aboutsummaryrefslogtreecommitdiffstats
path: root/python/fatcat_tools/importers/datacite.py
blob: 322e3db9400ec15da1e84b906807b80013a149aa (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
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
"""
Prototype Importer for datacite.org data.

Example doc at: https://gist.github.com/miku/5610a2d64e3fee82d16f5d3f3a295fc8
"""

from .common import EntityImporter, clean
import dateparser
import datetime
import fatcat_openapi_client
import hashlib
import json
import pycountry
import langdetect
import sqlite3
import sys
from fatcat_tools.transforms import entity_to_dict


# Cutoff length for abstracts.
MAX_ABSTRACT_LENGTH = 2048

# https://guide.fatcat.wiki/entity_container.html#container_type-vocabulary
CONTAINER_TYPE_MAP = {
    'Journal': 'journal',
    'Series': 'journal',
    'Book Series': 'book-series',
}

# The docs/guide should be the cannonical home for these mappings; update there
# first.  Map various datacite type types to CSL-ish types. None means TODO or
# remove.
DATACITE_TYPE_MAP = {
    'ris': {
        'THES': 'thesis',
        'SOUND': None,
        'CHAP': 'chapter',
        'FIGURE': None,
        'RPRT': 'report',
        'JOUR': 'article-journal',
        'MPCT': None,
        'GEN': None,
        'BOOK': 'book',
        'DATA': 'dataset',
        'COMP': None,
    },
    'schemaOrg': {
        'Dataset': 'dataset',
        'Book': 'book',
        'ScholarlyArticle': 'article',
        'ImageObject': 'graphic',
        'Collection': None,
        'MediaObject': None,
        'Event': None,
        'SoftwareSourceCode': None,
        'Chapter': 'chapter',
        'CreativeWork': None,
        'PublicationIssue': 'article',
        'AudioObject': None,
        'Thesis': 'thesis',
    },
    'citeproc': {
        'article': 'article',
        'article-journal': 'article-journal',
        'article-magazine': 'article-magazine',
        'article-newspaper': 'article-newspaper',
        'bill': 'bill',
        'book': 'book',
        'broadcast': 'broadcast',
        'chapter': 'chapter',
        'dataset': 'dataset',
        'entry-dictionary': 'entry-dictionary',
        'entry-encyclopedia': 'entry-encyclopedia',
        'entry': 'entry',
        'figure': 'figure',
        'graphic': 'graphic',
        'interview': 'interview',
        'legal_case': 'legal_case',
        'legislation': 'legislation',
        'manuscript': 'manuscript',
        'map': 'map',
        'motion_picture': 'motion_picture',
        'musical_score': 'musical_score',
        'pamphlet': 'pamphlet',
        'paper-conference': 'paper-conference',
        'patent': 'patent',
        'personal_communication': 'personal_communication',
        'post': 'post',
        'post-weblog': 'post-weblog',
        'report': 'report',
        'review-book': 'review-book',
        'review': 'review',
        'song': 'song',
        'speech': 'speech',
        'thesis': 'thesis',
        'treaty': 'treaty',
        'webpage': 'webpage',
    },  # https://docs.citationstyles.org/en/master/specification.html#appendix-iii-types
    'bibtex': {
        'phdthesis': 'thesis',
        'inbook': 'chapter',
        'misc': None,
        'article': 'article-journal',
        'book': 'book',
    },
    'resourceTypeGeneral': {
        'Image': None,
        'Dataset': 'dataset',
        'PhysicalObject': None,
        'Collection': None,
        'Text': None,
        'Sound': None,
        'InteractiveResource': None,
        'Event': None,
        'Software': None,
        'Other': None,
        'Workflow': None,
        'Audiovisual': None,
    }
}

