From 14c4c8ebb828d862261324a13616aad1f2f0c721 Mon Sep 17 00:00:00 2001 From: Justin Littman Date: Wed, 13 Sep 2017 13:04:25 -0400 Subject: [PATCH] Upgraded to version 2.0 of ORCID API --- orcid2vivo.py | 31 +- orcid2vivo_app/affiliations.py | 54 +- orcid2vivo_app/bio.py | 107 +- orcid2vivo_app/fundings.py | 122 +- orcid2vivo_app/works.py | 493 +-- orcid2vivo_loader.py | 28 +- tests/app/__init__.py | 1 - tests/app/test_affiliations.py | 294 +- tests/app/test_bio.py | 595 ++-- tests/app/test_fundings.py | 539 ++- tests/app/test_works.py | 2865 ++++++---------- tests/fixtures/fundings/no.yaml | 424 --- tests/fixtures/fundings/null.yaml | 42 - .../null_external_identifier_funding.yaml | 2947 ----------------- tests/fixtures/fundings/with_funding.yaml | 1397 -------- tests/fixtures/loader/load_single.yaml | 2452 +++++++++----- tests/test_loader.py | 42 +- 17 files changed, 4007 insertions(+), 8426 deletions(-) delete mode 100644 tests/fixtures/fundings/no.yaml delete mode 100644 tests/fixtures/fundings/null.yaml delete mode 100644 tests/fixtures/fundings/null_external_identifier_funding.yaml delete mode 100644 tests/fixtures/fundings/with_funding.yaml diff --git a/orcid2vivo.py b/orcid2vivo.py index 92331a0..aa1d2c5 100644 --- a/orcid2vivo.py +++ b/orcid2vivo.py @@ -45,7 +45,7 @@ def should_create(self, clazz, uri): def to_uri(self, clazz, attrs, general_clazz=None): uri = self._identifier_strategy.to_uri(clazz, attrs, general_clazz=None) - #Need to remember vcard uri for this person so that can skip. + # Need to remember vcard uri for this person so that can skip. if clazz == VCARD.Name and attrs.get("person_uri") == self.person_uri: self.person_name_vcard_uri = uri return uri @@ -62,19 +62,19 @@ def __init__(self, identifier_strategy, create_strategy): def crosswalk(self, orcid_id, person_uri, person_class=None, confirmed_orcid_id=False): - #Create an RDFLib Graph + # Create an RDFLib Graph graph = Graph(namespace_manager=ns.ns_manager) - #0000-0003-3441-946X + # 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 + # Determine the class to use for the person person_clazz = FOAF.Person if person_class: person_clazz = getattr(VIVO, person_class) - #ORCID + # 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) @@ -95,9 +95,8 @@ def _add_orcid_id(person_uri, orcid_id, graph, confirmed): def fetch_orcid_profile(orcid_id): orcid = clean_orcid(orcid_id) - #curl -H "Accept: application/orcid+json" 'http://pub.orcid.org/v1.2/0000-0003-3441-946X/orcid-profile' -L -i - r = requests.get('http://pub.orcid.org/v1.2/%s/orcid-profile' % orcid, - headers={"Accept": "application/orcid+json"}) + r = requests.get('https://pub.orcid.org/v2.0/%s' % orcid, + headers={"Accept": "application/json"}) if r: return r.json() else: @@ -105,7 +104,7 @@ def fetch_orcid_profile(orcid_id): def set_namespace(namespace=None): - #Set default VIVO namespace + # Set default VIVO namespace if namespace: ns.D = Namespace(namespace) ns.ns_manager.bind('d', ns.D, replace=True) @@ -113,14 +112,14 @@ def set_namespace(namespace=None): def default_execute(orcid_id, namespace=None, person_uri=None, person_id=None, skip_person=False, person_class=None, confirmed_orcid_id=False): - #Set namespace + # Set namespace set_namespace(namespace) this_identifier_strategy = HashIdentifierStrategy() this_person_uri = URIRef(person_uri) if person_uri \ else this_identifier_strategy.to_uri(FOAF.Person, {"id": person_id or orcid_id}) - #this_create_strategy will implement both create strategy and identifier strategy + # this_create_strategy will implement both create strategy and identifier strategy this_create_strategy = SimpleCreateEntitiesStrategy(this_identifier_strategy, skip_person=skip_person, person_uri=this_person_uri) @@ -155,25 +154,25 @@ def default_execute(orcid_id, namespace=None, person_uri=None, person_id=None, s help="Skip adding triples declaring the person and the person's name.") parser.add_argument("--confirmed", action="store_true", help="Mark the orcid id as confirmed.") - #Parse + # Parse args = parser.parse_args() - #Excute with default strategies + # Excute with default strategies (g, p, per_uri) = default_execute(args.orcid_id, namespace=args.namespace, person_uri=args.person_uri, person_id=args.person_id, skip_person=args.skip_person, person_class=args.person_class, confirmed_orcid_id=args.confirmed) - #Write to file + # Write to file if args.file: with codecs.open(args.file, "w") as out: g.serialize(format=args.format, destination=out) - #Post to SPARQL Update + # Post to SPARQL Update if args.endpoint: if not args.username or not args.password: raise Exception("If an endpoint is specified, --username and --password must be provided.") sparql_insert(g, args.endpoint, args.username, args.password) - #If not writing to file to posting to SPARQL Update then serialize to stdout + # If not writing to file to posting to SPARQL Update then serialize to stdout if not args.file and not args.endpoint: print g.serialize(format=args.format) diff --git a/orcid2vivo_app/affiliations.py b/orcid2vivo_app/affiliations.py index a5e1d20..be6aede 100644 --- a/orcid2vivo_app/affiliations.py +++ b/orcid2vivo_app/affiliations.py @@ -6,78 +6,76 @@ import orcid2vivo_app.vivo_namespace as ns -class AffiliationsCrosswalk(): +class AffiliationsCrosswalk: def __init__(self, identifier_strategy, create_strategy): self.identifier_strategy = identifier_strategy self.create_strategy = create_strategy def crosswalk(self, orcid_profile, person_uri, graph): - #Education - for affiliation in ((orcid_profile["orcid-profile"].get("orcid-activities") or {}) - .get("affiliations", {}) or {}).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") + # 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 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 affiliation["organization"]: - city = affiliation["organization"]["address"]["city"] - state = affiliation["organization"]["address"]["region"] + 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 + # 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 + # Has participants graph.add((educational_process_uri, OBO.RO_0000057, organization_uri)) graph.add((educational_process_uri, OBO.RO_0000057, person_uri)) - #Department - if affiliation.get("department-name"): + # Department + if education.get("department-name"): graph.add((educational_process_uri, VIVO.departmentOrSchool, - Literal(affiliation["department-name"]))) + Literal(education["department-name"]))) - #Interval + # 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 affiliation: - degree_name = affiliation["role-title"] + if "role-title" in education: + degree_name = education["role-title"] - #Awarded degree + # 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 + # Assigned by organization graph.add((awarded_degree_uri, VIVO.assignedBy, organization_uri)) - #Related to educational process + # Related to educational process graph.add((awarded_degree_uri, OBO.RO_0002353, educational_process_uri)) - #Relates to degree + # 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 + # Relates to person graph.add((awarded_degree_uri, VIVO.relates, person_uri)) - diff --git a/orcid2vivo_app/bio.py b/orcid2vivo_app/bio.py index a918156..e827df6 100644 --- a/orcid2vivo_app/bio.py +++ b/orcid2vivo_app/bio.py @@ -4,59 +4,66 @@ from vivo_namespace import VCARD, OBO, FOAF -class BioCrosswalk(): +class BioCrosswalk: def __init__(self, identifier_strategy, create_strategy): self.identifier_strategy = identifier_strategy self.create_strategy = create_strategy def crosswalk(self, orcid_profile, person_uri, graph, person_class=FOAF.Person): - #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)) + # 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 + # 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))) + # 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 - biography = (orcid_profile["orcid-profile"]["orcid-bio"].get("biography") or {}).get("value") - if biography: - graph.add((person_uri, VIVO.overview, Literal(biography))) + # 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. - 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"]))) + # 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-common-name"]["value"] == "ResearcherID": - graph.add((person_uri, VIVO.researcherId, Literal(external_identifier["external-id-reference"]["value"]))) + # ISI Research ID + if external_identifier["external-id-type"] == "ResearcherID": + graph.add((person_uri, VIVO.researcherId, Literal(external_identifier["external-id-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"]))) + # 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 + # Following is vcard bio information - #Add main vcard + # 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 + # Will only add vcard if there is a child vcard add_main_vcard = False - #Name vcard + # 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)) @@ -67,21 +74,21 @@ def crosswalk(self, orcid_profile, person_uri, graph, person_class=FOAF.Person): 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 researcher_url in researcher_urls: - url = researcher_url["url"]["value"] - url_name = (researcher_url["url-name"] or {}).get("value") - 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 + # 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 + # Contact info for graph.add((vcard_uri, OBO.ARG_2000029, person_uri)) diff --git a/orcid2vivo_app/fundings.py b/orcid2vivo_app/fundings.py index fb84974..d395142 100644 --- a/orcid2vivo_app/fundings.py +++ b/orcid2vivo_app/fundings.py @@ -3,82 +3,80 @@ from utility import add_date, add_date_interval -class FundingCrosswalk(): +class FundingCrosswalk: def __init__(self, identifier_strategy, create_strategy): self.identifier_strategy = identifier_strategy self.create_strategy = create_strategy def crosswalk(self, orcid_profile, person_uri, graph): - if orcid_profile["orcid-profile"]["orcid-activities"] \ - and "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": + 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["funding-title"]["title"]["value"] - grant_uri = self.identifier_strategy.to_uri(VIVO.Grant, {"title": title}) - #Type - graph.add((grant_uri, RDF.type, VIVO.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)) + # Person + graph.add((grant_uri, VIVO.relates, person_uri)) - #Title - graph.add((grant_uri, RDFS.label, Literal(title))) + # 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)) + # 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) + # 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)) + 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 = "${:,}".format(int(value)) - graph.add((grant_uri, VIVO.totalAwardAmount, Literal(award_amount))) + # Award amount + funding_amount = funding.get("amount") + if funding_amount is not None: + value = funding_amount.get("value") + if value is not None: + award_amount = "${:,}".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))) + # 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 "funding-external-identifiers" in funding and funding.get("funding-external-identifiers"): - 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"]))) - identifier_url = (external_identifier.get("funding-external-identifier-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))) + # 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))) @staticmethod def _get_date_parts(field_name, funding): diff --git a/orcid2vivo_app/works.py b/orcid2vivo_app/works.py index fe06b46..30f7dc5 100644 --- a/orcid2vivo_app/works.py +++ b/orcid2vivo_app/works.py @@ -83,7 +83,7 @@ } -class WorksCrosswalk(): +class WorksCrosswalk: def __init__(self, identifier_strategy, create_strategy): self.identifier_strategy = identifier_strategy self.create_strategy = create_strategy @@ -94,224 +94,241 @@ def crosswalk(self, orcid_profile, person_uri, graph): # 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) + person_surname = orcid_profile.get("person", {}).get("name", {}).get("family-name", {}).get("value", "") + + # Publications + if "works" in orcid_profile["activities-summary"]: + for work_group in orcid_profile["activities-summary"]["works"]["group"]: + for work in work_group["work-summary"]: + self.crosswalk_work(self._fetch_work(work["path"]), person_uri, person_surname, graph) + + @staticmethod + def _fetch_work(path): + r = requests.get('https://pub.orcid.org/v2.0%s' % path, + headers={"Accept": "application/json"}) + if r: + return r.json() + else: + raise Exception("Request to fetch %s returned %s" % (path, r.status_code)) + + 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 = 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)) + 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"]] + 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: - journal = (work.get("journal-title", {}) or {}).get("value") - + 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: - 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))) + 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))) @staticmethod def _fetch_crossref_doi(doi): - #curl 'http://api.crossref.org/works/10.1177/1049732304268657' -L -i + # curl 'http://api.crossref.org/works/10.1177/1049732304268657' -L -i r = requests.get('http://api.crossref.org/works/%s' % doi) if r.status_code == 404: - #Not a crossref DOI. + # Not a crossref DOI. return {} if r: return r.json()["message"] @@ -321,9 +338,9 @@ def _fetch_crossref_doi(doi): @staticmethod def _parse_bibtex(work): bibtex = {} - if work and (work.get("work-citation", {}) or {}).get("work-citation-type") == "BIBTEX": - citation = work["work-citation"]["citation"] - #Need to add \n for bibtexparser to work + if work and (work.get("citation", {}) or {}).get("citation-type") == "BIBTEX": + citation = work["citation"]["citation-value"] + # Need to add \n for bibtexparser to work curly_level = 0 new_citation = "" for c in citation: @@ -347,8 +364,8 @@ def _get_crossref_title(crossref_record): @staticmethod