class TestSearchAnnotations(unittest.TestCase):
def test_search_for_uri(self):
for url in annotation_urls:
g, target, selector = specific_resource(self.canvas,
res=URIRef(uuid.uuid4()),
selector=URIRef(uuid.uuid4()))
g, anno, body, target = annotation(g=g,
anno=URIRef(uuid.uuid4()),
target=target,
body=URIRef(uuid.uuid4()))
response = self.client.post(url, data=g.serialize(),
content_type="text/xml")
self.assertEqual(response.status_code, 201)
for uri in [anno, body, target, selector, self.canvas]:
response = self.client.get(url, {'uri': uri})
self.assertEqual(response.status_code, 200)
validate_return_content(self, response, g)
def tearDown(self):
pass
def setUp(self):
url = reverse('semantic_store_annotations', kwargs=dict())
self.client = Client()
fixture_filename = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"semantic_store_test_fixture.xml")
self.g = ConjunctiveGraph(rdfstore.rdfstore(),
identifier=rdfstore.default_identifier)
self.g.parse(fixture_filename)
canvases = self.g.subjects(URIRef(NS.rdf['type']), URIRef(NS.dms['Canvas']))
self.canvas = list(canvases)[0]
primer.add((myNS.pat, myNS.knows, myNS.jo)) # or: primer.add((myNS['pat'], myNS['age'], long(24))) # Now, with just that, lets see how the system # recorded *way* too many details about what # you just asserted as fact. # from pprint import pprint pprint(list(primer)) # just think .whatever((s, p, o)) # here we report on what we know pprint(list(primer.subjects())) pprint(list(primer.predicates())) pprint(list(primer.objects())) # and other things that make sense # what do we know about pat? pprint(list(primer.predicate_objects(myNS.pat))) # who is what age? pprint(list(primer.subject_objects(myNS.age))) # Okay, so lets now work with a bigger # dataset from the example, and start # with a fresh new graph.
def testFormulaStore(store="default", configString=None):
try:
g = ConjunctiveGraph(store=store)
except ImportError:
raise SkipTest("Dependencies for store '%s' not available!" % store)
if configString:
g.destroy(configString)
g.open(configString)
else:
if store == 'SQLite':
_, path = mkstemp(prefix='test', dir='/tmp', suffix='.sqlite')
g.open(path, create=True)
else:
g.open(mkdtemp(), create=True)
g.parse(data=testN3, format="n3")
try:
for s, p, o in g.triples((None, implies, None)):
formulaA = s
formulaB = o
assert type(formulaA) == QuotedGraph and type(formulaB) == QuotedGraph
# a = URIRef('http://test/a')
b = URIRef('http://test/b')
c = URIRef('http://test/c')
d = URIRef('http://test/d')
v = Variable('y')
universe = ConjunctiveGraph(g.store)
#test formula as terms
assert len(list(universe.triples((formulaA, implies, formulaB)))) == 1
#test variable as term and variable roundtrip
assert len(list(formulaB.triples((None, None, v)))) == 1
for s, p, o in formulaB.triples((None, d, None)):
if o != c:
assert isinstance(o, Variable)
assert o == v
s = list(universe.subjects(RDF.type, RDFS.Class))[0]
assert isinstance(s, BNode)
assert len(list(universe.triples((None, implies, None)))) == 1
assert len(list(universe.triples((None, RDF.type, None)))) == 1
assert len(list(formulaA.triples((None, RDF.type, None)))) == 1
assert len(list(formulaA.triples((None, None, None)))) == 2
assert len(list(formulaB.triples((None, None, None)))) == 2
assert len(list(universe.triples((None, None, None)))) == 3
assert len(list(formulaB.triples(
(None, URIRef('http://test/d'), None)))) == 2
assert len(list(universe.triples(
(None, URIRef('http://test/d'), None)))) == 1
# #context tests
# #test contexts with triple argument
# assert len(list(universe.contexts((a, d, c)))) == 1, \
# [ct for ct in universe.contexts((a, d, c))]
# FAIL: test.test_graph_formula.testFormulaStores('SQLite',)
# --------------------------------------------------------------------
# Traceback (most recent call last):
# File ".../site-packages/nose/case.py", line 197, in runTest
# self.test(*self.arg)
# File ".../test_graph_formula.py", line 80, in testFormulaStore
# [ct for ct in universe.contexts((a, d, c))]
# AssertionError: [
# <Graph identifier=N52fd4417ef7641089b2e4045ef19ad87
# (<class 'rdflib.graph.Graph'>)>,
# <Graph identifier=_:Formula16 (<class 'rdflib.graph.Graph'>)>
# ]
#Remove test cases
