def __get_by_subquery(self, params):
context = params.get("context", None)
inner_query = select("?s")
inner_params = params.copy()
if "order" in params:
# "order" needs to stay in subquery,
# but doesn't do anything useful in main query
del params["order"]
self.__apply_limit_offset_order_get_by_filter(inner_params, inner_query)
query = select("?s", "?p", "?v", "?c").distinct()
query.group(('?s', '?p', '?v'), optional_group(('?v', a, '?c')))
query.where(inner_query)
if not (context is None):
query.from_(context)
# Need ordering in outer query
if "order" in params:
if params["order"] == True:
# Order by subject URI
query.order_by("?s")
else:
# Match another variable, order by it
query.optional_group(("?s", params["order"], "?order"))
query.order_by("?order")
table = self._to_table(self._execute(query))
subjects = {}
results = []
for match in table:
# Make sure subject and predicate are URIs (they have to be!),
# this works around bug in Virtuoso -- it sometimes returns
# URIs as Literals.
subject = URIRef(match["s"])
predicate = URIRef(match["p"])
value = match["v"]
# Add subject to result list if it's not there
if not subject in subjects:
instance_data = {"direct" : {}}
subjects[subject] = instance_data
results.append((subject, instance_data))
# Add predicate to subject's direct predicates if it's not there
direct_attributes = subjects[subject]["direct"]
if not predicate in direct_attributes:
direct_attributes[predicate] = {}
# Add value to subject->predicate if ...
predicate_values = direct_attributes[predicate]
if not value in predicate_values:
predicate_values[value] = []
# Add RDF type of the value to subject->predicate->value list
if "c" in match:
predicate_values[value].append(match["c"])
return results
def get_schema_label(uri,prefix,format):
#store = surf.Store(reader='rdflib',writer='rdflib',rdflib_store='IOMemory')
store = surf.Store(**{"reader": "librdf", "writer" : "librdf", })
session = surf.Session(store)
try:
store.load_triples(source='file://'+settings.PROJECT_PATH+'/d2rq/vocab/'+prefix+'.'+format)
print "Loading from file : "+prefix+"."+format
except:
store.load_triples(source=uri)
print "Loading from Internet : "+uri
#store.enable_logging(True)
ontology = session.get_class(ns.OWL.Ontology)
if(ontology.all().first()): #contient un node Ontology
print "Le schema est une ontologie OWL"
vocab_type = 'owl'
titles = ['rdfs_comment','rdfs_label','dc_title','dcterms_title']
#import pdb; pdb.set_trace()
for o in ontology.all():
for title in titles:
if(len(o.__getattr__(title))>0):
lookup = literal_lang_select(o.__getattr__(title))
if(lookup != None):label=lookup
if not label:
label = unicode(uri)
else: # là c'est la vraie methode,
#au-dessus c'est juste pour les OWL dont l'URL ≠ de l'URI sujet
#donc pas forcément obligatoire à garder non plus
try:
print "Le schema est un vocabulaire RDFS"
vocab_type = 'rdfs'
label = get_label(rdflib.term.URIRef(uri),uri,store)
except:
raise
lookup_args = { 'owl': (ns.OWL.Class,ns.OWL.ObjectProperty),
'rdfs': (ns.RDFS.Class,ns.RDF.Property)}
vocab_classes = list(store.reader._to_table(store.reader._execute(
select("?s").where(("?s", a, lookup_args[vocab_type][0])).filter('(regex(str(?s),"'+uri+'","i"))')# vocab own classes only
)))
vocab_proprietes = list(store.reader._to_table(store.reader._execute(
select("?s").where(("?s", a, lookup_args[vocab_type][1])).filter('(regex(str(?s),"'+uri+'","i"))')
)))
cp = {'classes':[],'proprietes':[]}
for items in ((vocab_classes,'classes'),(vocab_proprietes,'proprietes')):
for triple in items[0]:
if(isinstance(triple['s'],rdflib.term.URIRef) and bool(re.compile(uri).match(unicode(triple['s'])))): #ugly patch waiting for query to work
clabel = get_label(triple['s'],uri,store) #on envoie le subject pour l'identifier
cp[items[1]].append((unicode(triple['s']),clabel))
print items[1]+':'+clabel
store.clear()
store.close()
session.close()
return((label,vocab_type,cp))
def __get_by_n_queries(self, params):
context = params.get("context", None)
query = select("?s")
if not (context is None):
query.from_(context)
self.__apply_limit_offset_order_get_by_filter(params, query)
# Load details, for now the simplest approach with N queries.
# Use _to_table instead of convert to preserve order.
results = []
for match in self._to_table(self._execute(query)):
subject = match["s"]
instance_data = {}
result = self._execute(query_S(subject, True, context))
result = self.convert(result, 'p', 'v', 'c')
instance_data["direct"] = result
if not params.get("only_direct"):
result = self._execute(query_S(subject, False, context))
result = self.convert(result, 'p', 'v', 'c')
instance_data["inverse"] = result
results.append((subject, instance_data))
return results
def process(self, input, output):