def _get_orcid_title(work): - return join_if_not_empty((work["work-title"]["title"]["value"], - (work["work-title"].get("subtitle") or {}).get("value")), ": ") + return join_if_not_empty((work["title"]["title"]["value"], + (work["title"].get("subtitle") or {}).get("value")), ": ") @staticmethod def _get_orcid_publication_date(work): @@ -369,7 +386,7 @@ def _get_bibtext_publication_date(bibtex): year = bibtex.get("year") if year and not re.match("\d{4}", year): year = None - #Not going to try to parse month and day + # Not going to try to parse month and day if not year: return None return year, None, None @@ -378,19 +395,19 @@ def _get_bibtext_publication_date(bibtex): def _get_crossref_publication_date(doi_record): if "issued" in doi_record and "date-parts" in doi_record["issued"]: date_parts = doi_record["issued"]["date-parts"][0] - return date_parts[0], \ - date_parts[1] if len(date_parts) > 1 else None, date_parts[2] if len(date_parts) > 2 else None + return date_parts[0], date_parts[1] if len(date_parts) > 1 else None, date_parts[2] if len( + date_parts) > 2 else None return None @staticmethod def _get_work_identifiers(work): ids = {} - external_identifiers = work.get("work-external-identifiers") + external_identifiers = work.get("external-ids") if external_identifiers: - for external_identifier in external_identifiers["work-external-identifier"]: - if external_identifier["work-external-identifier-id"] is not None: - ids[external_identifier["work-external-identifier-type"]] = \ - external_identifier["work-external-identifier-id"]["value"] + for external_identifier in (external_identifiers.get("external-id") or []): + if external_identifier["external-id-value"] is not None: + ids[external_identifier["external-id-type"].upper()] = \ + external_identifier["external-id-value"] return ids @staticmethod @@ -403,15 +420,15 @@ def _get_crossref_authors(doi_record): @staticmethod def _get_orcid_contributors(work): contributors = [] - for contributor in (work.get("work-contributors") or {}).get("contributor", []): - #Last name, first name + for contributor in (work.get("contributors") or {}).get("contributor", []): + # Last name, first name credit_name = (contributor.get("credit-name") or {}).get("value") - #Some entries will not have a credit name, meaning the entry is for the person. - #Using None, None to indicate the person. + # Some entries will not have a credit name, meaning the entry is for the person. + # Using None, None to indicate the person. first_name = None surname = None if credit_name: - #Normalize with BibtexParser's getnames() + # Normalize with BibtexParser's getnames() clean_name = bibtexparser.customization.getnames([credit_name])[0] (first_name, surname) = WorksCrosswalk._parse_reversed_name(clean_name) role = (contributor.get("contributor-attributes", {}) or {}).get("contributor-role") @@ -457,7 +474,7 @@ def _bibtex_convert_to_unicode(record): for k, v in itertools.chain(unicode_to_crappy_latex1, unicode_to_latex): if v in record[val]: record[val] = record[val].replace(v, k) - #Try without space + # Try without space elif v.rstrip() in record[val]: record[val] = record[val].replace(v.rstrip(), k) @@ -467,13 +484,13 @@ def _bibtex_convert_to_unicode(record): if v in record[val]: parts = record[val].split(str(v)) for key, record[val] in enumerate(parts): - if key+1 < len(parts) and len(parts[key+1]) > 0: + if key + 1 < len(parts) and len(parts[key + 1]) > 0: # Change order to display accents - parts[key] = parts[key] + parts[key+1][0] - parts[key+1] = parts[key+1][1:] + parts[key] = parts[key] + parts[key + 1][0] + parts[key + 1] = parts[key + 1][1:] record[val] = k.join(parts) - #Also replace {\\&} + # Also replace {\\&} if '{\\&}' in record[val]: record[val] = record[val].replace('{\\&}', '&') return record @@ -481,9 +498,9 @@ def _bibtex_convert_to_unicode(record): def _add_work_url(self, url, work_uri, graph): vcard_uri = self.identifier_strategy.to_uri(VCARD.Kind, {"url": url}) graph.add((vcard_uri, RDF.type, VCARD.Kind)) - #Has contact info + # Has contact info graph.add((work_uri, OBO.ARG_2000028, vcard_uri)) - #Url vcard + # 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)) @@ -491,7 +508,7 @@ def _add_work_url(self, url, work_uri, graph): @staticmethod def _use_url(url): - #Use url if it does not match one of the patterns in identifier_map + # Use url if it does not match one of the patterns in identifier_map for (identifier_predicate, url_template) in identifier_map.itervalues(): if url_template: base_url = url_template[:url_template.index("%s")] @@ -502,8 +519,8 @@ def _use_url(url): @staticmethod def _get_crossref_journal(crossref_record): journal = None - #May be multiple container titles. Take the longest. + # May be multiple container titles. Take the longest. for j in crossref_record.get("container-title", []): if not journal or len(j) > len(journal): journal = j - return journal \ No newline at end of file + return journal diff --git a/orcid2vivo_loader.py b/orcid2vivo_loader.py index 98182dd..d6ed197 100644 --- a/orcid2vivo_loader.py +++ b/orcid2vivo_loader.py @@ -17,7 +17,7 @@ DATETIME_FORMAT = "%Y-%m-%d %H:%M:%S" -class Store(): +class Store: def __init__(self, data_path): self.db_filepath = os.path.join(data_path, "orcid2vivo.db") log.debug("Db filepath is %s", self.db_filepath) @@ -32,7 +32,8 @@ def _create_db(self): # Creating a new table c.execute(""" - create table orcid_ids (orcid_id primary key, active, last_update, person_uri, person_id, person_class, confirmed); + create table orcid_ids (orcid_id primary key, active, last_update, person_uri, person_id, person_class, + confirmed); """) self._conn.commit() @@ -68,7 +69,8 @@ def __getitem__(self, orcid_id): """ c = self._conn.cursor() c.execute(""" - select orcid_id, active, last_update, person_uri, person_id, person_class, confirmed from orcid_ids where orcid_id=? + select orcid_id, active, last_update, person_uri, person_id, person_class, confirmed from orcid_ids where + orcid_id=? """, (orcid_id,)) row = c.fetchone() if not row: @@ -156,7 +158,7 @@ def delete_all(self): """) self._conn.commit() - #Methods to make this a Context Manager. This is necessary to make sure the connection is closed properly. + # Methods to make this a Context Manager. This is necessary to make sure the connection is closed properly. def __enter__(self): return self @@ -167,32 +169,32 @@ def __exit__(self, exc_type, exc_val, exc_tb): def load_single(orcid_id, person_uri, person_id, person_class, data_path, endpoint, username, password, namespace=None, skip_person=False, confirmed_orcid_id=False): with Store(data_path) as store: - #Crosswalk + # Crosswalk (graph, profile, person_uri) = default_execute(orcid_id, namespace=namespace, person_uri=person_uri, person_id=person_id, skip_person=skip_person, person_class=person_class, confirmed_orcid_id=confirmed_orcid_id) graph_filepath = os.path.join(data_path, "%s.ttl" % orcid_id.lower()) previous_graph = Graph(namespace_manager=ns_manager) - #Load last graph + # Load last graph if os.path.exists(graph_filepath): log.debug("Loading previous graph %s", graph_filepath) previous_graph.parse(graph_filepath, format="turtle") - #Diff against last graph + # Diff against last graph (both_graph, delete_graph, add_graph) = graph_diff(previous_graph, graph) - #SPARQL Update + # SPARQL Update log.info("Adding %s, deleting %s triples for %s", len(add_graph), len(delete_graph), orcid_id) sparql_delete(delete_graph, endpoint, username, password) sparql_insert(add_graph, endpoint, username, password) - #Save new last graph + # Save new last graph log.debug("Saving new graph %s", graph_filepath) with codecs.open(graph_filepath, "w") as out: graph.serialize(format="turtle", destination=out) - #Touch + # Touch store.touch(orcid_id) return graph, add_graph, delete_graph @@ -202,7 +204,7 @@ def load(data_path, endpoint, username, password, limit=None, before_datetime=No orcid_ids = [] failed_orcid_ids = [] with Store(data_path) as store: - #Get the orcid ids to update + # Get the orcid ids to update results = store.get_least_recent(limit=limit, before_datetime=before_datetime) for (orcid_id, person_uri, person_id, person_class, confirmed) in results: try: @@ -267,7 +269,7 @@ def load(data_path, endpoint, username, password, limit=None, before_datetime=No list_parser = subparsers.add_parser("list", help="Lists orcid_id records in the db.", parents=[data_path_parent_parser]) - #Parse + # Parse args = parser.parse_args() if args.debug: @@ -323,4 +325,4 @@ def load(data_path, endpoint, username, password, limit=None, before_datetime=No print "Loaded: %s" % ", ".join(main_orcid_ids) print "Failed: %s" % ", ".join(main_failed_orcid_ids) - print "Done" \ No newline at end of file + print "Done" diff --git a/tests/app/__init__.py b/tests/app/__init__.py index 25be156..e69de29 100644 --- a/tests/app/__init__.py +++ b/tests/app/__init__.py @@ -1 +0,0 @@ -__author__ = 'justinlittman' diff --git a/tests/app/test_affiliations.py b/tests/app/test_affiliations.py index bbe469b..fdf9f4c 100644 --- a/tests/app/test_affiliations.py +++ b/tests/app/test_affiliations.py @@ -14,29 +14,13 @@ def setUp(self): self.person_uri = ns.D["test"] self.create_strategy = SimpleCreateEntitiesStrategy(HashIdentifierStrategy(), person_uri=self.person_uri) self.crosswalker = AffiliationsCrosswalk(identifier_strategy=self.create_strategy, - create_strategy=self.create_strategy) - - def test_no_activities(self): - orcid_profile = json.loads(""" -{ - "message-version": "1.2", - "orcid-profile": { - "orcid-activities": null - } -} - """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) - self.assertEqual(0, len(self.graph)) + create_strategy=self.create_strategy) def test_no_affiliations(self): orcid_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-activities": { - "affiliations": null - } - } + "activities-summary": { + } } """) self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) @@ -45,145 +29,79 @@ def test_no_affiliations(self): def test_no_education(self): orcid_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "orcid-activities": { - "affiliations": { - "affiliation": [ - { - "type": "EMPLOYMENT", - "department-name": "Gelman Library", - "role-title": "Science & Engineering Librarian", - "start-date": { - "year": { - "value": "2013" - }, - "month": { - "value": "07" - }, - "day": null - }, - "end-date": null, - "organization": { - "name": "George Washington University", - "address": { - "city": "Washington", - "region": "DC", - "country": "US" - }, - "disambiguated-organization": { - "disambiguated-organization-identifier": "8367", - "disambiguation-source": "RINGGOLD" - } - }, - "source": { - "source-orcid": { - "value": null, - "uri": "http://orcid.org/0000-0002-4192-3392", - "path": "0000-0002-4192-3392", - "host": "orcid.org" - }, - "source-client-id": null, - "source-name": { - "value": "Hope Lappen" - }, - "source-date": { - "value": 1386877638912 - } - }, - "created-date": { - "value": 1386877638912 - }, - "last-modified-date": { - "value": 1386877750045 - }, - "visibility": "PUBLIC", - "put-code": "25495" - } - ] - } - } - } + "activities-summary": { + "educations": { + "education-summary": [] } + } } - """) +""") self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) self.assertEqual(0, len(self.graph)) def test_education(self): orcid_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-activities": { - "affiliations": { - "affiliation": [ - { - "type": "EDUCATION", - "department-name": "Neurosciences", - "role-title": "PhD", - "start-date": { - "year": { - "value": "1995" - }, - "month" : { - "value" : "06" - }, - "day" : { - "value" : "11" - } - }, - "end-date": { - "year": { - "value": "1997" - }, - "month" : { - "value" : "07" - }, - "day" : { - "value" : "03" - } - }, - "organization": { - "name": "Stanford University School of Medicine", - "address": { - "city": "Stanford", - "region": "California", - "country": "US" - }, - "disambiguated-organization": null - }, - "source": { - "source-orcid": { - "value": null, - "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" - }, - "source-date": { - "value": 1385568459467 - } - }, - "created-date": { - "value": 1385568459467 - }, - "last-modified-date": { - "value": 1406092743932 - }, - "visibility": "PUBLIC", - "put-code": "1006" - } - ] + "activities-summary": { + "educations": { + "last-modified-date": { + "value": 1486085029078 + }, + "education-summary": [ + { + "created-date": { + "value": 1385568459467 + }, + "last-modified-date": { + "value": 1486085026897 + }, + "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" } + }, + "department-name": "Neurosciences", + "role-title": "PhD", + "start-date": { + "year": { + "value": "1995" + }, + "month": null, + "day": null + }, + "end-date": { + "year": { + "value": "1997" + }, + "month": null, + "day": null + }, + "organization": { + "name": "Stanford University School of Medicine", + "address": { + "city": "Stanford", + "region": "California", + "country": "US" + }, + "disambiguated-organization": null + }, + "visibility": "PUBLIC", + "put-code": 1006, + "path": "/0000-0001-5109-3700/education/1006" } + ], + "path": "/0000-0001-5109-3700/educations" } + } } """) + # Changed start date to 1995 self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) self.assertTrue(bool(self.graph.query(""" ask where { @@ -217,53 +135,51 @@ def test_education(self): def test_education_minimal(self): orcid_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-activities": { - "affiliations": { - "affiliation": [ - { - "type": "EDUCATION", - "department-name": null, - "start-date": null, - "end-date": null, - "organization": { - "name": "Stanford University School of Medicine", - "address": { - "city": "Stanford", - "region": "California", - "country": "US" - }, - "disambiguated-organization": null - }, - "source": { - "source-orcid": { - "value": null, - "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" - }, - "source-date": { - "value": 