cognee 0.4.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

cognee/__init__.py

@@ -19,6 +19,7 @@ from .api.v1.add import add
 from .api.v1.delete import delete
 from .api.v1.cognify import cognify
 from .modules.memify import memify
+from .modules.run_custom_pipeline import run_custom_pipeline
 from .api.v1.update import update
 from .api.v1.config.config import config
 from .api.v1.datasets.datasets import datasets

cognee/api/client.py

@@ -21,8 +21,9 @@ from cognee.api.v1.notebooks.routers import get_notebooks_router
 from cognee.api.v1.permissions.routers import get_permissions_router
 from cognee.api.v1.settings.routers import get_settings_router
 from cognee.api.v1.datasets.routers import get_datasets_router
-from cognee.api.v1.cognify.routers import get_code_pipeline_router, get_cognify_router
+from cognee.api.v1.cognify.routers import get_cognify_router
 from cognee.api.v1.search.routers import get_search_router
+from cognee.api.v1.ontologies.routers.get_ontology_router import get_ontology_router
 from cognee.api.v1.memify.routers import get_memify_router
 from cognee.api.v1.add.routers import get_add_router
 from cognee.api.v1.delete.routers import get_delete_router
@@ -39,6 +40,8 @@ from cognee.api.v1.users.routers import (
 )
 from cognee.modules.users.methods.get_authenticated_user import REQUIRE_AUTHENTICATION
 
+# Ensure application logging is configured for container stdout/stderr
+setup_logging()
 logger = get_logger()
 
 if os.getenv("ENV", "prod") == "prod":
@@ -74,6 +77,9 @@ async def lifespan(app: FastAPI):
 
     await get_default_user()
 
+    # Emit a clear startup message for docker logs
+    logger.info("Backend server has started")
+
     yield
 
 
@@ -258,6 +264,8 @@ app.include_router(
 
 app.include_router(get_datasets_router(), prefix="/api/v1/datasets", tags=["datasets"])
 
+app.include_router(get_ontology_router(), prefix="/api/v1/ontologies", tags=["ontologies"])
+
 app.include_router(get_settings_router(), prefix="/api/v1/settings", tags=["settings"])
 
 app.include_router(get_visualize_router(), prefix="/api/v1/visualize", tags=["visualize"])
@@ -270,10 +278,6 @@ app.include_router(get_responses_router(), prefix="/api/v1/responses", tags=["re
 
 app.include_router(get_sync_router(), prefix="/api/v1/sync", tags=["sync"])
 
-codegraph_routes = get_code_pipeline_router()
-if codegraph_routes:
-    app.include_router(codegraph_routes, prefix="/api/v1/code-pipeline", tags=["code-pipeline"])
-
 app.include_router(
     get_users_router(),
     prefix="/api/v1/users",

cognee/api/v1/add/add.py

@@ -155,7 +155,7 @@ async def add(
         - LLM_API_KEY: API key for your LLM provider (OpenAI, Anthropic, etc.)
 
         Optional:
-        - LLM_PROVIDER: "openai" (default), "anthropic", "gemini", "ollama", "mistral"
+        - LLM_PROVIDER: "openai" (default), "anthropic", "gemini", "ollama", "mistral", "bedrock"
         - LLM_MODEL: Model name (default: "gpt-5-mini")
         - DEFAULT_USER_EMAIL: Custom default user email
         - DEFAULT_USER_PASSWORD: Custom default user password
@@ -205,6 +205,7 @@ async def add(
         pipeline_name="add_pipeline",
         vector_db_config=vector_db_config,
         graph_db_config=graph_db_config,
+        use_pipeline_cache=True,
         incremental_loading=incremental_loading,
         data_per_batch=data_per_batch,
     ):

cognee/api/v1/add/routers/get_add_router.py

@@ -82,7 +82,9 @@ def get_add_router() -> APIRouter:
                 datasetName,
                 user=user,
                 dataset_id=datasetId,
-                node_set=node_set if node_set else None,
+                node_set=node_set
+                if node_set != [""]
+                else None,  # Transform default node_set endpoint value to None
             )
 
             if isinstance(add_run, PipelineRunErrored):

cognee/api/v1/cognify/cognify.py

@@ -3,6 +3,7 @@ from pydantic import BaseModel
 from typing import Union, Optional
 from uuid import UUID
 