universe.remove((None, implies, None))
assert len(list(universe.triples((None, implies, None)))) == 0
assert len(list(formulaA.triples((None, None, None)))) == 2
assert len(list(formulaB.triples((None, None, None)))) == 2
formulaA.remove((None, b, None))
assert len(list(formulaA.triples((None, None, None)))) == 1
formulaA.remove((None, RDF.type, None))
assert len(list(formulaA.triples((None, None, None)))) == 0
universe.remove((None, RDF.type, RDFS.Class))
#remove_context tests
universe.remove_context(formulaB)
assert len(list(universe.triples((None, RDF.type, None)))) == 0
assert len(universe) == 1
assert len(formulaB) == 0
universe.remove((None, None, None))
assert len(universe) == 0
g.close()
if store == 'SQLite':
os.unlink(path)
else:
g.store.destroy(configString)
except:
g.close()
if store == 'SQLite':
os.unlink(path)
else:
g.store.destroy(configString)
raise
def make_property_graph(properties, args):
graph = ConjunctiveGraph()
output_graph = ConjunctiveGraph()
GH = 'https://raw.githubusercontent.com'
OBO = 'https://purl.obolibrary.org/obo'
ontologies = [
OBO + '/sepio.owl',
OBO + '/geno.owl',
OBO + '/iao.owl',
OBO + '/ero.owl',
OBO + '/pco.owl',
OBO + '/xco.owl',
OBO + '/ro.owl',
GH + '/jamesmalone/OBAN/master/ontology/oban_core.ttl',
]
for ontology in ontologies:
print("parsing: " + ontology)
try:
graph.parse(ontology, format=rdflib_util.guess_format(ontology))
except SAXParseException as e:
logger.error(e)
logger.error('Retrying: ' + ontology)
graph.parse(ontology, format="turtle")
except OSError as e: # URLError:
# simple retry
logger.error(e)
logger.error('Retrying: ' + ontology)
graph.parse(ontology, format=rdflib_util.guess_format(ontology))
# Get object properties
output_graph = add_property_to_graph(
graph.subjects(RDF['type'], OWL['ObjectProperty']), output_graph,
OWL['ObjectProperty'], properties)
# Get annotation properties
output_graph = add_property_to_graph(
graph.subjects(RDF['type'], OWL['AnnotationProperty']), output_graph,
OWL['AnnotationProperty'], properties)
# Get data properties
output_graph = add_property_to_graph(
graph.subjects(RDF['type'], OWL['DatatypeProperty']), output_graph,
OWL['DatatypeProperty'], properties)
# Hardcoded properties
output_graph.add(
(URIRef('https://monarchinitiative.org/MONARCH_cliqueLeader'),
RDF['type'], OWL['AnnotationProperty']))
output_graph.add(
(URIRef('https://monarchinitiative.org/MONARCH_anonymous'),
RDF['type'], OWL['AnnotationProperty']))
# Check monarch data triple
data_url = "https://data.monarchinitiative.org/ttl/{0}".format(
re.sub(r".*/", "", args.input))
new_url = "https://data.monarchinitiative.org/ttl/{0}".format(
re.sub(r".*/", "", args.output))
if (URIRef(data_url), RDF.type, OWL['Ontology']) in output_graph:
output_graph.remove(URIRef(data_url), RDF.type, OWL['Ontology'])
output_graph.add((URIRef(new_url), RDF.type, OWL['Ontology']))
for row in output_graph.predicates(DC['source'],
OWL['AnnotationProperty']):
if row == RDF['type']:
output_graph.remove(
(DC['source'], RDF['type'], OWL['AnnotationProperty']))
output_graph.add((DC['source'], RDF['type'], OWL['ObjectProperty']))
return output_graph
def testN3Store(store="default", configString=None):
storetest = True
g = ConjunctiveGraph(store=store)
if configString is not None:
g.destroy(configString)
g.open(configString, create=True)
g.parse(data=testN3, format="n3")
# op = g.serialize(format="n3")
# print(op)
formulaA = BNode()
formulaB = BNode()
try:
for s,p,o in g.triples((None,implies,None)):
formulaA = s
formulaB = o
assert type(formulaA)==QuotedGraph and type(formulaB)==QuotedGraph
a = URIRef('http://test/a')
b = URIRef('http://test/b')
c = URIRef('http://test/c')
d = URIRef('http://test/d')
v = Variable('y')
universe = ConjunctiveGraph(g.store)
#test formula as terms
assert len(list(universe.triples((formulaA,implies,formulaB))))==1
#test variable as term and variable roundtrip
assert len(list(formulaB.triples((None,None,v))))==1
for s,p,o in formulaB.triples((None,d,None)):
if o != c:
assert isinstance(o,Variable)
