def test_smartonfhir_collection(self):
""" Pull a sample of the smartonfhir observation data and generate the results in """
from fhirtordf.loaders.fhircollectionloader import FHIRCollection
output_dir = os.path.join(self.test_output_directory,
'smartonfhir_testdata', 'obs_sample')
make_and_clear_directory(output_dir)
collection = \
FHIRCollection(self.fhir_ontology,
os.path.join(self.test_input_directory, 'smartonfhir_testdata', 'json', 'obs_sample.json'),
"https://sb-fhir-dstu2.smarthealthit.org/api/smartdstu2/open/")
generated_files = []
for entry in collection.entries:
os.makedirs(os.path.join(output_dir, entry.resource_type),
exist_ok=True)
with open(
os.path.join(output_dir, entry.resource_type,
entry.resource_id + '.ttl'), 'w') as output:
output.write(str(entry))
generated_files.append(
os.path.join(entry.resource_type, entry.resource_id + ".ttl"))
self.assertEqual([
'Observation/SMART-Observation-5-smokingstatus.ttl',
'Observation/SMART-Observation-6-smokingstatus.ttl',
'Observation/SMART-Observation-18-smokingstatus.ttl',
'Observation/SMART-Observation-1098667-gestage.ttl',
'Observation/SMART-Observation-1681-lab.ttl',
'Observation/SMART-Observation-1682-lab.ttl',
'Observation/SMART-Observation-1683-lab.ttl',
'Observation/SMART-Observation-1684-lab.ttl',
'Observation/SMART-Observation-1685-lab.ttl'
], generated_files)
print("\n*****> Check outputs in {}".format(output_dir))
def test_careplan_instancenum(self):
# This is creating the correct parsing for this resource. Once the FHIR resource is fixed, we should
# pull this
from fhirtordf.loaders.fhircollectionloader import FHIRCollection
collection = FHIRCollection(self.fhir_ontology,
os.path.join(self.test_input_directory, 'synthea_data',
'CarePlan.json'),
"http://standardhealthrecord.org/fhir/")
for entry in collection.entries:
print(entry)
self.assertTrue(False)
def test_synthea_collection(self):
from fhirtordf.loaders.fhircollectionloader import FHIRCollection
output_dir = os.path.join(self.test_output_directory, 'synthea_data',
'ttl')
make_and_clear_directory(output_dir)
collection = FHIRCollection(
self.fhir_ontology,
os.path.join(self.test_input_directory, 'synthea_data',
'Adams301_Keyshawn30_74.json'),
"http://standardhealthrecord.org/fhir/")
generated_files = []
for entry in collection.entries:
output_fname = os.path.join(output_dir, entry.resource_type,
entry.resource_id + ".ttl")
os.makedirs(os.path.join(output_dir, entry.resource_type),
exist_ok=True)
with open(output_fname, 'w') as output:
output.write(str(entry))
generated_files.append(
os.path.join(
entry.resource_type,
(entry.resource_id if entry.resource_type
not in ["CarePlan", "MedicationRequest"] else "<UUID>") +
".ttl"))
self.assertEqual([
'Patient/526238ef-dec3-401d-a1c1-2974962df23f.ttl',
'Organization/9c00d82c-8deb-4e3c-80ee-2e9221addbc0.ttl',
'Encounter/ff4f9269-5036-45dc-b0fb-d8133ae13c76.ttl',
'Condition/9eba3a2a-b040-4697-8b46-41f87f3bbe71.ttl',
'Condition/e69d5da5-4408-44e5-9ed0-2e93aacae4fa.ttl',
'Condition/ccbc87d7-8439-4558-9672-7d58c56aa56c.ttl',
'Condition/0b901fad-ecc3-4135-9ee8-ff4534010c44.ttl',
'Observation/1d52ae90-6721-476c-ad4c-ec978eac4a34.ttl',
'DiagnosticReport/4d7445b4-d001-4679-8053-d564fddbb973.ttl',
'CarePlan/<UUID>.ttl', 'MedicationRequest/<UUID>.ttl',
'MedicationRequest/<UUID>.ttl', 'MedicationRequest/<UUID>.ttl',
'MedicationRequest/<UUID>.ttl', 'MedicationRequest/<UUID>.ttl',
'MedicationRequest/<UUID>.ttl', 'MedicationRequest/<UUID>.ttl',
'MedicationRequest/<UUID>.ttl', 'MedicationRequest/<UUID>.ttl',
'MedicationRequest/<UUID>.ttl', 'MedicationRequest/<UUID>.ttl',
'MedicationRequest/<UUID>.ttl', 'MedicationRequest/<UUID>.ttl'
], generated_files)
print("\n*****> Check outputs in {}".format(output_dir))
def fhir_json_to_rdf(
json_fname: str,
base_uri: str = "http://hl7.org/fhir/",
target_graph: Optional[Graph] = None,
add_ontology_header: bool = True,
do_continuations: bool = True,
replace_narrative_text: bool = False,
metavoc: Optional[Union[Graph, FHIRMetaVoc]] = None) -> Graph:
"""
Convert a FHIR JSON resource image to RDF
:param json_fname: Name or URI of the file to convert
:param base_uri: Base URI to use for relative references.
:param target_graph: If supplied, add RDF to this graph. If not, start with an empty graph.
:param add_ontology_header: True means add owl:Ontology declaration to output
:param do_continuations: True means follow continuation records on bundles and queries
:param replace_narrative_text: True means replace any narrative text longer than 120 characters with
'<div xmlns="http://www.w3.org/1999/xhtml">(removed)</div>'
:param metavoc: FHIR Metadata Vocabulary (fhir.ttl) graph
:return: resulting graph
"""
def check_for_continuation(data_: JsonObj) -> Optional[str]:
if do_continuations and 'link' in data_ and isinstance(
data_.link, list):
for link_e in data_.link:
if 'relation' in link_e and link_e.relation == 'next':
return link_e.url
return None
if target_graph is None:
target_graph = Graph()
if metavoc is None:
metavoc = FHIRMetaVoc().g
elif isinstance(metavoc, FHIRMetaVoc):
metavoc = metavoc.g
page_fname = json_fname
while page_fname:
data = load(page_fname)
if 'resourceType' in data and data.resourceType != 'Bundle':
FHIRResource(metavoc,
None,
base_uri,
data,
target=target_graph,
add_ontology_header=add_ontology_header,
replace_narrative_text=replace_narrative_text)
page_fname = check_for_continuation(data)
elif 'entry' in data and isinstance(
data.entry, list) and 'resource' in data.entry[0]:
FHIRCollection(metavoc,
None,
base_uri,
data,
target=target_graph,
add_ontology_header=add_ontology_header
if 'resourceType' in data else False,
replace_narrative_text=replace_narrative_text)
page_fname = check_for_continuation(data)
else:
page_fname = None
target_graph = None
return target_graph