def parse_record(self, row: Dict[str, Any]) -> FileEntity:
# bezerk mode doesn't make sense for this importer
assert self.bezerk_mode is False
file_ident = uuid2fcid(row["file_ident"])
wrong_release_ident = uuid2fcid(row["wrong_release_ident"])
edit_extra = row["edit_extra"]
assert edit_extra["link_source"] in ["unpaywall", "doi"]
file_edit_doi = clean_doi(edit_extra["link_source_id"])
if not file_edit_doi:
self.counts["skip-bad-doi"] += 1
return False
# check that the "wrong" release exists and doesn't have the DOI
wrong_release = None
try:
wrong_release = self.api.get_release(wrong_release_ident)
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
if not wrong_release:
self.counts["skip-wrong-release-missing"] += 1
return None
if clean_doi(wrong_release.ext_ids.doi) == file_edit_doi:
self.counts["skip-wrong-release-is-ok"] += 1
return None
# fetch the "correct" release, if any
fixed_release_ids = []
correct_release = None
try:
correct_release = self.api.lookup_release(doi=file_edit_doi)
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
if correct_release:
fixed_release_ids.append(correct_release.ident)
fe = FileEntity(
ident=file_ident,
release_ids=fixed_release_ids,
edit_extra=edit_extra,
)
fe._wrong_release_ident = wrong_release_ident
return fe
def doaj_ext_ids(
self, identifiers: List[dict],
doaj_article_id: str) -> fatcat_openapi_client.ReleaseExtIds:
"""
bibjson.identifier {
id (string),
type (string)
}
"""
assert doaj_article_id.isalnum() and len(doaj_article_id) == 32
doi: Optional[str] = None
pmid: Optional[str] = None
pmcid: Optional[str] = None
for id_obj in identifiers:
if not id_obj.get("id"):
continue
if id_obj["type"].lower() == "doi":
doi = clean_doi(id_obj["id"])
elif id_obj["type"].lower() == "pmid":
pmid = clean_pmid(id_obj["id"])
elif id_obj["type"].lower() == "pmcid":
pmcid = clean_pmcid(id_obj["id"])
return fatcat_openapi_client.ReleaseExtIds(
doaj=doaj_article_id,
doi=doi,
pmid=pmid,
pmcid=pmcid,
)
def dblp_ext_ids(self, xml_elem: Any,
dblp_key: str) -> fatcat_openapi_client.ReleaseExtIds:
"""
Takes a full XML object and returns external identifiers.
Currently these can be arixv identifiers, DOI, or wikidata QID
- ee (electronic edition; often DOI?)
=> in some cases a "local" URL
=> publisher URL; often DOI
=> type attr
- url
=> dblp internal link to table-of-contents
"""
doi: Optional[str] = None
wikidata_qid: Optional[str] = None
arxiv_id: Optional[str] = None
hdl: Optional[str] = None
for ee in xml_elem.find_all("ee"):
url = ee.text
# convert DOI-like domains, which mostly have DOIs anyways
if "://doi.acm.org/" in url:
url = url.replace("://doi.acm.org/", "://doi.org/")
elif "://doi.ieeecomputersociety.org/" in url:
url = url.replace("://doi.ieeecomputersociety.org/",
"://doi.org/")
if "doi.org/10." in url and not doi:
doi = clean_doi(url)
elif "wikidata.org/entity/Q" in url and not wikidata_qid:
wikidata_qid = clean_wikidata_qid(url)
elif "://arxiv.org/abs/" in url and not arxiv_id:
arxiv_id = (url.replace("http://",
"").replace("https://", "").replace(
"arxiv.org/abs/", ""))
arxiv_id = clean_arxiv_id(arxiv_id)
elif "://hdl.handle.net" in url and not hdl:
hdl = clean_hdl(url)
return fatcat_openapi_client.ReleaseExtIds(
dblp=dblp_key,
doi=doi,
wikidata_qid=wikidata_qid,
arxiv=arxiv_id,
hdl=hdl,
)
def parse_record(self, obj: Dict[str, Any]) -> Optional[FileEntity]:
dois = [d.lower() for d in obj.get("dois", [])]
# lookup dois
re_list = set()
for doi in dois:
doi = clean_doi(doi)
if not doi:
self.counts["skip-bad-doi"] += 1
return None
try:
re = self.api.lookup_release(doi=doi)
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
re = None
if re is None:
# print("DOI not found: {}".format(doi))
pass
else:
re_list.add(re.ident)
# look up other external ids
for extid_type in (
"arxiv",
"pmid",
"pmcid",
"jstor",
"wikidata_qid",
"core",
"isbn13",
"ark",
):
extid = obj.get(extid_type)
if extid:
try:
re = self.api.lookup_release(**{extid_type: extid})
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
re = None
if re is None:
pass
else:
re_list.add(re.ident)
release_ids = list(re_list)
if len(release_ids) == 0:
self.counts["skip-no-releases"] += 1
return None
if len(release_ids) > SANE_MAX_RELEASES:
self.counts["skip-too-many-releases"] += 1
return None
# parse URLs and CDX
urls_set = set()
for url in obj.get("urls", []):
url = make_rel_url(url, default_link_rel=self.default_link_rel)
if url is not None:
urls_set.add(url)
for cdx in obj.get("cdx", []):
original = cdx["url"]
if cdx.get("dt"):
wayback = "https://web.archive.org/web/{}/{}".format(cdx["dt"], original)
urls_set.add(("webarchive", wayback))
url = make_rel_url(original, default_link_rel=self.default_link_rel)
if url is not None:
urls_set.add(url)
urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls_set]
if len(urls) == 0:
self.counts["skip-no-urls"] += 1
return None
if len(urls) > SANE_MAX_URLS:
self.counts["skip-too-many-urls"] += 1
return None
size = obj.get("size")
if size:
size = int(size)
mimetype = obj.get("mimetype", self.default_mimetype)
if not mimetype and urls:
if urls[0].url.endswith(".pdf"):
mimetype = "application/pdf"
fe = FileEntity(
md5=obj.get("md5"),
sha1=obj["sha1"],
sha256=obj.get("sha256"),
size=size,
mimetype=mimetype,
release_ids=release_ids,
urls=urls,
)
return fe
def parse_record(self, article: Any) -> Optional[ReleaseEntity]:
journal_meta = article.front.find("journal-meta")
article_meta = article.front.find("article-meta")
extra: Dict[str, Any] = dict()
extra_jstor: Dict[str, Any] = dict()
release_type = JSTOR_TYPE_MAP.get(article["article-type"])
title = article_meta.find("article-title")
if title and title.get_text():
title = title.get_text().replace("\n", " ").strip()
elif title and not title.get_text():
title = None
if (not title and release_type and release_type.startswith("review")
and article_meta.product.source):
title = "Review: {}".format(
article_meta.product.source.replace("\n", " ").get_text())
if not title:
return None
if title.endswith("."):
title = title[:-1]
if "[Abstract]" in title:
# TODO: strip the "[Abstract]" bit?
release_type = "abstract"
elif "[Editorial" in title:
release_type = "editorial"
elif "[Letter" in title:
release_type = "letter"
elif "[Poem" in title or "[Photograph" in title:
release_type = None
if title.startswith("[") and title.endswith("]"):
# strip brackets if that is all that is there (eg, translation or non-english)
title = title[1:-1]
# JSTOR journal-id
journal_ids = [j.string for j in journal_meta.find_all("journal-id")]
if journal_ids:
extra_jstor["journal_ids"] = journal_ids
journal_title = journal_meta.find("journal-title").get_text().replace(
"\n", " ")
publisher = journal_meta.find("publisher-name").get_text().replace(
"\n", " ")
issn = journal_meta.find("issn")
if issn:
issn = issn.string
if len(issn) == 8:
issn = "{}-{}".format(issn[0:4], issn[4:8])
else:
assert len(issn) == 9
issnl = self.issn2issnl(issn)
container_id = None
if issnl:
container_id = self.lookup_issnl(issnl)
# create container if it doesn't exist
if (container_id is None and self.create_containers
and (issnl is not None) and journal_title):
ce = fatcat_openapi_client.ContainerEntity(
issnl=issnl,
publisher=publisher,
container_type=self.map_container_type(release_type),
name=clean_str(journal_title, force_xml=True),
)
ce_edit = self.create_container(ce)
container_id = ce_edit.ident
self._issnl_id_map[issnl] = container_id
doi = article_meta.find("article-id", {"pub-id-type": "doi"})
if doi:
doi = clean_doi(doi.string.lower())
else:
doi = None
jstor_id = article_meta.find("article-id", {"pub-id-type": "jstor"})
if jstor_id:
jstor_id = jstor_id.string.strip()
if not jstor_id and doi:
assert doi.startswith("10.2307/")
jstor_id = doi.replace("10.2307/", "")
assert jstor_id and int(jstor_id)
contribs = []
cgroup = article_meta.find("contrib-group")
if cgroup:
for c in cgroup.find_all("contrib"):
given = c.find("given-names")
if given:
given = clean_str(given.get_text().replace("\n", " "))
surname = c.find("surname")
if surname:
surname = clean_str(surname.get_text().replace("\n", " "))
raw_name = c.find("string-name")
if raw_name:
raw_name = clean_str(raw_name.get_text().replace(
"\n", " "))
if not raw_name:
if given and surname:
raw_name = "{} {}".format(given, surname)
elif surname:
raw_name = surname
role = JSTOR_CONTRIB_MAP.get(c.get("contrib-type", "author"))
if not role and c.get("contrib-type"):
sys.stderr.write("NOT IN JSTOR_CONTRIB_MAP: {}\n".format(
c["contrib-type"]))
contribs.append(
fatcat_openapi_client.ReleaseContrib(
role=role,
raw_name=raw_name,
given_name=given,
surname=surname,
))
for i, contrib in enumerate(contribs):
if contrib.raw_name != "et al.":
contrib.index = i
release_year = None
release_date = None
pub_date = article_meta.find("pub-date")
if pub_date and pub_date.year:
release_year = int(pub_date.year.string)
if pub_date.month and pub_date.day:
release_date = datetime.date(release_year,
int(pub_date.month.string),
int(pub_date.day.string))
if release_date.day == 1 and release_date.month == 1:
# suspect jan 1st dates get set by JSTOR when actual
# date not known (citation needed), so drop them
release_date = None
volume = None
if article_meta.volume:
volume = article_meta.volume.string or None
issue = None
if article_meta.issue:
issue = article_meta.issue.string or None
pages = None
if article_meta.find("page-range"):
pages = article_meta.find("page-range").string
elif article_meta.fpage:
pages = article_meta.fpage.string
language = None
cm = article_meta.find("custom-meta")
if cm.find("meta-name").string == "lang":
language = cm.find("meta-value").string.split()[0]
language = LANG_MAP_MARC.get(language)
if not language:
warnings.warn("MISSING MARC LANG: {}".format(
cm.find("meta-value").string))
# JSTOR issue-id
if article_meta.find("issue-id"):
issue_id = clean_str(article_meta.find("issue-id").string)
if issue_id:
extra_jstor["issue_id"] = issue_id
# everything in JSTOR is published
release_stage = "published"
# extra:
# withdrawn_date
# translation_of
# subtitle
# aliases
# container_name
# group-title
# pubmed: retraction refs
if extra_jstor:
extra["jstor"] = extra_jstor
re = fatcat_openapi_client.ReleaseEntity(
# work_id
title=title,
# original_title
release_type=release_type,
release_stage=release_stage,
release_date=release_date,
release_year=release_year,
ext_ids=fatcat_openapi_client.ReleaseExtIds(
doi=doi,
jstor=jstor_id,
),
volume=volume,
issue=issue,
pages=pages,
publisher=publisher,
language=language,
# license_slug
# content, mimetype, lang
# abstracts=abstracts,
contribs=contribs,
# key, year, container_name, title, locator
# extra: volume, authors, issue, publisher, identifiers
# refs=refs,
# name, type, publisher, issnl
# extra: issnp, issne, original_name, languages, country
container_id=container_id,
extra=extra or None,
)
return re
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 = clean_doi(attributes.get('doi', '').lower())
if not doi:
print('skipping record without a DOI', file=sys.stderr)
return
if not isascii(doi):
print('[{}] skipping non-ascii doi for now'.format(doi))
return None
creators = attributes.get('creators', []) or []
contributors = attributes.get('contributors', []) or [
] # Much fewer than creators.
contribs = self.parse_datacite_creators(
creators, doi=doi) + self.parse_datacite_creators(
contributors, role=None, set_index=False, doi=doi)
# 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 title is None:
print('[{}] skipping record w/o title: {}'.format(doi, obj),
file=sys.stderr)
return False
title = clean(title)
if not title:
print('[{}] skipping record w/o title: {}'.format(doi, obj),
file=sys.stderr)
return False
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_month, release_year = parse_datacite_dates(
attributes.get('dates', []))
# Some records do not use the "dates" field (e.g. micropub), but:
# "attributes.published" or "attributes.publicationYear"
if not any((release_date, release_month, release_year)):
release_date, release_month, release_year = parse_single_date(
attributes.get('publicationYear'))
if not any((release_date, release_month, release_year)):
release_date, release_month, release_year = parse_single_date(
attributes.get('published'))
if not any((release_date, release_month, release_year)):
print('[{}] record w/o date: {}'.format(doi, obj), file=sys.stderr)
# 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 = 'published'
# TODO(martin): If 'state' is not 'findable' or 'isActive' is not true,
# we might want something else than 'published'. See also:
# https://support.datacite.org/docs/doi-states.
# Publisher. A few NA values. A few bogus values.
publisher = attributes.get('publisher')
if publisher in UNKNOWN_MARKERS | set(('Unpublished', 'Unknown')):
publisher = None
release_stage = 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]
# Exception: https://www.micropublication.org/, see: !MR24.
if container_id is None and container_name is None:
if publisher and publisher.lower().startswith('micropublication'):