assert o == v
s = list(universe.subjects(RDF.type, RDFS.Class))[0]
assert isinstance(s,BNode)
assert len(list(universe.triples((None,implies,None)))) == 1
assert len(list(universe.triples((None,RDF.type,None)))) ==1
assert len(list(formulaA.triples((None,RDF.type,None))))==1
assert len(list(formulaA.triples((None,None,None))))==2
assert len(list(formulaB.triples((None,None,None))))==2
assert len(list(universe.triples((None,None,None))))==3
assert len(list(formulaB.triples((None,URIRef('http://test/d'),None))))==2
assert len(list(universe.triples((None,URIRef('http://test/d'),None))))==1
#context tests
#test contexts with triple argument
assert len(list(universe.contexts((a,d,c))))==1
#Remove test cases
universe.remove((None,implies,None))
assert len(list(universe.triples((None,implies,None))))==0
assert len(list(formulaA.triples((None,None,None))))==2
assert len(list(formulaB.triples((None,None,None))))==2
formulaA.remove((None,b,None))
assert len(list(formulaA.triples((None,None,None))))==1
formulaA.remove((None,RDF.type,None))
assert len(list(formulaA.triples((None,None,None))))==0
universe.remove((None,RDF.type,RDFS.Class))
#remove_context tests
universe.remove_context(formulaB)
assert len(list(universe.triples((None,RDF.type,None))))==0
assert len(universe)==1
assert len(formulaB)==0
universe.remove((None,None,None))
assert len(universe)==0
g.store.destroy(configString)
except:
g.store.destroy(configString)
raise
def testN3Store(store="default", configString=None):
storetest = True
del storetest
g = ConjunctiveGraph(store=store)
if configString:
# g.destroy(configString)
g.open(configString, create=True)
g.parse(data=testN3, format="n3")
# op = g.serialize(format="n3")
# print(op)
formulaA = BNode()
formulaB = BNode()
try:
for s, p, o in g.triples((None, implies, None)):
formulaA = s
formulaB = o
assert type(formulaA) == QuotedGraph \
and type(formulaB) == QuotedGraph
a = URIRef('http://test/a')
b = URIRef('http://test/b')
c = URIRef('http://test/c')
d = URIRef('http://test/d')
v = Variable('y')
universe = ConjunctiveGraph(g.store)
#test formula as terms
assert len(list(universe.triples((formulaA, implies, formulaB)))) == 1
#test variable as term and variable roundtrip
assert len(list(formulaB.triples((None, None, v)))) == 1
for s, p, o in formulaB.triples((None, d, None)):
if o != c:
assert isinstance(o, Variable)
assert o == v
s = list(universe.subjects(RDF.type, RDFS.Class))[0]
assert isinstance(s, BNode)
assert len(list(universe.triples((None, implies, None)))) == 1
assert len(list(universe.triples((None, RDF.type, None)))) == 1
assert len(list(formulaA.triples((None, RDF.type, None)))) == 1
assert len(list(formulaA.triples((None, None, None)))) == 2
assert len(list(formulaB.triples((None, None, None)))) == 2
assert len(list(universe.triples((None, None, None)))) == 3
assert len(
list(formulaB.triples((None, URIRef('http://test/d'), None)))) == 2
assert len(
list(universe.triples((None, URIRef('http://test/d'), None)))) == 1
#context tests
#test contexts with triple argument
assert len(list(universe.contexts((a, d, c)))) == 1
#Remove test cases
universe.remove((None, implies, None))
assert len(list(universe.triples((None, implies, None)))) == 0
assert len(list(formulaA.triples((None, None, None)))) == 2
assert len(list(formulaB.triples((None, None, None)))) == 2
formulaA.remove((None, b, None))
assert len(list(formulaA.triples((None, None, None)))) == 1
formulaA.remove((None, RDF.type, None))
assert len(list(formulaA.triples((None, None, None)))) == 0
universe.remove((None, RDF.type, RDFS.Class))
#remove_context tests
universe.remove_context(formulaB)
assert len(list(universe.triples((None, RDF.type, None)))) == 0
assert len(universe) == 1
assert len(formulaB) == 0
universe.remove((None, None, None))
assert len(universe) == 0
g.store.destroy(configString)
except:
g.store.destroy(configString)
raise
def test_n3_store(self):
# Thorough test suite for formula-aware store
implies = URIRef("http://www.w3.org/2000/10/swap/log#implies")
testN3 = """
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix : <http://test/> .