# TODO(martin): merge this with other maps, maybe.
LICENSE_SLUG_MAP = {
    "//creativecommons.org/licenses/by/2.0/": "CC-BY",
    "//creativecommons.org/licenses/by/2.0/uk/legalcode": "CC-BY",
    "//creativecommons.org/licenses/by/3.0/": "CC-BY",
    "//creativecommons.org/licenses/by/3.0/us": "CC-BY",
    "//creativecommons.org/licenses/by/4.0/": "CC-BY",
    "//creativecommons.org/licenses/by/4.0/deed.de/": "CC-BY",
    "//creativecommons.org/licenses/by/4.0/deed.en_US/": "CC-BY",
    "//creativecommons.org/licenses/by/4.0/legalcode/": "CC-BY",
    "//creativecommons.org/licenses/by-nc/2.0/": "CC-BY-NC",
    "//creativecommons.org/licenses/by-nc/3.0/": "CC-BY-NC",
    "//creativecommons.org/licenses/by-nc/4.0/": "CC-BY-NC",
    "//creativecommons.org/licenses/by-nc/4.0/legalcode": "CC-BY-NC",
    "//creativecommons.org/licenses/by-nc-nd/3.0/": "CC-BY-NC-ND",
    "//creativecommons.org/licenses/by-nc-nd/3.0/gr": "CC-BY-NC-ND",
    "//creativecommons.org/licenses/by-nc-nd/4.0/": "CC-BY-ND",
    "//creativecommons.org/licenses/by-nc-nd/4.0/legalcode": "CC-BY-ND",
    "//creativecommons.org/licenses/by-nc-sa/4.0/": "CC-BY-NC-SA",
    "//creativecommons.org/licenses/by-nd/4.0/": "CC-BY-ND",
    "//creativecommons.org/licenses/by-sa/3.0/de": "CC-BY-SA",
    "//creativecommons.org/licenses/by-sa/3.0/gr": "CC-BY-SA",
    "//creativecommons.org/licenses/by-sa/4.0/": "CC-BY-SA",
    "//creativecommons.org/licenses/by-sa/4.0/legalcode": "CC-BY-SA",
    "//creativecommons.org/licenses/CC-BY/4.0/": "CC-BY",
    "//creativecommons.org/licenses/publicdomain/zero/1.0/": "CC-0",
    "//creativecommons.org/publicdomain/zero/1.0/": "CC-0",
    "//creativecommons.org/publicdomain/zero/1.0/legalcode": "CC-0",
    "//opensource.org/licenses/MIT": "MIT",
    "//www.elsevier.com/open-access/userlicense/1.0": "ELSEVIER-USER-1.0",
    "//www.gnu.org/licenses/gpl-3.0.en.html": "GPLv3",
    "//www.gnu.org/licenses/old-licenses/gpl-2.0.en.html": "GPLv2",
    "//www.karger.com/Services/SiteLicenses": "KARGER",
    "//www.opensource.org/licenses/Apache-2.0": "Apache-2.0",
    "//www.opensource.org/licenses/BSD-3-Clause": "BSD-3-Clause",
    "//www.opensource.org/licenses/EUPL-1.1":
    "EUPL-1.1",  # redirects to EUPL-1.2
    "//www.opensource.org/licenses/MIT": "MIT",
    # "http://royalsocietypublishing.org/licence": "", # OA and "normal", https://royalsociety.org/journals/authors/licence-to-publish/
    # "http://rsc.li/journals-terms-of-use": "RSC",
    # "http://www.fu-berlin.de/sites/refubium/rechtliches/Nutzungsbedingungen": "", # 53 UrhG.
    # "http://www.nrcresearchpress.com/page/about/CorporateTextAndDataMining": "",
    # "http://www.springer.com/tdm": "",
    # "https://cds.unistra.fr/vizier-org/licences_vizier.html": "", # Maybe try to "SPN" those: https://web.archive.org/web/*/https://cds.unistra.fr/vizier-org/licences_vizier.html
    # "https://link.aps.org/licenses/aps-default-accepted-manuscript-license": "",
    # "https://oparu.uni-ulm.de/xmlui/license_opod_v1": "",
    # "https://publikationen.bibliothek.kit.edu/kitopen-lizenz": "",
    # "https://rightsstatements.org/page/InC/1.0?language=en": "",
    # "https://services.ceda.ac.uk/cedasite/register/info": "",
    # "https://wdc.dlr.de/ndmc/userfiles/file/NDMC-Data_Sharing_Principles.pdf": "", # 404
    # "https://www.cambridge.org/core/terms": "",
    # "https://www.elsevier.com/tdm/userlicense/1.0",
    # "info:eu-repo/semantics/closedAccess": "", # https://wiki.surfnet.nl/display/standards/info-eu-repo/#info-eu-repo-AccessRights
    # "info:eu-repo/semantics/embargoedAccess": "",
    # "info:eu-repo/semantics/openAccess": "",
    # Note: Some URLs pointing to licensing terms are not in WB yet (but would be nice).
}


