fix chunk deletion

llama_stack/providers/inline/vector_io/faiss/faiss.py

@@ -33,6 +33,7 @@ from llama_stack.providers.utils.kvstore import kvstore_impl
 from llama_stack.providers.utils.kvstore.api import KVStore
 from llama_stack.providers.utils.memory.openai_vector_store_mixin import OpenAIVectorStoreMixin
 from llama_stack.providers.utils.memory.vector_store import (
+    ChunkForDeletion,
     EmbeddingIndex,
     VectorDBWithIndex,
 )
@@ -128,11 +129,12 @@ class FaissIndex(EmbeddingIndex):
         # Save updated index
         await self._save_index()
 
-    async def delete_chunk(self, chunk_id: str) -> None:
+    async def delete_chunks(self, chunks_for_deletion: list[ChunkForDeletion]) -> None:
-        if chunk_id not in self.chunk_ids:
+        chunk_ids = [c.chunk_id for c in chunks_for_deletion]
+        if not set(chunk_ids).issubset(self.chunk_ids):
             return
 
-        async with self.chunk_id_lock:
+        def remove_chunk(chunk_id: str):
             index = self.chunk_ids.index(chunk_id)
             self.index.remove_ids(np.array([index]))
 
@@ -146,6 +148,10 @@ class FaissIndex(EmbeddingIndex):
             self.chunk_by_index = new_chunk_by_index
             self.chunk_ids.pop(index)
 
+        async with self.chunk_id_lock:
+            for chunk_id in chunk_ids:
+                remove_chunk(chunk_id)
+
         await self._save_index()
 
     async def query_vector(
@@ -297,8 +303,7 @@ class FaissVectorIOAdapter(OpenAIVectorStoreMixin, VectorIO, VectorDBsProtocolPr
 
         return await index.query_chunks(query, params)
 
-    async def delete_chunks(self, store_id: str, chunk_ids: list[str]) -> None:
+    async def delete_chunks(self, store_id: str, chunks_for_deletion: list[ChunkForDeletion]) -> None:
-        """Delete a chunk from a faiss index"""
+        """Delete chunks from a faiss index"""
         faiss_index = self.cache[store_id].index
-        for chunk_id in chunk_ids:
+        await faiss_index.delete_chunks(chunks_for_deletion)
-            await faiss_index.delete_chunk(chunk_id)

llama_stack/providers/inline/vector_io/sqlite_vec/sqlite_vec.py

@@ -31,6 +31,7 @@ from llama_stack.providers.utils.memory.openai_vector_store_mixin import OpenAIV
 from llama_stack.providers.utils.memory.vector_store import (
     RERANKER_TYPE_RRF,
     RERANKER_TYPE_WEIGHTED,
+    ChunkForDeletion,
     EmbeddingIndex,
     VectorDBWithIndex,
 )
@@ -426,34 +427,35 @@ class SQLiteVecIndex(EmbeddingIndex):
 
         return QueryChunksResponse(chunks=chunks, scores=scores)
 
-    async def delete_chunk(self, chunk_id: str) -> None:
+    async def delete_chunks(self, chunks_for_deletion: list[ChunkForDeletion]) -> None:
         """Remove a chunk from the SQLite vector store."""
+        chunk_ids = [c.chunk_id for c in chunks_for_deletion]
 
-        def _delete_chunk():
+        def _delete_chunks():
             connection = _create_sqlite_connection(self.db_path)
             cur = connection.cursor()
             try:
                 cur.execute("BEGIN TRANSACTION")
 
                 # Delete from metadata table
-                cur.execute(f"DELETE FROM {self.metadata_table} WHERE id = ?", (chunk_id,))
+                cur.execute(f"DELETE FROM {self.metadata_table} WHERE id = ANY(?)", (chunk_ids,))
 
                 # Delete from vector table
-                cur.execute(f"DELETE FROM {self.vector_table} WHERE id = ?", (chunk_id,))
+                cur.execute(f"DELETE FROM {self.vector_table} WHERE id = ANY(?)", (chunk_ids,))
 