{:a :b :c;a :foo} => {:a :d :c,?y}.
_:foo a rdfs:Class.
:a :d :c."""
g = self.open_graph()
g.parse(data=testN3, format="n3")
formulaA = BNode()
formulaB = BNode()
for s,o in g.subject_objects(predicate=implies):
formulaA = s
formulaB = o
assert type(formulaA)==QuotedGraph and type(formulaB)==QuotedGraph
a = URIRef('http://test/a')
b = URIRef('http://test/b')
c = URIRef('http://test/c')
d = URIRef('http://test/d')
v = Variable('y')
universe = ConjunctiveGraph(g.store)
# test formula as terms
assert len(list(universe.triples((formulaA, implies, formulaB)))) == 1
# test variable as term and variable roundtrip
assert len(list(formulaB.triples((None,None,v)))) == 1
for s,p,o in formulaB.triples((None,d,None)):
if o != c:
assert isinstance(o, Variable)
assert o == v
s = list(universe.subjects(RDF.type, RDFS.Class))[0]
assert isinstance(s, BNode)
assert len(list(universe.triples((None,implies,None)))) == 1
assert len(list(universe.triples((None,RDF.type,None)))) == 1
assert len(list(formulaA.triples((None,RDF.type,None)))) == 1
assert len(list(formulaA.triples((None,None,None)))) == 2
assert len(list(formulaB.triples((None,None,None)))) == 2
assert len(list(formulaB.triples((None,d,None)))) == 2
assert len(list(universe.triples((None,None,None)))) == 3
assert len(list(universe.triples((None,d,None)))) == 1
# context tests
# test contexts with triple argument
assert len(list(universe.contexts((a,d,c))))==1
# remove test cases
universe.remove((None,implies,None))
assert len(list(universe.triples((None,implies,None)))) == 0
assert len(list(formulaA.triples((None,None,None)))) == 2
assert len(list(formulaB.triples((None,None,None)))) == 2
formulaA.remove((None,b,None))
assert len(list(formulaA.triples((None,None,None)))) == 1
formulaA.remove((None,RDF.type,None))
assert len(list(formulaA.triples((None,None,None)))) == 0
universe.remove((None,RDF.type,RDFS.Class))
# remove_context tests
universe.remove_context(formulaB)
assert len(list(universe.triples((None,RDF.type,None)))) == 0
assert len(universe) == 1
assert len(formulaB) == 0
universe.remove((None,None,None))
assert len(universe) == 0
def test_rdflib_mysql_test(self):
"""
test taken from rdflib/test/test_mysql.py
"""
implies = URIRef("http://www.w3.org/2000/10/swap/log#implies")
testN3="""
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix : <http://test/> .
{:a :b :c;a :foo} => {:a :d :c,?y}.
_:foo a rdfs:Class.
:a :d :c."""
