Merge remote-tracking branch 'origin/dev' into feature/cog-2516-refactor-cognify-pipeline

cognee-frontend/src/app/(graph)/GraphVisualization.tsx

@@ -1,6 +1,6 @@
 "use client";
 
-import { MutableRefObject, useEffect, useImperativeHandle, useRef, useState } from "react";
+import { MutableRefObject, useEffect, useImperativeHandle, useRef, useState, useCallback } from "react";
 import { forceCollide, forceManyBody } from "d3-force-3d";
 import ForceGraph, { ForceGraphMethods, GraphData, LinkObject, NodeObject } from "react-force-graph-2d";
 import { GraphControlsAPI } from "./GraphControls";
@@ -22,6 +22,45 @@ export default function GraphVisualization({ ref, data, graphControls }: GraphVi
   const nodeSize = 15;
   // const addNodeDistanceFromSourceNode = 15;
 
+  // State for tracking container dimensions
+  const [dimensions, setDimensions] = useState({ width: 0, height: 0 });
+  const containerRef = useRef<HTMLDivElement>(null);
+
+  // Handle resize
+  const handleResize = useCallback(() => {
+    if (containerRef.current) {
+      const { clientWidth, clientHeight } = containerRef.current;
+      setDimensions({ width: clientWidth, height: clientHeight });
+
+      // Trigger graph refresh after resize
+      if (graphRef.current) {
+        // Small delay to ensure DOM has updated
+        setTimeout(() => {
+          graphRef.current?.zoomToFit(1000,50);
+        }, 100);
+      }
+    }
+  }, []);
+
+  // Set up resize observer
+  useEffect(() => {
+    // Initial size calculation
+    handleResize();
+
+    // ResizeObserver 
+    const resizeObserver = new ResizeObserver(() => {
+      handleResize();
+    });
+
+    if (containerRef.current) {
+      resizeObserver.observe(containerRef.current);
+    }
+
+    return () => {
+      resizeObserver.disconnect();
+    };
+  }, [handleResize]);
+
   const handleNodeClick = (node: NodeObject) => {
     graphControls.current?.setSelectedNode(node);
     // ref.current?.d3ReheatSimulation()
@@ -174,10 +213,12 @@ export default function GraphVisualization({ ref, data, graphControls }: GraphVi
   }));
 
   return (
-    <div className="w-full h-full" id="graph-container">
+    <div ref={containerRef} className="w-full h-full" id="graph-container">
       {(data && typeof window !== "undefined") ? (
         <ForceGraph
           ref={graphRef}
+          width={dimensions.width}
+          height={dimensions.height}
           dagMode={graphShape as unknown as undefined}
           dagLevelDistance={300}
           onDagError={handleDagError}
@@ -201,6 +242,8 @@ export default function GraphVisualization({ ref, data, graphControls }: GraphVi
       ) : (
         <ForceGraph
           ref={graphRef}
+          width={dimensions.width}
+          height={dimensions.height}
           dagMode={graphShape as unknown as undefined}
           dagLevelDistance={100}
           graphData={{

cognee/api/v1/add/add.py

@@ -22,6 +22,7 @@ async def add(
     user: Optional[User] = None,
     node_set: Optional[List[str]] = None,
     dataset_id: Optional[UUID] = None,
+    incremental_loading: bool = True,
 ):
     """
     Add data to Cognee for knowledge graph processing.
@@ -178,6 +179,7 @@ async def add(
         dataset=authorized_dataset,
         user=user,
         pipeline_name="add_pipeline",
+        incremental_loading=incremental_loading,
     ):
         pipeline_run_info = run_info
 

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

@@ -12,6 +12,7 @@ from typing import BinaryIO, List, Literal, Optional, Union
 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.modules.pipelines.models import PipelineRunErrored
 from cognee.shared.logging_utils import get_logger
 
 logger = get_logger()
@@ -107,6 +108,9 @@ def get_add_router() -> APIRouter:
                     data, dataset_name=datasetName, user=user, dataset_id=datasetId
                 )
 
