def writeFile(self, stmts, ctx, fileWords):
outfile = "commentstore/post-%s.nt" % ("-".join(fileWords))
graph = ConjunctiveGraph()
graph.add(*stmts, **{'context' : ctx})
graph.graph.serialize(outfile, format='n3')
log.info("wrote new comment to %s", outfile)
class Db(_shared):
def __init__(self):
self.lastTimes = []
def getGraph(self):
t1 = time.time()
mtimes = []
for f in (["/my/proj/openid_proxy/access.n3"] +
glob.glob("commentstore/*.nt")):
mtimes.append(os.path.getmtime(f))
if mtimes == self.lastTimes and hasattr(self, 'currentGraph'):
return self.currentGraph
self.lastTimes = mtimes
tf = tempfile.NamedTemporaryFile()
os.system("cat /my/proj/openid_proxy/access.n3 commentstore/*.nt > %s" % tf.name)
self.currentGraph = ConjunctiveGraph()
self.currentGraph.parse(tf.name, format="n3")
log.info("reloaded comments from disk in %f sec" % (time.time() - t1))
return self.currentGraph
def writeFile(self, stmts, ctx, fileWords):
outfile = "commentstore/post-%s.nt" % ("-".join(fileWords))
graph = ConjunctiveGraph()
graph.add(*stmts, **{'context' : ctx})
graph.graph.serialize(outfile, format='n3')
log.info("wrote new comment to %s", outfile)
def test_url(self):
if self.html5lib_installed():
g = ConjunctiveGraph()
g.parse(location='http://oreilly.com/catalog/9780596516499/',
format='rdfa',
lax=True)
self.assertTrue(len(g) > 0)
class TestSparqlJsonResults(unittest.TestCase):
def setUp(self):
self.graph = ConjunctiveGraph()
self.graph.parse(StringIO(test_data), format="n3")
def _query_result_contains(self, query, correct):
results = self.graph.query(query)
result_json = json.loads(results.serialize(format='json').decode('utf-8'))
msg = "Expected:\n %s \n- to contain:\n%s" % (result_json, correct)
self.assertEqual(sorted(result_json["head"], key=repr),
sorted(correct["head"], key=repr), msg)
# Sort by repr - rather a hack, but currently the best way I can think
# of to ensure the results are in the same order.
result_bindings = sorted(result_json["results"]["bindings"], key=repr)
correct_bindings = sorted(correct["results"]["bindings"], key=repr)
msg = "Expected:\n %s \n- to contain:\n%s" % (result_bindings, correct_bindings)
self.failUnless(result_bindings==correct_bindings, msg)
testOptional = make_method('optional')
testWildcard = make_method('wildcard')
testUnion = make_method('union')
testUnion3 = make_method('union3')
testSelectVars = make_method('select_vars')
testWildcardVars = make_method('wildcard_vars')
def test4_DAWG_DATASET_COMPLIANCE_is_True(self):
raise SkipTest("known DAWG_DATATSET_COMPLIANCE SPARQL issue")
graph = Graph()
graph.parse(data=test4data, format='n3')
res = graph.query(test4query, dSCompliance=True)
# print("json", res.serialize(format='json'))
assert len(res) == 2
def has_correct_hash(self, resource):
f = RdfUtils.get_format(resource.get_filename())
cg = ConjunctiveGraph()
cg.parse(data=resource.get_content(), format=f)
quads = RdfUtils.get_quads(cg)
h = RdfHasher.make_hash(quads, resource.get_hashstr())
return resource.get_hashstr() == h
def main():
parser = argparse.ArgumentParser(
description='OMIA integration test',
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument(
'--input', '-i', type=str, required=True,
help='Location of input ttl file')
args = parser.parse_args()
graph = ConjunctiveGraph()
graph.parse(args.input, format=rdflib_util.guess_format(args.input))
model_of = URIRef('http://purl.obolibrary.org/obo/RO_0003301')
models = graph.subject_objects(model_of)
model_len = len(list(models))
if model_len < EXPECTED_PAIRS:
logger.error("Not enough model_of predicates in graph:"
" {} expected {} check omia log for"
" warnings".format(model_len, EXPECTED_PAIRS))
exit(1)
omim_diseases = graph.objects(
subject=URIRef('https://monarchinitiative.org/model/OMIA-breed:18'),
predicate=model_of
)
if list(omim_diseases) != [URIRef('http://purl.obolibrary.org/obo/OMIM_275220')]:
logger.error("Missing breed to omim triple for {}".format('OMIA-breed:18'))
exit(1)
logger.info("PASSED")
class TestIssue06(unittest.TestCase):
debug = False
sparql = True
def setUp(self):
self.graph = ConjunctiveGraph()
self.graph.parse(data=testgraph, publicID="testgraph")
def test_issue_6(self):
query = """
PREFIX ex: <http://temp.example.org/terms/>
PREFIX loc: <http://simile.mit.edu/2005/05/ontologies/location#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
SELECT *
WHERE {
{?event ex:date ?date .
