aboutsummaryrefslogtreecommitdiffstats
path: root/fatcat_scholar/transform.py
blob: 41ed4176f05345f42bce5e22068323ca15493586 (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
import sys
import argparse
import datetime
import xml.etree.ElementTree as ET
from typing import List, Dict, Optional, Any, Sequence

from fatcat_openapi_client import ReleaseEntity, FileEntity, WebcaptureEntity

from fatcat_scholar.api_entities import *
from fatcat_scholar.schema import *
from fatcat_scholar.config import settings
from fatcat_scholar.grobid2json import teixml2json


def es_fulltext_from_sim(sim: Dict[str, Any]) -> Optional[ScholarFulltext]:
    if not sim["page_texts"]:
        return None
    first_page = sim["page_texts"][0]["page_num"]
    issue_item = sim["issue_item"]
    return ScholarFulltext(
        lang_code=None,  # TODO: pub/issue metadata? or langdetect?
        body="\n".join([p["raw_text"] for p in sim["page_texts"]]),
        # acknowledgement=None,
        # annex=None,
        release_ident=sim.get("release_ident"),
        # file_ident=None,
        # file_sha1=None,
        # file_mimetype=None,
        thumbnail_url=f"https://archive.org/serve/{issue_item}/__ia_thumb.jpg",
        access_url=f"https://archive.org/details/{issue_item}/page/{first_page}",
        access_type=AccessType.ia_sim,
    )


def es_sim_from_sim(sim: Dict[str, Any]) -> ScholarSim:
    first_page = None
    if sim["page_texts"]:
        first_page = sim["page_texts"][0]["page_num"]
    return ScholarSim(
        issue_item=sim["issue_item"],
        pub_collection=sim["pub_item_metadata"]["metadata"]["identifier"],
        sim_pubid=sim["issue_item_metadata"]["metadata"]["sim_pubid"],
        first_page=first_page,
    )


SIM_RELEASE_TYPE_MAP = {
    "Scholarly Journals": "article-journal",
    "Trade Journals": "article-magazine",
    "Historical Journals": "article",
    "Magazines": "article-magazine",
    "Government Documents": "article",
    "Law Journals": "article",
    # TODO: more categories?
}
SIM_LANG_MAP = {
    "English": "en",
    "German": "de",
    "Italian": "it",
    "French": "fr",
    "Afrikaans": "af",
    "Spanish": "es",
    "Portuguese": "pt",
    "Polish": "pl",
    # TODO: more languages in SIM corpus
}
SIM_COUNTRY_MAP = {
    "United States": "us",
    "Germany": "de",
    "Netherlands": "nl",
    "United Kingdom": "",
    "Canada": "ca",
    "Switzerland": "ch",
    "South Africa": "za",
    "Japan": "jp",
    "France": "fr",
    "India": "in",
    "Chile": "cl",
    "Brazil": "br",
    "Australia": "au",
    "Argentina": "ar",
    "Uganda": "ug",
    "Thailand": "th",
    "Puerto Rico": "pr",
    "Poland": "pl",
    "Philippines": "ph",
    "Mexico": "mx",
    "Jamaica": "jm",
    "Italy": "it",
    "Ireland": "ie",
    "Finland": "fi",
    "Bulgaria": "bg",
    # TODO: more countries in SIM corpus
}


def es_biblio_from_sim(sim: Dict[str, Any]) -> ScholarBiblio:

    issue_meta = sim["issue_item_metadata"]["metadata"]
    pub_meta = sim["pub_item_metadata"]["metadata"]

    first_page = None
    if sim["page_texts"]:
        first_page = sim["page_texts"][0]["page_num"] or None
    first_page_int = clean_small_int(first_page)

    container_name = sim["pub_item_metadata"]["metadata"]["title"]