+                if isinstance(add_run, PipelineRunErrored):
+                    return JSONResponse(status_code=420, content=add_run.model_dump(mode="json"))
+
                 return add_run.model_dump() if add_run else None
         except Exception as error:
             return JSONResponse(status_code=409, content={"error": str(error)})

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

@@ -41,6 +41,7 @@ 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.
@@ -204,6 +205,7 @@ async def cognify(
             datasets=user_datasets,
             vector_db_config=vector_db_config,
             graph_db_config=graph_db_config,
+            incremental_loading=incremental_loading,
         )
     else:
         return await run_cognify_blocking(
@@ -212,6 +214,7 @@ async def cognify(
             datasets=user_datasets,
             vector_db_config=vector_db_config,
             graph_db_config=graph_db_config,
+            incremental_loading=incremental_loading,
         )
 
 
@@ -221,6 +224,7 @@ async def run_cognify_blocking(
     datasets,
     graph_db_config: dict = None,
     vector_db_config: dict = False,
+    incremental_loading: bool = True,
 ):
     total_run_info = {}
 
@@ -231,6 +235,7 @@ 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
@@ -246,6 +251,7 @@ async def run_cognify_as_background_process(
     datasets,
     graph_db_config: dict = None,
     vector_db_config: dict = False,
+    incremental_loading: bool = True,
 ):
     # Convert dataset to list if it's a string
     if isinstance(datasets, str):
@@ -256,6 +262,7 @@ async def run_cognify_as_background_process(
 
     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:
@@ -280,6 +287,7 @@ 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/api/v1/cognify/routers/get_cognify_router.py

@@ -16,7 +16,11 @@ from cognee.modules.graph.methods import get_formatted_graph_data
 from cognee.modules.users.get_user_manager import get_user_manager_context
 from cognee.infrastructure.databases.relational import get_relational_engine
 from cognee.modules.users.authentication.default.default_jwt_strategy import DefaultJWTStrategy
-from cognee.modules.pipelines.models.PipelineRunInfo import PipelineRunCompleted, PipelineRunInfo
+from cognee.modules.pipelines.models.PipelineRunInfo import (
+    PipelineRunCompleted,
+    PipelineRunInfo,
+    PipelineRunErrored,
+)
 from cognee.modules.pipelines.queues.pipeline_run_info_queues import (
     get_from_queue,
     initialize_queue,
@@ -105,6 +109,9 @@ def get_cognify_router() -> APIRouter:
                 datasets, user, run_in_background=payload.run_in_background
             )
 
+            # If any cognify run errored return JSONResponse with proper error status code
+            if any(isinstance(v, PipelineRunErrored) for v in cognify_run.values()):
+                return JSONResponse(status_code=420, content=cognify_run)
             return cognify_run
         except Exception as error:
             return JSONResponse(status_code=409, content={"error": str(error)})

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
@@ -21,7 +22,11 @@ class Data(Base):
     tenant_id = Column(UUID, index=True, nullable=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)
     data_size = Column(Integer, nullable=True)  # File size in bytes
     created_at = Column(DateTime(timezone=True), default=lambda: datetime.now(timezone.utc))

cognee/modules/data/processing/document_types/PdfDocument.py

@@ -5,7 +5,6 @@ from cognee.modules.chunking.Chunker import Chunker
 from cognee.infrastructure.files.utils.open_data_file import open_data_file
 
 from .Document import Document
-from .exceptions.exceptions import PyPdfInternalError
 
 logger = get_logger("PDFDocument")
 
@@ -17,18 +16,12 @@ class PdfDocument(Document):
         async with open_data_file(self.raw_data_location, mode="rb") as stream:
             logger.info(f"Reading PDF: {self.raw_data_location}")
 