FILTER (xsd:date(?date) >= xsd:date("2007-12-31") && xsd:date(?date) <= xsd:date("2008-01-11"))}
UNION
{?event ex:starts ?start; ex:finishes ?end .
FILTER (xsd:date(?start) >= xsd:date("2008-01-02") && xsd:date(?end) <= xsd:date("2008-01-10"))}
}
ORDER BY ?event
"""
self.graph.query(query, DEBUG=False)
class GraphAggregates2(unittest.TestCase):
known_issue = True
sparql = True
def setUp(self):
memStore = plugin.get('IOMemory',Store)()
self.graph1 = Graph(memStore,URIRef("http://example.com/graph1"))
self.graph2 = Graph(memStore,URIRef("http://example.com/graph2"))
self.graph3 = Graph(memStore,URIRef("http://example.com/graph3"))
for n3Str,graph in [(testGraph1N3,self.graph1),
(testGraph2N3,self.graph2),
(testGraph3N3,self.graph3)]:
graph.parse(StringIO(n3Str),format='n3')
self.graph4 = Graph(memStore,RDFS)
self.graph4.parse(RDFS.uri)
self.G = ConjunctiveGraph(memStore)
def testAggregateSPARQL(self):
print sparqlQ
rt = self.G.query(sparqlQ)
assert len(rt) > 1
#print rt.serialize(format='xml')
LOG_NS = Namespace(u'http://www.w3.org/2000/10/swap/log#')
rt=self.G.query(sparqlQ2,initBindings={u'?graph' : URIRef("http://example.com/graph3")})
#print rt.serialize(format='json')
assert rt.serialize('python')[0] == LOG_NS.N3Document,repr(list(rt.serialize('python')))
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]
def test_file(self):
if self.html5lib_installed():
g = ConjunctiveGraph()
g.parse(location='test/rdfa/oreilly.html',
format='rdfa',
lax=True)
self.assertEqual(len(g), 77)
def test_01_query(self):
g = ConjunctiveGraph(self.store)
count = 0
for statement in g.triples((None, None, None)):
count += 1
break
assert count == 1, "Should have found at least one triple"
def check(kws):
cg = ConjunctiveGraph()
cg.parse(**kws)
for g in cg.contexts():
gid = g.identifier
assert isinstance(gid, Identifier)
class RecursionTests(unittest.TestCase):
def setUp(self):
self.graph = ConjunctiveGraph()
self.graph.load(StringIO(testContent), format='n3')
def test_simple_recursion(self):
graph = ConjunctiveGraph()
graph.load(StringIO(BASIC_KNOWS_DATA), format='n3')
results = graph.query(KNOWS_QUERY,
DEBUG=False).serialize(format='python')
results = set([tuple(result) for result in results])
person1 = URIRef('ex:person.1')
person2 = URIRef('ex:person.2')
nose.tools.assert_equal(
results,
set([(person1, None), (person1, Literal('person 3')),
(person2, Literal('person 3'))]))
def test_secondary_recursion(self):
graph = ConjunctiveGraph()
graph.load(StringIO(SUBCLASS_DATA), format='n3')
results = graph.query(SUBCLASS_QUERY,
DEBUG=False).serialize(format='python')
results = set([tuple(result) for result in results])
ob = URIRef('ex:ob')
class1 = URIRef('ex:class.1')
class2 = URIRef('ex:class.2')
class3 = URIRef('ex:class.3')
nose.tools.assert_equal(
results,
set([(ob, class1), (ob, class2), (ob, class3)]))
class TestSparqlEquals(unittest.TestCase):
PREFIXES = {
'rdfs': "http://www.w3.org/2000/01/rdf-schema#"
}
def setUp(self):
testContent = """
@prefix rdfs: <%(rdfs)s> .
<http://example.org/doc/1> rdfs:label "Document 1"@en .
<http://example.org/doc/2> rdfs:label "Document 2"@en .
<http://example.org/doc/3> rdfs:label "Document 3"@en .
""" % self.PREFIXES
self.graph = ConjunctiveGraph()
self.graph.load(StringIO(testContent), format='n3')
def test_uri_equals(self):
uri = URIRef("http://example.org/doc/1")
query = ("""
PREFIX rdfs: <%(rdfs)s>
SELECT ?uri WHERE {
?uri rdfs:label ?label .
