def test_raises_for_missing_api_url(self) -> None:
self.recipient.fhir_api_url = ""
exported_task = ExportedTask(task=self.task, recipient=self.recipient)
exported_task_fhir = ExportedTaskFhir(exported_task)
with self.assertRaises(FhirExportException) as cm:
FhirTaskExporter(self.req, exported_task_fhir)
message = str(cm.exception)
self.assertIn("must be initialized with `base_uri`", message)
def test_raises_when_fhirclient_raises(self) -> None:
exported_task = ExportedTask(task=self.task, recipient=self.recipient)
exported_task_fhir = ExportedTaskFhir(exported_task)
exporter = MockFhirTaskExporter(self.req, exported_task_fhir)
exporter.client.server = None
with self.assertRaises(FhirExportException) as cm:
exporter.export_task()
message = str(cm.exception)
self.assertIn("Cannot create a resource without a server", message)
def test_patient_exported(self) -> None:
exported_task = ExportedTask(task=self.task, recipient=self.recipient)
exported_task_fhir = ExportedTaskFhir(exported_task)
exporter = MockFhirTaskExporter(self.req, exported_task_fhir)
response_json = {Fc.TYPE: Fc.TRANSACTION_RESPONSE}
with mock.patch.object(
exporter.client.server,
"post_json",
return_value=MockFhirResponse(response_json),
) as mock_post:
exporter.export_task()
args, kwargs = mock_post.call_args
sent_json = args[1]
self.assertEqual(sent_json[Fc.RESOURCE_TYPE], Fc.RESOURCE_TYPE_BUNDLE)
self.assertEqual(sent_json[Fc.TYPE], Fc.TRANSACTION)
patient = sent_json[Fc.ENTRY][0][Fc.RESOURCE]
self.assertEqual(patient[Fc.RESOURCE_TYPE], Fc.RESOURCE_TYPE_PATIENT)
identifier = patient[Fc.IDENTIFIER]
idnum_value = self.patient_rio.idnum_value
patient_id = self.patient.get_fhir_identifier(self.req, self.recipient)
self.assertEqual(identifier[0][Fc.SYSTEM], patient_id.system)
self.assertEqual(identifier[0][Fc.VALUE], str(idnum_value))
self.assertEqual(
patient[Fc.NAME][0][Fc.NAME_FAMILY], self.patient.surname
)
self.assertEqual(
patient[Fc.NAME][0][Fc.NAME_GIVEN], [self.patient.forename]
)
self.assertEqual(patient[Fc.GENDER], Fc.GENDER_FEMALE)
request = sent_json[Fc.ENTRY][0][Fc.REQUEST]
self.assertEqual(request[Fc.METHOD], HttpMethod.POST)
self.assertEqual(request[Fc.URL], Fc.RESOURCE_TYPE_PATIENT)
self.assertEqual(
request[Fc.IF_NONE_EXIST],
fhir_reference_from_identifier(patient_id),
)
def test_raises_when_http_error(self) -> None:
exported_task = ExportedTask(task=self.task, recipient=self.recipient)
exported_task_fhir = ExportedTaskFhir(exported_task)
exporter = MockFhirTaskExporter(self.req, exported_task_fhir)
errmsg = "Something bad happened"
with mock.patch.object(
exporter.client.server,
"post_json",
side_effect=HTTPError(response=mock.Mock(text=errmsg)),
):
with self.assertRaises(FhirExportException) as cm:
exporter.export_task()
message = str(cm.exception)
self.assertIn(errmsg, message)
def test_questionnaire_response_exported(self) -> None:
exported_task = ExportedTask(task=self.task, recipient=self.recipient)
exported_task_fhir = ExportedTaskFhir(exported_task)
exporter = MockFhirTaskExporter(self.req, exported_task_fhir)
response_json = {Fc.TYPE: Fc.TRANSACTION_RESPONSE}
with mock.patch.object(
exporter.client.server,
"post_json",
return_value=MockFhirResponse(response_json),
) as mock_post:
exporter.export_task()
args, kwargs = mock_post.call_args
sent_json = args[1]
response = sent_json[Fc.ENTRY][1][Fc.RESOURCE]
self.assertEqual(
response[Fc.RESOURCE_TYPE], Fc.RESOURCE_TYPE_QUESTIONNAIRE_RESPONSE
)
q_id = self.task._get_fhir_questionnaire_id(self.req)
self.assertEqual(response[Fc.QUESTIONNAIRE], fhir_sysval_from_id(q_id))
self.assertEqual(
response[Fc.AUTHORED], self.task.when_created.isoformat()
)
self.assertEqual(response[Fc.STATUS], Fc.QSTATUS_COMPLETED)
request = sent_json[Fc.ENTRY][1][Fc.REQUEST]
self.assertEqual(request[Fc.METHOD], HttpMethod.POST)
self.assertEqual(request[Fc.URL], "QuestionnaireResponse")
qr_id = self.task._get_fhir_questionnaire_response_id(self.req)
self.assertEqual(
request[Fc.IF_NONE_EXIST], fhir_reference_from_identifier(qr_id)
)
self.assertEqual(len(response[Fc.ITEM]), 5)
(
q1_choice,
q2_choice,
q3_choice,
q1_satisfaction,
q2_satisfaction,
) = response[Fc.ITEM]
# q1_choice
self.assertEqual(q1_choice[Fc.LINK_ID], "q1_choice")
self.assertEqual(q1_choice[Fc.TEXT], GIVEN_INFO)
q1_choice_answer = q1_choice[Fc.ANSWER][0]
self.assertEqual(
q1_choice_answer[Fc.VALUE_INTEGER], self.task.q1_choice
)
# q2_choice
self.assertEqual(q2_choice[Fc.LINK_ID], "q2_choice")
self.assertEqual(q2_choice[Fc.TEXT], PREFER_ANY)
q2_choice_answer = q2_choice[Fc.ANSWER][0]
self.assertEqual(
q2_choice_answer[Fc.VALUE_INTEGER], self.task.q2_choice
)
# q3_choice
self.assertEqual(q3_choice[Fc.LINK_ID], "q3_choice")
self.assertEqual(q3_choice[Fc.TEXT], OFFERED_PREFERENCE)
q3_choice_answer = q3_choice[Fc.ANSWER][0]
self.assertEqual(
q3_choice_answer[Fc.VALUE_INTEGER], self.task.q3_choice
)
# q1_satisfaction
self.assertEqual(q1_satisfaction[Fc.LINK_ID], "q1_satisfaction")
self.assertEqual(q1_satisfaction[Fc.TEXT], SATISFIED_ASSESSMENT)
q1_satisfaction_answer = q1_satisfaction[Fc.ANSWER][0]
self.assertEqual(
q1_satisfaction_answer[Fc.VALUE_INTEGER], self.task.q1_satisfaction
)
# q2 satisfaction
self.assertEqual(q2_satisfaction[Fc.LINK_ID], "q2_satisfaction")
self.assertEqual(q2_satisfaction[Fc.TEXT], TELL_US)
q2_satisfaction_answer = q2_satisfaction[Fc.ANSWER][0]
self.assertEqual(
q2_satisfaction_answer[Fc.VALUE_STRING], self.task.q2_satisfaction
)
def test_questionnaire_exported(self) -> None:
exported_task = ExportedTask(task=self.task, recipient=self.recipient)
exported_task_fhir = ExportedTaskFhir(exported_task)
exporter = MockFhirTaskExporter(self.req, exported_task_fhir)
response_json = {Fc.TYPE: Fc.TRANSACTION_RESPONSE}
with mock.patch.object(
exporter.client.server,
"post_json",
return_value=MockFhirResponse(response_json),
) as mock_post:
exporter.export_task()
args, kwargs = mock_post.call_args
sent_json = args[1]
questionnaire = sent_json[Fc.ENTRY][0][Fc.RESOURCE]
self.assertEqual(
questionnaire[Fc.RESOURCE_TYPE], Fc.RESOURCE_TYPE_QUESTIONNAIRE
)
self.assertEqual(questionnaire[Fc.STATUS], Fc.QSTATUS_ACTIVE)
identifier = questionnaire[Fc.IDENTIFIER]
questionnaire_url = (
f"{self.camcops_root_url}/{Routes.FHIR_QUESTIONNAIRE_SYSTEM}"
)
self.assertEqual(identifier[0][Fc.SYSTEM], questionnaire_url)
self.assertEqual(
identifier[0][Fc.VALUE], f"apeqpt/{CAMCOPS_SERVER_VERSION_STRING}"
)
self.assertEqual(len(questionnaire[Fc.ITEM]), 5)
(
q1_choice,
q2_choice,
q3_choice,
q1_satisfaction,
q2_satisfaction,
) = questionnaire[Fc.ITEM]
# q1_choice
self.assertEqual(q1_choice[Fc.LINK_ID], "q1_choice")
self.assertEqual(q1_choice[Fc.TEXT], GIVEN_INFO)
self.assertEqual(q1_choice[Fc.TYPE], Fc.QITEM_TYPE_CHOICE)
options = q1_choice[Fc.ANSWER_OPTION]
self.assertEqual(options[0][Fc.VALUE_CODING][Fc.CODE], "0")
self.assertEqual(options[0][Fc.VALUE_CODING][Fc.DISPLAY], "No")
self.assertEqual(options[1][Fc.VALUE_CODING][Fc.CODE], "1")
self.assertEqual(options[1][Fc.VALUE_CODING][Fc.DISPLAY], "Yes")
# q2_choice
self.assertEqual(q2_choice[Fc.LINK_ID], "q2_choice")
self.assertEqual(q2_choice[Fc.TEXT], PREFER_ANY)
self.assertEqual(q2_choice[Fc.TYPE], Fc.QITEM_TYPE_CHOICE)
options = q2_choice[Fc.ANSWER_OPTION]
self.assertEqual(options[0][Fc.VALUE_CODING][Fc.CODE], "0")
self.assertEqual(options[0][Fc.VALUE_CODING][Fc.DISPLAY], "No")
self.assertEqual(options[1][Fc.VALUE_CODING][Fc.CODE], "1")
self.assertEqual(options[1][Fc.VALUE_CODING][Fc.DISPLAY], "Yes")
# q3_choice
self.assertEqual(q3_choice[Fc.LINK_ID], "q3_choice")
self.assertEqual(q3_choice[Fc.TEXT], OFFERED_PREFERENCE)
self.assertEqual(q3_choice[Fc.TYPE], Fc.QITEM_TYPE_CHOICE)
options = q3_choice[Fc.ANSWER_OPTION]
self.assertEqual(options[0][Fc.VALUE_CODING][Fc.CODE], "0")
self.assertEqual(options[0][Fc.VALUE_CODING][Fc.DISPLAY], "No")
self.assertEqual(options[1][Fc.VALUE_CODING][Fc.CODE], "1")
self.assertEqual(options[1][Fc.VALUE_CODING][Fc.DISPLAY], "Yes")
self.assertEqual(options[2][Fc.VALUE_CODING][Fc.CODE], "2")
self.assertEqual(options[2][Fc.VALUE_CODING][Fc.DISPLAY], "N/A")
# q1_satisfaction
self.assertEqual(q1_satisfaction[Fc.LINK_ID], "q1_satisfaction")
self.assertEqual(q1_satisfaction[Fc.TEXT], SATISFIED_ASSESSMENT)