1385568459467 - } - }, - "created-date": { - "value": 1385568459467 - }, - "last-modified-date": { - "value": 1406092743932 - }, - "visibility": "PUBLIC", - "put-code": "1006" - } - ] + "activities-summary": { + "educations": { + "last-modified-date": { + "value": 1486085029078 + }, + "education-summary": [ + { + "created-date": { + "value": 1385568459467 + }, + "last-modified-date": { + "value": 1486085026897 + }, + "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" } + }, + "department-name": null, + "role-title": "PhD", + "start-date": null, + "end-date": null, + "organization": { + "name": "Stanford University School of Medicine", + "address": { + "city": "Stanford", + "region": "California", + "country": "US" + }, + "disambiguated-organization": null + }, + "visibility": "PUBLIC", + "put-code": 1006, + "path": "/0000-0001-5109-3700/education/1006" } + ], + "path": "/0000-0001-5109-3700/educations" } + } } """) self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) diff --git a/tests/app/test_bio.py b/tests/app/test_bio.py index aa01b5b..f33ce3e 100644 --- a/tests/app/test_bio.py +++ b/tests/app/test_bio.py @@ -12,7 +12,6 @@ class TestBio(TestCase): - def setUp(self): self.graph = Graph(namespace_manager=ns.ns_manager) self.person_uri = ns.D["test"] @@ -23,162 +22,268 @@ def setUp(self): def test_no_external_identifiers(self): orcid_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "external-identifiers": null - } - } + "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(""" { - "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" + "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")]) + # 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" - } + "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" }, - "external-identifiers": null + "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 + # Laurel is a person self.assertTrue(self.graph[D["test"]: RDF.type: FOAF.Person]) - #with a label + # with a label self.assertTrue(self.graph[D["test"]: RDFS.label: Literal("Laurel Haak")]) - #vcard test + # vcard test self.assertTrue(bool(self.graph.query(""" ask where { ?vcn a vcard:Name . @@ -192,82 +297,130 @@ def test_name(self): 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" - } - } + "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.")]) + # 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(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "biography": null - } + "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 + # 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" + "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" }, - "contact-details": { - "email": [], - "address": { - "country": { - "value": "US", - "visibility": "PUBLIC" - } - } + "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 + # LinkedIn self.assertTrue(bool(self.graph.query(""" ask where { ?vcw a vcard:URL . @@ -278,7 +431,7 @@ def test_websites(self): } """))) - #ResearchGate + # ResearchGate self.assertTrue(bool(self.graph.query(""" ask where { ?vcw a vcard:URL . @@ -294,67 +447,81 @@ def test_websites(self): def test_no_websites(self): orcid_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "researcher-urls": { - "researcher-url": [], - "visibility": "PUBLIC" - } - } + "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 + # 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 - } + "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 + # 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" + "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(3, len(self.graph)) + self.assertEqual(8, len(self.graph)) self.assertTrue(bool(self.graph.query(""" ask where { @@ -362,4 +529,4 @@ def test_keywords(self): d:test vivo:freetextKeyword "research policy" . d:test vivo:freetextKeyword "science workforce" . } - """))) \ No newline at end of file + """))) diff --git a/tests/app/test_fundings.py b/tests/app/test_fundings.py index 2f36687..c530ddf 100644 --- a/tests/app/test_fundings.py +++ b/tests/app/test_fundings.py @@ -1,17 +1,14 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + from unittest import TestCase -from tests import FIXTURE_PATH from orcid2vivo_app.fundings import FundingCrosswalk -import orcid2vivo import orcid2vivo_app.vivo_namespace as ns from orcid2vivo_app.vivo_uri import HashIdentifierStrategy from orcid2vivo import SimpleCreateEntitiesStrategy from rdflib import Graph, RDFS -import vcr - -my_vcr = vcr.VCR( - cassette_library_dir=FIXTURE_PATH, -) +import json class TestFundings(TestCase): @@ -21,29 +18,428 @@ def setUp(self): 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) - + 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) + 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) - - @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) + 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( @@ -52,17 +448,100 @@ def test_with_funding(self): ) # 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) + self.assertEqual(len(pi_roles), 4) - @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) + 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 Drugs:" - u" Application to Synthetic Cannabinoids and Bath Salts " + 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 : ]))) diff --git a/tests/app/test_works.py b/tests/app/test_works.py index 19329a4..d48bfad 100644 --- a/tests/app/test_works.py +++ b/tests/app/test_works.py @@ -10,9 +10,11 @@ from orcid2vivo_app.vivo_uri import HashIdentifierStrategy from orcid2vivo import SimpleCreateEntitiesStrategy -#Saving this because will be monkey patching +# Saving this because will be monkey patching orig_fetch_crossref_doi = WorksCrosswalk._fetch_crossref_doi +# curl -H "Accept: application/json" https://pub.orcid.org/v2.0/0000-0003-3441-946X/work/15628639 | jq '.' | pbcopy + class TestWorks(TestCase): @@ -24,95 +26,45 @@ def setUp(self): self.crosswalker = WorksCrosswalk(identifier_strategy=self.create_strategy, create_strategy=self.create_strategy) - def test_no_actitivities(self): - orcid_profile = json.loads(""" -{ - "message-version": "1.2", - "orcid-profile": { - "orcid-activities": null - } -} - """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) - self.assertEqual(0, len(self.graph)) - def test_no_works(self): orcid_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-activities": { - "orcid-works": null - } + "activities-summary": { + "works": { + "group": [] } + } } """) self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) self.assertEqual(0, len(self.graph)) def test_only_handled_work_types(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "NOT_A_JOURNAL_ARTICLE" - } - ] - } - } - } + "type": "NOT_A_BOOK_CHAPTER" } """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "nobody", self.graph) self.assertEqual(0, len(self.graph)) def test_authorship(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" - } - }, - "work-type": "JOURNAL_ARTICLE" - }, - { - "work-title": { - "title": { - "value": "Persistent identifiers can improve provenance and attribution and encourage sharing of research results" - } - }, - "work-type": "JOURNAL_ARTICLE" - } - ] - } - } - } + "path": "/0000-0001-5109-3700/work/15643392", + "title": { + "title": { + "value": "Persistent identifiers can improve provenance and attribution and encourage sharing of research results" + }, + "subtitle": null, + "translated-title": null + }, + "type": "JOURNAL_ARTICLE" } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) - self.assertEqual(2, len(list(self.graph[: RDF["type"]: VIVO["Authorship"]]))) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) + self.assertEqual(1, len(list(self.graph[: RDF["type"]: VIVO["Authorship"]]))) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -123,176 +75,105 @@ def test_authorship(self): """))) def test_orcid_title_no_subtitle(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" - }, - "subtitle": null, - "translated-title": null - }, - "work-type": "JOURNAL_ARTICLE" - } - ] - } - } - } + "path": "/0000-0001-5109-3700/work/15643384", + "title": { + "title": { + "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "type": "JOURNAL_ARTICLE" } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(list(self.graph[: RDFS["label"]: Literal( - "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?")])) + "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for " + "physician investigators?")])) def test_orcid_title_and_subtitle(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Jennifer" - }, - "family-name": { - "value": "Wisdom" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title" : { - "value" : "Substance use disorder among people with first-episode psychosis" - }, - "subtitle" : { - "value" : "A systematic review of course and treatment" - }, - "translated-title": null - }, - "work-type": "JOURNAL_ARTICLE" - } - ] - } - } - } + "path": "/0000-0003-3441-946X/work/15628639", + "title": { + "title": { + "value": "Substance use disorder among people with first-episode psychosis" + }, + "subtitle": { + "value": "A systematic review of course and treatment" + }, + "translated-title": null + }, + "type": "JOURNAL_ARTICLE" } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Wisdom", self.graph) self.assertTrue(list(self.graph[: RDFS["label"]: Literal( - "Substance use disorder among people with first-episode psychosis: A systematic review of course and treatment")])) + "Substance use disorder among people with first-episode psychosis: A systematic review of course and " + "treatment")])) def test_bibtex_title(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Not the title" - }, - "subtitle": null, - "translated-title": null - }, - "work-type": "JOURNAL_ARTICLE", - "work-citation" : { - "work-citation-type" : "BIBTEX", - "citation" : "@article { haak2012,title = {Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?},journal = {Academic Medicine},year = {2012},volume = {87},number = {11},pages = {1516-1524},author = {Ginther, D.K. and Haak, L.L. and Schaffer, W.T. and Kington, R.}}" - } - } - ] - } - } - } + "path": "/0000-0001-5109-3700/work/15643384", + "title": { + "title": { + "value": "Not the title" + }, + "subtitle": null, + "translated-title": null + }, + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@article{Haak2012,title = {Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?},journal = {Academic Medicine},year = {2012},volume = {87},number = {11},pages = {1516-1524},author = {Ginther, D.K. and Haak, L.L. and Schaffer, W.T. and Kington, R.}}" + }, + "type": "JOURNAL_ARTICLE" } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(list(self.graph[: RDFS["label"]: Literal( - "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?")])) + "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for " + "physician investigators?")])) def test_crossref_title(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Not the title" - }, - "subtitle": null, - "translated-title": null - }, - "work-type": "JOURNAL_ARTICLE", - "work-citation": { - "work-citation-type": "BIBTEX", - "citation": "@article { haak2012,title = {Not the title},journal = {Academic Medicine},year = {2012},volume = {87},number = {11},pages = {1516-1524},author = {Ginther, D.K. and Haak, L.L. and Schaffer, W.T. and Kington, R.}}" - }, - "work-external-identifiers": { - "work-external-identifier": [ - { - "work-external-identifier-type": "DOI", - "work-external-identifier-id": { - "value": "10.1097/ACM.0b013e31826d726b" - } - } - ], - "scope": null - } - } - ] - } - } - } + "path": "/0000-0001-5109-3700/work/15643384", + "title": { + "title": { + "value": "Not the title" + }, + "subtitle": null, + "translated-title": null + }, + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@article{Haak2012,title = {Not the title},journal = {Academic Medicine},year = {2012},volume = {87},number = {11},pages = {1516-1524},author = {Ginther, D.K. and Haak, L.L. and Schaffer, W.T. and Kington, R.}}" + }, + "type": "JOURNAL_ARTICLE", + "external-ids": { + "external-id": [ + { + "external-id-type": "doi", + "external-id-value": "10.1097/ACM.0b013e31826d726b", + "external-id-url": null, + "external-id-relationship": "SELF" + }, + { + "external-id-type": "eid", + "external-id-value": "2-s2.0-84869886841", + "external-id-url": null, + "external-id-relationship": "SELF" + } + ] + } } + """) WorksCrosswalk._fetch_crossref_doi = staticmethod(lambda doi: json.loads(""" @@ -303,43 +184,25 @@ def test_crossref_title(self): } """)) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(list(self.graph[: RDFS["label"]: Literal( - "Are Race, Ethnicity, and Medical School Affiliation Associated With NIH R01 Type 1 Award Probability for Physician Investigators?")])) + "Are Race, Ethnicity, and Medical School Affiliation Associated With NIH R01 Type 1 Award Probability for " + "Physician Investigators?")])) def test_bibtex_publisher(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Heidi" - }, - "family-name": { - "value": "Hardt" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "BOOK", - "work-citation" : { - "work-citation-type" : "BIBTEX", - "citation": "@book{Hardt_2014,doi = {10.1093/acprof:oso/9780199337118.001.0001},url = {http://dx.doi.org/10.1093/acprof:oso/9780199337118.001.0001},year = 2014,month = {Feb},publisher = {Oxford University Press},author = {Heidi Hardt},title = {Time to React}}" - } - } - ] - } - } - } + "path": "/0000-0001-5014-4975/work/13266925", + "short-description": null, + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@book{Hardt_2014,doi = {10.1093/acprof:oso/9780199337118.001.0001},url = {http://dx.doi.org/10.1093/acprof:oso/9780199337118.001.0001},year = 2014,month = {Feb},publisher = {Oxford University Press},author = {Heidi Hardt},title = {Time to React}}" + }, + "type": "BOOK" } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Hardt", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:Book . @@ -350,46 +213,32 @@ def test_bibtex_publisher(self): """))) def test_crossref_publisher(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-citation": { - "work-citation-type": "BIBTEX", - "citation": "@article { haak2012,title = {Are Race, Ethnicity, and Medical School Affiliation Associated With NIH R01 Type 1 Award Probability for Physician Investigators?