-            try:
             file = PdfReader(stream, strict=False)
-            except Exception:
-                raise PyPdfInternalError()
 
             async def get_text():
-                try:
                 for page in file.pages:
                     page_text = page.extract_text()
                     yield page_text
-                except Exception:
-                    raise PyPdfInternalError()
 
             chunker = chunker_cls(self, get_text=get_text, max_chunk_size=max_chunk_size)
 

cognee/modules/engine/utils/generate_edge_id.py

@@ -0,0 +1,5 @@
+from uuid import NAMESPACE_OID, uuid5
+
+
+def generate_edge_id(edge_id: str) -> str:
+    return uuid5(NAMESPACE_OID, edge_id.lower().replace(" ", "_").replace("'", ""))

cognee/modules/graph/cognee_graph/CogneeGraph.py

@@ -170,28 +170,19 @@ class CogneeGraph(CogneeAbstractGraph):
 
             for edge in self.edges:
                 relationship_type = edge.attributes.get("relationship_type")
-                if relationship_type and relationship_type in embedding_map:
-                    edge.attributes["vector_distance"] = embedding_map[relationship_type]
+                distance = embedding_map.get(relationship_type, None)
+                if distance is not None:
+                    edge.attributes["vector_distance"] = distance
 
         except Exception as ex:
             logger.error(f"Error mapping vector distances to edges: {str(ex)}")
             raise ex
 
     async def calculate_top_triplet_importances(self, k: int) -> List:
-        min_heap = []
+        def score(edge):
+            n1 = edge.node1.attributes.get("vector_distance", 1)
+            n2 = edge.node2.attributes.get("vector_distance", 1)
+            e = edge.attributes.get("vector_distance", 1)
+            return n1 + n2 + e
 
-        for i, edge in enumerate(self.edges):
-            source_node = self.get_node(edge.node1.id)
-            target_node = self.get_node(edge.node2.id)
-
-            source_distance = source_node.attributes.get("vector_distance", 1) if source_node else 1
-            target_distance = target_node.attributes.get("vector_distance", 1) if target_node else 1
-            edge_distance = edge.attributes.get("vector_distance", 1)
-
-            total_distance = source_distance + target_distance + edge_distance
-
-            heapq.heappush(min_heap, (-total_distance, i, edge))
-            if len(min_heap) > k:
-                heapq.heappop(min_heap)
-
-        return [edge for _, _, edge in sorted(min_heap)]
+        return heapq.nsmallest(k, self.edges, key=score)

cognee/modules/pipelines/exceptions/__init__.py

@@ -0,0 +1 @@
+from .exceptions import PipelineRunFailedError

cognee/modules/pipelines/exceptions/exceptions.py

@@ -0,0 +1,12 @@
+from cognee.exceptions import CogneeApiError
+from fastapi import status
+
+
+class PipelineRunFailedError(CogneeApiError):
+    def __init__(
+        self,
+        message: str = "Pipeline run failed.",
+        name: str = "PipelineRunFailedError",
+        status_code: int = status.HTTP_422_UNPROCESSABLE_ENTITY,
+    ):
+        super().__init__(message, name, status_code)

cognee/modules/pipelines/models/DataItemStatus.py

@@ -0,0 +1,5 @@
+import enum
+
+
+class DataItemStatus(str, enum.Enum):
+    DATA_ITEM_PROCESSING_COMPLETED = "DATA_ITEM_PROCESSING_COMPLETED"

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[list] = None
 
     model_config = {
         "arbitrary_types_allowed": True,
@@ -30,6 +31,11 @@ class PipelineRunCompleted(PipelineRunInfo):
     pass
 
 
+class PipelineRunAlreadyCompleted(PipelineRunInfo):
+    status: str = "PipelineRunAlreadyCompleted"
+    pass
+
+
 class PipelineRunErrored(PipelineRunInfo):
     status: str = "PipelineRunErrored"
     pass

cognee/modules/pipelines/models/__init__.py

@@ -6,3 +6,4 @@ from .PipelineRunInfo import (
     PipelineRunCompleted,
     PipelineRunErrored,
 )
+from .DataItemStatus import DataItemStatus

cognee/modules/pipelines/operations/pipeline.py

@@ -46,6 +46,7 @@ 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.
@@ -100,6 +101,7 @@ async def cognee_pipeline(
             data=data,
             pipeline_name=pipeline_name,
             context={"dataset": dataset},
+            incremental_loading=incremental_loading,
         ):
             yield run_info
 