container_name = publisher
# 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:
# TODO(martin): This is more debug than info.
# 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" is
# uncontrolled (170000+ unique values, from "null", "Dataset" to
# "Jupyter Notebook" and "Macroseismic Data Points" or "2 days of IP
# flows in 2009") citeproc may be the closest, but not always supplied.
# Order lookup roughly by completeness of mapping.
for typeType in ('citeproc', 'ris', 'schemaOrg', 'bibtex',
'resourceTypeGeneral'):
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)
# release_type exception: Global Biodiversity Information Facility
# publishes highly interesting datasets, but titles are mostly the same
# ("GBIF Occurrence Download" or "Occurrence Download"); set
# release_type to "stub" (CSL/FC).
if publisher == 'The Global Biodiversity Information Facility':
release_type = 'stub'
# release_type exception: lots of "Experimental Crystal Structure Determination"
if publisher == 'Cambridge Crystallographic Data Centre':
release_type = 'entry'
# Supplement files, e.g. "Additional file 1: ASE constructs in questionnaire."
if title.lower().startswith('additional file'):
release_type = 'stub'
# 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:
pass
# TODO(martin): Print this on debug level, only.
# 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
# Description maybe a string or list.
text = desc.get('description', '')
if not text:
continue
if isinstance(text, list):
try:
text = "\n".join(text)
except TypeError as err:
continue # Bail out, if it is not a list of strings.
# Limit length.
if len(text) < 10:
continue
if len(text) > MAX_ABSTRACT_LENGTH:
text = text[:MAX_ABSTRACT_LENGTH] + " [...]"
# Detect language. This is fuzzy and may be removed, if too unreliable.
lang = None
try:
lang = langdetect.detect(text)
except (langdetect.lang_detect_exception.LangDetectException,
TypeError) as err:
print('[{}] language detection failed with {} on {}'.format(
doi, err, text),
file=sys.stderr)
abstracts.append(
fatcat_openapi_client.ReleaseAbstract(
mimetype="text/plain",
content=clean(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', '') in ('References', 'Cites'):
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
# More specific release_type via 'Reviews' relationsship.
for rel in relIds:
if rel.get('relatedIdentifierType', '') != 'Reviews':
continue
release_type = 'review'
# Extra information.
extra_datacite = dict()
if license_extra:
extra_datacite['license'] = license_extra
if attributes.get('subjects'):
extra_datacite['subjects'] = attributes['subjects']
# Include version information.
metadata_version = attributes.get('metadataVersion') or ''
if metadata_version:
extra_datacite['metadataVersion'] = metadata_version
# Include resource types.
types = attributes.get('types', {}) or {}
resource_type = types.get('resourceType', '') or ''
resource_type_general = types.get('resourceTypeGeneral', '') or ''
if resource_type and resource_type.lower(
) not in UNKNOWN_MARKERS_LOWER:
extra_datacite['resourceType'] = resource_type
if resource_type_general and resource_type_general.lower(
) not in UNKNOWN_MARKERS_LOWER:
extra_datacite['resourceTypeGeneral'] = resource_type_general
# 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()
# "1.0.0", "v1.305.2019", "Final", "v1.0.0", "v0.3.0", "1", "0.19.0",
# "3.1", "v1.1", "{version}", "4.0", "10329", "11672", "11555",
# "v1.4.5", "2", "V1", "v3.0", "v0", "v0.6", "11124", "v1.0-beta", "1st
# Edition", "20191024", "v2.0.0", "v0.9.3", "10149", "2.0", null,
# "v0.1.1", "3.0", "1.0", "3", "v1.12.2", "20191018", "v0.3.1", "v1.0",
# "10161", "10010691", "10780", # "Presentación"
version = attributes.get('version')
# top-level extra keys
if not container_id and container_name:
extra['container_name'] = container_name
# Always include datacite key, even if value is empty (dict).
extra['datacite'] = extra_datacite
# Preparation for a schema update.
if release_month:
extra['release_month'] = release_month
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,
version=version,
)
return re
def parse_record(self, record: Any) -> Optional[List[ReleaseEntity]]:
if not record:
return None
metadata = record.arXivRaw
if not metadata:
return None
extra: Dict[str, Any] = dict()
extra_arxiv: Dict[str, Any] = dict()
# don't know!
release_type = "article"
base_id = metadata.id.string
doi = None
if metadata.doi and metadata.doi.string:
doi = clean_doi(metadata.doi.string.lower().split()[0].strip())
if doi and not (doi.startswith("10.") and "/" in doi
and doi.split("/")[1]):
sys.stderr.write("BOGUS DOI: {}\n".format(doi))
doi = None
title = latex_to_text(metadata.title.get_text().replace("\n", " "))
authors = parse_arxiv_authors(metadata.authors.get_text().replace(
"\n", " "))
contribs = [
fatcat_openapi_client.ReleaseContrib(index=i,
raw_name=a,
role="author")
for i, a in enumerate(authors)
]
lang: Optional[str] = "en" # the vast majority in english
if metadata.comments and metadata.comments.get_text():
comments = metadata.comments.get_text().replace("\n", " ").strip()
extra_arxiv["comments"] = comments
if "in french" in comments.lower():
lang = "fr"
elif "in spanish" in comments.lower():
lang = "es"
elif "in portuguese" in comments.lower():
lang = "pt"
elif "in hindi" in comments.lower():
lang = "hi"
elif "in japanese" in comments.lower():
lang = "ja"
elif "in german" in comments.lower():
lang = "de"
elif "simplified chinese" in comments.lower():
lang = "zh"
elif "in russian" in comments.lower():
lang = "ru"
# more languages?
number = None
if metadata.find("journal-ref") and metadata.find(
"journal-ref").get_text():
journal_ref = metadata.find("journal-ref").get_text().replace(
"\n", " ").strip()
extra_arxiv["journal_ref"] = journal_ref
if "conf." in journal_ref.lower() or "proc." in journal_ref.lower(
):
release_type = "paper-conference"
if metadata.find("report-no") and metadata.find("report-no").string:
number = metadata.find("report-no").string.strip()
