Merge branch 'dev' into incremental-loading

cognee/api/v1/add/add.py

@@ -15,6 +15,7 @@ async def add(
     vector_db_config: dict = None,
     graph_db_config: dict = None,
     dataset_id: UUID = None,
+    incremental_loading: bool = True,
 ):
     """
     Add data to Cognee for knowledge graph processing.
@@ -153,6 +154,7 @@ async def add(
         pipeline_name="add_pipeline",
         vector_db_config=vector_db_config,
         graph_db_config=graph_db_config,
+        incremental_loading=incremental_loading,
     ):
         pipeline_run_info = run_info
 

cognee/api/v1/cognify/code_graph_pipeline.py

@@ -79,7 +79,9 @@ async def run_code_graph_pipeline(repo_path, include_docs=False):
         async for run_status in non_code_pipeline_run:
             yield run_status
 
-    async for run_status in run_tasks(tasks, dataset.id, repo_path, user, "cognify_code_pipeline"):
+    async for run_status in run_tasks(
+        tasks, dataset.id, repo_path, user, "cognify_code_pipeline", incremental_loading=False
+    ):
         yield run_status
 
 

cognee/api/v1/cognify/cognify.py

@@ -39,6 +39,7 @@ async def cognify(
     vector_db_config: dict = None,
     graph_db_config: dict = None,
     run_in_background: bool = False,
+    incremental_loading: bool = True,
 ):
     """
     Transform ingested data into a structured knowledge graph.
@@ -194,6 +195,7 @@ async def cognify(
             datasets=datasets,
             vector_db_config=vector_db_config,
             graph_db_config=graph_db_config,
+            incremental_loading=incremental_loading,
         )
     else:
         return await run_cognify_blocking(
@@ -202,6 +204,7 @@ async def cognify(
             datasets=datasets,
             vector_db_config=vector_db_config,
             graph_db_config=graph_db_config,
+            incremental_loading=incremental_loading,
         )
 
 
@@ -211,6 +214,7 @@ async def run_cognify_blocking(
     datasets,
     graph_db_config: dict = None,
     vector_db_config: dict = False,
+    incremental_loading: bool = True,
 ):
     total_run_info = {}
 
@@ -221,6 +225,7 @@ async def run_cognify_blocking(
         pipeline_name="cognify_pipeline",
         graph_db_config=graph_db_config,
         vector_db_config=vector_db_config,
+        incremental_loading=incremental_loading,
     ):
         if run_info.dataset_id:
             total_run_info[run_info.dataset_id] = run_info
@@ -236,12 +241,14 @@ async def run_cognify_as_background_process(
     datasets,
     graph_db_config: dict = None,
     vector_db_config: dict = False,
+    incremental_loading: bool = True,
 ):
     # Store pipeline status for all pipelines
     pipeline_run_started_info = []
 
     async def handle_rest_of_the_run(pipeline_list):
         # Execute all provided pipelines one by one to avoid database write conflicts
+        # TODO: Convert to async gather task instead of for loop when Queue mechanism for database is created
         for pipeline in pipeline_list:
             while True:
                 try:
@@ -266,6 +273,7 @@ async def run_cognify_as_background_process(
             pipeline_name="cognify_pipeline",
             graph_db_config=graph_db_config,
             vector_db_config=vector_db_config,
+            incremental_loading=incremental_loading,
         )
 
         # Save dataset Pipeline run started info

cognee/modules/data/models/Data.py

@@ -1,6 +1,7 @@
 from datetime import datetime, timezone
 from uuid import uuid4
 from sqlalchemy import UUID, Column, DateTime, String, JSON, Integer
+from sqlalchemy.ext.mutable import MutableDict
 from sqlalchemy.orm import relationship
 
 from cognee.infrastructure.databases.relational import Base
@@ -20,7 +21,11 @@ class Data(Base):
     owner_id = Column(UUID, index=True)
     content_hash = Column(String)
     external_metadata = Column(JSON)
-    node_set = Column(JSON, nullable=True)  # Store NodeSet as JSON list of strings
+    # Store NodeSet as JSON list of strings
+    node_set = Column(JSON, nullable=True)
+    # MutableDict allows SQLAlchemy to notice key-value pair changes, without it changing a value for a key
+    # wouldn't be noticed when commiting a database session
+    pipeline_status = Column(MutableDict.as_mutable(JSON))
     token_count = Column(Integer)
     created_at = Column(DateTime(timezone=True), default=lambda: datetime.now(timezone.utc))
     updated_at = Column(DateTime(timezone=True), onupdate=lambda: datetime.now(timezone.utc))

