style: clean up/rename errors

docs/source/api/etl_api.rst

@@ -9,13 +9,6 @@ Update methods
 .. automodule:: gene.etl.update
    :members:
 
-Exceptions
-----------
-
-.. automodule:: gene.etl.exceptions
-    :members:
-    :show-inheritance:
-
 NCBI
 ----
 

docs/source/api/query_api.rst

@@ -7,9 +7,3 @@ Query API
     :members:
     :special-members: __init__
     :undoc-members:
-
-.. autoexception:: gene.query.InvalidParameterException
-    :members:
-    :undoc-members:
-    :show-inheritance:
-

src/gene/cli.py

@@ -6,7 +6,7 @@
 import click
 
 from gene.database import create_db
-from gene.database.database import DatabaseException
+from gene.database.database import DatabaseError
 from gene.etl.update import update_all_sources, update_normalized, update_source
 from gene.schemas import SourceName
 
@@ -137,7 +137,7 @@ def update_from_remote(data_url: Optional[str], db_url: str, silent: bool) -> No
             f"Error: Fetching remote data dump not supported for {db.__class__.__name__}"
         )  # noqa: E501
         click.get_current_context().exit(1)
-    except DatabaseException as e:
+    except DatabaseError as e:
         click.echo(f"Encountered exception during update: {str(e)}")
         click.get_current_context().exit(1)
 
@@ -220,7 +220,7 @@ def dump_database(output_directory: Path, db_url: str, silent: bool) -> None:
             f"Error: Dumping data to file not supported for {db.__class__.__name__}"
         )  # noqa: E501
         click.get_current_context().exit(1)
-    except DatabaseException as e:
+    except DatabaseError as e:
         click.echo(f"Encountered exception during update: {str(e)}")
         click.get_current_context().exit(1)
 

src/gene/database/__init__.py

@@ -2,9 +2,9 @@
 from .database import (
     AWS_ENV_VAR_NAME,
     AbstractDatabase,
-    DatabaseException,
-    DatabaseInitializationException,
-    DatabaseReadException,
-    DatabaseWriteException,
+    DatabaseError,
+    DatabaseInitializationError,
+    DatabaseReadError,
+    DatabaseWriteError,
     create_db,
 )

src/gene/database/database.py

@@ -11,19 +11,19 @@
 from gene.schemas import RecordType, RefType, SourceMeta, SourceName
 
 
-class DatabaseException(Exception):  # noqa: N818
+class DatabaseError(Exception):
     """Create custom class for handling database exceptions"""
 
 
-class DatabaseInitializationException(DatabaseException):
+class DatabaseInitializationError(DatabaseError):
     """Create custom exception for errors during DB connection initialization."""
 
 
-class DatabaseReadException(DatabaseException):
+class DatabaseReadError(DatabaseError):
     """Create custom exception for lookup/read errors"""
 
 
-class DatabaseWriteException(DatabaseException):
+class DatabaseWriteError(DatabaseError):
     """Create custom exception for write errors"""
 
 
@@ -43,7 +43,7 @@ def __init__(self, db_url: Optional[str] = None, **db_args) -> None:
 
         :param db_url: address/connection description for database
         :param db_args: any DB implementation-specific parameters
-        :raise DatabaseInitializationException: if initial setup fails
+        :raise DatabaseInitializationError: if initial setup fails
         """
 
     @abc.abstractmethod
@@ -58,12 +58,12 @@ def _check_delete_okay() -> bool:
         """Check that environmental conditions permit DB deletion, and require
         confirmation.
 
-        :raise DatabaseWriteException: if skip confirmation variable is set -- manual
+        :raise DatabaseWriteError: if skip confirmation variable is set -- manual
         approval is required.
         """
         if environ.get(AWS_ENV_VAR_NAME, "") == AwsEnvName.PRODUCTION:
             if environ.get(SKIP_AWS_DB_ENV_NAME, "") == "true":
-                raise DatabaseWriteException(
+                raise DatabaseWriteError(
                     f"Must unset {SKIP_AWS_DB_ENV_NAME} env variable to enable drop_db()"  # noqa: E501
                 )
             return click.confirm("Are you sure you want to delete existing data?")
@@ -75,8 +75,8 @@ def drop_db(self) -> None:
         """Initiate total teardown of DB. Useful for quickly resetting the entirety of
         the data. Requires manual confirmation.
 
