oqmd
This commit is contained in:
0
database/__init__.py
Normal file
0
database/__init__.py
Normal file
163
database/material_project_router.py
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163
database/material_project_router.py
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@@ -0,0 +1,163 @@
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"""
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Author: Yutang LI
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Institution: SIAT-MIC
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Contact: yt.li2@siat.ac.cn
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"""
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from fastapi import APIRouter, Request
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import json
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import asyncio
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import logging
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from mp_api.client import MPRester
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from multiprocessing import Process, Manager
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from typing import Dict, Any, List
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from constant import MP_API_KEY, TIME_OUT, TOPK_RESULT
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router = APIRouter(prefix="/mp", tags=["Material Project"])
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logger = logging.getLogger(__name__)
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@router.get("/search")
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async def search_from_material_project(request: Request):
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# 打印请求日志
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logger.info(f"Received request: {request.method} {request.url}")
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logger.info(f"Query parameters: {request.query_params}")
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# 解析查询参数
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search_args = parse_search_parameters(request.query_params)
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# 检查API key
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if MP_API_KEY is None or MP_API_KEY == '':
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return 'Material Project API CANNOT Be None'
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try:
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# 执行搜索
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docs = await execute_search(search_args)
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# 处理搜索结果
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res = process_search_results(docs)
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# 返回结果
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if len(res) >= TOPK_RESULT:
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return json.dumps(res[:TOPK_RESULT], indent=2)
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return json.dumps(res, indent=2)
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except asyncio.TimeoutError:
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logger.error(f"Request timed out after {TIME_OUT} seconds, please simplify your query and try again.")
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return {"error": f"Request timed out after {TIME_OUT} seconds, please simplify your query and try again."}
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def parse_bool(param: str) -> bool | None:
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if not param:
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return None
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return param.lower() == 'true'
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def parse_list(param: str) -> List[str] | None:
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if not param:
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return None
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return param.split(',')
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def parse_tuple(param: str) -> tuple[float, float] | None:
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if not param:
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return None
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try:
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values = param.split(',')
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return (float(values[0]), float(values[1]))
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except (ValueError, IndexError):
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return None
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def parse_search_parameters(query_params: Dict[str, str]) -> Dict[str, Any]:
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"""解析搜索参数"""
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return {
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'band_gap': parse_tuple(query_params.get('band_gap')),
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'chemsys': parse_list(query_params.get('chemsys')),
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'crystal_system': parse_list(query_params.get('crystal_system')),
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'density': parse_tuple(query_params.get('density')),
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'formation_energy': parse_tuple(query_params.get('formation_energy')),
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'elements': parse_list(query_params.get('elements')),
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'exclude_elements': parse_list(query_params.get('exclude_elements')),
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'formula': parse_list(query_params.get('formula')),
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'is_gap_direct': parse_bool(query_params.get('is_gap_direct')),
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'is_metal': parse_bool(query_params.get('is_metal')),
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'is_stable': parse_bool(query_params.get('is_stable')),
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'magnetic_ordering': query_params.get('magnetic_ordering'),
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'material_ids': parse_list(query_params.get('material_ids')),
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'total_energy': parse_tuple(query_params.get('total_energy')),
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'num_elements': parse_tuple(query_params.get('num_elements')),
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'volume': parse_tuple(query_params.get('volume')),
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'chunk_size': int(query_params.get('chunk_size', '5'))
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}
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def process_search_results(docs: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
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"""处理搜索结果"""
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fields = [
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'formula_pretty', 'nsites', 'nelements', 'material_id', 'chemsys',
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'volume', 'density', 'density_atomic', 'cbm', 'vbm', 'band_gap',
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'is_gap_direct', 'is_stable', 'formation_energy_per_atom',
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'energy_above_hull', 'is_metal', 'total_magnetization', 'efermi',
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'is_magnetic', 'ordering', 'bulk_modulus', 'shear_modulus',
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'universal_anisotropy', 'theoretical'
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]
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res = []
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for doc in docs:
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try:
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new_docs = {}
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for field_name in fields:
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new_docs[field_name] = doc.get(field_name, '')
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res.append(new_docs)
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except Exception as e:
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logger.warning(f"Error processing document: {str(e)}")
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continue
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return res
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async def execute_search(search_args: Dict[str, Any], timeout: int = TIME_OUT) -> List[Dict[str, Any]]:
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"""执行搜索"""
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manager = Manager()
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queue = manager.Queue()
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p = Process(target=_search_worker, args=(queue, MP_API_KEY), kwargs=search_args)
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p.start()
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logger.info(f"Started worker process with PID: {p.pid}")
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p.join(timeout=timeout)
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if p.is_alive():
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logger.warning(f"Terminating worker process {p.pid} due to timeout")
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p.terminate()
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p.join()
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raise asyncio.TimeoutError(f"Request timed out after {timeout} seconds")
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try:
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if queue.empty():
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logger.warning("Queue is empty after process completion")
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else:
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logger.info("Queue contains data, retrieving...")