class DataciteImporter(EntityImporter):
    """
    Importer for datacite records.
    """
    def __init__(self,
                 api,
                 issn_map_file,
                 debug=False,
                 lang_detect=False,
                 insert_log_file=None,
                 **kwargs):

        eg_desc = kwargs.get(
            'editgroup_description',
            "Automated import of Datacite DOI metadata, harvested from REST API"
        )
        eg_extra = kwargs.get('editgroup_extra', dict())
        eg_extra['agent'] = eg_extra.get('agent',
                                         'fatcat_tools.DataciteImporter')
        super().__init__(api,
                         issn_map_file=issn_map_file,
                         editgroup_description=eg_desc,
                         editgroup_extra=eg_extra,
                         **kwargs)

        self.create_containers = kwargs.get('create_containers', True)
        extid_map_file = kwargs.get('extid_map_file')
        self.extid_map_db = None
        if extid_map_file:
            db_uri = "file:{}?mode=ro".format(extid_map_file)
            print("Using external ID map: {}".format(db_uri), file=sys.stderr)
            self.extid_map_db = sqlite3.connect(db_uri, uri=True)
        else:
            print("Not using external ID map", file=sys.stderr)

        self.read_issn_map_file(issn_map_file)
        self.debug = debug
        self.lang_detect = lang_detect
        self.insert_log_file = insert_log_file

        print('datacite with debug={}, lang_detect={}'.format(
            self.debug, self.lang_detect),
              file=sys.stderr)

    def lookup_ext_ids(self, doi):
        """
        Return dictionary of identifiers refering to the same things as the given DOI.
        """
        if self.extid_map_db is None:
            return dict(core_id=None,
                        pmid=None,
                        pmcid=None,
                        wikidata_qid=None,
                        arxiv_id=None,
                        jstor_id=None)
        row = self.extid_map_db.execute(
            "SELECT core, pmid, pmcid, wikidata FROM ids WHERE doi=? LIMIT 1",
            [doi.lower()]).fetchone()
        if row is None:
            return dict(core_id=None,
                        pmid=None,
                        pmcid=None,
                        wikidata_qid=None,
                        arxiv_id=None,
                        jstor_id=None)
        row = [str(cell or '') or None for cell in row]
        return dict(
            core_id=row[0],
            pmid=row[1],
            pmcid=row[2],
            wikidata_qid=row[3],
            # TODO:
            arxiv_id=None,
            jstor_id=None,
        )

    def parse_record(self, obj):
        """
        Mapping datacite JSON to ReleaseEntity.
        """
        if not obj or not isinstance(obj, dict):
            return None
        if 'attributes' not in obj:
            return None

        attributes = obj['attributes']
        doi = attributes.get('doi', '').lower()

        # Contributors. Many nameIdentifierSchemes, we do not use (yet):
        # "attributes.creators[].nameIdentifiers[].nameIdentifierScheme":
        # ["LCNA", "GND", "email", "NAF", "OSF", "RRID", "ORCID",
        # "SCOPUS", "NRCPID", "schema.org", "GRID", "MGDS", "VIAF", "JACoW-ID"].
        contribs = []

        for i, c in enumerate(attributes['creators']):
            nameType = c.get('nameType', '') or ''
            if nameType == 'Personal':
                creator_id = None
                for nid in c.get('nameIdentifiers', []):
                    if not nid.get('nameIdentifierScheme').lower() == "orcid":
                        continue
                    orcid = nid.get('nameIdentifier',
                                    '').replace('https://orcid.org/', '')
                    if not orcid:
                        continue
                    creator_id = self.lookup_orcid(orcid)
                    # TODO(martin): If creator_id is None, should we create creators?