print 'processing ' + input.subject
# prefix void: <http://rdfs.org/ns/void#>
#
# select ?from ?to ?overlap
# where {
# ?from void:subset [
# a void:Linkset;
# void:target ?from,
# ?to;
# void:triples ?overlap;
# ] .
# filter( ?from != ?to )
# }
query = select('?to ?overlap').where((input.subject, ns.VOID['subset'], '?linkset'),
('?linkset', a, ns.VOID['Linkset']),
('?linkset', ns.VOID['target'], input.subject),
('?linkset', ns.VOID['target'], '?to'),
('?linkset', ns.VOID['triples'], '?overlap')).filter('(?to != <'+input.subject+'>)')
results = input.session.default_store.execute(query)
for binding in results:
target = binding[0]
overlap = binding[1]
#print target + ' ' + overlap
if overlap >= 50: # "We arbitrarily require at least 50 links." -http://richard.cyganiak.de/2007/10/lod/
output.rdf_type.append(ns.DATAFAQS['Satisfactory'])
if ns.DATAFAQS['Satisfactory'] not in output.rdf_type:
output.rdf_type.append(ns.DATAFAQS['Unsatisfactory'])
output.save()
def test_same_as_inference_works(self):
""" Test owl:sameAs inferencing. """
store, session = self._get_store_session()
self._create_persons(session)
# Let's say Jonathan is the same Person as John
Person = session.get_class(surf.ns.FOAF["Person"])
john = session.get_resource("http://John", Person)
john.load()
jonathan = session.get_resource("http://Jonathan", Person)
jonathan.foaf_homepage = 'http://example.com'
john[surf.ns.OWL['sameAs']] = jonathan
session.commit()
store.reader.define = 'input:same-as "yes"'
query = select("?s").from_(self.CONTEXT)\
.where((jonathan.subject, surf.ns.FOAF['name'], '?s'))
r = store.execute_sparql(unicode(query))
self.assertEquals(set(entry['s']['value'] for entry in r["results"]["bindings"]),
set([john.foaf_name[0]]))
def _classification_search(query, start, limit, **kw):
crdf = CignoRDF()
rootNode = kw.get('node','').split('|')[-1]
rootResource = crdf.Collections(rootNode)
where = crdf.get_where_tree(rootResource)
query_obj = select("?s").where(*where).distinct()
resources = crdf.session.default_store.execute_sparql("%s" % query_obj)
results = []
for resource in resources['results']['bindings']:
res = crdf.CignoResources(resource['s']['value'])
result = {}
result['title'] = res.rdfs_label.first.format()
result['uuid'] = res.cigno_uuid.first.format()
result['detail'] = res.subject.format()
results.append(result)
result = {'rows': results,
'total': len(results)}
result['query_info'] = {
'start': start,
'limit': limit,
'q': query
}
if start > 0:
prev = max(start - limit, 0)
params = urlencode({'q': query, 'start': prev, 'limit': limit})
result['prev'] = reverse('geonode.maps.views.metadata_search') + '?' + params
next = 3
if next > 0:
params = urlencode({'q': query, 'start': next - 1, 'limit': limit})
result['next'] = reverse('geonode.maps.views.metadata_search') + '?' + params
return result
def query_p_s(c, p, direct, context):
"""
Construct :class:`surf.query.Query` with `?s` and `?c` as unknowns.
:param c: the `class`
:param p: the `predicate`
:param bool direct: whether the predicate is direct or inverse
:param context: the context
:return: the query
:rtype: :class:`surf.query.Query`
"""
query = select('?s', '?c').distinct()
if context:
query.from_(context)
for i in range(len(p)):
s, v = ('?s', '?v{0:d}'.format(i)) if direct else ('?v{0:d}'.format(i),
'?s')
if type(p[i]) is URIRef:
query.where((s, p[i], v))
query.optional_group(('?s', a, '?c'))
return query
def _get_by_n_queries(self, params):
context = params.get("context", None)
query = select("?s")
if not (context is None):
query.from_(context)
_apply_solution_modifiers(params, query)
# Load details, for now the simplest approach with N queries.
# Use _to_table instead of convert to preserve order.
results = []
for match in self._to_table(self._execute(query)):
subject = match["s"]
instance_data = {}
result = self._execute(query_s(subject, True, context))
result = self.convert(result, 'p', 'v', 'c')
instance_data["direct"] = result
if not params.get("direct_only"):
result = self._execute(query_s(subject, False, context))
result = self.convert(result, 'p', 'v', 'c')
instance_data["inverse"] = result
results.append((subject, instance_data))
return results
def __get_by_n_queries(self, params):
contexts = params.get("contexts", None)
query = select("?s")
if contexts:
query.from_(*contexts)
query.from_named(*contexts)
self.__apply_limit_offset_order_get_by_filter(params, query)
# Load details, for now the simplest approach with N queries.
# Use _to_table instead of convert to preserve order.
results = []
for match in self._to_table(self._execute(query)):
subject = match["s"]
instance_data = {}
result = self._execute(query_S(subject, True, contexts))
result = self.convert(result, 'p', 'v', 'g', 'c')
instance_data["direct"] = result
if not params.get("only_direct"):
result = self._execute(query_S(subject, False, contexts))
result = self.convert(result, 'p', 'v', 'g', 'c')
instance_data["inverse"] = result
results.append((subject, instance_data))
return results
def test_from_none():
"""
Check that .from_(None) raises.