-        :raise DatabaseWriteException: if called in a protected setting with
-            confirmation silenced.
+        :raise DatabaseWriteError: if called in a protected setting with confirmation
+            silenced.
         """
 
     @abc.abstractmethod
@@ -103,7 +103,7 @@ def initialize_db(self) -> None:
         existing content -- ie, this method is also responsible for checking whether
         the DB is already set up.
 
-        :raise DatabaseInitializationException: if initialization fails
+        :raise DatabaseInitializationError: if initialization fails
         """
 
     @abc.abstractmethod
@@ -168,7 +168,7 @@ def add_source_metadata(self, src_name: SourceName, data: SourceMeta) -> None:
 
         :param src_name: name of source
         :param data: known source attributes
-        :raise DatabaseWriteException: if write fails
+        :raise DatabaseWriteError: if write fails
         """
 
     @abc.abstractmethod
@@ -192,27 +192,27 @@ def update_merge_ref(self, concept_id: str, merge_ref: Any) -> None:  # noqa: AN
 
         :param concept_id: record to update
         :param merge_ref: new ref value
-        :raise DatabaseWriteException: if attempting to update non-existent record
+        :raise DatabaseWriteError: if attempting to update non-existent record
         """
 
     @abc.abstractmethod
     def delete_normalized_concepts(self) -> None:
         """Remove merged records from the database. Use when performing a new update
         of normalized data.
 
-        :raise DatabaseReadException: if DB client requires separate read calls and
+        :raise DatabaseReadError: if DB client requires separate read calls and
             encounters a failure in the process
-        :raise DatabaseWriteException: if deletion call fails
+        :raise DatabaseWriteError: if deletion call fails
         """
 
     @abc.abstractmethod
     def delete_source(self, src_name: SourceName) -> None:
         """Delete all data for a source. Use when updating source data.
 
         :param src_name: name of source to delete
-        :raise DatabaseReadException: if DB client requires separate read calls and
+        :raise DatabaseReadError: if DB client requires separate read calls and
             encounters a failure in the process
-        :raise DatabaseWriteException: if deletion call fails
+        :raise DatabaseWriteError: if deletion call fails
         """
 
     @abc.abstractmethod

src/gene/database/dynamodb.py

@@ -17,9 +17,9 @@
     VALID_AWS_ENV_NAMES,
     AbstractDatabase,
     AwsEnvName,
-    DatabaseInitializationException,
-    DatabaseReadException,
-    DatabaseWriteException,
+    DatabaseInitializationError,
+    DatabaseReadError,
+    DatabaseWriteError,
     confirm_aws_db_use,
 )
 from gene.schemas import (
@@ -44,20 +44,20 @@ def __init__(self, db_url: Optional[str] = None, **db_args) -> None:
         :Keyword Arguments:
             * region_name: AWS region (defaults to "us-east-2")
             * silent: if True, suppress console output
-        :raise DatabaseInitializationException: if initial setup fails
+        :raise DatabaseInitializationError: if initial setup fails
         """
         self.gene_table = environ.get("GENE_DYNAMO_TABLE", "gene_normalizer")
         region_name = db_args.get("region_name", "us-east-2")
 
         if AWS_ENV_VAR_NAME in environ:
             if "GENE_TEST" in environ:
-                raise DatabaseInitializationException(
+                raise DatabaseInitializationError(
                     f"Cannot have both GENE_TEST and {AWS_ENV_VAR_NAME} set."
                 )  # noqa: E501
             try:
                 aws_env = AwsEnvName(environ[AWS_ENV_VAR_NAME])
             except ValueError:
-                raise DatabaseInitializationException(
+                raise DatabaseInitializationError(
                     f"{AWS_ENV_VAR_NAME} must be one of {VALID_AWS_ENV_NAMES}: found {environ[AWS_ENV_VAR_NAME]} instead."
                 )
             skip_confirmation = environ.get(SKIP_AWS_DB_ENV_NAME)
@@ -108,13 +108,13 @@ def list_tables(self) -> List[str]:
     def drop_db(self) -> None:
         """Delete all tables from database. Requires manual confirmation.
 
