from pathlib import Path import time import chromadb import numpy as np import pandas as pd # ============================================================ # AYARLAR # ============================================================ INPUT_FILE = Path( "data/chunks_with_embeddings.parquet" ) CHROMA_DIR = Path( "data/chroma_db" ) COLLECTION_NAME = ( "turkish_medical_chunks" ) # ============================================================ # INDEX AYARLARI # ============================================================ DISTANCE_METRIC = "cosine" # Chroma'ya kaç kayıtlık batch'ler halinde veri gönderilecek? INSERT_BATCH_SIZE = 250 # ============================================================ # COLLECTION YENİDEN OLUŞTURMA # ============================================================ # True: # Script her çalıştırıldığında yalnızca bu collection # silinir ve baştan oluşturulur. # # Bu aşamada reproducibility açısından bunu istiyoruz. # # ChromaDB'nin tamamı silinmez. # Yalnızca COLLECTION_NAME silinir. RECREATE_COLLECTION = True # ============================================================ # BAŞLANGIÇ # ============================================================ print( "\n" + "=" * 70 ) print( "CHROMADB INDEX OLUŞTURMA" ) print( "=" * 70 ) # ============================================================ # INPUT KONTROLÜ # ============================================================ if not INPUT_FILE.exists(): raise FileNotFoundError( f"{INPUT_FILE} bulunamadı.\n" "Önce 03_embed_chunks.py çalıştırılmalıdır." ) # ============================================================ # VERİYİ OKU # ============================================================ print( f"\nInput dosyası:\n" f"{INPUT_FILE}" ) df = pd.read_parquet( INPUT_FILE ) print( f"\nToplam kayıt sayısı: " f"{len(df)}" ) if len(df) == 0: raise ValueError( "Input dosyasında hiç kayıt yok." ) # ============================================================ # GEREKLİ KOLONLAR # ============================================================ required_columns = [ "article_id", "parent_id", "parent_index", "child_id", "child_index", "url", "title", "parent_text", "chunk_text", "parent_token_count", "chunk_token_count", "embedding_model", "embedding_dimension", "chunk_vector", ] missing_columns = [ column for column in required_columns if column not in df.columns ] if missing_columns: raise ValueError( "Eksik kolonlar bulundu:\n" + "\n".join( missing_columns ) ) # ============================================================ # CHILD ID KONTROLÜ # ============================================================ duplicate_mask = ( df[ "child_id" ] .duplicated( keep=False ) ) if duplicate_mask.any(): duplicate_ids = ( df.loc[ duplicate_mask, "child_id" ] .tolist() ) raise ValueError( "Duplicate child_id bulundu:\n" + "\n".join( duplicate_ids[:20] ) ) print( "Child ID kontrolü: OK" ) # ============================================================ # BOŞ DOCUMENT KONTROLÜ # ============================================================ empty_document_mask = ( df[ "chunk_text" ] .fillna("") .astype(str) .str.strip() .eq("") ) empty_document_count = int( empty_document_mask.sum() ) if empty_document_count > 0: raise ValueError( f"{empty_document_count} adet " "boş chunk_text bulundu." ) print( "Boş document kontrolü: OK" ) # ============================================================ # EMBEDDING MODEL KONTROLÜ # ============================================================ embedding_models = ( df[ "embedding_model" ] .dropna() .astype(str) .unique() ) if len( embedding_models ) != 1: raise ValueError( "Input içerisinde birden fazla " "embedding modeli bulundu:\n" f"{embedding_models}" ) EMBEDDING_MODEL = ( embedding_models[0] ) print( f"\nEmbedding modeli:\n" f"{EMBEDDING_MODEL}" ) # ============================================================ # EMBEDDING DIMENSION KONTROLÜ # ============================================================ embedding_dimensions = ( df[ "embedding_dimension" ] .dropna() .astype(int) .unique() ) if len( embedding_dimensions ) != 1: raise ValueError( "Input içerisinde birden fazla " "embedding dimension bulundu:\n" f"{embedding_dimensions}" ) EMBEDDING_DIMENSION = int( embedding_dimensions[0] ) print( f"Embedding dimension: " f"{EMBEDDING_DIMENSION}" ) # ============================================================ # VECTORLERİ NUMPY ARRAY'E ÇEVİR # ============================================================ print( "\nEmbedding vectorleri hazırlanıyor..." ) try: embeddings = np.stack( [ np.asarray( vector, dtype=np.float32 ) for vector in df[ "chunk_vector" ] ] ) except Exception as error: raise ValueError( "chunk_vector kolonundaki " "embedding'ler numpy array'e " "çevrilemedi." ) from error print( f"Embedding matrix shape: " f"{embeddings.shape}" ) # ============================================================ # SHAPE KONTROLÜ # ============================================================ expected_shape = ( len(df), EMBEDDING_DIMENSION ) if ( embeddings.shape != expected_shape ): raise ValueError( "Embedding matrix shape hatalı.\n" f"Beklenen : {expected_shape}\n" f"Gelen : {embeddings.shape}" ) print( "Embedding shape kontrolü: OK" ) # ============================================================ # NaN / INF KONTROLÜ # ============================================================ if not np.isfinite( embeddings ).all(): raise ValueError( "Embedding vectorlerinde " "NaN veya Inf bulundu." ) print( "NaN / Inf kontrolü: OK" ) # ============================================================ # L2 NORM KONTROLÜ # ============================================================ embedding_norms = np.linalg.norm( embeddings, axis=1 ) print( "\nEmbedding norm istatistikleri:" ) print( f"Ortalama : " f"{embedding_norms.mean():.8f}" ) print( f"Minimum : " f"{embedding_norms.min():.8f}" ) print( f"Maksimum : " f"{embedding_norms.max():.8f}" ) if not np.allclose( embedding_norms, 1.0, atol=1e-5 ): raise ValueError( "Embedding'lerin tamamı " "L2-normalize değil." ) print( "L2 normalization kontrolü: OK" ) # ============================================================ # CHROMA KLASÖRÜ # ============================================================ CHROMA_DIR.mkdir( parents=True, exist_ok=True ) print( "\n" + "=" * 70 ) print( "CHROMADB CLIENT" ) print( "=" * 70 ) print( f"\nDatabase dizini:\n" f"{CHROMA_DIR}" ) # ============================================================ # PERSISTENT CLIENT # ============================================================ client = chromadb.PersistentClient( path=str( CHROMA_DIR ) ) print( "\nPersistentClient oluşturuldu." ) # ============================================================ # CHROMA VERSION # ============================================================ try: chroma_version = ( client.get_version() ) print( f"Chroma version: " f"{chroma_version}" ) except Exception: print( "Chroma version bilgisi " "alınamadı." ) # ============================================================ # MEVCUT COLLECTION'LAR # ============================================================ existing_collections = ( client.list_collections() ) existing_collection_names = { collection.name for collection in existing_collections } print( "\nMevcut collection sayısı: " f"{len(existing_collection_names)}" ) # ============================================================ # COLLECTION VARSA SİL # ============================================================ if ( COLLECTION_NAME in existing_collection_names ): if RECREATE_COLLECTION: print( f"\n'{COLLECTION_NAME}' " "zaten mevcut." ) print( "Eski collection siliniyor..." ) client.delete_collection( name=COLLECTION_NAME ) print( "Eski collection silindi." ) else: raise RuntimeError( f"'{COLLECTION_NAME}' " "collection'ı zaten mevcut.