cwyodmodules 0.3.44__py3-none-any.whl → 0.3.46__py3-none-any.whl

cwyodmodules/graphrag/indexing/extraction.py

@@ -1,230 +1,237 @@
-from graphrag.indexing.types import (
-    EntityModel, 
-    RelationshipModel, 
-    ChunkModel, 
-    HighLevelKeywords
-)
-
-from graphrag.database.base import get_db
-from graphrag.database.models import Chunk, Entity, Relationship
-
-from graphrag.indexing.utils import calculate_hash
-from graphrag.llm.llm import extract_entities_completion
-
-from typing import (List, 
-                    Tuple, 
-                    Dict, 
-                    Any, 
-                    Set)
-from fuzzywuzzy import fuzz
-from openai import RateLimitError
-
-import uuid
-import asyncio
-import uuid
-
-
-def _extract_chunk_info_from_db_if_exists(chunk: str) -> Tuple[List[EntityModel], List[RelationshipModel], ChunkModel] | None:
-
-    db = next(get_db())
-    hash = "chunk-" + calculate_hash(text=chunk)
-    exists = db.query(Chunk).filter(Chunk.hash == hash).first()
-    if exists:
-        entities_models, relationships_models = [], [] 
-        entities = db.query(Entity).filter(Entity.chunk_id == exists.chunk_id).all()
-        for entity in entities:
-            entity_model = EntityModel(
-                entity_name=entity.entity_name, 
-                entity_type=entity.entity_type, 
-                entity_description=entity.description,
-                chunk_id=str(exists.chunk_id)
-            )
-            entities_models.append(entity_model)
-        relationships = db.query(Relationship).filter(Relationship.chunk_id == exists.chunk_id).all()
-        for rel in relationships:
-            rel_model = RelationshipModel(
-                source_entity=rel.source_entity.entity_name, 
-                target_entity=rel.target_entity.entity_name,
-                relationship_description=rel.description,
-                relationship_strength=rel.weight,
-                chunk_id=str(exists.chunk_id),
-                relationship_keywords=rel.keywords
-            )
-            relationships_models.append(rel_model)
-        db.close()
-        return entities_models, relationships_models, ChunkModel(text=exists.text, id=str(exists.chunk_id))
-    db.close()
-    return None
-    
-
-def _merge_entities(entities: List[EntityModel], threshold: int=75) -> Tuple[List[EntityModel], Dict[str, Set[str]]]:
-    
-    def find_most_similar(entity: EntityModel, candidates: List[EntityModel], threshold: int) -> List[EntityModel]:
-        
-        most_sim_entity: List[EntityModel] = []
-        for candidate_entity in candidates:
-            if (entity.entity_type != candidate_entity.entity_type): continue
-            try:
-                score = fuzz.ratio(entity.entity_name, candidate_entity.entity_name)
-            except IndexError:
-                continue
-            if score > threshold:
-                most_sim_entity.append(candidate_entity)
-
-        return most_sim_entity
-    
-    kept_vs_merged = {}
-
-    merged_entities = set()
-    modified_entities: Dict[Tuple[str, str, str, str], List[EntityModel]] = {}
-    for index, entity in enumerate(entities):
-        most_sim_entities = find_most_similar(entity=entity, candidates=entities[index+1:], threshold=threshold)
-        entity_key = (entity.entity_name, entity.entity_type, entity.entity_description)
-
-        if entity_key in merged_entities:
-            print(f"{entity_key} already exists as an entity")
-            continue
-    
-        if (entity.entity_name, entity.entity_type, entity.entity_description, entity.get_chunk_id) not in modified_entities:
-            modified_entities[(entity.entity_name, entity.entity_type, entity.entity_description, entity.get_chunk_id)] = []
-        if most_sim_entities:
-            for most_sim_entity in most_sim_entities:
-                most_sim_key = (most_sim_entity.entity_name, most_sim_entity.entity_type, most_sim_entity.entity_description)
-                print(f"{most_sim_key[:2]} has been identified as similar to another entity")
-                merged_entities.add(most_sim_key)
-                modified_entities[(entity.entity_name, entity.entity_type, entity.entity_description, entity.get_chunk_id)].append(most_sim_entity)
-                if most_sim_entity.entity_name not in kept_vs_merged:
-                    kept_vs_merged[most_sim_entity.entity_name] = {entity.entity_name}
-                else:
-                    kept_vs_merged[most_sim_entity.entity_name].add(entity.entity_name)
-
-    updated_entities = []
-    for entity_info, sim_entities in modified_entities.items():
-
-        if entity_info[:-1] in merged_entities and not len(sim_entities): continue