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result = queue.get(timeout=15)
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except queue.Empty:
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logger.error("Failed to retrieve data from queue")
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raise RuntimeError("Failed to retrieve data from worker process")
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if isinstance(result, Exception):
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logger.error(f"Error in search worker: {str(result)}")
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raise result
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logger.info(f"Successfully retrieved {len(result)} documents")
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return result
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def _search_worker(queue, api_key, **kwargs):
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"""搜索工作线程"""
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try:
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mpr = MPRester(api_key)
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result = mpr.materials.summary.search(**kwargs)
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queue.put([doc.model_dump() for doc in result])
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except Exception as e:
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queue.put(e)
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305
database/oqmd_router.py
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305
database/oqmd_router.py
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@@ -0,0 +1,305 @@
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"""
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Author: Yutang LI
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Institution: SIAT-MIC
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Contact: yt.li2@siat.ac.cn
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"""
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import os
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import boto3
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from fastapi import APIRouter, Request
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from io import StringIO
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import logging
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import httpx
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import datetime
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import pandas as pd
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from bs4 import BeautifulSoup
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from PIL import Image
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from playwright.async_api import async_playwright
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from constant import MINIO_ENDPOINT, MINIO_ACCESS_KEY, MINIO_SECRET_KEY, MINIO_BUCKET, INTERNEL_MINIO_ENDPOINT
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router = APIRouter(prefix="/oqmd", tags=["OQMD"])
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logger = logging.getLogger(__name__)
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@router.get("/search")
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async def search_from_oqmd_by_composition(request: Request):
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# 打印请求日志
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logger.info(f"Received request: {request.method} {request.url}")
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logger.info(f"Query parameters: {request.query_params}")
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try:
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# 获取并解析数据
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composition = request.query_params['composition']
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html = await fetch_oqmd_data(composition)
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basic_data, table_data, phase_data = parse_oqmd_html(html)
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# 渲染并保存图表
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phase_diagram_name = await render_and_save_charts(phase_data)
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# 返回格式化后的响应
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return format_response(basic_data, table_data, phase_diagram_name)
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except httpx.HTTPStatusError as e:
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logger.error(f"OQMD API request failed: {str(e)}")
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return {
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"status": "error",
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"message": f"OQMD API request failed: {str(e)}"
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}
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except Exception as e:
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logger.error(f"Unexpected error: {str(e)}")
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return {
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"status": "error",
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"message": f"Unexpected error: {str(e)}"
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}
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async def fetch_oqmd_data(composition: str) -> str:
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"""
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从OQMD获取数据
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Args:
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composition: 材料组成字符串
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Returns:
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HTML内容字符串
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Raises:
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httpx.HTTPError: 当发生HTTP相关错误时抛出
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ValueError: 当响应内容无效时抛出
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"""
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url = f"https://www.oqmd.org/materials/composition/{composition}"
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try:
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async with httpx.AsyncClient(timeout=30.0) as client:
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response = await client.get(url)
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response.raise_for_status()
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# 验证响应内容
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if not response.text or len(response.text) < 100:
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raise ValueError("Invalid response content from OQMD API")
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return response.text
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except httpx.HTTPStatusError as e:
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status_code = e.response.status_code
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if status_code == 401:
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logger.error("OQMD API: Unauthorized access")
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raise httpx.HTTPError("Unauthorized access to OQMD API") from e
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elif status_code == 403:
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logger.error("OQMD API: Forbidden access")
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raise httpx.HTTPError("Forbidden access to OQMD API") from e
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elif status_code == 404:
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logger.error("OQMD API: Resource not found")
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raise httpx.HTTPError("Resource not found on OQMD API") from e
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elif status_code >= 500:
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logger.error(f"OQMD API: Server error ({status_code})")
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raise httpx.HTTPError(f"OQMD API server error ({status_code})") from e
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else:
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logger.error(f"OQMD API request failed: {str(e)}")
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raise httpx.HTTPError(f"OQMD API request failed: {str(e)}") from e
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except httpx.TimeoutException as e:
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logger.error("OQMD API request timed out")
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raise httpx.HTTPError("OQMD API request timed out") from e
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except httpx.NetworkError as e:
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logger.error(f"Network error occurred: {str(e)}")
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raise httpx.HTTPError(f"Network error: {str(e)}") from e
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except ValueError as e:
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logger.error(f"Invalid response content: {str(e)}")
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raise ValueError(f"Invalid response content: {str(e)}") from e
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def parse_oqmd_html(html: str) -> tuple[list, str, list]:
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"""
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解析OQMD HTML数据
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"""
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soup = BeautifulSoup(html, 'html.parser')
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# 解析基本数据
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basic_data = []
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basic_data.append(soup.find('h1').text.strip())
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for script in soup.find_all('p'):
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if script:
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combined_text = ""
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for element in script.contents: # 遍历 <p> 的子元素
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if element.name == 'a': # 如果是 <a> 标签
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url = "https://www.oqmd.org" + element['href']
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combined_text += f"[{element.text.strip()}]({url}) "
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else: # 如果是文本
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combined_text += element.text.strip() + " "
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basic_data.append(combined_text.strip())
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# import pdb
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# pdb.set_trace()
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# 解析表格数据
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table = soup.find('table')
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if table:
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df = pd.read_html(StringIO(str(table)))[0]
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df = df.fillna('')
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df = df.replace([float('inf'), float('-inf')], '')
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# table_data = df.to_dict(orient='records')
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table_data = df.to_markdown(index=False)
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# 提取JavaScript数据
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phase_data = []
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for script in soup.find_all('script'):
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if script.string and '$(function()' in script.string:
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phase_data.append({
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'type': script.get('type', 'text/javascript'),
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'content': script.string.strip()
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})
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return basic_data, table_data, phase_data
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async def render_and_save_charts(script_data: list) -> str:
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"""
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渲染并保存图表到MinIO
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Returns:
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str: 图片的预签名URL
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Raises:
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RuntimeError: 如果图片生成或上传失败
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"""
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browser = None
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temp_files = []
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try:
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# 初始化Playwright
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async with async_playwright() as p:
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browser = await p.chromium.launch(headless=True)
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page = await browser.new_page()
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# 构建包含 JavaScript 的 HTML 代码
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html_content = """
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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="UTF-8">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.0/jquery.min.js"></script>
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<script src="https://cdn.jsdelivr.net/npm/jquery.flot@0.8.3/jquery.flot.js"></script>
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<title>Phase Diagram</title>
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</head>
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<body>
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<div class="diagram">
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<div id="placeholder" width="200" height="400" style="direction: ltr; position: absolute; left: 550px; top: 0px; width: 200px; height: 400px;"></div>
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<script>
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{placeholder_content}
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</script>
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<div id="phasediagram" width="500" height="400" style="direction: ltr; position: absolute; left: 0px; top: 0px; width: 500px; height: 400px;"></div>
