def crosswalk_funding(orcid_profile, person_uri, graph):
if "funding-list" in orcid_profile["orcid-profile"]["orcid-activities"] \
and orcid_profile["orcid-profile"]["orcid-activities"]["funding-list"] \
and "funding" in orcid_profile["orcid-profile"]["orcid-activities"]["funding-list"]:
#Funding
fundings = orcid_profile["orcid-profile"]["orcid-activities"]["funding-list"]["funding"]
for funding in fundings:
if funding["funding-type"] == "GRANT":
title = funding["funding-title"]["title"]["value"]
grant_uri = ns.D[to_hash_identifier(PREFIX_GRANT, (title,))]
#Type
graph.add((grant_uri, RDF.type, VIVO.Grant))
#Person
graph.add((grant_uri, VIVO.relates, person_uri))
#Title
graph.add((grant_uri, RDFS.label, Literal(title)))
#Role
role_uri = grant_uri + "-role"
graph.add((role_uri, RDF.type, VIVO.PrincipalInvestigatorRole))
#Inheres in
graph.add((role_uri, OBO.RO_0000052, person_uri))
graph.add((role_uri, VIVO.relatedBy, grant_uri))
#Date interval
interval_uri = grant_uri + "-interval"
interval_start_uri = interval_uri + "-start"
interval_end_uri = interval_uri + "-end"
start_year = funding["start-date"]["year"]["value"] \
if "start-date" in funding and "year" in funding["start-date"] else None
start_month = funding["start-date"]["month"]["value"] \
if "start-date" in funding and "month" in funding["start-date"] else None
start_day = funding["start-date"]["day"]["value"] \
if "start-date" in funding and "day" in funding["start-date"] else None
end_year = funding["end-date"]["year"]["value"] \
if "end-date" in funding and "year" in funding["start-date"] else None
end_month = funding["end-date"]["month"]["value"] \
if "end-date" in funding and "month" in funding["start-date"] else None
end_day = funding["end-date"]["day"]["value"] \
if "end-date" in funding and "day" in funding["start-date"] else None
add_date_interval(interval_uri, grant_uri, graph,
interval_start_uri if add_date(interval_start_uri,
start_year,
graph,
start_month,
start_day) else None,
interval_end_uri if add_date(interval_end_uri,
end_year,
graph,
end_month,
end_day) else None)
#Award amount
if "amount" in funding:
award_amount = "${:,}".format(int(funding["amount"]["value"]))
graph.add((grant_uri, VIVO.totalAwardAmount, Literal(award_amount)))
#Awarded by
if "organization" in funding:
organization_name = funding["organization"]["name"]
organization_uri = ns.D[to_hash_identifier(PREFIX_ORGANIZATION, (organization_name,))]
graph.add((organization_uri, RDF.type, FOAF.Organization))
graph.add((organization_uri, RDFS.label, Literal(organization_name)))
graph.add((grant_uri, VIVO.assignedBy, organization_uri))
#Identifiers
if "funding-external-identifiers" in funding:
for external_identifier in funding["funding-external-identifiers"]["funding-external-identifier"]:
if "funding-external-identifier-value" in external_identifier:
graph.add((grant_uri, VIVO.sponsorAwardId,
Literal(external_identifier["funding-external-identifier-value"])))
if "funding-external-identifier-url" in external_identifier:
identifier_url = external_identifier["funding-external-identifier-url"]["value"]
vcard_uri = ns.D[to_hash_identifier("vcard", (identifier_url,))]
graph.add((vcard_uri, RDF.type, VCARD.Kind))
#Has contact info
graph.add((grant_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)))
def crosswalk(self, orcid_profile, person_uri, graph):
if "fundings" in orcid_profile["activities-summary"]:
# Funding
for funding_group in orcid_profile["activities-summary"]["fundings"]["group"]:
for funding in funding_group["funding-summary"]:
if funding["type"] == "GRANT":
