Replace ChromaDB with pgvector for vector storage

Consolidate onto PostgreSQL by using pgvector instead of a separate
ChromaDB instance. This removes a Docker volume, a large dependency,
and simplifies the stack without meaningful performance impact at
our document scale.

- Swap langchain-chroma for langchain-postgres (PGVector)
- Use pgvector/pgvector:pg16 Docker image with init script
- Lazy-initialize vector store to avoid eager DB connections
- Add SQL helpers for stats/delete/list (replacing _collection access)
- Remove legacy main.py, chunker, petmd scraper, and /api/query endpoint

Re-index required after deploy (POST /api/rag/index + /index-obsidian).

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

.env.example

@@ -19,11 +19,6 @@ BASE_URL=192.168.1.5:8000
 LLAMA_SERVER_URL=http://192.168.1.213:8080/v1
 LLAMA_MODEL_NAME=llama-3.1-8b-instruct
 
-# ChromaDB Configuration
-# For Docker: This is automatically set to /app/data/chromadb
-# For local development: Set to a local directory path
-CHROMADB_PATH=./data/chromadb
-
 # OpenAI Configuration
 OPENAI_API_KEY=your-openai-api-key
 

.gitignore

@@ -13,9 +13,6 @@ wheels/
 .env
 
 # Database files
-chromadb/
-chromadb_openai/
-chroma_db/
 database/
 *.db
 

CLAUDE.md

@@ -4,7 +4,7 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 ## Project Overview
 
-SimbaRAG is a RAG (Retrieval-Augmented Generation) conversational AI system for querying information about Simba (a cat). It ingests documents from Paperless-NGX, stores embeddings in ChromaDB, and uses LLMs (Ollama or OpenAI) to answer questions.
+SimbaRAG is a RAG (Retrieval-Augmented Generation) conversational AI system for querying information about Simba (a cat). It ingests documents from Paperless-NGX, stores embeddings in PostgreSQL via pgvector, and uses LLMs (Ollama or OpenAI) to answer questions.
 