                 # Delete from FTS table
-                cur.execute(f"DELETE FROM {self.fts_table} WHERE id = ?", (chunk_id,))
+                cur.execute(f"DELETE FROM {self.fts_table} WHERE id = ANY(?)", (chunk_ids,))
 
                 connection.commit()
             except Exception as e:
                 connection.rollback()
-                logger.error(f"Error deleting chunk {chunk_id}: {e}")
+                logger.error(f"Error deleting chunks: {e}")
                 raise
             finally:
                 cur.close()
                 connection.close()
 
-        await asyncio.to_thread(_delete_chunk)
+        await asyncio.to_thread(_delete_chunks)
 
 
 class SQLiteVecVectorIOAdapter(OpenAIVectorStoreMixin, VectorIO, VectorDBsProtocolPrivate):
@@ -551,12 +553,10 @@ class SQLiteVecVectorIOAdapter(OpenAIVectorStoreMixin, VectorIO, VectorDBsProtoc
             raise VectorStoreNotFoundError(vector_db_id)
         return await index.query_chunks(query, params)
 
-    async def delete_chunks(self, store_id: str, chunk_ids: list[str]) -> None:
+    async def delete_chunks(self, store_id: str, chunks_for_deletion: list[ChunkForDeletion]) -> None:
-        """Delete a chunk from a sqlite_vec index."""
+        """Delete chunks from a sqlite_vec index."""
         index = await self._get_and_cache_vector_db_index(store_id)
         if not index:
             raise VectorStoreNotFoundError(store_id)
 
-        for chunk_id in chunk_ids:
+        await index.index.delete_chunks(chunks_for_deletion)
-            # Use the index's delete_chunk method
-            await index.index.delete_chunk(chunk_id)

llama_stack/providers/registry/vector_io.py

@@ -342,6 +342,7 @@ See [Chroma's documentation](https://docs.trychroma.com/docs/overview/introducti
 """,
             ),
             api_dependencies=[Api.inference],
+            optional_api_dependencies=[Api.files],
         ),
         InlineProviderSpec(
             api=Api.vector_io,
@@ -350,6 +351,7 @@ See [Chroma's documentation](https://docs.trychroma.com/docs/overview/introducti
             module="llama_stack.providers.inline.vector_io.chroma",
             config_class="llama_stack.providers.inline.vector_io.chroma.ChromaVectorIOConfig",
             api_dependencies=[Api.inference],
+            optional_api_dependencies=[Api.files],
             description="""
 [Chroma](https://www.trychroma.com/) is an inline and remote vector
 database provider for Llama Stack. It allows you to store and query vectors directly within a Chroma database.
@@ -731,6 +733,7 @@ For more details on TLS configuration, refer to the [TLS setup guide](https://mi
 """,
             ),
             api_dependencies=[Api.inference],
+            optional_api_dependencies=[Api.files],
         ),
         InlineProviderSpec(
             api=Api.vector_io,

llama_stack/providers/remote/vector_io/chroma/chroma.py

@@ -26,6 +26,7 @@ from llama_stack.providers.utils.kvstore import kvstore_impl
 from llama_stack.providers.utils.kvstore.api import KVStore
 from llama_stack.providers.utils.memory.openai_vector_store_mixin import OpenAIVectorStoreMixin
 from llama_stack.providers.utils.memory.vector_store import (
+    ChunkForDeletion,
     EmbeddingIndex,
     VectorDBWithIndex,
 )
@@ -115,8 +116,10 @@ class ChromaIndex(EmbeddingIndex):
     ) -> QueryChunksResponse:
         raise NotImplementedError("Keyword search is not supported in Chroma")
 
-    async def delete_chunk(self, chunk_id: str) -> None:
+    async def delete_chunks(self, chunks_for_deletion: list[ChunkForDeletion]) -> None:
-        raise NotImplementedError("delete_chunk is not supported in Chroma")
+        """Delete a single chunk from the Chroma collection by its ID."""
+        ids = [f"{chunk.document_id}:{chunk.chunk_id}" for chunk in chunks_for_deletion]
+        await maybe_await(self.collection.delete(ids=ids))
 
     async def query_hybrid(
         self,
@@ -144,6 +147,7 @@ class ChromaVectorIOAdapter(OpenAIVectorStoreMixin, VectorIO, VectorDBsProtocolP
         self.cache = {}
         self.kvstore: KVStore | None = None
         self.vector_db_store = None
+        self.files_api = files_api
 
     async def initialize(self) -> None:
         self.kvstore = await kvstore_impl(self.config.kvstore)
@@ -227,5 +231,10 @@ class ChromaVectorIOAdapter(OpenAIVectorStoreMixin, VectorIO, VectorDBsProtocolP
         self.cache[vector_db_id] = index
         return index
 