title = funding["title"]["title"]["value"]
grant_uri = self.identifier_strategy.to_uri(VIVO.Grant, {"title": title})
# Type
graph.add((grant_uri, RDF.type, VIVO.Grant))
# Person
graph.add((grant_uri, VIVO.relates, person_uri))
# Title
graph.add((grant_uri, RDFS.label, Literal(title)))
# Role
role_uri = self.identifier_strategy.to_uri(VIVO.PrincipalInvestigatorRole,
{"grant_uri": grant_uri})
graph.add((role_uri, RDF.type, VIVO.PrincipalInvestigatorRole))
# Inheres in
graph.add((role_uri, OBO.RO_0000052, person_uri))
graph.add((role_uri, VIVO.relatedBy, grant_uri))
# Date interval
(start_year, start_month, start_day) = FundingCrosswalk._get_date_parts("start-date", funding)
(end_year, end_month, end_day) = FundingCrosswalk._get_date_parts("end-date", funding)
add_date_interval(grant_uri, graph, self.identifier_strategy,
add_date(start_year, graph, self.identifier_strategy, start_month, start_day),
add_date(end_year, graph, self.identifier_strategy, end_month, end_day))
# Award amount
funding_amount = funding.get("amount")
if funding_amount is not None:
value = funding_amount.get("value")
if value is not None:
award_amount = "${:,}".format(int(value))
graph.add((grant_uri, VIVO.totalAwardAmount, Literal(award_amount)))
# Awarded by
if "organization" in funding:
organization_name = funding["organization"]["name"]
organization_uri = self.identifier_strategy.to_uri(FOAF.Organization,
{"name": organization_name})
graph.add((grant_uri, VIVO.assignedBy, organization_uri))
if self.create_strategy.should_create(FOAF.Organization, organization_uri):
graph.add((organization_uri, RDF.type, FOAF.Organization))
graph.add((organization_uri, RDFS.label, Literal(organization_name)))
# Identifiers
if "external-ids" in funding and funding.get("external-ids"):
for external_identifier in funding["external-ids"]["external-id"]:
if "funding-external-identifier-value" in external_identifier:
graph.add((grant_uri, VIVO.sponsorAwardId,
Literal(external_identifier["external-id-value"])))
identifier_url = (external_identifier.get("external-id-url", {}) or {}).get("value")
if identifier_url:
vcard_uri = self.identifier_strategy.to_uri(VCARD.Kind, {"url": identifier_url})
graph.add((vcard_uri, RDF.type, VCARD.Kind))
# Has contact info
graph.add((grant_uri, OBO.ARG_2000028, vcard_uri))
# Url vcard
vcard_url_uri = self.identifier_strategy.to_uri(VCARD.URL, {"vcard_uri": vcard_uri})
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)))
def crosswalk(self, orcid_profile, person_uri, graph):
# Education
if "educations" in orcid_profile["activities-summary"]:
for education in orcid_profile["activities-summary"]["educations"][
"education-summary"]:
# Gather some values
degree_name = education.get("role-title")
organization_name = education["organization"]["name"]
start_date_year = (education["start-date"]
or {}).get("year", {}).get("value")
end_date_year = (education["end-date"]
or {}).get("year", {}).get("value")
# Organization
organization_uri = self.identifier_strategy.to_uri(
FOAF.Organization, {"name": organization_name})
if self.create_strategy.should_create(FOAF.Organization,
organization_uri):
graph.add((organization_uri, RDF.type, FOAF.Organization))
graph.add((organization_uri, RDFS.label,
Literal(organization_name)))
if "address" in education["organization"]:
city = education["organization"]["address"]["city"]
state = education["organization"]["address"]["region"]
address_uri = ns.D[to_hash_identifier(
"geo", (city, state))]
graph.add((address_uri, RDF.type, VIVO.GeographicLocation))
graph.add((organization_uri, OBO.RO_0001025, address_uri))