    # can't remember what this hack is for...
    last_word = container_name.split()[-1]
    if len(last_word) == 9 and last_word[4] == "-":
        container_name = container_name[:-10]

    issns = []
    raw_issn = issue_meta.get("issn")
    if raw_issn and len(raw_issn) == 9:
        issns.append(raw_issn)

    volume = issue_meta.get("volume")
    volume_int = clean_small_int(volume)
    issue = issue_meta.get("issue")
    issue_int = clean_small_int(issue)

    date = issue_meta.get("date")
    release_year = None
    if date and len(date) > 4 and date[:4].isdigit():
        release_year = int(date[:4])

    release_date = None
    if len(date) == len("2000-01-01"):
        try:
            datetime.date.fromisoformat(date)
            release_date = date
        except ValueError:
            pass

    if release_year and abs(release_year) > 2050:
        release_year = None

    return ScholarBiblio(
        # release_ident=release.ident,
        title=None,
        # subtitle=None,
        # original_title=release.original_title,
        release_date=release_date,
        release_year=release_year,
        release_type=SIM_RELEASE_TYPE_MAP.get(issue_meta.get("pub_type"))
        or SIM_RELEASE_TYPE_MAP.get(pub_meta.get("pub_type")),
        release_stage="published",  # as a default
        # withdrawn_status=release.withdrawn_status,
        lang_code=SIM_LANG_MAP.get(issue_meta.get("language"))
        or SIM_LANG_MAP.get(pub_meta.get("language")),
        country_code=SIM_COUNTRY_MAP.get(pub_meta.get("country")),
        volume=volume,
        volume_int=volume_int,
        issue=issue,
        issue_int=issue_int,
        pages=sim.get("pages"),
        first_page=first_page,
        first_page_int=first_page_int,
        # number=None,
        # no external identifiers
        # license_slug=release.license_slug,
        publisher=issue_meta.get("publisher") or pub_meta.get("publisher"),
        container_name=container_name,
        container_original_name=None,
        container_ident=None,  # TODO
        container_type=None,  # TODO
        container_issnl=None,  # TODO
        issns=issns,
        # no contrib/affiliation info
        contrib_names=[],
        affiliations=[],
    )


def _add_file_release_meta(
    fulltext: ScholarFulltext,
    pdf_meta: Optional[dict],
    re: ReleaseEntity,
    fe: FileEntity,
) -> ScholarFulltext:
    best_url = None
    best_url_type = None
    for url in fe.urls:
        best_url = url.url
        best_url_type = AccessType.web
        if "//archive.org/" in url.url:
            best_url_type = AccessType.ia_file
            break
        elif "//web.archive.org/" in url.url:
            best_url_type = AccessType.wayback
            break
        if url.rel == "repository":
            best_url_type = AccessType.repository
        # TODO: more file-to-access logic

    fulltext.release_ident = re.ident
    fulltext.file_ident = fe.ident
    fulltext.file_sha1 = fe.sha1
    fulltext.file_mimetype = fe.mimetype
    fulltext.access_url = best_url
    fulltext.access_type = best_url_type
    if pdf_meta is not None and pdf_meta["pdf_meta"].get("has_page0_thumbnail"):
        # eg: https://blobs.fatcat.wiki/thumbnail/pdf/32/29/322909fe57cef73b10a166996a4528d337026d16.180px.jpg
        fulltext.thumbnail_url = f"{ settings.THUMBNAIL_URL_PREFIX }{ fe.sha1[0:2] }/{ fe.sha1[2:4] }/{ fe.sha1 }.180px.jpg"
    return fulltext


def es_fulltext_from_grobid(
    tei_dict: dict, pdf_meta: Optional[dict], re: ReleaseEntity, fe: FileEntity
) -> Optional[ScholarFulltext]:
    if not tei_dict.get("body"):
        return None
    ret = ScholarFulltext(
        lang_code=tei_dict.get("lang"),
        body=tei_dict.get("body"),
        acknowledgement=tei_dict.get("acknowledgement"),
        annex=tei_dict.get("annex"),
    )
    return _add_file_release_meta(ret, pdf_meta, re, fe)


def es_fulltext_from_pdftotext(
    raw_text: str, pdf_meta: Optional[dict], re: ReleaseEntity, fe: FileEntity
) -> Optional[ScholarFulltext]:

    ret = ScholarFulltext(
        lang_code=re.language, body=raw_text, acknowledgement=None, annex=None,
    )
    return _add_file_release_meta(ret, pdf_meta, re, fe)


def es_fulltext_from_html(
    html_fulltext: Dict[str, Any], re: ReleaseEntity, wc: WebcaptureEntity,
) -> Optional[ScholarFulltext]:

    if not wc.archive_urls or not html_fulltext.get("tei_xml"):
        return None

    ns = {"tei": "http://www.tei-c.org/ns/1.0"}
    tree = ET.fromstring(html_fulltext["tei_xml"])
    body = tree.find(".//tei:body", ns)
    if body:
        raw_text = " ".join(body.itertext())
    else:
        return None

    ret = ScholarFulltext(
        lang_code=re.language,
        body=raw_text,
        acknowledgement=None,
        annex=None,
        release_ident=re.ident,
        # webcapture_ident=wc.ident,
        file_sha1=html_fulltext.get("html_meta", {}).get("sha1hex"),
        file_mimetype="text/html",
        access_url=wc.archive_urls[0].url,
        access_type=AccessType.wayback,
    )
    return ret


def biblio_metadata_hacks(biblio: ScholarBiblio) -> ScholarBiblio:  # noqa: C901
    """
    This function does platform/publisher specific metadata hacks.

    Really these should be updated in the fatcat catalog directly, but in the
    short term want to work around some large-ish transforms for our prototype
    index.

    This function is long, but simple in structure, so not likely to refactor
    into smaller functions.
    """

    # valid year
    if biblio.release_year and biblio.release_year > 2025:
        biblio.release_year = None
        biblio.release_date = None

    # figshare
    if biblio.doi_prefix in ("10.6084", "10.25384"):
        if not biblio.container_name:
            biblio.container_name = "Figshare"

    # zenodo
    if biblio.doi_prefix == "10.5281":
        if not biblio.container_name:
            biblio.container_name = "Zenodo"

    # biorxiv/medrxiv
    # NOTE: there is a further hack that determines which of biorxiv/medrxiv
    # based on access URL
    if biblio.doi_prefix == "10.1101":
        if not biblio.container_name:
            biblio.container_name = "biorxiv/medrxiv"
        if not biblio.release_stage:
            biblio.release_stage = "submitted"
        if biblio.release_type == "post":
            biblio.release_type = "article"

    # arxiv
    if biblio.arxiv_id and not (biblio.doi or biblio.pmid):
        if not biblio.container_name:
            biblio.container_name = "arXiv"
        if biblio.release_type in (None, "report", "post"):
            biblio.release_type = "article"

    # IEEE
    if biblio.doi_prefix == "10.1109":
        if (
            not biblio.release_stage
            and biblio.container_name
            and (
                "IEEE" in biblio.container_name
                or "Conference" in biblio.container_name
                or "Proceedings" in biblio.container_name
                or biblio.release_type == "paper-conference"
            )
        ):
            biblio.release_stage = "published"

    # ACM
    if biblio.doi_prefix == "10.1145":
        if (
            not biblio.release_stage
            and biblio.container_name
            and (
                "ACM" in biblio.container_name
                or "Conference" in biblio.container_name
                or "Proceedings" in biblio.container_name
            )
        ):
            biblio.release_stage = "published"

    # IOP, ACM, IEEE, AIP, World Scientific (large conference publishers)
    if biblio.doi_prefix in ("10.1145", "10.1109", "10.1117", "10.1063", "10.1142"):
        if not biblio.release_stage and biblio.release_type == "paper-conference":
            biblio.release_stage = "published"

    # F1000
    if biblio.doi_prefix == "10.3510":
        if biblio.title and biblio.title.startswith("Faculty of 1000 evaluation for"):
            biblio.release_type = "peer_review"
            biblio.release_stage = "published"

    # protocols.io
    if biblio.doi_prefix == "10.17504":
        if not biblio.release_stage:
            biblio.release_stage = "published"

    return biblio


def generate_tags(
    biblio: ScholarBiblio, primary_release: Optional[ReleaseEntity]
) -> List[str]:

    tags = []

    # tags
    if biblio.license_slug and biblio.license_slug.lower().startswith("cc-"):
        tags.append("oa")
    if primary_release and primary_release.container:
        container = primary_release.container
        if container.extra:
            if container.extra.get("doaj"):
                tags.append("doaj")
                tags.append("oa")
            if container.extra.get("road"):
                tags.append("road")
                tags.append("oa")
            if container.extra.get("szczepanski"):
                tags.append("szczepanski")
                tags.append("oa")
            if container.extra.get("ia", {}).get("longtail_oa"):
                tags.append("longtail")
                tags.append("oa")
            if container.extra.get("sherpa_romeo", {}).get("color") == "white":
                tags.append("oa")
            if container.extra.get("default_license", "").lower().startswith("cc-"):
                tags.append("oa")
            if container.extra.get("platform"):
                # scielo, ojs, wordpress, etc
                tags.append(container.extra["platform"].lower())
    if biblio.doi_prefix == "10.2307":
        tags.append("jstor")
    return list(set(tags))