-    async def delete_chunks(self, store_id: str, chunk_ids: list[str]) -> None:
+    async def delete_chunks(self, store_id: str, chunks_for_deletion: list[ChunkForDeletion]) -> None:
-        raise NotImplementedError("OpenAI Vector Stores API is not supported in Chroma")
+        """Delete chunks from a Chroma vector store."""
+        index = await self._get_and_cache_vector_db_index(store_id)
+        if not index:
+            raise ValueError(f"Vector DB {store_id} not found")
+
+        await index.index.delete_chunks(chunks_for_deletion)

llama_stack/providers/remote/vector_io/milvus/milvus.py

@@ -28,6 +28,7 @@ from llama_stack.providers.utils.kvstore.api import KVStore
 from llama_stack.providers.utils.memory.openai_vector_store_mixin import OpenAIVectorStoreMixin
 from llama_stack.providers.utils.memory.vector_store import (
     RERANKER_TYPE_WEIGHTED,
+    ChunkForDeletion,
     EmbeddingIndex,
     VectorDBWithIndex,
 )
@@ -287,14 +288,15 @@ class MilvusIndex(EmbeddingIndex):
 
         return QueryChunksResponse(chunks=filtered_chunks, scores=filtered_scores)
 
-    async def delete_chunk(self, chunk_id: str) -> None:
+    async def delete_chunks(self, chunks_for_deletion: list[ChunkForDeletion]) -> None:
         """Remove a chunk from the Milvus collection."""
+        chunk_ids_str = ",".join(f"'{c.chunk_id}'" for c in chunks_for_deletion)
         try:
             await asyncio.to_thread(
-                self.client.delete, collection_name=self.collection_name, filter=f'chunk_id == "{chunk_id}"'
+                self.client.delete, collection_name=self.collection_name, filter=f"chunk_id IN [{chunk_ids_str}]"
             )
         except Exception as e:
-            logger.error(f"Error deleting chunk {chunk_id} from Milvus collection {self.collection_name}: {e}")
+            logger.error(f"Error deleting chunks from Milvus collection {self.collection_name}: {e}")
             raise
 
 
@@ -420,12 +422,10 @@ class MilvusVectorIOAdapter(OpenAIVectorStoreMixin, VectorIO, VectorDBsProtocolP
 
         return await index.query_chunks(query, params)
 
-    async def delete_chunks(self, store_id: str, chunk_ids: list[str]) -> None:
+    async def delete_chunks(self, store_id: str, chunks_for_deletion: list[ChunkForDeletion]) -> None:
         """Delete a chunk from a milvus vector store."""
         index = await self._get_and_cache_vector_db_index(store_id)
         if not index:
             raise VectorStoreNotFoundError(store_id)
 
-        for chunk_id in chunk_ids:
+        await index.index.delete_chunks(chunks_for_deletion)
-            # Use the index's delete_chunk method
-            await index.index.delete_chunk(chunk_id)

llama_stack/providers/remote/vector_io/pgvector/pgvector.py

@@ -27,6 +27,7 @@ from llama_stack.providers.utils.kvstore import kvstore_impl
 from llama_stack.providers.utils.kvstore.api import KVStore
 from llama_stack.providers.utils.memory.openai_vector_store_mixin import OpenAIVectorStoreMixin
 from llama_stack.providers.utils.memory.vector_store import (
+    ChunkForDeletion,
     EmbeddingIndex,
     VectorDBWithIndex,
 )
@@ -163,10 +164,11 @@ class PGVectorIndex(EmbeddingIndex):
         with self.conn.cursor(cursor_factory=psycopg2.extras.DictCursor) as cur:
             cur.execute(f"DROP TABLE IF EXISTS {self.table_name}")
 