cognee/modules/ingestion/methods/__init__.py

@@ -0,0 +1,2 @@
+from .get_s3_fs import get_s3_fs
+from .open_data_file import open_data_file

cognee/modules/ingestion/methods/get_s3_fs.py

@@ -0,0 +1,14 @@
+from cognee.api.v1.add.config import get_s3_config
+
+
+def get_s3_fs():
+    s3_config = get_s3_config()
+
+    fs = None
+    if s3_config.aws_access_key_id is not None and s3_config.aws_secret_access_key is not None:
+        import s3fs
+
+        fs = s3fs.S3FileSystem(
+            key=s3_config.aws_access_key_id, secret=s3_config.aws_secret_access_key, anon=False
+        )
+    return fs

cognee/modules/ingestion/methods/open_data_file.py

@@ -0,0 +1,6 @@
+def open_data_file(file_path: str, s3fs):
+    if file_path.startswith("s3://"):
+        return s3fs.open(file_path, mode="rb")
+    else:
+        local_path = file_path.replace("file://", "")
+        return open(local_path, mode="rb")

cognee/modules/pipelines/models/PipelineRunInfo.py

@@ -9,6 +9,7 @@ class PipelineRunInfo(BaseModel):
     dataset_id: UUID
     dataset_name: str
     payload: Optional[Any] = None
+    data_ingestion_info: Optional[dict] = None
 
     model_config = {
         "arbitrary_types_allowed": True,

cognee/modules/pipelines/operations/pipeline.py

@@ -2,6 +2,7 @@ import asyncio
 from typing import Union
 from uuid import NAMESPACE_OID, uuid5, UUID
 
+from cognee.modules.ingestion.exceptions import IngestionError
 from cognee.shared.logging_utils import get_logger
 from cognee.modules.data.methods.get_dataset_data import get_dataset_data
 from cognee.modules.data.models import Data, Dataset
@@ -52,6 +53,7 @@ async def cognee_pipeline(
     pipeline_name: str = "custom_pipeline",
     vector_db_config: dict = None,
     graph_db_config: dict = None,
+    incremental_loading: bool = True,
 ):
     # Note: These context variables allow different value assignment for databases in Cognee
     #       per async task, thread, process and etc.
@@ -106,6 +108,7 @@ async def cognee_pipeline(
             data=data,
             pipeline_name=pipeline_name,
             context={"dataset": dataset},
+            incremental_loading=incremental_loading,
         ):
             yield run_info
 
@@ -117,6 +120,7 @@ async def run_pipeline(
     data=None,
     pipeline_name: str = "custom_pipeline",
     context: dict = None,
+    incremental_loading=True,
 ):
     check_dataset_name(dataset.name)
 
@@ -184,7 +188,9 @@ async def run_pipeline(
         if not isinstance(task, Task):
             raise ValueError(f"Task {task} is not an instance of Task")
 
-    pipeline_run = run_tasks(tasks, dataset_id, data, user, pipeline_name, context)
+    pipeline_run = run_tasks(
+        tasks, dataset_id, data, user, pipeline_name, context, incremental_loading
+    )
 
     async for pipeline_run_info in pipeline_run:
         yield pipeline_run_info

cognee/modules/pipelines/operations/run_tasks.py

@@ -1,14 +1,20 @@
 import os
+import cognee.modules.ingestion as ingestion
+
 from uuid import UUID
 from typing import Any
 from functools import wraps
+from sqlalchemy import select
 
 from cognee.infrastructure.databases.relational import get_relational_engine
 from cognee.modules.pipelines.operations.run_tasks_distributed import run_tasks_distributed
 from cognee.modules.users.models import User
+from cognee.modules.data.models import Data
+from cognee.modules.ingestion.methods import get_s3_fs, open_data_file
 from cognee.shared.logging_utils import get_logger
 from cognee.modules.users.methods import get_default_user
 from cognee.modules.pipelines.utils import generate_pipeline_id
+from cognee.tasks.ingestion import save_data_item_to_storage, resolve_data_directories
 from cognee.modules.pipelines.models.PipelineRunInfo import (
     PipelineRunCompleted,
     PipelineRunErrored,
@@ -55,6 +61,7 @@ async def run_tasks(
     user: User = None,
     pipeline_name: str = "unknown_pipeline",
     context: dict = None,
+    incremental_loading: bool = True,
 ):
     if not user:
         user = get_default_user()
@@ -79,10 +86,45 @@ async def run_tasks(
         payload=data,
     )
 