FILTER( ?uri = <"""+uri+"""> )
}
""") % self.PREFIXES
res = self.graph.query(query)
expected = [(uri,)]
self.assertEqual(list(res),expected)
class GraphAggregates2(unittest.TestCase):
# known_issue = True
def setUp(self):
memStore = plugin.get("SQLAlchemy", Store)(identifier="rdflib_test", configuration=Literal("sqlite://"))
self.graph1 = Graph(memStore, URIRef("http://example.com/graph1"))
self.graph2 = Graph(memStore, URIRef("http://example.com/graph2"))
self.graph3 = Graph(memStore, URIRef("http://example.com/graph3"))
for n3Str, graph in [(testGraph1N3, self.graph1), (testGraph2N3, self.graph2), (testGraph3N3, self.graph3)]:
graph.parse(StringIO(n3Str), format="n3")
self.graph4 = Graph(memStore, RDFS.uri)
self.graph4.parse(RDFS.uri)
self.G = ConjunctiveGraph(memStore)
def testAggregateSPARQL(self):
raise SkipTest("known_issue with SELECT from NAMED")
rt = self.G.query(sparqlQ)
assert len(rt) > 1
rt = self.G.query(sparqlQ2, initBindings={u"?graph": URIRef(u"http://example.com/graph3")})
try:
import json
assert json
except ImportError:
import simplejson as json
res = json.loads(rt.serialize(format="json").decode("utf-8"))
assert len(res["results"]["bindings"]) == 20, len(res["results"]["bindings"])
def test_issue_250(self):
"""
https://github.com/RDFLib/rdflib/issues/250
When I have a ConjunctiveGraph with the default namespace set,
for example
import rdflib
g = rdflib.ConjunctiveGraph()
g.bind(None, "http://defaultnamespace")
then the Trix serializer binds the default namespace twice in its XML
output, once for the Trix namespace and once for the namespace I used:
print(g.serialize(format='trix').decode('UTF-8'))
<?xml version="1.0" encoding="utf-8"?>
<TriX
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns="http://defaultnamespace"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns="http://www.w3.org/2004/03/trix/trix-1/"
/>
"""
graph = ConjunctiveGraph()
graph.bind(None, "http://defaultnamespace")
sg = graph.serialize(format='trix').decode('UTF-8')
self.assertTrue(
'xmlns="http://defaultnamespace"' not in sg, sg)
self.assertTrue(
'xmlns="http://www.w3.org/2004/03/trix/trix-1/' in sg, sg)
def fromuri(self, uri):
self.uri = uri
if not uri.startswith('http://rdf.freebase.com'):
self.checkuri()
try:
g = ConjunctiveGraph()
g.load(self.uri)
if g:
logger.info("INFO process_rdf.py - returning graph for " + self.uri)
return g
else:
raise Exception('Nothing was returned, probably caused URL serving no RDF or bad RDF (eg. Freebase): '
'"No handlers could be found for logger "process_rdf.py" -- uri was ' + self.uri)
except URLError as e:
logger.error("URLError process_rdf.py - " + e.message)
raise Exception('URLError, cause either bad URL or no internet connection - ' + e.message + '(uri was ' + self.uri + ')')
except SAXParseException as e:
logger.error("SAXParseException process_rdf.py - " + e.message + '(uri was' + self.uri + ')')
raise Exception('SAXParseException')
except AttributeError as e:
logger.error("AttributeError process_rdf.py - " + e.message + '(uri was' + self.uri + ')')
raise Exception('AttributeError')
else:
self.fromfreebaseuri()
class TestSparqlJsonResults(unittest.TestCase):
def setUp(self):
self.graph = ConjunctiveGraph()
self.graph.parse(StringIO(test_data), format="n3")
def _query_result_contains(self, query, correct):
results = self.graph.query(query)
result_json = json.loads(results.serialize(format='json'))
msg = "Expected:\n %s \n- to contain:\n%s" % (result_json, correct)
self.failUnless(result_json["head"]==correct["head"], msg)
result_bindings = sorted(result_json["results"]["bindings"])
correct_bindings = sorted(correct["results"]["bindings"])
msg = "Expected:\n %s \n- to contain:\n%s" % (result_bindings, correct_bindings)
self.failUnless(result_bindings==correct_bindings, msg)
testOptional = make_method('optional')
testWildcard = make_method('wildcard')
