sethmcknight
fix(chroma): recover from corrupted persistent DB by cleaning and retrying init
b3b90ec
import logging
import os
from pathlib import Path
from typing import Any, Dict, List, Optional
import chromadb
from src.config import VECTOR_STORAGE_TYPE
from src.utils.memory_utils import log_memory_checkpoint, memory_monitor
from src.vector_db.postgres_adapter import PostgresVectorAdapter
def create_vector_database(persist_path: Optional[str] = None, collection_name: Optional[str] = None):
"""
Factory function to create the appropriate vector database implementation.
Args:
persist_path: Path for persistence (used by ChromaDB)
collection_name: Name of the collection
Returns:
Vector database implementation
"""
# Allow runtime override via environment variable to make tests and
# deploy-time configuration consistent. Prefer explicit env var when set.
storage_type = os.getenv("VECTOR_STORAGE_TYPE") or VECTOR_STORAGE_TYPE
if storage_type == "postgres":
return PostgresVectorAdapter(table_name=collection_name or "document_embeddings")
else:
# Default to ChromaDB
from src.config import COLLECTION_NAME, VECTOR_DB_PERSIST_PATH
return VectorDatabase(
persist_path=persist_path or VECTOR_DB_PERSIST_PATH,
collection_name=collection_name or COLLECTION_NAME,
)
class VectorDatabase:
"""ChromaDB integration for vector storage and similarity search"""
def __init__(
self,
persist_path: str,
collection_name: str,
):
"""
Initialize the vector database
Args:
persist_path: Path to persist the database
collection_name: Name of the collection to use
"""
self.persist_path = persist_path
self.collection_name = collection_name
# Ensure persist directory exists
Path(persist_path).mkdir(parents=True, exist_ok=True)
# Get chroma settings from config for memory optimization
from chromadb.config import Settings
from src.config import CHROMA_SETTINGS
# Convert CHROMA_SETTINGS dict to Settings object
chroma_settings = Settings(**CHROMA_SETTINGS)
# Initialize ChromaDB client with persistence and memory optimization
log_memory_checkpoint("vector_db_before_client_init")
try:
self.client = chromadb.PersistentClient(path=persist_path, settings=chroma_settings)
except Exception as e:
# Detect common sqlite corrupt/partial-init state where Chroma's sysdb
# tables (like `tenants`) are missing. Attempt a safe one-time cleanup
# of the persistence directory and retry initialization. This helps
# recover when a previous failed startup left an inconsistent DB.
import glob
import shutil
import sqlite3
logging.warning(
"ChromaDB persistent client init failed: %s; attempting cleanup and retry",
e,
)
# Only perform aggressive cleanup for sqlite OperationalError or
# Chroma UniqueConstraint/Operational style issues.
if isinstance(e, sqlite3.OperationalError) or "no such table" in str(e).lower():
try:
# Remove sqlite files and chroma DB folders under persist_path
pattern = os.path.join(persist_path, "*")
for p in glob.glob(pattern):
try:
if os.path.isdir(p):
shutil.rmtree(p)
else:
os.remove(p)
except Exception:
# Best-effort cleanup; continue
logging.debug("Failed to remove %s during cleanup", p)
# Recreate the directory and retry
Path(persist_path).mkdir(parents=True, exist_ok=True)
self.client = chromadb.PersistentClient(path=persist_path, settings=chroma_settings)
logging.info("ChromaDB persistence cleaned and client reinitialized")
except Exception as e2:
logging.error("ChromaDB recovery attempt failed: %s", e2)
# Re-raise original exception to let caller handle failure
raise
else:
# If it's an unexpected error, re-raise to be handled upstream
raise
log_memory_checkpoint("vector_db_after_client_init")
# Get or create collection
self.collection = self.client.get_or_create_collection(name=collection_name)
logging.info(f"Initialized VectorDatabase with collection " f"'{collection_name}' at '{persist_path}'")
def get_collection(self):
"""Get the ChromaDB collection"""
return self.collection
@memory_monitor
def add_embeddings_batch(
self,
batch_embeddings: List[List[List[float]]],
batch_chunk_ids: List[List[str]],
batch_documents: List[List[str]],
batch_metadatas: List[List[Dict[str, Any]]],
) -> int:
"""
Add embeddings in batches to prevent memory issues with large datasets
Args:
batch_embeddings: List of embedding batches
batch_chunk_ids: List of chunk ID batches
batch_documents: List of document batches
batch_metadatas: List of metadata batches
Returns:
Number of embeddings added
"""
total_added = 0
for i, (embeddings, chunk_ids, documents, metadatas) in enumerate(
zip(
batch_embeddings,
batch_chunk_ids,
batch_documents,
batch_metadatas,
)
):
log_memory_checkpoint(f"before_add_batch_{i}")
# add_embeddings may return True on success (or raise on failure)
added = self.add_embeddings(