+from cognee.modules.cognify.config import get_cognify_config
 from cognee.modules.ontology.ontology_env_config import get_ontology_env_config
 from cognee.shared.logging_utils import get_logger
 from cognee.shared.data_models import KnowledgeGraph
@@ -19,7 +20,6 @@ from cognee.modules.ontology.get_default_ontology_resolver import (
 from cognee.modules.users.models import User
 
 from cognee.tasks.documents import (
-    check_permissions_on_dataset,
     classify_documents,
     extract_chunks_from_documents,
 )
@@ -53,6 +53,7 @@ async def cognify(
     custom_prompt: Optional[str] = None,
     temporal_cognify: bool = False,
     data_per_batch: int = 20,
+    **kwargs,
 ):
     """
     Transform ingested data into a structured knowledge graph.
@@ -78,12 +79,11 @@ async def cognify(
 
     Processing Pipeline:
         1. **Document Classification**: Identifies document types and structures
-        2. **Permission Validation**: Ensures user has processing rights
-        3. **Text Chunking**: Breaks content into semantically meaningful segments
-        4. **Entity Extraction**: Identifies key concepts, people, places, organizations
-        5. **Relationship Detection**: Discovers connections between entities
-        6. **Graph Construction**: Builds semantic knowledge graph with embeddings
-        7. **Content Summarization**: Creates hierarchical summaries for navigation
+        2. **Text Chunking**: Breaks content into semantically meaningful segments
+        3. **Entity Extraction**: Identifies key concepts, people, places, organizations
+        4. **Relationship Detection**: Discovers connections between entities
+        5. **Graph Construction**: Builds semantic knowledge graph with embeddings
+        6. **Content Summarization**: Creates hierarchical summaries for navigation
 
     Graph Model Customization:
         The `graph_model` parameter allows custom knowledge structures:
@@ -224,6 +224,7 @@ async def cognify(
             config=config,
             custom_prompt=custom_prompt,
             chunks_per_batch=chunks_per_batch,
+            **kwargs,
         )
 
     # By calling get pipeline executor we get a function that will have the run_pipeline run in the background or a function that we will need to wait for
@@ -238,6 +239,7 @@ async def cognify(
         vector_db_config=vector_db_config,
         graph_db_config=graph_db_config,
         incremental_loading=incremental_loading,
+        use_pipeline_cache=True,
         pipeline_name="cognify_pipeline",
         data_per_batch=data_per_batch,
     )
@@ -251,6 +253,7 @@ async def get_default_tasks(  # TODO: Find out a better way to do this (Boris's
     config: Config = None,
     custom_prompt: Optional[str] = None,
     chunks_per_batch: int = 100,
+    **kwargs,
 ) -> list[Task]:
     if config is None:
         ontology_config = get_ontology_env_config()
@@ -272,9 +275,11 @@ async def get_default_tasks(  # TODO: Find out a better way to do this (Boris's
     if chunks_per_batch is None:
         chunks_per_batch = 100
 
+    cognify_config = get_cognify_config()
+    embed_triplets = cognify_config.triplet_embedding
+
     default_tasks = [
         Task(classify_documents),
-        Task(check_permissions_on_dataset, user=user, permissions=["write"]),
         Task(
             extract_chunks_from_documents,
             max_chunk_size=chunk_size or get_max_chunk_tokens(),
@@ -286,12 +291,17 @@ async def get_default_tasks(  # TODO: Find out a better way to do this (Boris's
             config=config,
             custom_prompt=custom_prompt,
             task_config={"batch_size": chunks_per_batch},
+            **kwargs,
         ),  # Generate knowledge graphs from the document chunks.
         Task(
             summarize_text,
             task_config={"batch_size": chunks_per_batch},
         ),
-        Task(add_data_points, task_config={"batch_size": chunks_per_batch}),
+        Task(
+            add_data_points,
+            embed_triplets=embed_triplets,
+            task_config={"batch_size": chunks_per_batch},
+        ),
     ]
 
     return default_tasks
@@ -305,14 +315,13 @@ async def get_temporal_tasks(
 
     The pipeline includes:
     1. Document classification.
-    2. Dataset permission checks (requires "write" access).
-    3. Document chunking with a specified or default chunk size.
-    4. Event and timestamp extraction from chunks.
-    5. Knowledge graph extraction from events.
-    6. Batched insertion of data points.
+    2. Document chunking with a specified or default chunk size.
+    3. Event and timestamp extraction from chunks.
+    4. Knowledge graph extraction from events.
+    5. Batched insertion of data points.
 
