ddi-fw 0.0.95__py3-none-any.whl → 0.0.97__py3-none-any.whl

ddi_fw/pipeline/pipeline.py

@@ -47,7 +47,7 @@ class Pipeline:
         self.combinations = combinations
         self.model = model
 
-    def __create_or_update_embeddings__(embedding_dict, vector_db_persist_directory, vector_db_collection_name, column):
+    def __create_or_update_embeddings__(self, embedding_dict, vector_db_persist_directory, vector_db_collection_name, column=None):
         """
         Fetch embeddings and metadata from a persistent Chroma vector database and update the provided embedding_dict.
 
@@ -56,8 +56,6 @@ class Pipeline:
         - vector_db_collection_name (str): The name of the collection to query.
         - embedding_dict (dict): The existing dictionary to update with embeddings.
 
-        Returns:
-        - embedding_dict (dict): The updated dictionary where embeddings are grouped by 'type' and 'id'.
         """
         if vector_db_persist_directory:
             # Initialize the Chroma client and get the collection
@@ -67,9 +65,11 @@ class Pipeline:
 
             # Fetch the embeddings and metadata
             if column == None:
-                dictionary = collection.get(include=['embeddings', 'metadatas'])
+                dictionary = collection.get(
+                    include=['embeddings', 'metadatas'])
             else:
-                dictionary = collection.get(include=['embeddings', 'metadatas'], where= {"type": {"$eq": f"{column}"}})
+                dictionary = collection.get(include=['embeddings', 'metadatas'], where={
+                                            "type": {"$eq": f"{column}"}})
             # Populate the embedding dictionary with embeddings from the vector database
             for metadata, embedding in zip(dictionary['metadatas'], dictionary['embeddings']):
                 embedding_dict[metadata["type"]
@@ -79,7 +79,7 @@ class Pipeline:
         else:
             raise ValueError(
                 "Persistent directory for the vector DB is not specified.")
-        
+
     def build(self):
         # 'enzyme','target','pathway','smile','all_text','indication', 'description','mechanism_of_action','pharmacodynamics', 'tui', 'cui', 'entities'
         kwargs = {"columns": self.columns}
@@ -91,14 +91,16 @@ class Pipeline:
             if self.vector_db_persist_directory:
                 self.__create_or_update_embeddings__(
                     embedding_dict, self.vector_db_persist_directory, self.vector_db_collection_name)
-                
+
             if self.column_embedding_configs:
                 for item in self.column_embedding_configs:
                     col = item["column"]
                     col_db_dir = item["vector_db_persist_directory"]
                     col_db_collection = item["vector_db_collection_name"]
-                    self.__create_or_update_embeddings__(embedding_dict, col_db_dir, col_db_collection, col)
-                    print(f"Embedings of {col} is calculated from {col_db_collection}")
+                    self.__create_or_update_embeddings__(
+                        embedding_dict, col_db_dir, col_db_collection, col)
+                    print(
+                        f"Embedings of {col} is calculated from {col_db_collection}")
 
         # if self.embedding_dict == None:
         #     if self.vector_db_persist_directory:

{ddi_fw-0.0.95.dist-info → ddi_fw-0.0.97.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ddi_fw
-Version: 0.0.95
+Version: 0.0.97
 Summary: Do not use :)
 Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
 Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>

{ddi_fw-0.0.95.dist-info → ddi_fw-0.0.97.dist-info}/RECORD

@@ -72,7 +72,7 @@ ddi_fw/pipeline/__init__.py,sha256=tKDM_rW4vPjlYTeOkNgi9PujDzb4e9O3LK1w5wqnebw,2
 ddi_fw/pipeline/multi_modal_combination_strategy.py,sha256=qIst7vxHaOAhRv4lgozszwa3b1QE4aIrN74t41Xnvr4,1637
 ddi_fw/pipeline/multi_pipeline.py,sha256=t_Z7d7xRfDnhpQTlqCf7c0isZ5hZlyXavKhC7ePsnJY,5903
 ddi_fw/pipeline/ner_pipeline.py,sha256=wB7hz4YCOv7UAz6bGE6sSpPXXIdoOflOVK5UCc1fO-o,5586
-ddi_fw/pipeline/pipeline.py,sha256=JhjsF5-JIGebGT_J7Lk82ymGNWCoxy6teM78jUDhkK8,8475
+ddi_fw/pipeline/pipeline.py,sha256=VX3GcoTjY7_ehX_rmpa-uh0NyBFoxF24AxbwruEWw4A,8457
 ddi_fw/test/basic_test.py,sha256=fEOGcZm1ObnsDvMiXNmdmz6YCeUrGc8V0DwlSwGhsq8,376
 ddi_fw/test/combination_test.py,sha256=TWNE8sf-DSh1Q9-yRaRBc774Sn1kSMGXLwQhd2_Qynk,324
 ddi_fw/test/compress_json_test.py,sha256=BGny56YqiG-pzhMoDzLKQBQI1E7o3jU0S7VYWtclAx4,1045
@@ -89,7 +89,7 @@ ddi_fw/utils/enums.py,sha256=19eJ3fX5eRK_xPvkYcukmug144jXPH4X9zQqtsFBj5A,671
 ddi_fw/utils/py7zr_helper.py,sha256=gOqaFIyJvTjUM-btO2x9AQ69jZOS8PoKN0wetYIckJw,4747
 ddi_fw/utils/utils.py,sha256=szwnxMTDRrZoeNRyDuf3aCbtzriwtaRk4mHSH3asLdA,4301
 ddi_fw/utils/zip_helper.py,sha256=YRZA4tKZVBJwGQM0_WK6L-y5MoqkKoC-nXuuHK6CU9I,5567
-ddi_fw-0.0.95.dist-info/METADATA,sha256=B0XmNCFk6GWOt7-9bNGIGK7n0gd5M_MqbxW-Ygm_t20,1966
-ddi_fw-0.0.95.dist-info/WHEEL,sha256=R06PA3UVYHThwHvxuRWMqaGcr-PuniXahwjmQRFMEkY,91
-ddi_fw-0.0.95.dist-info/top_level.txt,sha256=PMwHICFZTZtcpzQNPV4UQnfNXYIeLR_Ste-Wfc1h810,7
-ddi_fw-0.0.95.dist-info/RECORD,,
+ddi_fw-0.0.97.dist-info/METADATA,sha256=wdTxARxGIxFpSzXZMgU22Arwx7NiomfNFMYR4NTxXlk,1966
+ddi_fw-0.0.97.dist-info/WHEEL,sha256=R06PA3UVYHThwHvxuRWMqaGcr-PuniXahwjmQRFMEkY,91
+ddi_fw-0.0.97.dist-info/top_level.txt,sha256=PMwHICFZTZtcpzQNPV4UQnfNXYIeLR_Ste-Wfc1h810,7
+ddi_fw-0.0.97.dist-info/RECORD,,