graph.add((address_uri, RDFS.label,
Literal("%s, %s" % (city, state))))
# Output of educational process
educational_process_uri = self.identifier_strategy.to_uri(
VIVO.EducationalProcess, {
"organization_name": organization_name,
"degree_name": degree_name,
"start_year": start_date_year,
"end_year": end_date_year
})
graph.add((educational_process_uri, RDF.type,
VIVO.EducationalProcess))
# Has participants
graph.add((educational_process_uri, OBO.RO_0000057,
organization_uri))
graph.add(
(educational_process_uri, OBO.RO_0000057, person_uri))
# Department
if education.get("department-name"):
graph.add(
(educational_process_uri, VIVO.departmentOrSchool,
Literal(education["department-name"])))
# Interval
add_date_interval(
educational_process_uri, graph, self.identifier_strategy,
add_date(start_date_year, graph, self.identifier_strategy),
add_date(end_date_year, graph, self.identifier_strategy))
if "role-title" in education:
degree_name = education["role-title"]
# Awarded degree
awarded_degree_uri = self.identifier_strategy.to_uri(
VIVO.AwardedDegree,
{"educational_process_uri": educational_process_uri})
graph.add(
(awarded_degree_uri, RDF.type, VIVO.AwardedDegree))
graph.add(
(awarded_degree_uri, RDFS.label, Literal(degree_name)))
# Assigned by organization
graph.add((awarded_degree_uri, VIVO.assignedBy,
organization_uri))
# Related to educational process
graph.add((awarded_degree_uri, OBO.RO_0002353,
educational_process_uri))
# Relates to degree
degree_uri = self.identifier_strategy.to_uri(
VIVO.AcademicDegree, {"name": degree_name})
graph.add((awarded_degree_uri, VIVO.relates, degree_uri))
if self.create_strategy.should_create(
VIVO.AcademicDegree, degree_uri):
graph.add((degree_uri, RDF.type, VIVO.AcademicDegree))
graph.add(
(degree_uri, RDFS.label, Literal(degree_name)))
# Relates to person
graph.add((awarded_degree_uri, VIVO.relates, person_uri))
def crosswalk(self, orcid_profile, person_uri, graph):
# Education
if "educations" in orcid_profile["activities-summary"]:
for education in orcid_profile["activities-summary"]["educations"]["education-summary"]:
# Gather some values
degree_name = education.get("role-title")
organization_name = education["organization"]["name"]
start_date_year = (education["start-date"] or {}).get("year", {}).get("value")
end_date_year = (education["end-date"] or {}).get("year", {}).get("value")
# Organization
organization_uri = self.identifier_strategy.to_uri(FOAF.Organization, {"name": organization_name})
if self.create_strategy.should_create(FOAF.Organization, organization_uri):
graph.add((organization_uri, RDF.type, FOAF.Organization))
graph.add((organization_uri, RDFS.label, Literal(organization_name)))
if "address" in education["organization"]:
city = education["organization"]["address"]["city"]
state = education["organization"]["address"]["region"]
address_uri = ns.D[to_hash_identifier("geo", (city, state))]
graph.add((address_uri, RDF.type, VIVO.GeographicLocation))
graph.add((organization_uri, OBO.RO_0001025, address_uri))
graph.add((address_uri, RDFS.label, Literal("%s, %s" % (city, state))))
# Output of educational process
educational_process_uri = self.identifier_strategy.to_uri(VIVO.EducationalProcess,
{"organization_name": organization_name,
"degree_name": degree_name,
"start_year": start_date_year,
"end_year": end_date_year})
graph.add((educational_process_uri, RDF.type, VIVO.EducationalProcess))
# Has participants
graph.add((educational_process_uri, OBO.RO_0000057, organization_uri))
graph.add((educational_process_uri, OBO.RO_0000057, person_uri))
