def crosswalk_bio(orcid_profile, person_uri, graph, skip_person=False, person_class=FOAF.Person):
#If skip_person, then don't create person and add names
if not skip_person:
person_details = orcid_profile["orcid-profile"]["orcid-bio"]["personal-details"]
given_names = person_details["given-names"]["value"] if "given-names" in person_details else None
family_name = person_details["family-name"]["value"] if "family-name" in person_details else None
full_name = join_if_not_empty((given_names, family_name))
##Person
graph.add((person_uri, RDF.type, person_class))
graph.add((person_uri, RDFS.label, Literal(full_name)))
#Note that not assigning class here.
##vcard
#Main vcard
vcard_uri = person_uri + "-vcard"
graph.add((vcard_uri, RDF.type, VCARD.Individual))
#Contact info for
graph.add((vcard_uri, OBO.ARG_2000029, person_uri))
#Name vcard
vcard_name_uri = person_uri + "-vcard-name"
graph.add((vcard_name_uri, RDF.type, VCARD.Name))
graph.add((vcard_uri, VCARD.hasName, vcard_name_uri))
if given_names:
graph.add((vcard_name_uri, VCARD.givenName, Literal(given_names)))
if family_name:
graph.add((vcard_name_uri, VCARD.familyName, Literal(family_name)))
#Other identifiers
if "external-identifiers" in orcid_profile["orcid-profile"]["orcid-bio"] \
and orcid_profile["orcid-profile"]["orcid-bio"]["external-identifiers"] \
and "external-identifier" in orcid_profile["orcid-profile"]["orcid-bio"]["external-identifiers"]:
external_identifiers = orcid_profile["orcid-profile"]["orcid-bio"]["external-identifiers"]["external-identifier"]
for external_identifier in external_identifiers:
if external_identifier["external-id-common-name"]["value"] == "Scopus Author ID":
graph.add((person_uri, VIVO.scopusId, Literal(external_identifier["external-id-reference"]["value"])))
def gen_triples(cr_result, matchlist, publisher_list, journal_list, doi=None):
pub_uri = uri_gen('pub', g)
# Article info
subjects = cr_result["subject"] if "subject" in cr_result else None
if "title" in cr_result:
if cr_result["title"][0]:
title = cr_result["title"][0]
elif cr_result["title"]:
title = cr_result["title"].strip()
else:
title = None
else:
title = None
# Publication type
if cr_result["type"] == 'journal-article':
pubtype = BIBO.AcademicArticle
elif cr_result["type"] == 'book-chapter':
pubtype = BIBO.Chapter
elif cr_result["type"] == 'dataset':
pubtype = VIVO.Dataset
elif cr_result["type"] == 'proceedings-article':
pubtype = VIVO.ConferencePaper
elif cr_result["type"] == 'abstract':
pubtype = VIVO.Abstract
else:
pubtype = URIRef(raw_input('Unknown publication type for {}.'
' Enter a valid URI for the type'
.format(doi)))
# Choose the longer (hopefully non-abbreviated) title
journal = (max(cr_result["container-title"], key=len) if
"container-title" in cr_result and
cr_result["container-title"] else None)
if journal:
if journal in journal_list:
journal_uri = journal_list[journal]
print 'found existing '+journal
g.add((D[pub_uri], VIVO.hasPublicationVenue,
URIRef(journal_uri)))
else:
# publisher_list = get_publishers()
# raw_input(publisher_list)
journal_uri = D[uri_gen('n', g)]
journal_list[journal] = str(journal_uri)
g.add((D[pub_uri], VIVO.hasPublicationVenue,
URIRef(journal_uri)))
if pubtype == VIVO.ConferencePaper:
g.add((URIRef(journal_uri), RDF.type, BIBO.Proceedings))
elif pubtype == BIBO.Chapter:
g.add((URIRef(journal_uri), RDF.type, BIBO.Book))
else:
g.add((URIRef(journal_uri), RDF.type, BIBO.Journal))
g.add((URIRef(journal_uri), RDFS.label, Literal(journal)))
if "publisher" in cr_result:
publisher = cr_result["publisher"]
if publisher in publisher_list:
publisher_uri = publisher_list[publisher]
else:
publisher_uri = D[uri_gen('n', g)]
g.add(((URIRef(publisher_uri)), RDF.type, VIVO.Publisher))
g.add(((URIRef(publisher_uri)), RDFS.label,
Literal(publisher)))
publisher_list[publisher] = str(publisher_uri)
print('Created new publisher "' + publisher + '"')
g.add(((URIRef(journal_uri)), VIVO.publisher,
URIRef(publisher_uri)))
print 'Made new '+journal
issue = cr_result["issue"] if "issue" in cr_result else None
volume = cr_result["volume"] if "volume" in cr_result else None
pages = (cr_result["page"] if "page" in cr_result and 'n/a' not in
cr_result["page"] else None)
# Authors
authors = (parse_authors(cr_result) if "author" in cr_result
else None)
date = parse_publication_date(cr_result)
# Publication date
if date:
(publication_year, publication_month, publication_day) = date
else:
(publication_year, publication_month, publication_day) = (None,
None,
None)
date_uri = uri_gen('n', g)
g.add((D[pub_uri], VIVO.dateTimeValue, D[date_uri]))
add_date(D[date_uri], publication_year, g, publication_month,
publication_day)
# Add things to the graph
if pubtype:
g.add((D[pub_uri], RDF.type, pubtype))
if doi:
g.add((D[pub_uri], BIBO.doi, Literal(doi)))
if issue:
g.add((D[pub_uri], BIBO.issue, Literal(issue)))
if volume:
g.add((D[pub_uri], BIBO.volume, Literal(volume)))
if title:
g.add((D[pub_uri], RDFS.label, Literal(title)))
# Loop through the list of authors, trying to check for existing
# authors in the database
if authors:
for idx, (first_name, surname) in enumerate(authors):
full_name = join_if_not_empty((first_name, surname))
rank = idx+1
if full_name in matchlist[0]:
pos = matchlist[0].index(full_name)
assign_authorship(matchlist[1][pos], g, pub_uri,
full_name, matchlist, rank)
else:
roll = name_lookup(surname)
matchlist = name_selecter(roll, full_name, g,
first_name, surname, pub_uri,
matchlist, rank)
# subjects
if subjects:
for subject in subjects:
# NEED TO FIND SUBJECT IN VIVO
concept_uri = get_subject(subject, g)
if concept_uri:
# print 'found existing '+subject
g.add((D[pub_uri], VIVO.hasSubjectArea,
URIRef(concept_uri)))
elif subject in subjectlist[0]:
# print 'already made a new one this round '+subject
match = subjectlist[0].index(subject)
subject_uri = subjectlist[1][match]
g.add((D[pub_uri], VIVO.hasSubjectArea,
D[subject_uri]))
else:
# print 'made new '+subject
subject_uri = uri_gen('sub', g)
subjectlist[0].append(subject)
subjectlist[1].append(subject_uri)
g.add((D[pub_uri], VIVO.hasSubjectArea,
D[subject_uri]))
g.add((D[subject_uri], RDF.type, SKOS.Concept))
g.add((D[subject_uri], RDFS.label, Literal(subject)))
if pages:
pages = pages.split("-")
startpage = pages[0]
g.add((D[pub_uri], BIBO.pageStart, Literal(startpage)))
if len(pages) > 1:
endpage = pages[1]
g.add((D[pub_uri], BIBO.pageEnd, Literal(endpage)))
else:
endpage = None
def crosswalk_bio(orcid_profile, person_uri, graph, skip_person=False, person_class=FOAF.Person,
existing_vcard_uri=None, skip_name_vcard=False):
#Get names (for person and name vcard)
person_details = orcid_profile["orcid-profile"]["orcid-bio"].get("personal-details", {})
given_names = person_details.get("given-names", {}).get("value")
family_name = person_details.get("family-name", {}).get("value")
full_name = join_if_not_empty((given_names, family_name))
#Following is non-vcard bio information
#If skip_person, then don't create person and add names
if not skip_person:
#Add person
graph.add((person_uri, RDF.type, person_class))
graph.add((person_uri, RDFS.label, Literal(full_name)))
#Biography
biography = (orcid_profile["orcid-profile"]["orcid-bio"].get("biography") or {}).get("value")
if biography:
graph.add((person_uri, VIVO.overview, Literal(biography)))
#Other identifiers
#Default VIVO-ISF only supports a limited number of identifier types.
external_identifiers = \
(orcid_profile["orcid-profile"]["orcid-bio"].get("external-identifiers", {}) or {}).get("external-identifier", [])
for external_identifier in external_identifiers:
#Scopus ID
if external_identifier["external-id-common-name"]["value"] == "Scopus Author ID":
graph.add((person_uri, VIVO.scopusId, Literal(external_identifier["external-id-reference"]["value"])))
#ISI Research ID
if external_identifier["external-id-common-name"]["value"] == "ResearcherID":
graph.add((person_uri, VIVO.researcherId, Literal(external_identifier["external-id-reference"]["value"])))
#Keywords
keywords = \
(orcid_profile["orcid-profile"]["orcid-bio"].get("keywords", {}) or {}).get("keyword", [])
for keyword in keywords:
graph.add((person_uri, VIVO.freetextKeyword, Literal(keyword["value"])))
#Following is vcard bio information
#Add main vcard
vcard_uri = existing_vcard_uri or person_uri + "-vcard"
#Will only add vcard if there is a child vcard
add_main_vcard = False
if not skip_name_vcard and (given_names or family_name):
#Name vcard
vcard_name_uri = person_uri + "-vcard-name"
graph.add((vcard_name_uri, RDF.type, VCARD.Name))
graph.add((vcard_uri, VCARD.hasName, vcard_name_uri))
if given_names:
graph.add((vcard_name_uri, VCARD.givenName, Literal(given_names)))
if family_name:
graph.add((vcard_name_uri, VCARD.familyName, Literal(family_name)))
add_main_vcard = True
#Websites
researcher_urls = \
(orcid_profile["orcid-profile"]["orcid-bio"].get("researcher-urls", {}) or {}).get("researcher-url", [])
for index, researcher_url in enumerate(researcher_urls):
url = researcher_url["url"]["value"]
url_name = (researcher_url["url-name"] or {}).get("value")
vcard_website_uri = person_uri + "-vcard-website" + str(index)
graph.add((vcard_website_uri, RDF.type, VCARD.URL))
graph.add((vcard_uri, VCARD.hasURL, vcard_website_uri))
graph.add((vcard_website_uri, VCARD.url, Literal(url, datatype=XSD.anyURI)))
if url_name:
graph.add((vcard_website_uri, RDFS.label, Literal(url_name)))
if add_main_vcard and not existing_vcard_uri:
graph.add((vcard_uri, RDF.type, VCARD.Individual))
#Contact info for
graph.add((vcard_uri, OBO.ARG_2000029, person_uri))
def crosswalk(self, orcid_profile, person_uri, graph, person_class=FOAF.Person):
# Get names (for person and name vcard)
given_names = None
family_name = None
if "name" in orcid_profile["person"]:
person_details = orcid_profile["person"]["name"]
given_names = person_details.get("given-names", {}).get("value")
family_name = person_details.get("family-name", {}).get("value")
full_name = join_if_not_empty((given_names, family_name))
# Following is non-vcard bio information
# If skip_person, then don't create person and add names
if full_name and self.create_strategy.should_create(person_class, person_uri):
# Add person
graph.add((person_uri, RDF.type, person_class))
graph.add((person_uri, RDFS.label, Literal(full_name)))
# Biography
if "biography" in orcid_profile["person"]:
biography = orcid_profile["person"]["biography"]["content"]
if biography:
graph.add((person_uri, VIVO.overview, Literal(biography)))
