def test_composite_type(self):
""" """
results = self.load_contents()
self.admin_browser.open(results[3] + "/++add++Observation")
self.admin_browser.getControl(
name="form.widgets.IBasic.title").value = "Carbon dioxide in blood"
with open(os.path.join(FHIR_FIXTURE_PATH, "Observation.json"),
"rb") as f:
fhir_json = json_loads(f.read())
self.admin_browser.getControl(name="form.widgets.observation_resource"
).value = json_dumps(fhir_json)
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
# Let's flush
self.es.connection.indices.flush()
context = self.get_context("Observation", True)
# Test simple composite
params = (("code-value-quantity", "http://loinc.org|11557-6$6.2"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
def test_catalogsearch_missing_modifier(self):
""" """
results = self.load_contents()
org1_url = results[0]
# add another patient
self.admin_browser.open(org1_url + "/++add++Patient")
self.admin_browser.getControl(
name="form.widgets.IBasic.title").value = "Test Patient"
with open(str(FHIR_FIXTURE_PATH / "Patient.json"), "rb") as f:
data = json_loads(f.read())
data["id"] = "20c5245f-89a8-49f8-b244-666b32adb92e"
data["gender"] = None
self.admin_browser.getControl(
name="form.widgets.patient_resource").value = json_dumps(data)
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
# Let's flush
self.es.connection.indices.flush()
# Let's test
context = self.get_context("Patient", False)
params = (("gender:missing", "true"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(1, len(brains))
self.assertIsNone(brains[0].getObject().patient_resource.gender)
params = (("gender:missing", "false"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(1, len(brains))
self.assertIsNotNone(brains[0].getObject().patient_resource.gender)
def test_IN_OR(self):
""" """
results = self.load_contents()
new_id = str(uuid.uuid4())
new_patient_id = str(uuid.uuid4())
new_procedure_request_id = str(uuid.uuid4())
self.admin_browser.open(results[3] + "/++add++Task")
with open(os.path.join(FHIR_FIXTURE_PATH, "SubTask_HAQ.json"),
"rb") as f:
json_value = json_loads(f.read())
json_value["id"] = new_id
json_value["status"] = "completed"
json_value["for"]["reference"] = "Patient/" + new_patient_id
json_value["basedOn"][0]["reference"] = ("ProcedureRequest/" +
new_procedure_request_id)
self.admin_browser.getControl(name="form.widgets.task_resource"
).value = json_dumps(json_value)
self.admin_browser.getControl(name="form.widgets.IBasic.title"
).value = json_value["description"]
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
# Let's flush
self.es.connection.indices.flush()
context = self.get_context("Task", True)
params = (("status", "ready,draft"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
# should All three tasks
self.assertEqual(len(brains), 3)
params = ((
"patient",
"Patient/19c5245f-89a8-49f8-b244-666b32adb92e,Patient/" +
new_patient_id,
), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
# should All three tasks + one
self.assertEqual(len(brains), 4)
params = ((
"based-on",
("ProcedureRequest/0c57a6c9-c275-4a0a-"
"bd96-701daf7bd7ce,ProcedureRequest/") + new_procedure_request_id,
), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
# should two tasks
self.assertEqual(len(brains), 2)
def _get_mapping(fhir_release: str, resource_type: str):
"""
:param fhir_release:
:param resource_type:
:return:
"""
filename = (ELASTICSEARCH_STATIC_MAPPINGS / fhir_release /
f"{resource_type}.mapping.json")
try:
with open(str(filename), "rb") as fp:
data = json_loads(fp.read())
return data["mapping"]
except FileNotFoundError:
raise LookupError(
f"No mapping has been found for {fhir_release}.{resource_type}")
async def test_create_patient(hyperfhir_site, es_setup):
""" """
client = hyperfhir_site
with open(str(FHIR_EXAMPLE_RESOURCES / "Patient.json"), "rb") as fp:
json_data = json_loads(fp.read())
res = await client.post(
"/api/v1/fhir/Patient",
json=json_data,
headers={"Accept": "application/json"},
)
assert res.status_code == 201
db = get_db()
result = await db.fetch_all(
f"SELECT * FROM {ResourceHistoryModel.__tablename__} ORDER BY id ASC")
assert len(result) == 1
async def setup_elasticsearch(
release_name: str,
es_conn: AsyncElasticsearchConnection = None,
create: bool = False,
):
"""
:param release_name:
:param es_conn:
:param create:
:return:
"""
conn = es_conn.raw_connection
real_index_name = _get_index_name(release_name)
exist = await conn.indices.exists(real_index_name)
if create is True:
if exist:
# xxx: es_conn.indices.delete_alias(real_index_name, alias_name="")
await conn.indices.delete(real_index_name)
else:
if exist:
return
body = {
"settings": {
"analysis": {
"analyzer": {
"fhir_reference_analyzer": {
"tokenizer": "keyword",
"filter": ["fhir_reference_filter"],
},
},
"filter": {
"fhir_reference_filter": {
"type": "pattern_capture",
"preserve_original": True,
"patterns":
[r"(?:\w+\/)?(https?\:\/\/.*|[a-zA-Z0-9_-]+)"],
},
},
"char_filter": {},
"tokenizer": {},
},
"index": {
"mapping": {
"total_fields": {
"limit":
int(
os.environ.get(
"ELASTICSEARCH_INDEX_MAPPING_TOTAL_FIELDS",
"10000"))
},
"depth": {
"limit":
int(
os.environ.get("ELASTICSEARCH_INDEX_MAPPING_DEPTH",
"50"))
},
"nested_fields": {
"limit":
int(
os.environ.get(
"ELASTICSEARCH_INDEX_MAPPING_NESTED_FIELDS",
"1200"))
},
}
},
},
"mappings": {
"dynamic": False,
"properties": {
"access_scopes": {
"index": True,
"store": True,
"type": "keyword"
},
"access_users": {
"index": True,
"store": True,
"type": "keyword"
},
},
},
}
for jsonfile in (ELASTICSEARCH_STATIC_MAPPINGS /
release_name).glob("*.mapping.json"):
with open(str(jsonfile), "rb") as fp:
data = json_loads(fp.read())
body["mappings"]["properties"][
data["resourceType"]] = data["mapping"]
await conn.indices.create(real_index_name, body=body)
# xxx: create alias
await conn.indices.refresh(index=real_index_name)
async def deserialize_json_request_body(
request: Request,
) -> typing.Union[typing.Dict[str, typing.Any], typing.List[typing.Any]]:
""" """
raw = await request.body()
return json_loads(raw)
def test_reference_with_below_above(self):
""" """
results = self.load_contents()
context = self.get_context("Task", True)
# Should Get All Tasks
params = (("patient:below", "Patient"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 3)
self.admin_browser.open(results[3] + "/++add++Observation")
with open(os.path.join(FHIR_FIXTURE_PATH, "Observation.json"),
"rb") as f:
json_value1 = json_loads(f.read())
self.admin_browser.getControl(
name="form.widgets.observation_resource").value = json_dumps(
json_value1)
self.admin_browser.getControl(
name="form.widgets.IBasic.title").value = (
json_value1["resourceType"] + json_value1["id"])
self.admin_browser.getControl(name="form.buttons.save").click()
with open("output.html", "w") as fp:
fp.write(self.admin_browser.contents)
self.assertIn("Item created", self.admin_browser.contents)
device_id = str(uuid.uuid4())
self.admin_browser.open(results[3] + "/++add++Observation")
with open(os.path.join(FHIR_FIXTURE_PATH, "Observation.json"),
"rb") as f:
json_value = json_loads(f.read())
json_value["id"] = str(uuid.uuid4())
json_value["subject"] = {"reference": "Device/" + device_id}
self.admin_browser.getControl(
name="form.widgets.observation_resource").value = json_dumps(
json_value)
self.admin_browser.getControl(
name="form.widgets.IBasic.title").value = (
json_value["resourceType"] + json_value["id"])
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
self.es.connection.indices.flush()
context = self.get_context("Observation", True)
# Should One
params = (("subject:below", "Device"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
# Little bit complex
params = (("subject:below", "Device,Patient"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 2)
# Search By Multiple Ids
# no need above
params = (("subject",
device_id + "," + json_value1["subject"]["reference"]), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 2)
params = (("subject", device_id), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
def test_issue_21_code_and_coding(self):
"""Add Support for IN/OR query for token and other if possible search type"""
results = self.load_contents()
with open(os.path.join(FHIR_FIXTURE_PATH, "ChargeItem.json"),
"rb") as f:
fhir_json = json_loads(f.read())
fhir_json_copy = copy.deepcopy(fhir_json)
fhir_json_copy["id"] = str(uuid.uuid4())
fhir_json_copy["code"]["coding"] = [
{
"code": "387517004",
"display": "Paracetamol",
"system": "http://snomed.info/387517004",
},
{
"code": "91107009",
"display": "Caffeine",
"system": "http://snomed.info/91107009",
},
]
fhir_json_copy["code"]["text"] = "Paracetamol (substance)"
self.admin_browser.open(results[3] + "/++add++ChargeItem")
self.admin_browser.getControl(name="form.widgets.IBasic.title"
).value = "Test Clinical Bill (USD)"
self.admin_browser.getControl(name="form.widgets.chargeitem_resource"
).value = json_dumps(fhir_json_copy)
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
fhir_json_copy = copy.deepcopy(fhir_json)