},publisher = {Not the publisher},journal = {Academic Medicine},year = {2012},volume = {87},number = {11},pages = {1516-1524},author = {Ginther, D.K. and Haak, L.L. and Schaffer, W.T. and Kington, R.}}" - }, - "work-external-identifiers": { - "work-external-identifier": [ - { - "work-external-identifier-type": "DOI", - "work-external-identifier-id": { - "value": "10.1097/ACM.0b013e31826d726b" - } - } - ], - "scope": null - } - } - ] - } - } - } + "path": "/0000-0001-5109-3700/work/15643382", + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@article{Haak2012,title = {Standards and infrastructure for innovation data exchange},journal = {Science},year = {2012},volume = {338},number = {6104},pages = {196-197},author = {Haak, L.L. and Baker, D. and Ginther, D.K. and Gordon, G.J. and Probus, M.A. and Kannankutty, N. and Weinberg, B.A.}}" + }, + "type": "JOURNAL_ARTICLE", + "external-ids": { + "external-id": [ + { + "external-id-type": "doi", + "external-id-value": "10.1126/science.1221840", + "external-id-url": null, + "external-id-relationship": "SELF" + }, + { + "external-id-type": "eid", + "external-id-value": "2-s2.0-84867318319", + "external-id-url": null, + "external-id-relationship": "SELF" + } + ] + } } + """) WorksCrosswalk._fetch_crossref_doi = staticmethod(lambda doi: json.loads(""" @@ -398,7 +247,7 @@ def test_crossref_publisher(self): } """)) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -409,86 +258,50 @@ def test_crossref_publisher(self): """))) def test_bibtex_volume_and_number_and_pages(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "F." - }, - "family-name": { - "value": "Viladomat" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "BOOK", - "work-citation" : { - "work-citation-type" : "BIBTEX", - "citation": "@article { viladomat1997,title = {Narcissus alkaloids},journal = {Studies in Natural Products Chemistry},year = {1997},volume = {20},number = {PART F},pages = {323-405}}" - } - } - ] - } - } - } + "path": "/0000-0001-5003-0230/work/13540323", + "type": "BOOK", + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@article { viladomat1997,title = {Narcissus alkaloids},journal = {Studies in Natural Products Chemistry},year = {1997},volume = {20},number = {PART F},pages = {323-405},author = {Bastida, J. and Viladomat, F. and Codina, C.}}" + } } + """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Viladomat", self.graph) self.assertTrue(list(self.graph[: ns.BIBO["volume"]: Literal("20")])) self.assertTrue(list(self.graph[: ns.BIBO["issue"]: Literal("PART F")])) self.assertTrue(list(self.graph[: ns.BIBO["pageStart"]: Literal("323")])) self.assertTrue(list(self.graph[: ns.BIBO["pageEnd"]: Literal("405")])) - def test_bibtex_volume_and_number_and_pages(self): - orcid_profile = json.loads(""" + def test_crossref_volume_and_number_and_pages(self): + work_profile = json.loads(""" + { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-citation": { - "work-citation-type": "BIBTEX", - "citation": "@article { haak2012,title = {Are Race, Ethnicity, and Medical School Affiliation Associated With NIH R01 Type 1 Award Probability for Physician Investigators?},publisher = {Not the publisher},journal = {Academic Medicine},year = {2012},volume = {Not 87},number = {Not 11},pages = {1536-1554},author = {Ginther, D.K. and Haak, L.L. and Schaffer, W.T. and Kington, R.}}" - }, - "work-external-identifiers": { - "work-external-identifier": [ - { - "work-external-identifier-type": "DOI", - "work-external-identifier-id": { - "value": "10.1097/ACM.0b013e31826d726b" - } - } - ], - "scope": null - } - } - ] - } - } - } + "path": "/0000-0001-5109-3700/work/8289794", + "type": "JOURNAL_ARTICLE", + "title": { + "title": { + "value": "Are Race, Ethnicity, and Medical School Affiliation Associated With NIH R01 Type 1 Award Probability for Physician Investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "external-ids": { + "external-id": [ + { + "external-id-type": "doi", + "external-id-value": "10.1097/acm.0b013e31826d726b", + "external-id-url": null, + "external-id-relationship": "SELF" + } + ] + } } + """) - WorksCrosswalk._fetch_crossref_doi = staticmethod(lambda doi: json.loads(""" { "page": "1516-1524", @@ -496,60 +309,40 @@ def test_bibtex_volume_and_number_and_pages(self): "volume": "11" } """)) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(list(self.graph[: ns.BIBO["volume"]: Literal("11")])) self.assertTrue(list(self.graph[: ns.BIBO["issue"]: Literal("87")])) self.assertTrue(list(self.graph[: ns.BIBO["pageStart"]: Literal("1516")])) self.assertTrue(list(self.graph[: ns.BIBO["pageEnd"]: Literal("1524")])) def test_orcid_pubdate(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title": { - "title": { - "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" - }, - "subtitle": null, - "translated-title": null - }, - "publication-date" : { - "year" : { - "value" : "2013" - }, - "month" : { - "value" : "11" - }, - "day" : { - "value" : "01" - }, - "media-type" : null - } - } - ] - } - } - } + "path": "/0000-0001-5109-3700/work/8289794", + "type": "JOURNAL_ARTICLE", + "title": { + "title": { + "value": "Are Race, Ethnicity, and Medical School Affiliation Associated With NIH R01 Type 1 Award Probability for Physician Investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "publication-date": { + "year": { + "value": "2013" + }, + "month": { + "value": "11" + }, + "day": { + "value": "01" + }, + "media-type": null + } } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -562,49 +355,29 @@ def test_orcid_pubdate(self): """))) def test_orcid_pubdate_year_only(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title": { - "title": { - "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" - }, - "subtitle": null, - "translated-title": null - }, - "publication-date" : { - "year" : { - "value" : "2013" - }, - "month" : null, - "day" : null, - "media-type" : null - } - } - ] - } - } - } + "path": "/0000-0001-5109-3700/work/8289794", + "type": "JOURNAL_ARTICLE", + "title": { + "title": { + "value": "Are Race, Ethnicity, and Medical School Affiliation Associated With NIH R01 Type 1 Award Probability for Physician Investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "publication-date": { + "year": { + "value": "2013" + }, + "month": null, + "day": null, + "media-type": null + } } - """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + """) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -617,58 +390,37 @@ def test_orcid_pubdate_year_only(self): """))) def test_crossref_pubdate(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title": { - "title": { - "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" - }, - "subtitle": null, - "translated-title": null - }, - "publication-date" : { - "year" : { - "value" : "2013" - }, - "month" : null, - "day" : null, - "media-type" : null - }, - "work-external-identifiers": { - "work-external-identifier": [ - { - "work-external-identifier-type": "DOI", - "work-external-identifier-id": { - "value": "10.1097/ACM.0b013e31826d726b" - } - } - ], - "scope": null - } - } - ] - } - } - } + "path": "/0000-0001-5109-3700/work/8289794", + "type": "JOURNAL_ARTICLE", + "title": { + "title": { + "value": "Are Race, Ethnicity, and Medical School Affiliation Associated With NIH R01 Type 1 Award Probability for Physician Investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "publication-date": { + "year": { + "value": "2013" + }, + "month": null, + "day": null, + "media-type": null + }, + "external-ids": { + "external-id": [ + { + "external-id-type": "doi", + "external-id-value": "10.1097/acm.0b013e31826d726b", + "external-id-url": null, + "external-id-relationship": "SELF" + } + ] + } } - """) +""") WorksCrosswalk._fetch_crossref_doi = staticmethod(lambda doi: json.loads(""" { @@ -676,7 +428,7 @@ def test_crossref_pubdate(self): } """)) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -689,57 +441,36 @@ def test_crossref_pubdate(self): """))) def test_crossref_pubdate_year_only(self): - orcid_profile = json.loads(""" -{ - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title": { - "title": { - "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" - }, - "subtitle": null, - "translated-title": null - }, - "publication-date" : { - "year" : { - "value" : "2013" - }, - "month" : null, - "day" : null, - "media-type" : null - }, - "work-external-identifiers": { - "work-external-identifier": [ - { - "work-external-identifier-type": "DOI", - "work-external-identifier-id": { - "value": "10.1097/ACM.0b013e31826d726b" - } - } - ], - "scope": null - } - } - ] - } + work_profile = json.loads(""" + { + "path": "/0000-0001-5109-3700/work/8289794", + "type": "JOURNAL_ARTICLE", + "title": { + "title": { + "value": "Are Race, Ethnicity, and Medical School Affiliation Associated With NIH R01 Type 1 Award Probability for Physician Investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "publication-date": { + "year": { + "value": "2013" + }, + "month": null, + "day": null, + "media-type": null + }, + "external-ids": { + "external-id": [ + { + "external-id-type": "doi", + "external-id-value": "10.1097/acm.0b013e31826d726b", + "external-id-url": null, + "external-id-relationship": "SELF" + } + ] + } } - } -} """) WorksCrosswalk._fetch_crossref_doi = staticmethod(lambda doi: json.loads(""" @@ -748,7 +479,7 @@ def test_crossref_pubdate_year_only(self): } """)) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -761,44 +492,18 @@ def test_crossref_pubdate_year_only(self): """))) def test_bibtex_pubdate(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "M." - }, - "family-name": { - "value": "Chichorro" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title": { - "title": { - "value": "Chronological link between deep-seated processes in magma chambers and eruptions: Permo-Carboniferous magmatism in the core of Pangaea (Southern Pyrenees)" - }, - "subtitle": null - }, - "work-citation": { - "work-citation-type": "BIBTEX", - "citation": "@article { chichorro2014,title = {Chronological link between deep-seated processes in magma chambers and eruptions: Permo-Carboniferous magmatism in the core of Pangaea (Southern Pyrenees)},journal = {Gondwana Research},year = {2014},volume = {25},number = {1},pages = {290-308}}" - } - } - ] - } - } - } + "path": "/0000-0001-5000-0736/work/11557873", + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@article { chichorro2014,title = {Chronological link between deep-seated processes in magma chambers and eruptions: Permo-Carboniferous magmatism in the core of Pangaea (Southern Pyrenees)},journal = {Gondwana Research},year = {2014},volume = {25},number = {1},pages = {290-308},author = {Pereira, M.F. and Castro, A. and Chichorro, M. and Fernández, C. and Díaz-Alvarado, J. and Martí, J. and Rodríguez, C.}}" + }, + "type": "JOURNAL_ARTICLE" } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Chichorro", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -811,44 +516,18 @@ def test_bibtex_pubdate(self): """))) def test_bibtex_pubdate_in_press(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "M." - }, - "family-name": { - "value": "Chichorro" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title": { - "title": { - "value": "Chronological link between deep-seated processes in magma chambers and eruptions: Permo-Carboniferous magmatism in the core of Pangaea (Southern Pyrenees)" - }, - "subtitle": null - }, - "work-citation": { - "work-citation-type": "BIBTEX", - "citation": "@article { chichorro2014,title = {Chronological link between deep-seated processes in magma chambers and eruptions: Permo-Carboniferous magmatism in the core of Pangaea (Southern Pyrenees)},journal = {Gondwana Research},year = {in press},volume = {25},number = {1},pages = {290-308}}" - } - } - ] - } - } - } + "path": "/0000-0001-5000-0736/work/11557873", + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@article { chichorro2014,title = {Chronological link between deep-seated processes in magma chambers and eruptions: Permo-Carboniferous magmatism in the core of Pangaea (Southern Pyrenees)},journal = {Gondwana Research},year = {in press},volume = {25},number = {1},pages = {290-308}}" + }, + "type": "JOURNAL_ARTICLE" } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Chichorro", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -859,44 +538,24 @@ def test_bibtex_pubdate_in_press(self): """))) def test_book_chapter(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "N.J." - }, - "family-name": { - "value": "Ford" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Numerical methods for multi-term fractional boundary value problems, Differential and Difference Equations with Applications" - }, - "subtitle": null - }, - "work-citation": { - "work-citation-type": "BIBTEX", - "citation": "@incollection{\\nyear={2013},\\nisbn={978-1-4614-7332-9},\\nbooktitle={Differential and Difference Equations with Applications},\\nvolume={47},\\nseries={Springer Proceedings in Mathematics & Statistics},\\neditor={Pinelas, Sandra and Chipot, Michel and Dosla, Zuzana},\\ndoi={10.1007/978-1-4614-7333-6_48},\\ntitle={Numerical Methods for Multi-term Fractional Boundary Value Problems},\\nurl={http://dx.doi.org/10.1007/978-1-4614-7333-6_48},\\npublisher={Springer New York},\\npages={535-542},\\nlanguage={English}\\n}\\n" - }, - "work-type": "BOOK_CHAPTER" - } - ] - } - } - } -} + "path": "/0000-0002-9446-437X/work/35153466", + "title": { + "title": { + "value": "Numerical Methods for Multi-term Fractional Boundary Value Problems" + }, + "subtitle": null, + "translated-title": null + }, + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@incollection{\\nyear={2013},\\nisbn={978-1-4614-7332-9},\\nbooktitle={Differential and Difference Equations with Applications},\\nvolume={47},\\nseries={Springer Proceedings in Mathematics & Statistics},\\neditor={Pinelas, Sandra and Chipot, Michel and Dosla, Zuzana},\\ndoi={10.1007/978-1-4614-7333-6_48},\\ntitle={Numerical Methods for Multi-term Fractional Boundary Value Problems},\\nurl={http://dx.doi.org/10.1007/978-1-4614-7333-6_48},\\npublisher={Springer New York},\\npages={535-542},\\nlanguage={English}\\n}\\n" + }, + "type": "BOOK_CHAPTER" +} """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Ford", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:Chapter . @@ -910,58 +569,47 @@ def test_book_chapter(self): """))) def test_crossref_subject(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Jennifer" - }, - "family-name": { - "value": "Wisdom" - } - } + "path": "/0000-0003-3441-946X/work/15628641", + "title": { + "title": { + "value": "Substance abuse treatment programs' data management capacity: An exploratory study" + }, + "subtitle": null, + "translated-title": null + }, + "type": "JOURNAL_ARTICLE", + "external-ids": { + "external-id": [ + { + "external-id-type": "doi", + "external-id-value": "10.1007/s11414-010-9221-z", + "external-id-url": { + "value": "" }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title" : { - "title" : { - "value" : "Substance abuse treatment programs' data management capacity: An exploratory study" - }, - "subtitle" : null, - "translated-title" : null - }, - "work-external-identifiers": { - "work-external-identifier": [ - { - "work-external-identifier-type": "DOI", - "work-external-identifier-id": { - "value": "10.1007/s11414-010-9221-z" - } - } - ], - "scope": null - } - } - ] - } - } - } + "external-id-relationship": "SELF" + }, + { + "external-id-type": "eid", + "external-id-value": "2-s2.0-79955719929", + "external-id-url": { + "value": "" + }, + "external-id-relationship": "SELF" + } + ] + } } + """) - WorksCrosswalk._fetch_crossref_doi = staticmethod(lambda doi: json.loads(""" { "subject":["Health(social science)","Public Health, Environmental and Occupational Health","Health Policy"] } """)) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Wisdom", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -978,58 +626,45 @@ def test_crossref_subject(self): """))) def test_crossref_authors(self): - orcid_profile = json.loads(""" -{ - "message-version": "1.2", - "orcid-profile": { - "orcid-bio" : { - "personal-details" : { - "given-names" : { - "value" : "Laurel" - }, - "family-name" : { - "value" : "Haak" + work_profile = json.loads(""" + { + "path": "/0000-0001-5109-3700/work/8289794", + "type": "JOURNAL_ARTICLE", + "title": { + "title": { + "value": "Are Race, Ethnicity, and Medical School Affiliation Associated With NIH R01 Type 1 Award Probability for Physician Investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "publication-date": { + "year": { + "value": "2013" + }, + "month": null, + "day": null, + "media-type": null + }, + "external-ids": { + "external-id": [ + { + "external-id-type": "doi", + "external-id-value": "10.1097/acm.0b013e31826d726b", + "external-id-url": null, + "external-id-relationship": "SELF" + } + ] + } } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title" : { - "title" : { - "value" : "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" - }, - "subtitle" : null, - "translated-title" : null - }, - "work-external-identifiers": { - "work-external-identifier": [ - { - "work-external-identifier-type": "DOI", - "work-external-identifier-id": { - "value": "10.1097/ACM.0b013e31826d726b" - } - } - ], - "scope": null - } - } - ] - } - } - } -} - """) + """) WorksCrosswalk._fetch_crossref_doi = staticmethod(lambda doi: json.loads(""" -{ - "author":[{"affiliation":[],"family":"Ginther","given":"Donna K."},{"affiliation":[],"family":"Haak","given":"Laurel L."},{"affiliation":[],"family":"Schaffer","given":"Walter T."},{"affiliation":[],"family":"Kington","given":"Raynard"}] -} - """)) + { + "author":[{"affiliation":[],"family":"Ginther","given":"Donna K."},{"affiliation":[],"family":"Haak","given":"Laurel L."},{"affiliation":[],"family":"Schaffer","given":"Walter T."},{"affiliation":[],"family":"Kington","given":"Raynard"}] + } + """)) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -1051,80 +686,58 @@ def test_crossref_authors(self): """))) def test_orcid_authors_reversed(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } + "path": "/0000-0001-5109-3700/work/15643384", + "title": { + "title": { + "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "type": "JOURNAL_ARTICLE", + "contributors": { + "contributor": [ + { + "contributor-orcid": null, + "credit-name": { + "value": "Ginther, D.K." }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title": { - "title": { - "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" - }, - "subtitle": null, - "translated-title": null - }, - "work-contributors": { - "contributor": [ - { - "contributor-orcid": null, - "credit-name": { - "value": "Ginther, D.K.", - "visibility": "PUBLIC" - }, - "contributor-email": null, - "contributor-attributes": null - }, - { - "contributor-orcid": null, - "credit-name": { - "value": "Haak, L.L.", - "visibility": "PUBLIC" - }, - "contributor-email": null, - "contributor-attributes": null - }, - { - "contributor-orcid": null, - "credit-name": { - "value": "Schaffer, W.T.", - "visibility": "PUBLIC" - }, - "contributor-email": null, - "contributor-attributes": null - }, - { - "contributor-orcid": null, - "credit-name": { - "value": "Kington, R.", - "visibility": "PUBLIC" - }, - "contributor-email": null, - "contributor-attributes": null - } - ] - } - } - ] - } - } - } -} """) + "contributor-email": null, + "contributor-attributes": null + }, + { + "contributor-orcid": null, + "credit-name": { + "value": "Haak, L.L." + }, + "contributor-email": null, + "contributor-attributes": null + }, + { + "contributor-orcid": null, + "credit-name": { + "value": "Schaffer, W.T." + }, + "contributor-email": null, + "contributor-attributes": null + }, + { + "contributor-orcid": null, + "credit-name": { + "value": "Kington, R." + }, + "contributor-email": null, + "contributor-attributes": null + } + ] + } +} + + """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -1146,41 +759,25 @@ def test_orcid_authors_reversed(self): """))) def test_no_orcid_authors(self): - orcid_profile = json.loads(""" -{ - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title": { - "title": { - "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" - }, - "subtitle": null, - "translated-title": null - }, - "work-contributors": null - } - ] - } + work_profile = json.loads(""" + { + "path": "/0000-0001-5109-3700/work/15643384", + "title": { + "title": { + "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "type": "JOURNAL_ARTICLE", + "contributors": { + "contributor": [] + } } - } -} """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + """) + + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -1190,53 +787,32 @@ def test_no_orcid_authors(self): """))) def test_null_credit_name(self): - orcid_profile = json.loads(""" -{ - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title": { - "title": { - "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" - }, - "subtitle": null, - "translated-title": null - }, - "work-contributors": { - "contributor": [ - { - "contributor-orcid": null, - "credit-name": null, - "contributor-email": null, - "contributor-attributes": { - "contributor-sequence": null, - "contributor-role": "SUPPORT_STAFF" - } - } - ] - } - } - ] - } + work_profile = json.loads(""" + { + "path": "/0000-0001-5109-3700/work/15643384", + "title": { + "title": { + "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "type": "JOURNAL_ARTICLE", + "contributors": { + "contributor": [ + { + "contributor-orcid": null, + "credit-name": null, + "contributor-email": null, + "contributor-attributes": null + } + ] + } } - } -} """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + """) + + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -1246,80 +822,57 @@ def test_null_credit_name(self): """))) def test_orcid_authors_not_reversed(self): - orcid_profile = json.loads(""" -{ - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" + work_profile = json.loads(""" + { + "path": "/0000-0001-5109-3700/work/15643384", + "title": { + "title": { + "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "type": "JOURNAL_ARTICLE", + "contributors": { + "contributor": [ + { + "contributor-orcid": null, + "credit-name": { + "value": "D.K. Ginther" }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title": { - "title": { - "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" - }, - "subtitle": null, - "translated-title": null - }, - "work-contributors": { - "contributor": [ - { - "contributor-orcid": null, - "credit-name": { - "value": "D.K. Ginther", - "visibility": "PUBLIC" - }, - "contributor-email": null, - "contributor-attributes": null - }, - { - "contributor-orcid": null, - "credit-name": { - "value": "Haak, L.L.", - "visibility": "PUBLIC" - }, - "contributor-email": null, - "contributor-attributes": null - }, - { - "contributor-orcid": null, - "credit-name": { - "value": " W.T. Schaffer", - "visibility": "PUBLIC" - }, - "contributor-email": null, - "contributor-attributes": null - }, - { - "contributor-orcid": null, - "credit-name": { - "value": "R. Kington", - "visibility": "PUBLIC" - }, - "contributor-email": null, - "contributor-attributes": null - } - ] - } - } - ] - } + "contributor-email": null, + "contributor-attributes": null + }, + { + "contributor-orcid": null, + "credit-name": { + "value": "L.L. Haak" + }, + "contributor-email": null, + "contributor-attributes": null + }, + { + "contributor-orcid": null, + "credit-name": { + "value": "W.T. Schaffer" + }, + "contributor-email": null, + "contributor-attributes": null + }, + { + "contributor-orcid": null, + "credit-name": { + "value": "R. Kington" + }, + "contributor-email": null, + "contributor-attributes": null + } + ] + } } - } -} """) + """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -1341,44 +894,25 @@ def test_orcid_authors_not_reversed(self): """))) def test_bibtex_authors_reversed(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title": { - "title": { - "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" - }, - "subtitle": null, - "translated-title": null - }, - "work-citation" : { - "work-citation-type" : "BIBTEX", - "citation" : "@article { haak2012,title = {Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?},journal = {Academic Medicine},year = {2012},volume = {87},number = {11},pages = {1516-1524},author = {Ginther, D.K. and Haak, L.L. and Schaffer, W.T. and Kington, R.}}" - } - } - ] - } - } - } -} """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + "path": "/0000-0001-5109-3700/work/15643384", + "title": { + "title": { + "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@article{Haak2012,title = {Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?},journal = {Academic Medicine},year = {2012},volume = {87},number = {11},pages = {1516-1524},author = {Ginther, D.K. and Haak, L.L. and Schaffer, W.T. and Kington, R.}}" + }, + "type": "JOURNAL_ARTICLE" +} + + """) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -1400,44 +934,25 @@ def test_bibtex_authors_reversed(self): """))) def test_bibtex_authors_not_reversed(self): - orcid_profile = json.loads(""" -{ - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title": { - "title": { - "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" - }, - "subtitle": null, - "translated-title": null - }, - "work-citation" : { - "work-citation-type" : "BIBTEX", - "citation" : "@article { haak2012,title = {Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?},journal = {Academic Medicine},year = {2012},volume = {87},number = {11},pages = {1516-1524},author = {D.K. Ginther and L.L. Haak and W.T. Schaffer and R. Kington}}" - } - } - ] - } + work_profile = json.loads(""" + { + "path": "/0000-0001-5109-3700/work/15643384", + "title": { + "title": { + "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@article{Haak2012,title = {Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?