# Other identifiers
# Default VIVO-ISF only supports a limited number of identifier types.
if "external-identifiers" in orcid_profile["person"]:
external_identifiers = orcid_profile["person"]["external-identifiers"]["external-identifier"]
for external_identifier in external_identifiers:
# Scopus ID
if external_identifier["external-id-type"] == "Scopus Author ID":
graph.add((person_uri, VIVO.scopusId, Literal(external_identifier["external-id-value"])))
# ISI Research ID
if external_identifier["external-id-type"] == "ResearcherID":
graph.add((person_uri, VIVO.researcherId, Literal(external_identifier["external-id-value"])))
# Keywords
if "keywords" in orcid_profile["person"]:
keywords = orcid_profile["person"]["keywords"]["keyword"]
for keyword in keywords:
keywords_content = keyword["content"]
if keywords_content:
for keyword_content in keywords_content.split(", "):
graph.add((person_uri, VIVO.freetextKeyword, Literal(keyword_content)))
# Following is vcard bio information
# Add main vcard
vcard_uri = self.identifier_strategy.to_uri(VCARD.Individual, {"person_uri": person_uri})
# Will only add vcard if there is a child vcard
add_main_vcard = False
# Name vcard
vcard_name_uri = self.identifier_strategy.to_uri(VCARD.Name, {"person_uri": person_uri})
if (given_names or family_name) and self.create_strategy.should_create(VCARD.Name, vcard_name_uri):
graph.add((vcard_name_uri, RDF.type, VCARD.Name))
graph.add((vcard_uri, VCARD.hasName, vcard_name_uri))
if given_names:
graph.add((vcard_name_uri, VCARD.givenName, Literal(given_names)))
if family_name:
graph.add((vcard_name_uri, VCARD.familyName, Literal(family_name)))
add_main_vcard = True
# Websites
if "researcher-urls" in orcid_profile["person"]:
researcher_urls = orcid_profile["person"]["researcher-urls"]["researcher-url"]
for researcher_url in researcher_urls:
url = researcher_url["url"]["value"]
url_name = researcher_url["url-name"]
vcard_website_uri = self.identifier_strategy.to_uri(VCARD.URL, {"url": url})
graph.add((vcard_website_uri, RDF.type, VCARD.URL))
graph.add((vcard_uri, VCARD.hasURL, vcard_website_uri))
graph.add((vcard_website_uri, VCARD.url, Literal(url, datatype=XSD.anyURI)))
if url_name:
graph.add((vcard_website_uri, RDFS.label, Literal(url_name)))
add_main_vcard = True
if add_main_vcard and self.create_strategy.should_create(VCARD.Individual, vcard_uri):
graph.add((vcard_uri, RDF.type, VCARD.Individual))
# Contact info for
graph.add((vcard_uri, OBO.ARG_2000029, person_uri))
def crosswalk(self,
orcid_profile,
person_uri,
graph,
person_class=FOAF.Person):
# Get names (for person and name vcard)
given_names = None
family_name = None
if "name" in orcid_profile["person"]:
person_details = orcid_profile["person"]["name"]
given_names = person_details.get("given-names", {}).get("value")
family_name = person_details.get("family-name", {}).get("value")
full_name = join_if_not_empty((given_names, family_name))
# Following is non-vcard bio information
# If skip_person, then don't create person and add names
if full_name and self.create_strategy.should_create(
person_class, person_uri):
# Add person
graph.add((person_uri, RDF.type, person_class))
graph.add((person_uri, RDFS.label, Literal(full_name)))
# Biography
if "biography" in orcid_profile["person"]:
biography = orcid_profile["person"]["biography"]["content"]
if biography:
graph.add((person_uri, VIVO.overview, Literal(biography)))