                # If there are multiple affiliation strings, use the first one.
                affiliations = c.get('affiliation', []) or []
                raw_affiliation = None
                if len(affiliations) == 0:
                    raw_affiliation = None
                else:
                    raw_affiliation = clean(affiliations[0])

                name = c.get('name')
                given_name = c.get('givenName')
                surname = c.get('familyName')

                if name:
                    name = clean(name)

                if given_name:
                    given_name = clean(given_name)

                if surname:
                    surname = clean(surname)

                contribs.append(
                    fatcat_openapi_client.ReleaseContrib(
                        creator_id=creator_id,
                        index=i,
                        raw_name=c.get('name'),
                        given_name=c.get('givenName'),
                        surname=c.get('familyName'),
                        role='author',
                        raw_affiliation=raw_affiliation,
                    ))
            elif nameType == 'Organizational':
                name = c.get('name', '') or ''
                if name == 'NN':
                    continue
                if len(name) < 3:
                    continue
                extra = {'organization': name}
                contribs.append(fatcat_openapi_client.ReleaseContrib(
                    index=i, extra=extra))
            else:
                print('[{}] unknown name type: {}'.format(doi, nameType), file=sys.stderr)

        # Title, may come with "attributes.titles[].titleType", like
        # "AlternativeTitle", "Other", "Subtitle", "TranslatedTitle"
        titles = attributes.get('titles', []) or []
        title, original_language_title, subtitle = parse_datacite_titles(
            titles)

        if not title:
            print('[{}] skipping record w/o title: {}'.format(doi, obj), file=sys.stderr)
            return False
        else:
            title = clean(title)

        if not subtitle:
            subtitle = None
        else:
            subtitle = clean(subtitle)

        # Dates. A few internal dates (registered, created, updated) and
        # published (0..2554). We try to work with typed date list, in
        # "attributes.dates[].dateType", values: "Accepted", "Available"
        # "Collected", "Copyrighted", "Created", "Issued", "Submitted",
        # "Updated", "Valid".
        release_date, release_year = parse_datacite_dates(
            attributes.get('dates', []))

        # Publisher. A few NA values. A few bogus values.
        publisher = attributes.get('publisher')

        if publisher in ('(:unav)', 'Unknown', 'n.a.', '[s.n.]', '(:unap)',
                         '(:none)'):
            publisher = None
        if publisher is not None and len(publisher) > 80:
            # Arbitrary magic value max length. TODO(martin): better heuristic,
            # but factored out; first we have to log misses. Example:
            # "ETH-Bibliothek Zürich, Bildarchiv / Fotograf: Feller,
            # Elisabeth, Empfänger, Unbekannt, Fotograf / Fel_041033-RE /
            # Unbekannt, Nutzungsrechte müssen durch den Nutzer abgeklärt
            # werden"
            publisher = None

        if publisher:
            publisher = clean(publisher)

        # Container. For the moment, only ISSN as container.
        container_id = None
        container_name = None

        container = attributes.get('container', {}) or {}
        if container.get('type') in CONTAINER_TYPE_MAP.keys():
            container_type = CONTAINER_TYPE_MAP.get(container['type'])
            if container.get('identifier') and container.get(
                    'identifierType') == 'ISSN':
                issn = container.get('identifier')
                if len(issn) == 8:
                    issn = issn[:4] + "-" + issn[4:]
                issnl = self.issn2issnl(issn)
                if issnl is not None:
                    container_id = self.lookup_issnl(issnl)

                    if container_id is None and container.get('title'):
                        container_name = container.get('title')
                        if isinstance(container_name, list):
                            if len(container_name) > 0:
                                print('[{}] too many container titles: {}'.format(doi,
                                    len(container_name)))
                                container_name = container_name[0]
                        assert isinstance(container_name, str)
                        ce = fatcat_openapi_client.ContainerEntity(
                            issnl=issnl,
                            container_type=container_type,
                            name=container_name,
                        )
                        ce_edit = self.create_container(ce)
                        container_id = ce_edit.ident
                        self._issnl_id_map[issnl] = container_id
                else:
                    # TODO(martin): factor this out into a testable function.
                    # TODO(martin): "container_name": "№1(1) (2018)" / 10.26087/inasan.2018.1.1.013
                    container_name = container.get('title')
                    if isinstance(container_name, list):
                        if len(container_name) > 0:
                            print('[{}] too many container titles: {}'.format(doi,
                                len(container_name)))
                            container_name = container_name[0]