testUnion = make_method('union')
testUnion3 = make_method('union3')
testSelectVars = make_method('select_vars')
testWildcardVars = make_method('wildcard_vars')
class GraphAggregates2(unittest.TestCase):
def setUp(self):
memStore = plugin.get('SQLAlchemy', Store)(
identifier="rdflib_test", configuration=Literal("sqlite://"))
self.graph1 = Graph(memStore, URIRef("http://example.com/graph1"))
self.graph2 = Graph(memStore, URIRef("http://example.com/graph2"))
self.graph3 = Graph(memStore, URIRef("http://example.com/graph3"))
for n3Str,graph in [(testGraph1N3, self.graph1),
(testGraph2N3, self.graph2),
(testGraph3N3, self.graph3)]:
graph.parse(StringIO(n3Str), format='n3')
self.graph4 = Graph(memStore, RDFS.uri)
self.graph4.parse(RDFS.uri)
self.G = ConjunctiveGraph(memStore)
def testAggregateSPARQL(self):
rt = self.G.query(sparqlQ)
assert len(rt) > 1
rt = self.G.query(sparqlQ2, initBindings={u'?graph' : URIRef(u"http://example.com/graph3")})
try:
import json
except ImportError:
import simplejson as json
res = json.loads(rt.serialize(format='json'))
assert len(res['results']['bindings']) == 20, len(res['results']['bindings'])
def testParse(self):
g = ConjunctiveGraph()
try:
g.parse("http://groups.csail.mit.edu/dig/2005/09/rein/examples/troop42-policy.n3", format="n3")
except URLError:
from nose import SkipTest
raise SkipTest('No network to retrieve the information, skipping test')
def parse_n3(term_n3):
''' Disclaimer: Quick and dirty hack using the n3 parser. '''
prepstr = ("@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .\n"
"<urn:no_use> <urn:no_use> %s.\n" % term_n3)
g = ConjunctiveGraph()
g.parse(data=prepstr, format='n3')
return [t for t in g.triples((None, None, None))][0][2]
def main(fd, store_type=None, store_id=None, graph_id=None, gzipped=False):
"""
Converts MARC21 data stored in fd to a RDFlib graph.
"""
from rdflib import plugin
if store_type:
msg = "Need a {} identifier for a disk-based store."
assert store_id, msg.format('store')
assert graph_id, msg.format('graph')
store = plugin.get(store_type, Store)(store_id)
else:
store = 'default'
graph = Graph(store=store, identifier=graph_id)
if gzipped:
import gzip
open = gzip.open
try:
records = MARCReader(open(fd))
for i, triple in enumerate(process_records(records)):
graph.add(triple)
if i % 100 == 0:
graph.commit()
if i % 10000 == 0:
print i
finally:
records.close()
return graph
class TestSparqlASK(unittest.TestCase):
def setUp(self):
self.graph = Graph()
io = StringIO("""
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix : <http://goonmill.org/2007/skill.n3#> .
:Foo a rdfs:Class .
:bar a :Foo .
""")
self.graph.load(io, format='n3')
self.compliance_setting, algebra.DAWG_DATASET_COMPLIANCE = algebra.DAWG_DATASET_COMPLIANCE, False
def tearDown(self):
algebra.DAWG_DATASET_COMPLIANCE = self.compliance_setting
def test_ask_true(self):
"""
Ask for a triple that exists, assert that the response is True.
"""
res = self.graph.query('ASK { <http://goonmill.org/2007/skill.n3#bar> a <http://goonmill.org/2007/skill.n3#Foo> } ')
self.assertEquals(res.askAnswer, True, "The answer should have been that the triple was found")
def test_ask_false(self):
"""
Ask for a triple that does not exist, assert that the response is False.
"""
res = self.graph.query('ASK { <http://goonmill.org/2007/skill.n3#baz> a <http://goonmill.org/2007/skill.n3#Foo> } ')
self.assertEquals(res.askAnswer, False, "The answer should have been that the triple was not found")
def test_pretty_broken_xmlliteral(self):
# given:
g = ConjunctiveGraph()
g.add((BNode(), RDF.value, Literal(u'''<p ''', datatype=RDF.XMLLiteral)))
# when:
xmlrepr = g.serialize(format='pretty-xml')
# then:
assert u'''<rdf:value rdf:datatype="http://www.w3.org/1999/02/22-rdf-syntax-ns#XMLLiteral"><p '''.encode('utf-8') in xmlrepr
def testLimit2(self):
graph = ConjunctiveGraph(plugin.get('IOMemory',Store)())