@@ -111,6 +113,7 @@ async def run_pipeline(
     data=None,
     pipeline_name: str = "custom_pipeline",
     context: dict = None,
+    incremental_loading=True,
 ):
     # Will only be used if ENABLE_BACKEND_ACCESS_CONTROL is set to True
     await set_database_global_context_variables(dataset.id, dataset.owner_id)
@@ -149,7 +152,9 @@ async def run_pipeline(
             )
             return
 
-    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_add_pipeline.py

@@ -1,3 +1,4 @@
+from typing import Optional
 from cognee.shared.logging_utils import get_logger
 from cognee.modules.users.models import User
 from cognee.modules.data.models import Dataset
@@ -17,6 +18,7 @@ async def run_add_pipeline(
     dataset: Dataset,
     user: User,
     pipeline_name: str = "add_pipeline",
+    incremental_loading: Optional[bool] = True,
 ):
     await set_database_global_context_variables(dataset.id, dataset.owner_id)
 
@@ -30,6 +32,7 @@ async def run_add_pipeline(
             "user": user,
             "dataset": dataset,
         },
+        incremental_loading,
     )
 
     async for pipeline_run_info in pipeline_run:

cognee/modules/pipelines/operations/run_tasks.py

@@ -1,21 +1,31 @@
 import os
-from uuid import UUID
-from typing import Any
-from functools import wraps
 
+import asyncio
+from uuid import UUID
+from typing import Any, Optional
+from functools import wraps
+from sqlalchemy import select
+
+import cognee.modules.ingestion as ingestion
 from cognee.infrastructure.databases.graph import get_graph_engine
 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.infrastructure.files.utils.open_data_file import 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.modules.pipelines.exceptions import PipelineRunFailedError
+from cognee.tasks.ingestion import save_data_item_to_storage, resolve_data_directories
 from cognee.modules.pipelines.models.PipelineRunInfo import (
     PipelineRunCompleted,
     PipelineRunErrored,
     PipelineRunStarted,
     PipelineRunYield,
+    PipelineRunAlreadyCompleted,
 )
+from cognee.modules.pipelines.models.DataItemStatus import DataItemStatus
 
 from cognee.modules.pipelines.operations import (
     log_pipeline_run_start,
@@ -56,34 +66,57 @@ async def run_tasks(
     user: User = None,
     pipeline_name: str = "unknown_pipeline",
     context: dict = None,
+    incremental_loading: Optional[bool] = True,
+):
+    async def _run_tasks_data_item_incremental(
+        data_item,
+        dataset,
+        tasks,
+        pipeline_name,
+        pipeline_id,
+        pipeline_run_id,
+        context,
+        user,
     ):
-    if not user:
-        user = await get_default_user()
-
-    # Get Dataset object
         db_engine = get_relational_engine()
+        # If incremental_loading of data is set to True don't process documents already processed by pipeline
+        # 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)
+            # Ingest data and add metadata
+            async with open_data_file(file_path) as file:
+                classified_data = ingestion.classify(file)
+                # 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:
-        from cognee.modules.data.models import Dataset
-
-        dataset = await session.get(Dataset, dataset_id)
-
-    pipeline_id = generate_pipeline_id(user.id, dataset.id, pipeline_name)
-
-    pipeline_run = await log_pipeline_run_start(pipeline_id, pipeline_name, dataset_id, data)
-
-    pipeline_run_id = pipeline_run.pipeline_run_id
-
-    yield PipelineRunStarted(
+            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, {}).get(str(dataset.id))
+                    == DataItemStatus.DATA_ITEM_PROCESSING_COMPLETED
+                ):
+                    yield {
+                        "run_info": PipelineRunAlreadyCompleted(
                             pipeline_run_id=pipeline_run_id,
                             dataset_id=dataset.id,
                             dataset_name=dataset.name,
-        payload=data,
-    )
+                        ),
+                        "data_id": data_id,
+                    }
+                    return
 
         try:
+            # Process data based on data_item and list of tasks
             async for result in run_tasks_with_telemetry(
                 tasks=tasks,
-            data=data,
+                data=[data_item],
                 user=user,
                 pipeline_name=pipeline_id,
                 context=context,
@@ -95,6 +128,171 @@ async def run_tasks(
                     payload=result,
                 )
 