#Thorough test suite for formula-aware store
g = self.rdflib_graph
g.parse(data=testN3, format="n3")
#print g.store
for s,p,o in g.triples((None,implies,None)):
formulaA = s
formulaB = o
self.assertTrue(type(formulaA)==QuotedGraph and type(formulaB)==QuotedGraph)
a = URIRef('http://test/a')
b = URIRef('http://test/b')
c = URIRef('http://test/c')
d = URIRef('http://test/d')
v = Variable('y')
universe = ConjunctiveGraph(g.store)
#test formula as terms
self.assertTrue(len(list(universe.triples((formulaA,implies,formulaB))))==1)
#test variable as term and variable roundtrip
self.assertTrue(len(list(formulaB.triples((None,None,v))))==1)
for s,p,o in formulaB.triples((None,d,None)):
if o != c:
self.assertTrue(isinstance(o,Variable))
self.assertTrue(o == v)
s = list(universe.subjects(RDF.type, RDFS.Class))[0]
self.assertTrue(isinstance(s,BNode))
self.assertTrue( len(list(universe.triples((None,implies,None)))) == 1)
self.assertTrue( len(list(universe.triples((None,RDF.type,None)))) ==1)
self.assertTrue( len(list(formulaA.triples((None,RDF.type,None))))==1)
self.assertTrue( len(list(formulaA.triples((None,None,None))))==2)
self.assertTrue( len(list(formulaB.triples((None,None,None))))==2)
self.assertTrue( len(list(universe.triples((None,None,None))))==3)
self.assertTrue( len(list(formulaB.triples((None,URIRef('http://test/d'),None))))==2)
self.assertTrue( len(list(universe.triples((None,URIRef('http://test/d'),None))))==1)
#context tests
#test contexts with triple argument
self.assertTrue( len(list(universe.contexts((a,d,c))))==1)
#Remove test cases
universe.remove((None,implies,None))
self.assertTrue( len(list(universe.triples((None,implies,None))))==0)
self.assertTrue( len(list(formulaA.triples((None,None,None))))==2)
self.assertTrue( len(list(formulaB.triples((None,None,None))))==2)
formulaA.remove((None,b,None))
self.assertTrue( len(list(formulaA.triples((None,None,None))))==1)
formulaA.remove((None,RDF.type,None))
self.assertTrue( len(list(formulaA.triples((None,None,None))))==0)
universe.remove((None,RDF.type,RDFS.Class))
#remove_context tests
universe.remove_context(formulaB)
self.assertTrue( len(list(universe.triples((None,RDF.type,None))))==0)
self.assertTrue( len(universe)==1)
self.assertTrue( len(list(formulaB.triples((None,None,None))))==0)
universe.remove((None,None,None))
self.assertTrue( len(universe)==0)
class TestSingleAnnotation(unittest.TestCase):
def test_embedded_textual_body_bnode(self):
for url in annotation_urls:
g, target, selector = svg_specific_resource(source=self.canvas)
g, body = content_as_text_resource(g=g, chars=self.shortText)
g, anno, body, target = annotation(g=g, body=body, target=target)
data = g.serialize(initNs=ns)
response = self.client.post(url, data=data, content_type="text/xml")
self.assertEqual(response.status_code, 201)
validate_return_content(self, response, g)
def test_embedded_textual_body_uuids(self):
for url in annotation_urls:
g = Graph()
bind_namespaces(g)
anno = URIRef(uuid.uuid4())
body = URIRef(uuid.uuid4())
g.add((anno, NS.rdf['type'], NS.oa['Annotation']))
g.add((anno, NS.oa['hasTarget'], self.canvas))
g.add((anno, NS.oa['hasBody'], body))
g.add((body, NS.rdf['type'], NS.dctypes['Text']))
g.add((body, NS.rdf['type'], NS.cnt['ContentAsText']))
g.add((body, NS.cnt['chars'], self.shortText))
g.add((body, NS.dc['format'], Literal("text/plain")))
data = g.serialize(initNs=ns)
response = self.client.post(url, data=data, content_type="text/xml")
self.assertEqual(response.status_code, 201)
validate_return_content(self, response, g)
def test_body_uuid(self):
for url in annotation_urls:
g = Graph()
bind_namespaces(g)
anno = URIRef(uuid.uuid4())
body = URIRef(uuid.uuid4())
g.add((anno, NS.rdf['type'], NS.oa['Annotation']))
g.add((anno, NS.oa['hasTarget'], self.canvas))
g.add((anno, NS.oa['hasBody'], body))
g.add((body, NS.rdf['type'], NS.dctypes['Text']))
data = g.serialize(initNs=ns)