graph.parse(data=test_data2, format="n3")
results = list(graph.query(test_query2,DEBUG=False))
self.assertEqual(len(results), 1)
for title,price in results:
self.assertTrue(title in [Literal("Java Tutorial"),
Literal("COBOL Tutorial")])
def test_pretty_xmlliteral(self):
# given:
g = ConjunctiveGraph()
g.add((BNode(), RDF.value, Literal(u'''<p xmlns="http://www.w3.org/1999/xhtml">See also <a href="#aring">Å</a></p>''', datatype=RDF.XMLLiteral)))
# when:
xmlrepr = g.serialize(format='pretty-xml')
# then:
assert u'''<rdf:value rdf:parseType="Literal"><p xmlns="http://www.w3.org/1999/xhtml">See also <a href="#aring">Å</a></p></rdf:value>'''.encode('utf-8') in xmlrepr
def build_network(rules):
if isinstance(rules, basestring):
rules = StringIO(rules)
graph = ConjunctiveGraph()
graph.load(rules, publicID="test", format="n3")
network = NetworkFromN3(graph, additionalBuiltins={STRING_NS.startsWith: StringStartsWith})
network.feedFactsToAdd(generateTokenSet(extractBaseFacts(graph)))
return network
class TestEmptyBase(unittest.TestCase):
def setUp(self):
self.graph = ConjunctiveGraph()
self.graph.parse(StringIO(test_data),publicID=baseUri)
def test_base_ref(self):
self.failUnless(len(self.graph) == 1,"There should be at least one statement in the graph")
self.failUnless((baseUri,RDF.type,FOAF.Document) in self.graph,"There should be a triple with %s as the subject" % baseUri)
class TestRelativeBase(unittest.TestCase):
def setUp(self):
self.graph = ConjunctiveGraph()
self.graph.parse(StringIO(test_data2),publicID=baseUri2)
def test_base_ref(self):
self.failUnless(len(self.graph) == 1,"There should be at least one statement in the graph")
resolvedBase = URIRef('http://example.com/baz')
self.failUnless((resolvedBase,RDF.type,FOAF.Document) in self.graph,"There should be a triple with %s as the subject" % resolvedBase)
class TestRelativeBase(unittest.TestCase):
def setUp(self):
self.graph = ConjunctiveGraph()
self.graph.parse(StringIO(test_data2), publicID=baseUri2, format="xml")
def test_base_ref(self):
self.assertTrue(len(self.graph),
"There should be at least one statement in the graph")
resolvedBase = URIRef('http://example.com/baz')
self.assertTrue((resolvedBase, RDF.type, FOAF.Document) in self.graph,
"There should be a triple with %s as the subject" % resolvedBase)
def _convertJSONLD(self):
"""
Convert a RDF JSON-LDresult into an RDFLib triple store. This method can be overwritten
in a subclass for a different conversion method.
@return: converted result
@rtype: RDFLib Graph
"""
from rdflib import ConjunctiveGraph
retval = ConjunctiveGraph()
retval.load(self.response, format='json-ld', publicID=' ')
return retval
def test_pretty_broken_xmlliteral(self):
# given:
g = ConjunctiveGraph()
g.add((BNode(), RDF.value, Literal("""<p """,
datatype=RDF.XMLLiteral)))
# when:
xmlrepr = g.serialize(format="pretty-xml")
# then:
assert (
"""<rdf:value rdf:datatype="http://www.w3.org/1999/02/22-rdf-syntax-ns#XMLLiteral"><p """
in xmlrepr)
def testParse(self):
g = ConjunctiveGraph()
try:
g.parse(
"http://groups.csail.mit.edu/dig/2005/09/rein/examples/troop42-policy.n3",
format="n3",
)
except URLError:
from nose import SkipTest
raise SkipTest("No network to retrieve the information, skipping test")
def transform(args):
filename = args[0]
baseuristr = args[1]
with open(filename, "r") as f:
rdfFormat = RdfUtils.get_format(filename)
cg = ConjunctiveGraph()
cg.parse(data=f.read(), format=rdfFormat)
baseuri = URIRef(baseuristr)
outdir = os.path.abspath(os.path.join(str(filename), os.pardir))
RdfTransformer.transform_to_file(cg, baseuri, outdir, filename)
def _get_graph():
inputGraph = ConjunctiveGraph()
contentType = request.headers['Content-Type']
encoding = 'utf8' if not request.content_encoding else request.content_encoding
content = str(request.data, encoding)
fmt = sadi.mimeparse.best_match(
[mt for mt in list(dataFormats.keys()) if mt is not None],
