feat: implement chunk deletion for vector stores

Add support for deleting individual chunks from vector stores

- Add abstract delete_chunk() method to EmbeddingIndex base class
- Implement chunk deletion for Faiss provider with index tracking
- Add chunk_ids list to maintain chunk order in Faiss index
- Integrate chunk deletion into OpenAI vector store file deletion flow
- Add placeholder implementations for SQLite and Milvus providers

Closes: #2477

Signed-off-by: Derek Higgins <derekh@redhat.com>

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

@@ -55,6 +55,11 @@ class FaissIndex(EmbeddingIndex):
         self.kvstore = kvstore
         self.bank_id = bank_id
 
+        # A list of chunk id's in the same order as they are in the index,
+        # must be updated when chunks are added or removed
+        self.chunk_id_lock = asyncio.Lock()
+        self.chunk_ids: list[Any] = []
+
     @classmethod
     async def create(cls, dimension: int, kvstore: KVStore | None = None, bank_id: str | None = None):
         instance = cls(dimension, kvstore, bank_id)
@@ -75,6 +80,7 @@ class FaissIndex(EmbeddingIndex):
             buffer = io.BytesIO(base64.b64decode(data["faiss_index"]))
             try:
                 self.index = faiss.deserialize_index(np.load(buffer, allow_pickle=False))
+                self.chunk_ids = [chunk.chunk_id for chunk in self.chunk_by_index.values()]
             except Exception as e:
                 logger.debug(e, exc_info=True)
                 raise ValueError(
@@ -114,11 +120,33 @@ class FaissIndex(EmbeddingIndex):
         for i, chunk in enumerate(chunks):
             self.chunk_by_index[indexlen + i] = chunk
 
+        async with self.chunk_id_lock:
             self.index.add(np.array(embeddings).astype(np.float32))
+            self.chunk_ids.extend([chunk.chunk_id for chunk in chunks])
 
         # Save updated index
         await self._save_index()
 
+    async def delete_chunk(self, chunk_id: str) -> None:
+        if chunk_id not in self.chunk_ids:
+            return
+
+        async with self.chunk_id_lock:
+            index = self.chunk_ids.index(chunk_id)
+            self.index.remove_ids(np.array([index]))
+
+            new_chunk_by_index = {}
+            for idx, chunk in self.chunk_by_index.items():
+                # Shift all chunks after the removed chunk to the left
+                if idx > index:
+                    new_chunk_by_index[idx - 1] = chunk
+                else:
+                    new_chunk_by_index[idx] = chunk
+            self.chunk_by_index = new_chunk_by_index
+            self.chunk_ids.pop(index)
+
+        await self._save_index()
+
     async def query_vector(
         self,
         embedding: NDArray,
@@ -260,3 +288,8 @@ class FaissVectorIOAdapter(OpenAIVectorStoreMixin, VectorIO, VectorDBsProtocolPr
             raise ValueError(f"Vector DB {vector_db_id} not found")
 
         return await index.query_chunks(query, params)
+
+    async def _delete_openai_chunk_from_vector_store(self, store_id: str, chunk_id: str) -> None:
+        """Delete a chunk from a faiss index"""
+        faiss_index = self.cache[store_id].index
+        await faiss_index.delete_chunk(chunk_id)

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

@@ -520,3 +520,7 @@ class SQLiteVecVectorIOAdapter(OpenAIVectorStoreMixin, VectorIO, VectorDBsProtoc
         if not index:
             raise ValueError(f"Vector DB {vector_db_id} not found")
         return await index.query_chunks(query, params)
+
+    async def _delete_openai_chunk_from_vector_store(self, store_id: str, chunk_id: str) -> None:
+        """Delete a chunk from a sqlite_vec index."""
+        pass  # TODO

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

@@ -369,3 +369,7 @@ class MilvusVectorIOAdapter(OpenAIVectorStoreMixin, VectorIO, VectorDBsProtocolP
                 )
 
         return await index.query_chunks(query, params)
+
+    async def _delete_openai_chunk_from_vector_store(self, store_id: str, chunk_id: str) -> None:
+        """Delete a chunk from a milvus vector store."""
+        pass  # TODO

llama_stack/providers/utils/memory/openai_vector_store_mixin.py

@@ -152,6 +152,11 @@ class OpenAIVectorStoreMixin(ABC):
         """Load existing OpenAI vector stores into the in-memory cache."""
         self.openai_vector_stores = await self._load_openai_vector_stores()
 
+    @abstractmethod
+    async def _delete_openai_chunk_from_vector_store(self, store_id: str, chunk_id: str) -> None:
+        """Delete a chunk from a vector store."""
+        pass
+
     @abstractmethod
     async def register_vector_db(self, vector_db: VectorDB) -> None:
         """Register a vector database (provider-specific implementation)."""
@@ -763,6 +768,12 @@ class OpenAIVectorStoreMixin(ABC):
         if vector_store_id not in self.openai_vector_stores:
             raise ValueError(f"Vector store {vector_store_id} not found")
 
+        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]
+        for c in chunks:
+            if c.chunk_id:
+                await self._delete_openai_chunk_from_vector_store(vector_store_id, str(c.chunk_id))
+
         store_info = self.openai_vector_stores[vector_store_id].copy()
 
         file = await self.openai_retrieve_vector_store_file(vector_store_id, file_id)

llama_stack/providers/utils/memory/vector_store.py

@@ -231,6 +231,10 @@ class EmbeddingIndex(ABC):
     async def add_chunks(self, chunks: list[Chunk], embeddings: NDArray):
         raise NotImplementedError()
 
+    @abstractmethod
+    async def delete_chunk(self, chunk_id: str):
+        raise NotImplementedError()
+
     @abstractmethod
     async def query_vector(self, embedding: NDArray, k: int, score_threshold: float) -> QueryChunksResponse:
         raise NotImplementedError()