response = self.client.post(url, data=data, content_type="text/xml")
self.assertEqual(response.status_code, 201)
validate_return_content(self, response, g)
def test_specific_target_only(self):
# See http://www.openannotation.org/spec/core/specific.html#Specific
# and http://www.openannotation.org/spec/core/publishing.html#Embedding
for url in annotation_urls:
g, target, selector = svg_specific_resource(
Literal("<circle cx='300' cy='200' r='100'/>"))
g, anno, body, target = annotation(g=g, target=target)
data = g.serialize()
response = self.client.post(url, data=data, content_type="text/xml")
self.assertEqual(response.status_code, 201)
validate_return_content(self, response, g)
def test_no_annos(self):
for url in annotation_urls:
g, res, selector = svg_specific_resource(
Literal("<circle cx='300' cy='200' r='100'/>"))
data = g.serialize()
response = self.client.post(url, data=data, content_type="text/xml")
self.assertEqual(response.content, "No %s nodes found." %
NS.oa['Annotation'])
self.assertEqual(response.status_code, 400)
def test_specific_target_uuid(self):
for url in annotation_urls:
g = Graph()
bind_namespaces(g)
anno = URIRef(uuid.uuid4())
target = URIRef(uuid.uuid4())
svg = URIRef(uuid.uuid4())
g.add((anno, NS.rdf['type'], NS.oa['Annotation']))
g.add((anno, NS.oa['hasTarget'], target))
g.add((target, NS.rdf['type'], NS.oa['SpecificResource']))
g.add((target, NS.oa['hasSelector'], svg))
g.add((svg, NS.rdf['type'], NS.oa['SvgSelector']))
g.add((svg, NS.rdf['type'], NS.cnt['ContentAsText']))
g.add((svg, NS.cnt['chars'],
Literal("<circle cx='300' cy='200' r='100'/>")))
g.add((svg, NS.cnt['characterEncoding'], Literal("utf-8")))
data = g.serialize(initNs=ns)
response = self.client.post(url, data=data, content_type="text/xml")
self.assertEqual(response.status_code, 201)
def tearDown(self):
pass
def setUp(self):
self.client = Client()
fixture_filename = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"semantic_store_test_fixture.xml")
self.g = ConjunctiveGraph(rdfstore.rdfstore(),
identifier=rdfstore.default_identifier)
self.g.parse(fixture_filename)
canvases = self.g.subjects(URIRef(NS.rdf['type']), URIRef(NS.dms['Canvas']))
self.canvas = list(canvases)[0]
self.shortText = Literal("This is a short text.")
self.longText = """
def make_property_graph(properties, args):
graph = ConjunctiveGraph()
output_graph = ConjunctiveGraph()
ontologies = [
'https://raw.githubusercontent.com/monarch-initiative/SEPIO-ontology/master/src/ontology/sepio.owl',
'https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/src/ontology/geno.owl',
'http://purl.obolibrary.org/obo/ro.owl',
'http://purl.obolibrary.org/obo/iao.owl',
'http://purl.obolibrary.org/obo/ero.owl',
'https://raw.githubusercontent.com/jamesmalone/OBAN/master/ontology/oban_core.ttl',
'http://purl.obolibrary.org/obo/pco.owl',
'http://purl.obolibrary.org/obo/xco.owl'
]
for ontology in ontologies:
print("parsing: " + ontology)
try:
graph.parse(ontology, format=rdflib_util.guess_format(ontology))
except SAXParseException as e:
logger.error(e)
logger.error('Retrying: ' + ontology)
graph.parse(ontology, format="turtle")
except OSError as e: # URLError:
# simple retry
logger.error(e)
logger.error('Retrying: ' + ontology)
graph.parse(ontology, format=rdflib_util.guess_format(ontology))
# Get object properties
output_graph = add_property_to_graph(
graph.subjects(RDF['type'], OWL['ObjectProperty']),
output_graph, OWL['ObjectProperty'], properties)
# Get annotation properties
output_graph = add_property_to_graph(
graph.subjects(RDF['type'], OWL['AnnotationProperty']),
output_graph, OWL['AnnotationProperty'], properties)
# Get data properties
output_graph = add_property_to_graph(
graph.subjects(RDF['type'], OWL['DatatypeProperty']),
output_graph, OWL['DatatypeProperty'], properties)
# Hardcoded properties
output_graph.add(
(URIRef('https://monarchinitiative.org/MONARCH_cliqueLeader'),
