aboutsummaryrefslogtreecommitdiffstats
path: root/python/scripts/unpaywall2ingestrequest.py
blob: c51a152048e80452c3050f1551d91f44a7b449b1 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
#!/usr/bin/python3

"""
Transform an unpaywall dump (JSON) into ingest requests.
"""

import sys
import json
import argparse

DOMAIN_BLOCKLIST = [
    # large OA publishers (we get via DOI)

    # large repos and aggregators (we crawl directly)
    "://arxiv.org/",
    "://europepmc.org/",
    "ncbi.nlm.nih.gov/",
    "semanticscholar.org/",
    "://doi.org/",
    "zenodo.org/",
    "figshare.com/",
    "://archive.org/",
    ".archive.org/",
]

RELEASE_STAGE_MAP = {
    'draftVersion':     'draft',
    'submittedVersion': 'submitted',
    'acceptedVersion':  'accepted',
    'publishedVersion': 'published',
    'updatedVersion':   'updated',
}


def transform(obj):
    """
    Transforms from a single unpaywall object to zero or more ingest requests.
    Returns a list of dicts.
    """

    requests = []
    if not obj['doi'].startswith('10.'):
        return requests
    if not obj['oa_locations']:
        return requests

    for location in obj['oa_locations']:
        if not location['url_for_pdf']:
            continue
        skip = False
        for domain in DOMAIN_BLOCKLIST:
            if domain in location['url_for_pdf']:
                skip = True
        if skip:
            continue

        request = {
            'base_url': location['url_for_pdf'],
            'ingest_type': 'pdf',
            'link_source': 'unpaywall',
            'link_source_id': obj['doi'].lower(),
            'ingest_request_source': 'unpaywall',
            'release_stage': RELEASE_STAGE_MAP.get(location['version']),
            'rel': location['host_type'],
            'ext_ids': {
                'doi': obj['doi'].lower(),
            },
            'edit_extra': {},
        }
        if obj.get('oa_status'):
            request['edit_extra']['oa_status'] = obj['oa_status']
        if location.get('evidence'):
            request['edit_extra']['evidence'] = location['evidence']
        if location['pmh_id']:
            request['ext_ids']['pmh_id'] = location['pmh_id']
        requests.append(request)

    return requests

def run(args):
    for l in args.json_file:
        if not l.strip():
            continue
        row = json.loads(l)

        requests = transform(row) or []
        for r in requests:
            print("{}".format(json.dumps(r, sort_keys=True)))

def main():
    parser = argparse.ArgumentParser(
        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    parser.add_argument('json_file',
        help="unpaywall dump file to use",
        type=argparse.FileType('r'))
    subparsers = parser.add_subparsers()

    args = parser.parse_args()

    run(args)

if __name__ == '__main__':
    main()