contentType)
if fmt in dataFormats:
inputGraph.parse(data=content, format=dataFormats[fmt])
return inputGraph
def test_html_decoded_entity_xhtml(self):
if sys.version_info[0] == 3:
raise SkipTest('html5lib not yet available for Python 3')
if platform.system() == "Java":
raise SkipTest('problem with HTML entities for html5lib in Jython')
g = ConjunctiveGraph()
g.parse(data=htmlentitydecode(html), format='rdfa')
self.assertEqual(len(g), 1)
self.assertTrue(
g.value(
URIRef("http://example.com"),
URIRef("http://purl.org/dc/terms/title")).eq(u"Exampl\xe9"))
def test_html_entity_xhtml(self):
if sys.version_info[0] == 3:
raise SkipTest('minidom parser strips HTML entities in Python 3.2')
if platform.system() == "Java":
raise SkipTest('problem with HTML entities for html5lib in Jython')
g = ConjunctiveGraph()
warnings.simplefilter('ignore', UserWarning)
g.parse(data=html, format='rdfa')
self.assertEqual(len(g), 1)
self.assertTrue(
g.value(URIRef("http://example.com"),
URIRef("http://purl.org/dc/terms/title")).eq(u"Exampl"))
def test_etc_files():
assert p.exists(etc_dir)
for root, dirs, fnames in os.walk(etc_dir):
for fname in fnames:
name, ext = p.splitext(fname)
if ext != '.n3':
continue
n3_fpath = p.join(root, fname)
expected_graph = ConjunctiveGraph()
expected_graph.parse(n3_fpath, format='n3')
for json_fpath in glob.glob(p.join(root, name+"*.json")):
yield _run_case, json_fpath, expected_graph
def testBaseSerialize(self):
g = Graph()
g.add((
URIRef("http://example.com/people/Bob"),
URIRef("urn:knows"),
URIRef("http://example.com/people/Linda"),
))
s = g.serialize(base="http://example.com/", format="n3")
self.assertTrue("<people/Bob>".encode("latin-1") in s)
g2 = ConjunctiveGraph()
g2.parse(data=s, publicID="http://example.com/", format="n3")
self.assertEqual(list(g), list(g2))
class TestSparqlOPT_FILTER(unittest.TestCase):
def setUp(self):
self.graph = ConjunctiveGraph()
self.graph.load(StringIO(testContent), format='n3')
def test_OPT_FILTER(self):
xd3Objs = [
o for o in self.graph.objects(subject=exNS.xd3, predicate=exNS.p)
]
self.failUnless(
xd3Objs[0].datatype == XSD.double,
"Expecting %r, got instead : %r" % (double1, xd3Objs[0]))
def test_simple_recursion(self):
graph = ConjunctiveGraph()
graph.load(StringIO(BASIC_KNOWS_DATA), format='n3')
results = graph.query(KNOWS_QUERY,
DEBUG=False).serialize(format='python')
results = set([tuple(result) for result in results])
person1 = URIRef('ex:person.1')
person2 = URIRef('ex:person.2')
nose.tools.assert_equal(
results,
set([(person1, None), (person1, Literal('person 3')),
(person2, Literal('person 3'))]))
def test_secondary_recursion(self):
graph = ConjunctiveGraph()
graph.load(StringIO(SUBCLASS_DATA), format='n3')
results = graph.query(SUBCLASS_QUERY,
DEBUG=False).serialize(format='python')
results = set([tuple(result) for result in results])
ob = URIRef('ex:ob')
class1 = URIRef('ex:class.1')
class2 = URIRef('ex:class.2')
class3 = URIRef('ex:class.3')
nose.tools.assert_equal(
results, set([(ob, class1), (ob, class2), (ob, class3)]))
class TestSparqlJsonResults(unittest.TestCase):
sparql = True
def setUp(self):
self.graph = ConjunctiveGraph()
self.graph.parse(StringIO(test_data), format="n3")
def test_base_ref(self):
rt = list(self.graph.query(test_query))
self.failUnless(rt[0][0] == Literal("Alice"),
"Expected:\n 'Alice' \nGot:\n %s" % rt)
class TestEmptyBase(unittest.TestCase):
def setUp(self):
self.graph = ConjunctiveGraph()
self.graph.parse(StringIO(test_data), publicID=baseUri)
def test_base_ref(self):
self.assertTrue(
len(self.graph) == 1,
"There should be at least one statement in the graph")
self.assertTrue(
(baseUri, RDF.type, FOAF.Document) in self.graph,
"There should be a triple with %s as the subject" % baseUri)
def bundle_helper(descriptor,
graph=None,
bundles_directory=None,
homedir=None,
**kwargs):
'''
Helper for creating bundles for testing.
