async def test_async_fhir_client_patient_by_identifier_missing_true() -> None:
# Arrange
test_name = "test_fhir_client_patient_by_id_async"
mock_server_url = "http://mock-server:1080"
mock_client: MockServerFriendlyClient = MockServerFriendlyClient(
base_url=mock_server_url)
relative_url: str = test_name
absolute_url: str = mock_server_url + "/" + test_name
mock_client.clear(f"/{test_name}/*")
mock_client.reset()
response_text: str = json.dumps({"resourceType": "Patient", "id": "12355"})
mock_client.expect(
mock_request(
path=f"/{relative_url}/Patient",
method="GET",
querystring={"identifier:missing": "true"},
),
mock_response(body=response_text),
timing=times(1),
)
# Act
fhir_client = FhirClient()
fhir_client = (fhir_client.url(absolute_url).resource("Patient").filter(
[PropertyMissingFilter(property_="identifier", missing=True)]))
response: FhirGetResponse = await fhir_client.get_async()
# Assert
print(response.responses)
assert response.responses == response_text
def test_fhir_client_patient_by_id() -> None:
test_name = "test_fhir_client_patient_by_id"
mock_server_url = "http://mock-server:1080"
mock_client: MockServerFriendlyClient = MockServerFriendlyClient(
base_url=mock_server_url
)
relative_url: str = test_name
absolute_url: str = mock_server_url + "/" + test_name
mock_client.clear(f"/{test_name}/*.*")
mock_client.reset()
response_text: str = json.dumps({"resourceType": "Patient", "id": "12355"})
mock_client.expect(
mock_request(path=f"/{relative_url}/Patient/12355", method="GET"),
mock_response(body=response_text),
timing=times(1),
)
fhir_client = FhirClient()
fhir_client = fhir_client.url(absolute_url).resource("Patient").id_("12355")
response: FhirGetResponse = fhir_client.get()
print(response.responses)
assert response.responses == response_text
async def test_fhir_client_patient_delete_async() -> None:
test_name = "test_fhir_client_patient_delete_async"
mock_server_url = "http://mock-server:1080"
mock_client: MockServerFriendlyClient = MockServerFriendlyClient(
base_url=mock_server_url)
relative_url: str = test_name
absolute_url: str = mock_server_url + "/" + test_name
mock_client.clear(f"/{test_name}/*.*")
mock_client.reset()
mock_client.expect(
mock_request(path=f"/{relative_url}/Patient/12345", method="DELETE"),
mock_response(code=204),
timing=times(1),
)
# Act
fhir_client = FhirClient()
fhir_client = fhir_client.url(absolute_url).resource("Patient").id_(
"12345")
response: FhirDeleteResponse = await fhir_client.delete_async()
# Assert
assert response.status == 204
async def test_fhir_client_patient_update_async() -> None:
test_name = "test_fhir_client_patient_merge_async"
mock_server_url = "http://mock-server:1080"
mock_client: MockServerFriendlyClient = MockServerFriendlyClient(
base_url=mock_server_url)
relative_url: str = test_name
absolute_url: str = mock_server_url + "/" + test_name
mock_client.clear(f"/{test_name}/*.*")
mock_client.reset()
response_text_1: List[Dict[str, int]] = [{"created": 1, "updated": 0}]
resource = {"resourceType": "Patient", "id": "12355"}
# request_body = {"resourceType": "Bundle", "entry": [{"resource": resource}]}
mock_client.expect(
mock_request(
path=f"/{relative_url}/Patient/12355",
method="PUT",
body=json.dumps(resource),
),
mock_response(body=json.dumps(response_text_1)),
timing=times(1),
)
fhir_client = FhirClient()
fhir_client = fhir_client.url(absolute_url).resource("Patient")
fhir_client = fhir_client.id_(resource["id"])
response: FhirUpdateResponse = await fhir_client.update_async(
json.dumps(resource))
assert not response.error
def test_fhir_client_patient_merge() -> None:
