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"""
Originally wrote these as dataclasses using pydantic.dataclasses, but we don't
get serialization for free with those. This is useful for things like
auto-conversion of datetime objects.
"""
import ftfy
import datetime
from enum import Enum
from typing import Optional, List, Any
from xml.etree import cElementTree as ET
from pydantic import BaseModel
from fatcat_openapi_client import ReleaseEntity, ReleaseContrib
from fatcat_scholar.api_entities import entity_to_dict
class DocType(str, Enum):
work = "work"
sim_page = "sim_page"
class IntermediateBundle(BaseModel):
doc_type: DocType
releases: List[ReleaseEntity]
biblio_release_ident: Optional[str]
grobid_fulltext: Optional[Any]
pdftotext_fulltext: Optional[Any]
sim_fulltext: Optional[Any]
class Config:
arbitrary_types_allowed = True
json_encoders = {
ReleaseEntity: lambda re: entity_to_dict(re),
}
class AccessType(str, Enum):
ia_sim = "ia_sim"
ia_file = "ia_file"
wayback = "wayback"
web = "web"
repository = "repository"
paywall = "paywall"
loginwall = "loginwall"
shadow = "shadow"
class ScholarBiblio(BaseModel):
release_ident: Optional[str]
title: Optional[str]
subtitle: Optional[str]
original_title: Optional[str]
release_date: Optional[datetime.date]
release_year: Optional[int]
release_type: Optional[str]
release_stage: Optional[str]
withdrawn_status: Optional[str]
lang_code: Optional[str]
country_code: Optional[str]
volume: Optional[str]
volume_int: Optional[str] # TODO: needed?
issue: Optional[str]
issue_int: Optional[str] # TODO: needed?
pages: Optional[str]
first_page: Optional[str]
first_page_int: Optional[str] # TODO: needed?
number: Optional[str]
doi: Optional[str]
doi_prefix: Optional[str]
doi_registrar: Optional[str]
pmid: Optional[str]
pmcid: Optional[str]
isbn13: Optional[str]
wikidata_qid: Optional[str]
arxiv_id: Optional[str]
jstor_id: Optional[str]
mag_id: Optional[str]
license_slug: Optional[str]
publisher: Optional[str]
publisher_type: Optional[str]
container_name: Optional[str]
container_original_name: Optional[str]
container_ident: Optional[str]
container_issnl: Optional[str]
container_wikidata_qid: Optional[str]
issns: List[str]
container_type: Optional[str]
contrib_count: Optional[int]
contrib_names: List[str]
affiliations: List[str]
class ScholarFulltext(BaseModel):
lang_code: Optional[str]
body: str
acknowledgement: Optional[str]
annex: Optional[str]
release_ident: Optional[str]
file_ident: Optional[str]
file_sha1: Optional[str]
file_mimetype: Optional[str]
thumbnail_url: Optional[str]
access_url: Optional[str]
access_type: Optional[AccessType]
class ScholarRelease(BaseModel):
ident: Optional[str]
revision: Optional[str]
title: str
release_date: Optional[datetime.date]
release_year: Optional[int]
release_type: Optional[str]
release_stage: Optional[str]
withdrawn_status: Optional[str]
doi: Optional[str]
doi_prefix: Optional[str]
doi_registrar: Optional[str]
pmid: Optional[str]
pmcid: Optional[str]
isbn13: Optional[str]
wikidata_qid: Optional[str]
arxiv_id: Optional[str]
jstor_id: Optional[str]
mag_id: Optional[str]
license_slug: Optional[str]
container_name: Optional[str]
container_ident: Optional[str]
container_issnl: Optional[str]
container_type: Optional[str]
class ScholarSim(BaseModel):
issue_item: str
pub_collection: str
sim_pubid: str
first_page: Optional[str]
class ScholarAbstract(BaseModel):
body: str
lang_code: Optional[str]
class ScholarAccess(BaseModel):
access_type: AccessType
access_url: str
mimetype: Optional[str]
file_ident: Optional[str]
release_ident: Optional[str]
class ScholarDoc(BaseModel):
key: str
doc_type: str # enum: work or page
doc_index_ts: datetime.datetime
work_ident: Optional[str]
tags: List[str] = []
biblio: ScholarBiblio
fulltext: Optional[ScholarFulltext]
ia_sim: Optional[ScholarSim]
abstracts: List[ScholarAbstract]
releases: List[ScholarRelease]
access: List[ScholarAccess]
def doi_split_prefix(doi: str) -> str:
return doi.split('/')[0]
def release_doi_registrar(release: ReleaseEntity) -> Optional[str]:
if not release.ext_ids.doi or not release.extra:
return None
for registrar in ('crossref', 'datacite', 'jalc'):
if registrar in release.extra:
return registrar
# TODO: should we default to Crossref?
return None
def scrub_text(raw: str, mimetype: str = None) -> str:
"""
This function takes a mimetype-hinted string and tries to reduce it to a
simple token-and-punctuation scheme with any and all markup removed. Eg,
HTML tags, JATS XML tags, LaTeX, whatever.