"""
query = select("?s")
with pytest.raises(ValueError):
query.from_(None)
def test_subquery(self):
""" Try to produce query that contains subquery in WHERE clause. """
expected = canonical(u"""
SELECT ?s ?p ?o
WHERE {
?s ?p ?o.
{ SELECT ?s WHERE { ?s ?a ?b } LIMIT 3 }
}
""")
subquery = select("?s").where(("?s", "?a", "?b")).limit(3)
query = select("?s", "?p", "?o").where(("?s", "?p", "?o"), subquery)
result = canonical(SparqlTranslator(query).translate())
self.assertEqual(expected, result)
def test_subquery(self):
""" Try to produce query that contains subquery in WHERE clause. """
expected = canonical(u"""
SELECT ?s ?p ?o
WHERE {
?s ?p ?o.
{ SELECT ?s WHERE { ?s ?a ?b } LIMIT 3 }
}
""")
subquery = select("?s").where(("?s", "?a", "?b")).limit(3)
query = select("?s", "?p", "?o").where(("?s", "?p", "?o"), subquery)
result = canonical(SparqlTranslator(query).translate())
self.assertEqual(expected, result)
def test_from_none():
"""
Check that .from_(None) raises.
"""
query = select("?s")
with pytest.raises(ValueError):
query.from_(None)
def process(self, input, output):
print 'processing ' + input.subject
# Fails:
#
#PREFIX owl: <http://www.w3.org/2002/07/owl#>
#PREFIX dcterms: <http://purl.org/dc/terms/>
#PREFIX conversion: <http://purl.org/twc/vocab/conversion/>
#SELECT count(distinct ?o) as ?count
#WHERE {
# GRAPH <http://logd.tw.rpi.edu/source/nci-nih-gov/dataset/tobacco-law-coverage/version/2010-Aug-25/conversion/enhancement/1/subset/sample> {
# ?s ?p ?o .
# filter(regex(str(?o),'http://logd.tw.rpi.edu/id/us.*'))
# }
#}
# Passes:
#
#PREFIX owl: <http://www.w3.org/2002/07/owl#>
#PREFIX dcterms: <http://purl.org/dc/terms/>
#PREFIX conversion: <http://purl.org/twc/vocab/conversion/>
#SELECT count(distinct ?o) as ?count
#WHERE {
# GRAPH <http://logd.tw.rpi.edu/source/data-gov/dataset/1000/version/2010-Aug-30/conversion/enhancement/1/subset/sample> {
# ?s ?p ?o .
# filter(regex(str(?o),'http://logd.tw.rpi.edu/id/us.*'))
# }
#}
####
# Query a SPARQL endpoint
#store = Store(reader = 'sparql_protocol', endpoint = 'http://dbpedia.org/sparql')
#session = Session(store)
#session.enable_logging = False
#result = session.default_store.execute_sparql('select distinct ?type where {[] a ?type} limit 2')
#if result:
# for binding in result['results']['bindings']:
# type = binding['type']['value']
# print type
####
store = Store(reader = 'sparql_protocol', endpoint = 'http://logd.tw.rpi.edu/sparql')
session = Session(store)
session.enable_logging = False
query = select("?o").named_group(input.subject,('?s', '?p', '?o')).filter('regex(str(?o),"http://logd.tw.rpi.edu/id/us.*")')
print unicode(query)
result = session.default_store.execute(query)
if result:
for binding in result['results']['bindings']:
print binding['o']['value']
output.rdf_type.append(ns.DATAFAQS['Satisfactory'])
if ns.DATAFAQS['Satisfactory'] not in output.rdf_type:
output.rdf_type.append(ns.DATAFAQS['Unsatisfactory'])
output.save()
def query_SP(s, p, direct, context):
""" Construct :class:`surf.query.Query` with `?v` and `?c` as unknowns. """
s, v = direct and (s, '?v') or ('?v', s)
query = select('?v', '?c').distinct()
query.where((s, p, v)).optional_group(('?v', a, '?c'))
if context:
query.from_(context)
return query
def query_concept(s):
"""
Construct :class:`surf.query.Query` with `?c` as the unknown.
:param s: the `subject`
:return: the query
:rtype: :class:`surf.query.Query`
"""
return select('?c').distinct().where((s, a, '?c'))
def query_SP(s, p, direct, context):
""" Construct :class:`surf.query.Query` with `?v` and `?c` as unknowns. """
s, v = direct and (s, '?v') or ('?v', s)
query = select('?v', '?c').distinct()
query.where((s, p, v)).optional_group(('?v', a, '?c'))
if context:
query.from_(context)
return query
def query_concept(s):
"""
Construct :class:`surf.query.Query` with `?c` as the unknown.
