from tool_shed.util import repository_util -from tool_shed.util import shed_util_common as suc -from tool_shed.util import metadata_util log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/api/users.py b/lib/galaxy/webapps/tool_shed/api/users.py index 70846adeb78..9b81257ece7 100644 --- a/lib/galaxy/webapps/tool_shed/api/users.py +++ b/lib/galaxy/webapps/tool_shed/api/users.py @@ -1,12 +1,16 @@ import logging -from galaxy import util -from galaxy import web -from galaxy.web.base.controller import BaseAPIController -from galaxy.security.validate_user_input import validate_email -from galaxy.security.validate_user_input import validate_publicname -from galaxy.security.validate_user_input import validate_password import tool_shed.util.shed_util_common as suc +from galaxy import ( + util, + web +) +from galaxy.security.validate_user_input import ( + validate_email, + validate_password, + validate_publicname +) +from galaxy.web.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/app.py b/lib/galaxy/webapps/tool_shed/app.py index bfb4235af09..815d7aa4ee9 100644 --- a/lib/galaxy/webapps/tool_shed/app.py +++ b/lib/galaxy/webapps/tool_shed/app.py @@ -1,10 +1,13 @@ -import config +import logging import sys import time + import galaxy.datatypes.registry import galaxy.quota import galaxy.tools.data import galaxy.webapps.tool_shed.model +import tool_shed.repository_registry +import tool_shed.repository_types.registry from galaxy import tools from galaxy.config import configure_logging from galaxy.managers.tags import CommunityTagManager @@ -12,11 +15,9 @@ from galaxy.openid.providers import OpenIDProviders from galaxy.util.dbkeys import GenomeBuilds from galaxy.web import security from galaxy.web.stack import application_stack_instance -import tool_shed.repository_registry -import tool_shed.repository_types.registry from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager +from . import config -import logging log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/controllers/admin.py b/lib/galaxy/webapps/tool_shed/controllers/admin.py index 8cf7d5a81d1..96a571e7afd 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -1,19 +1,20 @@ import logging -from galaxy import util -from galaxy.util import inflector -from galaxy import web -from tool_shed.util.web_util import escape - -from galaxy.web.base.controller import BaseUIController -from tool_shed.util.admin_util import Admin - import tool_shed.grids.admin_grids as admin_grids +from galaxy import ( + util, + web +) +from galaxy.util import inflector +from galaxy.web.base.controller import BaseUIController from tool_shed.metadata import repository_metadata_manager - -from tool_shed.util import metadata_util -from tool_shed.util import repository_util -from tool_shed.util import shed_util_common as suc +from tool_shed.util import ( + metadata_util, + repository_util, + shed_util_common as suc +) +from tool_shed.util.admin_util import Admin +from tool_shed.util.web_util import escape log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py index 62f00bc20e7..b404f9fdbbe 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py @@ -1,20 +1,28 @@ import logging -from sqlalchemy import and_, func, false +from sqlalchemy import ( + and_, + false, + func +) import tool_shed.grids.repository_review_grids as repository_review_grids import tool_shed.grids.util as grids_util -from galaxy import util -from galaxy import web +from galaxy import ( + util, + web +) from galaxy.util.odict import odict from galaxy.web.base.controller import BaseUIController from galaxy.web.form_builder import CheckboxField from galaxy.webapps.tool_shed.util import ratings_util -from tool_shed.util import hg_util -from tool_shed.util import review_util -from tool_shed.util import metadata_util -from tool_shed.util import repository_util -from tool_shed.util import shed_util_common as suc +from tool_shed.util import ( + hg_util, + metadata_util, + repository_util, + review_util, + shed_util_common as suc +) from tool_shed.util.container_util import STRSEP from tool_shed.util.web_util import escape diff --git a/lib/galaxy/webapps/tool_shed/controllers/upload.py b/lib/galaxy/webapps/tool_shed/controllers/upload.py index 2fa3d3be406..8e16be8931c 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -5,28 +5,29 @@ import tarfile import tempfile import requests +from mercurial import commands -from galaxy import util -from galaxy import web +from galaxy import ( + util, + web +) from galaxy.util import checkers from galaxy.web.base.controller import BaseUIController -from tool_shed.util.web_util import escape - from tool_shed.dependencies import attribute_handlers from tool_shed.galaxy_install import dependency_display from tool_shed.metadata import repository_metadata_manager from tool_shed.repository_types import util as rt_util from tool_shed.tools import data_table_manager - -from tool_shed.util import basic_util -from tool_shed.util import commit_util -from tool_shed.util import hg_util -from tool_shed.util