def search_records(cls, query):
c = DemographicConnector()
res = c.sparql(query)
m = parse_rdf(res)
# for each person, look up their demographics object.
from smart.models.record_object import RecordObject
people = m.triples((None, rdf['type'], sp.Demographics))
pobj = RecordObject[sp.Demographics]
obtained = set()
return_graph = bound_graph()
for person in people:
p = person[0] # subject
# Connect to RDF Store
pid = re.search("\/records\/(.*?)\/demographics", str(p)).group(1)
if pid in obtained: continue
print "matched ", p," to ", pid
obtained.add(pid)
c = RecordStoreConnector(Record.objects.get(id=pid))
# Pull out demographics
p_uri = p.n3() # subject URI
p_subgraph = parse_rdf(c.sparql(pobj.query_one(p_uri)))
# Append to search result graph
return_graph += p_subgraph
return serialize_rdf(return_graph)
def search_records(cls, query):
c = DemographicConnector()
res = c.sparql(query)
m = parse_rdf(res)
# for each person, look up their demographics object.
from smart.models.record_object import RecordObject
people = m.triples((None, rdf['type'], sp.Demographics))
pobj = RecordObject[sp.Demographics]
obtained = set()
return_graph = bound_graph()
for person in people:
p = person[0] # subject
# Connect to RDF Store
pid = re.search("\/records\/(.*?)\/demographics", str(p)).group(1)
if pid in obtained: continue
print "matched ", p, " to ", pid
obtained.add(pid)
c = RecordStoreConnector(Record.objects.get(id=pid))
# Pull out demographics
p_uri = p.n3() # subject URI
p_subgraph = parse_rdf(c.sparql(pobj.query_one(p_uri)))
# Append to search result graph
return_graph += p_subgraph
return serialize_rdf(return_graph)
def record_get_allergies(request, *args, **kwargs):
record_id = kwargs['record_id']
a = RecordObject["http://smartplatforms.org/terms#Allergy"]
ae = RecordObject["http://smartplatforms.org/terms#AllergyExclusion"]
c = RecordStoreConnector(Record.objects.get(id=record_id))
ma = c.sparql(a.query_all())
m = parse_rdf(ma)
mae = c.sparql(ae.query_all())
parse_rdf(mae, model=m)
return rdf_response(serialize_rdf(m))
def record_get_allergies(request, *args, **kwargs):
record_id = kwargs['record_id']
a = RecordObject["http://smartplatforms.org/terms#Allergy"]
ae = RecordObject["http://smartplatforms.org/terms#AllergyExclusion"]
c = RecordStoreConnector(Record.objects.get(id=record_id))
ma = c.sparql(a.query_all())
m = parse_rdf(ma)
mae = c.sparql(ae.query_all())
parse_rdf(mae, model=m)
return rdf_response(serialize_rdf(m))
def record_get_allergies(request, *args, **kwargs):
record_id = kwargs['record_id']
a = RecordObject["http://smartplatforms.org/terms#Allergy"]
ae = RecordObject["http://smartplatforms.org/terms#AllergyExclusion"]
c = RecordTripleStore(Record.objects.get(id=record_id))
allergy_graph = c.get_objects(a)
exclusion_graph = c.get_objects(ae)
a = parse_rdf(allergy_graph)
ae = parse_rdf(exclusion_graph)
a += ae
return rdf_response(serialize_rdf(a))
def from_rdf(cls, rdfstring, record, app):
s = parse_rdf(rdfstring)
q = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX sp: <http://smartplatforms.org/terms#>
SELECT ?notes ?severity
WHERE {
?a rdf:type sp:Alert.
?a sp:notes ?notes.
?a sp:severity ?scv.
?scv sp:code ?severity.
}"""
r = list(s.query(q))
assert len(r) == 1, "Expected one alert in post, found %s"%len(r)
(notes, severity) = r[0]
assert type(notes) == Literal
spcodes = Namespace("http://smartplatforms.org/terms/code/alertLevel#")
assert severity in [spcodes.information, spcodes.warning, spcodes.critical]
a = RecordAlert(record=record,
alert_text=str(notes),
triggering_app=app)
a.save()
return a
def from_rdf(cls, rdfstring, record, app):
s = parse_rdf(rdfstring)
q = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX sp: <http://smartplatforms.org/terms#>
SELECT ?notes ?severity
WHERE {
?a rdf:type sp:Alert.
?a sp:notes ?notes.
?a sp:severity ?scv.
?scv sp:code ?severity.
