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|
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,
# size_bytes=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.size_bytes = fe.size
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",
# size_bytess
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 or biblio.release_year < 1500
):
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") or biblio.doaj_id:
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")
if biblio.publisher_type not in ["big5"]:
# szczepanski not accurate OA flag for some large publishers (eg, Springer)
tags.append("oa")
if container.extra.get("ia", {}).get("longtail_oa"):
tags.append("longtail")
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" or biblio.jstor_id:
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()
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