with requests_mock.Mocker() as mock:
url = "http://foo"
request_data = {"resourceType": "Patient", "id": "12355"}
response_json = [{"created": 1, "updated": 0}]
def custom_matcher(request: Any) -> Optional[Response]:
if request.path == "/patient/1/$merge" and request.text == json.dumps(
[request_data]):
resp: Response = requests.Response()
resp.status_code = 200
return resp
return None
mock.post(
f"{url}/Patient/1/$merge",
additional_matcher=custom_matcher,
text=f"{json.dumps(response_json)}",
)
fhir_client = FhirClient()
fhir_client = fhir_client.url(url).resource("Patient")
response: FhirMergeResponse = fhir_client.merge(
[json.dumps(request_data)])
print(response.responses)
assert response.responses == response_json
def test_dev_server_auth() -> None:
url = "https://fhir-auth.dev.bwell.zone/4_0_0"
fhir_client = FhirClient()
fhir_client = fhir_client.url(url).resource("Patient")
fhir_client = fhir_client.client_credentials(
client_id="4opocimdhppokn1ks0hpbo9fkv", client_secret="{Put secret here}"
).auth_scopes(["user/*.read"])
response: FhirGetResponse = fhir_client.get()
print(response.responses)
def test_fhir_client_patient_by_id() -> None:
with requests_mock.Mocker() as mock:
url = "http://foo"
response_text = {"resourceType": "Patient", "id": "12355"}
mock.get(f"{url}/Patient/12355", json=response_text)
fhir_client = FhirClient()
fhir_client = fhir_client.url(url).resource("Patient").id_("12355")
response: FhirGetResponse = fhir_client.get()
print(response.responses)
assert response.responses == json.dumps(response_text)
def test_fhir_client_patient_list_auth_fail() -> None:
with requests_mock.Mocker() as mock:
url = "http://foo"
mock.get(f"{url}/Patient", status_code=403)
fhir_client = FhirClient()
fhir_client = fhir_client.url(url).resource("Patient")
with pytest.raises(AssertionError):
response: FhirGetResponse = fhir_client.get()
print(response.responses)
assert response.error == "403"
async def test_fhir_graph_async() -> None:
test_name = "test_fhir_graph_async"
mock_server_url = "http://mock-server:1080"
mock_client: MockServerFriendlyClient = MockServerFriendlyClient(
base_url=mock_server_url)
relative_url: str = test_name
absolute_url: str = mock_server_url + "/" + test_name
mock_client.clear(f"/{test_name}/*.*")
mock_client.reset()
response_text = {"resourceType": "Patient", "id": "12355"}
graph_definition = GraphDefinition(
id_="123",
name="my_everything",
start="Patient",
link=[
GraphDefinitionLink(target=[
GraphDefinitionTarget(type_="Location",
params="managingOrganization={ref}")
]),
GraphDefinitionLink(target=[
GraphDefinitionTarget(
type_="HealthcareService",
params="providedBy={ref}",
link=[
GraphDefinitionLink(target=[
GraphDefinitionTarget(type_="Schedule",
params="actor={ref}")
])
],
)
]),
],
)
mock_client.expect(
mock_request(path=f"/{relative_url}/Patient/1/$graph", method="POST"),
mock_response(body=response_text),
timing=times(1),
)
fhir_client = FhirClient()
fhir_client = fhir_client.url(absolute_url).resource("Patient")
response: FhirGetResponse = await fhir_client.graph_async(
graph_definition=graph_definition, contained=False)
assert json.loads(response.responses) == response_text
async def test_fhir_client_patient_list_auth_fail_retry_async() -> None:
test_name = "test_fhir_client_patient_list_auth_fail_retry_async"
mock_server_url = "http://mock-server:1080"
mock_client: MockServerFriendlyClient = MockServerFriendlyClient(
base_url=mock_server_url
)
relative_url: str = test_name
absolute_url: str = mock_server_url + "/" + test_name
mock_client.clear(f"/{test_name}/*.*")
mock_client.reset()
mock_client.expect(