+            # 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] = {
+                    str(dataset.id): DataItemStatus.DATA_ITEM_PROCESSING_COMPLETED
+                }
+                await session.merge(data_point)
+                await session.commit()
+
+            yield {
+                "run_info": PipelineRunCompleted(
+                    pipeline_run_id=pipeline_run_id,
+                    dataset_id=dataset.id,
+                    dataset_name=dataset.name,
+                ),
+                "data_id": data_id,
+            }
+
+        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
+            logger.error(
+                f"Exception caught while processing data: {error}.\n Data processing failed for data item: {data_item}."
+            )
+            yield {
+                "run_info": PipelineRunErrored(
+                    pipeline_run_id=pipeline_run_id,
+                    payload=repr(error),
+                    dataset_id=dataset.id,
+                    dataset_name=dataset.name,
+                ),
+                "data_id": data_id,
+            }
+
+    async def _run_tasks_data_item_regular(
+        data_item,
+        dataset,
+        tasks,
+        pipeline_id,
+        pipeline_run_id,
+        context,
+        user,
+    ):
+        # Process data based on data_item and list of tasks
+        async for result in run_tasks_with_telemetry(
+            tasks=tasks,
+            data=[data_item],
+            user=user,
+            pipeline_name=pipeline_id,
+            context=context,
+        ):
+            yield PipelineRunYield(
+                pipeline_run_id=pipeline_run_id,
+                dataset_id=dataset.id,
+                dataset_name=dataset.name,
+                payload=result,
+            )
+
+        yield {
+            "run_info": PipelineRunCompleted(
+                pipeline_run_id=pipeline_run_id,
+                dataset_id=dataset.id,
+                dataset_name=dataset.name,
+            )
+        }
+
+    async def _run_tasks_data_item(
+        data_item,
+        dataset,
+        tasks,
+        pipeline_name,
+        pipeline_id,
+        pipeline_run_id,
+        context,
+        user,
+        incremental_loading,
+    ):
+        # Go through async generator and return data item processing result. Result can be PipelineRunAlreadyCompleted when data item is skipped,
+        # PipelineRunCompleted when processing was successful and PipelineRunErrored if there were issues
+        result = None
+        if incremental_loading:
+            async for result in _run_tasks_data_item_incremental(
+                data_item=data_item,
+                dataset=dataset,
+                tasks=tasks,
+                pipeline_name=pipeline_name,
+                pipeline_id=pipeline_id,
+                pipeline_run_id=pipeline_run_id,
+                context=context,
+                user=user,
+            ):
+                pass
+        else:
+            async for result in _run_tasks_data_item_regular(
+                data_item=data_item,
+                dataset=dataset,
+                tasks=tasks,
+                pipeline_id=pipeline_id,
+                pipeline_run_id=pipeline_run_id,
+                context=context,
+                user=user,
+            ):
+                pass
+
+        return result
+
+    if not user:
+        user = await get_default_user()
+
+    # Get Dataset object
+    db_engine = get_relational_engine()
+    async with db_engine.get_async_session() as session:
+        from cognee.modules.data.models import Dataset
+
+        dataset = await session.get(Dataset, dataset_id)
+
+    pipeline_id = generate_pipeline_id(user.id, dataset.id, pipeline_name)
+    pipeline_run = await log_pipeline_run_start(pipeline_id, pipeline_name, dataset_id, data)
+    pipeline_run_id = pipeline_run.pipeline_run_id
+
+    yield PipelineRunStarted(
+        pipeline_run_id=pipeline_run_id,
+        dataset_id=dataset.id,
+        dataset_name=dataset.name,
+        payload=data,
+    )
+
+    try:
+        if not isinstance(data, list):
+            data = [data]
+
+        if incremental_loading:
+            data = await resolve_data_directories(data)
+
+        # Create async tasks per data item that will run the pipeline for the data item
+        data_item_tasks = [
+            asyncio.create_task(
+                _run_tasks_data_item(
+                    data_item,
+                    dataset,
+                    tasks,
+                    pipeline_name,
+                    pipeline_id,
+                    pipeline_run_id,
+                    context,
+                    user,
+                    incremental_loading,
+                )
+            )
+            for data_item in data
+        ]
+        results = await asyncio.gather(*data_item_tasks)
+        # Remove skipped data items from results
+        results = [result for result in results if result]
+
+        # If any data item could not be processed propagate error
+        errored_results = [
+            result for result in results if isinstance(result["run_info"], PipelineRunErrored)
+        ]
+        if errored_results:
+            raise PipelineRunFailedError(
+                message="Pipeline run failed. Data item could not be processed."
+            )
+
         await log_pipeline_run_complete(
             pipeline_run_id, pipeline_id, pipeline_name, dataset_id, data
         )
@@ -103,6 +301,7 @@ async def run_tasks(
             pipeline_run_id=pipeline_run_id,
             dataset_id=dataset.id,
             dataset_name=dataset.name,
+            data_ingestion_info=results,
         )
 
