ragflow/graph/component/pubmed.py

#
#  Copyright 2024 The InfiniFlow Authors. All Rights Reserved.
#
#  Licensed under the Apache License, Version 2.0 (the "License");
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
#
#      http://www.apache.org/licenses/LICENSE-2.0
#
#  Unless required by applicable law or agreed to in writing, software
#  distributed under the License is distributed on an "AS IS" BASIS,
#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#  See the License for the specific language governing permissions and
#  limitations under the License.
#
import random
from abc import ABC
from functools import partial
from Bio import Entrez
import pandas as pd
import xml.etree.ElementTree as ET
from graph.settings import DEBUG
from graph.component.base import ComponentBase, ComponentParamBase


class PubMedParam(ComponentParamBase):
    """
    Define the PubMed component parameters.
    """

    def __init__(self):
        super().__init__()
        self.top_n = 5
        self.email = "A.N.Other@example.com"

    def check(self):
        self.check_positive_integer(self.top_n, "Top N")


class PubMed(ComponentBase, ABC):
    component_name = "PubMed"

    def _run(self, history, **kwargs):
        ans = self.get_input()
        ans = " - ".join(ans["content"]) if "content" in ans else ""
        if not ans:
            return PubMed.be_output("")

        try:
            Entrez.email = self._param.email
            pubmedids = Entrez.read(Entrez.esearch(db='pubmed', retmax=self._param.top_n, term=ans))['IdList']
            pubmedcnt = ET.fromstring(
                Entrez.efetch(db='pubmed', id=",".join(pubmedids), retmode="xml").read().decode("utf-8"))
            pubmed_res = [{"content": 'Title:' + child.find("MedlineCitation").find("Article").find(
                "ArticleTitle").text + '\nUrl:<a href=" https://pubmed.ncbi.nlm.nih.gov/' + child.find(
                "MedlineCitation").find("PMID").text + '">' + '</a>\n' + 'Abstract:' + child.find(
                "MedlineCitation").find("Article").find("Abstract").find("AbstractText").text} for child in
                          pubmedcnt.findall("PubmedArticle")]
        except Exception as e:
            return PubMed.be_output("**ERROR**: " + str(e))

        if not pubmed_res:
            return PubMed.be_output("")

        df = pd.DataFrame(pubmed_res)
        if DEBUG: print(df, ":::::::::::::::::::::::::::::::::")
        return df