fhir_json_copy["id"] = str(uuid.uuid4())
fhir_json_copy["code"]["coding"] = [{
"code":
"387137007",
"display":
"Omeprazole",
"system":
"http://snomed.info/387137007",
}]
fhir_json_copy["code"]["text"] = "Omeprazole (substance)"
self.admin_browser.open(results[3] + "/++add++ChargeItem")
self.admin_browser.getControl(
name="form.widgets.IBasic.title").value = "Test Clinical Bill(BDT)"
self.admin_browser.getControl(name="form.widgets.chargeitem_resource"
).value = json_dumps(fhir_json_copy)
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
# Let's flush
self.es.connection.indices.flush()
context = self.get_context("ChargeItem", True)
params = (("code", "387517004,387137007"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 2)
# Test with system+code with negetive
params = ((
"code:not",
("http://snomed.info/387517004|FF009,"
"http://snomed.info/387137007|387137007"),
), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
def test_code_datatype(self):
""" """
results = self.load_contents()
self.admin_browser.open(results[3] + "/++add++ChargeItem")
self.admin_browser.getControl(
name="form.widgets.IBasic.title").value = "Test Clinical Bill"
with open(os.path.join(FHIR_FIXTURE_PATH, "ChargeItem.json"),
"rb") as f:
fhir_json = json_loads(f.read())
self.admin_browser.getControl(name="form.widgets.chargeitem_resource"
).value = json_dumps(fhir_json)
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
# Let's flush
self.es.connection.indices.flush()
# Test code (Coding)
context = self.get_context("ChargeItem", True)
params = (("code", "F01510"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
# Test with system+code
params = (("code", "http://snomed.info/sct|F01510"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
# test with code only
params = (("code", "|F01510"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
# test with system only
params = (("code", "http://snomed.info/sct|"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
# test with text
params = (("code:text", "Nice Code"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
# test with .as(
self.admin_browser.open(results[3] + "/++add++MedicationRequest")
self.admin_browser.getControl(
name="form.widgets.IBasic.title").value = "Test Clinical Bill"
with open(os.path.join(FHIR_FIXTURE_PATH, "MedicationRequest.json"),
"rb") as f:
fhir_json = json_loads(f.read())
self.admin_browser.getControl(
name="form.widgets.medicationrequest_resource").value = json_dumps(
fhir_json)
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
# Let's flush
self.es.connection.indices.flush()
# test with only code
context = self.get_context("MedicationRequest", True)
params = (("code", "322254008"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
# test with system and code
params = (("code", "http://snomed.info/sct|"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
def test_number_type_search(self):
""" """
results = self.load_contents()
self.admin_browser.open(results[3] + "/++add++ChargeItem")
self.admin_browser.getControl(
name="form.widgets.IBasic.title").value = "Test Clinical Bill"
with open(os.path.join(FHIR_FIXTURE_PATH, "ChargeItem.json"),
"rb") as f:
fhir_json_charge_item = json_loads(f.read())
self.admin_browser.getControl(
name="form.widgets.chargeitem_resource").value = json_dumps(
fhir_json_charge_item)
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
# Let's flush
self.es.connection.indices.flush()
# Test so normal
context = self.get_context("ChargeItem", True)
# Test normal float value order
params = (("factor-override", "0.8"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
params = (("factor-override", "gt0.79"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
# Test for Encounter
self.admin_browser.open(results[3] + "/++add++Encounter")
self.admin_browser.getControl(
name="form.widgets.IBasic.title").value = "Test Encounter"
with open(os.path.join(FHIR_FIXTURE_PATH, "Encounter.json"),
"rb") as f:
fhir_json = json_loads(f.read())
self.admin_browser.getControl(name="form.widgets.encounter_resource"
).value = json_dumps(fhir_json)
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
# Let's flush
self.es.connection.indices.flush()
context = self.get_context("Encounter", True)
params = (("length", "gt139"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
# Test Issue#21
fhir_json_copy = copy.deepcopy(fhir_json_charge_item)
fhir_json_copy["id"] = str(uuid.uuid4())
fhir_json_copy["priceOverride"].update({
"value": 12,
"unit": "USD",
"code": "USD"