self.assertEqual(q1_satisfaction[Fc.TYPE], Fc.QITEM_TYPE_CHOICE)
options = q1_satisfaction[Fc.ANSWER_OPTION]
self.assertEqual(options[0][Fc.VALUE_CODING][Fc.CODE], "0")
self.assertEqual(
options[0][Fc.VALUE_CODING][Fc.DISPLAY], APEQ_SATIS_A0
)
self.assertEqual(options[1][Fc.VALUE_CODING][Fc.CODE], "1")
self.assertEqual(
options[1][Fc.VALUE_CODING][Fc.DISPLAY], APEQ_SATIS_A1
)
self.assertEqual(options[2][Fc.VALUE_CODING][Fc.CODE], "2")
self.assertEqual(
options[2][Fc.VALUE_CODING][Fc.DISPLAY], APEQ_SATIS_A2
)
self.assertEqual(options[3][Fc.VALUE_CODING][Fc.CODE], "3")
self.assertEqual(
options[3][Fc.VALUE_CODING][Fc.DISPLAY], APEQ_SATIS_A3
)
self.assertEqual(options[4][Fc.VALUE_CODING][Fc.CODE], "4")
self.assertEqual(
options[4][Fc.VALUE_CODING][Fc.DISPLAY], APEQ_SATIS_A4
)
# q2 satisfaction
self.assertEqual(q2_satisfaction[Fc.LINK_ID], "q2_satisfaction")
self.assertEqual(q2_satisfaction[Fc.TEXT], TELL_US)
self.assertEqual(q2_satisfaction[Fc.TYPE], Fc.QITEM_TYPE_STRING)
request = sent_json[Fc.ENTRY][0][Fc.REQUEST]
self.assertEqual(request[Fc.METHOD], HttpMethod.POST)
self.assertEqual(request[Fc.URL], Fc.RESOURCE_TYPE_QUESTIONNAIRE)
q_id = self.task._get_fhir_questionnaire_id(self.req)
self.assertEqual(
request[Fc.IF_NONE_EXIST], fhir_reference_from_identifier(q_id)
)
def test_exported_task_saved(self) -> None:
exported_task = ExportedTask(task=self.task, recipient=self.recipient)
# auto increment doesn't work for BigInteger with SQLite
exported_task.id = 1
self.dbsession.add(exported_task)
exported_task_fhir = ExportedTaskFhir(exported_task)
self.dbsession.add(exported_task_fhir)
exporter = MockFhirTaskExporter(self.req, exported_task_fhir)
response_json = {
Fc.RESOURCE_TYPE: Fc.RESOURCE_TYPE_BUNDLE,
Fc.ID: "cae48957-e7e6-4649-97f8-0a882076ad0a",
Fc.TYPE: Fc.TRANSACTION_RESPONSE,
Fc.LINK: [
{Fc.RELATION: Fc.SELF, Fc.URL: "http://localhost:8080/fhir"}
],
Fc.ENTRY: [
{
Fc.RESPONSE: {
Fc.STATUS: Fc.RESPONSE_STATUS_200_OK,
Fc.LOCATION: "Patient/1/_history/1",
Fc.ETAG: "1",
}
},
{
Fc.RESPONSE: {
Fc.STATUS: Fc.RESPONSE_STATUS_200_OK,
Fc.LOCATION: "Questionnaire/26/_history/1",
Fc.ETAG: "1",
}
},
{
Fc.RESPONSE: {
Fc.STATUS: Fc.RESPONSE_STATUS_201_CREATED,
Fc.LOCATION: "QuestionnaireResponse/42/_history/1",
Fc.ETAG: "1",
Fc.LAST_MODIFIED: "2021-05-24T09:30:11.098+00:00",
}
},
],
}
with mock.patch.object(
exporter.client.server,
"post_json",
return_value=MockFhirResponse(response_json),
):
exporter.export_task()
self.dbsession.commit()
entries = (
exported_task_fhir.entries
) # type: List[ExportedTaskFhirEntry] # noqa
entries.sort(key=lambda e: e.location)
self.assertEqual(entries[0].status, Fc.RESPONSE_STATUS_200_OK)
self.assertEqual(entries[0].location, "Patient/1/_history/1")
self.assertEqual(entries[0].etag, "1")