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<script>
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{phasediagram_content}
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</script>
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</div>
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</body>
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</html>
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"""
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html_content = html_content.format(
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placeholder_content=script_data[0]['content'],
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phasediagram_content=script_data[1]['content'])
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await page.set_content(html_content)
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await page.wait_for_timeout(5000)
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# 分别截图两个图表
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# 获取placeholder元素位置并扩大截图区域
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placeholder = page.locator('#placeholder')
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placeholder_box = await placeholder.bounding_box()
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await page.screenshot(
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path="placeholder.png",
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clip={
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'x': placeholder_box['x'],
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'y': placeholder_box['y'],
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'width': placeholder_box['width'] + 40,
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'height': placeholder_box['height'] + 40
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}
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)
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# 获取phasediagram元素位置并扩大截图区域
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phasediagram = page.locator('#phasediagram')
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phasediagram_box = await phasediagram.bounding_box()
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await page.screenshot(
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path="phasediagram.png",
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clip={
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'x': phasediagram_box['x'],
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'y': phasediagram_box['y'],
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'width': phasediagram_box['width'] + 40,
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'height': phasediagram_box['height'] + 40
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}
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)
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await browser.close()
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# 拼接图片
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try:
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img1 = Image.open("placeholder.png")
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temp_files.append("placeholder.png")
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img2 = Image.open("phasediagram.png")
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temp_files.append("phasediagram.png")
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new_img = Image.new('RGB', (img1.width + img2.width, max(img1.height, img2.height)))
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new_img.paste(img2, (0, 0))
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new_img.paste(img1, (img2.width, 0))
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timestamp = datetime.datetime.now().strftime("%Y%m%d%H%M%S")
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file_name = f"oqmd_phase_diagram_{timestamp}.png"
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new_img.save(file_name)
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temp_files.append(file_name)
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except Exception as e:
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logger.error(f"Failed to process images: {str(e)}")
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raise RuntimeError(f"Image processing failed: {str(e)}") from e
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# 上传到 MinIO 的逻辑
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try:
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minio_client = boto3.client(
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's3',
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endpoint_url=MINIO_ENDPOINT if INTERNEL_MINIO_ENDPOINT == "" else INTERNEL_MINIO_ENDPOINT,
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aws_access_key_id=MINIO_ACCESS_KEY,
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aws_secret_access_key=MINIO_SECRET_KEY
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)
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bucket_name = MINIO_BUCKET
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minio_client.upload_file(file_name, bucket_name, file_name, ExtraArgs={"ACL": "private"})
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# 生成预签名 URL
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url = minio_client.generate_presigned_url(
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'get_object',
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Params={'Bucket': bucket_name, 'Key': file_name},
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ExpiresIn=3600
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||||
)
|
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return url.replace(INTERNEL_MINIO_ENDPOINT, MINIO_ENDPOINT)
|
||||
|
||||
except Exception as e:
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logger.error(f"Failed to upload to MinIO: {str(e)}")
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raise RuntimeError(f"MinIO upload failed: {str(e)}") from e
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finally:
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# 清理临时文件
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for temp_file in temp_files:
|
||||
try:
|
||||
if os.path.exists(temp_file):
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||||
os.remove(temp_file)
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||||
except Exception as e:
|
||||
logger.warning(f"Failed to remove temporary file {temp_file}: {str(e)}")
|
||||
except Exception as e:
|
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logger.error(f"Failed to render and save charts: {str(e)}")
|
||||
raise RuntimeError(f"Chart rendering failed: {str(e)}") from e
|
||||
finally:
|
||||
# 确保浏览器关闭
|
||||
if browser:
|
||||
try:
|
||||
await browser.close()
|
||||
except Exception as e:
|
||||
logger.warning(f"Failed to close browser: {str(e)}")
|
||||
|
||||
def format_response(basic_data: list, table_data: str, phase_data: str) -> str:
|
||||
"""
|
||||
格式化响应数据
|
||||
"""
|
||||
response = "### OQMD Data\n"
|
||||
for item in basic_data:
|
||||
response += f"**{item}**\n"
|
||||
response += "\n### Phase Diagram\n\n"
|
||||
response += f"\n\n"
|
||||
response += "\n### Compounds at this composition\n\n"
|
||||
response += f"{table_data}\n"
|
||||
|
||||
return {
|
||||
"status": "success",
|
||||
"data": response
|
||||
}
|
||||
Reference in New Issue
Block a user