 ## Commands
 
@@ -54,9 +54,8 @@ docker compose up -d
 │                     Docker Compose                          │
 ├─────────────────────────────────────────────────────────────┤
 │  raggr (port 8080)              │  postgres (port 5432)    │
-│  ├── Quart backend              │  PostgreSQL 16           │
+│  ├── Quart backend              │  PostgreSQL 16 + pgvector│
-│  ├── React frontend (served)    │                          │
+│  └── React frontend (served)    │                          │
-│  └── ChromaDB (volume)          │                          │
 └─────────────────────────────────────────────────────────────┘
 ```
 

Dockerfile

@@ -37,15 +37,14 @@ WORKDIR /app/raggr-frontend
 RUN yarn install && yarn build
 WORKDIR /app
 
-# Create ChromaDB and database directories
+# Create database directory
-RUN mkdir -p /app/chromadb /app/database
+RUN mkdir -p /app/database
 
 # Expose port
 EXPOSE 8080
 
 # Set environment variables
 ENV PYTHONPATH=/app
-ENV CHROMADB_PATH=/app/chromadb
 
 # Run the startup script
 CMD ["./startup.sh"]

Dockerfile.dev

@@ -34,16 +34,15 @@ COPY . .
 WORKDIR /app/raggr-frontend
 RUN yarn build
 
-# Create ChromaDB and database directories
+# Create database directory
 WORKDIR /app
-RUN mkdir -p /app/chromadb /app/database
+RUN mkdir -p /app/database
 
 # Make startup script executable
 RUN chmod +x /app/startup-dev.sh
 
 # Set environment variables
 ENV PYTHONPATH=/app
-ENV CHROMADB_PATH=/app/chromadb
 ENV PYTHONUNBUFFERED=1
 
 # Expose port

app.py

@@ -3,7 +3,7 @@ import os
 from datetime import timedelta
 
 from dotenv import load_dotenv
-from quart import Quart, jsonify, render_template, request, send_from_directory
+from quart import Quart, jsonify, render_template, send_from_directory
 from quart_jwt_extended import JWTManager, get_jwt_identity, jwt_refresh_token_required
 from tortoise import Tortoise
 
@@ -15,7 +15,6 @@ import blueprints.users
 import blueprints.whatsapp
 import blueprints.users.models
 from config.db import TORTOISE_CONFIG
-from main import consult_simba_oracle
 
 # Load environment variables
 load_dotenv()
@@ -78,39 +77,6 @@ async def serve_react_app(path):
     return await render_template("index.html")
 
 
-@app.route("/api/query", methods=["POST"])
-@jwt_refresh_token_required
-async def query():
-    current_user_uuid = get_jwt_identity()
-    user = await blueprints.users.models.User.get(id=current_user_uuid)
-    data = await request.get_json()
-    query = data.get("query")
-    conversation_id = data.get("conversation_id")
-    conversation = await blueprints.conversation.logic.get_conversation_by_id(
-        conversation_id
-    )
-    await conversation.fetch_related("messages")
-    await blueprints.conversation.logic.add_message_to_conversation(
-        conversation=conversation,
-        message=query,
-        speaker="user",
-        user=user,
-    )
-
-    transcript = await blueprints.conversation.logic.get_conversation_transcript(
-        user=user, conversation=conversation
-    )
-
-    response = consult_simba_oracle(input=query, transcript=transcript)
-    await blueprints.conversation.logic.add_message_to_conversation(
-        conversation=conversation,
-        message=response,
-        speaker="simba",
-        user=user,
-    )
-    return jsonify({"response": response})
-
-
 @app.route("/api/messages", methods=["GET"])
 @jwt_refresh_token_required
 async def get_messages():

blueprints/conversation/agents.py

@@ -328,7 +328,7 @@ async def obsidian_search_notes(query: str) -> str:
         return "Obsidian integration is not configured. Please set OBSIDIAN_VAULT_PATH environment variable."
 
     try:
-        # Query ChromaDB for obsidian documents
+        # Query vector store for obsidian documents
         serialized, docs = await query_vector_store(query=query)
         return serialized
 

blueprints/rag/__init__.py

@@ -1,7 +1,12 @@
 from quart import Blueprint, jsonify
 from quart_jwt_extended import jwt_refresh_token_required
 
-from .logic import fetch_obsidian_documents, get_vector_store_stats, index_documents, index_obsidian_documents, vector_store
+from .logic import (
+    delete_all_documents,
+    get_vector_store_stats,
+    index_documents,
+    index_obsidian_documents,
+)
 from blueprints.users.decorators import admin_required
 
 rag_blueprint = Blueprint("rag_api", __name__, url_prefix="/api/rag")
@@ -32,14 +37,7 @@ async def trigger_index():
 async def trigger_reindex():
     """Clear and reindex all documents. Admin only."""
     try:
-        # Clear existing documents
+        delete_all_documents()
-        collection = vector_store._collection
-        all_docs = collection.get()
-
-        if all_docs["ids"]:
-            collection.delete(ids=all_docs["ids"])
-
-        # Reindex
         await index_documents()
         stats = get_vector_store_stats()
         return jsonify({"status": "success", "stats": stats})

blueprints/rag/logic.py

