pyresearch_subsection.py

from optparse import OptionParser
from Bio import Entrez
from openpyxl import load_workbook, Workbook
from authors import outputAuthors
from journals import outputJournals
from pubmedHelpers import getPubmedIds, saveWorksheet, pubmedData
import numpy
from operator import itemgetter
from datetime import datetime
from tqdm import tqdm
import warnings
warnings.filterwarnings("ignore")
with open('config.txt', 'r') as f:
    Entrez.email = f.readline()

parser = OptionParser()
parser.add_option("-s", "--search", dest="searchTerm", help="search term")
parser.add_option("-i", "--input", dest="input", help="Name of input file")
parser.add_option("-t", "--title", dest="title", help="Name of worksheet")
(options, args) = parser.parse_args()
if len(options.searchTerm) == 0:
	print("Please input a search term with -s or --search")
	exit(1)
print("Search Term: %s") % options.searchTerm

date = datetime.now().strftime('%Y-%m-%d')
suffix = "-%s" % date

idlist = getPubmedIds(options.searchTerm)
total = len(idlist)
print("Number of articles: %s") % total

data = numpy.load('%s.npy' % options.input)
matched = list()
for record in tqdm(data):
	if record['PMID'] in idlist:
		matched.append(record)
publications = sorted(matched, key=itemgetter('Citations Rate', 'Citations'), reverse=True)

print('Saving to excel')
wb = load_workbook('%s.xlsx' % options.input)
saveWorksheet(wb, options.title, publications, options.searchTerm, orderedEntries=True, autoFilter=True)

wb.save('%s.xlsx' % options.input)
directory = 'subsections'
numpy.save('%s/%s.npy' % (directory, options.title), publications)

wb = Workbook()
subsections = pubmedData(wb, publications, options.searchTerm, suffix)
numpy.save('%s/%s-subsections.npy' % (directory, options.title), subsections)

authorData = outputAuthors(publications)
saveWorksheet(wb, 'Authors', authorData, searchTerm=options.searchTerm, autoFilter=True)

journalData = outputJournals(publications)
saveWorksheet(wb, 'Journals', journalData)

wb.save('%s/%s.xlsx' % (directory, options.title))