Formatted code with ruff.

Author: jstone-dev

src/mavedb/lib/experiments.py

@@ -8,7 +8,9 @@
 from mavedb.models.contributor import Contributor
 from mavedb.models.controlled_keyword import ControlledKeyword
 from mavedb.models.experiment import Experiment
-from mavedb.models.experiment_controlled_keyword import ExperimentControlledKeywordAssociation
+from mavedb.models.experiment_controlled_keyword import (
+    ExperimentControlledKeywordAssociation,
+)
 from mavedb.models.publication_identifier import PublicationIdentifier
 from mavedb.models.score_set import ScoreSet
 from mavedb.models.user import User
@@ -117,6 +119,9 @@ def search_experiments(
         items = []
 
     save_to_logging_context({"matching_resources": len(items)})
-    logger.debug(msg="Experiment search yielded {len(items)} matching resources.", extra=logging_context())
+    logger.debug(
+        msg="Experiment search yielded {len(items)} matching resources.",
+        extra=logging_context(),
+    )
 
     return items

src/mavedb/lib/permissions.py

@@ -37,9 +37,15 @@ def __init__(self, permitted: bool, http_code: int = 403, message: Optional[str]
 
         save_to_logging_context({"permission_message": self.message, "access_permitted": self.permitted})
         if self.permitted:
-            logger.debug(msg="Access to the requested resource is permitted.", extra=logging_context())
+            logger.debug(
+                msg="Access to the requested resource is permitted.",
+                extra=logging_context(),
+            )
         else:
-            logger.debug(msg="Access to the requested resource is not permitted.", extra=logging_context())
+            logger.debug(
+                msg="Access to the requested resource is not permitted.",
+                extra=logging_context(),
+            )
 
 
 class PermissionException(Exception):
@@ -315,7 +321,11 @@ def has_permission(user_data: Optional[UserData], item: Base, action: Action) ->
             # TODO who should be allowed to delete an official collection? mavedb admins only?
             # A collection may be deleted even if it has been published, as long as it is not an official collection.
             if user_is_owner:
-                return PermissionResponse(not item.badge_name, 403, f"insufficient permissions for URN '{item.urn}'")
+                return PermissionResponse(
+                    not item.badge_name,
+                    403,
+                    f"insufficient permissions for URN '{item.urn}'",
+                )
             # MaveDB admins may delete official collections.
             elif roles_permitted(active_roles, [UserRole.admin]):
                 return PermissionResponse(True)

src/mavedb/models/collection.py

@@ -22,7 +22,13 @@ class Collection(Base):
 
     id = Column(Integer, primary_key=True)
 
-    urn = Column(String(64), nullable=True, default=generate_collection_urn, unique=True, index=True)
+    urn = Column(
+        String(64),
+        nullable=True,
+        default=generate_collection_urn,
+        unique=True,
+        index=True,
+    )
     private = Column(Boolean, nullable=False, default=True)
 
     name = Column(String, nullable=False)
@@ -37,7 +43,9 @@ class Collection(Base):
     modification_date = Column(Date, nullable=False, default=date.today, onupdate=date.today)
 
     user_associations: Mapped[list[mavedb.models.collection_user_association.CollectionUserAssociation]] = relationship(
-        "CollectionUserAssociation", back_populates="collection", cascade="all, delete-orphan"
+        "CollectionUserAssociation",
+        back_populates="collection",
+        cascade="all, delete-orphan",
     )
     users: AssociationProxy[list[User]] = association_proxy(
         "user_associations",
@@ -48,8 +56,12 @@ class Collection(Base):
     )
 
     experiments: Mapped[list[Experiment]] = relationship(
-        "Experiment", secondary=collection_experiments_association_table, back_populates="collections"
+        "Experiment",
+        secondary=collection_experiments_association_table,
+        back_populates="collections",
     )
     score_sets: Mapped[list[ScoreSet]] = relationship(
-        "ScoreSet", secondary=collection_score_sets_association_table, back_populates="collections"
+        "ScoreSet",
+        secondary=collection_score_sets_association_table,
+        back_populates="collections",
     )

src/mavedb/models/collection_user_association.py

@@ -18,7 +18,13 @@ class CollectionUserAssociation(Base):
     collection_id = Column("collection_id", Integer, ForeignKey("collections.id"), primary_key=True)
     user_id = Column("user_id", Integer, ForeignKey("users.id"), primary_key=True)
     contribution_role: Mapped["ContributionRole"] = Column(
-        Enum(ContributionRole, create_constraint=True, length=32, native_enum=False, validate_strings=True),
+        Enum(
+            ContributionRole,
+            create_constraint=True,
+            length=32,
+            native_enum=False,
+            validate_strings=True,
+        ),
         nullable=False,
     )
 

