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 = BioCrosswalk(
identifier_strategy=self.create_strategy,
create_strategy=self.create_strategy)
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))
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 = BioCrosswalk(identifier_strategy=self.create_strategy,
create_strategy=self.create_strategy)
class TestBio(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 = BioCrosswalk(identifier_strategy=self.create_strategy,
create_strategy=self.create_strategy)
def test_no_external_identifiers(self):
orcid_profile = json.loads("""
{
"person": {
"external-identifiers": {
"last-modified-date": null,
"external-identifier": [],
"path": "/0000-0003-4507-4735/external-identifiers"
},
"path": "/0000-0003-4507-4735/person"
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
self.assertEqual(0, len(self.graph))
def test_external_identifiers(self):
orcid_profile = json.loads("""
{
"person": {
"external-identifiers": {
"last-modified-date": {
"value": 1390435480189
},
"external-identifier": [
{
"created-date": {
"value": 1379686803951
},
"last-modified-date": {
"value": 1379686803951
},
"source": {
"source-orcid": null,
"source-client-id": {
"uri": "http://orcid.org/client/0000-0002-5982-8983",
"path": "0000-0002-5982-8983",
"host": "orcid.org"
},
"source-name": {
"value": "Scopus to ORCID"
}
},
"external-id-type": "Scopus Author ID",
"external-id-value": "6602258586",
"external-id-url": {
"value": "http://www.scopus.com/inward/authorDetails.url?authorID=6602258586&partnerID=MN8TOARS"
},
"external-id-relationship": "SELF",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/external-identifiers/142173",
"put-code": 142173,
"display-index": 0
},
{
"created-date": {
"value": 1379686803951
},
"last-modified-date": {
"value": 1379686803951
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-7707-4137",
"path": "0000-0001-7707-4137",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Clarivate Analytics"
}
},
"external-id-type": "ResearcherID",
"external-id-value": "C-4986-2008",
"external-id-url": {
"value": "http://www.researcherid.com/rid/C-4986-2008"
},
"external-id-relationship": "SELF",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/external-identifiers/38181",
"put-code": 38181,
"display-index": 0
},
{
"created-date": {
"value": 1390435480189
},
"last-modified-date": {
"value": 1390435480189
},
"source": {
"source-orcid": null,
"source-client-id": {
"uri": "http://orcid.org/client/0000-0003-0412-1857",
"path": "0000-0003-0412-1857",
"host": "orcid.org"
},
"source-name": {
"value": "ISNI2ORCID search and link"
}
},
"external-id-type": "ISNI",
"external-id-value": "0000000138352317",
"external-id-url": {
"value": "http://isni.org/isni/0000000138352317"
},
"external-id-relationship": "SELF",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/external-identifiers/187639",
"put-code": 187639,
"display-index": 0
}
],
"path": "/0000-0001-5109-3700/external-identifiers"
},
"path": "/0000-0001-5109-3700/person"
}
}
""")
self.create_strategy.skip_person = True
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
self.assertEqual(2, len(self.graph))
# ScopusID is added.
self.assertTrue(self.graph[D["test"]: VIVO["scopusId"]: Literal("6602258586")])