Uses `~owmeta_core.bundle.Installer` to lay out a bundle
Parameters
----------
descriptor : Descriptor
Describes the bundle
graph : rdflib.graph.ConjunctiveGraph, optional
Graph from which the bundle contexts will be generated. If not provided, a graph
will be created with the triple ``(ex:a, ex:b, ex:c)`` in a context named ``ex:ctx``,
where ``ex:`` expands to ``http://example.org/``
bundles_directory : str, optional
The directory where the bundles should be installed. If not provided, creates a
temporary directory to house the bundles and cleans them up afterwards
homedir : str, optional
Test home directory. If not provided, one will be created based on test directory
'''
res = BundleData()
with tempfile.TemporaryDirectory(prefix=__name__ + '.') as testdir:
res.testdir = testdir
res.test_homedir = homedir or p(res.testdir, 'homedir')
res.bundle_source_directory = p(res.testdir, 'bundle_source')
res.bundles_directory = bundles_directory or p(res.test_homedir,
'.owmeta', 'bundles')
if not homedir:
os.mkdir(res.test_homedir)
os.mkdir(res.bundle_source_directory)
if not bundles_directory:
os.makedirs(res.bundles_directory)
# This is a bit of an integration test since it would be a PITA to maintain the bundle
# format separately from the installer
res.descriptor = descriptor
if graph is None:
graph = ConjunctiveGraph()
ctxg = graph.get_context(URIRef('http://example.org/ctx'))
ctxg.add((URIRef('http://example.org/a'),
URIRef('http://example.org/b'),
URIRef('http://example.org/c')))
res.installer = Installer(res.bundle_source_directory,
res.bundles_directory,
graph=graph,
**kwargs)
res.bundle_directory = res.installer.install(res.descriptor)
yield res
def test_pretty_xmlliteral(self):
# given:
g = ConjunctiveGraph()
g.add((
BNode(), RDF.value,
Literal(
u'''<p xmlns="http://www.w3.org/1999/xhtml">See also <a href="#aring">Å</a></p>''',
datatype=RDF.XMLLiteral)))
# when:
xmlrepr = g.serialize(format='pretty-xml')
# then:
assert u'''<rdf:value rdf:parseType="Literal"><p xmlns="http://www.w3.org/1999/xhtml">See also <a href="#aring">Å</a></p></rdf:value>'''.encode(
'utf-8') in xmlrepr
def setUp(self):
memStore = plugin.get('SQLAlchemy',
Store)(identifier="rdflib_test",
configuration=Literal("sqlite://"))
self.graph1 = Graph(memStore, URIRef("graph1"))
self.graph2 = Graph(memStore, URIRef("graph2"))
self.graph3 = Graph(memStore, URIRef("graph3"))
for n3Str, graph in [(testGraph1N3, self.graph1),
(testGraph2N3, self.graph2),
(testGraph3N3, self.graph3)]:
graph.parse(StringIO(n3Str), format='n3')
self.G = ConjunctiveGraph(memStore)
class TestIssue11(unittest.TestCase):
debug = False
sparql = True
def setUp(self):
NS = u"http://example.org/"
self.graph = ConjunctiveGraph()
self.graph.parse(data=testgraph, format="n3", publicID=NS)
def testSPARQL_lessthan_filter_using_negative_integer(self):
rt = self.graph.query(testquery, initNs={'rdf':RDF }, DEBUG=True)
for row in rt:
assert str(row[0]) == "http://example.org/bar"
class TestSparqlOPT_FILTER(unittest.TestCase):
def setUp(self):
self.graph = ConjunctiveGraph()
self.graph.load(StringIO(testContent), format='n3')
def test_OPT_FILTER(self):
results = self.graph.query(QUERY,
DEBUG=False,
initBindings={
'?label': RDFS.label
}).serialize(format='python')
self.failUnless(
list(results) == [doc2], "expecting : %s" % repr([doc2]))
def parse_and_serialize(input_files,
input_format,
guess,
outfile,
output_format,
ns_bindings,
store_conn="",
store_type=None):
if store_type:
store = plugin.get(store_type, Store)()
store.open(store_conn)
graph = ConjunctiveGraph(store)
else:
store = None
graph = ConjunctiveGraph()
for prefix, uri in list(ns_bindings.items()):
graph.namespace_manager.bind(prefix, uri, override=False)
for fpath in input_files:
use_format, kws = _format_and_kws(input_format)
if fpath == '-':
fpath = sys.stdin
elif not input_format and guess:
use_format = guess_format(fpath) or DEFAULT_INPUT_FORMAT
graph.parse(fpath, format=use_format, **kws)
if outfile:
output_format, kws = _format_and_kws(output_format)
kws.setdefault('base', None)
graph.serialize(destination=outfile, format=output_format, **kws)
if store:
store.rollback()
def get_conjunctive_graph(store_id=None):
"""
Returns an open conjunctive graph.
"""
if not store_id:
store_id = DEFAULT_STORE
store = DjangoStore(DEFAULT_STORE)
graph = ConjunctiveGraph(store=store, identifier=store_id)
if graph.open(None) != VALID_STORE:
raise ValueError(
"The store identified by {0} is not a valid store".format(
store_id))
return graph
def load_cache(cache_filename):
cache = {'urls': set(), 'g': ConjunctiveGraph()}
if not cache_filename:
return cache
if not os.path.exists(cache_filename):
return cache
f = open(cache_filename, "rb")
cache = pickle.load(f)
g_serialized = cache['g']
g = ConjunctiveGraph()
g.parse(data=g_serialized)
cache['g'] = g
f.close()
return cache
def _mangled_copy(g):
"Makes a copy of the graph, replacing all bnodes with the bnode ``_blank``."
gcopy = ConjunctiveGraph()
def isbnode(v): return isinstance(v, BNode)
for s, p, o in g:
if isbnode(s):
s = _blank
if isbnode(p):
p = _blank
if isbnode(o):
o = _blank
gcopy.add((s, p, o))
return gcopy
def test_escaping_of_triple_doublequotes():
"""
Issue 186 - Check escaping of multiple doublequotes.