self.assertEqual(entries[1].status, Fc.RESPONSE_STATUS_200_OK)
self.assertEqual(entries[1].location, "Questionnaire/26/_history/1")
self.assertEqual(entries[1].etag, "1")
self.assertEqual(entries[2].status, Fc.RESPONSE_STATUS_201_CREATED)
self.assertEqual(
entries[2].location, "QuestionnaireResponse/42/_history/1"
)
self.assertEqual(entries[2].etag, "1")
self.assertEqual(
entries[2].last_modified,
datetime.datetime(2021, 5, 24, 9, 30, 11, 98000),
)
def test_questionnaire_response_exported(self) -> None:
exported_task = ExportedTask(task=self.task, recipient=self.recipient)
exported_task_fhir = ExportedTaskFhir(exported_task)
exporter = MockFhirTaskExporter(self.req, exported_task_fhir)
response_json = {Fc.TYPE: Fc.TRANSACTION_RESPONSE}
with mock.patch.object(
exporter.client.server,
"post_json",
return_value=MockFhirResponse(response_json),
) as mock_post:
exporter.export_task()
args, kwargs = mock_post.call_args
sent_json = args[1]
response = sent_json[Fc.ENTRY][2][Fc.RESOURCE]
self.assertEqual(
response[Fc.RESOURCE_TYPE], Fc.RESOURCE_TYPE_QUESTIONNAIRE_RESPONSE
)
q_id = self.task._get_fhir_questionnaire_id(self.req)
self.assertEqual(response[Fc.QUESTIONNAIRE], fhir_sysval_from_id(q_id))
self.assertEqual(
response[Fc.AUTHORED], self.task.when_created.isoformat()
)
self.assertEqual(response[Fc.STATUS], Fc.QSTATUS_COMPLETED)
subject = response[Fc.SUBJECT]
identifier = subject[Fc.IDENTIFIER]
self.assertEqual(subject[Fc.TYPE], Fc.RESOURCE_TYPE_PATIENT)
idnum_value = self.patient_rio.idnum_value
patient_id = self.patient.get_fhir_identifier(self.req, self.recipient)
if isinstance(identifier, list):
test_identifier = identifier[0]
else: # only one
test_identifier = identifier
self.assertEqual(test_identifier[Fc.SYSTEM], patient_id.system)
self.assertEqual(test_identifier[Fc.VALUE], str(idnum_value))
request = sent_json[Fc.ENTRY][2][Fc.REQUEST]
self.assertEqual(request[Fc.METHOD], HttpMethod.POST)
self.assertEqual(
request[Fc.URL], Fc.RESOURCE_TYPE_QUESTIONNAIRE_RESPONSE
)
qr_id = self.task._get_fhir_questionnaire_response_id(self.req)
self.assertEqual(
request[Fc.IF_NONE_EXIST], fhir_reference_from_identifier(qr_id)
)
item_1 = response[Fc.ITEM][0]
item_10 = response[Fc.ITEM][9]
self.assertEqual(item_1[Fc.LINK_ID], "q1")
self.assertEqual(
item_1[Fc.TEXT], "1. Little interest or pleasure in doing things"
)
answer_1 = item_1[Fc.ANSWER][0]
# noinspection PyUnresolvedReferences
self.assertEqual(answer_1[Fc.VALUE_INTEGER], self.task.q1)
self.assertEqual(item_10[Fc.LINK_ID], "q10")
self.assertEqual(
item_10[Fc.TEXT],
(
"10. If you checked off any problems, how difficult have "
"these problems made it for you to do your work, take care of "
"things at home, or get along with other people?"