@@ -1,11 +1,13 @@
 import datetime
+import logging
 import os
 
 from dotenv import load_dotenv
-from langchain_chroma import Chroma
 from langchain_core.documents import Document
 from langchain_openai import OpenAIEmbeddings
+from langchain_postgres import PGVector
 from langchain_text_splitters import RecursiveCharacterTextSplitter
+from sqlalchemy import create_engine, text
 
 from .fetchers import PaperlessNGXService
 from utils.obsidian_service import ObsidianService
@@ -13,13 +15,39 @@ from utils.obsidian_service import ObsidianService
 # Load environment variables
 load_dotenv()
 
+logger = logging.getLogger(__name__)
+
 embeddings = OpenAIEmbeddings(model="text-embedding-3-small")
 
-vector_store = Chroma(
+# Convert Tortoise-style postgres:// URL to SQLAlchemy-style postgresql+psycopg://
-    collection_name="simba_docs",
+_db_url = os.getenv(
-    embedding_function=embeddings,
+    "DATABASE_URL", "postgres://raggr:raggr_dev_password@localhost:5432/raggr"
-    persist_directory=os.getenv("CHROMADB_PATH", ""),
 )
+_pgvector_url = _db_url.replace("postgres://", "postgresql+psycopg://")
+
+# Lazy-initialized vector store (defers DB connection to first use)
+_vector_store = None
+
+
+def _get_vector_store() -> PGVector:
+    global _vector_store
+    if _vector_store is None:
+        _vector_store = PGVector(
+            embeddings=embeddings,
+            collection_name="simba_docs",
+            connection=_pgvector_url,
+            use_jsonb=True,
+            create_extension=False,  # created by docker init script
+        )
+    return _vector_store
+
+
+def _get_engine():
+    """Get a SQLAlchemy engine for direct queries."""
+    if not hasattr(_get_engine, "_engine"):
+        _get_engine._engine = create_engine(_pgvector_url)
+    return _get_engine._engine
+
 
 text_splitter = RecursiveCharacterTextSplitter(
     chunk_size=1000,  # chunk size (characters)
@@ -28,6 +56,18 @@ text_splitter = RecursiveCharacterTextSplitter(
 )
 
 
+def _get_collection_id():
+    """Get the UUID of our collection from the langchain_pg_collection table."""
+    engine = _get_engine()
+    with engine.connect() as conn:
+        result = conn.execute(
+            text("SELECT uuid FROM langchain_pg_collection WHERE name = :name"),
+            {"name": "simba_docs"},
+        )
+        row = result.fetchone()
+        return row[0] if row else None
+
+
 def date_to_epoch(date_str: str) -> float:
     split_date = date_str.split("-")
     date = datetime.datetime(
@@ -63,6 +103,7 @@ async def index_documents():
     documents = await fetch_documents_from_paperless_ngx()
 
     splits = text_splitter.split_documents(documents)
+    vector_store = _get_vector_store()
     await vector_store.aadd_documents(documents=splits)
 
 
@@ -92,13 +133,17 @@ async def fetch_obsidian_documents() -> list[Document]:
                     "filepath": parsed["filepath"],
                     "tags": parsed["tags"],
                     "created_at": parsed["metadata"].get("created_at"),
-                    **{k: v for k, v in parsed["metadata"].items() if k not in ["created_at", "created_by"]},
+                    **{
+                        k: v
+                        for k, v in parsed["metadata"].items()
+                        if k not in ["created_at", "created_by"]
+                    },
                 },
             )
             documents.append(document)
 
         except Exception as e:
-            print(f"Error reading {md_path}: {e}")
+            logger.warning(f"Error reading {md_path}: {e}")
             continue
 
     return documents
@@ -109,26 +154,25 @@ async def index_obsidian_documents():
 
     Deletes existing obsidian source chunks before re-indexing.
     """
-    obsidian_service = ObsidianService()
     documents = await fetch_obsidian_documents()
 
     if not documents:
-        print("No Obsidian documents found to index")
+        logger.info("No Obsidian documents found to index")
         return {"indexed": 0}
 
     # Delete existing obsidian chunks
-    existing_results = vector_store.get(where={"source": "obsidian"})
+    delete_documents_by_metadata("source", "obsidian")
-    if existing_results.get("ids"):
-        await vector_store.adelete(existing_results["ids"])
 
     # Split and index documents
     splits = text_splitter.split_documents(documents)
+    vector_store = _get_vector_store()
     await vector_store.aadd_documents(documents=splits)
 
     return {"indexed": len(documents)}
 
 
 async def query_vector_store(query: str):
+    vector_store = _get_vector_store()
     retrieved_docs = await vector_store.asimilarity_search(query, k=2)
     serialized = "\n\n".join(
         (f"Source: {doc.metadata}\nContent: {doc.page_content}")
@@ -137,32 +181,79 @@ async def query_vector_store(query: str):
     return serialized, retrieved_docs
 
 
+def delete_all_documents():
+    """Delete all documents from the vector store collection."""