# ResearcherId is added.
self.assertTrue(self.graph[D["test"]: VIVO["researcherId"]: Literal("C-4986-2008")])
def test_name(self):
orcid_profile = json.loads(u"""
{
"person": {
"name": {
"created-date": {
"value": 1460753221409
},
"last-modified-date": {
"value": 1460753221409
},
"given-names": {
"value": "Laurel"
},
"family-name": {
"value": "Haak"
},
"credit-name": {
"value": "Laurel L Haak"
},
"source": null,
"visibility": "PUBLIC",
"path": "0000-0001-5109-3700"
},
"other-names": {
"last-modified-date": {
"value": 1461191605426
},
"other-name": [
{
"created-date": {
"value": 1461191605416
},
"last-modified-date": {
"value": 1461191605416
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-5109-3700",
"path": "0000-0001-5109-3700",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Laurel L Haak"
}
},
"content": " L. L. Haak",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/other-names/721941",
"put-code": 721941,
"display-index": 0
},
{
"created-date": {
"value": 1461191605425
},
"last-modified-date": {
"value": 1461191605425
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-5109-3700",
"path": "0000-0001-5109-3700",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Laurel L Haak"
}
},
"content": "L Haak",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/other-names/721942",
"put-code": 721942,
"display-index": 0
},
{
"created-date": {
"value": 1461191605426
},
"last-modified-date": {
"value": 1461191605426
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-5109-3700",
"path": "0000-0001-5109-3700",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Laurel L Haak"
}
},
"content": "Laure Haak",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/other-names/721943",
"put-code": 721943,
"display-index": 0
},
{
"created-date": {
"value": 1461191605426
},
"last-modified-date": {
"value": 1461191605426
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-5109-3700",
"path": "0000-0001-5109-3700",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Laurel L Haak"
}
},
"content": "Laurela L Hāka",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/other-names/721944",
"put-code": 721944,
"display-index": 0
}
],
"path": "/0000-0001-5109-3700/other-names"
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# Laurel is a person
self.assertTrue(self.graph[D["test"]: RDF.type: FOAF.Person])
# with a label
self.assertTrue(self.graph[D["test"]: RDFS.label: Literal("Laurel Haak")])
# vcard test
self.assertTrue(bool(self.graph.query("""
ask where {
?vcn a vcard:Name .
?vcn vcard:familyName "Haak" .
?vcn vcard:givenName "Laurel" .
?vc obo:ARG_2000029 d:test .
?vc vcard:hasName ?vcn .
}
""")))
def test_biography(self):
orcid_profile = json.loads("""
{
"person": {
"biography": {
"created-date": {
"value": 1460753221411
},
"last-modified-date": {
"value": 1487932762756
},
"content": "Laurel L. Haak, PhD, is the Executive Director of ORCID, an international and interdisciplinary non-profit organization dedicated to providing the technical infrastructure to generate and maintain unique and persistent identifiers for researchers and scholars.",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/biography"
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# Has a biography
self.assertTrue(self.graph[D["test"]: VIVO["overview"]: Literal("Laurel L. Haak, PhD, is the Executive "
"Director of ORCID, an international and "
"interdisciplinary non-profit organization "
"dedicated to providing the technical "
"infrastructure to generate and maintain "
"unique and persistent identifiers for "
"researchers and scholars.")])
def test_no_biography(self):
orcid_profile = json.loads("""
{
"person": {
"biography": {
"created-date": {
"value": 1460766291133
},
"last-modified-date": {
"value": 1460766291133
},
"content": null,
"visibility": "PUBLIC",
"path": "/0000-0003-4507-4735/biography"
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# Has a biography
self.assertEqual(0, len(self.graph))
def test_websites(self):
orcid_profile = json.loads("""
{
"person": {
"researcher-urls": {
"last-modified-date": {
"value": 1463003428816
},
"researcher-url": [
{
"created-date": {
"value": 1461191605427
},
"last-modified-date": {
"value": 1463003428816
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-5109-3700",
"path": "0000-0001-5109-3700",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Laurel L Haak"
}
},
"url-name": "LinkedIn",
"url": {
"value": "http://www.linkedin.com/pub/laurel-haak/3/1b/4a3/"
},
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/researcher-urls/714700",
"put-code": 714700,
"display-index": 0
},
{
"created-date": {
"value": 1461191605427
},
"last-modified-date": {
"value": 1463003428816
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-5109-3700",
"path": "0000-0001-5109-3700",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Laurel L Haak"
}
},
"url-name": null,
"url": {
"value": "https://www.researchgate.net/profile/Laurel_Haak"
},
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/researcher-urls/714701",
"put-code": 714701,
"display-index": 0
}
],
"path": "/0000-0001-5109-3700/researcher-urls"
}
}
}
""")
# Set ResearchGate url-name to null.
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# LinkedIn
self.assertTrue(bool(self.graph.query("""
ask where {
?vcw a vcard:URL .
