def __init__(self, identifier_strategy, create_strategy):
self.identifier_strategy = identifier_strategy
self.create_strategy = create_strategy
self.bio_crosswalker = BioCrosswalk(identifier_strategy, create_strategy)
self.affiliations_crosswalker = AffiliationsCrosswalk(identifier_strategy, create_strategy)
self.funding_crosswalker = FundingCrosswalk(identifier_strategy, create_strategy)
self.works_crosswalker = WorksCrosswalk(identifier_strategy, create_strategy)
def setUp(self):
self.graph = Graph(namespace_manager=ns.ns_manager)
self.person_uri = ns.D["test"]
self.create_strategy = SimpleCreateEntitiesStrategy(
HashIdentifierStrategy(), person_uri=self.person_uri)
self.crosswalker = FundingCrosswalk(
identifier_strategy=self.create_strategy,
create_strategy=self.create_strategy)
def setUp(self):
self.graph = Graph(namespace_manager=ns.ns_manager)
self.person_uri = ns.D["test"]
self.create_strategy = SimpleCreateEntitiesStrategy(HashIdentifierStrategy(), person_uri=self.person_uri)
self.crosswalker = FundingCrosswalk(
identifier_strategy=self.create_strategy, create_strategy=self.create_strategy
)
class TestFundings(TestCase):
def setUp(self):
self.graph = Graph(namespace_manager=ns.ns_manager)
self.person_uri = ns.D["test"]
self.create_strategy = SimpleCreateEntitiesStrategy(
HashIdentifierStrategy(), person_uri=self.person_uri)
self.crosswalker = FundingCrosswalk(
identifier_strategy=self.create_strategy,
create_strategy=self.create_strategy)
@my_vcr.use_cassette('fundings/no.yaml')
def test_no_funding(self):
profile = orcid2vivo.fetch_orcid_profile('0000-0003-1527-0030')
self.crosswalker.crosswalk(profile, self.person_uri, self.graph)
# Assert no triples in graph
self.assertTrue(len(self.graph) == 0)
@my_vcr.use_cassette('fundings/null.yaml')
def test_no_funding(self):
profile = orcid2vivo.fetch_orcid_profile('0000-0002-7843-9422')
self.crosswalker.crosswalk(profile, self.person_uri, self.graph)
# Assert no triples in graph
self.assertTrue(len(self.graph) == 0)
@my_vcr.use_cassette('fundings/with_funding.yaml')
def test_with_funding(self):
profile = orcid2vivo.fetch_orcid_profile('0000-0001-5109-3700')
self.crosswalker.crosswalk(profile, self.person_uri, self.graph)
# Verify a grant exists.
grant_uri = ns.D['grant-9ea22d7c992375778b4a3066f5142624']
self.assertEqual(
self.graph.value(grant_uri, RDFS.label).toPython(),
u"Policy Implications of International Graduate Students and Postdocs in the United States"
)
# Verify three PI roles related to grants for this person uri.
pi_roles = [
guri
for guri in self.graph.subjects(predicate=ns.OBO['RO_0000052'],
object=self.person_uri)
]
self.assertEqual(len(pi_roles), 3)
@my_vcr.use_cassette('fundings/null_external_identifier_funding.yaml')
def test_with_funding(self):
profile = orcid2vivo.fetch_orcid_profile('0000-0003-3844-5120')
self.crosswalker.crosswalk(profile, self.person_uri, self.graph)