mock_request(path=f"/{relative_url}/Patient", method="GET"),
mock_response(code=401),
timing=times(1),
)
auth_response_text = {
"access_token": "my_access_token",
"expires_in": 86400,
"token_type": "Bearer",
}
mock_client.expect(
mock_request(path=f"/{relative_url}/auth", method="POST"),
mock_response(code=200, body=auth_response_text),
timing=times(1),
)
response_text: str = json.dumps({"resourceType": "Patient", "id": "12355"})
mock_client.expect(
mock_request(path=f"/{relative_url}/Patient", method="GET"),
mock_response(body=response_text),
timing=times(1),
)
fhir_client = FhirClient()
fhir_client = fhir_client.url(absolute_url).resource("Patient")
fhir_client = fhir_client.client_credentials(
client_id="client_id", client_secret="client_secret"
)
fhir_client = fhir_client.auth_server_url(absolute_url + "/" + "auth").auth_scopes(
["user/*.ready"]
)
response: FhirGetResponse = await fhir_client.get_async()
print(response.responses)
assert response.responses == response_text
async def test_fhir_client_patient_list_ids_async() -> None:
test_name = "test_fhir_client_patient_list_ids_async"
mock_server_url = "http://mock-server:1080"
mock_client: MockServerFriendlyClient = MockServerFriendlyClient(
base_url=mock_server_url)
relative_url: str = test_name
absolute_url: str = mock_server_url + "/" + test_name
mock_client.clear(f"/{test_name}/*.*")
mock_client.reset()
last_updated_after = datetime.datetime.strptime("2022-01-10", "%Y-%m-%d")
response_text: str = json.dumps([
{
"resourceType": "Patient",
"id": "12355"
},
{
"resourceType": "Patient",
"id": "5555"
},
])
mock_client.expect(
mock_request(
path=f"/{relative_url}/Patient",
method="GET",
querystring={
"_elements": "id",
"_count": "10000",
"_getpagesoffset": "9",
"_lastUpdated": "ge2022-01-10T00:00:00Z",
},
),
mock_response(body=response_text),
timing=times(1),
)
fhir_client = FhirClient()
fhir_client = fhir_client.url(absolute_url).resource("Patient")
fhir_client = fhir_client.last_updated_after(last_updated_after)
list_of_ids: List[str] = await fhir_client.get_ids_for_query_async()
print(json.dumps(list_of_ids))
assert list_of_ids == ["12355", "5555"]
def test_dev_server_get_patients() -> None:
clean_fhir_server()
url = "http://fhir:3000/4_0_0"
fhir_client = FhirClient()
fhir_client = fhir_client.url(url).resource("Patient")
resource = {
"resourceType": "Patient",
"id": "12355",
"meta": {
"security": [{
"system": "https://www.icanbwell.com/access",
"code": "bwell"
}]
},
}
merge_response: FhirMergeResponse = fhir_client.merge(
[json.dumps(resource)])
print(merge_response.responses)
assert merge_response.status == 200, merge_response.responses
assert merge_response.responses[0][
"created"] is True, merge_response.responses
fhir_client = fhir_client.url(url).resource("Patient")
response: FhirGetResponse = fhir_client.get()
print(response.responses)
responses_ = json.loads(response.responses)[0]
assert responses_["id"] == resource["id"]
assert responses_["resourceType"] == resource["resourceType"]
def test_fhir_client_patient_list_auth_fail_retry() -> None:
with requests_mock.Mocker() as mock:
url = "http://foo"
response_text = {"resourceType": "Patient", "id": "12355"}
mock.get(f"{url}/Patient", [{
"status_code": 403
}, {
"json": response_text
}])
auth_response = {
"access_token": "my_access_token",
"expires_in": 86400,
"token_type": "Bearer",
}
mock.post(
"http://auth",
[{
"status_code": 200
}, {
"json": auth_response,
"status_code": 200
}],
)
fhir_client = FhirClient()
fhir_client = fhir_client.url(url).resource("Patient")
fhir_client = fhir_client.client_credentials(