# at least some people plop extra metadata in here. hrmf!
if "ISSN " in number or "ISBN " in number or len(
number.split()) > 2:
extra_arxiv["report-no"] = number
number = None
else:
release_type = "report"
if metadata.find("acm-class") and metadata.find("acm-class").string:
extra_arxiv["acm_class"] = metadata.find(
"acm-class").string.strip()
if metadata.categories and metadata.categories.get_text():
extra_arxiv["categories"] = metadata.categories.get_text().split()
license_slug = None
if metadata.license and metadata.license.get_text():
license_slug = lookup_license_slug(metadata.license.get_text())
abstracts = None
if metadata.abstract:
# TODO: test for this multi-abstract code path
abstracts = []
abst = metadata.abstract.get_text().strip()
orig = None
if "-----" in abst:
both = abst.split("-----")
abst = both[0].strip()
orig = both[1].strip()
if "$" in abst or "{" in abst:
mime = "application/x-latex"
abst_plain = latex_to_text(abst)
abstracts.append(
fatcat_openapi_client.ReleaseAbstract(
content=abst_plain, mimetype="text/plain", lang="en"))
else:
mime = "text/plain"
abstracts.append(
fatcat_openapi_client.ReleaseAbstract(content=abst,
mimetype=mime,
lang="en"))
if orig:
abstracts.append(
fatcat_openapi_client.ReleaseAbstract(content=orig,
mimetype=mime))
# indicates that fulltext probably isn't english either
if lang == "en":
lang = None
# extra:
# withdrawn_date
# translation_of
# subtitle
# aliases
# container_name
# group-title
# arxiv: comments, categories, etc
extra_arxiv["base_id"] = base_id
extra["superceded"] = True
extra["arxiv"] = extra_arxiv
versions = []
for version in metadata.find_all("version"):
arxiv_id = base_id + version["version"]
release_date = version.date.string.strip()
release_date = datetime.datetime.strptime(
release_date, "%a, %d %b %Y %H:%M:%S %Z").date()
# TODO: source_type?
versions.append(
ReleaseEntity(
work_id=None,
title=title,
# original_title
version=version["version"],
release_type=release_type,
release_stage="submitted",
release_date=release_date.isoformat(),
release_year=release_date.year,
ext_ids=fatcat_openapi_client.ReleaseExtIds(
arxiv=arxiv_id, ),
number=number,
language=lang,
license_slug=license_slug,
abstracts=abstracts,
contribs=contribs,
extra=extra.copy(),
))
# TODO: assert that versions are actually in order?
assert versions
versions[-1].extra.pop("superceded")
# only apply DOI to most recent version (HACK)
if doi:
versions[-1].ext_ids.doi = doi
if len(versions) > 1:
versions[-1].release_stage = "accepted"
return versions
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 = clean_doi(attributes.get('doi', '').lower())
if not doi:
print('skipping record without a DOI', file=sys.stderr)
return
if not str.isascii(doi):
print('[{}] skipping non-ascii doi for now'.format(doi))
return None
creators = attributes.get('creators', []) or []
contributors = attributes.get('contributors', []) or [
] # Much fewer than creators.
contribs = self.parse_datacite_creators(creators, doi=doi)
# Beside creators, we have contributors in datacite. Sample:
# ContactPerson, DataCollector, DataCurator, DataManager, Distributor,
# Editor, Funder, HostingInstitution, Other, Producer, ProjectLeader,
# ProjectMember, RelatedPerson, ResearchGroup, Researcher,
# RightsHolder, Sponsor, Supervisor
#
# Datacite schema:
# https://schema.datacite.org/meta/kernel-4.3/doc/DataCite-MetadataKernel_v4.3.pdf#page=32
# -- could be used as a form of controlled vocab?
#
# Currently (07/2020) in release_contrib:
#
# select count(*), role from release_contrib group by role;
# count | role
# -----------+------------
# 500269665 | author
# 4386563 | editor
# 17871 | translator
# 10870584 |
# (4 rows)
#
# Related: https://guide.fatcat.wiki/entity_release.html -- role
# (string, of a set): the type of contribution, from a controlled
# vocabulary. TODO: vocabulary needs review.
contribs_extra_contributors = self.parse_datacite_creators(
contributors, set_index=False, doi=doi)
# Unfortunately, creators and contributors might overlap, refs GH59.
for cc in contribs_extra_contributors:
if contributor_list_contains_contributor(contribs, cc):
continue
contribs.append(cc)
# 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 title is None:
print('[{}] skipping record w/o title: {}'.format(doi, obj),
file=sys.stderr)
return False
title = clean(title)
if not title:
print('[{}] skipping record w/o title: {}'.format(doi, obj),
file=sys.stderr)
return False
# check for blocklisted "spam", e.g. "FULL MOVIE"
for rule in DATACITE_TITLE_SPAM_WORDGROUPS:
seen = set()
for token in rule.get("tokens", []):
if token in title.lower():
seen.add(token)
if len(seen) >= rule.get("min"):
print("[{}] skipping spammy title: {}".format(doi, obj),
file=sys.stderr)
return False
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_month, release_year = parse_datacite_dates(
attributes.get('dates', []))
# block bogus far-future years/dates
if release_year is not None and (release_year > (self.this_year + 5)
or release_year < 1000):
release_date = None
release_month = None
release_year = None
# Some records do not use the "dates" field (e.g. micropub), but:
# "attributes.published" or "attributes.publicationYear"
if not any((release_date, release_month, release_year)):
release_date, release_month, release_year = parse_single_date(
attributes.get('publicationYear'))
if not any((release_date, release_month, release_year)):
release_date, release_month, release_year = parse_single_date(
attributes.get('published'))
if not any((release_date, release_month, release_year)):
print('[{}] record w/o date: {}'.format(doi, obj), file=sys.stderr)
# 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 = 'published'
# TODO(martin): If 'state' is not 'findable' or 'isActive' is not true,
# we might want something else than 'published'. See also:
# https://support.datacite.org/docs/doi-states.
# Publisher. A few NA values. A few bogus values.
publisher = attributes.get('publisher')
if publisher in UNKNOWN_MARKERS | set(('Unpublished', 'Unknown')):
publisher = None
release_stage = 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]
# Exception: https://www.micropublication.org/, see: !MR24.
if container_id is None and container_name is None:
if publisher and publisher.lower().startswith('micropublication'):
container_name = publisher
# 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: # noqa: F841
# TODO(martin): This is more debug than info.
# print('[{}] {}'.format(doi, err), file=sys.stderr)
pass
if not pages and first_page:
pages = first_page
# License.
license_slug = None
license_extra = []
for lic in attributes.get('rightsList', []):
slug = lookup_license_slug(lic.get('rightsUri'))
if slug:
license_slug = slug
license_extra.append(lic)
release_type = self.datacite_release_type(doi, attributes)
# 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: # noqa: F841
pass
# TODO(martin): Print this on debug level, only.
# 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
# Description maybe a string, int or list.
text = desc.get('description', '')
if not text:
continue
if isinstance(text, int):
text = '{}'.format(text)
if isinstance(text, list):
try:
text = "\n".join(text)
except TypeError:
continue # Bail out, if it is not a list of strings.
# Limit length.
if len(text) < 10:
continue
if len(text) > MAX_ABSTRACT_LENGTH:
text = text[:MAX_ABSTRACT_LENGTH] + " [...]"