-        
-        updated_entities.append(
-            EntityModel(
-                entity_name=entity_info[0], 
-                entity_type=entity_info[1], 
-                entity_description=entity_info[2] + "\n".join([sim_entity.entity_description for sim_entity in sim_entities]), 
-                chunk_id=set([entity_info[3]] + [sim_entity.get_chunk_id for sim_entity in sim_entities])
-            )
-        )
-        
-    return updated_entities, kept_vs_merged
-
-
-def _merge_relationships(
-    relationships: List[RelationshipModel], kept_vs_merged_entities: Dict[str, List[str]]
-) -> List[RelationshipModel]:
-
-    for relationship in relationships:
-        source, target = relationship.source_entity, relationship.target_entity
-        try:
-            if source in kept_vs_merged_entities:
-                relationship.source_entity = list(kept_vs_merged_entities[source])[0]
-            if target in kept_vs_merged_entities:
-                relationship.target_entity = list(kept_vs_merged_entities[target])[0]
-        except (KeyError, IndexError):
-            print(f"Something went wrong for edge: {(source, target)}")
-            continue
-        
-
-    merged_relationships = {}
-    for relationship in relationships:
-        edge = (relationship.source_entity, relationship.target_entity)
-        if edge not in merged_relationships:
-            merged_relationships[edge] = relationship
-            continue
-        print(f"Edge: ({source}, {target}) already exists")
-        existing_edge = merged_relationships[edge]
-        existing_edge.relationship_description += "\n" + relationship.relationship_description
-        existing_edge.relationship_strength += relationship.relationship_strength
-        existing_edge.relationship_keywords += relationship.relationship_keywords
-        existing_edge.relationship_keywords = list(set(existing_edge.relationship_keywords))
-        existing_edge.update_chunk_ids(relationship.chunk_id)
-        
-    return list(merged_relationships.values())
-                
-
-async def _extract_graph_information_from_chunk(chunk: str, entity_types: Dict[str, str], gleaning: int=1) -> Tuple[List[EntityModel], List[RelationshipModel], ChunkModel] | None:
-    
-    already_exists = _extract_chunk_info_from_db_if_exists(chunk=chunk)
-    if already_exists is not None:
-        return already_exists
-    chunk_info: Dict[str, Any] = {}
-    for _ in range(gleaning):
-        gleaning_chunk_info = await extract_entities_completion(chunk=chunk, 
-                                                                history=None, 
-                                                                entity_types=entity_types)
-        if gleaning_chunk_info is None: continue
-    
-        more_chunk_info = await extract_entities_completion(
-            chunk=chunk, history=str(chunk_info), entity_types=entity_types
-        )
-        if more_chunk_info is not None:
-            chunk_info.update(more_chunk_info)
-    
-    chunk_model = ChunkModel(text=chunk, id=str(uuid.uuid4()))
-    try:
-        entities, relationships, high_level_keywords = [chunk_info[key] for key in ("entities", "relationships", "content_keywords")]
-    except KeyError as e:
-        print(f"KeyError -> {e}")
-        print(chunk_info)
-        raise e
-    if isinstance(high_level_keywords, list): high_level_keywords = {"content_keywords": high_level_keywords}
-    entities_models, relationships_models, high_level_keywords_models = [
-        [model(**val, chunk_id={chunk_model.id}) for val in values] if isinstance(values, list) else [model(**values, chunk_id={chunk_model.id})]
-        for model, values in zip((EntityModel, RelationshipModel, HighLevelKeywords), 
-                                 (entities, relationships, high_level_keywords))
-    ]
-    return entities_models, relationships_models, chunk_model
-
-
-async def extract_entities(chunks: List[str], entity_types: Dict[str, str], gleaning: int=1, batch: int=15) -> Tuple[List[EntityModel], List[RelationshipModel], Dict[str, Set[str]], List[ChunkModel]]:
-
-    if len(chunks) > batch:
-        results = []
-        for k in range(0, len(chunks), batch):
-            batch_chunks = chunks[k: k + batch]
-            try:
-                results.extend(
-                    await asyncio.gather(*[
-                        _extract_graph_information_from_chunk(chunk=chunk, gleaning=gleaning, entity_types=entity_types) for chunk in batch_chunks
-                    ])
-                )
-            except RateLimitError:
-                print("Rate limit error. Sleeping for a few seconds...")