},journal = {Academic Medicine},year = {2012},volume = {87},number = {11},pages = {1516-1524},author = {D.K. Ginther and L.L. Haak and W.T. Schaffer and R. Kington}}" + }, + "type": "JOURNAL_ARTICLE" } - } -} """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + """) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -1459,44 +974,26 @@ def test_bibtex_authors_not_reversed(self): """))) def test_bibtex_editor(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "N.J." - }, - "family-name": { - "value": "Ford" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Numerical methods for multi-term fractional boundary value problems, Differential and Difference Equations with Applications" - }, - "subtitle": null - }, - "work-citation": { - "work-citation-type": "BIBTEX", - "citation": "@incollection{\\nyear={2013},\\nisbn={978-1-4614-7332-9},\\nbooktitle={Differential and Difference Equations with Applications},\\nvolume={47},\\nseries={Springer Proceedings in Mathematics & Statistics},\\neditor={Pinelas, Sandra and Chipot, Michel and Dosla, Zuzana},\\ndoi={10.1007/978-1-4614-7333-6_48},\\ntitle={Numerical Methods for Multi-term Fractional Boundary Value Problems},\\nurl={http://dx.doi.org/10.1007/978-1-4614-7333-6_48},\\npublisher={Springer New York},\\npages={535-542},\\nlanguage={English}\\n}\\n" - }, - "work-type": "BOOK_CHAPTER" - } - ] - } - } - } + "path": "/0000-0002-9446-437X/work/35153466", + "title": { + "title": { + "value": "Numerical Methods for Multi-term Fractional Boundary Value Problems" + }, + "subtitle": null, + "translated-title": null + }, + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@incollection{\\nyear={2013},\\nisbn={978-1-4614-7332-9},\\nbooktitle={Differential and Difference Equations with Applications},\\nvolume={47},\\nseries={Springer Proceedings in Mathematics & Statistics},\\neditor={Pinelas, Sandra and Chipot, Michel and Dosla, Zuzana},\\ndoi={10.1007/978-1-4614-7333-6_48},\\ntitle={Numerical Methods for Multi-term Fractional Boundary Value Problems},\\nurl={http://dx.doi.org/10.1007/978-1-4614-7333-6_48},\\npublisher={Springer New York},\\npages={535-542},\\nlanguage={English}\\n}\\n" + }, + "type": "BOOK_CHAPTER" } + """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Ford", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:Chapter . @@ -1516,50 +1013,34 @@ def test_bibtex_editor(self): """))) def test_orcid_editor(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Maria Clotilde" - }, - "family-name": { - "value": "Almeida" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Media and Sports/Media e Desporto" - }, - "subtitle": null - }, - "work-type": "BOOK", - "work-contributors": { - "contributor": [ - { - "contributor-attributes": { - "contributor-sequence": "FIRST", - "contributor-role": "EDITOR" - } - } - ] - } - } - ] - } + "path": "/0000-0001-5014-7658/work/11269935", + "title": { + "title": { + "value": "Media and Sports/Media e Desporto" + }, + "subtitle": null, + "translated-title": null + }, + "type": "BOOK", + "contributors": { + "contributor": [ + { + "contributor-orcid": null, + "credit-name": null, + "contributor-email": null, + "contributor-attributes": { + "contributor-sequence": "FIRST", + "contributor-role": "EDITOR" } - } + } + ] + } } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Almeida", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:Book . @@ -1569,49 +1050,35 @@ def test_orcid_editor(self): """))) def test_external_identifier(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-type": "JOURNAL_ARTICLE", - "work-title": { - "title": { - "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" - }, - "subtitle": null, - "translated-title": null - }, - "work-external-identifiers": { - "work-external-identifier": [ - { - "work-external-identifier-type": "DOI", - "work-external-identifier-id": { - "value": "10.1097/ACM.0b013e31826d726b" - } - } - ], - "scope": null - } - } - ] - } - } - } + "path": "/0000-0001-5109-3700/work/15643384", + "title": { + "title": { + "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "type": "JOURNAL_ARTICLE", + "external-ids": { + "external-id": [ + { + "external-id-type": "doi", + "external-id-value": "10.1097/ACM.0b013e31826d726b", + "external-id-url": null, + "external-id-relationship": "SELF" + }, + { + "external-id-type": "eid", + "external-id-value": "2-s2.0-84869886841", + "external-id-url": null, + "external-id-relationship": "SELF" + } + ] + } } + """) WorksCrosswalk._fetch_crossref_doi = staticmethod(lambda doi: json.loads(""" @@ -1619,7 +1086,7 @@ def test_external_identifier(self): } """)) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -1633,142 +1100,96 @@ def test_external_identifier(self): """))) def test_isbn13(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.1", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Lara" - }, - "family-name": { - "value": "Milesi" - } - } + "path": "/0000-0001-9002-015X/work/13926662", + "title": { + "title": { + "value": "Estrategias de frontera desde la interculturalidad." + }, + "subtitle": { + "value": "El caso del we tripantü mapuche hoy" + }, + "translated-title": null + }, + "journal-title": { + "value": "Actas del XIII Congreso de Antropología de la Federación de Asociaciones de Antropología del Estado Español: Periferias, Fronteras y Diálogos. " + }, + "type": "CONFERENCE_PAPER", + "external-ids": { + "external-id": [ + { + "external-id-type": "isbn", + "external-id-value": "978-84-697-0505-6", + "external-id-url": { + "value": "" }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Estrategias de frontera desde la interculturalidad." - }, - "subtitle": { - "value": "El caso del we tripantü mapuche hoy" - } - }, - "journal-title": { - "value": "Actas del XIII Congreso de Antropología de la Federación de Asociaciones de Antropología del Estado Español: Periferias, Fronteras y Diálogos. " - }, - "work-type": "CONFERENCE_PAPER", - "work-external-identifiers": { - "work-external-identifier": [ - { - "work-external-identifier-type": "ISBN", - "work-external-identifier-id": { - "value": "978-84-697-0505-6" - } - } - ] - } - } - ] - } - } - } + "external-id-relationship": "PART_OF" + } + ] + } } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Milesi", self.graph) self.assertTrue(list(self.graph[: ns.BIBO["isbn13"]: Literal("978-84-697-0505-6")])) def test_isbn10(self): - orcid_profile = json.loads(""" -{ - "message-version": "1.1", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Lara" + work_profile = json.loads(""" + { + "path": "/0000-0001-9002-015X/work/13926662", + "title": { + "title": { + "value": "Estrategias de frontera desde la interculturalidad." + }, + "subtitle": { + "value": "El caso del we tripantü mapuche hoy" + }, + "translated-title": null + }, + "journal-title": { + "value": "Actas del XIII Congreso de Antropología de la Federación de Asociaciones de Antropología del Estado Español: Periferias, Fronteras y Diálogos. " + }, + "type": "CONFERENCE_PAPER", + "external-ids": { + "external-id": [ + { + "external-id-type": "isbn", + "external-id-value": "978-84-697-05", + "external-id-url": { + "value": "" }, - "family-name": { - "value": "Milesi" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Estrategias de frontera desde la interculturalidad." - }, - "subtitle": { - "value": "El caso del we tripantü mapuche hoy" - } - }, - "journal-title": { - "value": "Actas del XIII Congreso de Antropología de la Federación de Asociaciones de Antropología del Estado Español: Periferias, Fronteras y Diálogos. " - }, - "work-type": "CONFERENCE_PAPER", - "work-external-identifiers": { - "work-external-identifier": [ - { - "work-external-identifier-type": "ISBN", - "work-external-identifier-id": { - "value": "978-84-697-05" - } - } - ] - } - } - ] - } + "external-id-relationship": "PART_OF" + } + ] + } } - } -} - """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + """) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Milesi", self.graph) self.assertTrue(list(self.graph[: ns.BIBO["isbn10"]: Literal("978-84-697-05")])) def test_bibtex_doi(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Heidi" - }, - "family-name": { - "value": "Hardt" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "BOOK", - "work-citation" : { - "work-citation-type" : "BIBTEX", - "citation": "@book{Hardt_2014,doi = {10.1093/acprof:oso/9780199337118.001.0001},url = {http://dx.doi.org/10.1093/acprof:oso/9780199337118.001.0001},year = 2014,month = {Feb},publisher = {Oxford University Press},author = {Heidi Hardt},title = {Time to React}}" - } - } - ] - } - } - } + "path": "/0000-0001-5014-4975/work/13266925", + "title": { + "title": { + "value": "Time to React" + }, + "subtitle": { + "value": "The Efficiency of International Organizations in Crisis Response" + }, + "translated-title": null + }, + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@book{Hardt_2014,doi = {10.1093/acprof:oso/9780199337118.001.0001},url = {http://dx.doi.org/10.1093/acprof:oso/9780199337118.001.0001},year = 2014,month = {Feb},publisher = {Oxford University Press},author = {Heidi Hardt},title = {Time to React}}" + }, + "type": "BOOK" } """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Hardt", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:Book . @@ -1782,84 +1203,47 @@ def test_bibtex_doi(self): """))) def test_bibtex_isbn(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "N.J." - }, - "family-name": { - "value": "Ford" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Numerical methods for multi-term fractional boundary value problems, Differential and Difference Equations with Applications" - }, - "subtitle": null - }, - "work-citation": { - "work-citation-type": "BIBTEX", - "citation": "@incollection{\\nyear={2013},\\nisbn={978-1-4614-7332-9},\\nbooktitle={Differential and Difference Equations with Applications},\\nvolume={47},\\nseries={Springer Proceedings in Mathematics & Statistics},\\neditor={Pinelas, Sandra and Chipot, Michel and Dosla, Zuzana},\\ndoi={10.1007/978-1-4614-7333-6_48},\\ntitle={Numerical Methods for Multi-term Fractional Boundary Value Problems},\\nurl={http://dx.doi.org/10.1007/978-1-4614-7333-6_48},\\npublisher={Springer New York},\\npages={535-542},\\nlanguage={English}\\n}\\n" - }, - "work-type": "BOOK_CHAPTER" - } - ] - } - } - } + "title": { + "title": { + "value": "Numerical methods for multi-term fractional boundary value problems, Differential and Difference Equations with Applications" + }, + "subtitle": null, + "translated-title": null + }, + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@incollection{\\nyear={2013},\\nisbn={978-1-4614-7332-9},\\nbooktitle={Differential and Difference Equations with Applications},\\nvolume={47},\\nseries={Springer Proceedings in Mathematics & Statistics},\\neditor={Pinelas, Sandra and Chipot, Michel and Dosla, Zuzana},\\ndoi={10.1007/978-1-4614-7333-6_48},\\ntitle={Numerical Methods for Multi-term Fractional Boundary Value Problems},\\nurl={http://dx.doi.org/10.1007/978-1-4614-7333-6_48},\\npublisher={Springer New York},\\npages={535-542},\\nlanguage={English}\\n}\\n" + }, + "type": "BOOK_CHAPTER" } + """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Ford", self.graph) self.assertTrue(list(self.graph[: ns.BIBO["isbn13"]: Literal("978-1-4614-7332-9")])) def test_orcid_url(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.1", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Edwin" - }, - "family-name": { - "value": "Seroussi" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Popular Music and Israeli National Culture" - }, - "subtitle": null - }, - "work-type": "BOOK", - "url": { - "value": "http://www.ucpress.edu/book.php?isbn=9780520236547" - } - } - ] - } - } - } + "path": "/0000-0001-5006-1520/work/13637092", + "title": { + "title": { + "value": "Popular Music and Israeli National Culture" + }, + "subtitle": null, + "translated-title": null + }, + "type": "BOOK", + "url": { + "value": "http://www.ucpress.edu/book.php?isbn=9780520236547" + } } + """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Seroussi", self.graph) self.assertTrue(list(self.graph[: ns.VCARD["url"]: ])) self.assertTrue(bool(self.graph.query(""" ask where { @@ -1872,82 +1256,51 @@ def test_orcid_url(self): } """))) - - def test_ignore_orcid_url(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Heidi" - }, - "family-name": { - "value": "Hardt" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "BOOK", - "work-title": { - "title": { - "value": "Time to React" - }, - "subtitle": null, - "translated-title": null - }, - "url": { - "value": "http://dx.doi.org/10.1093/acprof:oso/9780199337118.001.0001" - } - } - ] - } - } - } + "path": "/0000-0001-5014-4975/work/13266925", + "title": { + "title": { + "value": "Time to React" + }, + "subtitle": { + "value": "The Efficiency of International Organizations in Crisis Response" + }, + "translated-title": null + }, + "type": "BOOK", + "url": { + "value": "http://dx.doi.org/10.1093/acprof:oso/9780199337118.001.0001" + } } - """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + + """) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Hardt", self.graph) self.assertFalse(list(self.graph[: ns.VCARD["url"]: ])) def test_bibtex_url(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Heidi" - }, - "family-name": { - "value": "Hardt" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "BOOK", - "work-citation" : { - "work-citation-type" : "BIBTEX", - "citation": "@book{Hardt_2014,url = {http://www.ucpress.edu/book.php?isbn=9780520236547},year = 2014,month = {Feb},publisher = {Oxford University Press},author = {Heidi Hardt},title = {Time to React}}" - } - } - ] - } - } - } + "path": "/0000-0001-5014-4975/work/13266925", + "title": { + "title": { + "value": "Time to React" + }, + "subtitle": { + "value": "The Efficiency of International Organizations in Crisis Response" + }, + "translated-title": null + }, + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@book{Hardt_2014,doi = {10.1093/acprof:oso/9780199337118.001.0001},url = {http://www.ucpress.edu/book.php?isbn=9780520236547},year = 2014,month = {Feb},publisher = {Oxford University Press},author = {Heidi Hardt},title = {Time to React}}" + }, + "type": "BOOK" } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Hardt", self.graph) self.assertTrue(list(self.graph[: ns.VCARD["url"]:])) self.assertTrue(bool(self.graph.query(""" ask where { @@ -1961,80 +1314,50 @@ def test_bibtex_url(self): """))) def test_ignore_bibtex_url(self): - orcid_profile = json.loads(""" -{ - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Heidi" - }, - "family-name": { - "value": "Hardt" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-type": "BOOK", - "work-citation" : { - "work-citation-type" : "BIBTEX", - "citation": "@book{Hardt_2014,url = {http://dx.doi.org/10.1093/acprof:oso/9780199337118.001.0001},year = 2014,month = {Feb},publisher = {Oxford University Press},author = {Heidi Hardt},title = {Time to React}}" - } - } - ] - } + work_profile = json.loads(""" + { + "path": "/0000-0001-5014-4975/work/13266925", + "title": { + "title": { + "value": "Time to React" + }, + "subtitle": { + "value": "The Efficiency of International Organizations in Crisis Response" + }, + "translated-title": null + }, + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@book{Hardt_2014,url = {http://dx.doi.org/10.1093/acprof:oso/9780199337118.001.0001},year = 2014,month = {Feb},publisher = {Oxford University Press},author = {Heidi Hardt},title = {Time to React}}" + }, + "type": "BOOK" } - } -} - """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + """) + + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Hardt", self.graph) self.assertFalse(list(self.graph[: ns.VCARD["url"]:])) def test_bibtex_journal(self): - orcid_profile = json.loads(""" -{ - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Not the title" - }, - "subtitle": null, - "translated-title": null - }, - "work-type": "JOURNAL_ARTICLE", - "work-citation" : { - "work-citation-type" : "BIBTEX", - "citation" : "@article { haak2012,title = {Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?