def transform_heavy(heavy: IntermediateBundle) -> Optional[ScholarDoc]:

    tags: List[str] = []
    work_ident: Optional[str] = None
    sim_issue: Optional[str] = None
    abstracts: List[ScholarAbstract] = []
    fulltext: Optional[ScholarFulltext] = None
    primary_release: Optional[ReleaseEntity] = None

    ia_sim: Optional[ScholarSim] = None
    if heavy.sim_fulltext is not None:
        ia_sim = es_sim_from_sim(heavy.sim_fulltext)
        fulltext = es_fulltext_from_sim(heavy.sim_fulltext)

    if heavy.doc_type == DocType.sim_page:
        assert ia_sim is not None
        assert heavy.sim_fulltext is not None
        if not ia_sim.first_page or not ia_sim.issue_item:
            # can't create a valid key if we don't have these fields, so shouldn't index
            return None
        key = f"page_{ia_sim.issue_item}_{ia_sim.first_page}"
        sim_issue = ia_sim.issue_item
        biblio = es_biblio_from_sim(heavy.sim_fulltext)
        # fulltext extracted from heavy.sim_fulltext above
    elif heavy.doc_type == DocType.work:
        work_ident = heavy.releases[0].work_id
        key = f"work_{work_ident}"
        assert heavy.biblio_release_ident
        primary_release = [
            r for r in heavy.releases if r.ident == heavy.biblio_release_ident
        ][0]
        biblio = es_biblio_from_release(primary_release)
        biblio = biblio_metadata_hacks(biblio)
        abstracts = es_abstracts_from_release(primary_release)

        # if no abstract from primary_release, try all the other releases
        for release in heavy.releases:
            if not abstracts:
                abstracts = es_abstracts_from_release(release)
    else:
        raise NotImplementedError(f"doc_type: {heavy.doc_type}")

    if heavy.grobid_fulltext:
        fulltext_release = [
            r
            for r in heavy.releases
            if r.ident == heavy.grobid_fulltext["release_ident"]
        ][0]
        fulltext_file = [
            f
            for f in fulltext_release.files
            if f.ident == heavy.grobid_fulltext["file_ident"]
        ][0]
        tei_dict = teixml2json(heavy.grobid_fulltext["tei_xml"])
        fulltext = es_fulltext_from_grobid(
            tei_dict, heavy.pdf_meta, fulltext_release, fulltext_file
        )
        if not abstracts:
            abstracts = es_abstracts_from_grobid(tei_dict)

    if not fulltext and heavy.pdftotext_fulltext:
        fulltext_release = [
            r
            for r in heavy.releases
            if r.ident == heavy.pdftotext_fulltext["release_ident"]
        ][0]
        fulltext_file = [
            f
            for f in fulltext_release.files
            if f.ident == heavy.pdftotext_fulltext["file_ident"]
        ][0]
        fulltext = es_fulltext_from_pdftotext(
            heavy.pdftotext_fulltext["raw_text"],
            heavy.pdf_meta,
            fulltext_release,
            fulltext_file,
        )

    if not fulltext and heavy.html_fulltext:
        fulltext_release = [
            r for r in heavy.releases if r.ident == heavy.html_fulltext["release_ident"]
        ][0]
        fulltext_webcapture = [
            f
            for f in fulltext_release.webcaptures
            if f.ident == heavy.html_fulltext["webcapture_ident"]
        ][0]
        fulltext = es_fulltext_from_html(
            heavy.html_fulltext, fulltext_release, fulltext_webcapture,
        )

    # TODO: additional access list (eg, HTML if only PDF currently)
    access_dict = dict()
    if fulltext and fulltext.access_type:
        access_dict[fulltext.access_type] = ScholarAccess(
            access_type=fulltext.access_type,
            access_url=fulltext.access_url,
            mimetype=fulltext.file_mimetype,
            file_ident=fulltext.file_ident,
            release_ident=fulltext.release_ident,
        )
    if ia_sim and not AccessType.ia_sim in access_dict:
        access_dict[AccessType.ia_sim] = ScholarAccess(
            access_type=AccessType.ia_sim,
            access_url=f"https://archive.org/details/{ia_sim.issue_item}/page/{ia_sim.first_page}",
        )

