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| # | |
| # 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. | |
| # | |
| from abc import ABC | |
| from Bio import Entrez | |
| import pandas as pd | |
| import xml.etree.ElementTree as ET | |
| from agent.settings import DEBUG | |
| from agent.component.base import ComponentBase, ComponentParamBase | |
| class PubMedParam(ComponentParamBase): | |
| """ | |
| Define the PubMed component parameters. | |
| """ | |
| def __init__(self): | |
| super().__init__() | |
| self.top_n = 5 | |
| self.email = "[email protected]" | |
| 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 | |