-    async def delete_chunk(self, chunk_id: str) -> None:
+    async def delete_chunks(self, chunks_for_deletion: list[ChunkForDeletion]) -> None:
         """Remove a chunk from the PostgreSQL table."""
+        chunk_ids = [c.chunk_id for c in chunks_for_deletion]
         with self.conn.cursor(cursor_factory=psycopg2.extras.DictCursor) as cur:
-            cur.execute(f"DELETE FROM {self.table_name} WHERE id = %s", (chunk_id,))
+            cur.execute(f"DELETE FROM {self.table_name} WHERE id = ANY(%s)", (chunk_ids,))
 
 
 class PGVectorVectorIOAdapter(OpenAIVectorStoreMixin, VectorIO, VectorDBsProtocolPrivate):
@@ -275,12 +277,10 @@ class PGVectorVectorIOAdapter(OpenAIVectorStoreMixin, VectorIO, VectorDBsProtoco
         self.cache[vector_db_id] = VectorDBWithIndex(vector_db, index, self.inference_api)
         return self.cache[vector_db_id]
 
-    async def delete_chunks(self, store_id: str, chunk_ids: list[str]) -> None:
+    async def delete_chunks(self, store_id: str, chunks_for_deletion: list[ChunkForDeletion]) -> None:
         """Delete a chunk from a PostgreSQL vector store."""
         index = await self._get_and_cache_vector_db_index(store_id)
         if not index:
             raise VectorStoreNotFoundError(store_id)
 
-        for chunk_id in chunk_ids:
+        await index.index.delete_chunks(chunks_for_deletion)
-            # Use the index's delete_chunk method
-            await index.index.delete_chunk(chunk_id)

llama_stack/providers/remote/vector_io/qdrant/qdrant.py

@@ -29,6 +29,7 @@ from llama_stack.providers.inline.vector_io.qdrant import QdrantVectorIOConfig a
 from llama_stack.providers.utils.kvstore import KVStore, kvstore_impl
 from llama_stack.providers.utils.memory.openai_vector_store_mixin import OpenAIVectorStoreMixin
 from llama_stack.providers.utils.memory.vector_store import (
+    ChunkForDeletion,
     EmbeddingIndex,
     VectorDBWithIndex,
 )
@@ -88,15 +89,16 @@ class QdrantIndex(EmbeddingIndex):
 
         await self.client.upsert(collection_name=self.collection_name, points=points)
 
-    async def delete_chunk(self, chunk_id: str) -> None:
+    async def delete_chunks(self, chunks_for_deletion: list[ChunkForDeletion]) -> None:
         """Remove a chunk from the Qdrant collection."""
+        chunk_ids = [convert_id(c.chunk_id) for c in chunks_for_deletion]
         try:
             await self.client.delete(
                 collection_name=self.collection_name,
-                points_selector=models.PointIdsList(points=[convert_id(chunk_id)]),
+                points_selector=models.PointIdsList(points=chunk_ids),
             )
         except Exception as e:
-            log.error(f"Error deleting chunk {chunk_id} from Qdrant collection {self.collection_name}: {e}")
+            log.error(f"Error deleting chunks from Qdrant collection {self.collection_name}: {e}")
             raise
 
     async def query_vector(self, embedding: NDArray, k: int, score_threshold: float) -> QueryChunksResponse:
@@ -266,10 +268,10 @@ class QdrantVectorIOAdapter(OpenAIVectorStoreMixin, VectorIO, VectorDBsProtocolP
         async with self._qdrant_lock:
             await super().openai_attach_file_to_vector_store(vector_store_id, file_id, attributes, chunking_strategy)
 
-    async def delete_chunks(self, store_id: str, chunk_ids: list[str]) -> None:
+    async def delete_chunks(self, store_id: str, chunks_for_deletion: list[ChunkForDeletion]) -> None:
         """Delete chunks from a Qdrant vector store."""
         index = await self._get_and_cache_vector_db_index(store_id)
         if not index:
             raise ValueError(f"Vector DB {store_id} not found")
-        for chunk_id in chunk_ids:
+
-            await index.index.delete_chunk(chunk_id)
+        await index.index.delete_chunks(chunks_for_deletion)

llama_stack/providers/utils/memory/openai_vector_store_mixin.py

@@ -38,7 +38,11 @@ from llama_stack.apis.vector_io import (
     VectorStoreSearchResponsePage,
 )
 from llama_stack.providers.utils.kvstore.api import KVStore
-from llama_stack.providers.utils.memory.vector_store import content_from_data_and_mime_type, make_overlapped_chunks
+from llama_stack.providers.utils.memory.vector_store import (
+    ChunkForDeletion,
+    content_from_data_and_mime_type,
+    make_overlapped_chunks,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -154,8 +158,8 @@ class OpenAIVectorStoreMixin(ABC):
         self.openai_vector_stores = await self._load_openai_vector_stores()
 