?vcw vcard:url "http://www.linkedin.com/pub/laurel-haak/3/1b/4a3/"^^xsd:anyURI .
?vcw rdfs:label "LinkedIn" .
?vc a vcard:Individual .
?vc vcard:hasURL ?vcw .
}
""")))
# ResearchGate
self.assertTrue(bool(self.graph.query("""
ask where {
?vcw a vcard:URL .
?vcw vcard:url "https://www.researchgate.net/profile/Laurel_Haak"^^xsd:anyURI .
?vc a vcard:Individual .
?vc vcard:hasURL ?vcw .
filter not exists {
?vcw rdfs:label ?label .
}
}
""")))
def test_no_websites(self):
orcid_profile = json.loads("""
{
"person": {
"researcher-urls": {
"last-modified-date": null,
"researcher-url": [],
"path": "/0000-0003-4507-4735/researcher-urls"
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# Has a biography
self.assertEqual(0, len(self.graph))
def test_no_keywords(self):
orcid_profile = json.loads("""
{
"person": {
"keywords": {
"last-modified-date": null,
"keyword": [],
"path": "/0000-0003-4507-4735/keywords"
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# Has a biography
self.assertEqual(0, len(self.graph))
def test_keywords(self):
orcid_profile = json.loads("""
{
"person": {
"keywords": {
"last-modified-date": {
"value": 1464800983143
},
"keyword": [
{
"created-date": {
"value": 1461191605415
},
"last-modified-date": {
"value": 1464800983143
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-5109-3700",
"path": "0000-0001-5109-3700",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Laurel L Haak"
}
},
"content": "persistent identifiers, research policy, science workforce, program evaluation, neuroscience, calcium imaging, oligodendrocytes, circadian rhythms",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/keywords/419740",
"put-code": 419740,
"display-index": 0
}
],
"path": "/0000-0001-5109-3700/keywords"
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
self.assertEqual(8, len(self.graph))
self.assertTrue(bool(self.graph.query("""
ask where {
d:test vivo:freetextKeyword "persistent identifiers" .
d:test vivo:freetextKeyword "research policy" .
d:test vivo:freetextKeyword "science workforce" .
}
""")))
class TestBio(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 = BioCrosswalk(
identifier_strategy=self.create_strategy,
create_strategy=self.create_strategy)
def test_no_external_identifiers(self):
orcid_profile = json.loads("""
{
"person": {
"external-identifiers": {
"last-modified-date": null,
"external-identifier": [],
"path": "/0000-0003-4507-4735/external-identifiers"
},
"path": "/0000-0003-4507-4735/person"
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
self.assertEqual(0, len(self.graph))
def test_external_identifiers(self):
orcid_profile = json.loads("""
{
"person": {
"external-identifiers": {
"last-modified-date": {
"value": 1390435480189
},
"external-identifier": [
{
"created-date": {
"value": 1379686803951
},
"last-modified-date": {
"value": 1379686803951
},
"source": {
"source-orcid": null,
"source-client-id": {
"uri": "http://orcid.org/client/0000-0002-5982-8983",
"path": "0000-0002-5982-8983",
"host": "orcid.org"
},
"source-name": {
"value": "Scopus to ORCID"
}
},
"external-id-type": "Scopus Author ID",
"external-id-value": "6602258586",
"external-id-url": {
"value": "http://www.scopus.com/inward/authorDetails.url?authorID=6602258586&partnerID=MN8TOARS"
},
"external-id-relationship": "SELF",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/external-identifiers/142173",
"put-code": 142173,
"display-index": 0
},
{
"created-date": {
"value": 1379686803951
},
"last-modified-date": {
"value": 1379686803951
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-7707-4137",
"path": "0000-0001-7707-4137",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Clarivate Analytics"
}
},
"external-id-type": "ResearcherID",
"external-id-value": "C-4986-2008",
"external-id-url": {
"value": "http://www.researcherid.com/rid/C-4986-2008"
},
"external-id-relationship": "SELF",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/external-identifiers/38181",
"put-code": 38181,
"display-index": 0
},
{
"created-date": {
"value": 1390435480189
},
"last-modified-date": {
"value": 1390435480189
},
"source": {
"source-orcid": null,
"source-client-id": {
"uri": "http://orcid.org/client/0000-0003-0412-1857",
"path": "0000-0003-0412-1857",
"host": "orcid.org"
},
"source-name": {
"value": "ISNI2ORCID search and link"
}
},
"external-id-type": "ISNI",
"external-id-value": "0000000138352317",
"external-id-url": {
"value": "http://isni.org/isni/0000000138352317"
},
"external-id-relationship": "SELF",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/external-identifiers/187639",
"put-code": 187639,
"display-index": 0
}
],
"path": "/0000-0001-5109-3700/external-identifiers"
},
"path": "/0000-0001-5109-3700/person"
}
}
""")
self.create_strategy.skip_person = True
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
self.assertEqual(2, len(self.graph))