import repository_util -from tool_shed.util import shed_util_common as suc -from tool_shed.util import repository_content_util -from tool_shed.util import xml_util - -from mercurial import commands +from tool_shed.util import ( + basic_util, + commit_util, + hg_util, + repository_content_util, + repository_util, + shed_util_common as suc, + xml_util +) +from tool_shed.util.web_util import escape log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/controllers/user.py b/lib/galaxy/webapps/tool_shed/controllers/user.py index 1f8bff9cd95..9f1e6e84639 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/user.py +++ b/lib/galaxy/webapps/tool_shed/controllers/user.py @@ -1,13 +1,15 @@ from datetime import datetime from markupsafe import escape +from sqlalchemy import ( + and_, + true +) -from sqlalchemy import and_ -from sqlalchemy import true - -from galaxy import util -from galaxy import web - +from galaxy import ( + util, + web +) from galaxy.security.validate_user_input import validate_email, validate_password, validate_publicname from galaxy.web import url_for from galaxy.webapps.galaxy.controllers.user import User as BaseUser diff --git a/lib/galaxy/webapps/tool_shed/search/tool_search.py b/lib/galaxy/webapps/tool_shed/search/tool_search.py index 9aba6761231..ca4154961c3 100644 --- a/lib/galaxy/webapps/tool_shed/search/tool_search.py +++ b/lib/galaxy/webapps/tool_shed/search/tool_search.py @@ -1,13 +1,19 @@ """Module for searching the toolshed tools within all repositories""" -import os import logging -from galaxy import exceptions -from galaxy.exceptions import ObjectNotFound +import os + import whoosh.index from whoosh import scoring -from whoosh.fields import Schema, STORED, TEXT +from whoosh.fields import ( + Schema, + STORED, + TEXT +) from whoosh.qparser import MultifieldParser +from galaxy import exceptions +from galaxy.exceptions import ObjectNotFound + log = logging.getLogger(__name__) tool_schema = Schema( diff --git a/lib/galaxy/webapps/tool_shed/util/hgweb_config.py b/lib/galaxy/webapps/tool_shed/util/hgweb_config.py index 28c36a3df32..b45bf887b20 100644 --- a/lib/galaxy/webapps/tool_shed/util/hgweb_config.py +++ b/lib/galaxy/webapps/tool_shed/util/hgweb_config.py @@ -1,6 +1,6 @@ -import os import ConfigParser import logging +import os import shutil import threading from datetime import date diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py index 53161117f70..5aab3df4690 100644 --- a/lib/galaxy/workflow/extract.py +++ b/lib/galaxy/workflow/extract.py @@ -15,7 +15,6 @@ from galaxy.tools.parameters.grouping import ( ) from galaxy.tools.parser import ToolOutputCollectionPart from galaxy.util.odict import odict - from .steps import ( attach_ordered_steps, order_workflow_steps_with_levels diff --git a/lib/galaxy/workflow/schedulers/core.py b/lib/galaxy/workflow/schedulers/core.py index 0fe303cc0eb..8eacd3abf8b 100644 --- a/lib/galaxy/workflow/schedulers/core.py +++ b/lib/galaxy/workflow/schedulers/core.py @@ -5,7 +5,6 @@ import logging from galaxy.work import context from galaxy.workflow import run, run_request - from ..schedulers import ActiveWorkflowSchedulingPlugin log = logging.getLogger(__name__) diff --git a/lib/tool_shed/dependencies/attribute_handlers.py b/lib/tool_shed/dependencies/attribute_handlers.py index b63c648f9bf..93d238c2ecd 100644 --- a/lib/tool_shed/dependencies/attribute_handlers.py +++ b/lib/tool_shed/dependencies/attribute_handlers.py @@ -4,7 +4,6 @@ import logging from galaxy.util import asbool from galaxy.util.odict import odict from galaxy.web import url_for - from tool_shed.dependencies.tool import tag_attribute_handler from tool_shed.repository_types.util import REPOSITORY_DEPENDENCY_DEFINITION_FILENAME from tool_shed.repository_types.util import TOOL_DEPENDENCY_DEFINITION_FILENAME @@ -12,6 +11,7 @@ from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import repository_util from tool_shed.util import xml_util + log = logging.getLogger(__name__) diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py index 0b40a1c8661..1f29fbf3fe0 100644 --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py @@ -12,13 +12,13 @@ from fabric import state from fabric.operations import _AttributeString from six.moves import queue -from galaxy.util import DATABASE_MAX_STRING_SIZE -from galaxy.util import DATABASE_MAX_STRING_SIZE_PRETTY -from galaxy.util import shrink_string_by_size -from galaxy.util import unicodify - +from galaxy.util import ( + DATABASE_MAX_STRING_SIZE, + DATABASE_MAX_STRING_SIZE_PRETTY, + shrink_string_by_size, + unicodify +) from tool_shed.galaxy_install.tool_dependencies.recipe import asynchronous_reader - from tool_shed.util import basic_util, tool_dependency_util log = logging.getLogger(__name__) diff --git a/lib/tool_shed/galaxy_install/tool_migration_manager.py b/lib/tool_shed/galaxy_install/tool_migration_manager.py index 570630476cd..e8de5dd15cb 100644 --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -12,22 +12,21 @@ from galaxy import util from