    # TODO: additional abstracts

    tags = generate_tags(biblio, primary_release)

    # biorxiv/medrxiv hacks
    if (
        biblio.doi_prefix == "10.1101"
        and biblio.container_name in (None, "biorxiv/medrxiv")
        and biblio.release_stage != "published"
    ):
        for _, acc in access_dict.items():
            if "://www.medrxiv.org/" in acc.access_url:
                biblio.container_name = "medRxiv"
                if biblio.release_stage == None:
                    biblio.release_stage = "submitted"
            elif "://www.biorxiv.org/" in acc.access_url:
                biblio.container_name = "bioRxiv"
                if biblio.release_stage == None:
                    biblio.release_stage = "submitted"

    return ScholarDoc(
        key=key,
        collapse_key=sim_issue or work_ident,
        doc_type=heavy.doc_type.value,
        doc_index_ts=datetime.datetime.utcnow(),
        work_ident=work_ident,
        tags=tags,
        biblio=biblio,
        fulltext=fulltext,
        ia_sim=ia_sim,
        abstracts=abstracts,
        releases=[es_release_from_release(r) for r in heavy.releases],
        access=list(access_dict.values()),
    )


def refs_from_grobid(release: ReleaseEntity, tei_dict: dict) -> Sequence[RefStructured]:
    output = []
    for ref in tei_dict.get("citations") or []:
        ref_date = ref.get("date") or None
        ref_year: Optional[int] = None
        if ref_date and len(ref_date) >= 4 and ref_date[:4].isdigit():
            ref_year = int(ref_date[:4])
        ref_authors = ref.get("authors") or []
        authors: List[str] = []
        for a in ref_authors:
            if isinstance(a, str):
                authors.append(a)
            elif isinstance(a, dict):
                if a.get("name"):
                    assert isinstance(a["name"], str)
                    authors.append(a["name"])
        output.append(
            RefStructured(
                biblio=RefBiblio(
                    unstructured=ref.get("unstructured"),
                    title=ref.get("title"),
                    # subtitle
                    contrib_raw_names=authors or None,
                    year=ref_year,
                    container_name=ref.get("journal"),
                    publisher=ref.get("publisher"),
                    volume=ref.get("volume"),
                    issue=ref.get("issue"),
                    pages=ref.get("pages"),
                    doi=ref.get("doi"),
                    pmid=ref.get("pmid"),
                    pmcid=ref.get("pmcid"),
                    arxiv_id=ref.get("arxiv_id"),
                    # isbn13: Optional[str]
                    url=clean_url_conservative(ref.get("url")),
                ),
                release_ident=release.ident,
                work_ident=release.work_id,
                release_year=release.release_year,
                index=ref.get("index"),
                key=ref.get("id"),
                locator=None,
                # target_release_id
                ref_source="grobid",
            )
        )
    return output


def refs_from_release_refs(release: ReleaseEntity) -> Sequence[RefStructured]:
    output = []
    for ref in release.refs:
        ref_source = "fatcat"
        if release.extra and release.extra.get("pubmed"):
            ref_source = "pubmed"
        elif release.extra and release.extra.get("crossref"):
            ref_source = "crossref"
        elif release.extra and release.extra.get("datacite"):
            ref_source = "datacite"
        extra = ref.extra or dict()
        authors = extra.get("authors") or []
        authors = [a for a in authors if type(a) == str]
        output.append(
            RefStructured(
                biblio=RefBiblio(
                    unstructured=extra.get("unstructured"),
                    title=ref.title,
                    subtitle=extra.get("subtitle"),
                    contrib_raw_names=authors or None,
                    year=ref.year,
                    container_name=ref.container_name,
                    publisher=extra.get("publisher"),
                    volume=extra.get("volume"),
                    issue=extra.get("issue"),
                    pages=extra.get("pages") or extra.get("page"),
                    doi=extra.get("doi"),
                    pmid=extra.get("pmid"),
                    pmcid=extra.get("pmcid"),
                    arxiv_id=extra.get("arxiv_id"),
                    isbn13=extra.get("isbn13"),
                    url=clean_url_conservative(extra.get("url")),
                ),
                release_ident=release.ident,
                work_ident=release.work_id,
                release_year=release.release_year,
                index=ref.index,
                key=ref.key,
                locator=ref.locator,
                target_release_id=ref.target_release_id,
                ref_source=ref_source,
            )
        )
    return output


