def testGetResource_withAddedPackages_retrievesResource(self):
vs_1 = value_set_pb2.ValueSet()
vs_1.url.value = 'vs1'
vs_2 = value_set_pb2.ValueSet()
vs_2.url.value = 'vs2'
package_1 = fhir_package.FhirPackage(
package_info=mock.MagicMock(),
structure_definitions=mock_resource_collection_containing([]),
search_parameters=mock_resource_collection_containing([]),
code_systems=mock_resource_collection_containing([]),
value_sets=mock_resource_collection_containing([vs_1]),
)
package_2 = fhir_package.FhirPackage(
package_info=mock.MagicMock(),
structure_definitions=mock_resource_collection_containing([]),
search_parameters=mock_resource_collection_containing([]),
code_systems=mock_resource_collection_containing([]),
value_sets=mock_resource_collection_containing([vs_2]),
)
manager = fhir_package.FhirPackageManager()
manager.add_package(package_1)
manager.add_package(package_2)
self.assertEqual(manager.get_resource('vs1'), vs_1)
self.assertEqual(manager.get_resource('vs2'), vs_2)
def testExpandValueSet_withIntensionalValueSet_makesExpectedCalls(
self, mock_expand_extensional_value_set):
mock_expand_extensional_value_set.return_value = None
expanded_value_set = value_set_pb2.ValueSet()
codes = [
value_set_pb2.ValueSet.Expansion.Contains(
system=datatypes_pb2.Uri(value='include-system-1'),
version=datatypes_pb2.String(value='include-version-1'),
code=datatypes_pb2.Code(value='code-1-2'),
),
value_set_pb2.ValueSet.Expansion.Contains(
system=datatypes_pb2.Uri(value='include-system-2'),
version=datatypes_pb2.String(value='include-version-2'),
code=datatypes_pb2.Code(value='code-2-1'),
),
]
expanded_value_set.expansion.contains.extend(codes)
mock_client = unittest.mock.MagicMock(
spec=terminology_service_client.TerminologyServiceClient)
mock_client.expand_value_set.return_value = expanded_value_set
value_set = value_set_pb2.ValueSet()
result = value_sets.expand_value_set(value_set, mock_client)
self.assertCountEqual(result.expansion.contains, codes)
def testValueSetExpansionFromTerminologyService_withMissingId_raisesError(
self):
value_set = value_set_pb2.ValueSet()
with self.assertRaises(ValueError):
client = terminology_service_client.TerminologyServiceClient({})
client.expand_value_set(value_set)
def testValueSetToInsertStatement_withValueSet_buildsValidQuery(self):
value_set = value_set_pb2.ValueSet()
value_set.url.value = 'vs-url'
value_set.version.value = 'vs-version'
for code, system in (('c1', 's1'), ('c2', 's2')):
coding = value_set.expansion.contains.add()
coding.code.value = code
coding.system.value = system
table = build_valueset_codes_table()
query = value_sets.valueset_codes_insert_statement_for(value_set, table)
query_string = str(query.compile(compile_kwargs={'literal_binds': True}))
self.assertEqual(query_string, (
'INSERT INTO valueset_codes (valueseturi, valuesetversion, system, code) '
'SELECT codes.valueseturi, codes.valuesetversion, codes.system, codes.code '
'\nFROM ('
"SELECT 'vs-url' AS valueseturi, 'vs-version' AS valuesetversion, 's1' AS system, 'c1' AS code "
'UNION ALL '
"SELECT 'vs-url' AS valueseturi, 'vs-version' AS valuesetversion, 's2' AS system, 'c2' AS code"
') AS codes '
'LEFT OUTER JOIN valueset_codes '
'ON codes.valueseturi = valueset_codes.valueseturi '
'AND codes.valuesetversion = valueset_codes.valuesetversion '
'AND codes.system = valueset_codes.system '
'AND codes.code = valueset_codes.code '
'\nWHERE valueset_codes.valueseturi IS NULL '
'AND valueset_codes.valuesetversion IS NULL '
'AND valueset_codes.system IS NULL '
'AND valueset_codes.code IS NULL'))
def testValueSetExpansionFromTerminologyService_withBadUrl_raisesError(
self):
value_set = value_set_pb2.ValueSet()
value_set.id.value = 'an-id'
value_set.url.value = 'mystery-url'
with self.assertRaises(ValueError):
client = terminology_service_client.TerminologyServiceClient({})
client.expand_value_set(value_set)
def testValueSetExpansionForExtensionalSets_withIntensionalSet_raisesError(
self):
value_set = value_set_pb2.ValueSet()
include = value_set.compose.include.add()
filter_ = include.filter.add()
filter_.op.value = 1
filter_.value.value = 'medicine'
self.assertIsNone(value_sets._expand_extensional_value_set(value_set))
def testValueSetExpansionForExtensionalSets_withExtensionalSet_expandsCodes(
self):
value_set = value_set_pb2.ValueSet()