# Other identifiers
# Default VIVO-ISF only supports a limited number of identifier types.
if "external-identifiers" in orcid_profile["person"]:
external_identifiers = orcid_profile["person"][
"external-identifiers"]["external-identifier"]
for external_identifier in external_identifiers:
# Scopus ID
if external_identifier[
"external-id-type"] == "Scopus Author ID":
graph.add(
(person_uri, VIVO.scopusId,
Literal(external_identifier["external-id-value"])))
# ISI Research ID
if external_identifier["external-id-type"] == "ResearcherID":
graph.add(
(person_uri, VIVO.researcherId,
Literal(external_identifier["external-id-value"])))
# Keywords
if "keywords" in orcid_profile["person"]:
keywords = orcid_profile["person"]["keywords"]["keyword"]
for keyword in keywords:
keywords_content = keyword["content"]
if keywords_content:
for keyword_content in keywords_content.split(", "):
graph.add((person_uri, VIVO.freetextKeyword,
Literal(keyword_content)))
# Following is vcard bio information
# Add main vcard
vcard_uri = self.identifier_strategy.to_uri(VCARD.Individual,
{"person_uri": person_uri})
# Will only add vcard if there is a child vcard
add_main_vcard = False
# Name vcard
vcard_name_uri = self.identifier_strategy.to_uri(
VCARD.Name, {"person_uri": person_uri})
if (given_names or family_name) and self.create_strategy.should_create(
VCARD.Name, vcard_name_uri):
graph.add((vcard_name_uri, RDF.type, VCARD.Name))
graph.add((vcard_uri, VCARD.hasName, vcard_name_uri))
if given_names:
graph.add(
(vcard_name_uri, VCARD.givenName, Literal(given_names)))
if family_name:
graph.add(
(vcard_name_uri, VCARD.familyName, Literal(family_name)))
add_main_vcard = True
# Websites
if "researcher-urls" in orcid_profile["person"]:
researcher_urls = orcid_profile["person"]["researcher-urls"][
"researcher-url"]
for researcher_url in researcher_urls:
url = researcher_url["url"]["value"]
url_name = researcher_url["url-name"]
vcard_website_uri = self.identifier_strategy.to_uri(
VCARD.URL, {"url": url})
graph.add((vcard_website_uri, RDF.type, VCARD.URL))
graph.add((vcard_uri, VCARD.hasURL, vcard_website_uri))
graph.add((vcard_website_uri, VCARD.url,
Literal(url, datatype=XSD.anyURI)))
if url_name:
graph.add(
(vcard_website_uri, RDFS.label, Literal(url_name)))
add_main_vcard = True
if add_main_vcard and self.create_strategy.should_create(
VCARD.Individual, vcard_uri):
graph.add((vcard_uri, RDF.type, VCARD.Individual))
# Contact info for
graph.add((vcard_uri, OBO.ARG_2000029, person_uri))
def _get_orcid_title(work):
return join_if_not_empty(
(work["title"]["title"]["value"],
(work["title"].get("subtitle") or {}).get("value")), ": ")
def crosswalk_work(self, work, person_uri, person_surname, graph):
# Work metadata may be available from the orcid profile, bibtex contained in the orcid profile, and/or crossref
# record. The preferred order (in general) for getting metadata is crossref, bibtex, orcid.
# Note that datacite records were considered, but not found to have additional/better metadata.
# Work Type
work_type = work["type"]
if work_type in work_type_map:
# Extract
# Get external identifiers so that can get DOI
external_identifiers = WorksCrosswalk._get_work_identifiers(work)
doi = external_identifiers.get("DOI")
crossref_record = WorksCrosswalk._fetch_crossref_doi(
doi) if doi else {}
# Bibtex
bibtex = WorksCrosswalk._parse_bibtex(work)
# Get title so that can construct work uri
title = WorksCrosswalk._get_crossref_title(
crossref_record) or bibtex.get(
"title") or WorksCrosswalk._get_orcid_title(work)
# Work-type
work_class = work_type_map[work_type]
if work_type == "TRANSLATION" and bibtex and bibtex[
"ENTRYTYPE"] in bibtex_type_map:
work_class = bibtex_type_map[bibtex["ENTRYTYPE"]]
# Construct work uri
work_uri = self.identifier_strategy.to_uri(work_class,
{"name": title})
graph.add((work_uri, RDF.type, work_class))
# Title
graph.add((work_uri, RDFS.label, Literal(title)))
# Publication date
(publication_year, publication_month, publication_day) = \
WorksCrosswalk._get_crossref_publication_date(crossref_record) \
or WorksCrosswalk._get_orcid_publication_date(work) \
or WorksCrosswalk._get_bibtext_publication_date(bibtex) or (None, None, None)
date_uri = add_date(publication_year, graph,
self.identifier_strategy, publication_month,
publication_day)
if date_uri:
graph.add((work_uri, VIVO.dateTimeValue, date_uri))
# Subjects
subjects = crossref_record[
"subject"] if crossref_record and "subject" in crossref_record else None
if subjects:
for subject in subjects:
subject_uri = self.identifier_strategy.to_uri(
SKOS.Concept, {"name": subject})
graph.add((work_uri, VIVO.hasSubjectArea, subject_uri))
if self.create_strategy.should_create(
SKOS.Concept, subject_uri):
graph.add((subject_uri, RDF.type, SKOS.Concept))
graph.add((subject_uri, RDFS.label, Literal(subject)))
# Contributors (an array of (first_name, surname, VIVO type, e.g., VIVO.Authorship))
bibtex_contributors = []
bibtex_contributors.extend(
WorksCrosswalk._get_bibtex_authors(bibtex))
bibtex_contributors.extend(
WorksCrosswalk._get_bibtex_editors(bibtex))
# Orcid is better for translations because has translator role
if work_type == "TRANSLATION":
contributors = WorksCrosswalk._get_orcid_contributors(work)
else:
contributors = WorksCrosswalk._get_crossref_authors(crossref_record) or bibtex_contributors \
or WorksCrosswalk._get_orcid_contributors(work)
if not contributors:
# Add person as author or editor.
# None, None means this person.
if work_type in ("EDITED_BOOK", ):
contributors.append((None, None, VIVO.Editorship))
elif work_type == "TRANSLATION":
# Translator is a predicate, not a -ship class.
contributors.append((None, None, "TRANSLATOR"))
else:
contributors.append((None, None, VIVO.Authorship))
for (first_name, surname, vivo_type) in contributors:
if not surname or person_surname.lower() == surname.lower():
contributor_uri = person_uri
else:
contributor_uri = self.identifier_strategy.to_uri(
FOAF.Person, {
"first_name": first_name,
"surname": surname
})
if self.create_strategy.should_create(
FOAF.Person, contributor_uri):
graph.add((contributor_uri, RDF.type, FOAF.Person))
full_name = join_if_not_empty((first_name, surname))
graph.add(
(contributor_uri, RDFS.label, Literal(full_name)))
# Translation is a special case
if vivo_type == "TRANSLATOR":
graph.add((contributor_uri, BIBO.translator, work_uri))
# So is patent assignee
elif work_type == "PATENT":
graph.add((contributor_uri, VIVO.assigneeFor, work_uri))
else:
contributorship_uri = self.identifier_strategy.to_uri(
vivo_type, {
"contributor_uri": contributor_uri,
"work_uri": work_uri
})
graph.add((contributorship_uri, RDF.type, vivo_type))
graph.add((contributorship_uri, VIVO.relates, work_uri))
graph.add(
(contributorship_uri, VIVO.relates, contributor_uri))
# Publisher
publisher = crossref_record.get("publisher") or bibtex.get(
"publisher")
if publisher:
publisher_uri = self.identifier_strategy.to_uri(
FOAF.Organization, {"name": publisher})
graph.add((work_uri, VIVO.publisher, publisher_uri))
if self.create_strategy.should_create(FOAF.Organization,
publisher_uri):
graph.add((publisher_uri, RDF.type, FOAF.Organization))
graph.add((publisher_uri, RDFS.label, Literal(publisher)))
# Volume
volume = crossref_record.get("volume") or bibtex.get("volume")
if volume:
graph.add((work_uri, BIBO.volume, Literal(volume)))
# Issue
issue = crossref_record.get("issue") or bibtex.get("number")
if issue:
graph.add((work_uri, BIBO.issue, Literal(issue)))
# Pages
pages = crossref_record.get("page") or bibtex.get("pages")
start_page = None
end_page = None
if pages and "-" in pages:
(start_page, end_page) = re.split(" *-+ *", pages, maxsplit=2)
if start_page:
graph.add((work_uri, BIBO.pageStart, Literal(start_page)))
if end_page:
graph.add((work_uri, BIBO.pageEnd, Literal(end_page)))
# Identifiers
# Add doi in bibtex, but not orcid profile
if bibtex and "doi" in bibtex and "DOI" not in external_identifiers:
external_identifiers["DOI"] = bibtex["doi"]
# Add isbn in bibtex, but not orcid profile
if bibtex and "isbn" in bibtex and "ISBN" not in external_identifiers:
external_identifiers["ISBN"] = bibtex["isbn"]
for identifier_type, identifier in external_identifiers.iteritems(
):
identifier_url = None
if identifier_type in ("PAT",
"OTHER-ID") and work_type == "PATENT":
identifier_predicate = VIVO.patentNumber
elif identifier_type == "ISBN":
clean_isbn = identifier.replace("-", "")
if len(clean_isbn) <= 10:
identifier_predicate = BIBO.isbn10
else:
identifier_predicate = BIBO.isbn13
else:
(identifier_predicate, url_template) = identifier_map.get(
identifier_type, (None, None))
if url_template:
identifier_url = url_template % identifier
if identifier_predicate:
graph.add(
(work_uri, identifier_predicate, Literal(identifier)))
if identifier_url:
self._add_work_url(identifier_url, work_uri, graph)
orcid_url = (work.get("url", {}) or {}).get("value")
if orcid_url and WorksCrosswalk._use_url(orcid_url):
self._add_work_url(orcid_url, work_uri, graph)
bibtex_url = bibtex.get("link")
if bibtex_url and WorksCrosswalk._use_url(
bibtex_url) and orcid_url != bibtex_url:
self._add_work_url(bibtex_url, work_uri, graph)
# Series
series = bibtex.get("series")
# TODO: Figure out how to model series in VIVO-ISF.
# Journal
# If Crossref has a journal use it
journal = WorksCrosswalk._get_crossref_journal(crossref_record)
issns = []
if journal:
issns = crossref_record.get("ISSN", [])