The output should be clean and "HTML safe" (though should still be escaped
in HTML to get entity encoding correct).
TODO: barely implemented yet
"""
if "<jats" in raw or (mimetype and "application/xml" in mimetype):
root = ET.fromstring(raw)
raw = " ".join(list(root.itertext())) or ""
raw = ftfy.fix_text(raw)
assert raw, "Empty abstract"
return raw
def contrib_name(contrib: ReleaseContrib) -> str:
# TODO: support more cultural normals for name presentation
if contrib.given_name and contrib.family_name:
return f"{contrib.given_name} {contrib.family_name}"
elif contrib.raw_name:
return contrib.raw_name
elif contrib.family_name:
return contrib.family_name
else:
return contrib.given_name
def contrib_affiliation(contrib: ReleaseContrib) -> Optional[str]:
# TODO
return None
def es_abstracts_from_release(release: ReleaseEntity) -> List[ScholarAbstract]:
d = dict()
for abst in release.abstracts:
if not abst.lang in d:
d[abst.lang] = ScholarAbstract(lang_code=abst.lang, body=scrub_text(abst.content))
return list(d.values())
def es_biblio_from_release(release: ReleaseEntity) -> ScholarBiblio:
if release.container:
publisher = release.publisher
container_name = release.container.name
container_original_name = release.container.extra and release.container.extra.get('original_name')
container_ident = release.container.ident
container_type = release.container.container_type
container_issnl = release.container.issnl
issns = [container_issnl,]
if release.extra.get('issne'):
issns.append(release.extra['issne'])
if release.extra.get('issnp'):
issns.append(release.extra['issnp'])
issns = list(set(issns))
else:
publisher = release.extra.get('publisher')
container_name = release.extra.get('container_name')
container_original_name = None
container_ident = None
container_type = None
container_issnl = None
issns = []
first_page: Optional[str] = None
if release.pages:
first_page = release.pages.split('-')[0]
first_page_int: Optional[int] = None
if first_page and first_page.isdigit():
first_page_int = int(first_page)
ret = ScholarBiblio(
release_ident=release.ident,
title=release.title,
subtitle=release.subtitle,
original_title=release.original_title,
release_date=release.release_date,
release_year=release.release_year,
release_type=release.release_type,
release_stage=release.release_stage,
withdrawn_status=release.withdrawn_status,
lang_code=release.language,
country_code=release.extra and release.extra.get('country'),
volume=release.volume,
volume_int=None,
issue=release.issue,
issue_int=None,
pages=release.pages,
first_page=first_page,
first_page_int=None,
number=release.number,
doi=release.ext_ids.doi,
doi_prefix=release.ext_ids.doi and doi_split_prefix(release.ext_ids.doi),
doi_registrar=release_doi_registrar(release),
pmid=release.ext_ids.pmid,
pmcid=release.ext_ids.pmcid,
isbn13=release.ext_ids.isbn13,
wikidata_qid=release.ext_ids.wikidata_qid,
arxiv_id=release.ext_ids.arxiv,
jstor_id=release.ext_ids.jstor,
mag_id=release.ext_ids.mag,
license_slug=release.license_slug,
publisher=publisher,
container_name=container_name,
container_original_name=container_original_name,
container_ident=container_ident,
container_type=container_type,
container_issnl=container_issnl,
issns=issns,
contrib_names=[contrib_name(c) for c in release.contribs if c.index],
contrib_count = len([c for c in release.contribs if c.index]),
affiliations=list(filter(lambda x: bool(x), [contrib_affiliation(c) for c in release.contribs if c.index])),
)
return ret
def es_release_from_release(release: ReleaseEntity) -> ScholarRelease:
if release.container:
container_name = release.container.name
container_ident = release.container.ident
container_issnl = release.container.issnl
container_type = release.container.container_type
else:
container_name = release.extra.get('container_name')
container_ident = None
container_issnl = None
container_type = None
ret = ScholarRelease(
ident=release.ident,
revision=release.revision,
title=release.title,
release_date=release.release_date,
release_year=release.release_year,
release_type=release.release_type,
release_stage=release.release_stage,
withdrawn_status=release.withdrawn_status,
doi=release.ext_ids.doi,
doi_prefix=release.ext_ids.doi and doi_split_prefix(release.ext_ids.doi),
doi_registrar=release_doi_registrar(release),
pmid=release.ext_ids.pmid,
pmcid=release.ext_ids.pmcid,
isbn13=release.ext_ids.isbn13,
wikidata_qid=release.ext_ids.wikidata_qid,
arxiv_id=release.ext_ids.arxiv,
jstor_id=release.ext_ids.jstor,
mag_id=release.ext_ids.mag,
license_slug=release.license_slug,
container_name=container_name,
container_ident=container_ident,
container_issnl=container_issnl,
container_type=container_type,
)
return ret
|
