clinical / app.py
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Update app.py
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from __future__ import annotations as _annotations
import os
import asyncio
import json
import sqlite3
import datetime
import fastapi
import logfire
import time
from collections.abc import AsyncIterator
from concurrent.futures.thread import ThreadPoolExecutor
from contextlib import asynccontextmanager
from dataclasses import dataclass
from datetime import datetime, timezone, date
from functools import partial
from pathlib import Path
from typing import Annotated, Any, Callable, Literal, TypeVar
from pydantic import BaseModel, Field, ValidationError, model_validator
from typing import List, Optional, Dict
from fastapi import Depends, Request
from fastapi.responses import FileResponse, Response, StreamingResponse
from typing_extensions import LiteralString, ParamSpec, TypedDict
from pydantic_ai import Agent
from pydantic_ai.exceptions import UnexpectedModelBehavior
from pydantic_ai.messages import (
ModelMessage,
ModelMessagesTypeAdapter,
ModelRequest,
ModelResponse,
TextPart,
UserPromptPart,
)
from pydantic_ai.models.openai import OpenAIModel
model = OpenAIModel(
'gemma-2-2b-it',
base_url='http://localhost:1234/v1',
api_key='your-local-api-key',
)
# 'if-token-present' means nothing will be sent (and the example will work) if you don't have logfire configured
logfire.configure(send_to_logfire='if-token-present')
class ClinicalNoteResult(BaseModel):
entities: list
message: str
# # Create a system prompt to guide the model
system_prompt="Anda adalah dokter medis yang membantu mengekstrak informasi dari catatan klinis. Hasil extract adalah menjadi format JSON"
#INI SAJA. SALAH SATU
agent = Agent('gemini-1.5-flash', system_prompt=system_prompt) # OK-Gemini
#agent = Agent(model) # OK-Lokal
THIS_DIR = Path(__file__).parent
@asynccontextmanager
async def lifespan(_app: fastapi.FastAPI):
async with Database.connect() as db:
yield {'db': db}
app = fastapi.FastAPI(lifespan=lifespan)
logfire.instrument_fastapi(app)
@app.get('/')
async def index() -> FileResponse:
return FileResponse((THIS_DIR / 'chat_app.html'), media_type='text/html')
@app.get('/chat_app.ts')
async def main_ts() -> FileResponse:
"""Get the raw typescript code, it's compiled in the browser, forgive me."""
return FileResponse((THIS_DIR / 'chat_app.ts'), media_type='text/plain')
async def get_db(request: Request) -> Database:
return request.state.db
@app.get('/chat/')
async def get_chat(database: Database = Depends(get_db)) -> Response:
msgs = await database.get_messages()
return Response(
b'\n'.join(json.dumps(to_chat_message(m)).encode('utf-8') for m in msgs),
media_type='text/plain',
)
class ChatMessage(TypedDict):
"""Format of messages sent to the browser."""
role: Literal['user', 'model']
timestamp: str
content: str
def to_chat_message(m: ModelMessage) -> ChatMessage:
first_part = m.parts[0]
if isinstance(m, ModelRequest):
first_part = m.parts[1]
if isinstance(first_part, UserPromptPart):
return {
'role': 'user',
'timestamp': first_part.timestamp.isoformat(),
'content': first_part.content,
}
elif isinstance(m, ModelResponse):
if isinstance(first_part, TextPart):
return {
'role': 'model',
'timestamp': m.timestamp.isoformat(),
'content': first_part.content,
}
raise UnexpectedModelBehavior(f'Unexpected message type for chat app: {m}')
def to_ds_message(m: ModelMessage) -> ChatMessage:
if isinstance(m, ModelRequest):
first_part = m.parts[1]
if isinstance(first_part, UserPromptPart):
return {
'role': 'user',
'timestamp': first_part.timestamp.isoformat(),
'content': first_part.content,
}
elif isinstance(m, ModelResponse):
first_part = m.parts[0]
if isinstance(first_part, TextPart):
return {
'role': 'model',
'timestamp': m.timestamp.isoformat(),
'content': first_part.content,
}
raise UnexpectedModelBehavior(f'Unexpected ds-message type for chat app: {m}')
@app.post('/chat/')
async def post_chat(
prompt: Annotated[str, fastapi.Form()], database: Database = Depends(get_db)
) -> StreamingResponse:
async def stream_messages():
"""Streams new line delimited JSON `Message`s to the client."""