\n" "RECREATE_COLLECTION=True yapabilir " "veya farklı bir collection adı " "kullanabilirsin." ) # ============================================================ # COLLECTION OLUŞTUR # ============================================================ print( "\n" + "=" * 70 ) print( "COLLECTION OLUŞTURULUYOR" ) print( "=" * 70 ) print( f"\nCollection adı : " f"{COLLECTION_NAME}" ) print( f"Distance metric: " f"{DISTANCE_METRIC}" ) collection = client.create_collection( name=COLLECTION_NAME, # Embeddingleri zaten Qwen3 ile kendimiz ürettik. # Chroma'nın tekrar embedding üretmesini istemiyoruz. embedding_function=None, configuration={ "hnsw": { "space": DISTANCE_METRIC } }, metadata={ "description": ( "Turkish medical RAG child chunks" ), "embedding_model": ( EMBEDDING_MODEL ), "embedding_dimension": ( EMBEDDING_DIMENSION ), "distance_metric": ( DISTANCE_METRIC ), "source_file": ( str(INPUT_FILE) ), } ) print( "\nCollection oluşturuldu." ) # ============================================================ # BATCH SIZE # ============================================================ batch_size = ( INSERT_BATCH_SIZE ) try: max_batch_size = ( client.get_max_batch_size() ) print( f"\nChroma max batch size: " f"{max_batch_size}" ) batch_size = min( batch_size, max_batch_size ) except (AttributeError, NotImplementedError): print( "\nChroma max batch size " "bilgisi alınamadı." ) print( f"Kullanılacak insert batch size: " f"{batch_size}" ) # ============================================================ # METADATA HAZIRLAMA YARDIMCILARI # ============================================================ def safe_string(value): """ Chroma metadata için None / NaN değerlerini güvenli string'e çevirir. """ if value is None: return "" try: if pd.isna(value): return "" except (TypeError, ValueError): pass return str( value ) def safe_int(value): """ Metadata için integer dönüşümü. """ if value is None: return -1 try: if pd.isna(value): return -1 except (TypeError, ValueError): pass return int( value ) # ============================================================ # CHROMA METADATA # ============================================================ print( "\nMetadata hazırlanıyor..." ) metadatas = [] for _, row in df.iterrows(): metadata = { # ---------------------------------------------------- # ARTICLE # ---------------------------------------------------- "article_id": ( safe_string( row[ "article_id" ] ) ), # ---------------------------------------------------- # PARENT # ---------------------------------------------------- "parent_id": ( safe_string( row[ "parent_id" ] ) ), "parent_index": ( safe_int( row[ "parent_index" ] ) ), # ---------------------------------------------------- # CHILD # ---------------------------------------------------- "child_index": ( safe_int( row[ "child_index" ] ) ), # ---------------------------------------------------- # SOURCE # ---------------------------------------------------- "title": ( safe_string( row[ "title" ] ) ), "url": ( safe_string( row[ "url" ] ) ), # ---------------------------------------------------- # TOKEN COUNTS # ---------------------------------------------------- "parent_token_count": ( safe_int( row[ "parent_token_count" ] ) ), "chunk_token_count": ( safe_int( row[ "chunk_token_count" ] ) ), # ---------------------------------------------------- # EMBEDDING # ---------------------------------------------------- "embedding_model": ( safe_string( row[ "embedding_model" ] ) ), "embedding_dimension": ( safe_int( row[ "embedding_dimension" ] ) ), } # __source varsa ekle. if "__source" in df.columns: metadata[ "source" ] = safe_string( row[ "__source" ] ) metadatas.append( metadata ) print( f"Metadata sayısı: " f"{len(metadatas)}" ) # ============================================================ # IDS # ============================================================ ids = ( df[ "child_id" ] .astype(str) .tolist() ) # ============================================================ # DOCUMENTS # ============================================================ documents = ( df[ "chunk_text" ] .astype(str) .tolist() ) # ============================================================ # CHROMADB'YE EKLE # ============================================================ print( "\n" + "=" * 70 ) print( "CHROMADB'YE VERİ EKLENİYOR" ) print( "=" * 70 ) insert_start = ( time.perf_counter() ) total_records = len( df ) for start in range( 0, total_records, batch_size ): end = min( start + batch_size, total_records ) batch_ids = ( ids[ start:end ] ) batch_documents = ( documents[ start:end ] ) batch_metadatas = ( metadatas[ start:end ] ) batch_embeddings = ( embeddings[ start:end ] .tolist() ) collection.add( ids=batch_ids, embeddings=batch_embeddings, documents=batch_documents, metadatas=batch_metadatas, ) print( f"{end}/{total_records} " "kayıt