-                await asyncio.sleep(2)
-                sub_batch = batch // 2
-                for j in range(0, len(batch_chunks), sub_batch):
-                    results.extend(
-                        await asyncio.gather(*[
-                            _extract_graph_information_from_chunk(chunk=chunk, gleaning=gleaning, entity_types=entity_types) for chunk in batch_chunks[j: j + sub_batch]
-                        ])
-                    )
-                    await asyncio.sleep(1)
-            await asyncio.sleep(1)
-    else:
-        results = await asyncio.gather(*[
-            _extract_graph_information_from_chunk(chunk=chunk, gleaning=gleaning, entity_types=entity_types) for chunk in chunks
-        ])
-    
-    if results is None:
-        return None
-    
-    entities, relationships, chunks_models = [], [], []
-        
-    for result in results:
-        if result is None:
-            continue
-        entities_n, relationships_n, chunk = result
-        entities.extend(entities_n)
-        relationships.extend(relationships_n)
-        chunks_models.append(chunk)
-        
-    entities, kept_vs_merged = _merge_entities(entities=entities)
-    relationships = _merge_relationships(relationships=relationships, kept_vs_merged_entities=kept_vs_merged)
-    
-    return entities, relationships, kept_vs_merged, chunks_models
+from .types import (
+    EntityExtractionResult,
+    RelationshipExtractionResult,
+    Chunk,
+    EntityModel, 
+    RelationshipModel, 
+    KeptVsMerged,
+    ChunkModel, 
+    HighLevelKeywords
+)
+from ..llm.entity_extraction import extract_entities as llm_extract_entities
+from typing import List, Dict, Tuple
+import pandas as pd
+
+from graphrag.database.base import get_db
+from graphrag.database.models import Chunk, Entity, Relationship
+
+from graphrag.indexing.utils import calculate_hash
+from graphrag.llm.llm import extract_entities_completion
+
+from typing import (List, 
+                    Tuple, 
+                    Dict, 
+                    Any, 
+                    Set)
+from fuzzywuzzy import fuzz
+from openai import RateLimitError
+
+import uuid
+import asyncio
+import uuid
+
+
+def _extract_chunk_info_from_db_if_exists(chunk: str) -> Tuple[List[EntityModel], List[RelationshipModel], ChunkModel] | None:
+
+    db = next(get_db())
+    hash = "chunk-" + calculate_hash(text=chunk)
+    exists = db.query(Chunk).filter(Chunk.hash == hash).first()
+    if exists:
+        entities_models, relationships_models = [], [] 
+        entities = db.query(Entity).filter(Entity.chunk_id == exists.chunk_id).all()
+        for entity in entities:
+            entity_model = EntityModel(
+                entity_name=entity.entity_name, 
+                entity_type=entity.entity_type, 
+                entity_description=entity.description,
+                chunk_id=str(exists.chunk_id)
+            )
+            entities_models.append(entity_model)
+        relationships = db.query(Relationship).filter(Relationship.chunk_id == exists.chunk_id).all()
+        for rel in relationships:
+            rel_model = RelationshipModel(
+                source_entity=rel.source_entity.entity_name, 
+                target_entity=rel.target_entity.entity_name,
+                relationship_description=rel.description,
+                relationship_strength=rel.weight,
+                chunk_id=str(exists.chunk_id),
+                relationship_keywords=rel.keywords
+            )
+            relationships_models.append(rel_model)
+        db.close()
+        return entities_models, relationships_models, ChunkModel(text=exists.text, id=str(exists.chunk_id))
+    db.close()
+    return None
+    
+
+def _merge_entities(entities: List[EntityModel], threshold: int=75) -> Tuple[List[EntityModel], Dict[str, Set[str]]]:
+    
+    def find_most_similar(entity: EntityModel, candidates: List[EntityModel], threshold: int) -> List[EntityModel]:
+        
+        most_sim_entity: List[EntityModel] = []
+        for candidate_entity in candidates:
+            if (entity.entity_type != candidate_entity.entity_type): continue
+            try:
+                score = fuzz.ratio(entity.entity_name, candidate_entity.entity_name)
+            except IndexError:
+                continue
+            if score > threshold:
+                most_sim_entity.append(candidate_entity)
+
+        return most_sim_entity
+    
+    kept_vs_merged = {}
+
+    merged_entities = set()
+    modified_entities: Dict[Tuple[str, str, str, str], List[EntityModel]] = {}
+    for index, entity in enumerate(entities):
+        most_sim_entities = find_most_similar(entity=entity, candidates=entities[index+1:], threshold=threshold)
+        entity_key = (entity.entity_name, entity.entity_type, entity.entity_description)
+
+        if entity_key in merged_entities:
+            print(f"{entity_key} already exists as an entity")
+            continue
+    
+        if (entity.entity_name, entity.entity_type, entity.entity_description, entity.get_chunk_id) not in modified_entities:
+            modified_entities[(entity.entity_name, entity.entity_type, entity.entity_description, entity.get_chunk_id)] = []
+        if most_sim_entities:
+            for most_sim_entity in most_sim_entities:
+                most_sim_key = (most_sim_entity.entity_name, most_sim_entity.entity_type, most_sim_entity.entity_description)
+                print(f"{most_sim_key[:2]} has been identified as similar to another entity")
+                merged_entities.add(most_sim_key)
+                modified_entities[(entity.entity_name, entity.entity_type, entity.entity_description, entity.get_chunk_id)].append(most_sim_entity)
+                if most_sim_entity.entity_name not in kept_vs_merged:
+                    kept_vs_merged[most_sim_entity.entity_name] = {entity.entity_name}
+                else:
+                    kept_vs_merged[most_sim_entity.entity_name].add(entity.entity_name)
+
+    updated_entities = []
+    for entity_info, sim_entities in modified_entities.items():
+
+        if entity_info[:-1] in merged_entities and not len(sim_entities): continue
+        
+        updated_entities.append(
+            EntityModel(
+                entity_name=entity_info[0], 
+                entity_type=entity_info[1], 
+                entity_description=entity_info[2] + "\n".join([sim_entity.entity_description for sim_entity in sim_entities]), 
+                chunk_id=set([entity_info[3]] + [sim_entity.get_chunk_id for sim_entity in sim_entities])
+            )
+        )
+        
+    return updated_entities, kept_vs_merged
+
+
+def _merge_relationships(
+    relationships: List[RelationshipModel], kept_vs_merged_entities: Dict[str, List[str]]
+) -> List[RelationshipModel]:
+
+    for relationship in relationships:
+        source, target = relationship.source_entity, relationship.target_entity
+        try:
+            if source in kept_vs_merged_entities:
+                relationship.source_entity = list(kept_vs_merged_entities[source])[0]
+            if target in kept_vs_merged_entities:
+                relationship.target_entity = list(kept_vs_merged_entities[target])[0]
+        except (KeyError, IndexError):
+            print(f"Something went wrong for edge: {(source, target)}")
+            continue
+        
+
+    merged_relationships = {}
+    for relationship in relationships:
+        edge = (relationship.source_entity, relationship.target_entity)
+        if edge not in merged_relationships:
+            merged_relationships[edge] = relationship
+            continue
+        print(f"Edge: ({source}, {target}) already exists")
+        existing_edge = merged_relationships[edge]
+        existing_edge.relationship_description += "\n" + relationship.relationship_description
+        existing_edge.relationship_strength += relationship.relationship_strength
+        existing_edge.relationship_keywords += relationship.relationship_keywords
+        existing_edge.relationship_keywords = list(set(existing_edge.relationship_keywords))
+        existing_edge.update_chunk_ids(relationship.chunk_id)
+        
+    return list(merged_relationships.values())
+                
+
+async def _extract_graph_information_from_chunk(chunk: str, entity_types: Dict[str, str], gleaning: int=1) -> Tuple[List[EntityModel], List[RelationshipModel], ChunkModel] | None:
+    
+    already_exists = _extract_chunk_info_from_db_if_exists(chunk=chunk)
+    if already_exists is not None:
+        return already_exists
+    chunk_info: Dict[str, Any] = {}
+    for _ in range(gleaning):
+        gleaning_chunk_info = await extract_entities_completion(chunk=chunk, 
+                                                                history=None, 
+                                                                entity_types=entity_types)
+        if gleaning_chunk_info is None: continue
+    
+        more_chunk_info = await extract_entities_completion(
+            chunk=chunk, history=str(chunk_info), entity_types=entity_types
+        )
+        if more_chunk_info is not None:
+            chunk_info.update(more_chunk_info)
+    
+    chunk_model = ChunkModel(text=chunk, id=str(uuid.uuid4()))
+    try:
+        entities, relationships, high_level_keywords = [chunk_info[key] for key in ("entities", "relationships", "content_keywords")]
+    except KeyError as e:
+        print(f"KeyError -> {e}")
+        print(chunk_info)
+        raise e
+    if isinstance(high_level_keywords, list): high_level_keywords = {"content_keywords": high_level_keywords}
+    entities_models, relationships_models, high_level_keywords_models = [
+        [model(**val, chunk_id={chunk_model.id}) for val in values] if isinstance(values, list) else [model(**values, chunk_id={chunk_model.id})]
+        for model, values in zip((EntityModel, RelationshipModel, HighLevelKeywords), 
+                                 (entities, relationships, high_level_keywords))
+    ]
+    return entities_models, relationships_models, chunk_model
+
+
+async def extract_entities(chunks: List[str], entity_types: Dict[str, str], gleaning: int=1, batch: int=15) -> Tuple[List[EntityModel], List[RelationshipModel], Dict[str, Set[str]], List[ChunkModel]]:
+
+    if len(chunks) > batch:
+        results = []
+        for k in range(0, len(chunks), batch):
+            batch_chunks = chunks[k: k + batch]
+            try:
+                results.extend(
+                    await asyncio.gather(*[
+                        _extract_graph_information_from_chunk(chunk=chunk, gleaning=gleaning, entity_types=entity_types) for chunk in batch_chunks
+                    ])
+                )
+            except RateLimitError:
+                print("Rate limit error. Sleeping for a few seconds...")
+                await asyncio.sleep(2)
+                sub_batch = batch // 2
+                for j in range(0, len(batch_chunks), sub_batch):
+                    results.extend(
+                        await asyncio.gather(*[
+                            _extract_graph_information_from_chunk(chunk=chunk, gleaning=gleaning, entity_types=entity_types) for chunk in batch_chunks[j: j + sub_batch]
+                        ])
+                    )
+                    await asyncio.sleep(1)
+            await asyncio.sleep(1)
+    else:
+        results = await asyncio.gather(*[
+            _extract_graph_information_from_chunk(chunk=chunk, gleaning=gleaning, entity_types=entity_types) for chunk in chunks
+        ])
+    
+    if results is None:
+        return None
+    
+    entities, relationships, chunks_models = [], [], []
+        
+    for result in results:
+        if result is None:
+            continue
+        entities_n, relationships_n, chunk = result
+        entities.extend(entities_n)
+        relationships.extend(relationships_n)
+        chunks_models.append(chunk)
+        
+    entities, kept_vs_merged = _merge_entities(entities=entities)
+    relationships = _merge_relationships(relationships=relationships, kept_vs_merged_entities=kept_vs_merged)
+    
+    return entities, relationships, kept_vs_merged, chunks_models

cwyodmodules/graphrag/main.py

@@ -1,34 +1,34 @@
-from graphrag.indexing import (create_chunks, 
-                               upsert_data_and_create_graph, 
-                               extract_entities)
-from graphrag.query.generate import _local_query, _global_query, _hybrid_query, _naive_rag
-