src/mavedb/models/experiment.py

@@ -10,12 +10,18 @@
 
 from mavedb.db.base import Base
 from mavedb.lib.temp_urns import generate_temp_urn
-from mavedb.models.collection_association import collection_experiments_association_table
+from mavedb.models.collection_association import (
+    collection_experiments_association_table,
+)
 from mavedb.models.contributor import Contributor
 from mavedb.models.controlled_keyword import ControlledKeyword
 from mavedb.models.doi_identifier import DoiIdentifier
-from mavedb.models.experiment_controlled_keyword import ExperimentControlledKeywordAssociation
-from mavedb.models.experiment_publication_identifier import ExperimentPublicationIdentifierAssociation
+from mavedb.models.experiment_controlled_keyword import (
+    ExperimentControlledKeywordAssociation,
+)
+from mavedb.models.experiment_publication_identifier import (
+    ExperimentPublicationIdentifierAssociation,
+)
 from mavedb.models.experiment_set import ExperimentSet
 from mavedb.models.legacy_keyword import LegacyKeyword
 from mavedb.models.publication_identifier import PublicationIdentifier
@@ -78,7 +84,9 @@ class Experiment(Base):
     score_sets: Mapped[List["ScoreSet"]] = relationship(back_populates="experiment", cascade="all, delete-orphan")
 
     collections: Mapped[list["Collection"]] = relationship(
-        "Collection", secondary=collection_experiments_association_table, back_populates="experiments"
+        "Collection",
+        secondary=collection_experiments_association_table,
+        back_populates="experiments",
     )
     official_collections: Mapped[list["Collection"]] = relationship(
         "Collection",
@@ -98,19 +106,27 @@ class Experiment(Base):
     creation_date = Column(Date, nullable=False, default=date.today)
     modification_date = Column(Date, nullable=False, default=date.today, onupdate=date.today)
     contributors: Mapped[list["Contributor"]] = relationship(
-        "Contributor", secondary=experiments_contributors_association_table, backref="experiments"
+        "Contributor",
+        secondary=experiments_contributors_association_table,
+        backref="experiments",
     )
     keyword_objs: Mapped[list["ExperimentControlledKeywordAssociation"]] = relationship(
         back_populates="experiment", cascade="all, delete-orphan"
     )
     legacy_keyword_objs: Mapped[list[LegacyKeyword]] = relationship(
-        "LegacyKeyword", secondary=experiments_legacy_keywords_association_table, backref="experiments"
+        "LegacyKeyword",
+        secondary=experiments_legacy_keywords_association_table,
+        backref="experiments",
     )
     doi_identifiers: Mapped[list[DoiIdentifier]] = relationship(
-        "DoiIdentifier", secondary=experiments_doi_identifiers_association_table, backref="experiments"
+        "DoiIdentifier",
+        secondary=experiments_doi_identifiers_association_table,
+        backref="experiments",
     )
     publication_identifier_associations: Mapped[list[ExperimentPublicationIdentifierAssociation]] = relationship(
-        "ExperimentPublicationIdentifierAssociation", back_populates="experiment", cascade="all, delete-orphan"
+        "ExperimentPublicationIdentifierAssociation",
+        back_populates="experiment",
+        cascade="all, delete-orphan",
     )
     publication_identifiers: AssociationProxy[List[PublicationIdentifier]] = association_proxy(
         "publication_identifier_associations",
@@ -120,7 +136,9 @@ class Experiment(Base):
 
     # sra_identifiers = relationship('SraIdentifier', secondary=experiments_sra_identifiers_association_table, backref='experiments')
     raw_read_identifiers: Mapped[list[RawReadIdentifier]] = relationship(
-        "RawReadIdentifier", secondary=experiments_raw_read_identifiers_association_table, backref="experiments"
+        "RawReadIdentifier",
+        secondary=experiments_raw_read_identifiers_association_table,
+        backref="experiments",
     )
 
