def test_no_args(self):
from fhirtordf.fhirtordf import fhirtordf
args = ""
output = self._push_stderr()
fhirtordf(args.split(), default_exit=False)
self._pop_stderr()
self.maxDiff = None
self.assertEqual(noargs_text, output.getvalue())
def test_version(self):
from fhirtordf.fhirtordf import fhirtordf
from fhirtordf import __version__
output = self._push_stdout()
fhirtordf(["-v"])
self._pop_stdout()
self.assertEqual(
"FHIR to RDF Conversion Tool -- Version {}".format(__version__),
output.getvalue().strip())
def test_help(self):
from fhirtordf.fhirtordf import fhirtordf
args = "-h"
output = self._push_stdout()
fhirtordf(args.split(), default_exit=False)
self._pop_stdout()
self.maxDiff = None
print(output.getvalue())
self.assertEqual(help_text, output.getvalue())
def test_two_uris(self):
from fhirtordf.fhirtordf import fhirtordf
if USE_BUILD_SERVER:
args = "-i {}/patient-example-f201-roel.json {}/patient-example-f201-roel.json".\
format(test_fhir_server, test_fhir_server)
else:
args = "-i {}Patient/f201 {}/Patient/pat1".format(
test_fhir_server, test_fhir_server)
output = self._push_stdout()
fhirtordf(args.split())
self._pop_stdout()
print(output.getvalue())
def test_two_infiles(self):
from fhirtordf.fhirtordf import fhirtordf
test_directory = os.path.join(
os.path.split(os.path.abspath(__file__))[0], '..', 'data')
tf1 = os.path.join(test_directory, "activitydefinition-example.json")
tf2 = os.path.join(test_directory,
"activitydefinition-predecessor-example.json")
args = "-i {} {}".format(tf1, tf2)
output = self._push_stdout()
fhirtordf(args.split())
self._pop_stdout()
print(output.getvalue())
def test_big_fhir_convert(self):
# This is a test of the complete FHIR directory conversion
from fhirtordf.fhirtordf import fhirtordf
input_directory = os.path.abspath(
'/Users/mrf7578/Development/fhir/build/publish')
output_directory = os.path.abspath(
os.path.join(
os.path.split(os.path.abspath(__file__))[0], 'data',
'publish'))
args = '-nc -nn -id {} -od {} -sd /v2/ /v3/ -sf .cs. .vs. .profile. .canonical. .schema. .diff.'.format(
input_directory, output_directory)
fhirtordf(args.split(), default_exit=False)
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_patient_example(self):
from fhirtordf.fhirtordf import fhirtordf
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(fhirtordf(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_output_directory(self):
from fhirtordf.fhirtordf import fhirtordf
output_directory = os.path.abspath(
os.path.join(
os.path.split(os.path.abspath(__file__))[0], 'data',
'patlist'))
shutil.rmtree(output_directory, ignore_errors=True)
fhirtordf(
"-i http://fhirtest.uhn.ca/baseDstu3/Patient"
"?_format=json&gender=male&birthdate=gt2013-01-01 -od {} -nn -nc".
format(output_directory).split())
self.assertTrue(os.path.exists(output_directory))
self.assertTrue(
os.path.exists(os.path.join(output_directory, '_url1.ttl')))
shutil.rmtree(output_directory)
def test_sd_issue(self):
from fhirtordf.fhirtordf import fhirtordf
test_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), '..', 'data'))
of = mktemp()
fhir_ttl = os.path.join(test_dir, 'fhir_metadata_vocabulary',
'fhir.ttl')
args = f"-id {test_dir} -mv {fhir_ttl} -u http://dss.cora/ -no -o {of}"
print(args)
output = StringIO()
with redirect_stdout(output):
fhirtordf(args.split())
print(output.getvalue())
# passes if we get here
self.assertTrue(True)
def test_subjects(self):
from fhirtordf.fhirtordf import fhirtordf
output = self._push_stdout()
if USE_BUILD_SERVER:
args = '-i {}/observation-example-vitals-panel.json'.format(test_fhir_server)
else:
args = "-i {}/Observation/vitals-panel".format(test_fhir_server)
fhirtordf(args.split())
self._pop_stdout()
g = Graph()
g.parse(data=output.getvalue(), format="turtle")
self.assertEqual({URIRef('http://hl7.org/fhir/Observation/respiratory-rate'),
URIRef('http://hl7.org/fhir/Observation/body-temperature'),
URIRef('http://hl7.org/fhir/Patient/example'),
URIRef('http://hl7.org/fhir/Observation/vitals-panel.ttl'),
URIRef('http://hl7.org/fhir/Observation/blood-pressure'),
URIRef('http://hl7.org/fhir/Observation/heart-rate'),
URIRef('http://hl7.org/fhir/Observation/vitals-panel')},
set(s for s in g.subjects() if isinstance(s, URIRef)))
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_continuations(self):
from fhirtordf.fhirtordf import fhirtordf
test_directory = os.path.join(
os.path.split(os.path.abspath(__file__))[0], 'data')
outfname = os.path.join(test_directory, "patlist1.ttl")
# The following query returned 310 entries on Sep 10, 2017
url = "http://fhirtest.uhn.ca/baseDstu3/Patient?_format=json&gender=male&birthdate=gt2013-01-01"
args = "-i {} -o {} -nc".format(url, outfname)
self.assertTrue(fhirtordf(args.split()))
out_graph = Graph()
out_graph.load(outfname, format="turtle")
self.assertTrue(
len([
s for s in set(out_graph.subjects()) if isinstance(s, URIRef)
]) < 50)
args = "-i {} -o {}".format(url, outfname)
self.assertTrue(fhirtordf(args.split()))
out_graph = Graph()
out_graph.load(outfname, format="turtle")
self.assertTrue(
len([
s for s in set(out_graph.subjects()) if isinstance(s, URIRef)
]) > 300)