# Verify a grant exists.
grant_uri = ns.D['grant-742228eecfbdacf092bf482f84151082']
self.assertEqual(
self.graph.value(grant_uri, RDFS.label).toPython(),
u"The Utility of Ultra High Performance Supercritical Fluid Chromatography for the Analysis of Seized Drugs:"
u" Application to Synthetic Cannabinoids and Bath Salts ")
self.assertEqual(
0, len(list(self.graph[grant_uri:ns.VIVO.sponsorAwardId:])))
class PersonCrosswalk():
def __init__(self, identifier_strategy, create_strategy):
self.identifier_strategy = identifier_strategy
self.create_strategy = create_strategy
self.bio_crosswalker = BioCrosswalk(identifier_strategy, create_strategy)
self.affiliations_crosswalker = AffiliationsCrosswalk(identifier_strategy, create_strategy)
self.funding_crosswalker = FundingCrosswalk(identifier_strategy, create_strategy)
self.works_crosswalker = WorksCrosswalk(identifier_strategy, create_strategy)
def crosswalk(self, orcid_id, person_uri, person_class=None, confirmed_orcid_id=False):
# Create an RDFLib Graph
graph = Graph(namespace_manager=ns.ns_manager)
# 0000-0003-3441-946X
clean_orcid_id = clean_orcid(orcid_id)
orcid_profile = fetch_orcid_profile(clean_orcid_id)
# Determine the class to use for the person
person_clazz = FOAF.Person
if person_class:
person_clazz = getattr(VIVO, person_class)
# ORCID
PersonCrosswalk._add_orcid_id(person_uri, clean_orcid_id, graph, confirmed_orcid_id)
self.bio_crosswalker.crosswalk(orcid_profile, person_uri, graph, person_class=person_clazz)
self.works_crosswalker.crosswalk(orcid_profile, person_uri, graph)
self.affiliations_crosswalker.crosswalk(orcid_profile, person_uri, graph)
self.funding_crosswalker.crosswalk(orcid_profile, person_uri, graph)
return graph, orcid_profile, person_uri
@staticmethod
def _add_orcid_id(person_uri, orcid_id, graph, confirmed):
orcid_id_uriref = URIRef("http://orcid.org/%s" % orcid_id)
graph.add((person_uri, VIVO.orcidId, orcid_id_uriref))
graph.add((orcid_id_uriref, RDF.type, OWL.Thing))
if confirmed:
graph.add((orcid_id_uriref, VIVO.confirmedOrcidId, person_uri))
class TestFundings(TestCase):
def setUp(self):
self.graph = Graph(namespace_manager=ns.ns_manager)
self.person_uri = ns.D["test"]
self.create_strategy = SimpleCreateEntitiesStrategy(HashIdentifierStrategy(), person_uri=self.person_uri)
self.crosswalker = FundingCrosswalk(
identifier_strategy=self.create_strategy, create_strategy=self.create_strategy
)
@my_vcr.use_cassette("fundings/no.yaml")
def test_no_funding(self):
profile = orcid2vivo.fetch_orcid_profile("0000-0003-1527-0030")
self.crosswalker.crosswalk(profile, self.person_uri, self.graph)
# Assert no triples in graph
self.assertTrue(len(self.graph) == 0)
@my_vcr.use_cassette("fundings/null.yaml")
def test_no_funding(self):
profile = orcid2vivo.fetch_orcid_profile("0000-0002-7843-9422")
self.crosswalker.crosswalk(profile, self.person_uri, self.graph)
# Assert no triples in graph
self.assertTrue(len(self.graph) == 0)
@my_vcr.use_cassette("fundings/with_funding.yaml")
def test_with_funding(self):
profile = orcid2vivo.fetch_orcid_profile("0000-0001-5109-3700")
self.crosswalker.crosswalk(profile, self.person_uri, self.graph)
# Verify a grant exists.
grant_uri = ns.D["grant-9ea22d7c992375778b4a3066f5142624"]
self.assertEqual(
self.graph.value(grant_uri, RDFS.label).toPython(),
u"Policy Implications of International Graduate Students and Postdocs in the United States",
)
# Verify three PI roles related to grants for this person uri.
pi_roles = [guri for guri in self.graph.subjects(predicate=ns.OBO["RO_0000052"], object=self.person_uri)]
self.assertEqual(len(pi_roles), 3)
@my_vcr.use_cassette("fundings/null_external_identifier_funding.yaml")
def test_with_funding(self):
profile = orcid2vivo.fetch_orcid_profile("0000-0003-3844-5120")
self.crosswalker.crosswalk(profile, self.person_uri, self.graph)
