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Harry Caufield "] license = "BSD-3" diff --git a/src/curategpt/store/db_adapter.py b/src/curategpt/store/db_adapter.py index 4ea01cc..ad9fc26 100644 --- a/src/curategpt/store/db_adapter.py +++ b/src/curategpt/store/db_adapter.py @@ -214,9 +214,7 @@ def collection_metadata( :return: """ - def set_collection_metadata( - self, collection_name: Optional[str], metadata: Metadata, **kwargs - ): + def set_collection_metadata(self, collection_name: Optional[str], metadata: Metadata, **kwargs): """ Set the metadata for a collection. @@ -488,6 +486,7 @@ def dump_then_load(self, collection: str = None, target: "DBAdapter" = None): """ raise NotImplementedError - def insert_from_huggingface(self, objs: Union[OBJECT, Iterable[OBJECT]], collection: str = None, **kwargs): + def insert_from_huggingface( + self, objs: Union[OBJECT, Iterable[OBJECT]], collection: str = None, **kwargs + ): raise NotImplementedError - diff --git a/src/curategpt/store/duckdb_adapter.py b/src/curategpt/store/duckdb_adapter.py index 9ce70b9..b17b660 100644 --- a/src/curategpt/store/duckdb_adapter.py +++ b/src/curategpt/store/duckdb_adapter.py @@ -292,7 +292,9 @@ def _process_objects( if collection not in self.list_collection_names(): self._create_table_if_not_exists( - collection, self.vec_dimension, venomx=updated_venomx, + collection, + self.vec_dimension, + venomx=updated_venomx, ) # if collection already exists, update metadata here @@ -409,17 +411,17 @@ def _process_objects( self.create_index(collection) def insert_from_huggingface( - self, - objs: Union[OBJECT, Iterable[OBJECT]], - collection: str = None, - batch_size: int = None, - text_field: Union[str, Callable] = None, - venomx: Optional[Metadata] = None, - object_type: Optional[str] = None, - distance: Optional[str] = None, - vec_dimension: Optional[int] = None, - method: str = "insert", - **kwargs, + self, + objs: Union[OBJECT, Iterable[OBJECT]], + collection: str = None, + batch_size: int = None, + text_field: Union[str, Callable] = None, + venomx: Optional[Metadata] = None, + object_type: Optional[str] = None, + distance: Optional[str] = None, + vec_dimension: Optional[int] = None, + method: str = "insert", + **kwargs, ): collection = self._get_collection(collection) model = None @@ -434,7 +436,9 @@ def insert_from_huggingface( vec_dimension = self._get_embedding_dimension(model) except Exception as e: - raise KeyError(f"Metadata from {collection} is not compatible with the current version of CurateGPT") from e + raise KeyError( + f"Metadata from {collection} is not compatible with the current version of CurateGPT" + ) from e updated_venomx = self.update_or_create_venomx( venomx.venomx, @@ -446,9 +450,11 @@ def insert_from_huggingface( ) if collection not in self.list_collection_names(): self._create_table_if_not_exists( - collection, vec_dimension, venomx=updated_venomx, + collection, + vec_dimension, + venomx=updated_venomx, ) - updated_venomx.venomx.id = collection # prevent name error + updated_venomx.venomx.id = collection # prevent name error self.set_collection_metadata(collection_name=collection, metadata=updated_venomx) if batch_size is None: batch_size = 100000 @@ -464,11 +470,17 @@ def insert_from_huggingface( for next_objs in chunk(objs, batch_size): next_objs = list(next_objs) - ids = [item['metadata']['id'] for item in next_objs] + ids = [item["metadata"]["id"] for item in next_objs] metadatas = [self._dict(o) for o in next_objs] - documents = [item['document'] for item in next_objs] - embeddings = [item['embeddings'].tolist() if isinstance(item['embeddings'], np.ndarray) - else item['embeddings'] for item in next_objs] + documents = [item["document"] for item in next_objs] + embeddings = [ + ( + item["embeddings"].tolist() + if isinstance(item["embeddings"], np.ndarray) + else item["embeddings"] + ) + for item in next_objs + ] try: self.conn.execute("BEGIN TRANSACTION;") self.conn.executemany( @@ -484,16 +496,14 @@ def insert_from_huggingface( finally: self.create_index(collection) - - def update_or_create_venomx( - self, - venomx: Optional[Index], - collection: str, - model: str, - distance: str, - object_type: str, - embeddings_dimension: Optional[int], + self, + venomx: Optional[Index], + collection: str, + model: str, + distance: str, + object_type: str, + embeddings_dimension: Optional[int], ) -> Metadata: """ Updates an existing Index instance (venomx) with additional values or creates a new one if none is provided. @@ -501,42 +511,42 @@ def update_or_create_venomx( # If venomx already exists, update its nested fields (as e.g. vec_dimension would not be given) if venomx: new_embedding_model = Model(name=model) - updated_index = venomx.model_copy(update={ # given venomx comes as