}"""
r = list(s.query(q))
assert len(r) == 1, "Expected one alert in post, found %s" % len(r)
(notes, severity) = r[0]
assert type(notes) == Literal
spcodes = Namespace("http://smartplatforms.org/terms/code/alertLevel#")
assert severity in [
spcodes.information, spcodes.warning, spcodes.critical
]
a = RecordAlert(record=record,
alert_text=str(notes),
triggering_app=app)
a.save()
return a
def search_records(cls, query):
c =TripleStore()
ids = parse_rdf(c.sparql(query))
from smart.models.record_object import RecordObject
demographics = RecordObject[sp.Demographics]
subjects = [p[0] for p in ids.triples((None, rdf['type'], sp.Demographics))]
ret = c.get_contexts(subjects)
return ret
def rdf_delete(record_connector, query, save=True):
to_delete = parse_rdf(record_connector.sparql(query))
deleted = bound_graph()
for r in to_delete:
deleted.add(r)
record_connector.pending_removes.append(r)
if (save): record_connector.execute_transaction()
return rdf_response(serialize_rdf(deleted))
def __init__(self, filename, target_id=None):
# 0. Read supplied data
self.target_id = target_id
self.data = parse_rdf(open(filename).read())
# 1. For each known data type, extract relevant nodes
var_bindings = {'record_id': self.target_id}
ro = RecordObject[sp.Statement]
ro.prepare_graph(self.data, None, var_bindings)
# 2. Copy extracted nodes to permanent RDF store
self.write_to_record()
def rdf_to_objects(cls, res):
m = parse_rdf(res)
record_list = []
q = """
PREFIX sp:<http://smartplatforms.org/terms#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dcterms:<http://purl.org/dc/terms/>
PREFIX v:<http://www.w3.org/2006/vcard/ns#>
PREFIX foaf:<http://xmlns.com/foaf/0.1/>
SELECT ?gn ?fn ?dob ?gender ?zipcode ?d
WHERE {
?d rdf:type sp:Demographics.
?d v:n ?n.
?n v:given-name ?gn.
?n v:family-name ?fn.
optional{ ?d foaf:gender ?gender.}
optional{ ?d v:bday ?dob.}
optional{ ?d v:adr ?a.
?a rdf:type v:Pref.
?a v:postal-code ?zipcode.
}
optional{ ?d v:adr ?a.
?a v:postal-code ?zipcode.
}
}"""
people = list(m.query(q))
for p in people:
record = Record()
record.id = re.search("\/records\/(.*?)\/demographics",
str(p[5])).group(1)
record.fn, record.ln, record.dob, record.gender, record.zipcode = p[:
5]
record_list.append(record)
return record_list
def internal_id(self, record_connector, external_id):
idquery = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
CONSTRUCT {%s <http://smartplatforms.org/terms#externalIDFor> ?o.}
FROM $context
WHERE {
%s <http://smartplatforms.org/terms#externalIDFor> ?o.
} """ % (external_id.n3(), external_id.n3())
id_graph = parse_rdf(record_connector.sparql(idquery))
l = list(id_graph)
if len(l) > 1:
raise Exception("MORE THAN ONE ENTITY WITH EXTERNAL ID %s : %s" %
(external_id, ", ".join([str(x[0]) for x in l])))
try:
s = l[0][2]
return s
except:
return None
def internal_id(self, record_connector, external_id):
idquery = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
CONSTRUCT {%s <http://smartplatforms.org/terms#externalIDFor> ?o.}
FROM $context
WHERE {
%s <http://smartplatforms.org/terms#externalIDFor> ?o.
} """%(external_id.n3(), external_id.n3())
id_graph = parse_rdf(record_connector.sparql(idquery))
l = list(id_graph)
if len(l) > 1:
raise Exception( "MORE THAN ONE ENTITY WITH EXTERNAL ID %s : %s"%(external_id, ", ".join([str(x[0]) for x in l])))
try:
s = l[0][2]
return s
except:
return None
def rdf_to_objects(cls, res):
m = parse_rdf(res)
record_list = []
q = """
PREFIX sp:<http://smartplatforms.org/terms#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dcterms:<http://purl.org/dc/terms/>
PREFIX v:<http://www.w3.org/2006/vcard/ns#>
PREFIX foaf:<http://xmlns.com/foaf/0.1/>
SELECT ?gn ?fn ?dob ?gender ?zipcode ?d
WHERE {
?d rdf:type sp:Demographics.
?d v:n ?n.
?n v:given-name ?gn.
?n v:family-name ?fn.
optional{ ?d foaf:gender ?gender.}
optional{ ?d v:bday ?dob.}
optional{ ?d v:adr ?a.
?a rdf:type v:Pref.
?a v:postal-code ?zipcode.
}
optional{ ?d v:adr ?a.
?a v:postal-code ?zipcode.
}
}"""
people = list(m.query(q))
for p in people:
record = Record()
record.id = re.search("\/records\/(.*?)\/demographics", str(p[5])).group(1)
record.fn, record.ln, record.dob, record.gender, record.zipcode = p[:5]
record_list.append(record)
return record_list
def __init__(self, filename, target_id=None):
# 0. Read supplied data
self.target_id = target_id
self.data = parse_rdf(open(filename).read())
# 1. For each known data type, extract relevant nodes
var_bindings = {'record_id': self.target_id}
self.ro = RecordObject[sp.Statement]
self.ro.prepare_graph(self.data, None, var_bindings)
print "Default context", len(self.data.default_context)
record_node = list(self.data.triples((None, rdf.type, sp.MedicalRecord)))
assert len(record_node) == 1, "Found statements about >1 patient in file: %s" % record_node
record_node = record_node[0][0]
self.record_node = record_node
self.ro.segregate_nodes(self.data, record_node)
self.data.remove_context(self.data.default_context)
# 2. Copy extracted nodes to permanent RDF store
self.write_to_record()
print self.data.default_context.identifier.n3()