# Verify a grant exists.
grant_uri = ns.D["grant-742228eecfbdacf092bf482f84151082"]
self.assertEqual(
self.graph.value(grant_uri, RDFS.label).toPython(),
u"The Utility of Ultra High Performance Supercritical Fluid Chromatography for the Analysis of Seized Drugs:"
u" Application to Synthetic Cannabinoids and Bath Salts ",
)
self.assertEqual(0, len(list(self.graph[grant_uri : ns.VIVO.sponsorAwardId :])))
class TestFundings(TestCase):
def setUp(self):
self.graph = Graph(namespace_manager=ns.ns_manager)
self.person_uri = ns.D["test"]
self.create_strategy = SimpleCreateEntitiesStrategy(
HashIdentifierStrategy(), person_uri=self.person_uri)
self.crosswalker = FundingCrosswalk(
identifier_strategy=self.create_strategy,
create_strategy=self.create_strategy)
def test_no_funding(self):
orcid_profile = json.loads("""
{
"activities-summary": {
"fundings": {
"group": []
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# Assert no triples in graph
self.assertTrue(len(self.graph) == 0)
def test_with_funding(self):
orcid_profile = json.loads("""
{
"activities-summary": {
"fundings": {
"last-modified-date": {
"value": 1444208097475
},
"group": [
{
"last-modified-date": {
"value": 1437078970386
},
"external-ids": {
"external-id": [
{
"external-id-type": "grant_number",
"external-id-value": "0536999",
"external-id-url": {
"value": "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0536999&HistoricalAwards=false"
},
"external-id-relationship": "SELF"
}
]
},
"funding-summary": [
{
"created-date": {
"value": 1427825460988
},
"last-modified-date": {
"value": 1437078970386
},
"source": {
"source-orcid": null,
"source-client-id": {
"uri": "http://orcid.org/client/0000-0003-2174-0924",
"path": "0000-0003-2174-0924",
"host": "orcid.org"
},
"source-name": {
"value": "ÜberWizard for ORCID"
}
},
"title": {
"title": {
"value": "ADVANCE Leadership Award: Women in Science and Engineering: A Guide to Maximizing their Potential"
},
"translated-title": null
},
"external-ids": {
"external-id": [
{
"external-id-type": "grant_number",
"external-id-value": "0536999",
"external-id-url": {
"value": "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0536999&HistoricalAwards=false"
},
"external-id-relationship": "SELF"
},
{
"external-id-type": "grant_number",
"external-id-value": "0536999",
"external-id-url": {
"value": "http://grants.uberresearch.com/100000081/0536999/ADVANCE-Leadership-Award-Women-in-Science-and-Engineering-A-Guide-to-Maximizing-their-Potential"
},
"external-id-relationship": "SELF"
}
]
},
"type": "GRANT",
"start-date": {
"year": {
"value": "2006"
},
"month": {
"value": "04"
},
"day": {
"value": "01"
}
},
"end-date": {
"year": {
"value": "2007"
},
"month": {
"value": "03"
},
"day": {
"value": "31"
}
},
"organization": {
"name": "National Science Foundation - Directorate for Education and Human Resources",
"address": {
"city": "n/a",
"region": null,
"country": "US"
},
"disambiguated-organization": null
},
"visibility": "PUBLIC",
"put-code": 74458,
"path": "/0000-0001-5109-3700/funding/74458",
"display-index": "0"
}
]
},
{
"last-modified-date": {
"value": 1440583684368
},
"external-ids": {
"external-id": [
{
"external-id-type": "grant_number",
"external-id-value": "0305602",
"external-id-url": {
"value": "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0305602&HistoricalAwards=false"
},
"external-id-relationship": "SELF"
}
]
},
"funding-summary": [
{
"created-date": {
"value": 1440583684368
},
"last-modified-date": {
"value": 1440583684368
},
"source": {
"source-orcid": null,
"source-client-id": {
"uri": "http://orcid.org/client/0000-0003-2174-0924",
"path": "0000-0003-2174-0924",