     Args:
-        user (User, optional): The user requesting task execution, used for permission checks.
+        user (User, optional): The user requesting task execution.
         chunker (Callable, optional): A text chunking function/class to split documents. Defaults to TextChunker.
         chunk_size (int, optional): Maximum token size per chunk. If not provided, uses system default.
         chunks_per_batch (int, optional): Number of chunks to process in a single batch in Cognify
@@ -325,7 +334,6 @@ async def get_temporal_tasks(
 
     temporal_tasks = [
         Task(classify_documents),
-        Task(check_permissions_on_dataset, user=user, permissions=["write"]),
         Task(
             extract_chunks_from_documents,
             max_chunk_size=chunk_size or get_max_chunk_tokens(),

cognee/api/v1/cognify/routers/__init__.py

@@ -1,2 +1 @@
 from .get_cognify_router import get_cognify_router
-from .get_code_pipeline_router import get_code_pipeline_router

cognee/api/v1/cognify/routers/get_cognify_router.py

@@ -41,6 +41,11 @@ class CognifyPayloadDTO(InDTO):
     custom_prompt: Optional[str] = Field(
         default="", description="Custom prompt for entity extraction and graph generation"
     )
+    ontology_key: Optional[List[str]] = Field(
+        default=None,
+        examples=[[]],
+        description="Reference to one or more previously uploaded ontologies",
+    )
 
 
 def get_cognify_router() -> APIRouter:
@@ -68,6 +73,7 @@ def get_cognify_router() -> APIRouter:
         - **dataset_ids** (Optional[List[UUID]]): List of existing dataset UUIDs to process. UUIDs allow processing of datasets not owned by the user (if permitted).
         - **run_in_background** (Optional[bool]): Whether to execute processing asynchronously. Defaults to False (blocking).
         - **custom_prompt** (Optional[str]): Custom prompt for entity extraction and graph generation. If provided, this prompt will be used instead of the default prompts for knowledge graph extraction.
+        - **ontology_key** (Optional[List[str]]): Reference to one or more previously uploaded ontology files to use for knowledge graph construction.
 
         ## Response
         - **Blocking execution**: Complete pipeline run information with entity counts, processing duration, and success/failure status
@@ -82,7 +88,8 @@ def get_cognify_router() -> APIRouter:
         {
             "datasets": ["research_papers", "documentation"],
             "run_in_background": false,
-            "custom_prompt": "Extract entities focusing on technical concepts and their relationships. Identify key technologies, methodologies, and their interconnections."
+            "custom_prompt": "Extract entities focusing on technical concepts and their relationships. Identify key technologies, methodologies, and their interconnections.",
+            "ontology_key": ["medical_ontology_v1"]
         }
         ```
 
@@ -108,13 +115,35 @@ def get_cognify_router() -> APIRouter:
             )
 
         from cognee.api.v1.cognify import cognify as cognee_cognify
+        from cognee.api.v1.ontologies.ontologies import OntologyService
 
         try:
             datasets = payload.dataset_ids if payload.dataset_ids else payload.datasets
+            config_to_use = None
+
+            if payload.ontology_key:
+                ontology_service = OntologyService()
+                ontology_contents = ontology_service.get_ontology_contents(
+                    payload.ontology_key, user
+                )
+
+                from cognee.modules.ontology.ontology_config import Config
+                from cognee.modules.ontology.rdf_xml.RDFLibOntologyResolver import (
+                    RDFLibOntologyResolver,
+                )
+                from io import StringIO
+
+                ontology_streams = [StringIO(content) for content in ontology_contents]
+                config_to_use: Config = {
+                    "ontology_config": {
+                        "ontology_resolver": RDFLibOntologyResolver(ontology_file=ontology_streams)
+                    }
+                }
 
             cognify_run = await cognee_cognify(
                 datasets,
                 user,
+                config=config_to_use,
                 run_in_background=payload.run_in_background,
                 custom_prompt=payload.custom_prompt,
             )

cognee/api/v1/datasets/routers/get_datasets_router.py

@@ -208,14 +208,14 @@ def get_datasets_router() -> APIRouter:
             },
         )
 
