From 3803774ad0d2683c6026ae9f8cdefaebcf601c2b Mon Sep 17 00:00:00 2001 From: guerler Date: Tue, 24 Oct 2023 19:10:04 +0300 Subject: [PATCH] Fix linting --- lib/galaxy/managers/visualizations.py | 47 ++++++++++--------- lib/galaxy/schema/visualization.py | 17 +++---- .../webapps/galaxy/api/visualizations.py | 9 ++-- .../webapps/galaxy/services/visualizations.py | 8 +--- 4 files changed, 36 insertions(+), 45 deletions(-) diff --git a/lib/galaxy/managers/visualizations.py b/lib/galaxy/managers/visualizations.py index d4750408f423..68b91b04a86b 100644 --- a/lib/galaxy/managers/visualizations.py +++ b/lib/galaxy/managers/visualizations.py @@ -5,7 +5,6 @@ reproduce a specific view in a Galaxy visualization. """ import logging - from typing import ( Dict, List, @@ -17,30 +16,25 @@ or_, true, ) -from sqlalchemy.orm import ( - aliased, -) +from sqlalchemy.orm import aliased from galaxy import ( exceptions, model, ) -from galaxy.managers import (base, sharable) +from galaxy.managers import ( + base, + sharable, +) from galaxy.managers.context import ProvidesUserContext - from galaxy.model.index_filter_util import ( append_user_filter, raw_text_column_filter, tag_filter, text_column_filter, ) - -from galaxy.schema.visualization import ( - VisualizationIndexQueryPayload, -) - +from galaxy.schema.visualization import VisualizationIndexQueryPayload from galaxy.structured_app import MinimalManagerApp - from galaxy.util.search import ( FilteredTerm, parse_filters_structured, @@ -188,17 +182,24 @@ def __init__(self, app: MinimalManagerApp): self.visualization_manager = self.manager self.default_view = "summary" - self.add_view("summary", [ - "id", - "title", - "type", - "dbkey", - ]) - self.add_view("detailed", [ - "create_time", - "tags", - "update_time", - ], include_keys_from="summary",) + self.add_view( + "summary", + [ + "id", + "title", + "type", + "dbkey", + ], + ) + self.add_view( + "detailed", + [ + "create_time", + "tags", + "update_time", + ], + include_keys_from="summary", + ) def add_serializers(self): super().add_serializers() diff --git a/lib/galaxy/schema/visualization.py b/lib/galaxy/schema/visualization.py index 26c5f2e7b4b6..ac16c0a0e477 100644 --- a/lib/galaxy/schema/visualization.py +++ b/lib/galaxy/schema/visualization.py @@ -8,22 +8,17 @@ Extra, Field, ) -from typing_extensions import ( - Literal, -) +from typing_extensions import Literal -from galaxy.schema.fields import ( - DecodedDatabaseIdField, -) +from galaxy.schema.fields import DecodedDatabaseIdField from galaxy.schema.schema import ( CreateTimeField, - TagCollection, - UpdateTimeField, Model, SharingStatus, + TagCollection, + UpdateTimeField, ) - VisualizationSortByEnum = Literal["create_time", "title", "update_time", "username"] @@ -32,7 +27,9 @@ class VisualizationIndexQueryPayload(Model): show_published: Optional[bool] = None show_shared: Optional[bool] = None user_id: Optional[DecodedDatabaseIdField] = None - sort_by: VisualizationSortByEnum = Field("update_time", title="Sort By", description="Sort pages by this attribute.") + sort_by: VisualizationSortByEnum = Field( + "update_time", title="Sort By", description="Sort pages by this attribute." + ) sort_desc: Optional[bool] = Field(default=True, title="Sort descending", description="Sort in descending order.") search: Optional[str] = Field(default=None, title="Filter text", description="Freetext to search.") limit: Optional[int] = Field(default=100, lt=1000, title="Limit", description="Maximum number of pages to return.") diff --git a/lib/galaxy/webapps/galaxy/api/visualizations.py b/lib/galaxy/webapps/galaxy/api/visualizations.py index 2e7ff41b8002..5f39926ff19f 100644 --- a/lib/galaxy/webapps/galaxy/api/visualizations.py +++ b/lib/galaxy/webapps/galaxy/api/visualizations.py @@ -6,10 +6,7 @@ """ import json import logging - -from typing import ( - Optional, -) +from typing import Optional from fastapi import ( Body, @@ -90,7 +87,9 @@ ShowPublishedQueryParam: bool = Query(default=True, title="Include published visualizations.", description="") -ShowSharedQueryParam: bool = Query(default=False, title="Include visualizations shared with authenticated user.", description="") +ShowSharedQueryParam: bool = Query( + default=False, title="Include visualizations shared with authenticated user.", description="" +) SortByQueryParam: VisualizationSortByEnum = Query( default="update_time", diff --git a/lib/galaxy/webapps/galaxy/services/visualizations.py b/lib/galaxy/webapps/galaxy/services/visualizations.py index 686ad4ce355c..5dd1cfcbbacb 100644 --- a/lib/galaxy/webapps/galaxy/services/visualizations.py +++ b/lib/galaxy/webapps/galaxy/services/visualizations.py @@ -1,5 +1,4 @@ import logging - from typing import ( Any, List, @@ -7,17 +6,13 @@ ) from galaxy import exceptions - from galaxy.managers.notification import NotificationManager from galaxy.managers.visualizations import ( VisualizationManager, VisualizationSerializer, ) +from galaxy.schema.visualization import VisualizationIndexQueryPayload from galaxy.security.idencoding import IdEncodingHelper - -from galaxy.schema.visualization import ( - VisualizationIndexQueryPayload, -) from galaxy.webapps.galaxy.services.base import ServiceBase from galaxy.webapps.galaxy.services.sharable import ShareableService @@ -51,7 +46,6 @@ def index( payload: VisualizationIndexQueryPayload, detailed: bool = False, include_total_count: bool = False, - sharing: bool = False, ) -> Tuple[List[Any], int]: """Return a list of Visualizations viewable by the user