def test_serialize(self):
# Issue #1 - serialize goes after the entire graph
WD = Namespace("http://www.wikidata.org/entity/")
g = SlurpyGraph(endpoint, agent=UserAgent)
_ = list(g.predicate_objects(WD.Q29017194))
g.debug_slurps = True
# Warning - this will go away forever if the bug isn't fixed
serialized_graph = g.serialize(format="turtle").decode()
g2 = Graph()
g2.parse(data=serialized_graph, format="turtle")
self.assertEqual(len(list(g)), len(list(g2)))
def test_debug_slurps(self):
WD = Namespace("http://www.wikidata.org/entity/")
g = SlurpyGraph(endpoint, agent=UserAgent)
g.debug_slurps = True
output = io.StringIO()
with redirect_stdout(output):
_ = list(g.predicate_objects(WD.Q29017194))
if not output.getvalue().startswith("SPARQL: "
"(SELECT ?s ?p ?o {<http://www.wikidata.org/entity/Q29017194> ?p ?o})"):
print("Unexpected:")
print(output.getvalue())
self.assertTrue(False)
def SlurpyGraphWithAgent(endpoint: str,
*args,
persistent_bnodes: bool = False,
agent: Optional[str] = None,
gdb_slurper: Optional[bool] = False,
**kwargs) -> SlurpyGraph:
rval = GraphDBSlurpyGraph(endpoint, *args, persistent_bnodes=persistent_bnodes, **kwargs) if gdb_slurper else \
SlurpyGraph(endpoint, *args, persistent_bnodes=persistent_bnodes, **kwargs)
rval.sparql.agent = agent if agent else UserAgent
return rval
def test_persistent_bnode(self):
""" Test the persistent_bnode argument """
g = SlurpyGraph("http://sparql-playground.nextprot.org/sparql")
with self.assertRaises(ValueError):
_ = list(g.objects(NEXTPROT['NATUR-NX_PEPT00119967-NX_Q9Y5X1-1'], NEXTPROT.evidence))
g.persistent_bnodes = True
evidence = g.value(NEXTPROT['NATUR-NX_PEPT00119967-NX_Q9Y5X1-1'], NEXTPROT.evidence)
self.assertTrue(isinstance(evidence, BNode))
peptide_name = g.value(evidence, NEXTPROT.peptideName)
if peptide_name != "NX_PEPT00119967":
print(f"Warning: {g.sparql.endpoint} does not support persistent BNodes!")
def test_reactome(self):
WD = Namespace("http://www.wikidata.org/entity/")
P = Namespace("http://www.wikidata.org/prop/")
g = SlurpyGraph(endpoint, agent=UserAgent)
g.debug_slurps = False
gpo = list(g.predicate_objects(WD.Q29017194))
orig_len = len(gpo)
# Test that we get something
self.assertTrue(30 < orig_len < 60) # Current value is 33
# Test that it is reproducable
self.assertEqual(orig_len, len(list(g.predicate_objects((WD.Q29017194)))))
# Test that it is cached
self.assertEqual(orig_len, len(g))
# Add a path
added_length = 0
for s in g.objects(WD.Q29017194, P.P31):
gp31s = list(g.predicate_objects(s))
added_length += len(gp31s)
self.assertEqual(orig_len + added_length, len(g))
print(f"{g.total_calls}, {g.total_queries}, {g.total_slurptime}, {g.total_triples}")
self.assertEqual((5, 3, 41), (g.total_calls, g.total_queries, g.total_triples))
self.assertTrue(g.total_slurptime > 0.1)
def test_already_resolved(self):
g = SlurpyGraph("endpoint")
EX = Namespace("http://example.org/")
g.resolved_nodes.append((EX.s1, EX.p1, EX.o1))
g.resolved_nodes.append((EX.s1, EX.p1, Literal("Steam")))
g.resolved_nodes.append((EX.s1, EX.p1, Literal(117)))
g.resolved_nodes.append((EX.s2, EX.p2, None))
g.resolved_nodes.append((EX.s3, None, EX.o3))
g.resolved_nodes.append((EX.s3, None, Literal("Gas")))
g.resolved_nodes.append((EX.s3, None, Literal(-42)))
g.resolved_nodes.append((EX.s4, None, None))
g.resolved_nodes.append((None, EX.p5, EX.o5))
g.resolved_nodes.append((None, EX.p5, Literal("Coal")))
g.resolved_nodes.append((None, EX.p5, Literal(11.2)))
g.resolved_nodes.append((None, EX.p6, None))
g.resolved_nodes.append((None, None, EX.o7))
g.resolved_nodes.append((None, None, Literal("Wood")))
g.resolved_nodes.append((None, None, Literal(3.14159)))
self.assertTrue(g.already_resolved((None, None, None)))
self.assertTrue(g.already_resolved((EX.s1, EX.p1, EX.o1)))
self.assertFalse(g.already_resolved((EX.s1, EX.p1, EX.o2)))
self.assertTrue(g.already_resolved((EX.s1, EX.p1, Literal("Steam"))))
self.assertFalse(g.already_resolved((EX.s1, EX.p1, Literal("Gas"))))
self.assertTrue(g.already_resolved((EX.s1, EX.p1, Literal(117))))
self.assertFalse(g.already_resolved((EX.s1, EX.p1, Literal(118))))
self.assertFalse(g.already_resolved((EX.s1, None, Literal(117))))
self.assertFalse(g.already_resolved((None, EX.p1, Literal(117))))
self.assertTrue(g.already_resolved((EX.s2, EX.p2, Literal(143))))
self.assertFalse(g.already_resolved((EX.s2, None, Literal(143))))
self.assertTrue(g.already_resolved((EX.s4, EX.p4, None)))
self.assertTrue(g.already_resolved((EX.s4, None, Literal(12))))
self.assertTrue(g.already_resolved((EX.s4, None, None)))
self.assertTrue(g.already_resolved((EX.s5, EX.p5, EX.o5)))
self.assertFalse(g.already_resolved((EX.s5, EX.p5, EX.o5n)))
self.assertTrue(g.already_resolved((EX.s7, None, EX.o7)))
self.assertTrue(g.already_resolved((None, EX.p7, EX.o7)))
self.assertFalse(g.already_resolved((EX.s7, None, None)))
def do_test(g: SlurpyGraph) -> str:
output = io.StringIO()
with redirect_stdout(output):
_ = list(g.predicate_objects(WD.Q29017194))
return output.getvalue()
def setup_test() -> SlurpyGraph:
g = SlurpyGraph(endpoint, agent=UserAgent)
g.bind("wd", WD)
g.bind("wdp", "http://www.wikidata.org/prop/")
g.bind("wdd", "http://www.wikidata.org/prop/direct/")
g.bind("sdo", "http://schema.org/")
g.bind("wds", "http://www.wikidata.org/entity/statement/")
g.bind("wikiba", "http://wikiba.se/ontology#")
g.add_result_hook(QueryResultPrinter)
return g