def get_concept_hierarchy(self):
# same as parent query, only:
# running against rdflib in-memory graph, not SPARQL endpoint
# a single graph, not a multi-graph (since it's an RDF/XML or Turtle file)
"""
Function to draw concept hierarchy for vocabulary
"""
def build_hierarchy(bindings_list, broader_concept=None, level=0):
"""
Recursive helper function to build hierarchy list from a bindings list
Returns list of tuples: (<level>, <concept>, <concept_preflabel>, <broader_concept>)
"""
level += 1 # Start with level 1 for top concepts
hierarchy = []
narrower_list = sorted(
[
binding_dict for binding_dict in bindings_list if
# Top concept
((broader_concept is None) and
(binding_dict.get("broader_concept") is None)) or
# Narrower concept
((binding_dict.get("broader_concept") is not None) and
(binding_dict["broader_concept"] == broader_concept))
],
key=lambda binding_dict: binding_dict["concept_preflabel"],
)
for binding_dict in narrower_list:
concept = binding_dict["concept"]
hierarchy += [(
level,
concept,
binding_dict["concept_preflabel"],
binding_dict["broader_concept"]
if binding_dict.get("broader_concept") else None,
)] + build_hierarchy(bindings_list, concept, level)
return hierarchy
vocab = g.VOCABS[self.vocab_id]
q = """
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX dct: <http://purl.org/dc/terms/>
SELECT DISTINCT ?concept ?concept_preflabel ?broader_concept
WHERE {{
{{ ?concept skos:inScheme <{vocab_uri}> . }}
UNION
{{ ?concept skos:topConceptOf <{vocab_uri}> . }}
UNION
{{ <{vocab_uri}> skos:hasTopConcept ?concept . }}
?concept skos:prefLabel ?concept_preflabel .
OPTIONAL {{ ?concept skos:broader ?broader_concept .
?broader_concept skos:inScheme <{vocab_uri}> .
}}
FILTER(lang(?concept_preflabel) = "{language}" || lang(?concept_preflabel) = "")
}}
ORDER BY ?concept_preflabel""".format(
vocab_uri=vocab.concept_scheme_uri, language=self.language)
bindings_list = []
for r in self.gr.query(q):
bindings_list.append({
# ?concept ?concept_preflabel ?broader_concept
"concept": r[0],
"concept_preflabel": r[1],
"broader_concept": r[2],
})
assert bindings_list is not None, "FILE concept hierarchy query failed"
hierarchy = build_hierarchy(bindings_list)
return Source.draw_concept_hierarchy(hierarchy, self.request,
self.vocab_id)
def get_concept_hierarchy(self):
# return FILE.hierarchy[self.vocab_id]
pass
g = FILE.load_pickle_graph(self.vocab_id)
result = g.query(
"""
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT (COUNT(?mid) AS ?length) ?c ?pl ?parent
WHERE {{
?c a skos:Concept .
?cs (skos:hasTopConcept | skos:narrower)* ?mid .
?mid (skos:hasTopConcept | skos:narrower)+ ?c .
?c skos:prefLabel ?pl .
?c (skos:topConceptOf | skos:broader) ?parent .
FILTER (?cs = <{}>)
}}
GROUP BY ?c ?pl ?parent
ORDER BY ?length ?parent ?pl
""".format(self.uri)
)
cs = []
for row in result:
cs.append({
'length': {'value': row['length']},
'c': {'value': row['c']},
'pl': {'value': row['pl']},
'parent': {'value': row['parent']}
})
hierarchy = []
previous_parent_uri = None
last_index = 0
for c in cs:
# insert all topConceptOf directly
if str(c['parent']['value']) == self.uri:
hierarchy.append((
int(c['length']['value']),
c['c']['value'],
c['pl']['value'],
None
))
else:
# If this is not a topConcept, see if it has the same URI as the previous inserted Concept
# If so, use that Concept's index + 1
this_parent = c['parent']['value']
if this_parent == previous_parent_uri:
# use last inserted index
hierarchy.insert(last_index + 1, (
int(c['length']['value']),
c['c']['value'],
c['pl']['value'],
c['parent']['value']
))
last_index += 1
# This is not a TopConcept and it has a differnt parent from the previous insert
# So insert it after it's parent
else:
i = 0
parent_index = 0
for t in hierarchy:
if this_parent in t[1]:
parent_index = i
i += 1
hierarchy.insert(parent_index + 1, (
int(c['length']['value']),
c['c']['value'],
c['pl']['value'],
c['parent']['value']
))
last_index = parent_index + 1
previous_parent_uri = this_parent
return Source.draw_concept_hierarchy(hierarchy, self.request, self.vocab_id)
def get_concept_hierarchy(self, concept_scheme_uri):
# returns an ordered list of tuples, (hierarchy level, Concept URI, Concept prefLabel)
s = VOCBENCH('x', self.request)._authed_request_object()
r = s.post(config.VB_ENDPOINT + '/SPARQL/evaluateQuery',
data={
'query':
'''
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT (COUNT(?mid) AS ?length) ?c ?pl ?parent
WHERE {{
?c a skos:Concept .
?cs (skos:hasTopConcept | skos:narrower)* ?mid .
?mid (skos:hasTopConcept | skos:narrower)+ ?c .
?c skos:prefLabel ?pl .
?c (skos:topConceptOf | skos:broader) ?parent .
FILTER (?cs = <{}>)
}}
GROUP BY ?c ?pl ?parent
ORDER BY ?length ?parent ?pl'''.format(concept_scheme_uri),
'ctx_project':
self.vocab_id
})
if r.status_code == 200:
test = r.content.decode('utf-8')
"""<?xml version="1.0" encoding="UTF-8"?><stresponse request="evaluateQuery" type="error">
<msg>org.eclipse.rdf4j.repository.http.HTTPQueryEvaluationException: Query evaluation error: com.ontotext.trree.util.NotEnoughMemoryForDistinctGroupBy: Insufficient free Heap Memory 172Mb for group by and distinct, threshold:250Mb, reached 0Mb (HTTP status 500)</msg>
</stresponse>
"""
cs = json.loads(r.content.decode(
'utf-8'))['result']['sparql']['results']['bindings']
hierarchy = []
previous_parent_uri = None
last_index = 0
for c in cs:
# insert all topConceptOf directly
test = c
if 'parent' not in c:
continue
if str(c['parent']['value']) == concept_scheme_uri:
hierarchy.append((int(c['length']['value']),
c['c']['value'], c['pl']['value'], None))
else:
# If this is not a topConcept, see if it has the same URI as the previous inserted Concept
# If so, use that Concept's index + 1
this_parent = c['parent']['value']
if this_parent == previous_parent_uri:
# use last inserted index
hierarchy.insert(
last_index + 1,
(int(c['length']['value']), c['c']['value'],
c['pl']['value'], c['parent']['value']))
last_index += 1
# This is not a TopConcept and it has a differnt parent from the previous insert
# So insert it after it's parent
else:
i = 0
parent_index = 0
for t in hierarchy:
if this_parent in t[1]:
parent_index = i
i += 1
hierarchy.insert(
parent_index + 1,
(int(c['length']['value']), c['c']['value'],
c['pl']['value'], c['parent']['value']))
last_index = parent_index + 1
previous_parent_uri = this_parent
return Source.draw_concept_hierarchy(hierarchy, self.request,
self.vocab_id)
else:
raise VbException('There was an error: ' +
r.content.decode('utf-8'))