def json_to_ttl(self: FHIRInstanceTestCase, dirpath: str, fname: str) -> bool:
json_file = os.path.join(dirpath, fname)
turtle_fname = fname.rsplit('.', 1)[0] + '.ttl'
source = FHIRResource(self.fhir_ontology, json_file,
FHIRInstanceTestCase.base_dir)
test_ttl_fname = os.path.join(dirpath, turtle_fname)
if os.path.exists(test_ttl_fname):
target = Graph()
target.load(test_ttl_fname, format="turtle")
diffs_nc = rdf_compare(target,
source.graph,
ignore_owl_version=True,
ignore_type_arcs=True)
diffs = rdf_compare(target,
source.graph,
ignore_owl_version=True,
ignore_type_arcs=True,
compare_filter=fhir_decimal_issue_filter)
if diffs_nc and not diffs:
print("---> {} has decimal precision issues".format(fname))
if diffs:
with open(os.path.join(self.output_directory, turtle_fname),
'w') as f:
f.write(diffs)
f.write('\n\n' + '=' * 40 + '\n')
f.write(str(source))
return False
return True
else:
print("===> {} does not exist!".format(test_ttl_fname))
return True
def test_patient_example(self):
from fhirtordf.fhirtordf import main
test_directory = os.path.join(
os.path.split(os.path.abspath(__file__))[0], '..', 'data')
infname = os.path.join(test_directory, "patient-example.json")
testfname = os.path.join(test_directory, "patient-example.ttl")
if save_output:
outfname = testfname
else:
outfname = os.path.join(test_directory, "patient-example-out.ttl")
args = "-i {} -o {} -s".format(infname, outfname)
self.assertTrue(main(args.split()))
self.assertFalse(save_output,
"Test file: {} generated".format(outfname))
out_graph = Graph()
out_graph.load(outfname, format="turtle")
test_graph = Graph()
test_graph.load(testfname, format="turtle")
comp_result = rdf_compare(test_graph,
out_graph,
ignore_owl_version=True,
ignore_type_arcs=True)
if len(comp_result):
print(comp_result)
self.assertTrue(len(comp_result) == 0)
def test_fhir_files(self):
from fhirtordf.fhirtordf import fhirtordf
fnames = [
'activitydefinition-example',
'activitydefinition-medicationorder-example',
'capabilitystatement-base', 'careplan-example-f001-heart',
'claim-example', 'patient-example'
]
for fname in fnames:
in_url = "{}{}.json".format(test_fhir_server, fname)
test_url = "{}{}.ttl".format(test_fhir_server, fname)
# fmv_url = "{}/fhir.ttl".format(target_fhir_build)
fmv_url = os.path.join(
os.path.split(os.path.abspath(__file__))[0], '..', 'data',
'fhir_metadata_vocabulary', 'fhir.ttl')
test_directory = os.path.join(
os.path.split(os.path.abspath(__file__))[0], 'data')
outfname = os.path.join(test_directory, "{}.ttl".format(fname))
args = "-i {} -o {} -mv {} -s".format(in_url, outfname, fmv_url)
self.assertTrue(fhirtordf(args.split()))
out_graph = Graph()
out_graph.load(outfname, format="turtle")
test_graph = Graph()
test_graph.load(test_url, format="turtle")
comp_result = rdf_compare(test_graph,
out_graph,
ignore_owl_version=True,
ignore_type_arcs=True)
if len(comp_result):
print(comp_result)
self.assertTrue(len(comp_result) == 0)
def test_reference(self):
test_json = loads(data)
from fhirtordf.loaders.fhirresourceloader import FHIRResource
test_rdf = FHIRResource(FHIRGraph(), None, "http://hl7.org/fhir", test_json)
g = test_rdf.graph
expected_graph = Graph()
diffs = rdf_compare(expected_graph, test_rdf.graph, ignore_owl_version=True, ignore_type_arcs=True)
self.assertEqual("", diffs)
def do_test(self, fname):
from fhirtordf.loaders.fhirresourceloader import FHIRResource
json_file = fname + ".json"
turtle_file = fname + ".ttl"
source = FHIRResource(self.fhir_ontology,
os.path.join(self.base_dir, json_file),
"http://hl7.org/fhir/")
turtle_fname = os.path.join(self.base_dir, turtle_file)
target = PrettyGraph()
target.load(turtle_fname, format="turtle")
self.maxDiff = None
self.assertEqual(
'', rdf_compare(source.graph, target, ignore_owl_version=False))
def bester_tester(self, args: str, test_fname: str):
from fhirtordf.fhirtordf import fhirtordf
output = self._push_stdout()
fhirtordf(args.split(), default_exit=False)
g2 = Graph()
g2.parse(data=output.getvalue(), format="turtle")
self._pop_stdout()
if save_sample_output:
with open(test_fname, 'w') as f:
f.write(output.getvalue())
g1 = Graph()
g1.parse(test_fname, format="turtle")
comp_result = rdf_compare(g1, g2)
if len(comp_result):
print(comp_result)
self.assertTrue(len(comp_result) == 0)
self.assertFalse(save_sample_output,
"save_sample_output is True -- test not applied")
def test_data_entry(self):
save_output = False
from fhirtordf.loaders.fhirresourceloader import FHIRResource
with open(
os.path.join(self.base_dir, 'synthea_data',
'Adams301_Keyshawn30_74.json')) as f:
collection = load(f)
source = FHIRResource(self.fhir_ontology,
None,
"http://standardhealthrecord.org/fhir/",
data=collection.entry[0].resource)
turtle_fname = os.path.join(self.base_dir, 'synthea_data',
'Adams301_Keyshawn30_74_entry0.ttl')
if save_output:
with open(turtle_fname, 'w') as output:
output.write(str(source))
target = PrettyGraph()
target.load(turtle_fname, format="turtle")
# Note: This will fail if we use the pure turtle serializer (vs our changes in this package)
self.maxDiff = None
self.assertEqual(
'', rdf_compare(source.graph, target, ignore_owl_version=True))
self.assertFalse(save_output, "Update output file always fails")