"host": "orcid.org"
},
"source-name": {
"value": "ÜberWizard for ORCID"
}
},
"title": {
"title": {
"value": "Postdoc Network Annual Policy Meeting; Berkeley, CA, March 15-17, 2003"
},
"translated-title": null
},
"external-ids": {
"external-id": [
{
"external-id-type": "grant_number",
"external-id-value": "0305602",
"external-id-url": {
"value": "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0305602&HistoricalAwards=false"
},
"external-id-relationship": "SELF"
},
{
"external-id-type": "grant_number",
"external-id-value": "0305602",
"external-id-url": {
"value": "http://grants.uberresearch.com/100000076/0305602/Postdoc-Network-Annual-Policy-Meeting-Berkeley-CA-March-15-17-2003"
},
"external-id-relationship": "SELF"
}
]
},
"type": "GRANT",
"start-date": {
"year": {
"value": "2003"
},
"month": {
"value": "03"
},
"day": {
"value": "01"
}
},
"end-date": {
"year": {
"value": "2004"
},
"month": {
"value": "02"
},
"day": {
"value": "29"
}
},
"organization": {
"name": "National Science Foundation - Directorate for Biological Sciences",
"address": {
"city": "n/a",
"region": null,
"country": "US"
},
"disambiguated-organization": null
},
"visibility": "PUBLIC",
"put-code": 105986,
"path": "/0000-0001-5109-3700/funding/105986",
"display-index": "0"
}
]
},
{
"last-modified-date": {
"value": 1440583684380
},
"external-ids": {
"external-id": [
{
"external-id-type": "grant_number",
"external-id-value": "0342159",
"external-id-url": {
"value": "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0342159&HistoricalAwards=false"
},
"external-id-relationship": "SELF"
}
]
},
"funding-summary": [
{
"created-date": {
"value": 1440583684380
},
"last-modified-date": {
"value": 1440583684380
},
"source": {
"source-orcid": null,
"source-client-id": {
"uri": "http://orcid.org/client/0000-0003-2174-0924",
"path": "0000-0003-2174-0924",
"host": "orcid.org"
},
"source-name": {
"value": "ÜberWizard for ORCID"
}
},
"title": {
"title": {
"value": "Policy Implications of International Graduate Students and Postdocs in the United States"
},
"translated-title": null
},
"external-ids": {
"external-id": [
{
"external-id-type": "grant_number",
"external-id-value": "0342159",
"external-id-url": {
"value": "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0342159&HistoricalAwards=false"
},
"external-id-relationship": "SELF"
},
{
"external-id-type": "grant_number",
"external-id-value": "0342159",
"external-id-url": {
"value": "http://grants.uberresearch.com/100000179/0342159/Policy-Implications-of-International-Graduate-Students-and-Postdocs-in-the-United-States"
},
"external-id-relationship": "SELF"
}
]
},
"type": "GRANT",
"start-date": {
"year": {
"value": "2004"
},
"month": {
"value": "03"
},
"day": {
"value": "01"
}
},
"end-date": {
"year": {
"value": "2006"
},
"month": {
"value": "02"
},
"day": {
"value": "28"
}
},
"organization": {
"name": "National Science Foundation - Office of the Director",
"address": {
"city": "n/a",
"region": null,
"country": "US"
},
"disambiguated-organization": null
},
"visibility": "PUBLIC",
"put-code": 105988,
"path": "/0000-0001-5109-3700/funding/105988",
"display-index": "0"
}
]
},
{
"last-modified-date": {
"value": 1444208097475
},
"external-ids": {
"external-id": [
{
"external-id-type": "grant_number",
"external-id-value": "5F31MH010500-03",
"external-id-url": {
"value": "http://projectreporter.nih.gov/project_info_description.cfm?aid=2241697"
},
"external-id-relationship": "SELF"
}
]
},
"funding-summary": [
{
"created-date": {
"value": 1444208097475
},
"last-modified-date": {
"value": 1444208097475
},
"source": {
"source-orcid": null,