def refs_from_heavy(heavy: IntermediateBundle) -> Sequence[RefStructured]:
    """
    Current behavior is to return *both* fatcat refs and GROBID refs if
    available.
    """

    if heavy.doc_type != DocType.work:
        return []

    # first, identify source of refs: fatcat release metadata or GROBID
    assert heavy.biblio_release_ident
    primary_release = [
        r for r in heavy.releases if r.ident == heavy.biblio_release_ident
    ][0]

    refs: List[RefStructured] = []

    if primary_release.refs:
        # TODO: what about other releases?
        refs.extend(refs_from_release_refs(primary_release))

    if heavy.grobid_fulltext:
        fulltext_release = [
            r
            for r in heavy.releases
            if r.ident == heavy.grobid_fulltext["release_ident"]
        ][0]
        tei_dict = teixml2json(heavy.grobid_fulltext["tei_xml"])
        refs.extend(refs_from_grobid(fulltext_release, tei_dict))

    return refs


def run_transform(infile: Sequence) -> None:
    for line in infile:
        obj = json.loads(line)

        heavy = IntermediateBundle(
            doc_type=DocType(obj["doc_type"]),
            releases=[
                entity_from_json(json.dumps(re), ReleaseEntity)
                for re in obj["releases"]
            ],
            biblio_release_ident=obj.get("biblio_release_ident"),
            grobid_fulltext=obj.get("grobid_fulltext"),
            pdftotext_fulltext=obj.get("pdftotext_fulltext"),
            pdf_meta=obj.get("pdf_meta"),
            sim_fulltext=obj.get("sim_fulltext"),
        )
        es_doc = transform_heavy(heavy)
        if not es_doc:
            continue
        print(es_doc.json(exclude_none=True, sort_keys=True))


def run_refs(infile: Sequence) -> None:
    for line in infile:
        obj = json.loads(line)

        heavy = IntermediateBundle(
            doc_type=DocType(obj["doc_type"]),
            releases=[
                entity_from_json(json.dumps(re), ReleaseEntity)
                for re in obj["releases"]
            ],
            biblio_release_ident=obj.get("biblio_release_ident"),
            grobid_fulltext=obj.get("grobid_fulltext"),
            pdftotext_fulltext=obj.get("pdftotext_fulltext"),
            pdf_meta=obj.get("pdf_meta"),
            sim_fulltext=obj.get("sim_fulltext"),
        )
        refs = refs_from_heavy(heavy)
        for ref in refs:
            print(ref.json(exclude_none=True, sort_keys=True))


def main() -> None:
    """
    Run this command like:

        python -m fatcat_scholar.transform
    """

    parser = argparse.ArgumentParser(
        formatter_class=argparse.ArgumentDefaultsHelpFormatter
    )
    subparsers = parser.add_subparsers()

    sub = subparsers.add_parser(
        "run_transform",
        help="takes 'heavy' intermediate, outputs scholar_fulltext ES documents",
    )
    sub.set_defaults(func="run_transform")
    sub.add_argument(
        "json_file",
        help="intermediate globs as JSON-lines",
        nargs="?",
        default=sys.stdin,
        type=argparse.FileType("r"),
    )

    sub = subparsers.add_parser(
        "run_refs", help="extracts references from 'heavy' intermediate"
    )
    sub.set_defaults(func="run_refs")
    sub.add_argument(
        "json_file",
        help="intermediate globs as JSON-lines",
        nargs="?",
        default=sys.stdin,
        type=argparse.FileType("r"),
    )

    args = parser.parse_args()
    if not args.__dict__.get("func"):
        parser.print_help(file=sys.stderr)
        sys.exit(-1)

    if args.func == "run_transform":
        run_transform(infile=args.json_file)
    elif args.func == "run_refs":
        run_refs(infile=args.json_file)
    else:
        raise NotImplementedError(args.func)


if __name__ == "__main__":
    main()