embeddings=embeddings,
chunk_ids=chunk_ids,
documents=documents,
metadatas=metadatas,
)
# If add_embeddings returns True, treat as all embeddings added
if isinstance(added, bool) and added:
added_count = len(embeddings)
elif isinstance(added, int):
added_count = int(added)
else:
added_count = 0
total_added += added_count
logging.info(f"Added batch {i+1}/{len(batch_embeddings)}")
# Force cleanup after each batch
import gc
gc.collect()
log_memory_checkpoint(f"after_add_batch_{i}")
return total_added
@memory_monitor
def add_embeddings(
self,
embeddings: List[List[float]],
chunk_ids: List[str],
documents: List[str],
metadatas: List[Dict[str, Any]],
) -> int:
"""
Add embeddings to the collection
Args:
embeddings: List of embedding vectors
chunk_ids: List of chunk IDs
documents: List of document texts
metadatas: List of metadata dictionaries
Returns:
Number of embeddings added
"""
# Validate input lengths
n = len(embeddings)
if not (len(chunk_ids) == n and len(documents) == n and len(metadatas) == n):
raise ValueError(f"Number of embeddings {n} must match number of ids {len(chunk_ids)}")
log_memory_checkpoint("before_add_embeddings")
try:
self.collection.add(
embeddings=embeddings,
documents=documents,
metadatas=metadatas,
ids=chunk_ids,
)
log_memory_checkpoint("after_add_embeddings")
logging.info(f"Added {n} embeddings to collection")
# Return boolean True for API compatibility tests
return True
except Exception as e:
logging.error(f"Failed to add embeddings: {e}")
# Re-raise to allow callers/tests to handle failures explicitly
raise
@memory_monitor
def search(self, query_embedding: List[float], top_k: int = 5) -> List[Dict[str, Any]]:
"""
Search for similar embeddings
Args:
query_embedding: Query vector to search for
top_k: Number of results to return
Returns:
List of search results with metadata
"""
try:
# Handle empty collection
if self.get_count() == 0:
return []
# Perform similarity search
log_memory_checkpoint("vector_db_before_query")
results = self.collection.query(
query_embeddings=[query_embedding],
n_results=min(top_k, self.get_count()),
)
log_memory_checkpoint("vector_db_after_query")
# Format results
formatted_results = []
if results["ids"] and len(results["ids"][0]) > 0:
for i in range(len(results["ids"][0])):
result = {
"id": results["ids"][0][i],
"document": results["documents"][0][i],
"metadata": results["metadatas"][0][i],
"distance": results["distances"][0][i],
}
formatted_results.append(result)
logging.info(f"Search returned {len(formatted_results)} results")
return formatted_results
except Exception as e:
logging.error(f"Search failed: {e}")
return []
def get_count(self) -> int:
"""Get the number of embeddings in the collection"""
try:
return self.collection.count()
except Exception as e:
logging.error(f"Failed to get count: {e}")
return 0
def delete_collection(self) -> bool:
"""Delete the collection"""
try:
self.client.delete_collection(name=self.collection_name)
logging.info(f"Deleted collection '{self.collection_name}'")
return True
except Exception as e:
logging.error(f"Failed to delete collection: {e}")
return False
def reset_collection(self) -> bool:
"""Reset the collection (delete and recreate)"""
try:
# Delete existing collection
try:
self.client.delete_collection(name=self.collection_name)
except ValueError:
# Collection doesn't exist, that's fine
pass
# Create new collection
self.collection = self.client.create_collection(name=self.collection_name)
logging.info(f"Reset collection '{self.collection_name}'")
return True
except Exception as e:
logging.error(f"Failed to reset collection: {e}")
return False
def get_embedding_dimension(self) -> int:
"""
Get the embedding dimension from existing data in the collection.
Returns 0 if collection is empty or has no embeddings.
"""
try:
count = self.get_count()
if count == 0:
return 0
# Retrieve one record to check its embedding dimension
record = self.collection.get(
ids=None, # None returns all records, but we only need one
include=["embeddings"],
limit=1,
)
if record and "embeddings" in record and record["embeddings"]:
return len(record["embeddings"][0])
return 0
except Exception as e:
logging.error(f"Failed to get embedding dimension: {e}")
return 0
def has_valid_embeddings(self, expected_dimension: int) -> bool:
"""
Check if the collection has embeddings with the expected dimension.
Args:
expected_dimension: The expected embedding dimension
Returns:
True if collection has embeddings with correct dimension, False otherwise
"""
try:
actual_dimension = self.get_embedding_dimension()
return actual_dimension == expected_dimension and actual_dimension > 0
except Exception as e:
logging.error(f"Failed to validate embeddings: {e}")
return False