# ScopusID is added.
self.assertTrue(
self.graph[D["test"]:VIVO["scopusId"]:Literal("6602258586")])
# ResearcherId is added.
self.assertTrue(
self.graph[D["test"]:VIVO["researcherId"]:Literal("C-4986-2008")])
def test_name(self):
orcid_profile = json.loads(u"""
{
"person": {
"name": {
"created-date": {
"value": 1460753221409
},
"last-modified-date": {
"value": 1460753221409
},
"given-names": {
"value": "Laurel"
},
"family-name": {
"value": "Haak"
},
"credit-name": {
"value": "Laurel L Haak"
},
"source": null,
"visibility": "PUBLIC",
"path": "0000-0001-5109-3700"
},
"other-names": {
"last-modified-date": {
"value": 1461191605426
},
"other-name": [
{
"created-date": {
"value": 1461191605416
},
"last-modified-date": {
"value": 1461191605416
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-5109-3700",
"path": "0000-0001-5109-3700",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Laurel L Haak"
}
},
"content": " L. L. Haak",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/other-names/721941",
"put-code": 721941,
"display-index": 0
},
{
"created-date": {
"value": 1461191605425
},
"last-modified-date": {
"value": 1461191605425
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-5109-3700",
"path": "0000-0001-5109-3700",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Laurel L Haak"
}
},
"content": "L Haak",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/other-names/721942",
"put-code": 721942,
"display-index": 0
},
{
"created-date": {
"value": 1461191605426
},
"last-modified-date": {
"value": 1461191605426
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-5109-3700",
"path": "0000-0001-5109-3700",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Laurel L Haak"
}
},
"content": "Laure Haak",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/other-names/721943",
"put-code": 721943,
"display-index": 0
},
{
"created-date": {
"value": 1461191605426
},
"last-modified-date": {
"value": 1461191605426
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-5109-3700",
"path": "0000-0001-5109-3700",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Laurel L Haak"
}
},
"content": "Laurela L Hāka",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/other-names/721944",
"put-code": 721944,
"display-index": 0
}
],
"path": "/0000-0001-5109-3700/other-names"
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# Laurel is a person
self.assertTrue(self.graph[D["test"]:RDF.type:FOAF.Person])
# with a label
self.assertTrue(
self.graph[D["test"]:RDFS.label:Literal("Laurel Haak")])
# vcard test
self.assertTrue(
bool(
self.graph.query("""
ask where {
?vcn a vcard:Name .
?vcn vcard:familyName "Haak" .
?vcn vcard:givenName "Laurel" .
?vc obo:ARG_2000029 d:test .
?vc vcard:hasName ?vcn .
}
""")))
def test_biography(self):
orcid_profile = json.loads("""
{
"person": {
"biography": {
"created-date": {
"value": 1460753221411
},
"last-modified-date": {
"value": 1487932762756
},
"content": "Laurel L. Haak, PhD, is the Executive Director of ORCID, an international and interdisciplinary non-profit organization dedicated to providing the technical infrastructure to generate and maintain unique and persistent identifiers for researchers and scholars.",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/biography"
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# Has a biography
self.assertTrue(self.graph[D["test"]:VIVO["overview"]:Literal(
"Laurel L. Haak, PhD, is the Executive "
"Director of ORCID, an international and "
"interdisciplinary non-profit organization "
"dedicated to providing the technical "
"infrastructure to generate and maintain "
"unique and persistent identifiers for "
"researchers and scholars.")])
