Преглед изворни кода

Add component pubmed (#1586)

### What problem does this PR solve?

### Type of change

- [x] New Feature (non-breaking change which adds functionality)
tags/v0.9.0
H пре 1 година
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5 измењених фајлова са 67 додато и 0 уклоњено
  1. 1
    0
      graph/component/__init__.py
  2. 63
    0
      graph/component/pubmed.py
  3. 1
    0
      requirements.txt
  4. 1
    0
      requirements_arm.txt
  5. 1
    0
      requirements_dev.txt

+ 1
- 0
graph/component/__init__.py Прегледај датотеку

from .baidu import Baidu, BaiduParam from .baidu import Baidu, BaiduParam
from .duckduckgo import DuckDuckGo, DuckDuckGoParam from .duckduckgo import DuckDuckGo, DuckDuckGoParam
from .wikipedia import Wikipedia, WikipediaParam from .wikipedia import Wikipedia, WikipediaParam
from .pubmed import PubMed, PubMedParam




def component_class(class_name): def component_class(class_name):

+ 63
- 0
graph/component/pubmed.py Прегледај датотеку

#
# 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("")

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")]

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

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

+ 1
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requirements.txt Прегледај датотеку

Aspose.Slides==24.2.0 Aspose.Slides==24.2.0
BCEmbedding==0.1.3 BCEmbedding==0.1.3
Bio==1.7.1
boto3==1.34.140 boto3==1.34.140
botocore==1.34.140 botocore==1.34.140
cachetools==5.3.3 cachetools==5.3.3

+ 1
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requirements_arm.txt Прегледај датотеку

google-generativeai==0.7.2 google-generativeai==0.7.2
groq==0.9.0 groq==0.9.0
wikipedia==1.4.0 wikipedia==1.4.0
Bio==1.7.1

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requirements_dev.txt Прегледај датотеку

google-generativeai==0.7.2 google-generativeai==0.7.2
groq==0.9.0 groq==0.9.0
wikipedia==1.4.0 wikipedia==1.4.0
Bio==1.7.1

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