def test_patch_resource(self, store: FHIRStore, test_patient):
"""patch() finds a document in the database"""
store.create(test_patient)
store.patch("Patient", test_patient["id"], {"gender": "other"})
assert store.read("Patient", test_patient["id"]) == {
**test_patient, "gender": "other"
}
def test_update_bad_resource_schema(self, store: FHIRStore, test_patient):
"""update() raises if json schema validation failed in mongo"""
store.create(test_patient)
with raises(ValidationError):
store.update("Patient", test_patient["id"], {
**test_patient, "gender": "elephant"
})
def test_delete_missing_param(self, store: FHIRStore, test_patient):
"""delete() returns None when no matching document was found"""
with raises(
BadRequestError,
match=
"one of: 'instance_id', 'resource_id' or 'source_id' are required",
):
store.delete("Patient")
def store():
client = MongoClient(username=MONGO_USERNAME, password=MONGO_PASSWORD)
try:
client.server_info()
except ServerSelectionTimeoutError as err:
print("MongoClient could not reach server, is it running ?")
raise
client_es = Elasticsearch([ES_URL], http_auth=("elastic", ES_PASSWORD))
fhirstore = FHIRStore(client, client_es, DB_NAME)
fhirstore.reset()
fhirstore.bootstrap(depth=2, resource="Patient")
fhirstore.bootstrap(depth=2, resource="Practitioner")
fhirstore.bootstrap(depth=2, resource="MedicationRequest")
return fhirstore
def test_create_resource(self, store: FHIRStore, mongo_client: MongoClient,
test_patient):
"""create() correctly inserts a document in the database"""
result = store.create(test_patient)
assert isinstance(result["_id"],
ObjectId), "result _id must be an objectId"
inserted = mongo_client["Patient"].find_one({"_id": result["_id"]})
assert inserted == test_patient
def test_search_identifier(store: FHIRStore):
result = store.comprehensive_search(
"Patient", ImmutableMultiDict([("managingOrganization:identifier", "98765")])
)
assert (
result.content["entry"][0]["resource"]["managingOrganization"]["identifier"][0]["value"]
== "98765"
)
def test_delete_by_source_id(self, store: FHIRStore, test_patient):
"""delete() finds a document in the database"""
store.create(test_patient)
source_id = "pyrogSourceId"
metadata = {
"tag": [
{
"system": ARKHN_CODE_SYSTEMS.source,
"code": source_id
},
{
"code": "some-other-tag"
},
]
}
store.create({
"resourceType": "Patient",
"id": "pat2",
"meta": metadata
})
store.create({
"resourceType": "Patient",
"id": "pat3",
"meta": metadata
})
result = store.delete("Patient", source_id=source_id)
assert result == 2
def test_search_one_param_modifier_str_not(store: FHIRStore):
"""Checks that "not" string modifier works
"""
result = store.comprehensive_search(
"Patient", ImmutableMultiDict([("name.family:not", "Donald")])
)
assert all(
element["resource"]["name"][0]["family"] != "Donald" for element in result.content["entry"]
)
def test_search_two_elements(store: FHIRStore):
result = store.comprehensive_search("Patient", ImmutableMultiDict([("_elements", "birthDate")]))
assert result.content["total"] == 3
assert result.content["tag"]["code"] == "SUBSETTED"
assert result.content["entry"] == [
{"resource": {}, "search": {"mode": "match"}},
{"resource": {"birthDate": "1932-09-24"}, "search": {"mode": "match"}},
{"resource": {"birthDate": "1974-12-25"}, "search": {"mode": "match"}},
]
def test_search_one_param_simple(store: FHIRStore):
"""Checks simple one parameter search
"""
result = store.comprehensive_search(
"Patient", ImmutableMultiDict([("identifier.value", "654321")])
)
assert len(result.content["entry"]) == 1
assert all(
element["resource"]["identifier"][0]["value"] == "654321"
for element in result.content["entry"]
)
def test_search_summary_text(store: FHIRStore):
result = store.comprehensive_search("Patient", ImmutableMultiDict([("_summary", "text")]))
assert result.content["total"] == 3
assert result.content["tag"]["code"] == "SUBSETTED"
assert result.content["entry"] == [
{
"resource": {
"meta": {
"tag": [
{
"system": "http://terminology.hl7.org/CodeSystem/v3-ActReason",
"code": "HTEST",
"display": "test health data",
}
]
},
"id": "pat1",
"text": {
"div": '<div xmlns="http://www.w3.org/1999/xhtml">\n \n <p>Patient Donald DUCK @ Acme Healthcare, Inc. MR = 654321</p>\n \n </div>',
"status": "generated",
},
},
"search": {"mode": "match"},
},
{
"resource": {
"id": "xcda",
"text": {
"div": '<div xmlns="http://www.w3.org/1999/xhtml">\n \n <p>Henry Levin the 7th</p>\n \n </div>',
"status": "generated",
},
},
"search": {"mode": "match"},
},
{
"resource": {
"meta": {
"tag": [
{
"system": "http://terminology.hl7.org/CodeSystem/v3-ActReason",