def test_no_biography(self):
orcid_profile = json.loads("""
{
"person": {
"biography": {
"created-date": {
"value": 1460766291133
},
"last-modified-date": {
"value": 1460766291133
},
"content": null,
"visibility": "PUBLIC",
"path": "/0000-0003-4507-4735/biography"
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# Has a biography
self.assertEqual(0, len(self.graph))
def test_websites(self):
orcid_profile = json.loads("""
{
"person": {
"researcher-urls": {
"last-modified-date": {
"value": 1463003428816
},
"researcher-url": [
{
"created-date": {
"value": 1461191605427
},
"last-modified-date": {
"value": 1463003428816
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-5109-3700",
"path": "0000-0001-5109-3700",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Laurel L Haak"
}
},
"url-name": "LinkedIn",
"url": {
"value": "http://www.linkedin.com/pub/laurel-haak/3/1b/4a3/"
},
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/researcher-urls/714700",
"put-code": 714700,
"display-index": 0
},
{
"created-date": {
"value": 1461191605427
},
"last-modified-date": {
"value": 1463003428816
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-5109-3700",
"path": "0000-0001-5109-3700",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Laurel L Haak"
}
},
"url-name": null,
"url": {
"value": "https://www.researchgate.net/profile/Laurel_Haak"
},
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/researcher-urls/714701",
"put-code": 714701,
"display-index": 0
}
],
"path": "/0000-0001-5109-3700/researcher-urls"
}
}
}
""")
# Set ResearchGate url-name to null.
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# LinkedIn
self.assertTrue(
bool(
self.graph.query("""
ask where {
?vcw a vcard:URL .
?vcw vcard:url "http://www.linkedin.com/pub/laurel-haak/3/1b/4a3/"^^xsd:anyURI .
?vcw rdfs:label "LinkedIn" .
?vc a vcard:Individual .
?vc vcard:hasURL ?vcw .
}
""")))
# ResearchGate
self.assertTrue(
bool(
self.graph.query("""
ask where {
?vcw a vcard:URL .
?vcw vcard:url "https://www.researchgate.net/profile/Laurel_Haak"^^xsd:anyURI .
?vc a vcard:Individual .
?vc vcard:hasURL ?vcw .
filter not exists {
?vcw rdfs:label ?label .
}
}
""")))
def test_no_websites(self):
orcid_profile = json.loads("""
{
"person": {
"researcher-urls": {
"last-modified-date": null,
"researcher-url": [],
"path": "/0000-0003-4507-4735/researcher-urls"
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# Has a biography
self.assertEqual(0, len(self.graph))
def test_no_keywords(self):
orcid_profile = json.loads("""
{
"person": {
"keywords": {
"last-modified-date": null,
"keyword": [],
"path": "/0000-0003-4507-4735/keywords"
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
# Has a biography
self.assertEqual(0, len(self.graph))
def test_keywords(self):
orcid_profile = json.loads("""
{
"person": {
"keywords": {
"last-modified-date": {
"value": 1464800983143
},
"keyword": [
{
"created-date": {
"value": 1461191605415
},
"last-modified-date": {
"value": 1464800983143
},
"source": {
"source-orcid": {
"uri": "http://orcid.org/0000-0001-5109-3700",
"path": "0000-0001-5109-3700",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": {
"value": "Laurel L Haak"
}
},
"content": "persistent identifiers, research policy, science workforce, program evaluation, neuroscience, calcium imaging, oligodendrocytes, circadian rhythms",
"visibility": "PUBLIC",
"path": "/0000-0001-5109-3700/keywords/419740",
"put-code": 419740,
"display-index": 0
}
],
"path": "/0000-0001-5109-3700/keywords"
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
self.assertEqual(8, len(self.graph))
self.assertTrue(
bool(
self.graph.query("""
ask where {
d:test vivo:freetextKeyword "persistent identifiers" .
d:test vivo:freetextKeyword "research policy" .
d:test vivo:freetextKeyword "science workforce" .
