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_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 test_cache_loc(self):
current_cache_directory = picklejarfactory.cache_directory
test_directory = os.path.join(
os.path.split(os.path.abspath(__file__))[0], 'data')
picklejarfactory.cache_directory = os.path.abspath(
os.path.join(test_directory, 'pjcache'))
make_and_clear_directory(picklejarfactory.cache_directory)
o1 = TestObj()
o1.foo = "bagels"
picklejar().add('o1', (2, 3), o1)
o2 = TestObj()
o2.foo = "cheese"
picklejar().add('o2', (2, 5), o2)
ot1 = picklejar().get('o1', (2, 3))
ot2 = picklejar().get('o2', (2, 5))
self.assertEqual("bagels", ot1.foo)
self.assertEqual("cheese", ot2.foo)
picklejar().clear()
picklejarfactory.cache_directory = current_cache_directory
ot1 = picklejar().get('o1', (2, 3))
ot2 = picklejar().get('o2', (2, 5))
self.assertIsNone(ot1)
self.assertIsNone(ot2)
self.assertIsNotNone(picklejar().get('cls', (1, )))
def test_make_and_clear_directory(self):
from tests.utils.base_test_case import make_and_clear_directory
test_dir = os.path.join(test_data_directory, 'mcd_test')
safety_file = os.path.join(test_dir, "generated")
test_file = os.path.join(test_dir, "test.txt")
self.assertFalse(os.path.exists(test_dir), "mcd_test directory should not exist at this point")
make_and_clear_directory(test_dir)
self.assertTrue(os.path.exists(test_dir))
self.assertTrue(os.path.exists(safety_file))
with open(test_file, "w") as f:
f.write("Test file")
make_and_clear_directory(test_dir)
self.assertFalse(os.path.exists(test_file))
with open(test_file, "w") as f:
f.write("Test file")
os.remove(safety_file)
with self.assertRaises(FileExistsError):
make_and_clear_directory(test_dir)
os.remove(test_file)
os.removedirs(test_dir)
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
FHIRInstanceTestCase.validation_function = json_to_ttl
if not FHIRInstanceTestCase.no_tests and not FHIRInstanceTestCase.single_file:
make_and_clear_directory(FHIRInstanceTestCase.output_directory)
FHIRInstanceTestCase.build_test_harness()
if __name__ == '__main__':
unittest.main()
def tearDown(self):
make_and_clear_directory(self.output_dir)
def setUp(self):
make_and_clear_directory(self.output_dir)