galaxy.tools.toolbox import ToolSection from galaxy.tools.toolbox.parser import ensure_tool_conf_item from galaxy.util.odict import odict - from tool_shed.galaxy_install import install_manager from tool_shed.galaxy_install.datatypes import custom_datatype_manager from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.tools import tool_panel_manager - from tool_shed.tools import data_table_manager - -from tool_shed.util import basic_util -from tool_shed.util import common_util -from tool_shed.util import hg_util -from tool_shed.util import repository_util -from tool_shed.util import shed_util_common as suc -from tool_shed.util import tool_dependency_util -from tool_shed.util import tool_util -from tool_shed.util import xml_util +from tool_shed.util import ( + basic_util, + common_util, + hg_util, + repository_util, + shed_util_common as suc, + tool_dependency_util, + tool_util, + xml_util +) log = logging.getLogger(__name__) diff --git a/lib/tool_shed/galaxy_install/tools/tool_panel_manager.py b/lib/tool_shed/galaxy_install/tools/tool_panel_manager.py index dfe48330edc..2fdbec7a0cd 100644 --- a/lib/tool_shed/galaxy_install/tools/tool_panel_manager.py +++ b/lib/tool_shed/galaxy_install/tools/tool_panel_manager.py @@ -1,6 +1,5 @@ import logging import threading - from xml.etree import cElementTree as XmlET from tool_shed.util import basic_util diff --git a/lib/tool_shed/repository_types/registry.py b/lib/tool_shed/repository_types/registry.py index c9406ff1afd..35563f74c8c 100644 --- a/lib/tool_shed/repository_types/registry.py +++ b/lib/tool_shed/repository_types/registry.py @@ -1,10 +1,11 @@ import logging from galaxy.util.odict import odict - -from . import repository_suite_definition -from . import tool_dependency_definition -from . import unrestricted +from . import ( + repository_suite_definition, + tool_dependency_definition, + unrestricted +) log = logging.getLogger(__name__) diff --git a/lib/tool_shed/tools/data_table_manager.py b/lib/tool_shed/tools/data_table_manager.py index be8590c4fde..9a89c1cb343 100644 --- a/lib/tool_shed/tools/data_table_manager.py +++ b/lib/tool_shed/tools/data_table_manager.py @@ -1,7 +1,6 @@ import logging import os import shutil - from xml.etree import ElementTree as XmlET from tool_shed.util import hg_util, xml_util diff --git a/lib/tool_shed/tools/tool_validator.py b/lib/tool_shed/tools/tool_validator.py index 24b55e17d46..1effbd784d7 100644 --- a/lib/tool_shed/tools/tool_validator.py +++ b/lib/tool_shed/tools/tool_validator.py @@ -8,14 +8,14 @@ from galaxy.tools import ( Tool ) from galaxy.tools.parameters import dynamic_options - from tool_shed.tools import data_table_manager - -from tool_shed.util import basic_util -from tool_shed.util import hg_util -from tool_shed.util import repository_util -from tool_shed.util import tool_util -from tool_shed.util import xml_util +from tool_shed.util import ( + basic_util, + hg_util, + repository_util, + tool_util, + xml_util +) log = logging.getLogger(__name__) diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py index 2b0811cdbff..63dde0ce62f 100644 --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -9,7 +9,6 @@ import sqlalchemy.orm.exc from sqlalchemy import and_, false, true import galaxy.tools.deps.requirements - from galaxy import util from galaxy.util import checkers from galaxy.web import url_for diff --git a/lib/tool_shed/util/tool_util.py b/lib/tool_shed/util/tool_util.py index a6b93e6eb42..b9aef505bdf 100644 --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -8,7 +8,6 @@ from galaxy.util import checkers from galaxy.util import unicodify from galaxy.util.expressions import ExpressionContext from galaxy.web.form_builder import SelectField - from tool_shed.util import basic_util log = logging.getLogger(__name__) diff --git a/lib/tool_shed/utility_containers/__init__.py b/lib/tool_shed/utility_containers/__init__.py index 9a6a19a6114..23141aa4800 100644 --- a/lib/tool_shed/utility_containers/__init__.py +++ b/lib/tool_shed/utility_containers/__init__.py @@ -2,10 +2,11 @@ import logging import threading from galaxy import util -from tool_shed.util import common_util -from tool_shed.util import container_util -from tool_shed.util import readme_util - +from tool_shed.util import ( + common_util, + container_util, + readme_util +) from . import utility_container_manager log = logging.getLogger(__name__) diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py index 33a7506263f..51228a384bb 100644 --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -13,10 +13,10 @@ galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pa sys.path[1:1] = [os.path.join(galaxy_root, "lib"), os.path.join(galaxy_root, "test")] from base import driver_util -log = driver_util.build_logger() - from base.api_util import get_master_api_key, get_user_api_key +log = driver_util.build_logger() + class MigratedToolsGalaxyTestDriver(driver_util.GalaxyTestDriver): """Instantiate a Galaxy-style nose TestDriver for testing migrated Galaxy tools.""" diff --git a/test/api/test_jobs.py b/test/api/test_jobs.py index 15c97c2dd88..6747b86e2ff 100644 --- a/test/api/test_jobs.py +++ b/test/api/test_jobs.py @@ -2,20 +2,19 @@ import datetime import json import os import time - from operator import itemgetter -from base import api -from base.api_asserts import assert_status_code_is_ok -from base.populators import ( +from requests import put + +from base import api # noqa: I100 +from base.api_asserts import assert_status_code_is_ok # noqa: I100 +from base.populators import ( # noqa: I100 DatasetCollectionPopulator, DatasetPopulator, wait_on, wait_on_state, ) -from requests import put - class JobsApiTestCase(api.ApiTestCase): diff --git a/test/api/test_page_revisions.py b/test/api/test_page_revisions.py index 051f0c85851..33d29d74fe6 100644 --- a/test/api/test_page_revisions.py +++ b/test/api/test_page_revisions.py @@ -1,5 +1,4 @@ from galaxy.exceptions import error_codes - from .test_pages import BasePageApiTestCase diff --git a/test/base/driver_util.py b/test/base/driver_util.py index b12655193ab..6095662fabc 100644 --- a/test/base/driver_util.py +++ b/test/base/driver_util.py @@ -20,9 +20,7 @@ import nose.config import nose.core import nose.loader import nose.plugins.manager - from paste import httpserver - from six.moves.urllib.parse import urlparse from galaxy.app import UniverseApplication as GalaxyUniverseApplication @@ -30,7 +28,6 @@ from galaxy.util import asbool, download_to_file from galaxy.util.properties import load_app_properties from galaxy.web import buildapp from galaxy.webapps.tool_shed.app import UniverseApplication as ToolshedUniverseApplication - from .api_util import get_master_api_key, get_user_api_key from .instrument import StructuredTestDataPlugin from .nose_util import run diff --git a/test/base/testcase.py b/test/base/testcase.py index df35ec268c7..bbe6bed3e5c 100644 --- a/test/base/testcase.py +++ b/test/base/testcase.py @@ -9,7 +9,6 @@ from json import loads from galaxy.tools.verify import verify from galaxy.tools.verify.test_data import TestDataResolver from galaxy.web import security - from .driver_util import GalaxyTestDriver log = logging.getLogger(__name__) diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py index 186eada279d..3ad1f34e985 100644 --- a/test/functional/test_toolbox.py +++ b/test/functional/test_toolbox.py @@ -15,7 +15,6 @@ from base.interactor import build_interactor, RunToolException, stage_data_in_hi from galaxy.tools import DataManagerTool from galaxy.tools.verify.asserts import verify_assertions from galaxy.util import bunch - from .twilltestcase import TwillTestCase log = logging.getLogger(__name__) diff --git a/test/galaxy_selenium/components.py b/test/galaxy_selenium/components.py index a71ade2fb0f..f9b76fc376c 100644 --- a/test/galaxy_selenium/components.py +++ b/test/galaxy_selenium/components.py @@ -1,13 +1,11 @@ import re import string - from abc import ( ABCMeta, abstractproperty, ) import six - from selenium.webdriver.common.by import By from galaxy.util.bunch import Bunch diff --git a/test/galaxy_selenium/data.py b/test/galaxy_selenium/data.py index f96a423c2c0..e79dd3aea36 100644 --- a/test/galaxy_selenium/data.py +++ b/test/galaxy_selenium/data.py @@ -1,5 +1,4 @@ import yaml - from pkg_resources import resource_string from .components import Component diff --git a/test/galaxy_selenium/navigates_galaxy.py b/test/galaxy_selenium/navigates_galaxy.py index 01c11f7e8dc..a4dffac14c3 100644 --- a/test/galaxy_selenium/navigates_galaxy.py +++ b/test/galaxy_selenium/navigates_galaxy.py @@ -15,7 +15,6 @@ import requests import yaml from galaxy.util.bunch import Bunch - from . import sizzle from .data import ( NAVIGATION, diff --git a/test/manual/workflows_scaling.py b/test/manual/workflows_scaling.py index 677eff160df..44f65f1efa9 100644 --- a/test/manual/workflows_scaling.py +++ b/test/manual/workflows_scaling.py @@ -24,7 +24,7 @@ from base.populators import ( # noqa: I100 GiDatasetPopulator, GiWorkflowPopulator, ) -from api.workflows_format_2.converter import python_to_workflow # noqa: I100 +from base.workflows_format_2.converter import python_to_workflow # noqa: I100 LONG_TIMEOUT = 1000000000 DESCRIPTION = "Script to exercise the workflow engine." diff --git a/test/selenium_tests/test_stock_tours.py b/test/selenium_tests/test_stock_tours.py index 66ac07a5409..77618488859 100644 --- a/test/selenium_tests/test_stock_tours.py +++ b/test/selenium_tests/test_stock_tours.py @@ -1,7 +1,6 @@ import os from galaxy.util import galaxy_root_path - from .framework import ( selenium_test, SeleniumTestCase diff --git a/test/shed_functional/base/twilltestcase.py b/test/shed_functional/base/twilltestcase.py index 61b71d10ad8..1bbd84d29c6 100644 --- a/test/shed_functional/base/twilltestcase.py +++ b/test/shed_functional/base/twilltestcase.py @@ -20,7 +20,6 @@ from functional.twilltestcase import TwillTestCase # noqa: I100 from galaxy.web import security from tool_shed.util import hg_util, xml_util from tool_shed.util.encoding_util