venomx=Index() - "embedding_model": new_embedding_model, - "embeddings_dimensions": embeddings_dimension, - }) - - venomx = Metadata( - venomx=updated_index, - hnsw_space=distance, - object_type=object_type + updated_index = venomx.model_copy( + update={ # given venomx comes as venomx=Index() + "embedding_model": new_embedding_model, + "embeddings_dimensions": embeddings_dimension, + } ) + venomx = Metadata(venomx=updated_index, hnsw_space=distance, object_type=object_type) + else: if distance is None: distance = self.distance_metric - venomx = self.populate_venomx(collection, model, distance, object_type, embeddings_dimension) + venomx = self.populate_venomx( + collection, model, distance, object_type, embeddings_dimension + ) return venomx @staticmethod def populate_venomx( - collection: Optional[str], - model: Optional[str], - distance: str, - object_type: str, - embeddings_dimension: int, + collection: Optional[str], + model: Optional[str], + distance: str, + object_type: str, + embeddings_dimension: int, ) -> Metadata: """ - Populate venomx with data currently given when inserting + Populate venomx with data currently given when inserting - :param collection: - :param model: - :param distance: - :param object_type: - :param embeddings_dimension: - :return: - """ + :param collection: + :param model: + :param distance: + :param object_type: + :param embeddings_dimension: + :return: + """ venomx = Metadata( venomx=Index( id=collection, @@ -544,7 +554,7 @@ def populate_venomx( embeddings_dimensions=embeddings_dimension, ), hnsw_space=distance, - object_type=object_type + object_type=object_type, ) return venomx @@ -764,15 +774,17 @@ def update_collection_metadata(self, collection: str, **kwargs): raise ValueError("Collection name must be provided.") metadata = self.collection_metadata(collection) current_venomx = {**kwargs} - if metadata is None: # should not be possible - logger.warning(f"No existing metadata found for collection {collection}. Initializing new metadata.") + if metadata is None: # should not be possible + logger.warning( + f"No existing metadata found for collection {collection}. Initializing new metadata." + ) metadata = Metadata(venomx=Index(**current_venomx)) else: metadata_dict = metadata.model_dump(exclude_none=True) # Check if the existing venomx has an embedding model and if it matches the one in kwargs - if 'venomx' in metadata_dict and metadata_dict['venomx'].get('embedding_model'): - existing_model_name = metadata_dict['venomx']['embedding_model'].get('name') - new_model_name = current_venomx.get('embedding_model', {}).get('name') + if "venomx" in metadata_dict and metadata_dict["venomx"].get("embedding_model"): + existing_model_name = metadata_dict["venomx"]["embedding_model"].get("name") + new_model_name = current_venomx.get("embedding_model", {}).get("name") if new_model_name and existing_model_name and new_model_name != existing_model_name: raise ValueError( @@ -781,10 +793,10 @@ def update_collection_metadata(self, collection: str, **kwargs): ) # Merge current_venomx (from kwargs) into the nested venomx dictionary - if 'venomx' in metadata_dict and isinstance(metadata_dict['venomx'], dict): - metadata_dict['venomx'].update(current_venomx) + if "venomx" in metadata_dict and isinstance(metadata_dict["venomx"], dict): + metadata_dict["venomx"].update(current_venomx) else: - metadata_dict['venomx'] = current_venomx + metadata_dict["venomx"] = current_venomx # Reconstruct the Metadata object from the updated dictionary metadata = Metadata(**metadata_dict) updated_metadata_dict = metadata.model_dump(exclude_none=True) @@ -799,9 +811,7 @@ def update_collection_metadata(self, collection: str, **kwargs): ) return metadata - def set_collection_metadata( - self, collection_name: Optional[str], metadata: Metadata, **kwargs - ): + def set_collection_metadata(self, collection_name: Optional[str], metadata: Metadata, **kwargs): """ Set the metadata for the collection :param collection_name: @@ -816,7 +826,9 @@ def set_collection_metadata( if metadata: if metadata.venomx.id != collection_name: - raise ValueError(f"venomx.id: {metadata.venomx.id} must match collection_name {collection_name}") + raise ValueError( + f"venomx.id: {metadata.venomx.id} must match collection_name {collection_name}" + ) new_model = metadata.venomx.embedding_model.name diff --git a/src/curategpt/store/duckdb_connection_handler.py b/src/curategpt/store/duckdb_connection_handler.py index 5e05c83..9735154 100644 --- a/src/curategpt/store/duckdb_connection_handler.py +++ b/src/curategpt/store/duckdb_connection_handler.py @@ -33,6 +33,7 @@ def _kill_process(pid: int) -> None: """Kill a process if it's holding the database lock.""" try: import psutil + if psutil.pid_exists(pid): process = psutil.Process(pid) process.terminate() @@ -65,11 +66,11 @@ def connect(self) -> duckdb.DuckDBPyConnection: - Now safely open the fixed database normally """ - wal_path = Path(self.path + '.wal') + wal_path = Path(self.path + ".wal") if wal_path.exists(): logger.info("Found WAL file, attempting recovery...") try: - temp_conn = duckdb.connect(':memory:') + temp_conn = duckdb.connect(":memory:") self._load_vss_extensions(temp_conn) temp_conn.execute(f"ATTACH '{self.path}' AS main_db") temp_conn.execute("CHECKPOINT;") diff --git a/src/curategpt/store/in_memory_adapter.py b/src/curategpt/store/in_memory_adapter.py index 736610b..9b6d8dd 100644 --- a/src/curategpt/store/in_memory_adapter.py +++ b/src/curategpt/store/in_memory_adapter.py @@ -101,12 +101,8 @@ def insert(self, objs: Union[OBJECT, Iterable[OBJECT]], collection: str = None, """ self._insert(objs, collection, **kwargs) - def _insert( - self, - objs: Union[OBJECT, Iterable[OBJECT]], - collection: str = None, - venomx: Metadata = None + self, objs: Union[OBJECT, Iterable[OBJECT]], collection: str = None, venomx: Metadata = None ): collection_obj = self._get_collection_object(collection) if venomx is None: @@ -121,33 +117,35 @@ def _insert( @staticmethod def populate_venomx( - collection: Optional[str], - model: Optional[str] = None, - distance: str = None, - object_type: str = None, - embeddings_dimension: int = None, - index_fields: Optional[Union[List[str], Tuple[str]]] = None, + collection: Optional[str], + model: Optional[str] = None, + distance: str = None, + object_type: str = None, + embeddings_dimension: int = None, + index_fields: Optional[Union[List[str], Tuple[str]]] = None, ) -> Metadata: """ - Populate venomx with data currently given when inserting + Populate venomx with data currently given when inserting - :param collection: - :param model: - :param distance: - :param object_type: - :param embeddings_dimension: - :param index_fields: - :return: - """ + :param collection: + :param model: + :param distance: + :param object_type: + :param embeddings_dimension: + :param index_fields: + :return: + """ venomx = Metadata( venomx=Index( id=collection, embedding_model=Model(name=model), embeddings_dimensions=embeddings_dimension, - embedding_input_method=ModelInputMethod(fields=index_fields) if index_fields else None + embedding_input_method=( + ModelInputMethod(fields=index_fields) if index_fields else None + ), ), hnsw_space=distance, - object_type=object_type + object_type=object_type, ) return venomx @@ -200,9 +198,7 @@ def collection_metadata( cm.object_count = len(collection_obj.objects) return cm - def set_collection_metadata( - self, collection_name: Optional[str], metadata: Metadata, **kwargs - ): + def set_collection_metadata(self, collection_name: Optional[str], metadata: Metadata, **kwargs): """ Set the metadata for a collection. @@ -215,7 +211,6 @@ def set_collection_metadata( # raise ValueError(f"venomx.id: {metadata.venomx.id} must match collection_name {collection_name} and should not be changed") collection_obj.metadata = metadata.model_dump(exclude_none=True) - def update_collection_metadata(self, collection_name: str, **kwargs) -> Metadata: """ Update the metadata for a collection. diff --git a/src/curategpt/store/metadata.py b/src/curategpt/store/metadata.py index 9d1dbd6..264d18d 100644 --- a/src/curategpt/store/metadata.py +++ b/src/curategpt/store/metadata.py @@ -46,13 +46,13 @@ def deserialize_venomx_metadata_from_adapter(cls, metadata_dict: dict, adapter: :param adapter: Adapter name (e.g., 'chroma', 'duckdb'). :return: Metadata instance. """ - if adapter == 'chromadb': + if adapter == "chromadb": # Deserialize '_venomx' (str) back into 'venomx' (dict) if "_venomx" in metadata_dict: venomx_json = metadata_dict.pop("_venomx") metadata_dict["venomx"] = Index(**json.loads(venomx_json)) # for 'duckdb', 'venomx' remains as is - if adapter == 'duckdb': + if adapter == "duckdb": metadata_dict = metadata_dict return cls(**metadata_dict) @@ -64,25 +64,18 @@ def serialize_venomx_metadata_for_adapter(self, adapter: str) -> dict: :param adapter: Adapter name (e.g., 'chroma', 'duckdb'). :return: Metadata dictionary. """ - if adapter == 'chromadb': + if adapter == "chromadb": # Serialize 'venomx' (dict) into '_venomx' (str) metadata_dict = self.model_dump( - exclude={"venomx"}, - exclude_unset=True, - exclude_none=True + exclude={"venomx"}, exclude_unset=True, exclude_none=True ) if self.venomx: metadata_dict["_venomx"] = json.dumps(self.venomx.model_dump()) return metadata_dict - elif adapter == 'duckdb': + elif adapter == "duckdb": metadata_dict = self.model_dump( - exclude={"_venomx"}, - exclude_unset=True, - exclude_none=True + exclude={"_venomx"}, exclude_unset=True, exclude_none=True ) return metadata_dict else: raise ValueError(f"Unsupported adapter: {adapter}") - - -