},journal = {Academic Medicine},issn = {1040-2446},year = {2012},volume = {87},number = {11},pages = {1516-1524},author = {Ginther, D.K. and Haak, L.L. and Schaffer, W.T. and Kington, R.}}" - } - } - ] - } + work_profile = json.loads(""" + { + "path": "/0000-0001-5109-3700/work/15643384", + "title": { + "title": { + "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@article { haak2012,title = {Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?},journal = {Academic Medicine},issn = {1040-2446},year = {2012},volume = {87},number = {11},pages = {1516-1524},author = {Ginther, D.K. and Haak, L.L. and Schaffer, W.T. and Kington, R.}}" + }, + "type": "JOURNAL_ARTICLE" } - } -} - """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + """) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -2046,63 +1369,45 @@ def test_bibtex_journal(self): """))) def test_crossref_journal(self): - orcid_profile = json.loads(""" -{ - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Not the title" - }, - "subtitle": null, - "translated-title": null - }, - "work-type": "JOURNAL_ARTICLE", - "work-citation" : { - "work-citation-type" : "BIBTEX", - "citation" : "@article { haak2012,title = {Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?},journal = {Not Academic Medicine},issn = {Not 1040-2446},year = {2012},volume = {87},number = {11},pages = {1516-1524},author = {Ginther, D.K. and Haak, L.L. and Schaffer, W.T. and Kington, R.}}" - }, - "work-external-identifiers": { - "work-external-identifier": [ - { - "work-external-identifier-type": "DOI", - "work-external-identifier-id": { - "value": "10.1097/ACM.0b013e31826d726b" - } - } - ], - "scope": null - } - } - ] - } + work_profile = json.loads(""" + { + "path": "/0000-0001-5109-3700/work/15643384", + "title": { + "title": { + "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "type": "JOURNAL_ARTICLE", + "external-ids": { + "external-id": [ + { + "external-id-type": "doi", + "external-id-value": "10.1097/ACM.0b013e31826d726b", + "external-id-url": null, + "external-id-relationship": "SELF" + }, + { + "external-id-type": "eid", + "external-id-value": "2-s2.0-84869886841", + "external-id-url": null, + "external-id-relationship": "SELF" + } + ] + } } - } -} - """) + + """) WorksCrosswalk._fetch_crossref_doi = staticmethod(lambda doi: json.loads(""" -{ - "container-title": ["Academic Medicine", "Acad. Med."], - "ISSN": ["1040-2446", "1938-808X"] -} - """)) + { + "container-title": ["Academic Medicine", "Acad. Med."], + "ISSN": ["1040-2446", "1938-808X"] + } + """)) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -2115,44 +1420,25 @@ def test_crossref_journal(self): """))) def test_orcid_journal(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.2", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Laurel" - }, - "family-name": { - "value": "Haak" - } - } - }, - "orcid-activities" : { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Not the title" - }, - "subtitle": null, - "translated-title": null - }, - "work-type": "JOURNAL_ARTICLE", - "journal-title": { - "value": "Academic Medicine" - } - } - ] - } - } - } + "path": "/0000-0001-5109-3700/work/15643384", + "title": { + "title": { + "value": "Are race, ethnicity, and medical school affiliation associated with NIH R01 type 1 award probability for physician investigators?" + }, + "subtitle": null, + "translated-title": null + }, + "journal-title": { + "value": "Academic Medicine" + }, + "type": "JOURNAL_ARTICLE" } + """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Haak", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:AcademicArticle . @@ -2163,85 +1449,71 @@ def test_orcid_journal(self): """))) def test_journal_issue(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.1", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Andrew" - }, - "family-name": { - "value": "Carlin" - } - } + "path": "/0000-0001-5138-9384/work/10341578", + "title": { + "title": { + "value": "Egon Bittner" + }, + "subtitle": { + "value": "Phenomenology in Action" + }, + "translated-title": null + }, + "journal-title": { + "value": "Ethnographic Studies" + }, + "short-description": "Special Memorial Issue", + "type": "JOURNAL_ISSUE", + "publication-date": { + "year": { + "value": "2013" + }, + "month": { + "value": "07" + }, + "day": { + "value": "01" + }, + "media-type": null + }, + "external-ids": { + "external-id": [ + { + "external-id-type": "issn", + "external-id-value": "1366-4964", + "external-id-url": null, + "external-id-relationship": "SELF" + } + ] + }, + "url": { + "value": "http://www.zhbluzern.ch/index.php?id=2583" + }, + "contributors": { + "contributor": [ + { + "contributor-orcid": { + "uri": null, + "path": null, + "host": null }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Egon Bittner" - }, - "subtitle": { - "value": "Phenomenology in Action" - } - }, - "journal-title": { - "value": "Ethnographic Studies" - }, - "short-description": "Special Memorial Issue", - "work-type": "JOURNAL_ISSUE", - "publication-date": { - "year": { - "value": "2013" - }, - "month": { - "value": "07" - }, - "day": { - "value": "01" - } - }, - "work-external-identifiers": { - "work-external-identifier": [ - { - "work-external-identifier-type": "ISSN", - "work-external-identifier-id": { - "value": "1366-4964" - } - } - ], - "scope": null - }, - "url": { - "value": "http://www.zhbluzern.ch/index.php?id=2583" - }, - "work-contributors": { - "contributor": [ - { - "credit-name": { - "value": "Andrew Carlin", - "visibility": "PUBLIC" - }, - "contributor-attributes": { - "contributor-sequence": "FIRST", - "contributor-role": "EDITOR" - } - } - ] - } - } - ] - } + "credit-name": { + "value": "Andrew Carlin" + }, + "contributor-email": null, + "contributor-attributes": { + "contributor-sequence": "FIRST", + "contributor-role": "EDITOR" } - } + } + ] + } } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Carlin", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:Issue . @@ -2258,45 +1530,27 @@ def test_journal_issue(self): } """))) - def test_journal_issue(self): - orcid_profile = json.loads(""" + def test_magazine(self): + work_profile = json.loads(""" { - "message-version": "1.1", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Victor" - }, - "family-name": { - "value": "Peinado" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "put-code": "13302713", - "work-title": { - "title": { - "value": "Software as a Communication Platform" - }, - "subtitle": null - }, - "journal-title": { - "value": "Kunststoffe international 2009/11" - }, - "work-type": "MAGAZINE_ARTICLE" - } - ] - } - } - } + "path": "/0000-0001-5019-3929/work/13302713", + "title": { + "title": { + "value": "Software as a Communication Platform" + }, + "subtitle": { + "value": "" + }, + "translated-title": null + }, + "journal-title": { + "value": "Kunststoffe international 2009/11" + }, + "type": "MAGAZINE_ARTICLE" } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Peinado", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:Article . @@ -2307,47 +1561,29 @@ def test_journal_issue(self): """))) def test_translation_with_bibtex(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.1", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "andrea" - }, - "family-name": { - "value": "sciandra" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Ambiguità nelle risposte al Position Generator" - }, - "subtitle": null - }, - "journal-title": { - "value": "SOCIOLOGIA E POLITICHE SOCIALI" - }, - "work-citation": { - "work-citation-type": "BIBTEX", - "citation": "@article{sciandra2012, author= {SCIANDRA A.}, doi= {10.3280/SP2012-002006}, issn= {1591-2027}, journal= {SOCIOLOGIA E POLITICHE SOCIALI}, pages= {113--141}, title= {Ambiguita nelle risposte al Position Generator}, url= {http://dx.medra.org/10.3280/SP2012-002006}, volume= {15}, year= {2012}}" - }, - "work-type": "TRANSLATION" - } - ] - } - } - } + + "path": "/0000-0001-5621-5463/work/14402996", + "title": { + "title": { + "value": "Ambiguità nelle risposte al Position Generator" + }, + "subtitle": null, + "translated-title": null + }, + "journal-title": { + "value": "SOCIOLOGIA E POLITICHE SOCIALI" + }, + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@article{sciandra2012, author= {SCIANDRA A.}, doi= {10.3280/SP2012-002006}, issn= {1591-2027}, journal= {SOCIOLOGIA E POLITICHE SOCIALI}, pages= {113--141}, title= {Ambiguita nelle risposte al Position Generator}, url= {http://dx.medra.org/10.3280/SP2012-002006}, volume= {15}, year= {2012}}" + }, + "type": "TRANSLATION" } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Sciandra", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:Article . @@ -2361,54 +1597,40 @@ def test_translation_with_bibtex(self): """))) def test_translation(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.1", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Manuel" - }, - "family-name": { - "value": "Alexandre Júnior" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Aristóteles, Retórica, Obras Completas de Aristóteles" - }, - "subtitle": { - "value": "com a colaboração de Paulo Farmhouse Alberto e Abel Nascimento Pena." - } - }, - "journal-title": { - "value": "São Paulo, WMF Martins Fontes, 2012." - }, - "work-type": "TRANSLATION", - "work-contributors": { - "contributor": [ - { - "contributor-attributes": { - "contributor-role": "CHAIR_OR_TRANSLATOR" - } - } - ] - } - } - ] - } + "path": "/0000-0001-5785-6342/work/11161159", + "title": { + "title": { + "value": "Aristóteles, Retórica, Obras Completas de Aristóteles" + }, + "subtitle": { + "value": "com a colaboração de Paulo Farmhouse Alberto e Abel Nascimento Pena." + }, + "translated-title": null + }, + "journal-title": { + "value": "São Paulo, WMF Martins Fontes, 2012." + }, + "type": "TRANSLATION", + "contributors": { + "contributor": [ + { + "contributor-orcid": null, + "credit-name": null, + "contributor-email": null, + "contributor-attributes": { + "contributor-sequence": null, + "contributor-role": "CHAIR_OR_TRANSLATOR" } - } + } + ] + } } + """) - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Manuel", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:Document . @@ -2422,44 +1644,24 @@ def test_translation(self): """))) def test_conference_paper(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.1", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Alexander" - }, - "family-name": { - "value": "Šatka" - } - } - }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "Noise in the InAlN/GaN HEMT transistors" - }, - "subtitle": null - }, - "work-citation": { - "work-citation-type": "BIBTEX", - "citation": "@article { atka2010,title = {Noise in the InAlN/GaN HEMT transistors},journal = {Conference Proceedings - The 8th International Conference on Advanced Semiconductor Devices and Microsystems, ASDAM 2010},year = {2010},pages = {53-56},author = {Rendek, K. and Šatka, A. and Kováč, J. and Donoval, D.}}" - }, - "work-type": "CONFERENCE_PAPER" - } - ] - } - } - } -} - """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + "path": "/0000-0001-5004-4536/work/14890522", + "title": { + "title": { + "value": "Noise in the InAlN/GaN HEMT transistors" + }, + "subtitle": null, + "translated-title": null + }, + "citation": { + "citation-type": "BIBTEX", + "citation-value": "@article { atka2010,title = {Noise in the InAlN/GaN HEMT transistors},journal = {Conference Proceedings - The 8th International Conference on Advanced Semiconductor Devices and Microsystems, ASDAM 2010},year = {2010},pages = {53-56},author = {Rendek, K. and Šatka, A. and Kováč, J. and Donoval, D.