eklendi." ) insert_seconds = ( time.perf_counter() - insert_start ) # ============================================================ # COLLECTION COUNT # ============================================================ stored_count = ( collection.count() ) print( "\n" + "=" * 70 ) print( "INDEX VALIDATION" ) print( "=" * 70 ) print( f"\nInput kayıt sayısı : " f"{total_records}" ) print( f"Chroma kayıt sayısı: " f"{stored_count}" ) if ( stored_count != total_records ): raise ValueError( "Chroma collection kayıt sayısı " "input ile eşleşmiyor." ) print( "\nCollection count kontrolü: OK" ) # ============================================================ # KAYIT GERİ OKUMA TESTİ # ============================================================ sample_id = ( ids[0] ) print( f"\nTest kaydı:\n" f"{sample_id}" ) stored_sample = collection.get( ids=[ sample_id ], include=[ "documents", "metadatas", "embeddings", ], ) if not stored_sample[ "ids" ]: raise ValueError( "Test kaydı ChromaDB'den " "geri okunamadı." ) stored_vector = np.asarray( stored_sample[ "embeddings" ][0], dtype=np.float32 ) if ( len(stored_vector) != EMBEDDING_DIMENSION ): raise ValueError( "ChromaDB'den geri okunan " "embedding dimension hatalı." ) print( "Stored embedding dimension: " f"{len(stored_vector)}" ) print( "Kayıt geri okuma kontrolü: OK" ) # ============================================================ # SELF-SIMILARITY QUERY # ============================================================ print( "\n" + "=" * 70 ) print( "COSINE SELF-QUERY TEST" ) print( "=" * 70 ) sample_embedding = ( embeddings[0] ) self_query = collection.query( query_embeddings=[ sample_embedding.tolist() ], n_results=min( 10, total_records ), include=[ "documents", "metadatas", "distances", ], ) result_ids = ( self_query[ "ids" ][0] ) result_distances = ( self_query[ "distances" ][0] ) if not result_ids: raise ValueError( "Self-query herhangi bir " "sonuç döndürmedi." ) # ============================================================ # TEST DOCUMENT SONUÇLARDA MI? # ============================================================ if ( sample_id not in result_ids ): raise ValueError( "Self-query sonucunda kendi " "child_id'si ilk 10 içerisinde bulunamadı." ) sample_result_index = ( result_ids.index( sample_id ) ) sample_distance = float( result_distances[ sample_result_index ] ) # Cosine distance: # # distance = 1 - cosine_similarity # # Dolayısıyla: # # similarity = 1 - distance sample_similarity = ( 1.0 - sample_distance ) print( f"\nSample child ID:" f"\n{sample_id}" ) print( f"\nSelf cosine distance:" f"\n{sample_distance:.8f}" ) print( f"\nSelf cosine similarity:" f"\n{sample_similarity:.8f}" ) print( "\nSelf-query kontrolü: OK" ) # ============================================================ # TOP 5 SELF QUERY SONUCU # ============================================================ print( "\n" + "-" * 70 ) print( "SELF-QUERY TOP 5" ) print( "-" * 70 ) top_count = min( 5, len(result_ids) ) for rank in range( top_count ): result_id = ( result_ids[ rank ] ) distance = float( result_distances[ rank ] ) similarity = ( 1.0 - distance ) result_metadata = ( self_query[ "metadatas" ][0][rank] ) title = "" if result_metadata: title = ( result_metadata.get( "title", "" ) ) print( f""" #{rank + 1} Child ID : {result_id} Başlık : {title} Distance : {distance:.6f} Similarity : {similarity:.6f} """ ) # ============================================================ # PERFORMANS # ============================================================ records_per_second = ( total_records / insert_seconds ) # ============================================================ # FINAL SONUÇ # ============================================================ print( "\n" + "=" * 70 ) print( "CHROMADB INDEX TAMAMLANDI" ) print( "=" * 70 ) print( f""" Collection : {COLLECTION_NAME} Database path : {CHROMA_DIR} Kayıt sayısı : {stored_count} Embedding model : {EMBEDDING_MODEL} Embedding dim : {EMBEDDING_DIMENSION} Distance metric : {DISTANCE_METRIC} Indexleme süresi : {insert_seconds:.2f} saniye Kayıt / saniye : {records_per_second:.2f} """ ) print( "=" * 70 ) print( "04_BUILD_CHROMADB BAŞARILI" ) print( "=" * 70 )