}
""")))
class TestBio(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 = BioCrosswalk(
identifier_strategy=self.create_strategy,
create_strategy=self.create_strategy)
def test_no_external_identifiers(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"external-identifiers": null
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
self.assertEqual(0, len(self.graph))
def test_external_identifiers(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"external-identifiers": {
"external-identifier": [
{
"orcid": null,
"external-id-orcid": null,
"external-id-common-name": {
"value": "ISNI"
},
"external-id-reference": {
"value": "0000000138352317"
},
"external-id-url": {
"value": "http://isni.org/isni/0000000138352317"
},
"external-id-source": null,
"source": {
"source-orcid": {
"value": null,
"uri": "http://orcid.org/0000-0003-0412-1857",
"path": "0000-0003-0412-1857",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": null,
"source-date": null
}
},
{
"orcid": null,
"external-id-orcid": null,
"external-id-common-name": {
"value": "ResearcherID"
},
"external-id-reference": {
"value": "C-4986-2008"
},
"external-id-url": {
"value": "http://www.researcherid.com/rid/C-4986-2008"
},
"external-id-source": null,
"source": {
"source-orcid": {
"value": null,
"uri": "http://orcid.org/0000-0001-7707-4137",
"path": "0000-0001-7707-4137",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": null,
"source-date": null
}
},
{
"orcid": null,
"external-id-orcid": null,
"external-id-common-name": {
"value": "Scopus Author ID"
},
"external-id-reference": {
"value": "6602258586"
},
"external-id-url": {
"value": "http://www.scopus.com/inward/authorDetails.url?authorID=6602258586&partnerID=MN8TOARS"
},
"external-id-source": null,
"source": {
"source-orcid": {
"value": null,
"uri": "http://orcid.org/0000-0002-5982-8983",
"path": "0000-0002-5982-8983",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": null,
"source-date": null
}
}
],
"visibility": "PUBLIC"
}
}
}
}
""")
self.create_strategy.skip_person = True
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
self.assertEqual(2, len(self.graph))
#ScopusID is added.
self.assertTrue(
self.graph[D["test"]:VIVO["scopusId"]:Literal("6602258586")])
#ResearcherId is added.
self.assertTrue(
self.graph[D["test"]:VIVO["researcherId"]:Literal("C-4986-2008")])
def test_name(self):
orcid_profile = json.loads(u"""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"personal-details": {
"given-names": {
"value": "Laurel"
},
"family-name": {
"value": "Haak"
},
"credit-name": {
"value": "Laurel L Haak",
"visibility": "PUBLIC"
},
"other-names": {
"other-name": [
{
"value": " L. L. Haak"
},
{
"value": "L Haak"
},
{
"value": "Laure Haak"
},
{
"value": "Laurela L Hāka"
}
],
"visibility": "PUBLIC"
}
},
"external-identifiers": null
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
#Laurel is a person
self.assertTrue(self.graph[D["test"]:RDF.type:FOAF.Person])
#with a label
self.assertTrue(
self.graph[D["test"]:RDFS.label:Literal("Laurel Haak")])
#vcard test
self.assertTrue(
bool(
self.graph.query("""
ask where {
?vcn a vcard:Name .
?vcn vcard:familyName "Haak" .
?vcn vcard:givenName "Laurel" .
?vc obo:ARG_2000029 d:test .
?vc vcard:hasName ?vcn .
}
""")))
def test_biography(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"biography": {
"value": "Laurel L. Haak, PhD, is the Executive Director of ORCID.",
"visibility": "PUBLIC"
}
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
#Has a biography
self.assertTrue(self.graph[D["test"]:VIVO["overview"]:Literal(
"Laurel L. Haak, PhD, is the Executive Director of ORCID.")])
def test_no_biography(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"biography": null
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
#Has a biography
self.assertEqual(0, len(self.graph))
def test_websites(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"researcher-urls": {
"researcher-url": [
{
"url-name": {
"value": "LinkedIn"
},
"url": {
"value": "http://www.linkedin.com/pub/laurel-haak/3/1b/4a3/"
}
},
{
"url-name": null,
"url": {
"value": "https://www.researchgate.net/profile/Laurel_Haak"
}
}
],
"visibility": "PUBLIC"
},
"contact-details": {
"email": [],
"address": {
"country": {
"value": "US",
"visibility": "PUBLIC"
}
}
}
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
#LinkedIn
self.assertTrue(
bool(
self.graph.query("""
ask where {
?vcw a vcard:URL .