# Otherwise, only use for some work types.
elif work_type in journal_map:
journal = bibtex.get("journal")
if journal:
if "issn" in bibtex:
issns = [bibtex["issn"]]
else:
journal = (work.get("journal-title", {})
or {}).get("value")
if journal:
journal_class = journal_map.get(work_type, BIBO.Journal)
journal_uri = self.identifier_strategy.to_uri(
journal_class, {"name": journal})
graph.add((work_uri, VIVO.hasPublicationVenue, journal_uri))
if self.create_strategy.should_create(journal_class,
journal_uri):
graph.add((journal_uri, RDF.type, journal_class))
graph.add((journal_uri, RDFS.label, Literal(journal)))
for issn in issns:
graph.add((journal_uri, BIBO.issn, Literal(issn)))
if work_type in ("BOOK_CHAPTER", ):
book_title = bibtex.get("booktitle")
if book_title:
book_uri = self.identifier_strategy.to_uri(
BIBO.Book, {"name": book_title})
graph.add((work_uri, VIVO.hasPublicationVenue, book_uri))
if self.create_strategy.should_create(BIBO.Book, book_uri):
graph.add((book_uri, RDF.type, BIBO.Book))
graph.add((book_uri, RDFS.label, Literal(book_title)))
if work_type in ("CONFERENCE_PAPER", ):
proceeding = bibtex.get("journal") or (work.get(
"journal-title", {}) or {}).get("value")
if proceeding:
proceeding_uri = self.identifier_strategy.to_uri(
BIBO.Proceedings, {"name": proceeding})
graph.add(
(work_uri, VIVO.hasPublicationVenue, proceeding_uri))
if self.create_strategy.should_create(
BIBO.Proceedings, proceeding_uri):
graph.add((proceeding_uri, RDF.type, BIBO.Proceedings))
graph.add(
(proceeding_uri, RDFS.label, Literal(proceeding)))
def crosswalk_works(orcid_profile, person_uri, graph, subjectlist, journlist, orglist):
person_surname = orcid_profile["orcid-profile"]["orcid-bio"]["personal-details"]["family-name"]["value"]
#Publications
if "orcid-works" in orcid_profile["orcid-profile"]["orcid-activities"] \
and orcid_profile["orcid-profile"]["orcid-activities"]["orcid-works"] \
and "orcid-work" in orcid_profile["orcid-profile"]["orcid-activities"]["orcid-works"]:
works = orcid_profile["orcid-profile"]["orcid-activities"]["orcid-works"]["orcid-work"]
for work in works:
##Extract
#Get external identifiers so that can get DOI
external_identifiers = _get_work_identifiers(work)
doi = external_identifiers.get("DOI")
doi_record = fetch_crossref_doi(doi) if doi else None
#Bibtex
bibtex = _parse_bibtex(work)
#Work Type
work_type = work["work-type"]
#Title
title = work["work-title"]["title"]["value"]
work_uri = ns.D[to_hash_identifier(PREFIX_DOCUMENT, (title, work_type))]
#Publication date
(publication_year, publication_month, publication_day) = _get_doi_publication_date(doi_record) \
if doi_record else _get_publication_date(work)
#Subjects
subjects = doi_record["subject"] if doi_record and "subject" in doi_record else None
#Authors
authors = _get_doi_authors(doi_record) if doi_record else None
#TODO: Get from ORCID profile if no doi record
#Publisher
publisher = bibtex.get("publisher")
##Add triples
#Title
graph.add((work_uri, RDFS.label, Literal(title)))
#Person (via Authorship)
authorship_uri = work_uri + "-auth"
graph.add((authorship_uri, RDF.type, VIVO.Authorship))
graph.add((authorship_uri, VIVO.relates, work_uri))
graph.add((authorship_uri, VIVO.relates, person_uri))
#Other authors
if authors:
for (first_name, surname) in authors:
if not person_surname.lower() == surname.lower():
author_uri = ns.D[to_hash_identifier(PREFIX_PERSON, (first_name, surname))]
graph.add((author_uri, RDF.type, FOAF.Person))
full_name = join_if_not_empty((first_name, surname))
graph.add((author_uri, RDFS.label, Literal(full_name)))
authorship_uri = author_uri + "-auth"
graph.add((authorship_uri, RDF.type, VIVO.Authorship))
graph.add((authorship_uri, VIVO.relates, work_uri))
graph.add((authorship_uri, VIVO.relates, author_uri))
#Date
date_uri = work_uri + "-date"
graph.add((work_uri, VIVO.dateTimeValue, date_uri))
add_date(date_uri, publication_year, graph, publication_month, publication_day)
#Subjects
if subjects:
for subject in subjects:
if subject in subjectlist[0]:
match = subjectlist[0].index(subject)
subject_uri = subjectlist[1][match]
graph.add((work_uri, VIVO.hasSubjectArea, subject_uri))
else:
subject_uri = ns.D[to_hash_identifier("sub", (subject,))]
subjectlist[0].append(subject)
subjectlist[1].append(subject_uri)
graph.add((work_uri, VIVO.hasSubjectArea, subject_uri))
graph.add((subject_uri, RDF.type, SKOS.Concept))
graph.add((subject_uri, RDFS.label, Literal(subject)))
#Identifier
if doi:
graph.add((work_uri, BIBO.doi, Literal(doi)))
#Also add as a website
identifier_url = "http://dx.doi.org/%s" % doi
vcard_uri = ns.D[to_hash_identifier("vcard", (identifier_url,))]
graph.add((vcard_uri, RDF.type, VCARD.Kind))
#Has contact info
graph.add((work_uri, OBO.ARG_2000028, vcard_uri))
#Url vcard
vcard_url_uri = vcard_uri + "-url"
graph.add((vcard_url_uri, RDF.type, VCARD.URL))
graph.add((vcard_uri, VCARD.hasURL, vcard_url_uri))
graph.add((vcard_url_uri, VCARD.url, Literal(identifier_url, datatype=XSD.anyURI)))
#Publisher
if publisher:
if publisher in orglist[0]:
match = orglist[0].index(publisher)
publisher_uri = orglist[1][match]
graph.add((work_uri, VIVO.publisher, publisher_uri))
else:
publisher_uri = ns.D[to_hash_identifier(PREFIX_ORGANIZATION, (publisher,))]
orglist[0].append(publisher)
orglist[1].append(publisher_uri)
graph.add((publisher_uri, RDF.type, FOAF.Organization))
graph.add((publisher_uri, RDFS.label, Literal(publisher)))
graph.add((work_uri, VIVO.publisher, publisher_uri))
if work_type == "JOURNAL_ARTICLE":
##Extract
#Journal
journal = bibtex.get("journal")
#Volume
volume = bibtex.get("volume")
#Number
number = bibtex.get("number")
#Pages
pages = bibtex.get("pages")
start_page = None
end_page = None
if pages and "-" in pages:
(start_page, end_page) = re.split(" *-+ *", pages, maxsplit=2)
##Add triples
#Type
graph.add((work_uri, RDF.type, BIBO.AcademicArticle))
#Journal
if journal:
if journal in journlist[0]:
match = journlist[0].index(journal)
journal_uri = journlist[1][match]
graph.add((work_uri, VIVO.hasPublicationVenue, journal_uri))
else:
journal_uri = ns.D[to_hash_identifier(PREFIX_JOURNAL, (BIBO.Journal, journal))]
journlist[0].append(journal)
journlist[1].append(journal_uri)
graph.add((journal_uri, RDF.type, BIBO.Journal))
graph.add((journal_uri, RDFS.label, Literal(journal)))
graph.add((work_uri, VIVO.hasPublicationVenue, journal_uri))
#Volume
if volume:
graph.add((work_uri, BIBO.volume, Literal(volume)))
#Number
if number:
graph.add((work_uri, BIBO.issue, Literal(number)))
#Pages
if start_page:
graph.add((work_uri, BIBO.pageStart, Literal(start_page)))
if end_page:
graph.add((work_uri, BIBO.pageEnd, Literal(end_page)))
elif work_type == "BOOK":
##Add triples
#Type
graph.add((work_uri, RDF.type, BIBO.Book))
elif work_type == "DATA_SET":
##Add triples
#Type
graph.add((work_uri, RDF.type, VIVO.Dataset))
def crosswalk(self, orcid_profile, person_uri, graph):
