From 7c5d90c97266f05a4ee9a47985da63350ebe298e Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 3 Jan 2023 15:22:37 +0000 Subject: [PATCH] Simplify imports --- lib/galaxy/auth/providers/alwaysreject.py | 2 +- lib/galaxy/auth/providers/ldap_ad.py | 2 +- lib/galaxy/auth/providers/localdb.py | 2 +- lib/galaxy/auth/providers/pam_auth.py | 2 +- lib/galaxy/authnz/custos_authnz.py | 2 +- lib/galaxy/authnz/psa_authnz.py | 6 +++--- lib/galaxy/exceptions/__init__.py | 2 +- lib/galaxy/files/sources/_pyfilesystem2.py | 2 +- lib/galaxy/files/sources/posix.py | 2 +- lib/galaxy/files/sources/s3fs.py | 2 +- lib/galaxy/job_metrics/__init__.py | 2 +- lib/galaxy/jobs/runners/util/cli/job/lsf.py | 2 +- lib/galaxy/jobs/runners/util/cli/job/slurm.py | 2 +- lib/galaxy/jobs/runners/util/cli/job/torque.py | 2 +- lib/galaxy/model/dataset_collections/types/list.py | 2 +- lib/galaxy/model/dataset_collections/types/paired.py | 2 +- lib/galaxy/objectstore/azure_blob.py | 2 +- lib/galaxy/objectstore/cloud.py | 4 ++-- lib/galaxy/objectstore/irods.py | 2 +- lib/galaxy/objectstore/pithos.py | 2 +- lib/galaxy/objectstore/pulsar.py | 2 +- lib/galaxy/objectstore/s3.py | 4 ++-- lib/galaxy/schema/tasks.py | 2 +- lib/galaxy/tool_util/deps/brew_util.py | 2 +- lib/galaxy/tool_util/deps/container_resolvers/explicit.py | 2 +- lib/galaxy/tool_util/locations/dockstore.py | 2 +- lib/galaxy/tool_util/locations/file.py | 2 +- lib/galaxy/tool_util/locations/http.py | 2 +- lib/galaxy/util/json.py | 2 +- lib/galaxy/workflow/reports/generators/markdown.py | 2 +- lib/galaxy/workflow/schedulers/core.py | 2 +- 31 files changed, 35 insertions(+), 35 deletions(-) diff --git a/lib/galaxy/auth/providers/alwaysreject.py b/lib/galaxy/auth/providers/alwaysreject.py index f64b243d9dd..1c21adc834f 100644 --- a/lib/galaxy/auth/providers/alwaysreject.py +++ b/lib/galaxy/auth/providers/alwaysreject.py @@ -5,7 +5,7 @@ Created on 16/07/2014 """ import logging -from ..providers import AuthProvider +from . import AuthProvider log = logging.getLogger(__name__) diff --git a/lib/galaxy/auth/providers/ldap_ad.py b/lib/galaxy/auth/providers/ldap_ad.py index cedd6a8f9f2..d115b693c65 100644 --- a/lib/galaxy/auth/providers/ldap_ad.py +++ b/lib/galaxy/auth/providers/ldap_ad.py @@ -12,7 +12,7 @@ from galaxy.util import ( string_as_bool, unicodify, ) -from ..providers import AuthProvider +from . import AuthProvider try: import ldap diff --git a/lib/galaxy/auth/providers/localdb.py b/lib/galaxy/auth/providers/localdb.py index 8acf20a3f66..bd5c765af20 100644 --- a/lib/galaxy/auth/providers/localdb.py +++ b/lib/galaxy/auth/providers/localdb.py @@ -5,7 +5,7 @@ Created on 16/07/2014 """ import logging -from ..providers import AuthProvider +from . import AuthProvider log = logging.getLogger(__name__) diff --git a/lib/galaxy/auth/providers/pam_auth.py b/lib/galaxy/auth/providers/pam_auth.py index d077a5f467f..65c15034bb7 100644 --- a/lib/galaxy/auth/providers/pam_auth.py +++ b/lib/galaxy/auth/providers/pam_auth.py @@ -10,7 +10,7 @@ from galaxy.util import ( commands, string_as_bool, ) -from ..providers import AuthProvider +from . import AuthProvider log = logging.getLogger(__name__) diff --git a/lib/galaxy/authnz/custos_authnz.py b/lib/galaxy/authnz/custos_authnz.py index 5ba223cb721..dc7101915ff 100644 --- a/lib/galaxy/authnz/custos_authnz.py +++ b/lib/galaxy/authnz/custos_authnz.py @@ -23,7 +23,7 @@ from galaxy.model import ( User, ) from galaxy.model.orm.util import add_object_to_object_session -from ..authnz import IdentityProvider +from . import IdentityProvider try: import pkce diff --git a/lib/galaxy/authnz/psa_authnz.py b/lib/galaxy/authnz/psa_authnz.py index de6a6b4d576..b8d1c636797 100644 --- a/lib/galaxy/authnz/psa_authnz.py +++ b/lib/galaxy/authnz/psa_authnz.py @@ -15,15 +15,15 @@ from social_core.utils import ( from sqlalchemy.exc import