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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
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