+    collection_id = _get_collection_id()
+    if not collection_id:
+        return
+    engine = _get_engine()
+    with engine.connect() as conn:
+        conn.execute(
+            text("DELETE FROM langchain_pg_embedding WHERE collection_id = :cid"),
+            {"cid": collection_id},
+        )
+        conn.commit()
+
+
+def delete_documents_by_metadata(key: str, value: str):
+    """Delete documents matching a metadata key/value pair."""
+    collection_id = _get_collection_id()
+    if not collection_id:
+        return
+    engine = _get_engine()
+    with engine.connect() as conn:
+        conn.execute(
+            text(
+                "DELETE FROM langchain_pg_embedding "
+                "WHERE collection_id = :cid AND cmetadata->>:key = :value"
+            ),
+            {"cid": collection_id, "key": key, "value": value},
+        )
+        conn.commit()
+
+
 def get_vector_store_stats():
     """Get statistics about the vector store."""
-    collection = vector_store._collection
+    collection_id = _get_collection_id()
-    count = collection.count()
+    count = 0
+    if collection_id:
+        engine = _get_engine()
+        with engine.connect() as conn:
+            result = conn.execute(
+                text(
+                    "SELECT COUNT(*) FROM langchain_pg_embedding WHERE collection_id = :cid"
+                ),
+                {"cid": collection_id},
+            )
+            count = result.scalar()
     return {
         "total_documents": count,
-        "collection_name": collection.name,
+        "collection_name": "simba_docs",
     }
 
 
 def list_all_documents(limit: int = 10):
     """List documents in the vector store with their metadata."""
-    collection = vector_store._collection
+    collection_id = _get_collection_id()
-    results = collection.get(limit=limit, include=["metadatas", "documents"])
+    if not collection_id:
+        return []
 
+    engine = _get_engine()
+    with engine.connect() as conn:
+        result = conn.execute(
+            text(
+                "SELECT id, document, cmetadata FROM langchain_pg_embedding "
+                "WHERE collection_id = :cid LIMIT :limit"
+            ),
+            {"cid": collection_id, "limit": limit},
+        )
         documents = []
-    for i, doc_id in enumerate(results["ids"]):
+        for row in result:
             documents.append(
                 {
-                "id": doc_id,
+                    "id": str(row[0]),
-                "metadata": results["metadatas"][i]
+                    "metadata": row[2],
-                if results.get("metadatas")
+                    "content_preview": row[1][:200] if row[1] else None,
-                else None,
-                "content_preview": results["documents"][i][:200]
-                if results.get("documents")
-                else None,
                 }
             )
 

docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.8"
 
 services:
   postgres:
-    image: postgres:16-alpine
+    image: pgvector/pgvector:pg16
     ports:
       - "5432:5432"
     environment:
@@ -11,6 +11,7 @@ services:
       - POSTGRES_DB=${POSTGRES_DB:-raggr}
     volumes:
       - postgres_data:/var/lib/postgresql/data
+      - ./docker/init-pgvector.sql:/docker-entrypoint-initdb.d/init-pgvector.sql
     healthcheck:
       test: ["CMD-SHELL", "pg_isready -U ${POSTGRES_USER:-raggr}"]
       interval: 10s
@@ -29,7 +30,6 @@ services:
       - PAPERLESS_TOKEN=${PAPERLESS_TOKEN}
       - BASE_URL=${BASE_URL}
       - OLLAMA_URL=${OLLAMA_URL:-http://localhost:11434}
-      - CHROMADB_PATH=/app/data/chromadb
       - OPENAI_API_KEY=${OPENAI_API_KEY}
       - JWT_SECRET_KEY=${JWT_SECRET_KEY}
       - LLAMA_SERVER_URL=${LLAMA_SERVER_URL}
@@ -66,10 +66,8 @@ services:
       postgres:
         condition: service_healthy
     volumes:
-      - chromadb_data:/app/data/chromadb
       - ./obvault:/app/data/obsidian
     restart: unless-stopped
 
 volumes:
-  chromadb_data:
   postgres_data:

docker/init-pgvector.sql

@@ -0,0 +1 @@
+CREATE EXTENSION IF NOT EXISTS vector;

main.py

@@ -1,278 +0,0 @@
-import argparse
-import datetime
-import logging
-import os
-import sqlite3
-import time
-
-from dotenv import load_dotenv
-
-import chromadb
-from utils.chunker import Chunker
-from utils.cleaner import pdf_to_image, summarize_pdf_image
-from llm import LLMClient
-from scripts.query import QueryGenerator
-from utils.request import PaperlessNGXService
-
-_dotenv_loaded = load_dotenv()
-
-client = chromadb.PersistentClient(path=os.getenv("CHROMADB_PATH", ""))
-simba_docs = client.get_or_create_collection(name="simba_docs2")
-feline_vet_lookup = client.get_or_create_collection(name="feline_vet_lookup")
-
-parser = argparse.ArgumentParser(
-    description="An LLM tool to query information about Simba <3"
-)
-
-parser.add_argument("query", type=str, help="questions about simba's health")
-parser.add_argument(