+    fs = get_s3_fs()
+    data_items_pipeline_run_info = {}
+    ingestion_error = None
+    try:
+        if not isinstance(data, list):
+            data = [data]
+
+        if incremental_loading:
+            data = await resolve_data_directories(data)
+
+        # TODO: Convert to async gather task instead of for loop (just make sure it can work there were some issues when async gathering datasets)
+        for data_item in data:
+            # If incremental_loading of data is set to True don't process documents already processed by pipeline
+            if incremental_loading:
+                # If data is being added to Cognee for the first time calculate the id of the data
+                if not isinstance(data_item, Data):
+                    file_path = await save_data_item_to_storage(data_item, dataset.name)
+                    # Ingest data and add metadata
+                    with open_data_file(file_path, s3fs=fs) as file:
+                        classified_data = ingestion.classify(file, s3fs=fs)
+                        # data_id is the hash of file contents + owner id to avoid duplicate data
+                        data_id = ingestion.identify(classified_data, user)
+                else:
+                    # If data was already processed by Cognee get data id
+                    data_id = data_item.id
+
+                    # Check pipeline status, if Data already processed for pipeline before skip current processing
+                    async with db_engine.get_async_session() as session:
+                        data_point = (
+                            await session.execute(select(Data).filter(Data.id == data_id))
+                        ).scalar_one_or_none()
+                        if data_point:
+                            if data_point.pipeline_status.get(pipeline_name) == "Completed":
+                                continue
+
             try:
                 async for result in run_tasks_with_telemetry(
                     tasks=tasks,
-            data=data,
+                    data=[data_item],
                     user=user,
                     pipeline_name=pipeline_id,
                     context=context,
@@ -94,6 +136,46 @@ async def run_tasks(
                         payload=result,
                     )
 
+                if incremental_loading:
+                    data_items_pipeline_run_info[data_id] = {
+                        "run_info": PipelineRunCompleted(
+                            pipeline_run_id=pipeline_run_id,
+                            dataset_id=dataset.id,
+                            dataset_name=dataset.name,
+                        ),
+                        "data_id": data_id,
+                    }
+
+                    # Update pipeline status for Data element
+                    async with db_engine.get_async_session() as session:
+                        data_point = (
+                            await session.execute(select(Data).filter(Data.id == data_id))
+                        ).scalar_one_or_none()
+                        data_point.pipeline_status[pipeline_name] = "Completed"
+                        await session.merge(data_point)
+                        await session.commit()
+
+            except Exception as error:
+                # Temporarily swallow error and try to process rest of documents first, then re-raise error at end of data ingestion pipeline
+                ingestion_error = error
+                logger.error(
+                    f"Exception caught while processing data: {error}.\n Data processing failed for data item: {data_item}."
+                )
+                if incremental_loading:
+                    data_items_pipeline_run_info = {
+                        "run_info": PipelineRunErrored(
+                            pipeline_run_id=pipeline_run_id,
+                            payload=error,
+                            dataset_id=dataset.id,
+                            dataset_name=dataset.name,
+                        ),
+                        "data_id": data_id,
+                    }
+
+        # re-raise error found during data ingestion
+        if ingestion_error:
+            raise ingestion_error
+
         await log_pipeline_run_complete(
             pipeline_run_id, pipeline_id, pipeline_name, dataset_id, data
         )
@@ -102,6 +184,7 @@ async def run_tasks(
             pipeline_run_id=pipeline_run_id,
             dataset_id=dataset.id,
             dataset_name=dataset.name,
+            data_ingestion_info=data_items_pipeline_run_info,
         )
 