# Department
if education.get("department-name"):
graph.add((educational_process_uri, VIVO.departmentOrSchool,
Literal(education["department-name"])))
# Interval
add_date_interval(educational_process_uri, graph, self.identifier_strategy,
add_date(start_date_year, graph, self.identifier_strategy),
add_date(end_date_year, graph, self.identifier_strategy))
if "role-title" in education:
degree_name = education["role-title"]
# Awarded degree
awarded_degree_uri = self.identifier_strategy.to_uri(VIVO.AwardedDegree,
{"educational_process_uri":
educational_process_uri})
graph.add((awarded_degree_uri, RDF.type, VIVO.AwardedDegree))
graph.add((awarded_degree_uri, RDFS.label, Literal(degree_name)))
# Assigned by organization
graph.add((awarded_degree_uri, VIVO.assignedBy, organization_uri))
# Related to educational process
graph.add((awarded_degree_uri, OBO.RO_0002353, educational_process_uri))
# Relates to degree
degree_uri = self.identifier_strategy.to_uri(VIVO.AcademicDegree, {"name": degree_name})
graph.add((awarded_degree_uri, VIVO.relates, degree_uri))
if self.create_strategy.should_create(VIVO.AcademicDegree, degree_uri):
graph.add((degree_uri, RDF.type, VIVO.AcademicDegree))
graph.add((degree_uri, RDFS.label, Literal(degree_name)))
# Relates to person
graph.add((awarded_degree_uri, VIVO.relates, person_uri))
def crosswalk(self, orcid_profile, person_uri, graph):
if "fundings" in orcid_profile["activities-summary"]:
# Funding
for funding_group in orcid_profile["activities-summary"][
"fundings"]["group"]:
for funding in funding_group["funding-summary"]:
if funding["type"] == "GRANT":
title = funding["title"]["title"]["value"]
grant_uri = self.identifier_strategy.to_uri(
VIVO.Grant, {"title": title})
# Type
graph.add((grant_uri, RDF.type, VIVO.Grant))
# Person
graph.add((grant_uri, VIVO.relates, person_uri))
# Title
graph.add((grant_uri, RDFS.label, Literal(title)))
# Role
role_uri = self.identifier_strategy.to_uri(
VIVO.PrincipalInvestigatorRole,
{"grant_uri": grant_uri})
graph.add((role_uri, RDF.type,
VIVO.PrincipalInvestigatorRole))
# Inheres in
graph.add((role_uri, OBO.RO_0000052, person_uri))
graph.add((role_uri, VIVO.relatedBy, grant_uri))
# Date interval
(start_year, start_month,
start_day) = FundingCrosswalk._get_date_parts(
"start-date", funding)
(end_year, end_month,
end_day) = FundingCrosswalk._get_date_parts(
"end-date", funding)
add_date_interval(
grant_uri, graph, self.identifier_strategy,
add_date(start_year, graph,
self.identifier_strategy, start_month,
start_day),
add_date(end_year, graph, self.identifier_strategy,
end_month, end_day))
# Award amount
funding_amount = funding.get("amount")
if funding_amount is not None:
value = funding_amount.get("value")
if value is not None:
award_amount = "${:,}".format(int(value))
graph.add((grant_uri, VIVO.totalAwardAmount,
Literal(award_amount)))
# Awarded by
if "organization" in funding:
organization_name = funding["organization"]["name"]
organization_uri = self.identifier_strategy.to_uri(
FOAF.Organization, {"name": organization_name})
graph.add(
(grant_uri, VIVO.assignedBy, organization_uri))
if self.create_strategy.should_create(
FOAF.Organization, organization_uri):
graph.add((organization_uri, RDF.type,
FOAF.Organization))
graph.add((organization_uri, RDFS.label,
Literal(organization_name)))
# Identifiers
if "external-ids" in funding and funding.get(
"external-ids"):
for external_identifier in funding["external-ids"][
"external-id"]:
if "funding-external-identifier-value" in external_identifier:
graph.add((grant_uri, VIVO.sponsorAwardId,
Literal(external_identifier[
