match_to_arxiv.py

import sys, os
import argparse
from adsputils import setup_logging
from pub_parser import get_pub_metadata
from from_oracle import get_matches
from common import get_filenames, format_results, write_for_inspection_hits

logger = setup_logging('docmatch_log')

def match_to_arXiv(filename):
    """
    read and parse arXiv metadata file
    return list of bibcodes and scores for the matches in decreasing order

    :param filename:
    :return:
    """
    try:
        with open(filename, 'rb') as pub_fp:
            return get_matches(get_pub_metadata(pub_fp.read()), 'article')
    except Exception as e:
        logger.error('Exception: %s'%e)
        return

def single_match_to_arXiv(pub_filename):
    """
    when user submits a single pub metadata file for matching

    :param pub_filename:
    :return:
    """
    results = match_to_arXiv(pub_filename)
    if results:
        return format_results(results, '\t')
    return None,None

def single_match_output(pub_filename):
    """

    :param pub_filename:
    :return:
    """
    a_match, for_inspection = single_match_to_arXiv(pub_filename)
    print(a_match)
    if for_inspection:
        print(for_inspection)

def batch_match_to_arXiv(filename, result_filename):
    """

    :param filename:
    :param result_filename:
    :return:
    """
    filenames = get_filenames(filename)
    if len(filenames) > 0:
        if result_filename:
            # output file
            with open(result_filename, 'w') as fp:
                # one file at a time, parse and score, and then write the result to the file
                for arXiv_filename in filenames:
                    a_match, for_inspection = single_match_to_arXiv(arXiv_filename)
                    fp.write('%s\r\n'%a_match)
                    if for_inspection:
                        write_for_inspection_hits(result_filename, for_inspection)
        else:
            for pub_filename in filenames:
                single_match_output(pub_filename)

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Match Publisher with arXiv')
    parser.add_argument('-i', '--input', help='the path to an input file containing list of arXiv metadata files for processing.')
    parser.add_argument('-s', '--single', help='the path to a single metadata file for processing.')
    parser.add_argument('-o', '--output', help='the output file name to write the result, else the result shall be written to console.')
    args = parser.parse_args()
    if args.input:
        batch_match_to_arXiv(filename=args.input, result_filename=args.output)
    elif args.single:
        single_match_output(pub_filename=args.single)
    # test mode
    else:
        pub_path = os.environ.get('PUB_DOCMATCHING_PATH')

        matched, _ = single_match_to_arXiv(pub_filename='%s%s'%(pub_path,'K47/K47-02665.abs'))
        matched = matched.split('\t')
        assert(matched[0] == '2018ApJS..236...24F')
        assert(matched[1] == '...................')
        assert(matched[2] == '0')
        assert(matched[3] == '')
        assert(matched[4] == 'No result from solr with Abstract, trying Title. No document was found in solr matching the request.')

        matched, _ = single_match_to_arXiv(pub_filename='%s%s'%(pub_path,'J05/J05-12407.abs'))
        matched = matched.split('\t')
        assert(matched[0] == '2005JASIS..56...36K')
        assert(matched[1] == '...................')
        assert(matched[2] == '0')
        assert(matched[3] == '')
        assert(matched[4] == 'No matches with Abstract, trying Title. No result from solr with Title. No document was found in solr matching the request.')

        print('both tests pass')

    sys.exit(0)