-    "--reindex", action="store_true", help="re-index the simba documents"
-)
-parser.add_argument("--classify", action="store_true", help="test classification")
-parser.add_argument("--index", help="index a file")
-
-ppngx = PaperlessNGXService()
-
-llm_client = LLMClient()
-
-
-def index_using_pdf_llm(doctypes):
-    logging.info("reindex data...")
-    files = ppngx.get_data()
-    for file in files:
-        document_id: int = file["id"]
-        pdf_path = ppngx.download_pdf_from_id(id=document_id)
-        image_paths = pdf_to_image(filepath=pdf_path)
-        logging.info(f"summarizing {file}")
-        generated_summary = summarize_pdf_image(filepaths=image_paths)
-        file["content"] = generated_summary
-
-    chunk_data(files, simba_docs, doctypes=doctypes)
-
-
-def date_to_epoch(date_str: str) -> float:
-    split_date = date_str.split("-")
-    date = datetime.datetime(
-        int(split_date[0]),
-        int(split_date[1]),
-        int(split_date[2]),
-        0,
-        0,
-        0,
-    )
-
-    return date.timestamp()
-
-
-def chunk_data(docs, collection, doctypes):
-    # Step 2: Create chunks
-    chunker = Chunker(collection)
-
-    logging.info(f"chunking {len(docs)} documents")
-    texts: list[str] = [doc["content"] for doc in docs]
-    with sqlite3.connect("database/visited.db") as conn:
-        to_insert = []
-        c = conn.cursor()
-        for index, text in enumerate(texts):
-            metadata = {
-                "created_date": date_to_epoch(docs[index]["created_date"]),
-                "filename": docs[index]["original_file_name"],
-                "document_type": doctypes.get(docs[index]["document_type"], ""),
-            }
-
-            if doctypes:
-                metadata["type"] = doctypes.get(docs[index]["document_type"])
-
-            chunker.chunk_document(
-                document=text,
-                metadata=metadata,
-            )
-            to_insert.append((docs[index]["id"],))
-
-        c.executemany(
-            "INSERT INTO indexed_documents (paperless_id) values (?)", to_insert
-        )
-        conn.commit()
-
-
-def chunk_text(texts: list[str], collection):
-    chunker = Chunker(collection)
-
-    for index, text in enumerate(texts):
-        metadata = {}
-        chunker.chunk_document(
-            document=text,
-            metadata=metadata,
-        )
-
-
-def classify_query(query: str, transcript: str) -> bool:
-    logging.info("Starting query generation")
-    qg_start = time.time()
-    qg = QueryGenerator()
-    query_type = qg.get_query_type(input=query, transcript=transcript)
-    logging.info(query_type)
-    qg_end = time.time()
-    logging.info(f"Query generation took {qg_end - qg_start:.2f} seconds")
-    return query_type == "Simba"
-
-
-def consult_oracle(
-    input: str,
-    collection,
-    transcript: str = "",
-):
-    chunker = Chunker(collection)
-
-    start_time = time.time()
-
-    # Ask
-    logging.info("Starting query generation")
-    qg_start = time.time()
-    qg = QueryGenerator()
-    doctype_query = qg.get_doctype_query(input=input)
-    # metadata_filter = qg.get_query(input)
-    metadata_filter = {**doctype_query}
-    logging.info(metadata_filter)
-    qg_end = time.time()
-    logging.info(f"Query generation took {qg_end - qg_start:.2f} seconds")
-
-    logging.info("Starting embedding generation")
-    embedding_start = time.time()
-    embeddings = chunker.embedding_fx(inputs=[input])
-    embedding_end = time.time()
-    logging.info(
-        f"Embedding generation took {embedding_end - embedding_start:.2f} seconds"
-    )
-
-    logging.info("Starting collection query")
-    query_start = time.time()
-    results = collection.query(
-        query_texts=[input],
-        query_embeddings=embeddings,
-        where=metadata_filter,
-    )
-    query_end = time.time()
-    logging.info(f"Collection query took {query_end - query_start:.2f} seconds")
-
-    # Generate
-    logging.info("Starting LLM generation")
-    llm_start = time.time()
-    system_prompt = "You are a helpful assistant that understands veterinary terms."
-    transcript_prompt = f"Here is the message transcript thus far {transcript}."
-    prompt = f"""Using the following data, help answer the user's query by providing as many details as possible.
-    Using this data: {results}. {transcript_prompt if len(transcript) > 0 else ""}
-    Respond to this prompt: {input}"""
-    output = llm_client.chat(prompt=prompt, system_prompt=system_prompt)
-    llm_end = time.time()
-    logging.info(f"LLM generation took {llm_end - llm_start:.2f} seconds")
-
-    total_time = time.time() - start_time
-    logging.info(f"Total consult_oracle execution took {total_time:.2f} seconds")
-
-    return output
-
-
-def llm_chat(input: str, transcript: str = "") -> str:
-    system_prompt = "You are a helpful assistant that understands veterinary terms."