client_id="client_id", client_secret="client_secret")
fhir_client = fhir_client.auth_server_url("http://auth").auth_scopes(
["user/*.ready"])
response: FhirGetResponse = fhir_client.get()
print(response.responses)
assert mock.call_count == 4, ",".join(
[r.url for r in mock.request_history])
assert response.responses == json.dumps(response_text)
def test_dev_server_no_auth() -> None:
url = "http://fhir:3000/4_0_0"
fhir_client = FhirClient()
fhir_client = fhir_client.url(url).resource("Patient")
response: FhirGetResponse = fhir_client.get()
print(response.responses)
async def test_fhir_client_patient_list_in_batches_async() -> None:
test_name = "test_fhir_client_patient_list_in_batches_async"
mock_server_url = "http://mock-server:1080"
mock_client: MockServerFriendlyClient = MockServerFriendlyClient(
base_url=mock_server_url
)
relative_url: str = test_name
absolute_url: str = mock_server_url + "/" + test_name
mock_client.clear(f"/{test_name}/*.*")
mock_client.reset()
# this is the first call made by the first concurrent request
mock_client.expect(
mock_request(
path=f"/{relative_url}/Patient",
method="GET",
querystring={
"_elements": "id",
"_count": "1",
"_getpagesoffset": "0",
"_total": "accurate",
},
),
mock_response(
body=json.dumps(
{
"resourceType": "Bundle",
"total": 2,
"entry": [{"resource": {"id": "1"}}],
}
)
),
timing=times(1),
)
# this is the second call made by first concurrent request
mock_client.expect(
mock_request(
path=f"/{relative_url}/Patient",
method="GET",
querystring={
"_elements": "id",
"_count": "1",
"_getpagesoffset": "3",
"_total": "accurate",
"id:above": "1",
},
),
mock_response(
body=json.dumps(
{
"resourceType": "Bundle",
"total": 2,
"entry": [],
}
)
),
timing=times(1),
)
# this is the first call made by the second concurrent request
mock_client.expect(
mock_request(
path=f"/{relative_url}/Patient",
method="GET",
querystring={
"_elements": "id",
"_count": "1",
"_getpagesoffset": "1",
"_total": "accurate",
},
),
mock_response(
body=json.dumps(
{
"resourceType": "Bundle",
"total": 2,
"entry": [{"resource": {"id": "2"}}],
}
)
),
timing=times(1),
)
# this is the second call made by second concurrent request
mock_client.expect(
mock_request(
path=f"/{relative_url}/Patient",
method="GET",
querystring={
"_elements": "id",
"_count": "1",
"_getpagesoffset": "3",
"_total": "accurate",
"id:above": "2",
},
),
mock_response(
body=json.dumps(
{
"resourceType": "Bundle",
"total": 2,
"entry": [],
}
)
),
timing=times(1),
)
# this is the call made by the third concurrent request
mock_client.expect(
mock_request(
path=f"/{relative_url}/Patient",
method="GET",
querystring={
"_elements": "id",
"_count": "1",
"_getpagesoffset": "2",
"_total": "accurate",
},
),
mock_response(
body=json.dumps(
{
"resourceType": "Bundle",
"total": 2,
"entry": [],
}
)
),
timing=times(1),
)
# now mock the actual calls to get resources
response_text_1: Dict[str, Any] = {
"resourceType": "Bundle",
"total": 2,
"entry": [
{"resource": {"resourceType": "Patient", "id": "1"}},
{"resource": {"resourceType": "Patient", "id": "2"}},
],
}
mock_client.expect(
mock_request(
path=f"/{relative_url}/Patient",
method="GET",
querystring={
"id": "1,2",
"_count": "1",
"_getpagesoffset": "0",
"_total": "accurate",
},
),
mock_response(body=json.dumps(response_text_1)),
timing=times(1),
)
fhir_client = FhirClient()
fhir_client = fhir_client.url(absolute_url).resource("Patient")
fhir_client = fhir_client.page_size(10)
fhir_client = fhir_client.include_total(True)
def handle_batch(
x: Optional[List[Dict[str, Any]]], page_number: Optional[int]
) -> bool:
if x:
resources_list.extend(x)
return True
