def test_rdf(self):
pub_uri = D["n123"]
article = Publication()
meta = article.prep(self.meta, pub_uri=pub_uri)
g = article.to_graph(meta)
g.namespace_manager = ns_mgr
# ids
pmid = g.value(subject=pub_uri, predicate=BCITE.pmid)
self.eq(u"23910982", pmid.toPython())
doi = g.value(subject=pub_uri, predicate=BCITE.doi)
self.eq(u"10.1016/j.jpeds.2013.06.032", doi.toPython())
# check venue
rq = """
select ?issn ?vtype
where {
?p bcite:hasVenue ?venue .
?venue bcite:issn ?issn ;
a ?vtype .
}
"""
for row in g.query(rq):
self.eq(u"0022-3476", row.issn.toPython())
self.eq(row.vtype, BCITE.Venue)
date = g.value(subject=pub_uri, predicate=BCITE.date)
dtv = date.toPython()
# Make sure our dates are datetime.date and not datetime.datetime.
assert type(dtv) == datetime.date
assert dtv.year == 2013
assert dtv.month == 12
def test_rdf(self):
pub_uri = D["n123"]
article = Publication()
meta = article.prep(self.meta, pub_uri=pub_uri)
g = article.to_graph(meta)
g.namespace_manager = ns_mgr
# ids
pmid = g.value(subject=pub_uri, predicate=BCITE.pmid)
self.eq(self.pmid, pmid.toPython())
doi = g.value(subject=pub_uri, predicate=BCITE.doi)
self.eq(u"10.1182/blood-2014-05-574871", doi.toPython())
title = g.value(subject=pub_uri, predicate=RDFS.label)
assert title.toPython().startswith(u"Survival trends in Waldenström macroglobulinemia:")
def test_rdf_venue_uri(self):
venue_uri = D["v123"]
article = Publication()
meta = article.prep(self.meta, venue_uri=venue_uri)
g = article.to_graph(meta)
g.namespace_manager = ns_mgr
# check venue
rq = """
select ?venue
where {
?p bcite:hasVenue ?v .
?v rdfs:label ?venue .
}
"""
for row in g.query(rq):
self.eq(u"The Journal of pediatrics", row.venue.toPython())
def test_rdf(self):
pub_uri = D["n123"]
book = Publication()
meta = book.prep(self.meta, pub_uri=pub_uri)
g = book.to_graph(meta)
g.namespace_manager = ns_mgr
# ids
pmid = g.value(subject=pub_uri, predicate=BCITE.pmid)
self.eq(self.pmid, pmid.toPython())
# No venue
venue = g.value(subject=pub_uri, predicate=BCITE.hasVenue)
assert venue == None
ctype = g.value(subject=pub_uri, predicate=RDF.type)
self.eq(ctype, BCITE.BookSection)
title = g.value(subject=pub_uri, predicate=RDFS.label)
assert title.toPython().startswith(u"Epidemiology")
book = g.value(subject=pub_uri, predicate=BCITE.book)
assert book.toPython().startswith(u"Medical Microbiology")
def test_contrib(self):
b = {}
uri = D["n123"]
b["articleids"] = [{"idtype": "pubmed", "value": "pm1234"}]
b["title"] = "Sample article"
# Try coauthors created as just strings with @baseuris and
# as RDFLib URI objects.
ca1 = ["jsmith", "jjones"]
ca2 = [D["jsmith"], D["jjones"]]
for coauthors in [ca1, ca2]:
pub = Publication()
prepped = pub.prep(b, pub_uri=uri, contributors=coauthors)
assert coauthors[0] in prepped["contributor"]
assert coauthors[1] in prepped["contributor"]
g = pub.to_graph(prepped)
# Test that all coathors are in the outputted RDF..
for ob in g.objects(subject=D["n123"], predicate=BCITE.hasContributor):
ca2.index(ob) > -1
assert type(ob) == URIRef
def test_rdf(self):
pub_uri = D["n123"]
book = Publication()
meta = book.prep(self.meta, pub_uri=pub_uri)
g = book.to_graph(meta)
g.namespace_manager = ns_mgr
# ids
pmid = g.value(subject=pub_uri, predicate=BCITE.pmid)
self.eq(self.pmid, pmid.toPython())
# No venue
venue = g.value(subject=pub_uri, predicate=BCITE.hasVenue)
assert venue == None
ctype = g.value(subject=pub_uri, predicate=RDF.type)
self.eq(ctype, BCITE.Book)
title = g.value(subject=pub_uri, predicate=RDFS.label)
assert title.toPython().startswith(
u"Comprehensive Overview of Methods and Reporting of Meta-Analyses of Test Accuracy"
)
url = g.value(subject=pub_uri, predicate=BCITE.url)
assert url.toPython() == u"http://www.ncbi.nlm.nih.gov/books/NBK92422/"