"source-client-id": {
"uri": "http://orcid.org/client/0000-0003-2174-0924",
"path": "0000-0003-2174-0924",
"host": "orcid.org"
},
"source-name": {
"value": "ÜberWizard for ORCID"
}
},
"title": {
"title": {
"value": "CELLULAR BASIS OF CIRCADIAN CLOCK IN SCN"
},
"translated-title": null
},
"external-ids": {
"external-id": [
{
"external-id-type": "grant_number",
"external-id-value": "5F31MH010500-03",
"external-id-url": {
"value": "http://projectreporter.nih.gov/project_info_description.cfm?aid=2241697"
},
"external-id-relationship": "SELF"
},
{
"external-id-type": "grant_number",
"external-id-value": "5F31MH010500-03",
"external-id-url": {
"value": "http://grants.uberresearch.com/100000025/F31MH010500/CELLULAR-BASIS-OF-CIRCADIAN-CLOCK-IN-SCN"
},
"external-id-relationship": "SELF"
}
]
},
"type": "GRANT",
"start-date": {
"year": {
"value": "1994"
},
"month": {
"value": "10"
},
"day": {
"value": "01"
}
},
"end-date": null,
"organization": {
"name": "National Institute of Mental Health",
"address": {
"city": "Bethesda",
"region": null,
"country": "US"
},
"disambiguated-organization": null
},
"visibility": "PUBLIC",
"put-code": 116401,
"path": "/0000-0001-5109-3700/funding/116401",
"display-index": "0"
}
]
}
],
"path": "/0000-0001-5109-3700/fundings"
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# Verify a grant exists.
grant_uri = ns.D['grant-9ea22d7c992375778b4a3066f5142624']
self.assertEqual(
self.graph.value(grant_uri, RDFS.label).toPython(),
u"Policy Implications of International Graduate Students and Postdocs in the United States"
)
# Verify three PI roles related to grants for this person uri.
pi_roles = [
guri
for guri in self.graph.subjects(predicate=ns.OBO['RO_0000052'],
object=self.person_uri)
]
self.assertEqual(len(pi_roles), 4)
def test_with_funding(self):
orcid_profile = json.loads("""
{
"activities-summary": {
"fundings": {
"last-modified-date": {
"value": 1449261003455
},
"group": [
{
"last-modified-date": {
"value": 1449261003455
},
"external-ids": {
"external-id": []
},
"funding-summary": [
{
"created-date": {
"value": 1449261003455
},
"last-modified-date": {
"value": 1449261003455
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0003-3844-5120",
"path": "0000-0003-3844-5120",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Ira Lurie"
}
},
"title": {
"title": {
"value": "The Utility of Ultra High Performance Supercritical Fluid Chromatography for the Analysis of Seized Drugs: Application to Synthetic Cannabinoids and Bath Salts "
},
"translated-title": null
},
"external-ids": null,
"type": "GRANT",
"start-date": {
"year": {
"value": "2015"
},
"month": {
"value": "01"
},
"day": null
},
"end-date": {
"year": {
"value": "2016"
},
"month": {
"value": "12"
},
"day": null
},
"organization": {
"name": "National Institute of Justice",
"address": {
"city": "DC",
"region": "DC",
"country": "US"
},
"disambiguated-organization": {
"disambiguated-organization-identifier": "http://dx.doi.org/10.13039/100005289",
"disambiguation-source": "FUNDREF"
}
},
"visibility": "PUBLIC",
"put-code": 132761,
"path": "/0000-0003-3844-5120/funding/132761",
"display-index": "0"
}
]
}
],
"path": "/0000-0003-3844-5120/fundings"
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# Verify a grant exists.
grant_uri = ns.D['grant-742228eecfbdacf092bf482f84151082']
self.assertEqual(
self.graph.value(grant_uri, RDFS.label).toPython(),
u"The Utility of Ultra High Performance Supercritical Fluid Chromatography for the Analysis of Seized "
u"Drugs: Application to Synthetic Cannabinoids and Bath Salts ")
self.assertEqual(
0, len(list(self.graph[grant_uri:ns.VIVO.sponsorAwardId:])))