?vcw vcard:url "http://www.linkedin.com/pub/laurel-haak/3/1b/4a3/"^^xsd:anyURI .
?vcw rdfs:label "LinkedIn" .
?vc a vcard:Individual .
?vc vcard:hasURL ?vcw .
}
""")))
#ResearchGate
self.assertTrue(
bool(
self.graph.query("""
ask where {
?vcw a vcard:URL .
?vcw vcard:url "https://www.researchgate.net/profile/Laurel_Haak"^^xsd:anyURI .
?vc a vcard:Individual .
?vc vcard:hasURL ?vcw .
filter not exists {
?vcw rdfs:label ?label .
}
}
""")))
def test_no_websites(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"researcher-urls": {
"researcher-url": [],
"visibility": "PUBLIC"
}
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
#Has a biography
self.assertEqual(0, len(self.graph))
def test_no_keywords(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"keywords": null
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
#Has a biography
self.assertEqual(0, len(self.graph))
def test_keywords(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"keywords": {
"keyword": [
{
"value": "persistent identifiers"
},
{
"value": "research policy"
},
{
"value": "science workforce"
}
],
"visibility": "PUBLIC"
}
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
self.assertEqual(3, len(self.graph))
self.assertTrue(
bool(
self.graph.query("""
ask where {
d:test vivo:freetextKeyword "persistent identifiers" .
d:test vivo:freetextKeyword "research policy" .
d:test vivo:freetextKeyword "science workforce" .
}
""")))
class TestBio(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 = BioCrosswalk(identifier_strategy=self.create_strategy,
create_strategy=self.create_strategy)
def test_no_external_identifiers(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"external-identifiers": null
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
self.assertEqual(0, len(self.graph))
def test_external_identifiers(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"external-identifiers": {
"external-identifier": [
{
"orcid": null,
"external-id-orcid": null,
"external-id-common-name": {
"value": "ISNI"
},
"external-id-reference": {
"value": "0000000138352317"
},
"external-id-url": {
"value": "http://isni.org/isni/0000000138352317"
},
"external-id-source": null,
"source": {
"source-orcid": {
"value": null,
"uri": "http://orcid.org/0000-0003-0412-1857",
"path": "0000-0003-0412-1857",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": null,
"source-date": null
}
},
{
"orcid": null,
"external-id-orcid": null,
"external-id-common-name": {
"value": "ResearcherID"
},
"external-id-reference": {
"value": "C-4986-2008"
},
"external-id-url": {
"value": "http://www.researcherid.com/rid/C-4986-2008"
},
"external-id-source": null,
"source": {
"source-orcid": {
"value": null,
"uri": "http://orcid.org/0000-0001-7707-4137",
"path": "0000-0001-7707-4137",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": null,
"source-date": null
}
},
{
"orcid": null,
"external-id-orcid": null,
"external-id-common-name": {
"value": "Scopus Author ID"
},
"external-id-reference": {
"value": "6602258586"
},
"external-id-url": {
"value": "http://www.scopus.com/inward/authorDetails.url?authorID=6602258586&partnerID=MN8TOARS"
},
"external-id-source": null,
"source": {
"source-orcid": {
"value": null,
"uri": "http://orcid.org/0000-0002-5982-8983",
"path": "0000-0002-5982-8983",
"host": "orcid.org"
},
"source-client-id": null,
"source-name": null,
"source-date": null
}
}
],
"visibility": "PUBLIC"
}
}
}
}
""")
self.create_strategy.skip_person = True
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
self.assertEqual(2, len(self.graph))
#ScopusID is added.