        # Volume and issue.
        volume = container.get('volume')
        issue = container.get('issue')

        if volume:
            volume = clean(volume)

        if issue:
            issue = clean(issue)

        # Pages.
        pages = None

        first_page = container.get('firstPage')
        last_page = container.get('lastPage')

        if first_page and last_page:
            try:
                int(first_page) < int(last_page)
                pages = '{}-{}'.format(first_page, last_page)
            except ValueError as err:
                print('[{}] {}'.format(doi, err), file=sys.stderr)
                pass

        if not pages and first_page:
            pages = first_page

        # License.
        license_slug = None
        license_extra = []

        for l in attributes.get('rightsList', []):
            slug = lookup_license_slug(l.get('rightsUri'))
            if slug:
                license_slug = slug
            license_extra.append(l)

        # Release type. Try to determine the release type from a variety of
        # types supplied in datacite. The "attributes.types.resourceType"
        # contains too many (176 in sample) things for now; citeproc may be the
        # closest, but not always supplied.
        for typeType in ('citeproc', 'resourceTypeGeneral', 'schemaOrg',
                         'bibtex', 'ris'):
            value = attributes.get('types', {}).get(typeType)
            release_type = DATACITE_TYPE_MAP.get(typeType, {}).get(value)
            if release_type is not None:
                break

        if release_type is None:
            print("[{}] no mapped type: {}".format(doi, value), file=sys.stderr)

        # Language values are varied ("ger", "es", "English", "ENG", "en-us",
        # "other", ...). Try to crush it with langcodes: "It may sound to you
        # like langcodes solves a pretty boring problem. At one level, that's
        # right. Sometimes you have a boring problem, and it's great when a
        # library solves it for you." -- TODO(martin): We need more of these.
        language = None

        value = attributes.get('language', '') or ''
        try:
            language = pycountry.languages.lookup(value).alpha_2
        except (LookupError, AttributeError) as err:
            print('[{}] language lookup miss for {}: {}'.format(doi, value, err), file=sys.stderr)

        # Abstracts appear in "attributes.descriptions[].descriptionType", some
        # of the observed values: "Methods", "TechnicalInfo",
        # "SeriesInformation", "Other", "TableOfContents", "Abstract". The
        # "Other" fields might contain references or related articles (with
        # DOI). TODO(martin): maybe try to parse out some of those refs.
        abstracts = []
        descs = attributes.get('descriptions', []) or []
        for desc in descs:
            if not desc.get('descriptionType') == 'Abstract':
                continue
            if len(desc.get('description', '')) < 10:
                continue
            text = desc.get('description')
            if len(text) > MAX_ABSTRACT_LENGTH:
                text = text[:MAX_ABSTRACT_LENGTH] + " [...]"
            lang = None
            if self.lang_detect:
                try:
                    lang = langdetect.detect(text)
                except langdetect.lang_detect_exception.LangDetectException as err:
                    print('[{}] language detection failed: {}'.format(doi, err),
                          file=sys.stderr)
            abstracts.append(
                fatcat_openapi_client.ReleaseAbstract(
                    mimetype="text/plain",
                    content=text,
                    lang=lang,
                ))

        # References and relations. Datacite include many relation types in
        # "attributes.relatedIdentifiers[].relationType", e.g.
        # "IsPartOf", "IsPreviousVersionOf", "Continues", "IsVariantFormOf",
        # "IsSupplementTo", "Cites", "IsSupplementedBy", "IsDocumentedBy", "HasVersion",
        # "IsCitedBy", "IsMetadataFor", "IsNewVersionOf", "IsIdenticalTo", "HasPart",
        # "References", "Reviews", "HasMetadata", "IsContinuedBy", "IsVersionOf",
        # "IsDerivedFrom", "IsSourceOf".
        #
        # For the moment, we only care about References.
        refs, ref_index = [], 0

        relIds = attributes.get('relatedIdentifiers', []) or []
        for rel in relIds:
            if not rel.get('relationType') == 'References':
                continue
            ref_extra = dict()
            if rel.get('relatedIdentifierType') == 'DOI':
                ref_extra['doi'] = rel.get('relatedIdentifier')
            if not ref_extra:
                ref_extra = None
            refs.append(
                fatcat_openapi_client.ReleaseRef(
                    index=ref_index,
                    extra=ref_extra,
                ))
            ref_index += 1