resources_list: List[Dict[str, Any]] = []
response: List[Dict[str, Any]] = await fhir_client.get_resources_by_query_async(
fn_handle_batch=handle_batch,
page_size_for_retrieving_ids=1,
page_size_for_retrieving_resources=2,
concurrent_requests=3,
)
print(response)
assert response == []
assert len(resources_list) == 2
print(resources_list)
assert resources_list == [
{"resourceType": "Patient", "id": "1"},
{"resourceType": "Patient", "id": "2"},
]
def test_fhir_client_bundle_separated() -> None:
test_name = "test_fhir_client_bundle_separated"
mock_server_url = "http://mock-server:1080"
mock_client: MockServerFriendlyClient = MockServerFriendlyClient(
base_url=mock_server_url)
relative_url: str = test_name
absolute_url: str = mock_server_url + "/" + test_name
mock_client.clear(f"/{test_name}/*.*")
mock_client.reset()
test_path = Path(__file__).parent
with open(test_path.joinpath("../practitioner_graph_sample.json")) as f:
response_text = json.load(f)
action_payload = {
"resourceType":
"GraphDefinition",
"id":
"o",
"name":
"provider_everything",
"status":
"active",
"start":
"Practitioner",
"link": [{
"description":
"Practitioner Roles for this Practitioner",
"target": [{
"type":
"PractitionerRole",
"params":
"practitioner={ref}",
"link": [
{
"path": "organization",
"target": [{
"type": "Organization"
}],
},
{
"path": "location[x]",
"target": [{
"type": "Location"
}],
},
{
"path": "healthcareService[x]",
"target": [{
"type": "HealthcareService"
}],
},
],
}],
}],
}
mock_client.expect(
mock_request(
path=f"/{relative_url}/Patient/$graph",
method="POST",
querystring={
"id": "1053306548,1710949219",
"contained": "true"
},
),
mock_response(body=response_text),
timing=times(1),
)
fhir_client = (FhirClient().action("$graph").id_(
["1710949219", "1053306548"]).additional_parameters([
"&contained=true"
]).action_payload(action_payload).separate_bundle_resources(True))
fhir_client = fhir_client.url(absolute_url).resource("Patient")
response: FhirGetResponse = fhir_client.get()
with open(test_path.joinpath(
"./practitioner_graph_sample_separated.json")) as f:
expected_response = json.load(f)
assert json.loads(response.responses) == expected_response
def test_fhir_client_bundle() -> None:
with requests_mock.Mocker() as mock:
url = "http://foo"
response_text = {
"resourceType":
"Bundle",
"id":
"1437321965",
"entry": [
{
"link":
"https://localhost:3000/4_0_0/Practitioner/1437321965",
"resource": {
"resourceType":
"Practitioner",
"id":
"1437321965",
"meta": {
"versionId": "1",
"lastUpdated": "2021-01-13T04:37:06+00:00",
"source": "http://medstarhealth.org/provider",
},
"identifier": [
{
"use": "usual",
"type": {
"coding": [{
"system":
"http://terminology.hl7.org/CodeSystem/v2-0203",
"code": "PRN",
}]
},
"system": "http://medstarhealth.org",
"value": "500524",
},
{
"use": "official",
"type": {
"coding": [{
"system":
"http://terminology.hl7.org/CodeSystem/v2-0203",
"code": "NPI",
}]
},
"system": "http://hl7.org/fhir/sid/us-npi",
"value": "1437321965",
},
],
"active":
True,
"name": [{
"use": "usual",
"text": "ZOOVIA AMAN MD",
"family": "AMAN",
"given": ["ZOOVIA", ""],
}],
"gender":
"female",
"qualification": [
{
"code": {
"coding": [{
"system":
"http://terminology.hl7.org/ValueSet/v2-2.7-030",
"code": "MD",
}]
}
},
{
"code": {
"coding": [{
"system":
"http://terminology.hl7.org/ValueSet/v2-2.7-030",
"code": "MD",
}]
},
"period": {
"start": "2011-01-01",
"end": "2023-12-31"
},
"issuer": {
"reference":
"Organization/Harpers_Ferry_Family_Medicine"
},
},
],
"communication": [{
"coding": [{
"system": "urn:ietf:bcp:47",
"code": "en"
}]
}],
},
},
{
"link":