}}" + }, + "type": "CONFERENCE_PAPER" +} +""") + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Sitka", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a vivo:ConferencePaper . @@ -2471,62 +1673,49 @@ def test_conference_paper(self): """))) def test_patent(self): - orcid_profile = json.loads(""" + work_profile = json.loads(""" { - "message-version": "1.1", - "orcid-profile": { - "orcid-bio": { - "personal-details": { - "given-names": { - "value": "Carlos C." - }, - "family-name": { - "value": "Romão" - } - } + "path": "/0000-0001-5061-3743/work/11259988", + "title": { + "title": { + "value": "TREATMENT OF INFECTIONS BY CARBON MONOXIDE" + }, + "subtitle": null, + "translated-title": null + }, + "type": "PATENT", + "external-ids": { + "external-id": [ + { + "external-id-type": "other-id", + "external-id-value": "US2010196516 (A1)", + "external-id-url": { + "value": "" }, - "orcid-activities": { - "orcid-works": { - "orcid-work": [ - { - "work-title": { - "title": { - "value": "TREATMENT OF INFECTIONS BY CARBON MONOXIDE" - }, - "subtitle": null - }, - "work-type": "PATENT", - "work-external-identifiers": { - "work-external-identifier": [ - { - "work-external-identifier-type": "OTHER_ID", - "work-external-identifier-id": { - "value": "US2010196516 (A1)" - } - } - ] - }, - "url": { - "value": "http://worldwide.espacenet.com/publicationDetails/biblio?II=17&ND=3&adjacent=true&locale=en_EP&FT=D&date=20100805&CC=US&NR=2010196516A1&KC=A1" - }, - "work-contributors": { - "contributor": [ - { - "contributor-attributes": { - "contributor-role": "CO_INVENTOR" - } - } - ] - } - } - ] - } + "external-id-relationship": "SELF" + } + ] + }, + "url": { + "value": "http://worldwide.espacenet.com/publicationDetails/biblio?II=5&ND=3&adjacent=true&locale=en_EP&FT=D&date=20100805&CC=US&NR=2010196516A1&KC=A1" + }, + "contributors": { + "contributor": [ + { + "contributor-orcid": null, + "credit-name": null, + "contributor-email": null, + "contributor-attributes": { + "contributor-sequence": null, + "contributor-role": "CO_INVENTOR" } - } + } + ] + } } + """) - - self.crosswalker.crosswalk(orcid_profile, self.person_uri, self.graph) + self.crosswalker.crosswalk_work(work_profile, self.person_uri, "Romão", self.graph) self.assertTrue(bool(self.graph.query(""" ask where { ?doc a bibo:Patent . diff --git a/tests/fixtures/fundings/no.yaml b/tests/fixtures/fundings/no.yaml deleted file mode 100644 index 243c53f..0000000 --- a/tests/fixtures/fundings/no.yaml +++ /dev/null @@ -1,424 +0,0 @@ -interactions: -- request: - body: null - headers: - Accept: [application/orcid+json] - Accept-Encoding: ['gzip, deflate, compress'] - User-Agent: [python-requests/2.2.1 CPython/2.7.6 Linux/3.13.0-37-generic] - method: GET - uri: http://pub.orcid.org/v1.2/0000-0003-1527-0030/orcid-profile - response: - body: {string: !!python/unicode "{\n \"message-version\" : \"1.2\",\n \"orcid-profile\" - : {\n \"orcid\" : null,\n \"orcid-id\" : null,\n \"orcid-identifier\" - : {\n \"value\" : null,\n \"uri\" : \"http://orcid.org/0000-0003-1527-0030\",\n - \ \"path\" : \"0000-0003-1527-0030\",\n \"host\" : \"orcid.org\"\n - \ },\n \"orcid-deprecated\" : null,\n \"orcid-preferences\" : {\n - \ \"locale\" : \"EN\"\n },\n \"orcid-history\" : {\n \"creation-method\" - : \"DIRECT\",\n \"completion-date\" : null,\n \"submission-date\" - : {\n \"value\" : 1424366272062\n },\n \"last-modified-date\" - : {\n \"value\" : 1432736260241\n },\n \"claimed\" : {\n - \ \"value\" : true\n },\n \"source\" : null,\n \"deactivation-date\" - : null,\n \"verified-email\" : {\n \"value\" : true\n },\n - \ \"verified-primary-email\" : {\n \"value\" : true\n },\n - \ \"visibility\" : null\n },\n \"orcid-bio\" : {\n \"personal-details\" - : {\n \"given-names\" : {\n \"value\" : \"Justin\"\n },\n - \ \"family-name\" : {\n \"value\" : \"Littman\"\n },\n - \ \"credit-name\" : null,\n \"other-names\" : null\n },\n - \ \"biography\" : null,\n \"researcher-urls\" : {\n \"researcher-url\" - : [ {\n \"url-name\" : {\n \"value\" : \"Github\"\n },\n - \ \"url\" : {\n \"value\" : \"https://github.com/justinlittman\"\n - \ }\n }, {\n \"url-name\" : {\n \"value\" - : \"Twitter\"\n },\n \"url\" : {\n \"value\" - : \"https://twitter.com/justin_littman\"\n }\n }, {\n \"url-name\" - : {\n \"value\" : \"LinkedIn\"\n },\n \"url\" - : {\n \"value\" : \"https://www.linkedin.com/pub/justin-littman/a7/aa3/11a\"\n - \ }\n } ],\n \"visibility\" : \"PUBLIC\"\n },\n - \ \"contact-details\" : null,\n \"keywords\" : {\n \"keyword\" - : [ {\n \"value\" : \"\"\n } ],\n \"visibility\" : - \"PUBLIC\"\n },\n \"external-identifiers\" : {\n \"external-identifier\" - : [ {\n \"orcid\" : null,\n \"external-id-orcid\" : null,\n - \ \"external-id-common-name\" : {\n \"value\" : \"Scopus - Author ID\"\n },\n \"external-id-reference\" : {\n \"value\" - : \"55926744500\"\n },\n \"external-id-url\" : {\n \"value\" - : \"http://www.scopus.com/inward/authorDetails.url?authorID=55926744500&partnerID=MN8TOARS\"\n - \ },\n \"external-id-source\" : null,\n \"source\" - : {\n \"source-orcid\" : {\n \"value\" : null,\n \"uri\" - : \"http://orcid.org/0000-0002-5982-8983\",\n \"path\" : \"0000-0002-5982-8983\",\n - \ \"host\" : \"orcid.org\"\n },\n \"source-client-id\" - : null,\n \"source-name\" : null,\n \"source-date\" - : null\n }\n } ],\n \"visibility\" : \"PUBLIC\"\n },\n - \ \"delegation\" : null,\n \"applications\" : null,\n \"scope\" - : null\n },\n \"orcid-activities\" : {\n \"affiliations\" : {\n - \ \"affiliation\" : [ {\n \"type\" : \"EMPLOYMENT\",\n \"department-name\" - : \"Scholarly Technology Group, Gelman Library\",\n \"role-title\" - : \"Software Developer / Librarian\",\n \"start-date\" : {\n \"year\" - : {\n \"value\" : \"2014\"\n },\n \"month\" - : null,\n \"day\" : null\n },\n \"end-date\" - : null,\n \"organization\" : {\n \"name\" : \"George Washington - University\",\n \"address\" : {\n \"city\" : \"Washington\",\n - \ \"region\" : \"DC\",\n \"country\" : \"US\"\n },\n - \ \"disambiguated-organization\" : {\n \"disambiguated-organization-identifier\" - : \"8367\",\n \"disambiguation-source\" : \"RINGGOLD\"\n }\n - \ },\n \"source\" : {\n \"source-orcid\" : {\n - \ \"value\" : null,\n \"uri\" : \"http://orcid.org/0000-0003-1527-0030\",\n - \ \"path\" : \"0000-0003-1527-0030\",\n \"host\" - : \"orcid.org\"\n },\n \"source-client-id\" : null,\n - \ \"source-name\" : {\n \"value\" : \"Justin Littman\"\n - \ },\n \"source-date\" : {\n \"value\" : - 1424367082233\n }\n },\n \"created-date\" : {\n - \ \"value\" : 1424367082233\n },\n \"last-modified-date\" - : {\n \"value\" : 1424367765508\n },\n \"visibility\" - : \"PUBLIC\",\n \"put-code\" : \"742819\"\n }, {\n \"type\" - : \"EMPLOYMENT\",\n \"department-name\" : \"Repository Development - Center, Office of Strategic Initiatives\",\n \"role-title\" : \"Software - Developer\",\n \"start-date\" : {\n \"year\" : {\n \"value\" - : \"2003\"\n },\n \"month\" : null,\n \"day\" - : null\n },\n \"end-date\" : {\n \"year\" : {\n - \ \"value\" : \"2014\"\n },\n \"month\" - : null,\n \"day\" : null\n },\n \"organization\" - : {\n \"name\" : \"Library of Congress\",\n \"address\" - : {\n \"city\" : \"Washington\",\n \"region\" : - \"DC\",\n \"country\" : \"US\"\n },\n \"disambiguated-organization\" - : {\n \"disambiguated-organization-identifier\" : \"8386\",\n - \ \"disambiguation-source\" : \"RINGGOLD\"\n }\n },\n - \ \"source\" : {\n \"source-orcid\" : {\n \"value\" - : null,\n \"uri\" : \"http://orcid.org/0000-0003-1527-0030\",\n - \ \"path\" : \"0000-0003-1527-0030\",\n \"host\" - : \"orcid.org\"\n },\n \"source-client-id\" : null,\n - \ \"source-name\" : {\n \"value\" : \"Justin Littman\"\n - \ },\n \"source-date\" : {\n \"value\" : - 1424367025562\n }\n },\n \"created-date\" : {\n - \ \"value\" : 1424367025562\n },\n \"last-modified-date\" - : {\n \"value\" : 1424367787455\n },\n \"visibility\" - : \"PUBLIC\",\n \"put-code\" : \"742815\"\n }, {\n \"type\" - : \"EDUCATION\",\n \"department-name\" : null,\n \"role-title\" - : \"M.L.I.S.\",\n \"start-date\" : null,\n \"end-date\" - : {\n \"year\" : {\n \"value\" : \"2002\"\n },\n - \ \"month\" : null,\n \"day\" : null\n },\n - \ \"organization\" : {\n \"name\" : \"University of Denver\",\n - \ \"address\" : {\n \"city\" : \"Denver\",\n \"region\" - : \"CO\",\n \"country\" : \"US\"\n },\n \"disambiguated-organization\" - : {\n \"disambiguated-organization-identifier\" : \"2927\",\n - \ \"disambiguation-source\" : \"RINGGOLD\"\n }\n },\n - \ \"source\" : {\n \"source-orcid\" : {\n \"value\" - : null,\n \"uri\" : \"http://orcid.org/0000-0003-1527-0030\",\n - \ \"path\" : \"0000-0003-1527-0030\",\n \"host\" - : \"orcid.org\"\n },\n \"source-client-id\" : null,\n - \ \"source-name\" : {\n \"value\" : \"Justin Littman\"\n - \ },\n \"source-date\" : {\n \"value\" : - 1424366945628\n }\n },\n \"created-date\" : {\n - \ \"value\" : 1424366945628\n },\n \"last-modified-date\" - : {\n \"value\" : 1424366945628\n },\n \"visibility\" - : \"PUBLIC\",\n \"put-code\" : \"742812\"\n }, {\n \"type\" - : \"EDUCATION\",\n \"department-name\" : null,\n \"role-title\" - : \"B.A.\",\n \"start-date\" : {\n \"year\" : {\n \"value\" - : \"1991\"\n },\n \"month\" : null,\n \"day\" - : null\n },\n \"end-date\" : {\n \"year\" : {\n - \ \"value\" : \"1995\"\n },\n \"month\" - : null,\n \"day\" : null\n },\n \"organization\" - : {\n \"name\" : \"Amherst College\",\n \"address\" - : {\n \"city\" : \"Amherst\",\n \"region\" : \"MA\",\n - \ \"country\" : \"US\"\n },\n \"disambiguated-organization\" - : {\n \"disambiguated-organization-identifier\" : \"1180\",\n - \ \"disambiguation-source\" : \"RINGGOLD\"\n }\n },\n - \ \"source\" : {\n \"source-orcid\" : {\n \"value\" - : null,\n \"uri\" : \"http://orcid.org/0000-0003-1527-0030\",\n - \ \"path\" : \"0000-0003-1527-0030\",\n \"host\" - : \"orcid.org\"\n },\n \"source-client-id\" : null,\n - \ \"source-name\" : {\n \"value\" : \"Justin Littman\"\n - \ },\n \"source-date\" : {\n \"value\" : - 1424366833252\n }\n },\n \"created-date\" : {\n - \ \"value\" : 1424366833252\n },\n \"last-modified-date\" - : {\n \"value\" : 1424366833252\n },\n \"visibility\" - : \"PUBLIC\",\n \"put-code\" : \"742807\"\n } ]\n },\n - \ \"orcid-works\" : {\n \"orcid-work\" : [ {\n \"put-code\" - : \"15473532\",\n \"work-title\" : {\n \"title\" : {\n - \ \"value\" : \"A Set of Transfer-Related Services\"\n },\n - \ \"subtitle\" : null,\n \"translated-title\" : null\n - \ },\n \"journal-title\" : {\n \"value\" : \"D-Lib - Magazine\"\n },\n \"short-description\" : null,\n \"work-citation\" - : {\n \"work-citation-type\" : \"BIBTEX\",\n \"citation\" - : \"@article{Littman_2009,doi = {10.1045/january2009-littman},url = {http://dx.doi.org/10.1045/january2009-littman},year - = 2009,month = {jan},publisher = {{CNRI} Acct},volume = {15},number = {1/2},author - 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[application/json;charset=UTF-8] + date: ['Wed, 13 Sep 2017 16:58:01 GMT'] + expires: ['0'] + pragma: [no-cache] + server: [nginx/1.4.6 (Ubuntu)] + set-cookie: [X-Mapping-fjhppofk=BB32ADE26669E4E542AAA075A6CC205A; path=/] + x-content-type-options: [nosniff] + x-frame-options: [DENY] + x-xss-protection: [1; mode=block] status: {code: 200, message: OK} version: 1 diff --git a/tests/test_loader.py b/tests/test_loader.py index d924bce..84dafc0 100644 --- a/tests/test_loader.py +++ b/tests/test_loader.py @@ -27,19 +27,19 @@ def test_persist(self): self.assertFalse(os.path.exists(self.db_filepath)) with Store(self.data_path) as store: self.assertEqual(self.db_filepath, store.db_filepath) - #Created + # Created self.assertTrue(os.path.exists(self.db_filepath)) - #Add + # Add store.add("0000-0003-1527-0030") - #Still exists after close + # Still exists after close self.assertTrue(os.path.exists(self.db_filepath)) with Store(self.data_path) as store: self.assertTrue("0000-0003-1527-0030" in store) def test_contains(self): with Store(self.data_path) as store: - #Add + # Add store.add("0000-0003-1527-0030") self.assertTrue("0000-0003-1527-0030" in store) self.assertFalse("X000-0003-1527-0030" in store) @@ -49,7 +49,7 @@ def test_contains(self): def test_add_item(self): with Store(self.data_path) as store: - #Insert + # Insert store.add("0000-0003-1527-0030") (orcid_id, active, last_update, person_uri, person_id, person_class, confirmed) = \ store["0000-0003-1527-0030"] @@ -59,7 +59,7 @@ def test_add_item(self): self.assertIsNone(person_class) self.assertIsNone(last_update) self.assertFalse(confirmed) - #Update + # Update store.add("0000-0003-1527-0030", person_uri="http://me", person_id="me", person_class="Librarian", confirmed=True) (orcid_id, active, last_update, person_uri, person_id, person_class, confirmed) = \ @@ -73,7 +73,7 @@ def test_add_item(self): def test_add_deleted_item(self): with Store(self.data_path) as store: - #Insert + # Insert store.add("0000-0003-1527-0030") (orcid_id, active, last_update, person_uri, person_id, person_class, confirmed) = \ store["0000-0003-1527-0030"] @@ -83,9 +83,9 @@ def test_add_deleted_item(self): self.assertIsNone(person_class) self.assertIsNone(last_update) self.assertFalse(confirmed) - #Delete + # Delete del store["0000-0003-1527-0030"] - #Add again + # Add again store.add("0000-0003-1527-0030") (orcid_id, active, last_update, person_uri, person_id, person_class, confirmed) = \ store["0000-0003-1527-0030"] @@ -118,9 +118,9 @@ def test_get_least_recent(self): store.add("0000-0003-1527-0030") store.add("0000-0003-1527-0031") store.add("0000-0003-1527-0032") - #Deactivate one to make sure not returned. + # Deactivate one to make sure not returned. del store["0000-0003-1527-0032"] - #Touch first + # Touch first time.sleep(1) t = datetime.datetime.utcnow() time.sleep(1) @@ -130,12 +130,12 @@ def test_get_least_recent(self): self.assertEqual("0000-0003-1527-0031", results[0][0]) self.assertEqual("0000-0003-1527-0030", results[1][0]) - #With limit + # With limit results = list(store.get_least_recent(limit=1)) self.assertEqual(1, len(results)) self.assertEqual("0000-0003-1527-0031", results[0][0]) - #Before + # Before results = list(store.get_least_recent(before_datetime=t)) self.assertEqual(1, len(results)) self.assertEqual("0000-0003-1527-0031", results[0][0]) @@ -177,27 +177,31 @@ def test_load_single(self, mock_sparql_delete, mock_sparql_insert): "http://vivo.mydomain.edu/sparql", "vivo@mydomain.edu", "password") - self.assertEqual(232, len(add_graph1)) + self.assertEqual(319, len(add_graph1)) self.assertEqual(0, len(delete_graph1)) self.assertEqual(to_isomorphic(graph1), to_isomorphic(add_graph1)) with Store(self.data_path) as store: - #Last update now set + # Last update now set (orcid_id, active, last_update, person_uri, person_id, person_class, confirmed) = \ store["0000-0003-1527-0030"] self.assertIsNotNone(last_update) - #Make sure turtle file created + # Make sure turtle file created self.assertTrue(os.path.exists(os.path.join(self.data_path, "0000-0003-1527-0030.ttl"))) - #Now change a fact and run again. Changed fact is provided by vcr recording. - #Changed year of Amherst degree. + # Now change a fact and run again. Changed fact is provided by vcr recording. + # Changed year of Amherst degree. + # Had to rig the Accept-Encoding to create the vcr recording with: + # r = requests.get('https://pub.orcid.org/v2.0/%s' % orcid, + # headers={"Accept": "application/json", "Accept-Encoding": "identity"}) + graph2, add_graph2, delete_graph2 = load_single("0000-0003-1527-0030", None, None, None, self.data_path, "http://vivo.mydomain.edu/sparql", "vivo@mydomain.edu", "password") - self.assertEqual(232, len(graph2)) + self.assertEqual(319, len(graph2)) self.assertEqual(17, len(add_graph2)) self.assertEqual(17, len(delete_graph2))