# Work metadata may be available from the orcid profile, bibtex contained in the orcid profile, and/or crossref
# record. The preferred order (in general) for getting metadata is crossref, bibtex, orcid.
# Note that datacite records were considered, but not found to have additional/better metadata.
#Publications
for work in ((orcid_profile["orcid-profile"].get("orcid-activities") or {}).get("orcid-works") or {})\
.get("orcid-work", []):
#Work Type
work_type = work["work-type"]
if work_type in work_type_map:
##Extract
#Get external identifiers so that can get DOI
external_identifiers = WorksCrosswalk._get_work_identifiers(work)
doi = external_identifiers.get("DOI")
crossref_record = WorksCrosswalk._fetch_crossref_doi(doi) if doi else {}
#Bibtex
bibtex = WorksCrosswalk._parse_bibtex(work)
#Get title so that can construct work uri
title = WorksCrosswalk._get_crossref_title(crossref_record) \
or bibtex.get("title") \
or WorksCrosswalk._get_orcid_title(work)
#Work-type
work_class = work_type_map[work_type]
if work_type == "TRANSLATION" and bibtex and bibtex["ENTRYTYPE"] in bibtex_type_map:
work_class = bibtex_type_map[bibtex["ENTRYTYPE"]]
#Construct work uri
work_uri = self.identifier_strategy.to_uri(work_class, {"name": title})
graph.add((work_uri, RDF.type, work_class))
#Title
graph.add((work_uri, RDFS.label, Literal(title)))
#Publication date
(publication_year, publication_month, publication_day) = \
WorksCrosswalk._get_crossref_publication_date(crossref_record) \
or WorksCrosswalk._get_orcid_publication_date(work) \
or WorksCrosswalk._get_bibtext_publication_date(bibtex) or (None, None, None)
date_uri = add_date(publication_year, graph, self.identifier_strategy,
publication_month, publication_day)
if date_uri:
graph.add((work_uri, VIVO.dateTimeValue, date_uri))
#Subjects
subjects = crossref_record["subject"] if crossref_record and "subject" in crossref_record else None
if subjects:
for subject in subjects:
subject_uri = self.identifier_strategy.to_uri(SKOS.Concept, {"name": subject})
graph.add((work_uri, VIVO.hasSubjectArea, subject_uri))
if self.create_strategy.should_create(SKOS.Concept, subject_uri):
graph.add((subject_uri, RDF.type, SKOS.Concept))
graph.add((subject_uri, RDFS.label, Literal(subject)))
#Contributors (an array of (first_name, surname, VIVO type, e.g., VIVO.Authorship))
bibtex_contributors = []
bibtex_contributors.extend(WorksCrosswalk._get_bibtex_authors(bibtex))
bibtex_contributors.extend(WorksCrosswalk._get_bibtex_editors(bibtex))
#Orcid is better for translations because has translator role
if work_type == "TRANSLATION":
contributors = WorksCrosswalk._get_orcid_contributors(work)
else:
contributors = WorksCrosswalk._get_crossref_authors(crossref_record) or bibtex_contributors \
or WorksCrosswalk._get_orcid_contributors(work)
person_surname = orcid_profile["orcid-profile"]["orcid-bio"]["personal-details"]["family-name"]["value"]
if not contributors:
#Add person as author or editor.
#None, None means this person.
if work_type in ("EDITED_BOOK",):
contributors.append((None, None, VIVO.Editorship))
elif work_type == "TRANSLATION":
#Translator is a predicate, not a -ship class.