import tool_shed_encode - from . import common, test_db_util log = logging.getLogger(__name__) diff --git a/test/unit/datatypes/dataproviders/test_base_dataproviders.py b/test/unit/datatypes/dataproviders/test_base_dataproviders.py index e081cc41ac4..0c071fe78a0 100644 --- a/test/unit/datatypes/dataproviders/test_base_dataproviders.py +++ b/test/unit/datatypes/dataproviders/test_base_dataproviders.py @@ -8,7 +8,6 @@ import unittest from six import StringIO from galaxy.datatypes.dataproviders import base, exceptions - from ...unittest_utils import tempfilecache, utility log = logging.getLogger(__name__) diff --git a/test/unit/datatypes/dataproviders/test_line_dataproviders.py b/test/unit/datatypes/dataproviders/test_line_dataproviders.py index 29dec9c9544..15962b7888d 100644 --- a/test/unit/datatypes/dataproviders/test_line_dataproviders.py +++ b/test/unit/datatypes/dataproviders/test_line_dataproviders.py @@ -6,7 +6,6 @@ import logging import unittest from galaxy.datatypes.dataproviders import line - from . import test_base_dataproviders log = logging.getLogger(__name__) diff --git a/test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py b/test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py index b62285fd0f3..7c9bfe5a7ef 100644 --- a/test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py +++ b/test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py @@ -7,7 +7,6 @@ from testfixtures import log_capture import galaxy.jobs.dynamic_tool_destination as dt from galaxy.jobs.dynamic_tool_destination import map_tool_to_destination from galaxy.jobs.mapper import JobMappingException - from . import mockGalaxy as mg from . import ymltests as yt diff --git a/test/unit/jobs/test_job_wrapper.py b/test/unit/jobs/test_job_wrapper.py index 268daf2315f..b60506681fe 100644 --- a/test/unit/jobs/test_job_wrapper.py +++ b/test/unit/jobs/test_job_wrapper.py @@ -13,7 +13,6 @@ from galaxy.model import ( ) from galaxy.tools import evaluation from galaxy.util.bunch import Bunch - from ..tools_support import UsesApp TEST_TOOL_ID = "cufftest" diff --git a/test/unit/jobs/test_mapper.py b/test/unit/jobs/test_mapper.py index 090d56f9b8e..db822d2ee6a 100644 --- a/test/unit/jobs/test_mapper.py +++ b/test/unit/jobs/test_mapper.py @@ -10,7 +10,6 @@ from galaxy.jobs.mapper import ( JobRunnerMapper, ) from galaxy.util import bunch - from . import test_rules WORKFLOW_UUID = uuid.uuid1().hex diff --git a/test/unit/jobs/test_runner_local.py b/test/unit/jobs/test_runner_local.py index 3d98f0011e9..0733bd77209 100644 --- a/test/unit/jobs/test_runner_local.py +++ b/test/unit/jobs/test_runner_local.py @@ -9,7 +9,6 @@ from galaxy import model from galaxy.jobs import metrics from galaxy.jobs.runners import local from galaxy.util import bunch - from ..tools_support import ( UsesApp, UsesTools diff --git a/test/unit/managers/base.py b/test/unit/managers/base.py index c1722e3c8dd..d87544a546c 100644 --- a/test/unit/managers/base.py +++ b/test/unit/managers/base.py @@ -9,7 +9,6 @@ import sqlalchemy from six import string_types from galaxy.managers.users import UserManager - from ..unittest_utils import galaxy_mock # ============================================================================= diff --git a/test/unit/managers/test_CollectionManager.py b/test/unit/managers/test_CollectionManager.py index 651fdc12000..d6052c81eac 100644 --- a/test/unit/managers/test_CollectionManager.py +++ b/test/unit/managers/test_CollectionManager.py @@ -8,7 +8,6 @@ from galaxy.managers.collections import DatasetCollectionManager from galaxy.managers.datasets import DatasetManager from galaxy.managers.hdas import HDAManager from galaxy.managers.histories import HistoryManager - from .base import BaseTestCase, CreatesCollectionsMixin # ============================================================================= diff --git a/test/unit/managers/test_DatasetManager.py b/test/unit/managers/test_DatasetManager.py index 6e99186ef4c..d4e0571bc35 100644 --- a/test/unit/managers/test_DatasetManager.py +++ b/test/unit/managers/test_DatasetManager.py @@ -18,7 +18,6 @@ from galaxy.managers.datasets import ( DatasetSerializer ) from galaxy.managers.roles import RoleManager - from .base import BaseTestCase # ============================================================================= diff --git a/test/unit/managers/test_HDAManager.py b/test/unit/managers/test_HDAManager.py index 1fd33108210..2d92dda94b3 100644 --- a/test/unit/managers/test_HDAManager.py +++ b/test/unit/managers/test_HDAManager.py @@ -8,7 +8,6 @@ from galaxy import exceptions, model from galaxy.managers import hdas from galaxy.managers.datasets import DatasetManager from galaxy.managers.histories import HistoryManager - from .base import BaseTestCase # ============================================================================= diff --git a/test/unit/managers/test_HDCAManager.py b/test/unit/managers/test_HDCAManager.py index aacbc0d8056..fe204b3c0dd 100644 --- a/test/unit/managers/test_HDCAManager.py +++ b/test/unit/managers/test_HDCAManager.py @@ -8,7 +8,6 @@ from galaxy.managers import ( ) from galaxy.managers.datasets import DatasetManager from galaxy.managers.histories import HistoryManager - from .base import ( BaseTestCase, CreatesCollectionsMixin diff --git a/test/unit/managers/test_HistoryContentsManager.py b/test/unit/managers/test_HistoryContentsManager.py index f45040a3177..4c2ab48f7a2 100644 --- a/test/unit/managers/test_HistoryContentsManager.py +++ b/test/unit/managers/test_HistoryContentsManager.py @@ -10,7 +10,6 @@ from sqlalchemy.sql import text from galaxy.managers import collections, hdas, history_contents from galaxy.managers.histories import HistoryManager - from .base import BaseTestCase from .base import CreatesCollectionsMixin diff --git a/test/unit/managers/test_HistoryManager.py b/test/unit/managers/test_HistoryManager.py index f14ee9512a8..f5067f8f896 100644 --- a/test/unit/managers/test_HistoryManager.py +++ b/test/unit/managers/test_HistoryManager.py @@ -21,7 +21,6 @@ from galaxy.managers.histories import ( HistoryManager, HistorySerializer ) - from .base import BaseTestCase from ..unittest_utils import galaxy_mock diff --git a/test/unit/managers/test_UserManager.py b/test/unit/managers/test_UserManager.py index 2ba7ba2408e..c4c9c962b27 100644 --- a/test/unit/managers/test_UserManager.py +++ b/test/unit/managers/test_UserManager.py @@ -12,7 +12,6 @@ from six import string_types from galaxy import exceptions, model from galaxy.managers import base as base_manager from galaxy.managers import histories, users - from .base import BaseTestCase diff --git a/test/unit/shed_unit/test_installed_repository_manager.py b/test/unit/shed_unit/test_installed_repository_manager.py index ffd3f57ff06..576ebe4e557 100644 --- a/test/unit/shed_unit/test_installed_repository_manager.py +++ b/test/unit/shed_unit/test_installed_repository_manager.py @@ -1,5 +1,4 @@ from tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager - from ..tools.test_toolbox import BaseToolBoxTestCase diff --git a/test/unit/shed_unit/test_tool_panel_manager.py b/test/unit/shed_unit/test_tool_panel_manager.py index 352b1b6d162..bf0ed4b319d 100644 --- a/test/unit/shed_unit/test_tool_panel_manager.py +++ b/test/unit/shed_unit/test_tool_panel_manager.py @@ -1,10 +1,8 @@ import os from galaxy.util import parse_xml - from tool_shed.galaxy_install.tools import tool_panel_manager from tool_shed.tools import tool_version_manager - from ..tools.test_toolbox import ( BaseToolBoxTestCase, SimplifiedToolBox diff --git a/test/unit/test_objectstore.py b/test/unit/test_objectstore.py index 689693fd9a5..5b1966e6a7d 100644 --- a/test/unit/test_objectstore.py +++ b/test/unit/test_objectstore.py @@ -1,5 +1,4 @@ import os - from contextlib import contextmanager from shutil import rmtree from string import Template diff --git a/test/unit/tools/test_actions.py b/test/unit/tools/test_actions.py index 5d0e0d83db1..7b2f067b6fb 100644 --- a/test/unit/tools/test_actions.py +++ b/test/unit/tools/test_actions.py @@ -9,7 +9,6 @@ from galaxy.tools.actions import ( on_text_for_names ) from galaxy.tools.parser.output_objects import ToolOutput - from .. import tools_support TEST_HANDLER_NAME = "test_handler_1" diff --git a/test/unit/tools/test_collect_primary_datasets.py b/test/unit/tools/test_collect_primary_datasets.py index 9c04b3301e0..4e10ad2132f 100644 --- a/test/unit/tools/test_collect_primary_datasets.py +++ b/test/unit/tools/test_collect_primary_datasets.py @@ -8,7 +8,6 @@ from galaxy import ( ) from galaxy.tools.parameters.output_collect import LegacyToolProvidedMetadata, NullToolProvidedMetadata from galaxy.tools.parser import output_collection_def - from .. import tools_support DEFAULT_TOOL_OUTPUT = "out1" diff --git a/test/unit/tools/test_column_parameters.py b/test/unit/tools/test_column_parameters.py index 9df583cdfcc..19fc9ea4029 100644 --- a/test/unit/tools/test_column_parameters.py +++ b/test/unit/tools/test_column_parameters.py @@ -3,7 +3,6 @@ test_select_parameters.py. """ from galaxy import model from galaxy.util import bunch - from .test_parameter_parsing import BaseParameterTestCase from ..tools_support import datatypes_registry diff --git a/test/unit/tools/test_data_parameters.py b/test/unit/tools/test_data_parameters.py index 9fd0f521042..c7e0aa2e4e4 100644 --- a/test/unit/tools/test_data_parameters.py +++ b/test/unit/tools/test_data_parameters.py @@ -1,6 +1,5 @@ from galaxy import model from galaxy.util import bunch - from .test_parameter_parsing import BaseParameterTestCase from ..unittest_utils import galaxy_mock diff --git a/test/unit/tools/test_dataset_matcher.py b/test/unit/tools/test_dataset_matcher.py index fe5b231eeb5..6962f1e4449 100644 --- a/test/unit/tools/test_dataset_matcher.py +++ b/test/unit/tools/test_dataset_matcher.py @@ -7,7 +7,6 @@ from galaxy.tools.parameters import ( dataset_matcher ) from galaxy.util import bunch - from .test_data_parameters import MockHistoryDatasetAssociation from ..tools_support import UsesApp