feat: implement chunk deletion for vector stores (#2701)

Add support for deleting individual chunks from vector stores

- Add abstract remove_chunk() method to EmbeddingIndex base class
- Implement chunk deletion for Faiss provider, SQLite Vec, Milvus,
PGVector
- Placeholder implementations with NotImplementedError for
Chroma/Qdrant/Weaviate
- Integrate chunk deletion into OpenAI vector store file deletion flow
- removed xfail from
test_openai_vector_store_delete_file_removes_from_vector_store

Closes: #2477

---------

Signed-off-by: Derek Higgins <derekh@redhat.com>
Co-authored-by: Francisco Arceo <arceofrancisco@gmail.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
 
-        self.index.add(np.array(embeddings).astype(np.float32))
+        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 +288,9 @@ 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_chunks(self, store_id: str, chunk_ids: list[str]) -> None:
+        """Delete a chunk from a faiss index"""
+        faiss_index = self.cache[store_id].index
+        for chunk_id in chunk_ids:
+            await faiss_index.delete_chunk(chunk_id)