:param s: the `subject`
:return: the query
:rtype: :class:`surf.query.Query`
"""
return select('?c').distinct().where((s, a, '?c'))
def test_simple(self):
""" Try to produce a simple "SELECT ... WHERE ..." query. """
expected = canonical(u"SELECT ?s ?p ?o WHERE { ?s ?p ?o }")
query = select("?s", "?p", "?o").where(("?s", "?p", "?o"))
result = SparqlTranslator(query).translate()
# Translated query should be unicode object.
self.assertTrue(isinstance(result, unicode))
result = canonical(result)
self.assertEqual(expected, result)
def get_label(subject,baseuri,store):
label = None
ns_titles = [ns.RDFS["comment"],ns.RDFS["label"],ns.DC["title"],ns.DCTERMS["title"]]
for title in ns_titles:
query = select("?o").where((subject,title,"?o"))
found_title = list(store.reader._to_table(store.reader._execute(query)))
#print 'Nombre de labels '+title+' :'+str(len(found_title))
if(len(found_title)>0):
label = literal_lang_select([found_title[x]['o'] for x in range(len(found_title))])
if(label==None): #on n'a rien trouvé du tout
label = unicode(subject).replace(baseuri,'')
return label
def test_simple(self):
""" Try to produce a simple "SELECT ... WHERE ..." query. """
expected = canonical(u"SELECT ?s ?p ?o WHERE { ?s ?p ?o }")
query = select("?s", "?p", "?o").where(("?s", "?p", "?o"))
result = SparqlTranslator(query).translate()
# Translated query should be unicode object.
self.assertTrue(isinstance(result, unicode))
result = canonical(result)
self.assertEqual(expected, result)
def test_simple():
"""
Try to produce a simple "SELECT ... WHERE ..." query.
"""
expected = canonical(u"SELECT ?s ?p ?o WHERE { ?s ?p ?o }")
query = select("?s", "?p", "?o").where(("?s", "?p", "?o"))
result = SparqlTranslator(query).translate()
# Translated query should be unicode object.
assert isinstance(result, basestring)
result = canonical(result)
assert expected == result
def test_union(self):
""" Try to produce query containing union. """
expected = canonical(u"""
SELECT ?s
WHERE {
{ ?s ?v1 ?v2} UNION { ?s ?v3 ?v4 }
}
""")
query = select("?s").union(("?s", "?v1", "?v2"), ("?s", "?v3", "?v4"))
result = canonical(SparqlTranslator(query).translate())
self.assertEqual(expected, result)
def test_union(self):
""" Try to produce query containing union. """
expected = canonical(u"""
SELECT ?s
WHERE {
{ ?s ?v1 ?v2} UNION { ?s ?v3 ?v4 }
}
""")
query = select("?s").union(("?s", "?v1", "?v2"), ("?s", "?v3", "?v4"))
result = canonical(SparqlTranslator(query).translate())
self.assertEqual(expected, result)
def query_P_S(c, p, direct, context):
""" Construct :class:`surf.query.Query` with `?s` and `?c` as unknowns. """
query = select('?s', '?c').distinct()
if context:
query.from_(context)
for i in range(len(p)):
s, v = direct and ('?s', '?v%d' % i) or ('?v%d' % i, '?s')
if type(p[i]) is URIRef:
query.where((s, p[i], v))
query.optional_group(('?s', a, '?c'))
return query
def query_P_S(c, p, direct, context):
""" Construct :class:`surf.query.Query` with `?s` and `?c` as unknowns. """
query = select('?s', '?c').distinct()
if context:
query.from_(context)
for i in range(len(p)):
s, v = direct and ('?s', '?v%d' % i) or ('?v%d' % i, '?s')
if type(p[i]) is URIRef:
query.where((s, p[i], v))
query.optional_group(('?s', a, '?c'))
return query
def test_str(self):
""" Try str(query). """
expected = canonical(u"""
SELECT ?s ?p ?o
WHERE {
?s ?p ?o
}
""")
query = select("?s", "?p", "?o").where(("?s", "?p", "?o"))
# test str()
self.assertEqual(expected, canonical(unicode(str(query))))
# test unicode()
self.assertEqual(expected, canonical(unicode(query)))
def test_str(self):
""" Try str(query). """
expected = canonical(u"""
SELECT ?s ?p ?o
WHERE {
?s ?p ?o
}
""")
query = select("?s", "?p", "?o").where(("?s", "?p", "?o"))
# test str()
self.assertEqual(expected, canonical(unicode(str(query))))
# test unicode()
self.assertEqual(expected, canonical(unicode(query)))
def query_s(s, direct, context):
"""
Construct :class:`surf.query.Query` with `?p`, `?v` and `?c` as unknowns.
:param s: the `subject`
:param bool direct: whether the predicate is direct or inverse
:param context: the context
:return: the query
:rtype: :class:`surf.query.Query`
"""
s, v = (s, '?v') if direct else ('?v', s)
query = select('?p', '?v', '?c').distinct()
query.where((s, '?p', v)).optional_group(('?v', a, '?c'))
if context:
query.from_(context)
return query
def test_from(self):
""" Try to produce query that contains FROM clauses. """
expected = canonical(u"""
SELECT ?s ?p ?o
FROM <http://uri1>
FROM <http://uri2>
WHERE {
?s ?p ?o
}
""")
query = select("?s", "?p", "?o").where(("?s", "?p", "?o"))
query.from_("http://uri1", URIRef("http://uri2"))
result = canonical(SparqlTranslator(query).translate())
self.assertEqual(expected, result)
def query_S(s, direct, contexts):
""" Construct :class:`surf.query.Query` with `?p`, `?v` and `?g`, `?c` as
unknowns. """
s, v = direct and (s, '?v') or ('?v', s)
query = select('?p', '?v', '?c', '?g').distinct()
# Get predicate, objects and optionally rdf:type & named graph of
# subject rdf:type and object rdf:type
# TODO fails under Virtuoso as V. doesn't allow ?g to be bound to two
# optional matches
query.where((s, '?p', v)).optional_group(('?v', a, '?c'))\
.optional_group(named_group('?g', (s, a, v)))\
.optional_group(named_group('?g', ('?v', a, '?c')))
if contexts:
query.from_(*contexts)
query.from_named(*contexts)
return query
def query_s(s, direct, context):
"""
Construct :class:`surf.query.Query` with `?p`, `?v` and `?c` as unknowns.
