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pdf_extractor.py
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pdf_extractor.py
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import argparse
import logging
import sys
from pathlib import Path
import pandas as pd
# https://github.com/py-pdf/benchmarks
import pypdfium2 as pdfium
from tqdm import tqdm
from utils import setup_log
_logger = logging.getLogger(__name__)
def extract_pdf_name(pdf_url: str, dirname: str, pdf_suffix: str) -> str:
pdf_name = pdf_url.split('/')[-1]
if pdf_name[-4:] == '.pdf':
return str(Path(dirname) / pdf_name)
else:
return str(Path(dirname) / f'{pdf_name.split("/")[-1]}{pdf_suffix}.pdf')
def extract_text(filepath: str) -> str:
text = ""
with open(filepath, "rb") as f:
data = f.read()
pdf = pdfium.PdfDocument(data)
for i in range(len(pdf)):
page = pdf.get_page(i)
text_page = page.get_textpage()
text += text_page.get_text_range()
text += "\n"
[g.close() for g in (text_page, page)]
pdf.close()
return text
def extract_title(page: str, conference: str, year: str) -> str:
lines = page.split('\n', 20)
begin = -1
end = 0
for i, line in enumerate(lines):
clean_line = line.strip()
if begin == -1 and len(clean_line) > 0 and conference not in clean_line.lower() and year not in clean_line:
begin = i
elif begin != -1 and (len(clean_line) == 0 or len(clean_line) > 50):
end = i
break
title = ' '.join(w.strip() for w in lines[begin:end]).strip()
if title.upper() == title:
title = title.title()
if title.isnumeric():
return ''
return title
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description="Extract papers' titles and abstracts.")
parser.add_argument('-c', '--conference', type=str, required=True,
help='conference to scrape data')
parser.add_argument('-f', '--file', type=str, default='',
help='part of file name to debug')
parser.add_argument('-i', '--index', type=int, default=-1,
help='file index to debug')
parser.add_argument('-l', '--log_level', type=str, default='warning',
choices=('debug', 'info', 'warning',
'error', 'critical', 'print'),
help='log level to debug')
parser.add_argument('-p', '--use_paper_info', action='store_true',
help='paper infos file')
parser.add_argument('--pdf_suffix', type=str, default='',
help='pdf suffix')
parser.add_argument('-s', '--separator', type=str, default='<#sep#>',
help='csv separator')
parser.add_argument('-y', '--year', type=str, required=True,
help='year of the conference')
args = parser.parse_args()
log_dir = Path('logs/').expanduser()
log_dir.mkdir(exist_ok=True)
setup_log(args.log_level, log_dir / 'pdf_extractor.log')
conference_year_dir = Path('data') / args.conference / args.year
papers = conference_year_dir / 'papers'
papers = [str(p) for p in papers.glob('*.pdf')]
if len(papers) == 0:
_logger.error(f"Couldn't find any paper in {conference_year_dir / 'papers'}")
sys.exit(0)
if args.index != -1:
paper = papers[args.index]
elif len(args.file) > 0:
file_to_find = args.file.lower()
found_papers = [
s for s in papers if file_to_find in Path(s).name.lower()]
if len(found_papers) == 0:
_logger.error(
f"Couldn't find any paper with {args.file} in file name")
sys.exit(0)
elif len(found_papers) > 1:
_logger.info(
f'Found {len(found_papers)} papers with "{args.file}" in name. Using the first one: {found_papers[0]}')
paper = found_papers[0]
else:
paper = ''
if len(paper) > 0:
text = extract_text(paper)
title = extract_title(text, args.conference, args.year)
_logger.debug(
f'\nText from PDF:\n###########################\n{text}\n###########################')
_logger.info(f'\nPaper:\n{paper}')
_logger.info(f'\nTitle: \n{title}')
# _logger.info(f'\nText: \n{repr(text)}')
else:
if args.use_paper_info:
paper_info = conference_year_dir / 'paper_info.csv'
if paper_info.exists():
paper_info_df = pd.read_csv(paper_info, sep=';')
paper_info_df.loc[:, 'pdf_url'] = paper_info_df['pdf_url'].astype(str)
paper_info_df.loc[:, 'pdf_url'] = paper_info_df['pdf_url'].apply(
extract_pdf_name, dirname=str(Path(papers[0]).parent), pdf_suffix=args.pdf_suffix)
paper_info_df = paper_info_df.drop(columns=['abstract_url'])
paper_info_df = paper_info_df[paper_info_df.pdf_url.isin(set(papers))]
if len(paper_info_df) == 0:
_logger.error(f'No paper info found in {paper_info}')
raise ValueError(f'No paper info found in {paper_info}')
else:
_logger.warning('Paper info file does not exists. Doing without it')
args.use_paper_info = False
with open(conference_year_dir / 'pdfs.csv', 'w') as corpus_file:
with open(conference_year_dir / 'errors.txt', 'w') as error_file:
corpus_file.write(f'title{args.separator}paper\n')
if args.use_paper_info:
with tqdm(paper_info_df.iterrows(), total=len(paper_info_df), unit='paper') as pbar:
for index, row in pbar:
pbar.set_description(Path(row['pdf_url']).name[:50])
try:
text = extract_text(row['pdf_url'])
title = row['title']
corpus_file.write(
f'{title}{args.separator}{repr(text)}\n')
except Exception:
_logger.exception(f'Error while extracting text of {Path(row["pdf_url"]).name}')
error_file.write(f'Error while extracting text of {Path(row["pdf_url"]).name}\n')
else:
with tqdm(papers, total=len(papers), unit='paper') as pbar:
for paper in pbar:
pbar.set_description(Path(paper).name[:50])
try:
text = extract_text(paper)
title = extract_title(text, args.conference, args.year)
corpus_file.write(
f'{title}{args.separator}{repr(text)}\n')
except Exception:
_logger.exception(f'Error while extracting text of {Path(paper).name}')
error_file.write(f'Error while extracting text of {Path(paper).name}\n')