IntegrityError from galaxy.exceptions import MalformedContents -from galaxy.util import DEFAULT_SOCKET_TIMEOUT -from ..authnz import IdentityProvider -from ..model import ( +from galaxy.model import ( PSAAssociation, PSACode, PSANonce, PSAPartial, UserAuthnzToken, ) +from galaxy.util import DEFAULT_SOCKET_TIMEOUT +from . import IdentityProvider # key: a component name which PSA requests. # value: is the name of a class associated with that key. diff --git a/lib/galaxy/exceptions/__init__.py b/lib/galaxy/exceptions/__init__.py index 8f5def61a88..f14a816d634 100644 --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -16,7 +16,7 @@ have nothing to do with the web - keep this in mind when defining exception name and messages. """ -from ..exceptions.error_codes import ( +from .error_codes import ( error_codes_by_name, ErrorCode, ) diff --git a/lib/galaxy/files/sources/_pyfilesystem2.py b/lib/galaxy/files/sources/_pyfilesystem2.py index 08abb9e4574..45162f86c5f 100644 --- a/lib/galaxy/files/sources/_pyfilesystem2.py +++ b/lib/galaxy/files/sources/_pyfilesystem2.py @@ -14,7 +14,7 @@ from typing import ( import fs from fs.base import FS -from ..sources import BaseFilesSource +from . import BaseFilesSource log = logging.getLogger(__name__) diff --git a/lib/galaxy/files/sources/posix.py b/lib/galaxy/files/sources/posix.py index 937c6be397a..b464b8f6351 100644 --- a/lib/galaxy/files/sources/posix.py +++ b/lib/galaxy/files/sources/posix.py @@ -13,7 +13,7 @@ from galaxy.util.path import ( safe_path, safe_walk, ) -from ..sources import BaseFilesSource +from . import BaseFilesSource DEFAULT_ENFORCE_SYMLINK_SECURITY = True DEFAULT_DELETE_ON_REALIZE = False diff --git a/lib/galaxy/files/sources/s3fs.py b/lib/galaxy/files/sources/s3fs.py index 2c85609dd33..8353b4d8d51 100644 --- a/lib/galaxy/files/sources/s3fs.py +++ b/lib/galaxy/files/sources/s3fs.py @@ -12,7 +12,7 @@ try: except ImportError: s3fs = None -from ..sources import BaseFilesSource +from . import BaseFilesSource DEFAULT_ENFORCE_SYMLINK_SECURITY = True DEFAULT_DELETE_ON_REALIZE = False diff --git a/lib/galaxy/job_metrics/__init__.py b/lib/galaxy/job_metrics/__init__.py index ab981cd6f3d..8fdb85f75a2 100644 --- a/lib/galaxy/job_metrics/__init__.py +++ b/lib/galaxy/job_metrics/__init__.py @@ -27,11 +27,11 @@ from typing import ( from galaxy import util from galaxy.util import plugin_config +from . import formatting from .safety import ( DEFAULT_SAFETY, Safety, ) -from ..job_metrics import formatting log = logging.getLogger(__name__) diff --git a/lib/galaxy/jobs/runners/util/cli/job/lsf.py b/lib/galaxy/jobs/runners/util/cli/job/lsf.py index 68c96345096..481b55c757d 100644 --- a/lib/galaxy/jobs/runners/util/cli/job/lsf.py +++ b/lib/galaxy/jobs/runners/util/cli/job/lsf.py @@ -3,7 +3,7 @@ from logging import getLogger from os import path -from ..job import ( +from . import ( BaseJobExec, job_states, ) diff --git a/lib/galaxy/jobs/runners/util/cli/job/slurm.py b/lib/galaxy/jobs/runners/util/cli/job/slurm.py index 5b694b13253..5c1626d7315 100644 --- a/lib/galaxy/jobs/runners/util/cli/job/slurm.py +++ b/lib/galaxy/jobs/runners/util/cli/job/slurm.py @@ -2,7 +2,7 @@ # non-submit host and using a Slurm cluster. from logging import getLogger -from ..job import ( +from . import ( BaseJobExec, job_states, ) diff --git a/lib/galaxy/jobs/runners/util/cli/job/torque.py b/lib/galaxy/jobs/runners/util/cli/job/torque.py index cb801ed1c0a..feb36dad949 100644 --- a/lib/galaxy/jobs/runners/util/cli/job/torque.py +++ b/lib/galaxy/jobs/runners/util/cli/job/torque.py @@ -1,7 +1,7 @@ from logging import getLogger from galaxy.util import parse_xml_string -from ..job import ( +from . import ( BaseJobExec, job_states, ) diff --git a/lib/galaxy/model/dataset_collections/types/list.py b/lib/galaxy/model/dataset_collections/types/list.py index 