"external-id-value"])))
identifier_url = (external_identifier.get(
"external-id-url", {}) or {}).get("value")
if identifier_url:
vcard_uri = self.identifier_strategy.to_uri(
VCARD.Kind, {"url": identifier_url})
graph.add(
(vcard_uri, RDF.type, VCARD.Kind))
# Has contact info
graph.add((grant_uri, OBO.ARG_2000028,
vcard_uri))
# Url vcard
vcard_url_uri = self.identifier_strategy.to_uri(
VCARD.URL, {"vcard_uri": vcard_uri})
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)))
def crosswalk_affiliations(orcid_profile, person_uri, graph):
#Education
for affiliation in (orcid_profile["orcid-profile"].get("orcid-activities") or {}).get("affiliations", {})\
.get("affiliation", []):
if affiliation["type"] == "EDUCATION":
#Gather some values
degree_name = affiliation.get("role-title")
organization_name=affiliation["organization"]["name"]
start_date_year = (affiliation["start-date"] or {}).get("year", {}).get("value")
end_date_year = (affiliation["end-date"] or {}).get("year", {}).get("value")
#Organization
organization_uri = ns.D[to_hash_identifier(PREFIX_ORGANIZATION, (organization_name,))]
graph.add((organization_uri, RDF.type, FOAF.Organization))
graph.add((organization_uri, RDFS.label, Literal(organization_name)))
if "address" in affiliation["organization"]:
city = affiliation["organization"]["address"]["city"]
state = affiliation["organization"]["address"]["region"]
address_uri = ns.D[to_hash_identifier("geo", (city, state))]
graph.add((address_uri, RDF.type, VIVO.GeographicLocation))
graph.add((organization_uri, OBO.RO_0001025, address_uri))
graph.add((address_uri, RDFS.label, Literal("%s, %s" % (city, state))))
#Output of educational process
educational_process_uri = ns.D[to_hash_identifier(PREFIX_EDUCATIONAL_PROCESS, (organization_name,
degree_name,
start_date_year,
end_date_year))]
graph.add((educational_process_uri, RDF.type, VIVO.EducationalProcess))
#Has participants
graph.add((educational_process_uri, OBO.RO_0000057, organization_uri))
graph.add((educational_process_uri, OBO.RO_0000057, person_uri))
#Department
if "department-name" in affiliation:
graph.add((educational_process_uri, VIVO.departmentOrSchool,
Literal(affiliation["department-name"])))
#Interval
interval_uri = educational_process_uri + "-interval"
interval_start_uri = interval_uri + "-start"
# start_date_year = affiliation["start-date"]["year"]["value"] if "start-date" in affiliation else None
interval_end_uri = interval_uri + "-end"
# end_date_year = affiliation["end-date"]["year"]["value"] if "end-date" in affiliation else None
add_date_interval(interval_uri, educational_process_uri, graph,
interval_start_uri if add_date(interval_start_uri, start_date_year, graph) else None,
interval_end_uri if add_date(interval_end_uri, end_date_year, graph) else None)
if "role-title" in affiliation:
degree_name = affiliation["role-title"]
#Awarded degree
awarded_degree_uri = educational_process_uri + "-dgre"
graph.add((awarded_degree_uri, RDF.type, VIVO.AwardedDegree))
graph.add((awarded_degree_uri, RDFS.label, Literal(degree_name)))
#Assigned by organization
graph.add((awarded_degree_uri, VIVO.assignedBy, organization_uri))
#Related to educational process
graph.add((awarded_degree_uri, OBO.RO_0002353, educational_process_uri))
#Relates to degree
degree_uri = ns.D[to_hash_identifier(PREFIX_DEGREE, (degree_name,))]
graph.add((degree_uri, RDF.type, VIVO.AcademicDegree))
graph.add((degree_uri, RDFS.label, Literal(degree_name)))
graph.add((awarded_degree_uri, VIVO.relates, degree_uri))
#Relates to person
graph.add((awarded_degree_uri, VIVO.relates, person_uri))