-    transcript_prompt = f"Here is the message transcript thus far {transcript}."
-    prompt = f"""Answer the user in as if you were a cat named Simba. Don't act too catlike. Be assertive.
-    {transcript_prompt if len(transcript) > 0 else ""}
-    Respond to this prompt: {input}"""
-    output = llm_client.chat(prompt=prompt, system_prompt=system_prompt)
-    return output
-
-
-def paperless_workflow(input):
-    # Step 1: Get the text
-    ppngx = PaperlessNGXService()
-    docs = ppngx.get_data()
-
-    chunk_data(docs, collection=simba_docs)
-    consult_oracle(input, simba_docs)
-
-
-def consult_simba_oracle(input: str, transcript: str = ""):
-    is_simba_related = classify_query(query=input, transcript=transcript)
-
-    if is_simba_related:
-        logging.info("Query is related to simba")
-        return consult_oracle(
-            input=input,
-            collection=simba_docs,
-            transcript=transcript,
-        )
-
-    logging.info("Query is NOT related to simba")
-
-    return llm_chat(input=input, transcript=transcript)
-
-
-def filter_indexed_files(docs):
-    with sqlite3.connect("database/visited.db") as conn:
-        c = conn.cursor()
-        c.execute(
-            "CREATE TABLE IF NOT EXISTS indexed_documents (id INTEGER PRIMARY KEY AUTOINCREMENT, paperless_id INTEGER)"
-        )
-        c.execute("SELECT paperless_id FROM indexed_documents")
-        rows = c.fetchall()
-        conn.commit()
-
-    visited = {row[0] for row in rows}
-    return [doc for doc in docs if doc["id"] not in visited]
-
-
-def reindex():
-    with sqlite3.connect("database/visited.db") as conn:
-        c = conn.cursor()
-        # Ensure the table exists before trying to delete from it
-        c.execute(
-            "CREATE TABLE IF NOT EXISTS indexed_documents (id INTEGER PRIMARY KEY AUTOINCREMENT, paperless_id INTEGER)"
-        )
-        c.execute("DELETE FROM indexed_documents")
-        conn.commit()
-
-    # Delete all documents from the collection
-    all_docs = simba_docs.get()
-    if all_docs["ids"]:
-        simba_docs.delete(ids=all_docs["ids"])
-
-    logging.info("Fetching documents from Paperless-NGX")
-    ppngx = PaperlessNGXService()
-    docs = ppngx.get_data()
-    docs = filter_indexed_files(docs)
-    logging.info(f"Fetched {len(docs)} documents")
-
-    # Delete all chromadb data
-    ids = simba_docs.get(ids=None, limit=None, offset=0)
-    all_ids = ids["ids"]
-    if len(all_ids) > 0:
-        simba_docs.delete(ids=all_ids)
-
-    # Chunk documents
-    logging.info("Chunking documents now ...")
-    doctype_lookup = ppngx.get_doctypes()
-    chunk_data(docs, collection=simba_docs, doctypes=doctype_lookup)
-    logging.info("Done chunking documents")
-
-
-if __name__ == "__main__":
-    args = parser.parse_args()
-    if args.reindex:
-        reindex()
-
-    if args.classify:
-        consult_simba_oracle(input="yohohoho testing")
-        consult_simba_oracle(input="write an email")
-        consult_simba_oracle(input="how much does simba weigh")
-
-    if args.query:
-        logging.info("Consulting oracle ...")
-        print(
-            consult_oracle(
-                input=args.query,
-                collection=simba_docs,
-            )
-        )
-    else:
-        logging.info("please provide a query")

pyproject.toml

@@ -5,7 +5,8 @@ description = "Add your description here"
 readme = "README.md"
 requires-python = ">=3.13"
 dependencies = [
-    "chromadb>=1.1.0",
+    "langchain-postgres>=0.0.13",
+    "psycopg[binary]>=3.1.0",
     "python-dotenv>=1.0.0",
     "flask>=3.1.2",
     "httpx>=0.28.1",
@@ -30,7 +31,6 @@ dependencies = [
     "asyncpg>=0.30.0",
     "langchain-openai>=1.1.6",
     "langchain>=1.2.0",
-    "langchain-chroma>=1.0.0",
     "langchain-community>=0.4.1",
     "jq>=1.10.0",
     "tavily-python>=0.7.17",

scripts/manage_vectorstore.py

@@ -6,19 +6,19 @@ import asyncio
 import sys
 
 from blueprints.rag.logic import (
+    delete_all_documents,
     get_vector_store_stats,
     index_documents,
     list_all_documents,
-    vector_store,
 )
 
 
 def stats():
     """Show vector store statistics."""
-    stats = get_vector_store_stats()
+    s = get_vector_store_stats()
     print("=== Vector Store Statistics ===")
-    print(f"Collection: {stats['collection_name']}")
+    print(f"Collection: {s['collection_name']}")
-    print(f"Total Documents: {stats['total_documents']}")
+    print(f"Total Documents: {s['total_documents']}")
 
 
 async def index():
@@ -26,23 +26,15 @@ async def index():
     print("Starting indexing process...")
     print("Fetching documents from Paperless-NGX...")
     await index_documents()
-    print("✓ Indexing complete!")
+    print("Indexing complete!")
     stats()
 
 
 async def reindex():
     """Clear and reindex all documents."""
     print("Clearing existing documents...")
-    collection = vector_store._collection
+    delete_all_documents()
-    all_docs = collection.get()