RDF['type'], OWL['AnnotationProperty']))
output_graph.add(
(URIRef('https://monarchinitiative.org/MONARCH_anonymous'),
RDF['type'], OWL['AnnotationProperty']))
# Check monarch data triple
data_url = "https://data.monarchinitiative.org/ttl/{0}".format(
re.sub(r".*/", "", args.input))
new_url = "https://data.monarchinitiative.org/ttl/{0}".format(
re.sub(r".*/", "", args.output))
if (URIRef(data_url), RDF.type, OWL['Ontology']) in output_graph:
output_graph.remove(URIRef(data_url), RDF.type, OWL['Ontology'])
output_graph.add((URIRef(new_url), RDF.type, OWL['Ontology']))
for row in output_graph.predicates(
DC['source'], OWL['AnnotationProperty']):
if row == RDF['type']:
output_graph.remove(
(DC['source'], RDF['type'], OWL['AnnotationProperty']))
output_graph.add((DC['source'], RDF['type'], OWL['ObjectProperty']))
return output_graph
def testFormulaStore(store="default", configString=None):
try:
g = ConjunctiveGraph(store=store)
except ImportError:
raise SkipTest("Dependencies for store '%s' not available!"%store)
if configString:
g.destroy(configString)
g.open(configString)
else:
g.open(mkdtemp(), create=True)
g.parse(data=testN3, format="n3")
print g.store
try:
for s,p,o in g.triples((None,implies,None)):
formulaA = s
formulaB = o
assert type(formulaA)==QuotedGraph and type(formulaB)==QuotedGraph
a = URIRef('http://test/a')
b = URIRef('http://test/b')
c = URIRef('http://test/c')
d = URIRef('http://test/d')
v = Variable('y')
universe = ConjunctiveGraph(g.store)
#test formula as terms
assert len(list(universe.triples((formulaA,implies,formulaB))))==1
#test variable as term and variable roundtrip
assert len(list(formulaB.triples((None,None,v))))==1
for s,p,o in formulaB.triples((None,d,None)):
if o != c:
assert isinstance(o,Variable)
assert o == v
s = list(universe.subjects(RDF.type, RDFS.Class))[0]
assert isinstance(s,BNode)
assert len(list(universe.triples((None,implies,None)))) == 1
assert len(list(universe.triples((None,RDF.type,None)))) ==1
assert len(list(formulaA.triples((None,RDF.type,None))))==1
assert len(list(formulaA.triples((None,None,None))))==2
assert len(list(formulaB.triples((None,None,None))))==2
assert len(list(universe.triples((None,None,None))))==3
assert len(list(formulaB.triples((None,URIRef('http://test/d'),None))))==2
assert len(list(universe.triples((None,URIRef('http://test/d'),None))))==1
#context tests
#test contexts with triple argument
assert len(list(universe.contexts((a,d,c))))==1
#Remove test cases
universe.remove((None,implies,None))
assert len(list(universe.triples((None,implies,None))))==0
assert len(list(formulaA.triples((None,None,None))))==2
assert len(list(formulaB.triples((None,None,None))))==2
formulaA.remove((None,b,None))
assert len(list(formulaA.triples((None,None,None))))==1
formulaA.remove((None,RDF.type,None))
assert len(list(formulaA.triples((None,None,None))))==0
universe.remove((None,RDF.type,RDFS.Class))
#remove_context tests
universe.remove_context(formulaB)
assert len(list(universe.triples((None,RDF.type,None))))==0
assert len(universe)==1
assert len(formulaB)==0
universe.remove((None,None,None))
assert len(universe)==0
g.close()
g.store.destroy(configString)
except:
g.close()
g.store.destroy(configString)
raise
primer.add((myNS['pat'], myNS['age'], long(24))) # Now, with just that, lets see how the system # recorded *way* too many details about what # you just asserted as fact. # from pprint import pprint pprint(list(primer)) # just think .whatever((s, p, o)) # here we report on what we know pprint(list(primer.subjects())) pprint(list(primer.predicates())) pprint(list(primer.objects())) # and other things that make sense # what do we know about pat? pprint(list(primer.predicate_objects(myNS.pat))) # who is what age? pprint(list(primer.subject_objects(myNS.age))) # Okay, so lets now work with a bigger # dataset from the example, and start