diff --git a/test/unit/tools/test_evaluation.py b/test/unit/tools/test_evaluation.py index d0e38fc561c..08db6eb8cb2 100644 --- a/test/unit/tools/test_evaluation.py +++ b/test/unit/tools/test_evaluation.py @@ -27,7 +27,6 @@ from galaxy.tools.parameters.grouping import ( ) from galaxy.tools.parser.output_objects import ToolOutput from galaxy.util.bunch import Bunch - # Test fixtures for Galaxy infrastructure. from ..tools_support import UsesApp diff --git a/test/unit/tools/test_execution.py b/test/unit/tools/test_execution.py index 3182a271995..ee0bca57d15 100644 --- a/test/unit/tools/test_execution.py +++ b/test/unit/tools/test_execution.py @@ -8,7 +8,6 @@ import galaxy.model from galaxy.tools.parameters import params_to_incoming from galaxy.util.bunch import Bunch from galaxy.util.odict import odict - from .. import tools_support BASE_REPEAT_TOOL_CONTENTS = ''' diff --git a/test/unit/tools/test_history_imp_exp.py b/test/unit/tools/test_history_imp_exp.py index 02a6f967e3f..c95845a7cfc 100644 --- a/test/unit/tools/test_history_imp_exp.py +++ b/test/unit/tools/test_history_imp_exp.py @@ -6,7 +6,6 @@ from tempfile import mkdtemp from galaxy import model from galaxy.exceptions import MalformedContents from galaxy.tools.imp_exp import JobImportHistoryArchiveWrapper, unpack_tar_gz_archive - from ..unittest_utils.galaxy_mock import MockApp diff --git a/test/unit/tools/test_parameter_parsing.py b/test/unit/tools/test_parameter_parsing.py index e6b3939b0b1..79b3ac35afd 100644 --- a/test/unit/tools/test_parameter_parsing.py +++ b/test/unit/tools/test_parameter_parsing.py @@ -4,7 +4,6 @@ from xml.etree.ElementTree import XML from galaxy import model from galaxy.tools.parameters import basic from galaxy.util import bunch - from ..tools_support import UsesApp diff --git a/test/unit/tools/test_parsing.py b/test/unit/tools/test_parsing.py index 2fa8c70374e..ccc5a562118 100644 --- a/test/unit/tools/test_parsing.py +++ b/test/unit/tools/test_parsing.py @@ -3,7 +3,6 @@ import os.path import shutil import tempfile import unittest - from math import isinf from galaxy.tools.parser.factory import get_tool_source diff --git a/test/unit/tools/test_select_parameters.py b/test/unit/tools/test_select_parameters.py index 6332a645aba..7e778c4602f 100644 --- a/test/unit/tools/test_select_parameters.py +++ b/test/unit/tools/test_select_parameters.py @@ -1,7 +1,6 @@ from galaxy import model from galaxy.tools.parameters import basic from galaxy.util import bunch - from .test_parameter_parsing import BaseParameterTestCase diff --git a/test/unit/tools/test_tool_deps.py b/test/unit/tools/test_tool_deps.py index 23cc30962cf..daac8549485 100644 --- a/test/unit/tools/test_tool_deps.py +++ b/test/unit/tools/test_tool_deps.py @@ -1,6 +1,5 @@ import os.path import tempfile - from contextlib import contextmanager from os import ( chmod, diff --git a/test/unit/tools/test_tool_loader.py b/test/unit/tools/test_tool_loader.py index 10a95e9eac3..3f2619973ae 100644 --- a/test/unit/tools/test_tool_loader.py +++ b/test/unit/tools/test_tool_loader.py @@ -1,5 +1,4 @@ import os - from shutil import rmtree from string import Template from tempfile import mkdtemp diff --git a/test/unit/tools/test_toolbox.py b/test/unit/tools/test_toolbox.py index d9366a8dab6..4610aac1aa2 100644 --- a/test/unit/tools/test_toolbox.py +++ b/test/unit/tools/test_toolbox.py @@ -13,7 +13,6 @@ from galaxy.model.tool_shed_install import mapping from galaxy.tools import ToolBox from galaxy.tools.cache import ToolCache from galaxy.webapps.galaxy.config_watchers import ConfigWatchers - from .test_tool_loader import ( SIMPLE_MACRO, SIMPLE_TOOL_WITH_MACRO diff --git a/test/unit/tools/test_watcher.py b/test/unit/tools/test_watcher.py index 6823552fc25..fd43eecbe33 100644 --- a/test/unit/tools/test_watcher.py +++ b/test/unit/tools/test_watcher.py @@ -1,6 +1,5 @@ import tempfile import time - from contextlib import contextmanager from os import path from shutil import rmtree diff --git a/test/unit/tools_support.py b/test/unit/tools_support.py index 29011ef926c..0f9e9d617fa 100644 --- a/test/unit/tools_support.py +++ b/test/unit/tools_support.py @@ -7,17 +7,14 @@ import os.path import shutil import string import tempfile - from collections import defaultdict -from unittest_utils import galaxy_mock - import galaxy.datatypes.registry import galaxy.model - from galaxy.tools import create_tool_from_source from galaxy.tools.parser import get_tool_source from galaxy.util.bunch import Bunch +from .unittest_utils import galaxy_mock datatypes_registry = galaxy.datatypes.registry.Registry() diff --git a/test/unit/visualizations/plugins/test_VisualizationPlugin.py b/test/unit/visualizations/plugins/test_VisualizationPlugin.py index eae02765c60..9fc80c3842a 100644 --- a/test/unit/visualizations/plugins/test_VisualizationPlugin.py +++ b/test/unit/visualizations/plugins/test_VisualizationPlugin.py @@ -10,7 +10,6 @@ from galaxy.visualization.plugins import ( resource_parser, utils as vis_utils ) - from ...unittest_utils