-        :raise DatabaseWriteException: if called in a protected setting with
-            confirmation silenced.
+        :raise DatabaseWriteError: if called in a protected setting with confirmation
+            silenced.
         """
         try:
             if not self._check_delete_okay():
                 return
-        except DatabaseWriteException as e:
+        except DatabaseWriteError as e:
             raise e
 
         if self.gene_table in self.list_tables():
@@ -226,7 +226,7 @@ def get_source_metadata(self, src_name: Union[str, SourceName]) -> Dict:
                 Key={"label_and_type": pk, "concept_id": concept_id}
             ).get("Item")
             if not metadata:
-                raise DatabaseReadException(
+                raise DatabaseReadError(
                     f"Unable to retrieve data for source {src_name}"
                 )
             self._cached_sources[src_name] = metadata
@@ -358,7 +358,7 @@ def add_source_metadata(self, src_name: SourceName, metadata: SourceMeta) -> Non
 
         :param src_name: name of source
         :param data: known source attributes
-        :raise DatabaseWriteException: if write fails
+        :raise DatabaseWriteError: if write fails
         """
         src_name_value = src_name.value
         metadata_item = metadata.model_dump()
@@ -369,7 +369,7 @@ def add_source_metadata(self, src_name: SourceName, metadata: SourceMeta) -> Non
         try:
             self.genes.put_item(Item=metadata_item)
         except ClientError as e:
-            raise DatabaseWriteException(e)
+            raise DatabaseWriteError(e)
 
     def add_record(self, record: Dict, src_name: SourceName) -> None:
         """Add new record to database.
@@ -450,7 +450,7 @@ def update_merge_ref(self, concept_id: str, merge_ref: Any) -> None:  # noqa: AN
 
         :param concept_id: record to update
         :param merge_ref: new ref value
-        :raise DatabaseWriteException: if attempting to update non-existent record
+        :raise DatabaseWriteError: if attempting to update non-existent record
         """
         label_and_type = f"{concept_id.lower()}##identity"
         key = {"label_and_type": label_and_type, "concept_id": concept_id}
@@ -467,7 +467,7 @@ def update_merge_ref(self, concept_id: str, merge_ref: Any) -> None:  # noqa: AN
         except ClientError as e:
             code = e.response.get("Error", {}).get("Code")
             if code == "ConditionalCheckFailedException":
-                raise DatabaseWriteException(
+                raise DatabaseWriteError(
                     f"No such record exists for keys {label_and_type}, {concept_id}"
                 )
             else:
@@ -479,9 +479,9 @@ def delete_normalized_concepts(self) -> None:
         """Remove merged records from the database. Use when performing a new update
         of normalized data.
 
-        :raise DatabaseReadException: if DB client requires separate read calls and
+        :raise DatabaseReadError: if DB client requires separate read calls and
             encounters a failure in the process
-        :raise DatabaseWriteException: if deletion call fails
+        :raise DatabaseWriteError: if deletion call fails
         """
         while True:
             with self.genes.batch_writer(
@@ -495,7 +495,7 @@ def delete_normalized_concepts(self) -> None:
                         ),
                     )
                 except ClientError as e:
-                    raise DatabaseReadException(e)
+                    raise DatabaseReadError(e)
                 records = response["Items"]
                 if not records:
                     break
@@ -511,9 +511,9 @@ def delete_source(self, src_name: SourceName) -> None:
         """Delete all data for a source. Use when updating source data.
 
         :param src_name: name of source to delete
-        :raise DatabaseReadException: if DB client requires separate read calls and
+        :raise DatabaseReadError: if DB client requires separate read calls and
             encounters a failure in the process
-        :raise DatabaseWriteException: if deletion call fails
+        :raise DatabaseWriteError: if deletion call fails
         """
         while True:
             try:
@@ -522,7 +522,7 @@ def delete_source(self, src_name: SourceName) -> None:
                     KeyConditionExpression=Key("src_name").eq(src_name.value),
                 )
             except ClientError as e:
-                raise DatabaseReadException(e)
+                raise DatabaseReadError(e)
             records = response["Items"]
             if not records:
                 break
@@ -538,7 +538,7 @@ def delete_source(self, src_name: SourceName) -> None:
                             }
                         )
                     except ClientError as e:
-                        raise DatabaseWriteException(e)
+                        raise DatabaseWriteError(e)
 
     def complete_write_transaction(self) -> None:
         """Conclude transaction or batch writing if relevant."""