     except Exception as error:
@@ -114,6 +197,7 @@ async def run_tasks(
             payload=error,
             dataset_id=dataset.id,
             dataset_name=dataset.name,
+            data_ingestion_info=data_items_pipeline_run_info,
         )
 
         raise error

cognee/tasks/ingestion/ingest_data.py

@@ -9,6 +9,7 @@ from cognee.modules.data.models import Data
 from cognee.modules.users.models import User
 from cognee.modules.users.methods import get_default_user
 from cognee.modules.users.permissions.methods import get_specific_user_permission_datasets
+from cognee.modules.ingestion.methods import get_s3_fs, open_data_file
 from cognee.modules.data.methods import (
     get_authorized_existing_datasets,
     get_dataset_data,
@@ -18,9 +19,6 @@ from cognee.modules.data.methods import (
 from .save_data_item_to_storage import save_data_item_to_storage
 
 
-from cognee.api.v1.add.config import get_s3_config
-
-
 async def ingest_data(
     data: Any,
     dataset_name: str,
@@ -31,22 +29,7 @@ async def ingest_data(
     if not user:
         user = await get_default_user()
 
-    s3_config = get_s3_config()
+    fs = get_s3_fs()
-
-    fs = None
-    if s3_config.aws_access_key_id is not None and s3_config.aws_secret_access_key is not None:
-        import s3fs
-
-        fs = s3fs.S3FileSystem(
-            key=s3_config.aws_access_key_id, secret=s3_config.aws_secret_access_key, anon=False
-        )
-
-    def open_data_file(file_path: str):
-        if file_path.startswith("s3://"):
-            return fs.open(file_path, mode="rb")
-        else:
-            local_path = file_path.replace("file://", "")
-            return open(local_path, mode="rb")
 
     def get_external_metadata_dict(data_item: Union[BinaryIO, str, Any]) -> dict[str, Any]:
         if hasattr(data_item, "dict") and inspect.ismethod(getattr(data_item, "dict")):
@@ -95,7 +78,7 @@ async def ingest_data(
             file_path = await save_data_item_to_storage(data_item, dataset_name)
 
             # Ingest data and add metadata
-            with open_data_file(file_path) as file:
+            with open_data_file(file_path, s3fs=fs) as file:
                 classified_data = ingestion.classify(file, s3fs=fs)
 
                 # data_id is the hash of file contents + owner id to avoid duplicate data
@@ -148,6 +131,7 @@ async def ingest_data(
                         content_hash=file_metadata["content_hash"],
                         external_metadata=ext_metadata,
                         node_set=json.dumps(node_set) if node_set else None,
+                        pipeline_status={},
                         token_count=-1,
                     )
 

cognee/tasks/ingestion/resolve_data_directories.py

@@ -40,6 +40,9 @@ async def resolve_data_directories(
                     if include_subdirectories:
                         base_path = item if item.endswith("/") else item + "/"
                         s3_keys = fs.glob(base_path + "**")
+                        # If path is not directory attempt to add item directly
+                        if not s3_keys:
+                            s3_keys = fs.ls(item)
                     else:
                         s3_keys = fs.ls(item)
                     # Filter out keys that represent directories using fs.isdir

cognee/tasks/repo_processor/get_repo_file_dependencies.py

@@ -103,6 +103,9 @@ async def get_repo_file_dependencies(
           extraction of dependencies (default is False). (default False)
     """
 
+    if isinstance(repo_path, list) and len(repo_path) == 1:
+        repo_path = repo_path[0]
+
     if not os.path.exists(repo_path):
         raise FileNotFoundError(f"Repository path {repo_path} does not exist.")
 

cognee/tests/test_deduplication.py

@@ -25,8 +25,8 @@ async def test_deduplication():
     explanation_file_path2 = os.path.join(
         pathlib.Path(__file__).parent, "test_data/Natural_language_processing_copy.txt"
     )
-    await cognee.add([explanation_file_path], dataset_name)
+    await cognee.add([explanation_file_path], dataset_name, incremental_loading=False)
-    await cognee.add([explanation_file_path2], dataset_name2)
+    await cognee.add([explanation_file_path2], dataset_name2, incremental_loading=False)
 
     result = await relational_engine.get_all_data_from_table("data")
     assert len(result) == 1, "More than one data entity was found."