"https://localhost:3000/4_0_0/PractitionerRole/1437321965-ML1-MLSW",
"resource": {
"resourceType":
"PractitionerRole",
"id":
"1437321965-ML1-MLSW",
"meta": {
"versionId": "1",
"lastUpdated": "2021-01-13T04:37:24+00:00",
"source": "http://medstarhealth.org/provider",
},
"practitioner": {
"reference": "Practitioner/1437321965"
},
"organization": {
"reference": "Organization/Medstar-15888213"
},
"code": [{
"coding": [{
"system":
"http://terminology.hl7.org/CodeSystem/practitioner-role",
"code": "doctor",
"display": "Doctor",
}],
"text":
"Doctor",
}],
"specialty": [
{
"coding": [{
"system":
"https://www.http://medstarhealth.org",
"code": "Family Medicine",
"display": "Family Medicine",
}],
"text":
"Family Medicine",
},
{
"coding": [{
"system":
"http://nucc.org/provider-taxonomy",
"code": "207Q00000X",
"display": "Family Medicine",
}],
"text":
"Family Medicine",
},
{
"coding": [{
"system":
"http://nucc.org/provider-taxonomy",
"code": "261QP2300X",
"display": "Primary Care",
}],
"text":
"Primary Care",
},
],
"location": [{
"reference":
"Location/Medstar-Alias-ML1-MLSW"
}],
},
},
],
}
expected_response = {
"practitioner": [{
"resourceType":
"Practitioner",
"id":
"1437321965",
"meta": {
"versionId": "1",
"lastUpdated": "2021-01-13T04:37:06+00:00",
"source": "http://medstarhealth.org/provider",
},
"identifier": [
{
"use": "usual",
"type": {
"coding": [{
"system":
"http://terminology.hl7.org/CodeSystem/v2-0203",
"code": "PRN",
}]
},
"system": "http://medstarhealth.org",
"value": "500524",
},
{
"use": "official",
"type": {
"coding": [{
"system":
"http://terminology.hl7.org/CodeSystem/v2-0203",
"code": "NPI",
}]
},
"system": "http://hl7.org/fhir/sid/us-npi",
"value": "1437321965",
},
],
"active":
True,
"name": [{
"use": "usual",
"text": "ZOOVIA AMAN MD",
"family": "AMAN",
"given": ["ZOOVIA", ""],
}],
"gender":
"female",
"qualification": [
{
"code": {
"coding": [{
"system":
"http://terminology.hl7.org/ValueSet/v2-2.7-030",
"code": "MD",
}]
}
},
{
"code": {
"coding": [{
"system":
"http://terminology.hl7.org/ValueSet/v2-2.7-030",
"code": "MD",
}]
},
"period": {
"start": "2011-01-01",
"end": "2023-12-31"
},
"issuer": {
"reference":
"Organization/Harpers_Ferry_Family_Medicine"
},
},
],
"communication": [{
"coding": [{
"system": "urn:ietf:bcp:47",
"code": "en"
}]
}],
}],
"practitionerrole": [{
"resourceType":
"PractitionerRole",
"id":
"1437321965-ML1-MLSW",
"meta": {
"versionId": "1",
"lastUpdated": "2021-01-13T04:37:24+00:00",
"source": "http://medstarhealth.org/provider",
},
"practitioner": {
"reference": "Practitioner/1437321965"
},
"organization": {
"reference": "Organization/Medstar-15888213"
},
"code": [{
"coding": [{
"system":
"http://terminology.hl7.org/CodeSystem/practitioner-role",
"code": "doctor",
"display": "Doctor",
}],
"text":
"Doctor",
}],
"specialty": [
{
"coding": [{
"system": "https://www.http://medstarhealth.org",
"code": "Family Medicine",
"display": "Family Medicine",
}],
"text":
"Family Medicine",
},
{
"coding": [{
"system": "http://nucc.org/provider-taxonomy",
"code": "207Q00000X",
"display": "Family Medicine",
}],
"text":
"Family Medicine",
},
{
"coding": [{
"system": "http://nucc.org/provider-taxonomy",
"code": "261QP2300X",
"display": "Primary Care",
}],
"text":
"Primary Care",
},
],
"location": [{
"reference": "Location/Medstar-Alias-ML1-MLSW"
}],
}],
}
mock.get(f"{url}/Patient", json=response_text)
fhir_client = FhirClient().separate_bundle_resources(True)
fhir_client = fhir_client.url(url).resource("Patient")
response: FhirGetResponse = fhir_client.get()
print(response.responses)
assert response.responses == json.dumps(expected_response)