        # Start with clear stages, e.g. published. TODO(martin): we could
        # probably infer a bit more from the relations, e.g.
        # "IsPreviousVersionOf" or "IsNewVersionOf".
        release_stage = None
        if attributes.get(
                'state') == 'findable' or attributes.get('isActive') is True:
            release_stage = 'published'

        # Extra information.
        extra_datacite = dict()

        if license_extra:
            extra_datacite['license'] = license_extra
        if attributes.get('subjects'):
            extra_datacite['subjects'] = attributes['subjects']

        # Include certain relations from relatedIdentifiers. Keeping the
        # original structure of data here, which is a list of dicts, with
        # relation type, identifer and identifier type (mostly).
        relations = []
        for rel in relIds:
            if rel.get('relationType') in ('IsPartOf', 'Reviews', 'Continues',
                                           'IsVariantFormOf', 'IsSupplementTo',
                                           'HasVersion', 'IsMetadataFor',
                                           'IsNewVersionOf', 'IsIdenticalTo',
                                           'IsVersionOf', 'IsDerivedFrom',
                                           'IsSourceOf'):
                relations.append(rel)

        if relations:
            extra_datacite['relations'] = relations

        extra = dict()

        # top-level extra keys
        if not container_id and container_name:
            extra['container_name'] = container_name

        if extra_datacite:
            extra['datacite'] = extra_datacite

        extids = self.lookup_ext_ids(doi=doi)

        # Assemble release.
        re = fatcat_openapi_client.ReleaseEntity(
            work_id=None,
            container_id=container_id,
            release_type=release_type,
            release_stage=release_stage,
            title=title,
            subtitle=subtitle,
            original_title=original_language_title,
            release_year=release_year,
            release_date=release_date,
            publisher=publisher,
            ext_ids=fatcat_openapi_client.ReleaseExtIds(
                doi=doi,
                pmid=extids['pmid'],
                pmcid=extids['pmcid'],
                wikidata_qid=extids['wikidata_qid'],
                core=extids['core_id'],
                arxiv=extids['arxiv_id'],
                jstor=extids['jstor_id'],
            ),
            contribs=contribs,
            volume=volume,
            issue=issue,
            pages=pages,
            language=language,
            abstracts=abstracts,
            refs=refs,
            extra=extra,
            license_slug=license_slug,
        )
        return re

    def try_update(self, re):
        """
        When debug is true, write the RE to stdout, not to the database. Might
        hide schema mismatch bugs.
        """
        if self.debug is True:
            print(json.dumps(entity_to_dict(re, api_client=None)))
            return False

        # lookup existing DOI (don't need to try other ext idents for crossref)
        existing = None
        try:
            existing = self.api.lookup_release(doi=re.ext_ids.doi)
        except fatcat_openapi_client.rest.ApiException as err:
            if err.status != 404:
                raise err
            # doesn't exist, need to update
            return True

        # eventually we'll want to support "updates", but for now just skip if
        # entity already exists
        if existing:
            self.counts['exists'] += 1
            return False

        return True

    def insert_batch(self, batch):
        print('inserting batch ({})'.format(len(batch)), file=sys.stderr)
        if self.insert_log_file:
            with open(self.insert_log_file, 'a') as f:
                for doc in batch:
                    json.dump(entity_to_dict(re, api_client=None), f)
                    f.write('\n')
        self.api.create_release_auto_batch(
            fatcat_openapi_client.ReleaseAutoBatch(
                editgroup=fatcat_openapi_client.Editgroup(
                    description=self.editgroup_description,
                    extra=self.editgroup_extra),
                entity_list=batch))