+    print("Cleared")
-
-    if all_docs["ids"]:
-        print(f"Deleting {len(all_docs['ids'])} existing documents...")
-        collection.delete(ids=all_docs["ids"])
-        print("✓ Cleared")
-    else:
-        print("Collection is already empty")
-
     await index()
 
 
@@ -113,7 +105,7 @@ Examples:
         print("\n\nOperation cancelled by user")
         sys.exit(1)
     except Exception as e:
-        print(f"\n❌ Error: {e}", file=sys.stderr)
+        print(f"\nError: {e}", file=sys.stderr)
         sys.exit(1)
 
 

scripts/petmd_scrape_index.py

@@ -1,24 +0,0 @@
-from bs4 import BeautifulSoup
-import chromadb
-import httpx
-
-client = chromadb.PersistentClient(path="/Users/ryanchen/Programs/raggr/chromadb")
-
-# Scrape
-BASE_URL = "https://www.vet.cornell.edu"
-LIST_URL = "/departments-centers-and-institutes/cornell-feline-health-center/health-information/feline-health-topics"
-
-QUERY_URL = BASE_URL + LIST_URL
-r = httpx.get(QUERY_URL)
-soup = BeautifulSoup(r.text)
-
-container = soup.find("div", class_="field-body")
-a_s = container.find_all("a", href=True)
-
-new_texts = []
-
-for link in a_s:
-    endpoint = link["href"]
-    query_url = BASE_URL + endpoint
-    r2 = httpx.get(query_url)
-    article_soup = BeautifulSoup(r2.text)

startup-dev.sh

@@ -1,9 +1,6 @@
 #!/bin/bash
 set -e
 
-echo "Initializing directories..."
-mkdir -p /app/data/chromadb
-
 echo "Rebuilding frontend..."
 cd /app/raggr-frontend
 yarn build

tests/unit/test_chunker.py

@@ -1,139 +0,0 @@
-"""Tests for text preprocessing functions in utils/chunker.py."""
-
-from utils.chunker import (
-    remove_headers_footers,
-    remove_special_characters,
-    remove_repeated_substrings,
-    remove_extra_spaces,
-    preprocess_text,
-)
-
-
-class TestRemoveHeadersFooters:
-    def test_removes_default_header(self):
-        text = "Header Line\nActual content here"
-        result = remove_headers_footers(text)
-        assert "Header" not in result
-        assert "Actual content here" in result
-
-    def test_removes_default_footer(self):
-        text = "Actual content\nFooter Line"
-        result = remove_headers_footers(text)
-        assert "Footer" not in result
-        assert "Actual content" in result
-
-    def test_custom_patterns(self):
-        text = "PAGE 1\nContent\nCopyright 2024"
-        result = remove_headers_footers(
-            text,
-            header_patterns=[r"^PAGE \d+$"],
-            footer_patterns=[r"^Copyright.*$"],
-        )
-        assert "PAGE 1" not in result
-        assert "Copyright" not in result
-        assert "Content" in result
-
-    def test_no_match_preserves_text(self):
-        text = "Just normal content"
-        result = remove_headers_footers(text)
-        assert result == "Just normal content"
-
-    def test_empty_string(self):
-        assert remove_headers_footers("") == ""
-
-
-class TestRemoveSpecialCharacters:
-    def test_removes_special_chars(self):
-        text = "Hello @world #test $100"
-        result = remove_special_characters(text)
-        assert "@" not in result
-        assert "#" not in result
-        assert "$" not in result
-
-    def test_preserves_allowed_chars(self):
-        text = "Hello, world! How's it going? Yes-no."
-        result = remove_special_characters(text)
-        assert "," in result
-        assert "!" in result
-        assert "'" in result
-        assert "?" in result
-        assert "-" in result
-        assert "." in result
-
-    def test_custom_pattern(self):
-        text = "keep @this but not #that"
-        result = remove_special_characters(text, special_chars=r"[#]")
-        assert "@this" in result
-        assert "#" not in result
-
-    def test_empty_string(self):
-        assert remove_special_characters("") == ""
-
-
-class TestRemoveRepeatedSubstrings:
-    def test_collapses_dots(self):
-        text = "Item.....Value"
-        result = remove_repeated_substrings(text)
-        assert result == "Item.Value"
-
-    def test_single_dot_preserved(self):
-        text = "End of sentence."
-        result = remove_repeated_substrings(text)
-        assert result == "End of sentence."
-
-    def test_custom_pattern(self):
-        text = "hello---world"
-        result = remove_repeated_substrings(text, pattern=r"-{2,}")
-        # Function always replaces matched pattern with "."
-        assert result == "hello.world"
-
-    def test_empty_string(self):
-        assert remove_repeated_substrings("") == ""
-
-
-class TestRemoveExtraSpaces:
-    def test_collapses_multiple_blank_lines(self):
-        text = "Line 1\n\n\n\nLine 2"
-        result = remove_extra_spaces(text)
-        # After collapsing newlines to \n\n, then \s+ collapses everything to single spaces
-        assert "\n\n\n" not in result
-
-    def test_collapses_multiple_spaces(self):
-        text = "Hello    world"
-        result = remove_extra_spaces(text)