     # Unfortunately, we can't use association_proxy here, because in spite of what the documentation seems to imply, it
@@ -170,7 +188,10 @@ async def set_keywords(self, db, keywords: list):
                 ExperimentControlledKeywordAssociation(
                     experiment=self,
                     controlled_keyword=await self._find_keyword(
-                        db, keyword_obj.keyword.key, keyword_obj.keyword.value, keyword_obj.keyword.vocabulary
+                        db,
+                        keyword_obj.keyword.key,
+                        keyword_obj.keyword.value,
+                        keyword_obj.keyword.vocabulary,
                     ),
                     description=keyword_obj.description,
                 )

src/mavedb/models/score_set.py

@@ -90,7 +90,13 @@ class ScoreSet(Base):
     approved = Column(Boolean, nullable=False, default=False)
     published_date = Column(Date, nullable=True)
     processing_state = Column(
-        Enum(ProcessingState, create_constraint=True, length=32, native_enum=False, validate_strings=True),
+        Enum(
+            ProcessingState,
+            create_constraint=True,
+            length=32,
+            native_enum=False,
+            validate_strings=True,
+        ),
         nullable=True,
     )
     processing_errors = Column(JSONB, nullable=True)
@@ -100,7 +106,13 @@ class ScoreSet(Base):
     variants: Mapped[list["Variant"]] = relationship(back_populates="score_set", cascade="all, delete-orphan")
 
     mapping_state = Column(
-        Enum(MappingState, create_constraint=True, length=32, native_enum=False, validate_strings=True),
+        Enum(
+            MappingState,
+            create_constraint=True,
+            length=32,
+            native_enum=False,
+            validate_strings=True,
+        ),
         nullable=True,
     )
     mapping_errors = Column(JSONB, nullable=True)
@@ -113,7 +125,10 @@ class ScoreSet(Base):
     license: Mapped["License"] = relationship("License")
     superseded_score_set_id = Column("replaces_id", Integer, ForeignKey("scoresets.id"), index=True, nullable=True)
     superseded_score_set: Mapped[Optional["ScoreSet"]] = relationship(
-        "ScoreSet", uselist=False, foreign_keys="ScoreSet.superseded_score_set_id", remote_side=[id]
+        "ScoreSet",
+        uselist=False,
+        foreign_keys="ScoreSet.superseded_score_set_id",
+        remote_side=[id],
     )
     superseding_score_set: Mapped[Optional["ScoreSet"]] = relationship(
         "ScoreSet", uselist=False, back_populates="superseded_score_set"
@@ -127,18 +142,26 @@ class ScoreSet(Base):
     modification_date = Column(Date, nullable=False, default=date.today, onupdate=date.today)
 
     legacy_keyword_objs: Mapped[list["LegacyKeyword"]] = relationship(
-        "LegacyKeyword", secondary=score_sets_legacy_keywords_association_table, backref="score_sets"
+        "LegacyKeyword",
+        secondary=score_sets_legacy_keywords_association_table,
+        backref="score_sets",
     )
     contributors: Mapped[list["Contributor"]] = relationship(
-        "Contributor", secondary=score_sets_contributors_association_table, backref="score_sets"
+        "Contributor",
+        secondary=score_sets_contributors_association_table,
+        backref="score_sets",
     )
     doi_identifiers: Mapped[list["DoiIdentifier"]] = relationship(
-        "DoiIdentifier", secondary=score_sets_doi_identifiers_association_table, backref="score_sets"
+        "DoiIdentifier",
+        secondary=score_sets_doi_identifiers_association_table,
+        backref="score_sets",
     )
     publication_identifier_associations: Mapped[
         list[mavedb.models.score_set_publication_identifier.ScoreSetPublicationIdentifierAssociation]
     ] = relationship(
-        "ScoreSetPublicationIdentifierAssociation", back_populates="score_set", cascade="all, delete-orphan"
+        "ScoreSetPublicationIdentifierAssociation",
+        back_populates="score_set",
+        cascade="all, delete-orphan",
     )
     publication_identifiers: AssociationProxy[List[PublicationIdentifier]] = association_proxy(
         "publication_identifier_associations",
@@ -162,7 +185,9 @@ class ScoreSet(Base):
     score_calibrations = Column(JSONB, nullable=True)
 
     collections: Mapped[list["Collection"]] = relationship(
-        "Collection", secondary=collection_score_sets_association_table, back_populates="score_sets"
+        "Collection",
+        secondary=collection_score_sets_association_table,
+        back_populates="score_sets",
     )
     official_collections: Mapped[list["Collection"]] = relationship(
         "Collection",