aboutsummaryrefslogtreecommitdiffstats
path: root/python/fatcat_tools/importers/grobid_metadata.py
blob: 5e61a154dc32a17143470ae7500384457fc2fe0d (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
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
#!/usr/bin/env python3

import sys
import json
import base64
import datetime
import fatcat_client
from .common import FatcatImporter

MAX_ABSTRACT_BYTES=4096


class GrobidMetadataImporter(FatcatImporter):

    def __init__(self, api, **kwargs):

        eg_desc = kwargs.get('editgroup_description',
            "Import of release and file metadata, as extracted from PDFs by GROBID.")
        eg_extra = kwargs.get('editgroup_extra', dict())
        eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.GrobidMetadataImporter')
        super().__init__(api,
            editgroup_description=eg_desc,
            editgroup_extra=eg_extra)
        self.default_link_rel = kwargs.get("default_link_rel", "web")

    def parse_grobid_json(self, obj):

        if not obj.get('title'):
            return None

        extra = dict()

        if obj.get('abstract') and len(obj.get('abstract')) < MAX_ABSTRACT_BYTES:
            abobj = dict(
                mimetype="text/plain",
                language=None,
                content=obj.get('abstract').strip())
            abstracts = [abobj]
        else:
            abstracts = None

        contribs = []
        for i, a in enumerate(obj.get('authors', [])):
            contribs.append(fatcat_client.ReleaseContrib(
                index=i,
                raw_name=a['name'],
                role="author",
                extra=None))

        refs = []
        for raw in obj.get('citations', []):
            cite_extra = dict()
            ref = dict()
            ref['key'] = raw.get('id')
            if raw.get('title'):
                ref['title'] = raw['title'].strip()
            if raw.get('date'):
                try:
                    year = int(raw['date'].strip()[:4])
                    ref['year'] = year
                except:
                    pass
            for key in ('volume', 'url', 'issue', 'publisher'):
                if raw.get(key):
                    cite_extra[key] = raw[key].strip()
            if raw.get('authors'):
                cite_extra['authors'] = [a['name'] for a in raw['authors']]
            if cite_extra:
                cite_extra = dict(grobid=cite_extra)
            else:
                cite_extra = None
            ref['extra'] = cite_extra
            refs.append(ref)

        release_date = None
        release_year = None
        if obj.get('date'):
            # only returns year, ever?
            release_year = int(obj['date'][:4])

        if obj.get('doi'):
            extra['doi'] = obj['doi']
        if obj['journal'] and obj['journal'].get('name'):
            extra['container_name'] = obj['journal']['name']

        extra['is_longtail_oa'] = True

        # TODO: ISSN/eISSN handling? or just journal name lookup?

        if extra:
            extra = dict(grobid=extra)
        else:
            extra = None

        re = fatcat_client.ReleaseEntity(
            title=obj['title'].strip(),
            release_type="article-journal",
            release_date=release_date,
            release_year=release_year,
            contribs=contribs,
            refs=refs,
            publisher=obj['journal'].get('publisher'),
            volume=obj['journal'].get('volume'),
            issue=obj['journal'].get('issue'),
            abstracts=abstracts,
            extra=extra)
        return re

    # TODO: make this a common function somewhere
    def make_url(self, raw):
        rel = self.default_link_rel
        # TODO: this is where we could map specific domains to rel types,
        # and also filter out bad domains, invalid URLs, etc
        if "//archive.org/" in raw or "//arxiv.org/" in raw:
            # TODO: special-case the arxiv.org bulk mirror?
            rel = "repository"
        elif "//web.archive.org/" in raw or "//archive.is/" in raw:
            rel = "webarchive"
        return fatcat_client.FileEntityUrls(url=raw, rel=rel)

    def parse_file_metadata(self, sha1_key, cdx, mimetype, file_size):

        sha1 = base64.b16encode(base64.b32decode(sha1_key.replace('sha1:', ''))).decode('ascii').lower()

        # lookup existing SHA1, or create new entity
        try:
            existing_file = self.api.lookup_file(sha1=sha1)
        except fatcat_client.rest.ApiException as err:
            if err.status != 404:
                raise err
            existing_file = None

        if existing_file:
            # if file is already in here, presumably not actually long-tail
            return None
        fe = fatcat_client.FileEntity(
            sha1=sha1,
            size=int(file_size),
            mimetype=mimetype,
            release_ids=[],
            urls=[],
        )

        # parse URLs and CDX
        original = cdx['url']
        wayback = "https://web.archive.org/web/{}/{}".format(
            cdx['dt'],
            original)
        fe.urls.append(
            fatcat_client.FileEntityUrls(url=wayback, rel="webarchive"))
        original_url = self.make_url(original)
        if original_url is not None:
            fe.urls.append(original_url)

        return fe

    def create_row(self, row, editgroup_id=None):
        if not row:
            return
        fields = row.split('\t')
        sha1_key = fields[0]
        cdx = json.loads(fields[1])
        mimetype = fields[2]
        file_size = int(fields[3])
        grobid_meta = json.loads(fields[4])
        fe = self.parse_file_metadata(sha1_key, cdx, mimetype, file_size)
        re = self.parse_grobid_json(grobid_meta)
        if fe and re:
            release_entity = self.api.create_release(re, editgroup_id=editgroup_id)
            # release ident can't already be in release list because we just
            # created it
            fe.release_ids.append(release_entity.ident)
            file_entity = self.api.create_file(fe, editgroup_id=editgroup_id)
            self.counts['insert'] += 1

    # NB: batch mode not implemented