-        assert result == "Hello world"
-
-    def test_strips_whitespace(self):
-        text = "  Hello world  "
-        result = remove_extra_spaces(text)
-        assert result == "Hello world"
-
-    def test_empty_string(self):
-        assert remove_extra_spaces("") == ""
-
-
-class TestPreprocessText:
-    def test_full_pipeline(self):
-        text = "Header Info\nHello @world...  with   spaces\nFooter Info"
-        result = preprocess_text(text)
-        assert "Header" not in result
-        assert "Footer" not in result
-        assert "@" not in result
-        assert "..." not in result
-        assert "   " not in result
-
-    def test_preserves_meaningful_content(self):
-        text = "The cat weighs 10 pounds."
-        result = preprocess_text(text)
-        assert "cat" in result
-        assert "10" in result
-        assert "pounds" in result
-
-    def test_empty_string(self):
-        assert preprocess_text("") == ""
-
-    def test_already_clean(self):
-        text = "Simple clean text here."
-        result = preprocess_text(text)
-        assert "Simple" in result
-        assert "clean" in result

utils/chunker.py

@@ -1,137 +0,0 @@
-import os
-from math import ceil
-import re
-from typing import Union
-from uuid import UUID, uuid4
-from chromadb.utils.embedding_functions.openai_embedding_function import (
-    OpenAIEmbeddingFunction,
-)
-from dotenv import load_dotenv
-from llm import LLMClient
-
-
-load_dotenv()
-
-
-def remove_headers_footers(text, header_patterns=None, footer_patterns=None):
-    if header_patterns is None:
-        header_patterns = [r"^.*Header.*$"]
-    if footer_patterns is None:
-        footer_patterns = [r"^.*Footer.*$"]
-
-    for pattern in header_patterns + footer_patterns:
-        text = re.sub(pattern, "", text, flags=re.MULTILINE)
-
-    return text.strip()
-
-
-def remove_special_characters(text, special_chars=None):
-    if special_chars is None:
-        special_chars = r"[^A-Za-z0-9\s\.,;:\'\"\?\!\-]"
-
-    text = re.sub(special_chars, "", text)
-    return text.strip()
-
-
-def remove_repeated_substrings(text, pattern=r"\.{2,}"):
-    text = re.sub(pattern, ".", text)
-    return text.strip()
-
-
-def remove_extra_spaces(text):
-    text = re.sub(r"\n\s*\n", "\n\n", text)
-    text = re.sub(r"\s+", " ", text)
-
-    return text.strip()
-
-
-def preprocess_text(text):
-    # Remove headers and footers
-    text = remove_headers_footers(text)
-
-    # Remove special characters
-    text = remove_special_characters(text)
-
-    # Remove repeated substrings like dots
-    text = remove_repeated_substrings(text)
-
-    # Remove extra spaces between lines and within lines
-    text = remove_extra_spaces(text)
-
-    # Additional cleaning steps can be added here
-
-    return text.strip()
-
-
-class Chunk:
-    def __init__(
-        self,
-        text: str,
-        size: int,
-        document_id: UUID,
-        chunk_id: int,
-        embedding,
-    ):
-        self.text = text
-        self.size = size
-        self.document_id = document_id
-        self.chunk_id = chunk_id
-        self.embedding = embedding
-
-
-class Chunker:
-    def __init__(self, collection) -> None:
-        self.collection = collection
-        self.llm_client = LLMClient()
-
-    def embedding_fx(self, inputs):
-        openai_embedding_fx = OpenAIEmbeddingFunction(
-            api_key=os.getenv("OPENAI_API_KEY"),
-            model_name="text-embedding-3-small",
-        )
-        return openai_embedding_fx(inputs)
-
-    def chunk_document(
-        self,
-        document: str,
-        chunk_size: int = 1000,
-        metadata: dict[str, Union[str, float]] = {},
-    ) -> list[Chunk]:
-        doc_uuid = uuid4()
-
-        chunk_size = min(chunk_size, len(document)) or 1
-
-        chunks = []
-        num_chunks = ceil(len(document) / chunk_size)
-        document_length = len(document)
-
-        for i in range(num_chunks):
-            curr_pos = i * num_chunks
-            to_pos = (
-                curr_pos + chunk_size
-                if curr_pos + chunk_size < document_length
-                else document_length
-            )
-            text_chunk = self.clean_document(document[curr_pos:to_pos])
-
-            embedding = self.embedding_fx([text_chunk])
-            self.collection.add(
-                ids=[str(doc_uuid) + ":" + str(i)],
-                documents=[text_chunk],
-                embeddings=embedding,
-                metadatas=[metadata],
-            )
-
-        return chunks
-
-    def clean_document(self, document: str) -> str:
-        """This function will remove information that is noise or already known.
-
-        Example: We already know all the things in here are Simba-related, so we don't need things like
-        "Sumamry of simba's visit"
-        """
-
-        document = document.replace("\\n", "")
-        document = document.strip()
-
-        return preprocess_text(document)