-        from cognee.modules.data.methods import get_dataset, delete_dataset
+        from cognee.modules.data.methods import delete_dataset
 
-        dataset = await get_dataset(user.id, dataset_id)
+        dataset = await get_authorized_existing_datasets([dataset_id], "delete", user)
 
         if dataset is None:
             raise DatasetNotFoundError(message=f"Dataset ({str(dataset_id)}) not found.")
 
-        await delete_dataset(dataset)
+        await delete_dataset(dataset[0])
 
     @router.delete(
         "/{dataset_id}/data/{data_id}",

cognee/api/v1/ontologies/__init__.py

@@ -0,0 +1,4 @@
+from .ontologies import OntologyService
+from .routers.get_ontology_router import get_ontology_router
+
+__all__ = ["OntologyService", "get_ontology_router"]

cognee/api/v1/ontologies/ontologies.py

@@ -0,0 +1,158 @@
+import os
+import json
+import tempfile
+from pathlib import Path
+from datetime import datetime, timezone
+from typing import Optional, List
+from dataclasses import dataclass
+from fastapi import UploadFile
+
+
+@dataclass
+class OntologyMetadata:
+    ontology_key: str
+    filename: str
+    size_bytes: int
+    uploaded_at: str
+    description: Optional[str] = None
+
+
+class OntologyService:
+    def __init__(self):
+        pass
+
+    @property
+    def base_dir(self) -> Path:
+        return Path(tempfile.gettempdir()) / "ontologies"
+
+    def _get_user_dir(self, user_id: str) -> Path:
+        user_dir = self.base_dir / str(user_id)
+        user_dir.mkdir(parents=True, exist_ok=True)
+        return user_dir
+
+    def _get_metadata_path(self, user_dir: Path) -> Path:
+        return user_dir / "metadata.json"
+
+    def _load_metadata(self, user_dir: Path) -> dict:
+        metadata_path = self._get_metadata_path(user_dir)
+        if metadata_path.exists():
+            with open(metadata_path, "r") as f:
+                return json.load(f)
+        return {}
+
+    def _save_metadata(self, user_dir: Path, metadata: dict):
+        metadata_path = self._get_metadata_path(user_dir)
+        with open(metadata_path, "w") as f:
+            json.dump(metadata, f, indent=2)
+
+    async def upload_ontology(
+        self, ontology_key: str, file: UploadFile, user, description: Optional[str] = None
+    ) -> OntologyMetadata:
+        if not file.filename:
+            raise ValueError("File must have a filename")
+        if not file.filename.lower().endswith(".owl"):
+            raise ValueError("File must be in .owl format")
+
+        user_dir = self._get_user_dir(str(user.id))
+        metadata = self._load_metadata(user_dir)
+
+        if ontology_key in metadata:
+            raise ValueError(f"Ontology key '{ontology_key}' already exists")
+
+        content = await file.read()
+
+        file_path = user_dir / f"{ontology_key}.owl"
+        with open(file_path, "wb") as f:
+            f.write(content)
+
+        ontology_metadata = {
+            "filename": file.filename,
+            "size_bytes": len(content),
+            "uploaded_at": datetime.now(timezone.utc).isoformat(),
+            "description": description,
+        }
+        metadata[ontology_key] = ontology_metadata
+        self._save_metadata(user_dir, metadata)
+
+        return OntologyMetadata(
+            ontology_key=ontology_key,
+            filename=file.filename,
+            size_bytes=len(content),
+            uploaded_at=ontology_metadata["uploaded_at"],
+            description=description,
+        )
+
+    async def upload_ontologies(
+        self,
+        ontology_key: List[str],
+        files: List[UploadFile],
+        user,
+        descriptions: Optional[List[str]] = None,
+    ) -> List[OntologyMetadata]:
+        """
+        Upload ontology files with their respective keys.
+
+        Args:
+            ontology_key: List of unique keys for each ontology
+            files: List of UploadFile objects (same length as keys)
+            user: Authenticated user
+            descriptions: Optional list of descriptions for each file
+
+        Returns:
+            List of OntologyMetadata objects for uploaded files
+
+        Raises:
+            ValueError: If keys duplicate, file format invalid, or array lengths don't match
+        """
+        if len(ontology_key) != len(files):
+            raise ValueError("Number of keys must match number of files")
+
+        if len(set(ontology_key)) != len(ontology_key):
+            raise ValueError("Duplicate ontology keys not allowed")
+
+        results = []
+
+        for i, (key, file) in enumerate(zip(ontology_key, files)):
+            results.append(
+                await self.upload_ontology(
+                    ontology_key=key,
+                    file=file,
+                    user=user,
+                    description=descriptions[i] if descriptions else None,
+                )
+            )
+        return results
+
+    def get_ontology_contents(self, ontology_key: List[str], user) -> List[str]:
+        """
+        Retrieve ontology content for one or more keys.
+
+        Args:
+            ontology_key: List of ontology keys to retrieve (can contain single item)
+            user: Authenticated user
+
+        Returns:
+            List of ontology content strings
+
+        Raises:
+            ValueError: If any ontology key not found
+        """
+        user_dir = self._get_user_dir(str(user.id))
+        metadata = self._load_metadata(user_dir)
+
+        contents = []
+        for key in ontology_key:
+            if key not in metadata:
+                raise ValueError(f"Ontology key '{key}' not found")
+
+            file_path = user_dir / f"{key}.owl"
+            if not file_path.exists():
+                raise ValueError(f"Ontology file for key '{key}' not found")
+
+            with open(file_path, "r", encoding="utf-8") as f:
+                contents.append(f.read())
+        return contents
+
+    def list_ontologies(self, user) -> dict:
+        user_dir = self._get_user_dir(str(user.id))
+        return self._load_metadata(user_dir)

