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30f6421760
### What problem does this PR solve? Use consistent log file names, introduced initLogger ### Type of change - [ ] Bug Fix (non-breaking change which fixes an issue) - [ ] New Feature (non-breaking change which adds functionality) - [ ] Documentation Update - [x] Refactoring - [ ] Performance Improvement - [ ] Other (please describe):
70 lines
2.7 KiB
Python
70 lines
2.7 KiB
Python
#
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# Copyright 2024 The InfiniFlow Authors. All Rights Reserved.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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import logging
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from abc import ABC
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from Bio import Entrez
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import re
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import pandas as pd
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import xml.etree.ElementTree as ET
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from agent.component.base import ComponentBase, ComponentParamBase
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class PubMedParam(ComponentParamBase):
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"""
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Define the PubMed component parameters.
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"""
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def __init__(self):
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super().__init__()
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self.top_n = 5
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self.email = "A.N.Other@example.com"
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def check(self):
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self.check_positive_integer(self.top_n, "Top N")
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class PubMed(ComponentBase, ABC):
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component_name = "PubMed"
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def _run(self, history, **kwargs):
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ans = self.get_input()
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ans = " - ".join(ans["content"]) if "content" in ans else ""
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if not ans:
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return PubMed.be_output("")
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try:
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Entrez.email = self._param.email
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pubmedids = Entrez.read(Entrez.esearch(db='pubmed', retmax=self._param.top_n, term=ans))['IdList']
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pubmedcnt = ET.fromstring(re.sub(r'<(/?)b>|<(/?)i>', '', Entrez.efetch(db='pubmed', id=",".join(pubmedids),
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retmode="xml").read().decode(
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"utf-8")))
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pubmed_res = [{"content": 'Title:' + child.find("MedlineCitation").find("Article").find(
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"ArticleTitle").text + '\nUrl:<a href=" https://pubmed.ncbi.nlm.nih.gov/' + child.find(
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"MedlineCitation").find("PMID").text + '">' + '</a>\n' + 'Abstract:' + (
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child.find("MedlineCitation").find("Article").find("Abstract").find(
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"AbstractText").text if child.find("MedlineCitation").find(
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"Article").find("Abstract") else "No abstract available")} for child in
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pubmedcnt.findall("PubmedArticle")]
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except Exception as e:
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return PubMed.be_output("**ERROR**: " + str(e))
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if not pubmed_res:
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return PubMed.be_output("")
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df = pd.DataFrame(pubmed_res)
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logging.debug(f"df: {df}")
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return df
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