),
)
answer_10 = item_10[Fc.ANSWER][0]
self.assertEqual(answer_10[Fc.VALUE_INTEGER], self.task.q10)
self.assertEqual(len(response[Fc.ITEM]), 10)
def test_questionnaire_exported(self) -> None:
exported_task = ExportedTask(task=self.task, recipient=self.recipient)
exported_task_fhir = ExportedTaskFhir(exported_task)
exporter = MockFhirTaskExporter(self.req, exported_task_fhir)
response_json = {Fc.TYPE: Fc.TRANSACTION_RESPONSE}
with mock.patch.object(
exporter.client.server,
"post_json",
return_value=MockFhirResponse(response_json),
) as mock_post:
exporter.export_task()
args, kwargs = mock_post.call_args
sent_json = args[1]
questionnaire = sent_json[Fc.ENTRY][1][Fc.RESOURCE]
self.assertEqual(
questionnaire[Fc.RESOURCE_TYPE], Fc.RESOURCE_TYPE_QUESTIONNAIRE
)
self.assertEqual(questionnaire[Fc.STATUS], Fc.QSTATUS_ACTIVE)
identifier = questionnaire[Fc.IDENTIFIER]
questionnaire_url = (
f"{self.camcops_root_url}/{Routes.FHIR_QUESTIONNAIRE_SYSTEM}"
)
self.assertEqual(identifier[0][Fc.SYSTEM], questionnaire_url)
self.assertEqual(
identifier[0][Fc.VALUE], f"phq9/{CAMCOPS_SERVER_VERSION_STRING}"
)
question_1 = questionnaire[Fc.ITEM][0]
question_10 = questionnaire[Fc.ITEM][9]
self.assertEqual(question_1[Fc.LINK_ID], "q1")
self.assertEqual(
question_1[Fc.TEXT],
"1. Little interest or pleasure in doing things",
)
self.assertEqual(question_1[Fc.TYPE], Fc.QITEM_TYPE_CHOICE)
options = question_1[Fc.ANSWER_OPTION]
self.assertEqual(options[0][Fc.VALUE_CODING][Fc.CODE], "0")
self.assertEqual(options[0][Fc.VALUE_CODING][Fc.DISPLAY], "Not at all")
self.assertEqual(options[1][Fc.VALUE_CODING][Fc.CODE], "1")
self.assertEqual(
options[1][Fc.VALUE_CODING][Fc.DISPLAY], "Several days"
)
self.assertEqual(options[2][Fc.VALUE_CODING][Fc.CODE], "2")
self.assertEqual(
options[2][Fc.VALUE_CODING][Fc.DISPLAY], "More than half the days"
)
self.assertEqual(options[3][Fc.VALUE_CODING][Fc.CODE], "3")
self.assertEqual(
options[3][Fc.VALUE_CODING][Fc.DISPLAY], "Nearly every day"
)
self.assertEqual(question_10[Fc.LINK_ID], "q10")
self.assertEqual(
question_10[Fc.TEXT],
(
"10. If you checked off any problems, how difficult have "
"these problems made it for you to do your work, take care of "
"things at home, or get along with other people?"
),
)
self.assertEqual(question_10[Fc.TYPE], Fc.QITEM_TYPE_CHOICE)
options = question_10[Fc.ANSWER_OPTION]
self.assertEqual(options[0][Fc.VALUE_CODING][Fc.CODE], "0")
self.assertEqual(
options[0][Fc.VALUE_CODING][Fc.DISPLAY], "Not difficult at all"
)
self.assertEqual(options[1][Fc.VALUE_CODING][Fc.CODE], "1")
self.assertEqual(
options[1][Fc.VALUE_CODING][Fc.DISPLAY], "Somewhat difficult"
)
self.assertEqual(options[2][Fc.VALUE_CODING][Fc.CODE], "2")
self.assertEqual(
options[2][Fc.VALUE_CODING][Fc.DISPLAY], "Very difficult"
)
self.assertEqual(options[3][Fc.VALUE_CODING][Fc.CODE], "3")
self.assertEqual(
options[3][Fc.VALUE_CODING][Fc.DISPLAY], "Extremely difficult"
)
self.assertEqual(len(questionnaire[Fc.ITEM]), 10)
request = sent_json[Fc.ENTRY][1][Fc.REQUEST]
self.assertEqual(request[Fc.METHOD], HttpMethod.POST)
self.assertEqual(request[Fc.URL], Fc.RESOURCE_TYPE_QUESTIONNAIRE)
q_id = self.task._get_fhir_questionnaire_id(self.req)
self.assertEqual(
request[Fc.IF_NONE_EXIST], fhir_reference_from_identifier(q_id)
)