         graph_engine = await get_graph_engine()
@@ -120,9 +319,14 @@ async def run_tasks(
 
         yield PipelineRunErrored(
             pipeline_run_id=pipeline_run_id,
-            payload=error,
+            payload=repr(error),
             dataset_id=dataset.id,
             dataset_name=dataset.name,
+            data_ingestion_info=locals().get(
+                "results"
+            ),  # Returns results if they exist or returns None
         )
 
+        # In case of error during incremental loading of data just let the user know the pipeline Errored, don't raise error
+        if not isinstance(error, PipelineRunFailedError):
             raise error

cognee/tasks/documents/extract_chunks_from_documents.py

@@ -8,7 +8,6 @@ from cognee.modules.data.models import Data
 from cognee.infrastructure.databases.relational import get_relational_engine
 from cognee.modules.chunking.TextChunker import TextChunker
 from cognee.modules.chunking.Chunker import Chunker
-from cognee.modules.data.processing.document_types.exceptions.exceptions import PyPdfInternalError
 
 
 async def update_document_token_count(document_id: UUID, token_count: int) -> None:
@@ -40,7 +39,7 @@ async def extract_chunks_from_documents(
     """
     for document in documents:
         document_token_count = 0
-        try:
+
         async for document_chunk in document.read(
             max_chunk_size=max_chunk_size, chunker_cls=chunker
         ):
@@ -49,6 +48,5 @@ async def extract_chunks_from_documents(
             yield document_chunk
 
         await update_document_token_count(document.id, document_token_count)
-        except PyPdfInternalError:
-            pass
+
         # todo rita

cognee/tasks/ingestion/ingest_data.py

@@ -5,12 +5,12 @@ from uuid import UUID
 from typing import Union, BinaryIO, Any, List, Optional
 
 import cognee.modules.ingestion as ingestion
-from cognee.infrastructure.files.utils.open_data_file import open_data_file
 from cognee.infrastructure.databases.relational import get_relational_engine
 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.infrastructure.files.utils.open_data_file import open_data_file
 from cognee.modules.data.methods import (
     get_authorized_existing_datasets,
     get_dataset_data,
@@ -134,6 +134,7 @@ async def ingest_data(
                         node_set=json.dumps(node_set) if node_set else None,
                         data_size=file_metadata["file_size"],
                         tenant_id=user.tenant_id if user.tenant_id 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/tasks/storage/index_graph_edges.py

@@ -1,3 +1,4 @@
+from cognee.modules.engine.utils.generate_edge_id import generate_edge_id
 from cognee.shared.logging_utils import get_logger, ERROR
 from collections import Counter
 
@@ -49,7 +50,9 @@ async def index_graph_edges(batch_size: int = 1024):
     )
 
     for text, count in edge_types.items():
-        edge = EdgeType(relationship_name=text, number_of_edges=count)
+        edge = EdgeType(
+            id=generate_edge_id(edge_id=text), relationship_name=text, number_of_edges=count
+        )
         data_point_type = type(edge)
 
         for field_name in edge.metadata["index_fields"]:

cognee/tests/test_deduplication.py

@@ -26,8 +26,8 @@ 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_path2], dataset_name2)
+    await cognee.add([explanation_file_path], dataset_name, incremental_loading=False)
+    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."