# Add an include set with three codes.
include_1 = value_set.compose.include.add()
include_1.version.value = 'include-version-1'
include_1.system.value = 'include-system-1'
code_1_1 = include_1.concept.add()
code_1_1.code.value = 'code-1-1'
code_1_2 = include_1.concept.add()
code_1_2.code.value = 'code-1-2'
code_1_3 = include_1.concept.add()
code_1_3.code.value = 'code-1-3'
# Add an include set with one code.
include_2 = value_set.compose.include.add()
include_2.version.value = 'include-version-2'
include_2.system.value = 'include-system-2'
code_2_1 = include_2.concept.add()
code_2_1.code.value = 'code-2-1'
# Add a copy of code_1_3 to the exclude set.
exclude = value_set.compose.exclude.add()
exclude.version.value = 'include-version-1'
exclude.system.value = 'include-system-1'
exclude_code = exclude.concept.add()
exclude_code.code.value = 'code-1-3'
result = value_sets._expand_extensional_value_set(value_set)
expected = [
value_set_pb2.ValueSet.Expansion.Contains(
system=datatypes_pb2.Uri(value='include-system-1'),
version=datatypes_pb2.String(value='include-version-1'),
code=datatypes_pb2.Code(value='code-1-1'),
),
value_set_pb2.ValueSet.Expansion.Contains(
system=datatypes_pb2.Uri(value='include-system-1'),
version=datatypes_pb2.String(value='include-version-1'),
code=datatypes_pb2.Code(value='code-1-2'),
),
value_set_pb2.ValueSet.Expansion.Contains(
system=datatypes_pb2.Uri(value='include-system-2'),
version=datatypes_pb2.String(value='include-version-2'),
code=datatypes_pb2.Code(value='code-2-1'),
),
]
self.assertCountEqual(result.expansion.contains, expected)
def testValueSetsFromFhirPackage_withValueSets_succeeds(self):
definition = structure_definition_pb2.StructureDefinition()
element = definition.differential.element.add()
element.binding.value_set.value = 'http://hl7.org/fhir/ValueSet/financial-taskcode'
another_definition = structure_definition_pb2.StructureDefinition()
another_element = definition.differential.element.add()
another_element.binding.value_set.value = 'http://hl7.org/fhir/ValueSet/action-participant-role'
value_set = value_set_pb2.ValueSet()
value_set.url.value = 'a-url'
another_value_set = value_set_pb2.ValueSet()
another_value_set.url.value = 'another-url'
duplicate_value_set = value_set_pb2.ValueSet()
duplicate_value_set.url.value = 'http://hl7.org/fhir/ValueSet/action-participant-role'
package = fhir_package.FhirPackage(
package_info=unittest.mock.MagicMock(),
structure_definitions=[definition, another_definition],
search_parameters=[],
code_systems=[],
value_sets=[value_set, another_value_set, duplicate_value_set],
)
result = get_resolver().value_sets_from_fhir_package(package)
self.assertCountEqual(
[vs.url.value for vs in result],
[
element.binding.value_set.value,
another_element.binding.value_set.value,
value_set.url.value,
another_value_set.url.value,
],
)
def testValueSetExpansionFromTerminologyService_withNoPagination_retrievesCodes(
self, mock_session):
mock_session().headers = {}
mock_session().__enter__().get('url').json.return_value = {
'resourceType': 'ValueSet',
'id': 'vs-id',
'url': 'vs-url',
'status': 'draft',
'expansion': {
'timestamp': '2022-02-14T15:51:40-05:00',
'contains': [{
'code': 'code-1'
}]