# stream the user prompt so that can be displayed straight away
yield (
json.dumps(
{
'role': 'user',
'timestamp': datetime.now(tz=timezone.utc).isoformat(),
'content': prompt,
}
).encode('utf-8')
+ b'\n'
)
## get the chat history so far to pass as context to the agent
#messages = await database.get_messages()
## run the agent with the user prompt and the chat history
async with agent.run_stream(prompt) as result:
async for text in result.stream(debounce_by=0.01):
# text here is a `str` and the frontend wants
# JSON encoded ModelResponse, so we create one
m = ModelResponse.from_text(content=text, timestamp=result.timestamp())
yield json.dumps(to_chat_message(m)).encode('utf-8') + b'\n'
# add new messages (e.g. the user prompt and the agent response in this case) to the database
print("---",result.new_messages_json(),"---")
#print("***",prompt,"***")
await database.add_messages(result.new_messages_json())
if prompt[0] == "@" :
#print("@@@", prompt, "@@@")
nn = len(prompt)
prompt = prompt[1:nn]
print(">>>", prompt, "<<<")
return StreamingResponse(stream_messages(), media_type='text/plain')
elif prompt[0] != "@" :
#print("biasa")
return StreamingResponse(stream_messages(), media_type='text/plain')
print("** selesai **")
return StreamingResponse(stream_messages(), media_type='text/plain')
P = ParamSpec('P')
R = TypeVar('R')
@dataclass
class Database:
"""Rudimentary database to store chat messages in SQLite.
The SQLite standard library package is synchronous, so we
use a thread pool executor to run queries asynchronously.
"""
con: sqlite3.Connection
_loop: asyncio.AbstractEventLoop
_executor: ThreadPoolExecutor
@classmethod
@asynccontextmanager
async def connect(
cls, file: Path = THIS_DIR / '.chat_messages.sqlite'
) -> AsyncIterator[Database]:
with logfire.span('connect to DB'):
loop = asyncio.get_event_loop()
executor = ThreadPoolExecutor(max_workers=1)
con = await loop.run_in_executor(executor, cls._connect, file)
slf = cls(con, loop, executor)
try:
yield slf
finally:
await slf._asyncify(con.close)
@staticmethod
def _connect(file: Path) -> sqlite3.Connection:
con = sqlite3.connect(str(file))
con = logfire.instrument_sqlite3(con)
cur = con.cursor()
cur.execute(
'CREATE TABLE IF NOT EXISTS messages (id INT PRIMARY KEY, message_list TEXT);'
)
con.commit()
return con
async def add_messages(self, messages: bytes):
await self._asyncify(
self._execute,
'INSERT INTO messages (message_list) VALUES (?);',
messages,
commit=True,
)
await self._asyncify(self.con.commit)
async def get_messages(self) -> list[ModelMessage]:
c = await self._asyncify(
self._execute, 'SELECT message_list FROM messages order by id asc'
)
rows = await self._asyncify(c.fetchall)
messages: list[ModelMessage] = []
for row in rows:
messages.extend(ModelMessagesTypeAdapter.validate_json(row[0]))
return messages
def _execute(
self, sql: LiteralString, *args: Any, commit: bool = False
) -> sqlite3.Cursor:
cur = self.con.cursor()
cur.execute(sql, args)
if commit:
self.con.commit()
return cur
async def _asyncify(
self, func: Callable[P, R], *args: P.args, **kwargs: P.kwargs
) -> R:
return await self._loop.run_in_executor( # type: ignore
self._executor,
partial(func, **kwargs),
*args, # type: ignore
)
if __name__ == '__main__':
import uvicorn
uvicorn.run(
'app:app', reload=True, host="0.0.0.0", port=7860, reload_dirs=[str(THIS_DIR)]
)