"code": "HTEST",
"display": "test health data",
}
]
},
"id": "example",
"text": {
"div": '<div xmlns="http://www.w3.org/1999/xhtml">\n\t\t\t<table>\n\t\t\t\t<tbody>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Name</td>\n\t\t\t\t\t\t<td>Peter James \n <b>Chalmers</b> ("Jim")\n </td>\n\t\t\t\t\t</tr>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Address</td>\n\t\t\t\t\t\t<td>534 Erewhon, Pleasantville, Vic, 3999</td>\n\t\t\t\t\t</tr>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Contacts</td>\n\t\t\t\t\t\t<td>Home: unknown. Work: (03) 5555 6473</td>\n\t\t\t\t\t</tr>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Id</td>\n\t\t\t\t\t\t<td>MRN: 12345 (Acme Healthcare)</td>\n\t\t\t\t\t</tr>\n\t\t\t\t</tbody>\n\t\t\t</table>\n\t\t</div>',
"status": "generated",
},
},
"search": {"mode": "match"},
},
]
def test_create_resource_with_extension(self, store: FHIRStore,
mongo_client: MongoClient):
"""resources using extensions are not
handled yet, an error should be raised"""
with open("test/fixtures/patient-example-with-extensions.json") as f:
patient = json.load(f)
result = store.create(patient)
assert isinstance(result["_id"],
ObjectId), "result _id must be an objectId"
inserted = mongo_client["Patient"].find_one({"_id": result["_id"]})
assert inserted == patient
mongo_client["Patient"].delete_one({"_id": patient["_id"]})
def test_search_one_param_modifier_str_exact(store: FHIRStore):
"""Checks that "exact" string modifier works
"""
result = store.comprehensive_search(
"Patient", ImmutableMultiDict([("name.family:exact", "Donald")])
)
assert len(result.content["entry"]) == 1
assert all(
element["resource"]["name"][0]["family"] == "Donald" for element in result.content["entry"]
)
assert all(
element["resource"]["name"][0]["family"] != ("Chalmers" or "Levin")
for element in result.content["entry"]
)
def test_search_one_param_multiple(store: FHIRStore):
"""Checks that multiple elements of one parameter are queried
"""
result = store.comprehensive_search(
"Patient", ImmutableMultiDict([("name.family", "Chalmers,Levin")])
)
assert len(result.content["entry"]) == 2
assert any(
element["resource"]["name"][0]["family"] == ("Chalmers" or "Levin")
for element in result.content["entry"]
)
assert all(
element["resource"]["name"][0]["family"] != "Donald" for element in result.content["entry"]
)
def test_handle_pipe(store: FHIRStore):
result = store.comprehensive_search(
"MedicationRequest",
ImmutableMultiDict([("contained.code.coding", "http://snomed.info/sct|324252006")]),
)
assert result.content["entry"][0]["resource"]["id"] == "medrx0302"
assert (
result.content["entry"][0]["resource"]["contained"][0]["code"]["coding"][0]["system"]
== "http://snomed.info/sct"
)
assert (
result.content["entry"][0]["resource"]["contained"][0]["code"]["coding"][0]["code"]
== "324252006"
)
def test_search_one_param_modifier_str_contains(store: FHIRStore):
"""Checks that "contains" string modifier works
"""
result = store.comprehensive_search(
"Patient",
ImmutableMultiDict([("managingOrganization.reference:contains", "Organization")]),
)
assert len(result.content["entry"]) == 3
assert any(
element["resource"]["managingOrganization"]["reference"] == "Organization/1"
for element in result.content["entry"]
)
assert any(
element["resource"]["managingOrganization"]["reference"]
!= "Organization/2.16.840.1.113883.19.5"
for element in result.content["entry"]
)
def test_search_one_params_and(store: FHIRStore):
"""Checks one parameter "and" search
"""
result = store.comprehensive_search(
"Patient", ImmutableMultiDict([("name.given", "Peter,James")])
)
assert len(result.content["entry"]) == 1
assert any(
element["resource"]["name"][0]["given"] == "Peter" or "James"
for element in result.content["entry"]
)
assert all(
element["resource"]["name"][0]["given"] != "Henry" for element in result.content["entry"]
)
assert all(
element["resource"]["name"][0]["given"] != "Duck" for element in result.content["entry"]
)
def test_search_and_or(store: FHIRStore):
"""Checks two parameter "and,or" search
"""
result = store.comprehensive_search(
"Patient",
ImmutableMultiDict([("name.family", "Levin,Chalmers"), ("identifier.value", "12345")]),
)
assert len(result.content["entry"]) == 2
assert all(
element["resource"]["identifier"][0]["value"] != "654321"
for element in result.content["entry"]
)
assert all(
element["resource"]["identifier"][0]["value"] == "12345"
for element in result.content["entry"]
)
assert all(
element["resource"]["name"][0]["family"] == "Levin" or "Chalmers"
for element in result.content["entry"]
)
assert all(