}
}
# Reset to hide the get('url') call we made above.
mock_session().__enter__().get.reset_mock()
value_set = value_set_pb2.ValueSet()
value_set.url.value = 'http://hl7.org/fhir/ValueSet/financial-taskcode'
client = terminology_service_client.TerminologyServiceClient({})
result = client.expand_value_set(value_set)
# Ensure we called requests correctly.
mock_session().__enter__().get.assert_called_once_with(
'https://tx.fhir.org/r4/ValueSet/$expand',
params={
'offset': 0,
'url': 'http://hl7.org/fhir/ValueSet/financial-taskcode'
})
self.assertEqual(mock_session().headers['Accept'], 'application/json')
# Ensure we got the expected protos back.
expected = [
value_set_pb2.ValueSet.Expansion.Contains(),
]
expected[0].code.value = 'code-1'
self.assertCountEqual(result.expansion.contains, expected)
def testValueSetExpansion_withValueSet_retrievesCodes(self, mock_session):
mock_session().headers = {}
mock_session().__enter__().get('url').json.side_effect = [
{
'resourceType': 'ValueSet',
'id': 'vs-id',
'url': 'vs-url',
'status': 'draft',
'expansion': {
'timestamp': '2022-02-14T15:51:40-05:00',
'offset': 0,
'total': 2,
'contains': [{
'code': 'code-1'
}]
}
},
{
'resourceType': 'ValueSet',
'id': 'vs-id',
'url': 'vs-url',
'status': 'draft',
'expansion': {
'timestamp': '2022-02-14T15:51:40-05:00',
'offset': 1,
'total': 2,
'contains': [{
'code': 'code-2'
}]
}
},
]
# Reset to hide the get('url') call we made above.
mock_session().__enter__().get.reset_mock()
value_set = value_set_pb2.ValueSet()
value_set.url.value = 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16'
value_set.version.value = '1.0'
client = terminology_service_client.TerminologyServiceClient(
{'https://cts.nlm.nih.gov/fhir/': 'the-api-key'})
result = client.expand_value_set(value_set)
# Ensure we called requests correctly.
self.assertEqual(mock_session().__enter__().get.call_args_list, [
unittest.mock.call(
'https://cts.nlm.nih.gov/fhir/r4/ValueSet/$expand',
params={
'url': 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16',
'offset': 0,
'valueSetVerson': '1.0'
}),
unittest.mock.call(
'https://cts.nlm.nih.gov/fhir/r4/ValueSet/$expand',
params={
'url': 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16',
'offset': 1,
'valueSetVerson': '1.0'
}),
])
self.assertEqual(mock_session().auth, ('apikey', 'the-api-key'))
self.assertEqual(mock_session().headers['Accept'], 'application/json')
# Ensure we got the expected protos back.
expected = [
value_set_pb2.ValueSet.Expansion.Contains(),
value_set_pb2.ValueSet.Expansion.Contains(),
]
expected[0].code.value = 'code-1'
expected[1].code.value = 'code-2'
self.assertCountEqual(result.expansion.contains, expected)
def testValueSetToInsertStatement_withEmptyCodes_raisesError(self):
value_set = value_set_pb2.ValueSet()
table = build_valueset_codes_table()
with self.assertRaises(ValueError):
value_sets.valueset_codes_insert_statement_for(value_set, table)