# Detect language. This is fuzzy and may be removed, if too unreliable.
lang = None
try:
lang = langdetect.detect(text)
except (langdetect.lang_detect_exception.LangDetectException,
TypeError) as err:
print('[{}] language detection failed with {} on {}'.format(
doi, err, text),
file=sys.stderr)
abstracts.append(
fatcat_openapi_client.ReleaseAbstract(
mimetype="text/plain",
content=clean(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', '') in ('References', 'Cites'):
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
# More specific release_type via 'Reviews' relationsship.
for rel in relIds:
if rel.get('relatedIdentifierType', '') != 'Reviews':
continue
release_type = 'review'
# Extra information.
extra_datacite = dict()
if license_extra:
extra_datacite['license'] = license_extra
if attributes.get('subjects'):
extra_datacite['subjects'] = attributes['subjects']
# Include version information.
metadata_version = attributes.get('metadataVersion') or ''
if metadata_version:
extra_datacite['metadataVersion'] = metadata_version
# Include resource types.
types = attributes.get('types', {}) or {}
resource_type = types.get('resourceType', '') or ''
resource_type_general = types.get('resourceTypeGeneral', '') or ''
if resource_type and resource_type.lower(
) not in UNKNOWN_MARKERS_LOWER:
extra_datacite['resourceType'] = resource_type
if resource_type_general and resource_type_general.lower(
) not in UNKNOWN_MARKERS_LOWER:
extra_datacite['resourceTypeGeneral'] = resource_type_general
# Include certain relations from relatedIdentifiers. Keeping the
# original structure of data here, which is a list of dicts, with
# relation type, identifier 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()
# "1.0.0", "v1.305.2019", "Final", "v1.0.0", "v0.3.0", "1", "0.19.0",
# "3.1", "v1.1", "{version}", "4.0", "10329", "11672", "11555",
# "v1.4.5", "2", "V1", "v3.0", "v0", "v0.6", "11124", "v1.0-beta", "1st
# Edition", "20191024", "v2.0.0", "v0.9.3", "10149", "2.0", null,
# "v0.1.1", "3.0", "1.0", "3", "v1.12.2", "20191018", "v0.3.1", "v1.0",
# "10161", "10010691", "10780", # "Presentación"
version = attributes.get('version') or None
# top-level extra keys
if not container_id and container_name:
extra['container_name'] = container_name
# Always include datacite key, even if value is empty (dict).
extra['datacite'] = extra_datacite
# Preparation for a schema update.
if release_month:
extra['release_month'] = release_month
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,
version=version,
)
re = self.biblio_hacks(re)
return re
def is_doi(self, doi: str) -> bool:
return clean_doi(doi) is not None
def parse_record(self, obj: Dict[str, Any]) -> Optional[ReleaseEntity]:
"""
obj is a python dict (parsed from json).
returns a ReleaseEntity
"""
# Ways to be out of scope (provisionally)
# journal-issue and journal-volume map to None, but allowed for now
if obj.get("type") in (
None,
"journal",
"proceedings",
"standard-series",
"report-series",
"book-series",
"book-set",
"book-track",
"proceedings-series",
):
self.counts["skip-release-type"] += 1
return None
# Do require the 'title' keys to exist, as release entities do
if ("title" not in obj) or (not obj["title"]):
self.counts["skip-blank-title"] += 1
return None
release_type = self.map_release_type(obj["type"])
# contribs
def do_contribs(obj_list: List[Dict[str, Any]],
ctype: str) -> List[ReleaseContrib]:
contribs = []
for i, am in enumerate(obj_list):
creator_id = None
if "ORCID" in am.keys():
creator_id = self.lookup_orcid(am["ORCID"].split("/")[-1])
# Sorry humans :(
if am.get("given") and am.get("family"):
raw_name: Optional[str] = "{} {}".format(
am["given"], am["family"])
elif am.get("family"):
raw_name = am["family"]
else:
# TODO: can end up empty
raw_name = am.get("name") or am.get("given")
extra: Dict[str, Any] = dict()
if ctype == "author":
index: Optional[int] = i
else:
index = None
raw_affiliation = None
affiliation_list = am.get("affiliation") or []
# TODO: currently requiring a "name" in all affiliations. Could
# add ROR support (via identifier) in the near future
affiliation_list = [a for a in affiliation_list if "name" in a]
if affiliation_list and len(affiliation_list) > 0:
raw_affiliation = affiliation_list[0]["name"]
if len(affiliation_list) > 1:
# note: affiliation => more_affiliations
extra["more_affiliations"] = [
clean_str(a["name"]) for a in affiliation_list[1:]
]
if am.get("sequence") and am.get("sequence") != "additional":
extra["seq"] = clean_str(am.get("sequence"))
assert ctype in ("author", "editor", "translator")
raw_name = clean_str(raw_name)
# TODO: what if 'raw_name' is None?
contribs.append(
ReleaseContrib(
creator_id=creator_id,
index=index,
raw_name=raw_name,
given_name=clean_str(am.get("given")),
surname=clean_str(am.get("family")),
raw_affiliation=clean_str(raw_affiliation),
role=ctype,
extra=extra or None,
))
return contribs
contribs = do_contribs(obj.get("author", []), "author")
contribs.extend(do_contribs(obj.get("editor", []), "editor"))
contribs.extend(do_contribs(obj.get("translator", []), "translator"))
# container
issn = obj.get("ISSN", [None])[0]
issnl = self.issn2issnl(issn)
container_id = None
if issnl:
container_id = self.lookup_issnl(issnl)
publisher = clean_str(obj.get("publisher"))
container_name = obj.get("container-title")
if container_name:
container_name = clean_str(container_name[0], force_xml=True)
if not container_name:
container_name = None
if (container_id is None and self.create_containers
and (issnl is not None) and container_name):
ce = fatcat_openapi_client.ContainerEntity(
issnl=issnl,
publisher=publisher,
container_type=self.map_container_type(release_type),
name=container_name,
)
ce_edit = self.create_container(ce)
container_id = ce_edit.ident
self._issnl_id_map[issnl] = container_id
# license slug
license_slug = None
license_extra = []
for lic in obj.get("license", []):
if lic["content-version"] not in ("vor", "unspecified"):
continue
slug = lookup_license_slug(lic["URL"])
if slug:
license_slug = slug
if "start" in lic:
lic["start"] = lic["start"]["date-time"]
license_extra.append(lic)
# references
refs = []
for i, rm in enumerate(obj.get("reference", [])):
try:
year: Optional[int] = int(rm.get("year"))