:param s: the `subject`
:param bool direct: whether the predicate is direct or inverse
:param context: the context
:return: the query
:rtype: :class:`surf.query.Query`
"""
s, v = (s, '?v') if direct else ('?v', s)
query = select('?p', '?v', '?c').distinct()
query.where((s, '?p', v)).optional_group(('?v', a, '?c'))
if context:
query.from_(context)
return query
def test_exceptions(self):
""" Test that exceptions are raised on invalid queries. """
store = surf.Store(reader="sparql_protocol",
writer="sparql_protocol",
endpoint="invalid")
def try_query():
store.execute(query)
query = select("?a")
self.assertRaises(SparqlReaderException, try_query)
def try_add_triple():
store.add_triple("?s", "?p", "?o")
self.assertRaises(SparqlWriterException, try_add_triple)
def test_from(self):
""" Try to produce query that contains FROM clauses. """
expected = canonical(u"""
SELECT ?s ?p ?o
FROM <http://uri1>
FROM <http://uri2>
WHERE {
?s ?p ?o
}
""")
query = select("?s", "?p", "?o").where(("?s", "?p", "?o"))
query.from_("http://uri1", URIRef("http://uri2"))
result = canonical(SparqlTranslator(query).translate())
self.assertEqual(expected, result)
def test_exceptions(self):
""" Test that exceptions are raised on invalid queries. """
store = surf.Store(reader = "sparql_protocol",
writer = "sparql_protocol",
endpoint = "invalid")
def try_query():
store.execute(query)
query = select("?a")
self.assertRaises(SparqlReaderException, try_query)
def try_add_triple():
store.add_triple("?s", "?p", "?o")
self.assertRaises(SparqlWriterException, try_add_triple)
def process(self, input, output):
store = surf.Store(reader = 'rdflib', writer = 'rdflib', rdflib_store = 'IOMemory')
session = surf.Session(store)
store.load_triples(source = input.subject)
output.datafaqs_resolved_triples = store.size();
query = select('?triples').where((input.subject, ns.VOID['triples'], '?triples'))
for count in store.execute(query):
output.void_triples.append(count)
output.rdf_type.append(ns.DATAFAQS['Satisfactory'])
print str(store.size()) + ' dereferenced RDF triples asserted that ' + input.subject + ' has ' + str(count) + ' triples.'
if ns.DATAFAQS['Satisfactory'] not in output.rdf_type:
output.rdf_type.append(ns.DATAFAQS['Unsatisfactory'])
print str(store.size()) + ' dereferenced RDF triples, but no void:triples asserted for ' + input.subject
output.save()
def _get_by(self, params):
# Decide which loading strategy to use
if "full" in params:
if self.use_subqueries:
return self.__get_by_subquery(params)
else:
return self.__get_by_n_queries(params)
# No details, just subjects and classes
query = select("?s", "?c", "?g")
self.__apply_limit_offset_order_get_by_filter(params, query)
query.optional_group(("?s", a, "?c"))
# Query for the same tuple to get the named graph if obtainable
query.optional_group(named_group("?g", ("?s", a, "?c")))
contexts = params.get("contexts", None)
if contexts:
query.from_(*contexts)
query.from_named(*contexts)
# Load just subjects and their types
table = self._to_table(self._execute(query))
# Create response structure, preserve order, don't include
# duplicate subjects if some subject has multiple types
subjects = {}
results = []
for match in table:
subject = match["s"]
if not subject in subjects:
instance_data = {"direct" : {a : {}}}
subjects[subject] = instance_data
results.append((subject, instance_data))
# "context" comes from an optional group and is missing if the
# triple is stored in the unamed graph
context = match.get("g")
if "c" in match:
concept = match["c"]
subjects[subject]["direct"][a][concept] = {context: []}
return results
def test_from_named():
"""
Try to produce query that contains FROM & FROM NAMED clauses.
"""
expected = canonical(u"""
SELECT ?s ?p ?o
FROM <http://uri1>
FROM NAMED <http://uri1>
FROM NAMED <http://uri2>
WHERE {
?s ?p ?o
}
""")
query = select("?s", "?p", "?o").where(("?s", "?p", "?o"))
query.from_("http://uri1")
query.from_named("http://uri1", URIRef("http://uri2"))
result = canonical(SparqlTranslator(query).translate())
assert expected == result
def test_from_named():
"""
Try to produce query that contains FROM & FROM NAMED clauses.