import galaxy_mock, utility diff --git a/test/unit/visualizations/plugins/test_VisualizationsRegistry.py b/test/unit/visualizations/plugins/test_VisualizationsRegistry.py index ef912bd433c..e658b235609 100644 --- a/test/unit/visualizations/plugins/test_VisualizationsRegistry.py +++ b/test/unit/visualizations/plugins/test_VisualizationsRegistry.py @@ -10,7 +10,6 @@ from six import string_types from galaxy import model from galaxy.visualization.plugins import plugin from galaxy.visualization.plugins.registry import VisualizationsRegistry - from ...unittest_utils import galaxy_mock, utility glx_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, os.pardir)) diff --git a/test/unit/web/framework/test_webapp.py b/test/unit/web/framework/test_webapp.py index 319b980498c..4794f65f926 100644 --- a/test/unit/web/framework/test_webapp.py +++ b/test/unit/web/framework/test_webapp.py @@ -7,7 +7,6 @@ import unittest import galaxy.config from galaxy.web.framework import webapp as Webapp - from ...unittest_utils import galaxy_mock log = logging.getLogger(__name__) diff --git a/test/unit/workflows/test_modules.py b/test/unit/workflows/test_modules.py index 2cca1fe6dc5..7d146860971 100644 --- a/test/unit/workflows/test_modules.py +++ b/test/unit/workflows/test_modules.py @@ -5,7 +5,6 @@ import mock from galaxy import model from galaxy.util import bunch from galaxy.workflow import modules - from .workflow_support import MockTrans, yaml_to_model diff --git a/test/unit/workflows/test_run_parameters.py b/test/unit/workflows/test_run_parameters.py index 744d650132c..93eea6c936b 100644 --- a/test/unit/workflows/test_run_parameters.py +++ b/test/unit/workflows/test_run_parameters.py @@ -3,7 +3,6 @@ from galaxy.workflow.run_request import ( _normalize_inputs, _normalize_step_parameters ) - from .workflow_support import MockTrans STEP_ID_OFFSET = 4 # Offset a little so ids and order index are different. diff --git a/test/unit/workflows/test_workflow_progress.py b/test/unit/workflows/test_workflow_progress.py index a91055161e4..21cb2341414 100644 --- a/test/unit/workflows/test_workflow_progress.py +++ b/test/unit/workflows/test_workflow_progress.py @@ -2,7 +2,6 @@ import unittest from galaxy import model from galaxy.workflow.run import WorkflowProgress - from .workflow_support import TestApp, yaml_to_model TEST_WORKFLOW_YAML = """ diff --git a/tools/filters/gff/gff_filter_by_attribute.py b/tools/filters/gff/gff_filter_by_attribute.py index f0e762b4bc2..d498056e29a 100644 --- a/tools/filters/gff/gff_filter_by_attribute.py +++ b/tools/filters/gff/gff_filter_by_attribute.py @@ -6,7 +6,6 @@ from __future__ import division, print_function import sys - from ast import Module, parse, walk from json import loads diff --git a/tools/filters/gff/gff_filter_by_feature_count.py b/tools/filters/gff/gff_filter_by_feature_count.py index d672c77b472..08f3cec6117 100644 --- a/tools/filters/gff/gff_filter_by_feature_count.py +++ b/tools/filters/gff/gff_filter_by_feature_count.py @@ -8,7 +8,6 @@ Usage: from __future__ import print_function import sys - from ast import Module, parse, walk from bx.intervals.io import GenomicInterval diff --git a/tools/phenotype_association/senatag.py b/tools/phenotype_association/senatag.py index 61e4e39df8c..1fffd53ee83 100755 --- a/tools/phenotype_association/senatag.py +++ b/tools/phenotype_association/senatag.py @@ -25,7 +25,6 @@ from __future__ import print_function import heapq import os - from getopt import getopt, GetoptError from sys import argv, exit, stderr diff --git a/tox.ini b/tox.ini index 34025cd0d85..9a75c38b03b 100644 --- a/tox.ini +++ b/tox.ini @@ -1,6 +1,6 @@ [tox] # envlist is the list of envs that are tested when `tox` is run without any option -envlist = first_startup, py27-lint, py27-lint-docstring-include-list, py27-lint-imports-include-list, py27-unit, py34-lint, qunit, validate-test-tools +envlist = first_startup, py27-lint, py27-lint-docstring-include-list, py27-unit, py34-lint, qunit, validate-test-tools skipsdist = True [testenv:check-python-dependencies] @@ -33,23 +33,6 @@ whitelist_externals = bash skip_install = True deps = -rlib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt -# Setup tox environments for linting all of Galaxy for imports and -# just a subset we expect to pass (the include import list). Once the -# include list is reduced to just the inverse of Galaxy's linting -# blacklist these can both just be removed and flake8-import-order can -# be added as a dependency to Galaxy's main linting task. -[testenv:py27-lint-imports] -commands = bash .ci/flake8_wrapper.sh -whitelist_externals = bash -skip_install = True -deps = -rlib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt - -[testenv:py27-lint-imports-include-list] -commands = bash .ci/flake8_wrapper_imports.sh -whitelist_externals = bash -skip_install = True -deps = -rlib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt - [testenv:py27-unit] commands = bash run_tests.sh --no-create-venv -u whitelist_externals = bash