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_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_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_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
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()
stats[example] = end - start
inserted.append(res)
values = stats.values()
print(f"insertions per second (on average): {1/statistics.mean(values):.2f}")
print(f"average: {statistics.mean(values)*1000:.2f} milliseconds")
print(f"median: {statistics.median(values)*1000:.2f} milliseconds")
print(f"min: {min(values)*1000:.2f} milliseconds")
print(f"max: {max(values)*1000:.2f} milliseconds")
print(f"spread: {statistics.variance(values)}")
examples = tqdm(inserted, desc="Running read benchmark")
stats = {}
for doc in examples:
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_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})
def test_create_bad_resource_type(self, store: FHIRStore):
"""create() raises if resource type is unknown"""
with raises(NotFoundError,
match='unsupported FHIR resource: "unknown"'):
store.create({"resourceType": "unknown"})
def test_create_missing_resource_type(self, store: FHIRStore):
"""create() raises if resource type is not specified"""
with raises(BadRequestError,
match="resourceType is missing in resource"):
store.create({})
def test_delete_instance(self, store: FHIRStore, test_patient):
"""delete() finds a document in the database"""
store.create(test_patient)
result = store.delete("Patient", test_patient["id"])
assert result == 1
def test_read_resource(self, store: FHIRStore, test_patient):
"""read() finds a document in the database"""
store.create(test_patient)
result = store.read("Patient", test_patient["id"])
assert result == test_patient
start = timer()
store.bootstrap(depth=3)
end = timer()
print(end - start, "seconds")
# creating document
print("Inserting documents...")
json_folder_path = os.path.join(os.getcwd(), "test/fixtures")
json_files = [
x for x in os.listdir(json_folder_path) if x.endswith(".json")
]
total = 0
for json_file in json_files:
json_file_path = os.path.join(json_folder_path, json_file)
with open(json_file_path, "r") as f:
data = json.load(f)
start = timer()
print("Creating", json_file_path, "...")
try:
store.create(data)
except Exception as e:
print(e)
end = timer()
print(end - start, "seconds")
total += (end - start)
print(f"Inserted {len(json_files)} documents in {total} seconds")
# srch = store.search(resource='patient',params="male")
# print(srch)
client.close()