contributors.append((None, None, "TRANSLATOR"))
else:
contributors.append((None, None, VIVO.Authorship))
for (first_name, surname, vivo_type) in contributors:
if not surname or person_surname.lower() == surname.lower():
contributor_uri = person_uri
else:
contributor_uri = self.identifier_strategy.to_uri(FOAF.Person, {"first_name": first_name,
"surname": surname})
if self.create_strategy.should_create(FOAF.Person, contributor_uri):
graph.add((contributor_uri, RDF.type, FOAF.Person))
full_name = join_if_not_empty((first_name, surname))
graph.add((contributor_uri, RDFS.label, Literal(full_name)))
#Translation is a special case
if vivo_type == "TRANSLATOR":
graph.add((contributor_uri, BIBO.translator, work_uri))
#So is patent assignee
elif work_type == "PATENT":
graph.add((contributor_uri, VIVO.assigneeFor, work_uri))
else:
contributorship_uri = self.identifier_strategy.to_uri(vivo_type,
{"contributor_uri": contributor_uri,
"work_uri": work_uri})
graph.add((contributorship_uri, RDF.type, vivo_type))
graph.add((contributorship_uri, VIVO.relates, work_uri))
graph.add((contributorship_uri, VIVO.relates, contributor_uri))
#Publisher
publisher = crossref_record.get("publisher") or bibtex.get("publisher")
if publisher:
publisher_uri = self.identifier_strategy.to_uri(FOAF.Organization, {"name": publisher})
graph.add((work_uri, VIVO.publisher, publisher_uri))
if self.create_strategy.should_create(FOAF.Organization, publisher_uri):
graph.add((publisher_uri, RDF.type, FOAF.Organization))
graph.add((publisher_uri, RDFS.label, Literal(publisher)))
#Volume
volume = crossref_record.get("volume") or bibtex.get("volume")
if volume:
graph.add((work_uri, BIBO.volume, Literal(volume)))
#Issue
issue = crossref_record.get("issue") or bibtex.get("number")
if issue:
graph.add((work_uri, BIBO.issue, Literal(issue)))
#Pages
pages = crossref_record.get("page") or bibtex.get("pages")
start_page = None
end_page = None
if pages and "-" in pages:
(start_page, end_page) = re.split(" *-+ *", pages, maxsplit=2)
if start_page:
graph.add((work_uri, BIBO.pageStart, Literal(start_page)))
if end_page:
graph.add((work_uri, BIBO.pageEnd, Literal(end_page)))
#Identifiers
#Add doi in bibtex, but not orcid profile
if bibtex and "doi" in bibtex and "DOI" not in external_identifiers:
external_identifiers["DOI"] = bibtex["doi"]
#Add isbn in bibtex, but not orcid profile
if bibtex and "isbn" in bibtex and "ISBN" not in external_identifiers:
external_identifiers["ISBN"] = bibtex["isbn"]
for identifier_type, identifier in external_identifiers.iteritems():
identifier_url = None
if identifier_type in ("PAT", "OTHER_ID") and work_type == "PATENT":
identifier_predicate = VIVO.patentNumber
elif identifier_type == "ISBN":
clean_isbn = identifier.replace("-", "")
if len(clean_isbn) <= 10:
identifier_predicate = BIBO.isbn10
else:
identifier_predicate = BIBO.isbn13
else:
(identifier_predicate, url_template) = identifier_map.get(identifier_type, (None, None))
if url_template:
identifier_url = url_template % identifier
if identifier_predicate:
graph.add((work_uri, identifier_predicate, Literal(identifier)))
if identifier_url:
self._add_work_url(identifier_url, work_uri, graph)
orcid_url = (work.get("url", {}) or {}).get("value")
if orcid_url and WorksCrosswalk._use_url(orcid_url):
self._add_work_url(orcid_url, work_uri, graph)
bibtex_url = bibtex.get("link")
if bibtex_url and WorksCrosswalk._use_url(bibtex_url) and orcid_url != bibtex_url:
self._add_work_url(bibtex_url, work_uri, graph)
#Series
series = bibtex.get("series")
#TODO: Figure out how to model series in VIVO-ISF.
#Journal
#If Crossref has a journal use it
journal = WorksCrosswalk._get_crossref_journal(crossref_record)
if journal:
issns = crossref_record.get("ISSN", [])
#Otherwise, only use for some work types.
elif work_type in journal_map:
issns = []
journal = bibtex.get("journal")
if journal:
if "issn" in bibtex:
issns = [bibtex["issn"]]
else:
journal = (work.get("journal-title", {}) or {}).get("value")
if journal:
journal_class = journal_map.get(work_type, BIBO.Journal)
journal_uri = self.identifier_strategy.to_uri(journal_class, {"name": journal})
graph.add((work_uri, VIVO.hasPublicationVenue, journal_uri))
if self.create_strategy.should_create(journal_class, journal_uri):
graph.add((journal_uri, RDF.type, journal_class))
graph.add((journal_uri, RDFS.label, Literal(journal)))
for issn in issns:
graph.add((journal_uri, BIBO.issn, Literal(issn)))
if work_type in ("BOOK_CHAPTER",):
book_title = bibtex.get("booktitle")
if book_title:
book_uri = self.identifier_strategy.to_uri(BIBO.Book, {"name": book_title})
graph.add((work_uri, VIVO.hasPublicationVenue, book_uri))
if self.create_strategy.should_create(BIBO.Book, book_uri):
graph.add((book_uri, RDF.type, BIBO.Book))
graph.add((book_uri, RDFS.label, Literal(book_title)))
if work_type in ("CONFERENCE_PAPER",):
proceeding = bibtex.get("journal") or (work.get("journal-title", {}) or {}).get("value")
if proceeding:
proceeding_uri = self.identifier_strategy.to_uri(BIBO.Proceedings, {"name": proceeding})
graph.add((work_uri, VIVO.hasPublicationVenue, proceeding_uri))
if self.create_strategy.should_create(BIBO.Proceedings, proceeding_uri):
graph.add((proceeding_uri, RDF.type, BIBO.Proceedings))
graph.add((proceeding_uri, RDFS.label, Literal(proceeding)))
def _get_orcid_title(work):
return join_if_not_empty((work["work-title"]["title"]["value"],
(work["work-title"].get("subtitle") or {}).get("value")), ": ")
