Summarize the publication of a researcher, and calculate their IFs for first and last authorships in a data range

ImpactHunter.py

#!/bin/python
from Bio import Entrez
import subprocess
import ast
import statistics
def search_publications(author_name, start_year, end_year):
    # Search PubMed for publications by the author within the specified date range
    query = f'({author_name}[Author]) AND (Journal Article[Publication Type]) NOT (Clinical Trial[Publication Type]) NOT preprint[pt] NOT review[pt] AND ({start_year}:{end_year}[PDAT])'
    handle = Entrez.esearch(db='pubmed', term=query)
    record = Entrez.read(handle)
    handle.close()

    # Retrieve publication IDs
    id_list = record['IdList']

    # Retrieve publication details
    publications = []
    for pub_id in id_list:
        pub_info = {'id': pub_id}

        handle = Entrez.esummary(db='pubmed', id=pub_id)
        summary = Entrez.read(handle)[0]
        handle.close()

        pub_info['title'] = summary['Title']
        pub_info['authors'] = summary['AuthorList']
        pub_info['first_author'] = pub_info['authors'][0]
        pub_info['last_author'] = pub_info['authors'][-1]

        if 'PubTypeList' in summary and summary['PubTypeList']:
            pub_info['article_type'] = summary['PubTypeList'][0]
        else:
            pub_info['article_type'] = 'N/A'

        # Retrieve journal name
        pub_info['journal_name'] = summary['FullJournalName']

        publications.append(pub_info)

    return publications


def get_if(journal_name):
    # journal_name = "nature"

    command = ["impact_factor", "search", journal_name]
    result = subprocess.run(command, capture_output=True, text=True)
    try:
        if result.returncode == 0:
            output = result.stdout.strip()
            output = ast.literal_eval(output)
            output = output[0]['factor']
        else:
            output = 0
    except:
        output = 0

    return output


# Main program
author_name = input('Enter author name: ')
start_year = int(input('Enter start year: '))
end_year = int(input('Enter end year: '))
# author_name = 'john Metcalfe'
# start_year = 2019
# end_year = 2023

surname = author_name.split()[-1].lower()

publications = search_publications(author_name, start_year, end_year)

total_publications = len(publications)
first_author_count = sum(surname in pub['first_author'].lower() for pub in publications)
last_author_count = sum(surname in pub['last_author'].lower() for pub in publications)
impacts_all = []
impacts = []

if not publications:
    print(f"No publications found for '{author_name}' within the specified date range.")
else:
    for pub in publications:
        imp_tmp = get_if(pub['journal_name'])
        impacts_all.append(imp_tmp)
        if surname in pub['first_author'].lower() or surname in pub['last_author'].lower():
            print(f"Publication ID: {pub['id']}")
            print(f"Title: {pub['title']}")
            print(f"Authors: {', '.join(pub['authors'])}")
            print(f"Article Type: {pub['article_type']}")
            print(f"Journal: {pub['journal_name']}")
            print('\n')
            impacts.append(imp_tmp)
    print(f"\nSummary for '{author_name}' (Publications from {start_year} to {end_year}):")
    print(f"Total publications: {total_publications}")
    print(f"Number of publications where '{author_name}' is the first author: {first_author_count}")
    print(f"Number of publications where '{author_name}' is the last author: {last_author_count}")
    print("\nPublications where the author is the first or last author:\n")
    print("First or Last")
    num_zeros = impacts.count(0)
    impacts = [x for x in impacts if x != 0]
    median = statistics.median(impacts)
    iqr = statistics.median_grouped(impacts)
    print("Number of zeros:", num_zeros)
    print("Median:", median)
    print("IQR:", iqr)

    print("\nALL")
    num_zeros = impacts_all.count(0)
    impacts = [x for x in impacts_all if x != 0]
    median = statistics.median(impacts_all)
    iqr = statistics.median_grouped(impacts_all)
    print("Number of zeros:", num_zeros)
    print("Median:", median)
    print("IQR:", iqr)