# TODO: will need to update/config in the future!
# NOTE: are there crossref works with year < 100?
if year is not None:
if year > 2025 or year < 100:
year = None
except (TypeError, ValueError):
year = None
ref_extra: Dict[str, Any] = dict()
key = rm.get("key")
if key and key.startswith(obj["DOI"].upper()):
key = key.replace(obj["DOI"].upper() + "-", "")
key = key.replace(obj["DOI"].upper(), "")
ref_container_name = rm.get("volume-title")
if not ref_container_name:
ref_container_name = rm.get("journal-title")
elif rm.get("journal-title"):
ref_extra["journal-title"] = rm["journal-title"]
if rm.get("DOI"):
ref_extra["doi"] = rm.get("DOI").lower()
author = clean_str(rm.get("author"))
if author:
ref_extra["authors"] = [author]
for k in (
"editor",
"edition",
"authority",
"version",
"genre",
"url",
"event",
"issue",
"volume",
"date",
"accessed_date",
"issued",
"page",
"medium",
"collection_title",
"chapter_number",
"unstructured",
"series-title",
"volume-title",
):
if clean_str(rm.get(k)):
ref_extra[k] = clean_str(rm[k])
refs.append(
fatcat_openapi_client.ReleaseRef(
index=i,
# doing lookups would be a second import pass
target_release_id=None,
key=key,
year=year,
container_name=clean_str(ref_container_name),
title=clean_str(rm.get("article-title")),
locator=clean_str(rm.get("first-page")),
# TODO: just dump JSON somewhere here?
extra=ref_extra or None,
))
# abstracts
abstracts = []
abstract = clean_str(obj.get("abstract"))
if abstract and len(abstract) > 10:
abstracts.append(
fatcat_openapi_client.ReleaseAbstract(
mimetype="application/xml+jats", content=abstract))
# extra fields
extra: Dict[str, Any] = dict()
extra_crossref: Dict[str, Any] = dict()
# top-level extra keys
if not container_id:
if obj.get("container-title"):
extra["container_name"] = container_name
for key in "group-title":
val = obj.get(key)
if val:
if type(val) == list:
val = val[0]
if type(val) == str:
val = clean_str(val)
if val:
extra[key] = clean_str(val)
else:
extra[key] = val
# crossref-nested extra keys
for key in ("subject", "type", "alternative-id", "archive", "funder"):
val = obj.get(key)
if val:
if type(val) == str:
extra_crossref[key] = clean_str(val)
else:
extra_crossref[key] = val
if license_extra:
extra_crossref["license"] = license_extra
if len(obj["title"]) > 1:
aliases = [clean_str(t) for t in obj["title"][1:]]
aliases = [t for t in aliases if t]
if aliases:
extra["aliases"] = aliases
# ISBN
isbn13 = None
for raw in obj.get("ISBN", []):
# TODO: convert if not ISBN-13 format
if len(raw) == 17:
isbn13 = raw
break
# release status
if obj["type"] in (
"journal-article",
"conference-proceeding",
"book",
"dissertation",
"book-chapter",
):
release_stage: Optional[str] = "published"
else:
# unknown
release_stage = None
# filter out unreasonably huge releases
if len(abstracts) > 100:
self.counts["skip-huge-abstracts"] += 1
return None
if len(contribs) > 2000:
self.counts["skip-huge-contribs"] += 1
return None
if len(refs) > 5000:
self.counts["skip-huge-refs"] += 1
return None
# release date parsing is amazingly complex
raw_date = obj["issued"]["date-parts"][0]
if not raw_date or not raw_date[0]:
# got some NoneType, even though at least year is supposed to be set
release_year = None
release_date = None
elif len(raw_date) == 3:
release_year = raw_date[0]
release_date = datetime.date(year=raw_date[0],
month=raw_date[1],
day=raw_date[2])
else:
# sometimes only the year is included, not the full date
release_year = raw_date[0]
release_date = None
original_title: Optional[str] = None
if obj.get("original-title"):
ot = obj.get("original-title")
if ot is not None:
original_title = clean_str(ot[0], force_xml=True)
title: Optional[str] = None
if obj.get("title"):
title = clean_str(obj["title"][0], force_xml=True)
if not title or len(title) <= 1:
# title can't be just a single character
self.counts["skip-blank-title"] += 1
return None
doi = clean_doi(obj["DOI"].lower())
if not doi:
self.counts["skip-bad-doi"] += 1
return None
subtitle = None
if obj.get("subtitle"):
subtitle = clean_str(obj["subtitle"][0], force_xml=True)
if not subtitle or len(subtitle) <= 1:
# subtitle can't be just a single character
subtitle = None
if extra_crossref:
extra["crossref"] = extra_crossref
re = ReleaseEntity(
work_id=None,
container_id=container_id,
title=title,
subtitle=subtitle,
original_title=original_title,
release_type=release_type,
release_stage=release_stage,
release_date=release_date,
release_year=release_year,
publisher=publisher,
ext_ids=fatcat_openapi_client.ReleaseExtIds(
doi=doi,
isbn13=isbn13,
),
volume=clean_str(obj.get("volume")),
issue=clean_str(obj.get("issue")),
pages=clean_str(obj.get("page")),
language=clean_str(obj.get("language")),
license_slug=license_slug,
extra=extra or None,
abstracts=abstracts or None,
contribs=contribs or None,
refs=refs or None,
)
return re
def parse_record(self, record: Any) -> Optional[ReleaseEntity]:
"""
record is a beautiful soup object
returns a ReleaseEntity, or None
In JALC metadata, both English and Japanese records are given for most
fields.
"""
extra: Dict[str, Any] = dict()
extra_jalc: Dict[str, Any] = dict()
titles = record.find_all("title")
if not titles:
return None
title = titles[0].get_text().replace("\n", " ").strip()
original_title = None
if title.endswith("."):
title = title[:-1]
if len(titles) > 1:
original_title = titles[1].get_text().replace("\n", " ").strip()
if original_title.endswith("."):
original_title = original_title[:-1]
doi = None
if record.doi:
doi = clean_doi(record.doi.string.strip().lower())
# TODO: following code is redundant with clean_doi()
if not doi:
return None
if doi.startswith("http://dx.doi.org/"):
doi = doi.replace("http://dx.doi.org/", "")
elif doi.startswith("https://dx.doi.org/"):
doi = doi.replace("https://dx.doi.org/", "")
elif doi.startswith("http://doi.org/"):
doi = doi.replace("http://doi.org/", "")
elif doi.startswith("https://doi.org/"):
doi = doi.replace("https://doi.org/", "")
if not (doi.startswith("10.") and "/" in doi):
sys.stderr.write("bogus JALC DOI: {}\n".format(doi))
doi = None
if not doi:
return None
people = record.find_all("Person")
contribs = parse_jalc_persons(people)
for i, contrib in enumerate(contribs):
if contrib.raw_name != "et al.":
contrib.index = i
release_year = None
release_date = None
date = record.date or None
if date:
date = date.string
if len(date) == 10:
release_date_date = datetime.datetime.strptime(
date["completed-date"], DATE_FMT).date()
release_year = release_date_date.year
release_date = release_date_date.isoformat()
elif len(date) == 4 and date.isdigit():
release_year = int(date)
pages = None
if record.startingPage and record.startingPage.string.strip():
pages = record.startingPage.string.strip()
if record.endingPage and record.endingPage.string.strip():
pages = "{}-{}".format(pages, record.endingPage.string.strip())
# double check to prevent "-" as pages
if pages and pages.strip() == "-":
pages = None
volume = None
if record.volume:
volume = record.volume.string
issue = None
if record.number:
# note: number/issue transform
issue = record.number.string
# container
issn = None
issn_list = record.find_all("issn")
if issn_list:
# if we wanted the other ISSNs, would also need to uniq the list.
# But we only need one to lookup ISSN-L/container
issn = issn_list[0].string
if issn:
issnl = self.issn2issnl(issn)
else:
issnl = None
container_id = None
if issnl:
container_id = self.lookup_issnl(issnl)
publisher = None
container_name = None
container_extra: Dict[str, Any] = dict()
if record.publicationName:
pubs = [
p.get_text().replace("\n", " ").strip()
for p in record.find_all("publicationName") if p.get_text()
]
pubs = [clean_str(p) for p in pubs if p]
assert pubs
if len(pubs) > 1 and pubs[0] == pubs[1]:
pubs = [pubs[0]]
if len(pubs) > 1 and is_cjk(pubs[0]):
# eng/jpn ordering is not reliable
pubs = [pubs[1], pubs[0]]
container_name = clean_str(pubs[0])
if len(pubs) > 1:
container_extra["original_name"] = clean_str(pubs[1])
if record.publisher:
pubs = [
p.get_text().replace("\n", " ").strip()
for p in record.find_all("publisher") if p.get_text()
]
pubs = [p for p in pubs if p]
if len(pubs) > 1 and pubs[0] == pubs[1]:
pubs = [pubs[0]]
if len(pubs) > 1 and is_cjk(pubs[0]):
# ordering is not reliable
pubs = [pubs[1], pubs[0]]
if pubs:
publisher = clean_str(pubs[0])
if len(pubs) > 1:
container_extra["publisher_aliases"] = pubs[1:]
if (container_id is None and self.create_containers
and (issnl is not None) and container_name):
# name, type, publisher, issnl
# extra: issnp, issne, original_name, languages, country
container_extra["country"] = "jp"
container_extra["languages"] = ["ja"]
ce = fatcat_openapi_client.ContainerEntity(
name=container_name,
container_type="journal",
publisher=publisher,
issnl=issnl,
extra=(container_extra or None),
)
ce_edit = self.create_container(ce)
container_id = ce_edit.ident
# short-cut future imports in same batch
self._issnl_id_map[issnl] = container_id
# the vast majority of works are in japanese
# TODO: any indication when *not* in japanese?
lang = "ja"
# reasonable default for this collection
release_type = "article-journal"
# extra:
# translation_of
# aliases
# container_name
# group-title
# always put at least an empty dict here to indicate the DOI registrar
# (informally)
extra["jalc"] = extra_jalc
title = clean_str(title)
if not title:
return None
re = ReleaseEntity(
work_id=None,
title=title,
original_title=clean_str(original_title),
release_type=release_type,
release_stage="published",
release_date=release_date,
release_year=release_year,
ext_ids=fatcat_openapi_client.ReleaseExtIds(doi=doi, ),
volume=volume,
issue=issue,
pages=pages,
publisher=publisher,
language=lang,
# license_slug
container_id=container_id,
contribs=contribs,
extra=extra,
)
return re
def parse_record(self, a: Any) -> ReleaseEntity:
medline = a.MedlineCitation
# PubmedData isn't required by DTD, but seems to always be present
pubmed = a.PubmedData
extra = dict()
extra_pubmed = dict()
identifiers = pubmed.ArticleIdList
pmid = medline.PMID.string.strip()
doi = identifiers.find("ArticleId", IdType="doi")
if doi and doi.string:
doi = clean_doi(doi.string)
else:
doi = None
pmcid = identifiers.find("ArticleId", IdType="pmc")
if pmcid:
pmcid = clean_pmcid(pmcid.string.strip().upper())
release_type = None
pub_types = []
for pub_type in medline.Article.PublicationTypeList.find_all("PublicationType"):
pub_types.append(pub_type.string)
if pub_type.string in PUBMED_RELEASE_TYPE_MAP:
release_type = PUBMED_RELEASE_TYPE_MAP[pub_type.string]
break
if pub_types:
extra_pubmed["pub_types"] = pub_types
if medline.Article.PublicationTypeList.find(string="Retraction of Publication"):
release_type = "retraction"
retraction_of = medline.find("CommentsCorrections", RefType="RetractionOf")
if retraction_of:
if retraction_of.RefSource:
extra_pubmed["retraction_of_raw"] = retraction_of.RefSource.string
if retraction_of.PMID:
extra_pubmed["retraction_of_pmid"] = retraction_of.PMID.string
# everything in medline is published
release_stage = "published"
if medline.Article.PublicationTypeList.find(string="Corrected and Republished Article"):
release_stage = "updated"
if medline.Article.PublicationTypeList.find(string="Retraction of Publication"):
release_stage = "retraction"
withdrawn_status = None
if medline.Article.PublicationTypeList.find(string="Retracted Publication"):
withdrawn_status = "retracted"
elif medline.find("CommentsCorrections", RefType="ExpressionOfConcernIn"):
withdrawn_status = "concern"
pages = medline.find("MedlinePgn")
if pages:
pages = pages.string
title = medline.Article.ArticleTitle.get_text() # always present
if title:
title = title.replace("\n", " ")
if title.endswith("."):
title = title[:-1]
# this hides some "special" titles, but the vast majority are
# translations; translations don't always include the original_title
if title.startswith("[") and title.endswith("]"):
title = title[1:-1]
else:
# will filter out later
title = None
original_title = medline.Article.find("VernacularTitle", recurse=False)
if original_title:
original_title = original_title.get_text() or None
original_title = original_title.replace("\n", " ")
if original_title and original_title.endswith("."):
original_title = original_title[:-1]
if original_title and not title:
# if we only have an "original" title, but not translated/english
# title, sub in the original title so the entity can be created
title = original_title
original_title = None
# TODO: happening in alpha order, not handling multi-language well.
language = medline.Article.Language
if language:
language = language.get_text()
if language in ("und", "un"):
# "undetermined"
language = None
else:
language = LANG_MAP_MARC.get(language)
if not language and not (medline.Article.Language.get_text() in LANG_MAP_MARC):
warnings.warn(
"MISSING MARC LANG: {}".format(medline.Article.Language.string)
)
### Journal/Issue Metadata
# MedlineJournalInfo is always present
issnl = None
container_id = None
container_name = None
container_extra = dict()
mji = medline.MedlineJournalInfo
if mji.find("Country"):
country_name = mji.Country.string.strip()
country_code = COUNTRY_NAME_MAP.get(country_name)
if country_code:
container_extra["country"] = country_code
elif country_name:
container_extra["country_name"] = country_name
if mji.find("ISSNLinking"):
issnl = mji.ISSNLinking.string
journal = medline.Article.Journal
issnp = journal.find("ISSN", IssnType="Print")
if issnp:
issnp = clean_issn(issnp.string)
else:
issnp = None
if not issnl and issnp:
issnl = self.issn2issnl(issnp)
else:
issnl = None
if issnl:
container_id = self.lookup_issnl(issnl)
pub_date = medline.Article.find("ArticleDate")
if not pub_date:
pub_date = journal.PubDate
if not pub_date:
pub_date = journal.JournalIssue.PubDate
release_date: Optional[str] = None
release_year: Optional[int] = None
if pub_date.Year:
release_year = int(pub_date.Year.string)
if pub_date.find("Day") and pub_date.find("Month"):
try:
release_date_date = datetime.date(
release_year,
MONTH_ABBR_MAP[pub_date.Month.string],
int(pub_date.Day.string),
)
release_date = release_date_date.isoformat()
except ValueError as ve:
print("bad date, skipping: {}".format(ve), file=sys.stderr)
release_date = None
elif pub_date.MedlineDate:
medline_date = pub_date.MedlineDate.string.strip()
if len(medline_date) >= 4 and medline_date[:4].isdigit():
release_year = int(medline_date[:4])
if release_year < 1300 or release_year > 2040:
print(
"bad medline year, skipping: {}".format(release_year), file=sys.stderr
)
release_year = None
else:
print(
"unparsable medline date, skipping: {}".format(medline_date),
file=sys.stderr,
)
if journal.find("Title"):
container_name = journal.Title.get_text()
if (
container_id is None
and self.create_containers
and (issnl is not None)
and container_name
):
# name, type, publisher, issnl
# extra: original_name, languages, country
ce = fatcat_openapi_client.ContainerEntity(
name=container_name,
container_type="journal",
# NOTE: publisher not included
issnl=issnl,
issnp=issnp,
extra=(container_extra or None),
)
ce_edit = self.create_container(ce)
container_id = ce_edit.ident
self._issnl_id_map[issnl] = container_id
ji = journal.JournalIssue
volume = None
if ji.find("Volume"):
volume = ji.Volume.string
issue = None
if ji.find("Issue"):
issue = ji.Issue.string
### Abstracts
# "All abstracts are in English"
abstracts = []
primary_abstract = medline.find("Abstract")
if primary_abstract and primary_abstract.AbstractText.get("NlmCategory"):
joined = "\n".join(
[m.get_text() for m in primary_abstract.find_all("AbstractText")]
)
abst = fatcat_openapi_client.ReleaseAbstract(
content=joined,
mimetype="text/plain",
lang="en",
)
if abst.content:
abstracts.append(abst)
elif primary_abstract:
for abstract in primary_abstract.find_all("AbstractText"):
abst = fatcat_openapi_client.ReleaseAbstract(
content=abstract.get_text().strip(),
mimetype="text/plain",
lang="en",
)
if abst.content:
abstracts.append(abst)
if abstract.find("math"):
abst = fatcat_openapi_client.ReleaseAbstract(
# strip the <AbstractText> tags
content=str(abstract)[14:-15],
mimetype="application/mathml+xml",
lang="en",
)
if abst.content:
abstracts.append(abst)
other_abstracts = medline.find_all("OtherAbstract")
for other in other_abstracts:
lang: Optional[str] = "en"
if other.get("Language"):
lang = LANG_MAP_MARC.get(other["Language"])
abst = fatcat_openapi_client.ReleaseAbstract(
content=other.AbstractText.get_text().strip(),
mimetype="text/plain",
lang=lang,
)
if abst.content:
abstracts.append(abst)
### Contribs
contribs = []
if medline.AuthorList:
for author in medline.AuthorList.find_all("Author"):
creator_id = None
given_name = None
surname = None
raw_name = None
if author.ForeName:
given_name = author.ForeName.get_text().replace("\n", " ")
if author.LastName:
surname = author.LastName.get_text().replace("\n", " ")
if given_name and surname:
raw_name = "{} {}".format(given_name, surname)
elif surname:
raw_name = surname
if not raw_name and author.CollectiveName and author.CollectiveName.get_text():
raw_name = author.CollectiveName.get_text().replace("\n", " ")
contrib_extra = dict()
orcid = author.find("Identifier", Source="ORCID")
if orcid:
# needs re-formatting from, eg, "0000000179841889"
orcid = orcid.string
if orcid.startswith("http://orcid.org/"):
orcid = orcid.replace("http://orcid.org/", "")
elif orcid.startswith("https://orcid.org/"):
orcid = orcid.replace("https://orcid.org/", "")
elif "-" not in orcid:
orcid = "{}-{}-{}-{}".format(
orcid[0:4],
orcid[4:8],
orcid[8:12],
orcid[12:16],
)
creator_id = self.lookup_orcid(orcid)
contrib_extra["orcid"] = orcid
affiliations = author.find_all("Affiliation")
raw_affiliation = None
if affiliations:
raw_affiliation = affiliations[0].get_text().replace("\n", " ")
if len(affiliations) > 1:
contrib_extra["more_affiliations"] = [
ra.get_text().replace("\n", " ") for ra in affiliations[1:]
]
if author.find("EqualContrib"):
# TODO: schema for this?
contrib_extra["equal"] = True
contribs.append(
fatcat_openapi_client.ReleaseContrib(
raw_name=raw_name,
given_name=given_name,
surname=surname,
role="author",
raw_affiliation=raw_affiliation,
creator_id=creator_id,
extra=contrib_extra,
)
)
if medline.AuthorList["CompleteYN"] == "N":
contribs.append(fatcat_openapi_client.ReleaseContrib(raw_name="et al."))
for i, contrib in enumerate(contribs):
if contrib.raw_name != "et al.":
contrib.index = i
### References
refs = []
if pubmed.ReferenceList:
# note that Reference always exists within a ReferenceList, but
# that there may be multiple ReferenceList (eg, sometimes one per
# Reference)
for ref in pubmed.find_all("Reference"):
ref_extra: Dict[str, Any] = dict()
ref_doi = ref.find("ArticleId", IdType="doi")
if ref_doi:
ref_doi = clean_doi(ref_doi.string)
ref_pmid = ref.find("ArticleId", IdType="pubmed")
if ref_pmid:
ref_pmid = clean_pmid(ref_pmid.string)
ref_release_id = None
if ref_doi:
ref_extra["doi"] = ref_doi
if self.lookup_refs:
ref_release_id = self.lookup_doi(ref_doi)
if ref_pmid:
ref_extra["pmid"] = ref_pmid
if self.lookup_refs:
ref_release_id = self.lookup_pmid(ref_pmid)
ref_raw = ref.Citation
if ref_raw:
ref_extra["unstructured"] = ref_raw.get_text()
refs.append(
fatcat_openapi_client.ReleaseRef(
target_release_id=ref_release_id,
extra=ref_extra or None,
)
)
# extra:
# translation_of
# aliases
# container_name
# group-title
# pubmed: retraction refs
if extra_pubmed:
extra["pubmed"] = extra_pubmed
title = clean_str(title)
if not title:
return None
re = fatcat_openapi_client.ReleaseEntity(
work_id=None,
title=title,
original_title=clean_str(original_title),
release_type=release_type,
release_stage=release_stage,
release_date=release_date,
release_year=release_year,
withdrawn_status=withdrawn_status,
ext_ids=fatcat_openapi_client.ReleaseExtIds(
doi=doi,
pmid=pmid,
pmcid=pmcid,
# isbn13 # never in Article
),
volume=volume,
issue=issue,
pages=pages,
# publisher # not included?
language=language,
# license_slug # not in MEDLINE
abstracts=abstracts or None,
contribs=contribs or None,
refs=refs or None,
container_id=container_id,
extra=extra or None,
)
return re