"""
expected = canonical(u"""
SELECT ?s ?p ?o
FROM <http://uri1>
FROM NAMED <http://uri1>
FROM NAMED <http://uri2>
WHERE {
?s ?p ?o
}
""")
query = select("?s", "?p", "?o").where(("?s", "?p", "?o"))
query.from_("http://uri1")
query.from_named("http://uri1", URIRef("http://uri2"))
result = canonical(SparqlTranslator(query).translate())
assert expected == result
def test_json_datatypes(self):
""" Test that proper datatypes are returned. """
# Tests for a bug wrt datatype uri with AllegroGraph
store, session = self._get_store_session(use_default_context=False)
Person = session.get_class(surf.ns.FOAF + "Person")
# Store datatype
jake = session.get_resource("http://Jake", Person)
jake.foaf_name = "Jake"
jake.foaf_age = 62
jake.save()
# Get birthday
query = select('?age').where(('?s', a, Person.uri),
('?s', ns.FOAF.age, '?age'))
result = store.execute_sparql(unicode(query))
assert len(result['results']['bindings']) == 1
entry = result['results']['bindings'][0]
# Test that rdflib type is properly constructed
age = json_to_rdflib(entry['age'])
self.assertEquals(age.toPython(), 62)
def test_json_datatypes(self):
""" Test that proper datatypes are returned. """
# Tests for a bug wrt datatype uri with AllegroGraph
store, session = self._get_store_session(use_default_context=False)
Person = session.get_class(surf.ns.FOAF + "Person")
# Store datatype
jake = session.get_resource("http://Jake", Person)
jake.foaf_name = "Jake"
jake.foaf_age = 62
jake.save()
# Get birthday
query = select('?age').where(('?s', a, Person.uri),
('?s', ns.FOAF.age, '?age'))
result = store.execute_sparql(unicode(query))
assert len(result['results']['bindings']) == 1
entry = result['results']['bindings'][0]
# Test that rdflib type is properly constructed
age = json_to_rdflib(entry['age'])
self.assertEquals(age.toPython(), 62)
def test_same_as_inference_works(self):
""" Test owl:sameAs inferencing. """
store, session = self._get_store_session()
# Let's say Jonathan is the same Person as John
Person = session.get_class(surf.ns.FOAF["Person"])
john = session.get_resource("http://John", Person)
john.load()
jonathan = session.get_resource("http://Jonathan", Person)
jonathan.foaf_homepage = 'http://example.com'
john[surf.ns.OWL['sameAs']] = jonathan
session.commit()
store.reader.define = 'input:same-as "yes"'
query = select("?s").from_(self.CONTEXT)\
.where((jonathan.subject, surf.ns.FOAF['name'], '?s'))
r = store.execute_sparql(unicode(query))
self.assertEquals(
set(entry['s'] for entry in r["results"]["bindings"]),
set([john.foaf_name[0]]))
def query_p_s(c, p, direct, context):
"""
Construct :class:`surf.query.Query` with `?s` and `?c` as unknowns.
:param c: the `class`
:param p: the `predicate`
:param bool direct: whether the predicate is direct or inverse
:param context: the context
:return: the query
:rtype: :class:`surf.query.Query`
"""
query = select('?s', '?c').distinct()
if context:
query.from_(context)
for i in range(len(p)):
s, v = ('?s', '?v{0:d}'.format(i)) if direct else ('?v{0:d}'.format(i), '?s')
if type(p[i]) is URIRef:
query.where((s, p[i], v))
query.optional_group(('?s', a, '?c'))
return query
def _get_by(self, params):
# Decide which loading strategy to use
if "full" in params:
if self.use_subqueries:
return self.__get_by_subquery(params)
else:
return self.__get_by_n_queries(params)
# No details, just subjects and classes
query = select("?s", "?c")
self.__apply_limit_offset_order_get_by_filter(params, query)
query.optional_group(("?s", a, "?c"))
context = params.get("context", None)
if not (context is None):
query.from_(context)
# Load just subjects and their types
table = self._to_table(self._execute(query))
# Create response structure, preserve order, don't include
# duplicate subjects if some subject has multiple types
subjects = {}
results = []
for match in table:
subject = match["s"]
if not subject in subjects:
instance_data = {"direct" : {a : {}}}
subjects[subject] = instance_data
results.append((subject, instance_data))
if "c" in match:
concept = match["c"]
subjects[subject]["direct"][a][concept] = []
return results
def _classification_search(query, start, limit, **kw):
crdf = CignoRDF()
rootNode = kw.get('node','').split('|')[-1]
rootResource = crdf.Collections(rootNode)
where = crdf.get_where_tree(rootResource)
query_obj = select("?s").where(*where).distinct()
querys = sanitize_sparql("%s" % query_obj)
resources = crdf.session.default_store.execute_sparql(querys)
results = []
for resource in resources['results']['bindings']:
res = crdf.CignoResources(resource['s']['value'])
result = {}
result['title'] = res.rdfs_label.first.format()
result['uuid'] = res.cigno_uuid.first.format()
result['detail'] = res.subject.format()
results.append(result)
result = {'rows': results,
'total': len(results)}
result['query_info'] = {
'start': start,
'limit': limit,
'q': query
}
if start > 0:
prev = max(start - limit, 0)
params = urlencode({'q': query, 'start': prev, 'limit': limit})
result['prev'] = reverse('geonode.maps.views.metadata_search') + '?' + params
next = 3
if next > 0:
params = urlencode({'q': query, 'start': next - 1, 'limit': limit})
result['next'] = reverse('geonode.maps.views.metadata_search') + '?' + params
return result
def _get_by(self, params):
# Decide which loading strategy to use
if "full" in params:
if self.use_subqueries:
return self._get_by_subquery(params)
else:
return self._get_by_n_queries(params)
# No details, just subjects and classes
query = select("?s", "?c")
_apply_solution_modifiers(params, query)
query.optional_group(("?s", a, "?c"))
context = params.get("context", None)
if not (context is None):
query.from_(context)
# Load just subjects and their types
table = self._to_table(self._execute(query))
# Create response structure, preserve order, don't include
# duplicate subjects if some subject has multiple types
subjects = {}
results = []
for match in table:
subject = match["s"]
if subject not in subjects:
instance_data = {"direct": {a: {}}}
subjects[subject] = instance_data
results.append((subject, instance_data))
if "c" in match:
concept = match["c"]
subjects[subject]["direct"][a][concept] = []
return results
def __get_by_subquery(self, params):
contexts = params.get("contexts", None)
inner_query = select("?s")
inner_params = params.copy()
if "order" in params:
# "order" needs to stay in subquery,
# but doesn't do anything useful in main query
del params["order"]
self.__apply_limit_offset_order_get_by_filter(inner_params, inner_query)
query = select("?s", "?p", "?v", "?c", "?g").distinct()
# Get values with object type & context
# TODO we need to query both contexts, from ?s -> rdf_type & ?v -> rdf_type but Virtuoso does not bind ?g twice. Bug or feature?