     @abstractmethod
-    async def delete_chunks(self, store_id: str, chunk_ids: list[str]) -> None:
+    async def delete_chunks(self, store_id: str, chunks_for_deletion: list[ChunkForDeletion]) -> None:
-        """Delete a chunk from a vector store."""
+        """Delete chunks from a vector store."""
         pass
 
     @abstractmethod
@@ -767,7 +771,21 @@ class OpenAIVectorStoreMixin(ABC):
 
         dict_chunks = await self._load_openai_vector_store_file_contents(vector_store_id, file_id)
         chunks = [Chunk.model_validate(c) for c in dict_chunks]
-        await self.delete_chunks(vector_store_id, [str(c.chunk_id) for c in chunks if c.chunk_id])
+
+        # Create ChunkForDeletion objects with both chunk_id and document_id
+        chunks_for_deletion = []
+        for c in chunks:
+            if c.chunk_id:
+                document_id = c.metadata.get("document_id") or (
+                    c.chunk_metadata.document_id if c.chunk_metadata else None
+                )
+                if document_id:
+                    chunks_for_deletion.append(ChunkForDeletion(chunk_id=str(c.chunk_id), document_id=document_id))
+                else:
+                    logger.warning(f"Chunk {c.chunk_id} has no document_id, skipping deletion")
+
+        if chunks_for_deletion:
+            await self.delete_chunks(vector_store_id, chunks_for_deletion)
 
         store_info = self.openai_vector_stores[vector_store_id].copy()
 

llama_stack/providers/utils/memory/vector_store.py

@@ -16,6 +16,7 @@ from urllib.parse import unquote
 import httpx
 import numpy as np
 from numpy.typing import NDArray
+from pydantic import BaseModel
 
 from llama_stack.apis.common.content_types import (
     URL,
@@ -34,6 +35,18 @@ from llama_stack.providers.utils.vector_io.vector_utils import generate_chunk_id
 
 log = logging.getLogger(__name__)
 
+
+class ChunkForDeletion(BaseModel):
+    """Information needed to delete a chunk from a vector store.
+
+    :param chunk_id: The ID of the chunk to delete
+    :param document_id: The ID of the document this chunk belongs to
+    """
+
+    chunk_id: str
+    document_id: str
+
+
 # Constants for reranker types
 RERANKER_TYPE_RRF = "rrf"
 RERANKER_TYPE_WEIGHTED = "weighted"
@@ -232,7 +245,7 @@ class EmbeddingIndex(ABC):
         raise NotImplementedError()
 
     @abstractmethod
-    async def delete_chunk(self, chunk_id: str):
+    async def delete_chunks(self, chunks_for_deletion: list[ChunkForDeletion]):
         raise NotImplementedError()
 
     @abstractmethod

tests/integration/vector_io/test_openai_vector_stores.py

@@ -588,16 +588,19 @@ def test_openai_vector_store_list_files(compat_client_with_empty_stores, client_
             file_buffer.name = f"openai_test_{i}.txt"
             file = compat_client.files.create(file=file_buffer, purpose="assistants")
 
-        compat_client.vector_stores.files.create(
+        response = compat_client.vector_stores.files.create(
             vector_store_id=vector_store.id,
             file_id=file.id,
         )
+        assert response.status == "completed", (
+            f"Failed to attach file {file.id} to vector store {vector_store.id}: {response=}"
+        )
         file_ids.append(file.id)
 
     files_list = compat_client.vector_stores.files.list(vector_store_id=vector_store.id)
     assert files_list
     assert files_list.object == "list"
-    assert files_list.data
+    assert files_list.data is not None
     assert not files_list.has_more
     assert len(files_list.data) == 3
     assert set(file_ids) == {file.id for file in files_list.data}