element["resource"]["name"][0]["family"] != "Donald" for element in result.content["entry"]
)
def test_search_no_parameters(store: FHIRStore):
"""Checks that all elements of the resource are returned
"""
result = store.comprehensive_search("Patient", ImmutableMultiDict([]))
assert len(result.content["entry"]) == 3
def test_search_medicationrequest(store: FHIRStore, insert_medicationrequest):
"""Check that medicationrequest was inserted properly
"""
result = store.comprehensive_search("MedicationRequest", {})
assert result.content["total"] == 2
def test_search_output_type(store: FHIRStore, insert_patient):
"""Check that the output type is correct
"""
result = store.comprehensive_search("Patient", ImmutableMultiDict([]))
assert result.content["resource_type"] == "Bundle"
def test_includes(store: FHIRStore):
result = store.comprehensive_search(
"MedicationRequest", ImmutableMultiDict([("_include", "MedicationRequest:subject")]),
)
assert len(result.content["entry"]) == 4
def test_sort_desc(store: FHIRStore):
result = store.comprehensive_search("Patient", ImmutableMultiDict([("_sort", "-birthDate")]))
assert (
result.content["entry"][0]["resource"]["birthDate"]
>= result.content["entry"][1]["resource"]["birthDate"]
)
def test_unique_indices(self, store: FHIRStore, mongo_client: MongoClient):
"""create() raises if index is already present"""
store.create({
"identifier": [
{
"value": "val",
"system": "sys"
},
{
"value": "just_value"
},
{
"value": "value",
"system": "system",
"type": {
"coding": [{
"system": "type_system",
"code": "type_code"
}]
},
},
],
"resourceType":
"Patient",
"id":
"pat1",
})
# index on id
with raises(DuplicateKeyError, match='dup key: { id: "pat1" }'):
store.create({"resourceType": "Patient", "id": "pat1"})
# index on (identifier.value, identifier.system)
with raises(
DuplicateKeyError,
match=
'dup key: { identifier.system: "sys", identifier.value: "val", \
identifier.type.coding.system: null, identifier.type.coding.code: null }',
):
store.create({
"identifier": [{
"value": "val",
"system": "sys"
}],
"resourceType": "Patient",
"id": "pat2",
})
with raises(
DuplicateKeyError,
match=
'dup key: { identifier.system: null, identifier.value: "just_value", \
identifier.type.coding.system: null, identifier.type.coding.code: null }',
):
store.create({
"identifier": [{
"value": "just_value"
}],
"resourceType": "Patient",
"id": "pat2",
})
with raises(
DuplicateKeyError,
match=
'dup key: { identifier.system: "system", identifier.value: "value", \
identifier.type.coding.system: "type_system", identifier.type.coding.code: "type_code" }',
):
store.create({
"identifier": [
{
"value": "new_val"
},
{
"value": "value",
"system": "system",
"type": {
"coding": [{
"system": "type_system",
"code": "type_code"
}]
},
},
],
"resourceType":
"Patient",
"id":
"pat2",
})
def test_search_bad_resource_type(store: FHIRStore):
"""search() raises error if resource type is unknown"""
with raises(NotFoundError, match='unsupported FHIR resource: "unknown"'):
store.comprehensive_search(resource_type="unknown", args={})
t = tqdm(total=total_size,
unit='B',
unit_scale=True,
desc="Downloading example resources")
with open('benchmark/examples.zip', 'wb') as f:
for data in r.iter_content(block_size):
t.update(len(data))
f.write(data)
t.close()
else:
print("Using cached resources")
download_resources()
client = MongoClient()
store = FHIRStore(client, "benchmark")
store.resume()
# store.reset()
# store.bootstrap(depth=3)
examples = tqdm(iter_examples(),
total=count_examples(),
desc="Running write benchmark")
stats = {}
inserted = []
for example, data in examples:
if not data.get('id'):
data["id"] = str(uuid4())
start = timer()
res = store.create(data)
end = timer()
def test_count_medicationrequest(store: FHIRStore):
result = store.comprehensive_search(
"MedicationRequest", ImmutableMultiDict([("_summary", "count")])
)
assert result.content["total"] == 2
def test_count_some(store: FHIRStore):
result = store.comprehensive_search(
"Patient", ImmutableMultiDict([("_summary", "count"), ("identifier.value", "ne12345")]),
)
assert result.content["total"] == 1
assert result.content["tag"]["code"] == "SUBSETTED"
def test_count_all(store: FHIRStore):
result = store.comprehensive_search("Patient", ImmutableMultiDict([("_summary", "count")]))
assert result.content["total"] == 3
assert result.content["tag"]["code"] == "SUBSETTED"
def test_create_bad_resource_schema(self, store: FHIRStore):
"""create() raises if json schema validation failed in mongo"""
with raises(ValidationError):
store.create({"resourceType": "Patient", "id": 42})