cognee/api/v1/ontologies/routers/get_ontology_router.py

@@ -0,0 +1,109 @@
+from fastapi import APIRouter, File, Form, UploadFile, Depends, Request
+from fastapi.responses import JSONResponse
+from typing import Optional, List
+
+from cognee.modules.users.models import User
+from cognee.modules.users.methods import get_authenticated_user
+from cognee.shared.utils import send_telemetry
+from cognee import __version__ as cognee_version
+from ..ontologies import OntologyService
+
+
+def get_ontology_router() -> APIRouter:
+    router = APIRouter()
+    ontology_service = OntologyService()
+
+    @router.post("", response_model=dict)
+    async def upload_ontology(
+        request: Request,
+        ontology_key: str = Form(...),
+        ontology_file: UploadFile = File(...),
+        description: Optional[str] = Form(None),
+        user: User = Depends(get_authenticated_user),
+    ):
+        """
+        Upload a single ontology file for later use in cognify operations.
+
+        ## Request Parameters
+        - **ontology_key** (str): User-defined identifier for the ontology.
+        - **ontology_file** (UploadFile): Single OWL format ontology file
+        - **description** (Optional[str]): Optional description for the ontology.
+
+        ## Response
+        Returns metadata about the uploaded ontology including key, filename, size, and upload timestamp.
+
+        ## Error Codes
+        - **400 Bad Request**: Invalid file format, duplicate key, multiple files uploaded
+        - **500 Internal Server Error**: File system or processing errors
+        """
+        send_telemetry(
+            "Ontology Upload API Endpoint Invoked",
+            user.id,
+            additional_properties={
+                "endpoint": "POST /api/v1/ontologies",
+                "cognee_version": cognee_version,
+            },
+        )
+
+        try:
+            # Enforce: exactly one uploaded file for "ontology_file"
+            form = await request.form()
+            uploaded_files = form.getlist("ontology_file")
+            if len(uploaded_files) != 1:
+                raise ValueError("Only one ontology_file is allowed")
+
+            if ontology_key.strip().startswith(("[", "{")):
+                raise ValueError("ontology_key must be a string")
+            if description is not None and description.strip().startswith(("[", "{")):
+                raise ValueError("description must be a string")
+
+            result = await ontology_service.upload_ontology(
+                ontology_key=ontology_key,
+                file=ontology_file,
+                user=user,
+                description=description,
+            )
+
+            return {
+                "uploaded_ontologies": [
+                    {
+                        "ontology_key": result.ontology_key,
+                        "filename": result.filename,
+                        "size_bytes": result.size_bytes,
+                        "uploaded_at": result.uploaded_at,
+                        "description": result.description,
+                    }
+                ]
+            }
+        except ValueError as e:
+            return JSONResponse(status_code=400, content={"error": str(e)})
+        except Exception as e:
+            return JSONResponse(status_code=500, content={"error": str(e)})
+
+    @router.get("", response_model=dict)
+    async def list_ontologies(user: User = Depends(get_authenticated_user)):
+        """
+        List all uploaded ontologies for the authenticated user.
+
+        ## Response
+        Returns a dictionary mapping ontology keys to their metadata including filename, size, and upload timestamp.
+
+        ## Error Codes
+        - **500 Internal Server Error**: File system or processing errors
+        """
+        send_telemetry(
+            "Ontology List API Endpoint Invoked",
+            user.id,
+            additional_properties={
+                "endpoint": "GET /api/v1/ontologies",
+                "cognee_version": cognee_version,
+            },
+        )
+
+        try:
+            metadata = ontology_service.list_ontologies(user)
+            return metadata
+        except Exception as e:
+            return JSONResponse(status_code=500, content={"error": str(e)})
+
+    return router