-from graphrag.config import GlobalConfig
-from typing import List, Dict, Tuple, Any, Set
-
-import networkx as nx
-
-
-async def insert(text: str, config: GlobalConfig) -> nx.Graph:
-    chunks = await create_chunks(text=text, 
-                                 min_token_size=config.min_chunk_size, 
-                                 max_token_size=config.max_chunk_size)
-    print(f"{len(chunks)} chunks created")
-    entities, relationships, kept_vs_merged, chunk_models = await extract_entities(chunks=chunks, entity_types=config.entity_types, gleaning=config.max_gleaning, batch=config.batch)
-    print(f"{len(entities)} entities extracted and {len(relationships)} relationships extracted. ")
-    graph = await upsert_data_and_create_graph(entities=entities, relationships=relationships, chunks=chunk_models)
-    return graph
-
-async def local_query(query: str, config: GlobalConfig) -> Tuple[str | None, List[str], Dict[str, Dict[str, Any]], List[str]]:
-    response, chunk_texts, nodes, keywords = await _local_query(query=query, top_k=config.keywords_top_k, max_nodes=config.graph_top_k, order_range=config.order_range)
-    return response, chunk_texts, nodes, keywords
-
-async def global_query(query: str, config: GlobalConfig) -> Tuple[str | None, List[str], Dict[str, Any], List[str]]:
-    response, chunk_texts, chunks, keywords = await _global_query(query=query, top_k=config.keywords_top_k, max_nodes=config.graph_top_k, alpha=config.alpha)
-    return response, chunk_texts, chunks, keywords
-
-async def hybrid_query(query: str, config: GlobalConfig) -> Tuple[str | None, List[str], Tuple[Dict[str, Any], Dict[str, Dict[str, Any]]], Set[str]]:
-    return await _hybrid_query(query=query, top_k=config.keywords_top_k, max_nodes=config.graph_top_k, alpha=config.alpha, order_range=config.order_range)
-
-async def naive_query(query: str, config: GlobalConfig) -> Tuple[str, List[str]]:
-    return await _naive_rag(query=query, top_k=config.graph_top_k)
+from .indexing import (create_chunks, 
+                               upsert_data_and_create_graph, 
+                               extract_entities)
+from .query.generate import _local_query, _global_query, _hybrid_query, _naive_rag
+
+from .config import GlobalConfig
+from typing import List, Dict, Tuple, Any, Set
+
+import networkx as nx
+
+
+async def insert(text: str, config: GlobalConfig) -> nx.Graph:
+    chunks = await create_chunks(text=text, 
+                                 min_token_size=config.min_chunk_size, 
+                                 max_token_size=config.max_chunk_size)
+    print(f"{len(chunks)} chunks created")
+    entities, relationships, kept_vs_merged, chunk_models = await extract_entities(chunks=chunks, entity_types=config.entity_types, gleaning=config.max_gleaning, batch=config.batch)
+    print(f"{len(entities)} entities extracted and {len(relationships)} relationships extracted. ")
+    graph = await upsert_data_and_create_graph(entities=entities, relationships=relationships, chunks=chunk_models)
+    return graph
+
+async def local_query(query: str, config: GlobalConfig) -> Tuple[str | None, List[str], Dict[str, Dict[str, Any]], List[str]]:
+    response, chunk_texts, nodes, keywords = await _local_query(query=query, top_k=config.keywords_top_k, max_nodes=config.graph_top_k, order_range=config.order_range)
+    return response, chunk_texts, nodes, keywords
+
+async def global_query(query: str, config: GlobalConfig) -> Tuple[str | None, List[str], Dict[str, Any], List[str]]:
+    response, chunk_texts, chunks, keywords = await _global_query(query=query, top_k=config.keywords_top_k, max_nodes=config.graph_top_k, alpha=config.alpha)
+    return response, chunk_texts, chunks, keywords
+
+async def hybrid_query(query: str, config: GlobalConfig) -> Tuple[str | None, List[str], Tuple[Dict[str, Any], Dict[str, Dict[str, Any]]], Set[str]]:
+    return await _hybrid_query(query=query, top_k=config.keywords_top_k, max_nodes=config.graph_top_k, alpha=config.alpha, order_range=config.order_range)
+
+async def naive_query(query: str, config: GlobalConfig) -> Tuple[str, List[str]]:
+    return await _naive_rag(query=query, top_k=config.graph_top_k)