})
fhir_json_copy["quantity"]["value"] = 3
fhir_json_copy["factorOverride"] = 0.54
self.admin_browser.open(results[3] + "/++add++ChargeItem")
self.admin_browser.getControl(name="form.widgets.IBasic.title"
).value = "Test Clinical Bill (USD)"
self.admin_browser.getControl(name="form.widgets.chargeitem_resource"
).value = json_dumps(fhir_json_copy)
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
fhir_json_copy = copy.deepcopy(fhir_json_charge_item)
fhir_json_copy["id"] = str(uuid.uuid4())
fhir_json_copy["priceOverride"].update({
"value": 850,
"unit": "BDT",
"code": "BDT"
})
fhir_json_copy["quantity"]["value"] = 8
fhir_json_copy["factorOverride"] = 0.21
self.admin_browser.open(results[3] + "/++add++ChargeItem")
self.admin_browser.getControl(
name="form.widgets.IBasic.title").value = "Test Clinical Bill(BDT)"
self.admin_browser.getControl(name="form.widgets.chargeitem_resource"
).value = json_dumps(fhir_json_copy)
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
# Let's flush
self.es.connection.indices.flush()
# Test with multiple equal values
context = self.get_context("ChargeItem", True)
params = (("factor-override", "0.8,0.21"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 2)
params = (("factor-override", "gt0.8,lt0.54"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
def test_quantity_type_search(self):
""" """
results = self.load_contents()
self.admin_browser.open(results[3] + "/++add++ChargeItem")
self.admin_browser.getControl(
name="form.widgets.IBasic.title").value = "Test Clinical Bill"
with open(os.path.join(FHIR_FIXTURE_PATH, "ChargeItem.json"),
"rb") as f:
fhir_json = json_loads(f.read())
self.admin_browser.getControl(name="form.widgets.chargeitem_resource"
).value = json_dumps(fhir_json)
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
self.assertIn("chargeitem/view", self.admin_browser.url)
# Let's flush
self.es.connection.indices.flush()
# Test so normal
context = self.get_context("ChargeItem", True)
# Test ascending order
params = (("quantity", "5"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
params = (("quantity", "lt5.1"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
# Test with value code/unit and system
params = (("price-override", "gt39.99|urn:iso:std:iso:4217|EUR"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
# Test with code/unit and system
params = (("price-override", "40||EUR"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 1)
# Test Issue#21
fhir_json_copy = copy.deepcopy(fhir_json)
fhir_json_copy["id"] = str(uuid.uuid4())
fhir_json_copy["priceOverride"].update({
"value": 12,
"unit": "USD",
"code": "USD"
})
fhir_json_copy["quantity"]["value"] = 3
fhir_json_copy["factorOverride"] = 0.54
self.admin_browser.open(results[3] + "/++add++ChargeItem")
self.admin_browser.getControl(name="form.widgets.IBasic.title"
).value = "Test Clinical Bill (USD)"
self.admin_browser.getControl(name="form.widgets.chargeitem_resource"
).value = json_dumps(fhir_json_copy)
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
fhir_json_copy = copy.deepcopy(fhir_json)
fhir_json_copy["id"] = str(uuid.uuid4())
fhir_json_copy["priceOverride"].update({
"value": 850,
"unit": "BDT",
"code": "BDT"
})
fhir_json_copy["quantity"]["value"] = 8
fhir_json_copy["factorOverride"] = 0.21
self.admin_browser.open(results[3] + "/++add++ChargeItem")
self.admin_browser.getControl(
name="form.widgets.IBasic.title").value = "Test Clinical Bill(BDT)"
self.admin_browser.getControl(name="form.widgets.chargeitem_resource"
).value = json_dumps(fhir_json_copy)
self.admin_browser.getControl(name="form.buttons.save").click()
self.assertIn("Item created", self.admin_browser.contents)
# Let's flush
self.es.connection.indices.flush()
params = ((
"price-override",
"gt39.99|urn:iso:std:iso:4217|EUR,le850|urn:iso:std:iso:4217|BDT",
), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
self.assertEqual(len(brains), 2)
params = (("price-override", "ge12,le850"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
# should be all three now
self.assertEqual(len(brains), 3)
# serach by only system and code
params = ((
"price-override",
("|urn:iso:std:iso:4217|USD,"
"|urn:iso:std:iso:4217|BDT,"
"|urn:iso:std:iso:4217|DKK"),
), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
# should be 2
self.assertEqual(len(brains), 2)
# serach by unit only
params = (("price-override", "|BDT,|DKK"), )
brains = zcatalog_fhir_search(context, query_string=urlencode(params))
# should be one
self.assertEqual(len(brains), 1)