A serialization/deserialization roundtrip of a certain class of
Literals fails when there are both, newline characters and multiple subsequent
quotation marks in the lexical form of the Literal. In this case invalid N3
is emitted by the serializer, which in turn cannot be parsed correctly.
"""
g = ConjunctiveGraph()
g.add((URIRef('http://foobar'), URIRef('http://fooprop'),
Literal('abc\ndef"""""')))
# assert g.serialize(format='n3') == '@prefix ns1: <http:// .\n\nns1:foobar ns1:fooprop """abc\ndef\\"\\"\\"\\"\\"""" .\n\n'
g2 = ConjunctiveGraph()
g2.parse(data=g.serialize(format='n3'), format='n3')
assert g.isomorphic(g2) is True
def deserialize(self, stream, rdf_format='trig', **kwargs):
"""
Deserialize from the `Prov-O <https://www.w3.org/TR/prov-o/>`_
representation to a :class:`~prov.model.ProvDocument` instance.
:param stream: Input data.
"""
newargs = kwargs.copy()
newargs['format'] = rdf_format
container = ConjunctiveGraph()
container.parse(stream, **newargs)
document = ProvDocument()
self.document = document
self.decode_document(container, document)
return document
def __init__(self, *args, **kw):
"""Inicializa o agregador RDF.
"""
super(RDFAggregator, self).__init__('csv', *args, **kw)
self.aggregator = ConjunctiveGraph()
self.aggregator.bind(u'owl', OWL)
self.aggregator.bind(u'lic', LIC)
self.aggregator.bind(u'siorg', SIORG)
self.aggregator.bind(u'siafi', SIAFI)
self.aggregator.bind(u'geo', GEO)
self.aggregator.bind(u'dbpedia', DBPEDIA)
self.aggregator.bind(u'dbprop', DBPROP)
self.aggregator.bind(u'dbo', DBONT)
self.aggregator.bind(u'void', VOID)
self.aggregator.bind(u'foaf', FOAF)
self.aggregator.bind(u'vcard', VCARD)
def _convertRDF(self):
"""
Convert an RDF/XML result into an RDFLib triple store. This method can be overwritten
in a subclass for a different conversion method.
@return: converted result
@rtype: RDFLib Graph
"""
try:
from rdflib.graph import ConjunctiveGraph
except ImportError:
from rdflib import ConjunctiveGraph
retval = ConjunctiveGraph()
# this is a strange hack. If the publicID is not set, rdflib (or the underlying xml parser) makes a funny
#(and, as far as I could see, meaningless) error message...
retval.load(self.response, publicID=' ')
return retval
def update(nanopub_uri):
'''gets called whenever there is a change in the knowledge graph.
Performs a breadth-first knowledge expansion of the current change.'''
#print "Updating on", nanopub_uri
#if not app.nanopub_manager.is_current(nanopub_uri):
# print("Skipping retired nanopub", nanopub_uri)
# return
nanopub = app.nanopub_manager.get(nanopub_uri)
nanopub_graph = ConjunctiveGraph(nanopub.store)
if 'inferencers' in self.config:
for name, service in list(self.config['inferencers'].items()):
service.app = self
if service.query_predicate == self.NS.whyis.updateChangeQuery:
if service.getInstances(nanopub_graph):
print("invoking", name, nanopub_uri)
process_nanopub.apply_async(kwargs={
'nanopub_uri': nanopub_uri,
'service_name': name
},
priority=1)
for name, service in list(self.config['inferencers'].items()):
service.app = self
if service.query_predicate == self.NS.whyis.globalChangeQuery:
process_resource.apply_async(
kwargs={'service_name': name}, priority=5)
def parse(self, source, sink, **kwargs):
# TODO: docstring w. args and return value
encoding = kwargs.get('encoding') or 'utf-8'
if encoding not in ('utf-8', 'utf-16'):
warnings.warn("JSON should be encoded as unicode. " +
"Given encoding was: %s" % encoding)
base = kwargs.get('base') or sink.absolutize(
source.getPublicId() or source.getSystemId() or "")
context_data = kwargs.get('context')
if not context_data and isinstance(source, URLInputSource):
context_data = context_from_urlinputsource(source)
produce_generalized_rdf = kwargs.get('produce_generalized_rdf', False)
data = source_to_json(source)
# NOTE: A ConjunctiveGraph parses into a Graph sink, so no sink will be
# context_aware. Keeping this check in case RDFLib is changed, or
# someone passes something context_aware to this parser directly.
if not sink.context_aware:
conj_sink = ConjunctiveGraph(store=sink.store,
identifier=sink.identifier)
else:
conj_sink = sink
to_rdf(data, conj_sink, base, context_data)