cognee/api/v1/permissions/routers/get_permissions_router.py

@@ -1,15 +1,20 @@
 from uuid import UUID
-from typing import List
+from typing import List, Union
 
 from fastapi import APIRouter, Depends
 from fastapi.responses import JSONResponse
 
 from cognee.modules.users.models import User
+from cognee.api.DTO import InDTO
 from cognee.modules.users.methods import get_authenticated_user
 from cognee.shared.utils import send_telemetry
 from cognee import __version__ as cognee_version
 
 
+class SelectTenantDTO(InDTO):
+    tenant_id: UUID | None = None
+
+
 def get_permissions_router() -> APIRouter:
     permissions_router = APIRouter()
 
@@ -226,4 +231,39 @@ def get_permissions_router() -> APIRouter:
             status_code=200, content={"message": "Tenant created.", "tenant_id": str(tenant_id)}
         )
 
+    @permissions_router.post("/tenants/select")
+    async def select_tenant(payload: SelectTenantDTO, user: User = Depends(get_authenticated_user)):
+        """
+        Select current tenant.
+
+        This endpoint selects a tenant with the specified UUID. Tenants are used
+        to organize users and resources in multi-tenant environments, providing
+        isolation and access control between different groups or organizations.
+
+        Sending a null/None value as tenant_id selects his default single user tenant
+
+        ## Request Parameters
+        - **tenant_id** (Union[UUID, None]): UUID of the tenant to select, If null/None is provided use the default single user tenant
+
+        ## Response
+        Returns a success message along with selected tenant id.
+        """
+        send_telemetry(
+            "Permissions API Endpoint Invoked",
+            user.id,
+            additional_properties={
+                "endpoint": f"POST /v1/permissions/tenants/{str(payload.tenant_id)}",
+                "tenant_id": str(payload.tenant_id),
+            },
+        )
+
+        from cognee.modules.users.tenants.methods import select_tenant as select_tenant_method
+
+        await select_tenant_method(user_id=user.id, tenant_id=payload.tenant_id)
+
+        return JSONResponse(
+            status_code=200,
+            content={"message": "Tenant selected.", "tenant_id": str(payload.tenant_id)},
+        )
+
     return permissions_router

cognee/api/v1/search/search.py

@@ -31,6 +31,8 @@ async def search(
     only_context: bool = False,
     use_combined_context: bool = False,
     session_id: Optional[str] = None,
+    wide_search_top_k: Optional[int] = 100,
+    triplet_distance_penalty: Optional[float] = 3.5,
 ) -> Union[List[SearchResult], CombinedSearchResult]:
     """
     Search and query the knowledge graph for insights, information, and connections.
@@ -200,6 +202,8 @@ async def search(
         only_context=only_context,
         use_combined_context=use_combined_context,
         session_id=session_id,
+        wide_search_top_k=wide_search_top_k,
+        triplet_distance_penalty=triplet_distance_penalty,
     )
 
     return filtered_search_results