def determine_remap_target(self,g,c,s,var_bindings):
full_path = None
if type(s) == Literal: return None
node_type = get_property(g, s, rdf.type)
subject_uri = str(s)
if type(s) == BNode:
assert node_type != None, "%s is a bnode with no type"%s.n3()
t = RecordObject[node_type]
if (t.path == None): return None
elif type(s) == URIRef:
if subject_uri.startswith("urn:smart_external_id:"):
full_path = self.internal_id(c, s)
assert full_path or node_type != None, "%s is a new external URI node with no type"%s.n3()
if full_path == None:
t = RecordObject[node_type]
assert t.path != None, "Non-gettable type %s shouldn't be a URI node."%t
elif subject_uri.startswith(smart_path("")):
return None
else:
self.assert_never_a_subject(g,s)
return None
# If we got here, we need to remap the node "s".
if full_path == None:
full_path = t.determine_full_path(var_bindings)
return full_path
def augment_data(g, var_bindings, new_nodes):
# Quick and dirty CodedValue augmentation to start.
# TODO: generalize this mechanism to allow plug-in extensibility!
code_q = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX sp: <http://smartplatforms.org/terms#>
SELECT ?c
WHERE { ?cv rdf:type sp:CodedValue .
?cv sp:code ?c. }"""
codes = set(g.query(code_q))
print "queried ", code_q, codes
codes = filter(lambda s: type(s) == URIRef and \
not str(s).startswith("urn:smart_external_id:") and \
not str(s).startswith(smart_path("")), codes)
# For any URI nodes referencing external vocabularies...
for c in codes:
augment_code_uri(g,c)
# Attach each data element (med, problem, lab, etc), to the
# base record URI with the sp:hasDataElement predicate.
recordURI = URIRef(smart_path("/records/%s"%var_bindings['record_id']))
for n in new_nodes:
node_type = get_property(g, n, rdf.type)
# Make sure this is a "medical data element" type
t = ontology[node_type]
if (t.base_path == None): continue
if (not t.base_path.startswith("/records")): continue
if (n == recordURI): continue # don't assert that the record has itself as an element
g.add((recordURI, sp.hasMedicalDataElement, n))
g.add((recordURI, rdf.type, sp.MedicalRecord))