def test_basics(self):
g = fhir_json_to_rdf("http://hl7.org/fhir/Observation/vitals-panel")
self.assertEqual(['http://hl7.org/fhir/Observation/blood-pressure',
'http://hl7.org/fhir/Observation/body-temperature',
'http://hl7.org/fhir/Observation/heart-rate',
'http://hl7.org/fhir/Observation/respiratory-rate',
'http://hl7.org/fhir/Observation/vitals-panel',
'http://hl7.org/fhir/Observation/vitals-panel.ttl',
'http://hl7.org/fhir/Patient/example'],
sorted(str(s) for s in set(g.subjects()) if isinstance(s, URIRef)))
mv = FHIRMetaVoc()
self.assertTrue(mv.from_cache)
g = fhir_json_to_rdf("http://hl7.org/fhir/DiagnosticReport/f201", target_graph=g, metavoc=mv)
self.assertEqual({URIRef('http://hl7.org/fhir/Observation/blood-pressure'),
URIRef('http://hl7.org/fhir/Observation/heart-rate'),
URIRef('http://hl7.org/fhir/DiagnosticReport/f201.ttl'),
URIRef('http://hl7.org/fhir/Patient/example'),
URIRef('http://hl7.org/fhir/Observation/body-temperature'),
URIRef('http://hl7.org/fhir/Observation/respiratory-rate'),
URIRef('http://hl7.org/fhir/Observation/vitals-panel.ttl'),
URIRef('http://hl7.org/fhir/Patient/f201'),
URIRef('http://hl7.org/fhir/DiagnosticReport/f201'),
URIRef('http://hl7.org/fhir/Organization/f203'),
URIRef('http://hl7.org/fhir/Observation/vitals-panel')},
set(s for s in g.subjects() if isinstance(s, URIRef)))
def proc_file(infile: str, outfile: str, opts: Namespace) -> bool:
"""
Process infile.
:param infile: input file to be processed
:param outfile: target output file.
:param opts:
:return:
"""
g = fhir_json_to_rdf(infile,
opts.uribase,
opts.graph,
add_ontology_header=not opts.noontology,
do_continuations=not opts.nocontinuation,
replace_narrative_text=bool(opts.nonarrative),
metavoc=opts.fhir_metavoc)
os.makedirs(os.path.dirname(outfile), exist_ok=True)
# If we aren't carrying graph in opts, we're doing a file by file transformation
if g:
if not opts.graph:
serialize_graph(g, outfile, opts)
return True
else:
print("{} : Not a FHIR collection or resource".format(infile))
return False
def load_file(dirname: str, fname: str) -> None:
filepath = fname if '://' in fname else os.path.join(dirname, fname)
print("--> loading {}".format(filepath))
if '://' in fname:
if opts.filetype == 'rdf':
rdf_str = read_rdf_uri(fname)
if not rdf_str:
print(" Read Failed")
g.parse(data=rdf_str, format="turtle")
else:
fhir_json_to_rdf(fname, opts.uribase, g, metavoc=fmv)
else:
if filepath.endswith('.json'):
fhir_json_to_rdf(filepath, opts.uribase, g, metavoc=fmv)
else:
g.load(filepath, format="turtle")
def test_basics(self):
# TODO: The test below fails. See: https://github.com/fhircat/FHIRCat/issues/36
print(
"http://hl7.org/fhir/Observation/vitals-panel test skipped -- See: FHIRCat issue #36 for details"
)
# g = fhir_json_to_rdf("http://hl7.org/fhir/Observation/vitals-panel")
g = fhir_json_to_rdf(
"http://hl7.org/fhir/observation-example-vitals-panel.json")
self.assertEqual([
'http://hl7.org/fhir/Observation/blood-pressure',
'http://hl7.org/fhir/Observation/body-temperature',
'http://hl7.org/fhir/Observation/heart-rate',
'http://hl7.org/fhir/Observation/respiratory-rate',
'http://hl7.org/fhir/Observation/vitals-panel',
'http://hl7.org/fhir/Observation/vitals-panel.ttl',
'http://hl7.org/fhir/Patient/example'
], sorted(str(s) for s in set(g.subjects()) if isinstance(s, URIRef)))
mv = FHIRMetaVoc()
self.assertTrue(mv.from_cache)
print(
"http://hl7.org/fhir/DiagnosticReport/f201 test skipped -- See: FHIRCat issue #36 for details"
)
# g = fhir_json_to_rdf("http://hl7.org/fhir/DiagnosticReport/f201")
g = fhir_json_to_rdf(
"http://hl7.org/fhir/diagnosticreport-example-f201-brainct.json",
target_graph=g,
metavoc=mv)
self.assertEqual(
{
URIRef('http://hl7.org/fhir/Observation/blood-pressure'),
URIRef('http://hl7.org/fhir/Observation/heart-rate'),
URIRef('http://hl7.org/fhir/DiagnosticReport/f201.ttl'),
URIRef('http://hl7.org/fhir/Patient/example'),
URIRef('http://hl7.org/fhir/Observation/body-temperature'),
URIRef('http://hl7.org/fhir/Observation/respiratory-rate'),
URIRef('http://hl7.org/fhir/Observation/vitals-panel.ttl'),
URIRef('http://hl7.org/fhir/Patient/f201'),
URIRef('http://hl7.org/fhir/DiagnosticReport/f201'),
URIRef('http://hl7.org/fhir/Organization/f203'),
URIRef('http://hl7.org/fhir/Observation/vitals-panel')
}, set(s for s in g.subjects() if isinstance(s, URIRef)))
def test_statement(self):
test_json = os.path.join(ISSUE_TEST_DATA_DIR, 'issue_15.json')
mvg = Graph()
mvg.load(FHIR_R4_TTL, format="turtle")
g = fhir_json_to_rdf(test_json, metavoc=mvg)
expected_graph = Graph()
g.load(os.path.join(ISSUE_TEST_DATA_DIR, 'issue_15.ttl'),
format="turtle")
expected, actual = rdf_compare_split(expected_graph,
g,
ignore_owl_version=False,
ignore_type_arcs=False)
self.assertEqual('', expected)
self.assertEqual('', actual)