def lookup_license_slug(raw):
    """
    TODO(martin): reuse from or combine with crossref, maybe.
    """
    if not raw:
        return None
    raw = raw.strip().replace('http://', '//').replace('https://', '//')
    if 'creativecommons.org' in raw.lower():
        raw = raw.lower()
        raw = raw.replace('/legalcode', '/').replace('/uk', '')
        if not raw.endswith('/'):
            raw = raw + '/'
    return LICENSE_SLUG_MAP.get(raw)


def find_original_language_title(item, min_length=4, max_questionmarks=3):
    """
    Perform a few checks before returning a potential original language title.
    """
    if not 'original_language_title' in item:
        return None
    title = item.get('title')
    if not title:
        return None
    original_language_title = item.get('original_language_title')
    if isinstance(original_language_title,
                  str) and title != original_language_title:
        if len(original_language_title) < min_length:
            return None
        if original_language_title.count('?') > max_questionmarks:
            return None
        return original_language_title
    if isinstance(original_language_title, dict):
        content = original_language_title.get('__content__', '') or ''
        if content and content != title and not content.count(
                '?') > max_questionmarks:
            return content
    return None


def parse_datacite_titles(titles):
    """
    Given a list of title items from datacite, return 3-tuple (title,
    original_language_title, subtitle).

    Example input:

        [
            {
                 "title": "Meeting Heterogeneity in Consumer Demand"
            }
        ]
    """
    title, original_language_title, subtitle = None, None, None

    if titles is None:
        return title, original_language_title, subtitle
    if len(titles) == 0:
        return title, original_language_title, subtitle
    elif len(titles) == 1:
        original_language_title = find_original_language_title(titles[0])
        title = titles[0].get('title', '') or ''
        title = title.strip()
        if not title:
            title = None
        return title, original_language_title, subtitle
    else:
        for entry in titles:
            if not title and ('titleType' not in entry
                              or not entry.get('titleType')):
                title = entry.get('title').strip()
            if not subtitle and entry.get('titleType') == 'Subtitle':
                subtitle = entry.get('title', '').strip()
            if not original_language_title:
                original_language_title = find_original_language_title(entry)

    return title, original_language_title, subtitle


def parse_datacite_dates(dates):
    """
    Given a list of date fields (under .dates), return tuple, (release_date,
    release_year).
    """
    release_date, release_year = None, None

    if not dates:
        return release_date, release_year

    if not isinstance(dates, list):
        raise ValueError('expected a list of date items')

    # Ignored: Collected, Issued.
    date_type_prio = (
        'Valid',
        'Available',
        'Accepted',
        'Submitted',
        'Copyrighted',
        'Created',
        'Updated',
    )

    # Before using (expensive) dateparser, try a few common patterns.
    common_patterns = ('%Y-%m-%d', '%Y-%m', '%Y-%m-%dT%H:%M:%SZ',
                       '%Y-%m-%dT%H:%M:%S', '%Y')

    def parse_item(item):
        result, value, year_only = None, item.get('date', ''), False
        release_date, release_year = None, None

        for pattern in common_patterns:
            try:
                result = datetime.datetime.strptime(value, pattern)
            except ValueError:
                continue
            else:
                if pattern == '%Y':
                    year_only = True
                break

        if result is None:
            print('fallback for {}'.format(value), file=sys.stderr)
            try:
                result = dateparser.parse(value)
            except TypeError as err:
                print("{} date parsing failed with: {}".format(value, err),
                      file=sys.stderr)
                return result_date, result_year

        if result is None:
            # Unparsable date.
            return release_date, release_year

        if not year_only:
            release_date = result.date()
        release_year = result.year

        return release_date, release_year

    for prio in date_type_prio:
        for item in dates:
            if not item.get('dateType') == prio:
                continue

            release_date, release_year = parse_item(item)
            if release_date is None and release_year is None:
                continue

            if release_year < 1000 or release_year > datetime.date.today(
            ).year + 5:
                # Skip possibly bogus dates.
                release_year = None
                continue
            break
        else:
            continue
        break

    if release_date is None and release_year is None:
        for item in dates:
            release_date, release_year = parse_item(item)
            if release_year or release_date:
                break

    return release_date, release_year