74a274138c7..6fccedf1728 100644 --- a/lib/galaxy/model/dataset_collections/types/list.py +++ b/lib/galaxy/model/dataset_collections/types/list.py @@ -1,5 +1,5 @@ from galaxy.model import DatasetCollectionElement -from ..types import BaseDatasetCollectionType +from . import BaseDatasetCollectionType class ListDatasetCollectionType(BaseDatasetCollectionType): diff --git a/lib/galaxy/model/dataset_collections/types/paired.py b/lib/galaxy/model/dataset_collections/types/paired.py index 71e24f471c8..3ac8d7da4d8 100644 --- a/lib/galaxy/model/dataset_collections/types/paired.py +++ b/lib/galaxy/model/dataset_collections/types/paired.py @@ -2,7 +2,7 @@ from galaxy.model import ( DatasetCollectionElement, HistoryDatasetAssociation, ) -from ..types import BaseDatasetCollectionType +from . import BaseDatasetCollectionType FORWARD_IDENTIFIER = "forward" REVERSE_IDENTIFIER = "reverse" diff --git a/lib/galaxy/objectstore/azure_blob.py b/lib/galaxy/objectstore/azure_blob.py index 7326d506781..daefbd71922 100644 --- a/lib/galaxy/objectstore/azure_blob.py +++ b/lib/galaxy/objectstore/azure_blob.py @@ -28,7 +28,7 @@ from galaxy.util import ( ) from galaxy.util.path import safe_relpath from galaxy.util.sleeper import Sleeper -from ..objectstore import ( +from . import ( ConcreteObjectStore, convert_bytes, ) diff --git a/lib/galaxy/objectstore/cloud.py b/lib/galaxy/objectstore/cloud.py index 26986eb2114..5835fc000b0 100644 --- a/lib/galaxy/objectstore/cloud.py +++ b/lib/galaxy/objectstore/cloud.py @@ -23,11 +23,11 @@ from galaxy.util import ( unlink, ) from galaxy.util.sleeper import Sleeper -from .s3 import parse_config_xml -from ..objectstore import ( +from . import ( ConcreteObjectStore, convert_bytes, ) +from .s3 import parse_config_xml try: from cloudbridge.factory import ( diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py index c885662600a..cf0f8a7770d 100644 --- a/lib/galaxy/objectstore/irods.py +++ b/lib/galaxy/objectstore/irods.py @@ -30,7 +30,7 @@ from galaxy.util import ( unlink, ) from galaxy.util.path import safe_relpath -from ..objectstore import DiskObjectStore +from . import DiskObjectStore IRODS_IMPORT_MESSAGE = "The Python irods package is required to use this feature, please install it" # 1 MB diff --git a/lib/galaxy/objectstore/pithos.py b/lib/galaxy/objectstore/pithos.py index 6f8094026f7..f28baf6c31d 100644 --- a/lib/galaxy/objectstore/pithos.py +++ b/lib/galaxy/objectstore/pithos.py @@ -26,7 +26,7 @@ from galaxy.util import ( umask_fix_perms, ) from galaxy.util.path import safe_relpath -from ..objectstore import ConcreteObjectStore +from . import ConcreteObjectStore NO_KAMAKI_ERROR_MESSAGE = ( "ObjectStore configured, but no kamaki.clients dependency available." diff --git a/lib/galaxy/objectstore/pulsar.py b/lib/galaxy/objectstore/pulsar.py index 39a54ca5650..04eab33d5fa 100644 --- a/lib/galaxy/objectstore/pulsar.py +++ b/lib/galaxy/objectstore/pulsar.py @@ -1,4 +1,4 @@ -from ..objectstore import BaseObjectStore +from . import BaseObjectStore try: from pulsar.client.manager import ObjectStoreClientManager diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py index c1e83643827..01efc4a2152 100644 --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -32,11 +32,11 @@ 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 ( +from . import ( ConcreteObjectStore, convert_bytes, ) +from .s3_multipart_upload import multipart_upload NO_BOTO_ERROR_MESSAGE = ( "S3/Swift object store configured, but no boto dependency available." diff --git a/lib/galaxy/schema/tasks.py b/lib/galaxy/schema/tasks.py index 8eca3b54a5a..be120cf74b5 100644 --- a/lib/galaxy/schema/tasks.py +++ b/lib/galaxy/schema/tasks.py @@ -7,6 +7,7 @@ from pydantic import ( ) from galaxy.util.hash_util import HashFunctionNameEnum +from . import PdfDocumentType from .schema import ( BcoGenerationParametersMixin, DatasetSourceType, @@ -15,7 +16,6 @@ from .schema import ( ShortTermStoreExportPayload, WriteStoreToPayload, ) -from ..schema import PdfDocumentType class SetupHistoryExportJob(BaseModel): diff --git a/lib/galaxy/tool_util/deps/brew_util.py b/lib/galaxy/tool_util/deps/brew_util.py index d513a23461f..a2e19d7d5cc 100644 --- a/lib/galaxy/tool_util/deps/brew_util.py +++ b/lib/galaxy/tool_util/deps/brew_util.py @@ -2,7 +2,7 @@ builds on those abstraction and provides Galaxy specific functionality not useful to the brew external commands. """ -from ..deps import brew_exts +from . import brew_exts DEFAULT_TAP = "homebrew/science" diff --git a/lib/galaxy/tool_util/deps/container_resolvers/explicit.py b/lib/galaxy/tool_util/deps/container_resolvers/explicit.py index db6569d19b1..a15bc5d5039 100644 --- a/lib/galaxy/tool_util/deps/container_resolvers/explicit.py +++ b/lib/galaxy/tool_util/deps/container_resolvers/explicit.py @@ -4,9 +4,9 @@ import os from typing import cast from galaxy.util.commands import shell +from . import ContainerResolver from .mulled import CliContainerResolver from ..container_classes import SingularityContainer -from ..container_resolvers import ContainerResolver from ..requirements import ContainerDescription log = logging.getLogger(__name__) diff --git a/lib/galaxy/tool_util/locations/dockstore.py b/lib/galaxy/tool_util/locations/dockstore.py index 3ef9c929889..68526b5ce6f 100644 --- a/lib/galaxy/tool_util/locations/dockstore.py +++ b/lib/galaxy/tool_util/locations/dockstore.py @@ -4,7 +4,7 @@ import requests import yaml from galaxy.util import DEFAULT_SOCKET_TIMEOUT -from ..locations import ToolLocationResolver +from . import ToolLocationResolver class DockStoreResolver(ToolLocationResolver): diff --git a/lib/galaxy/tool_util/locations/file.py b/lib/galaxy/tool_util/locations/file.py index cdc09981f17..daa09b56609 100644 --- a/lib/galaxy/tool_util/locations/file.py +++ b/lib/galaxy/tool_util/locations/file.py @@ -1,4 +1,4 @@ -from ..locations import ToolLocationResolver +from . import ToolLocationResolver class HttpToolResolver(ToolLocationResolver): diff --git a/lib/galaxy/tool_util/locations/http.py b/lib/galaxy/tool_util/locations/http.py index e8fb7372cb0..3b13abf82c6 100644 --- a/lib/galaxy/tool_util/locations/http.py +++ b/lib/galaxy/tool_util/locations/http.py @@ -1,5 +1,5 @@ from galaxy.util import download_to_file -from ..locations import ToolLocationResolver +from . import ToolLocationResolver class HttpToolResolver(ToolLocationResolver): diff --git a/lib/galaxy/util/json.py b/lib/galaxy/util/json.py index a6980f94036..1b3d03f6c47 100644 --- a/lib/galaxy/util/json.py +++ b/lib/galaxy/util/json.py @@ -11,7 +11,7 @@ from collections.abc import ( ) from decimal import Decimal -from ..util import unicodify +from . import unicodify __all__ = ("safe_dumps", "validate_jsonrpc_request", "validate_jsonrpc_response", "jsonrpc_request", "jsonrpc_response") diff --git a/lib/galaxy/workflow/reports/generators/markdown.py b/lib/galaxy/workflow/reports/generators/markdown.py index 44ccbb759ec..bcc65eebc8d 100644 --- a/lib/galaxy/workflow/reports/generators/markdown.py +++ b/lib/galaxy/workflow/reports/generators/markdown.py @@ -3,7 +3,7 @@ import logging import string -from ..generators import WorkflowMarkdownGeneratorPlugin +from . import WorkflowMarkdownGeneratorPlugin log = logging.getLogger(__name__) diff --git a/lib/galaxy/workflow/schedulers/core.py b/lib/galaxy/workflow/schedulers/core.py index a66c6db44eb..427e23f4818 100644 --- a/lib/galaxy/workflow/schedulers/core.py +++ b/lib/galaxy/workflow/schedulers/core.py @@ -9,7 +9,7 @@ from galaxy.workflow import ( run, run_request, ) -from ..schedulers import ActiveWorkflowSchedulingPlugin +from . import ActiveWorkflowSchedulingPlugin if TYPE_CHECKING: from galaxy.model import WorkflowInvocation