query.group(('?s', '?p', '?v'),
optional_group(('?v', a, '?c')),
optional_group(named_group("?g", ("?s", a, "?v"))))
#optional_group(named_group("?g", ("?v", a, "?c"))))
query.where(inner_query)
if contexts:
query.from_(*contexts)
query.from_named(*contexts)
# Need ordering in outer query
if "order" in params:
if params["order"] == True:
# Order by subject URI
query.order_by("?s")
else:
# Match another variable, order by it
query.optional_group(("?s", params["order"], "?order"))
query.order_by("?order")
table = self._to_table(self._execute(query))
subjects = {}
results = []
for match in table:
# Make sure subject and predicate are URIs (they have to be!),
# this works around bug in Virtuoso -- it sometimes returns
# URIs as Literals.
subject = URIRef(match["s"])
predicate = URIRef(match["p"])
value = match["v"]
# Add subject to result list if it's not there
if not subject in subjects:
instance_data = {"direct" : {}}
subjects[subject] = instance_data
results.append((subject, instance_data))
# Add predicate to subject's direct predicates if it's not there
direct_attributes = subjects[subject]["direct"]
if not predicate in direct_attributes:
direct_attributes[predicate] = {}
# "context" comes from an optional group and is missing if the
# triple is stored in the unamed graph
context = match.get("g")
# Add value to subject->predicate if ...
predicate_values = direct_attributes[predicate]
if not value in predicate_values:
predicate_values[value] = {context: []}
# Add RDF type of the value to subject->predicate->value list
if "c" in match:
predicate_values[value][context].append(match["c"])
return results
def _get_by_subquery(self, params):
context = params.get("context", None)
inner_query = select("?s")
inner_params = params.copy()
if "order" in params:
# "order" needs to stay in subquery,
# but doesn't do anything useful in main query
del params["order"]
_apply_solution_modifiers(inner_params, inner_query)
if params.get('direct_only'):
query = select("?s", "?p", "?v", "?c").distinct()
query.group(('?s', '?p', '?v'), optional_group(('?v', a, '?c')))
else:
direct_query = select("?s", "?p", "?v", "?c", '("0" AS ?i)')
direct_query.distinct()
direct_query.group(('?s', '?p', '?v'),
optional_group(('?v', a, '?c')))
indirect_query = select("?s", "?p", "?v", "?c", '("1" AS ?i)')
indirect_query.distinct()
indirect_query.group(('?v', '?p', '?s'),
optional_group(('?v', a, '?c')))
query = select("?s", "?p", "?v", "?c", "?i")
query.union(direct_query, indirect_query)
query.where(inner_query)
if not (context is None):
query.from_(context)
# Need ordering in outer query
if "order" in params:
if params["order"]:
# Order by subject URI
query.order_by("?s")
else:
# Match another variable, order by it
query.optional_group(("?s", params["order"], "?order"))
query.order_by("?order")
table = self._to_table(self._execute(query))
subjects = {}
results = []
for match in table:
# Make sure subject and predicate are URIs (they have to be!),
# this works around bug in Virtuoso -- it sometimes returns
# URIs as Literals.
subject = URIRef(match["s"])
predicate = URIRef(match["p"])
value = match["v"]
# Inverse given if direct_only is False
inverse = match.get("i") == "1"
# Add subject to result list if it's not there
if subject not in subjects:
instance_data = {"direct": {}, "inverse": {}}
subjects[subject] = instance_data
results.append((subject, instance_data))
if inverse:
attributes = subjects[subject]["inverse"]
else:
attributes = subjects[subject]["direct"]
# Add predicate to subject's predicates if it's not there
if predicate not in attributes:
attributes[predicate] = {}
# Add value to subject->predicate if ...
predicate_values = attributes[predicate]
if value not in predicate_values:
predicate_values[value] = []
# Add RDF type of the value to subject->predicate->value list
if "c" in match:
predicate_values[value].append(match["c"])
return results
def get_not_empty_members(self, res):
where = self.get_where_tree(res)
query = select("?c").where(*where).distinct()
querys = sanitize_sparql("%s" % query)
result = self.session.default_store.execute_sparql(querys)
return result['results']['bindings']
def process(self, input, output):
print 'processing ' + input.subject
endpoint = False
# TODO: add dcat:distribution [ a sd:NamedGraph; sd:name ; prov:hadLocation
# like https://github.com/timrdf/DataFAQs/blob/master/services/sadi/ckan/add-metadata-materials/sample-inputs/arrayexpress-e-afmx-1.ttl#L49
if len(input.void_sparqlEndpoint) > 0:
# <http://datahub.io/dataset/dbpedia>
# void:sparqlEndpoint <http://dbpedia.org/sparql> .
endpoint = self.surfSubject(input.void_sparqlEndpoint.first)
print 'void:sparqlEndpoint: ' + endpoint
else:
# <http://datahub.io/dataset/dbpedia>
# dcat:distribution [
# dct:format [
# a dct:IMT;
# rdf:value "api/sparql";
# rdfs:label "api/sparql"
# ];
# a dcat:Distribution ;
# dcat:accessURL <http://dbpedia.org/sparql>
# ]; .
query = select("?url").where((input.subject, ns.DCAT['distribution'], "?distro"),
("?distro", ns.DCTERMS['format'], "?format"),
("?format", ns.RDF['value'], rdflib.Literal('api/sparql')),
("?distro", ns.DCAT['accessURL'], "?url"))
for bindings in input.session.default_store.execute(query):
#print 'creator: ' + bindings[0] + ' ' + bindings[1]
endpoint = self.surfSubject(bindings[0])
print 'dcat:distribution dcat:accessURL: ' + endpoint
if endpoint is False:
print 'WARNING: could not find SPARQL endpoint to query; skipping ' + input.subject
output.rdf_type.append(ns.DATAFAQS['Unsatisfactory'])
output.save()
return
ng='http://purl.org/twc/health/source/healthdata-tw-rpi-edu/dataset/cr-full-dump/version/latest'
Class = output.session.get_class(ns.RDFS['Class'])
Predicate = output.session.get_class(ns.RDF['Property'])
####
# Query a SPARQL endpoint
store = Store(reader = 'sparql_protocol', endpoint = endpoint)
session = Session(store)
session.enable_logging = False
for predicate in self.predicates:
results = session.default_store.execute_sparql( # TODO: handle optional named graph.
'''
select (count(*) as ?count)
where {
[] <'''+predicate+'''> []
}'''
)
#graph <'''+ng+'''> {
count = False
if isinstance(results, xml.dom.minidom.Document):
for result in results.getElementsByTagName('result'):
for binding in result.getElementsByTagName('binding'):
for value in result.getElementsByTagName('literal'):
count = int(value.firstChild.data)
predR = output.session.get_resource(predicate, Predicate)
predR.sio_count = count
predR.save()
output.rdf_type.append(ns.DATAFAQS['Satisfactory'])
print str(count) + ' ' + predicate
elif results:
print results
for binding in results['results']['bindings']:
count = binding['count']['value']
print count
for classU in self.classes:
results = session.default_store.execute_sparql( # TODO: handle optional named graph.
'''
select (count(*) as ?count)
where {
[] a <'''+classU+'''>
}'''
)
#graph <'''+ng+'''> {
count = False
if isinstance(results, xml.dom.minidom.Document):
for result in results.getElementsByTagName('result'):
for binding in result.getElementsByTagName('binding'):
for value in result.getElementsByTagName('literal'):
count = int(value.firstChild.data)
classR = output.session.get_resource(classU, Class)
classR.sio_count = count
classR.save()
output.rdf_type.append(ns.DATAFAQS['Satisfactory'])
print str(count) + ' ' + classU
elif results:
print results
for binding in results['results']['bindings']:
count = binding['count']['value']
print count
####
# Query the RDF graph POSTed: input.session.default_store.execute
# Walk through all Things in the input graph (using SuRF):
# Thing = input.session.get_class(ns.OWL['Thing'])
# for person in Thing.all():
# Create a class in the output graph:
# Document = output.session.get_class(ns.FOAF['Document'])
if ns.DATAFAQS['Satisfactory'] not in output.rdf_type:
output.rdf_type.append(ns.DATAFAQS['Unsatisfactory'])
else:
Ontology = output.session.get_class(ns.OWL['Ontology'])
output.void_vocabulary.append(Ontology('http://www.w3.org/ns/prov#'))
output.save()
def test_from_none(self):
""" Check that .from_(None) raises. """
query = select("?s")
self.assertRaises(ValueError, lambda: query.from_(None))
def test_from_none(self):
""" Check that .from_(None) raises. """
query = select("?s")
self.assertRaises(ValueError, lambda: query.from_(None))
def query_Concept(subject):
""" Construct :class:`surf.query.Query` with `?c` as the unknown. """
return select('?c').distinct().where((subject, a, '?c'))
def query_Concept(subject):
""" Construct :class:`surf.query.Query` with `?c` as the unknown. """
return select('?c').distinct().where((subject, a, '?c'))