self.assertTrue(self.graph[D["test"]: VIVO["scopusId"] : Literal("6602258586")])
#ResearcherId is added.
self.assertTrue(self.graph[D["test"]: VIVO["researcherId"] : Literal("C-4986-2008")])
def test_name(self):
orcid_profile = json.loads(u"""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"personal-details": {
"given-names": {
"value": "Laurel"
},
"family-name": {
"value": "Haak"
},
"credit-name": {
"value": "Laurel L Haak",
"visibility": "PUBLIC"
},
"other-names": {
"other-name": [
{
"value": " L. L. Haak"
},
{
"value": "L Haak"
},
{
"value": "Laure Haak"
},
{
"value": "Laurela L Hāka"
}
],
"visibility": "PUBLIC"
}
},
"external-identifiers": null
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
#Laurel is a person
self.assertTrue(self.graph[D["test"]: RDF.type: FOAF.Person])
#with a label
self.assertTrue(self.graph[D["test"]: RDFS.label: Literal("Laurel Haak")])
#vcard test
self.assertTrue(bool(self.graph.query("""
ask where {
?vcn a vcard:Name .
?vcn vcard:familyName "Haak" .
?vcn vcard:givenName "Laurel" .
?vc obo:ARG_2000029 d:test .
?vc vcard:hasName ?vcn .
}
""")))
def test_biography(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"biography": {
"value": "Laurel L. Haak, PhD, is the Executive Director of ORCID.",
"visibility": "PUBLIC"
}
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
#Has a biography
self.assertTrue(self.graph[D["test"]: VIVO["overview"]:
Literal("Laurel L. Haak, PhD, is the Executive Director of ORCID.")])
def test_no_biography(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"biography": null
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
#Has a biography
self.assertEqual(0, len(self.graph))
def test_websites(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"researcher-urls": {
"researcher-url": [
{
"url-name": {
"value": "LinkedIn"
},
"url": {
"value": "http://www.linkedin.com/pub/laurel-haak/3/1b/4a3/"
}
},
{
"url-name": null,
"url": {
"value": "https://www.researchgate.net/profile/Laurel_Haak"
}
}
],
"visibility": "PUBLIC"
},
"contact-details": {
"email": [],
"address": {
"country": {
"value": "US",
"visibility": "PUBLIC"
}
}
}
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
#LinkedIn
self.assertTrue(bool(self.graph.query("""
ask where {
?vcw a vcard:URL .
?vcw vcard:url "http://www.linkedin.com/pub/laurel-haak/3/1b/4a3/"^^xsd:anyURI .
?vcw rdfs:label "LinkedIn" .
?vc a vcard:Individual .
?vc vcard:hasURL ?vcw .
}
""")))
#ResearchGate
self.assertTrue(bool(self.graph.query("""
ask where {
?vcw a vcard:URL .
?vcw vcard:url "https://www.researchgate.net/profile/Laurel_Haak"^^xsd:anyURI .
?vc a vcard:Individual .
?vc vcard:hasURL ?vcw .
filter not exists {
?vcw rdfs:label ?label .
}
}
""")))
def test_no_websites(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"researcher-urls": {
"researcher-url": [],
"visibility": "PUBLIC"
}
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
#Has a biography
self.assertEqual(0, len(self.graph))
def test_no_keywords(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"keywords": null
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
#Has a biography
self.assertEqual(0, len(self.graph))
def test_keywords(self):
orcid_profile = json.loads("""
{
"message-version": "1.2",
"orcid-profile": {
"orcid-bio": {
"keywords": {
"keyword": [
{
"value": "persistent identifiers"
},
{
"value": "research policy"
},
{
"value": "science workforce"
}
],
"visibility": "PUBLIC"
}
}
}
}
""")
self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph)
self.assertEqual(3, len(self.graph))
self.assertTrue(bool(self.graph.query("""
ask where {
d:test vivo:freetextKeyword "persistent identifiers" .
d:test vivo:freetextKeyword "research policy" .
d:test vivo:freetextKeyword "science workforce" .
}
""")))
