def test_json_with_resource(self, mock_jsonify, mock_get_store):
resource = Patient(id="test")
mock_get_store.return_value.normalize_resource.return_value = resource
r = BaseResource(resource=resource)
r.json()
mock_jsonify.assert_called_once_with(resource.dict())
def test_issue_28():
"""Running the following code:
from fhir.resources import construct_fhir_element
d = {'resourceType': 'Patient', 'contained':[{'resourceType': 'Patient'}]}
construct_fhir_element('Patient', d)
end up changing the value of d to {'resourceType': 'Patient', 'contained': [{}]}
I would expect it to not change the given object. Moreover, because it doesn't
delete resourceType from the outter dictionary, I assume this behavior is not expected.
Is it on purpose?
Thanks,
Itay"""
data = {
"resourceType": "Patient",
"contained": [{
"resourceType": "Patient"
}]
}
construct_fhir_element(
"Patient",
data,
)
# should not change data
assert data == {
"resourceType": "Patient",
"contained": [{
"resourceType": "Patient"
}],
}
data = {
"resourceType": "Patient",
"contained": [{
"resourceType": "Patient"
}]
}
Patient.parse_obj(data)
# should not change data
assert data == {
"resourceType": "Patient",
"contained": [{
"resourceType": "Patient"
}],
}
data = {
"resourceType": "Patient",
"contained": [{
"resourceType": "Patient"
}]
}
Patient(**data)
# should not change data
assert data == {
"resourceType": "Patient",
"contained": [{
"resourceType": "Patient"
}],
}
def test_init_with_resource(self, mock_get_store):
"""Initializes resource and resource_type"""
resource_data = {"gender": "female"}
mock_get_store.return_value.normalize_resource.return_value = Patient(
**resource_data)
r = BaseResource(resource=resource_data)
assert mock_get_store.call_count == 1
assert r.db == mock_get_store.return_value
assert r.id is None
assert r.resource == Patient(**resource_data)
assert r.resource_type == "BaseResource"
def test_patch(self, mock_get_store):
"""Applies a patch on the resource by reading and then updating it"""
resource = Patient(id="test")
mock_get_store.return_value.normalize_resource.return_value = resource
mock_get_store.return_value.patch.return_value = Patient(
id="test", gender="other")
patch_data = {"gender": "other"}
r = BaseResource(id="test", resource=resource)
r.patch(patch_data)
mock_get_store.return_value.patch.assert_called_once_with(
"BaseResource", "test", patch_data)
assert r.resource == Patient(id="test", gender="other")
def test_search_not_found(self, mock_get_store):
"""
Calls the search method and handles the case
where no result is found.
"""
resource = Patient(id="test")
error = OperationOutcome(id="notfound",
issue=[{
"severity": "error",
"code": "noop",
"diagnostics": "bobo"
}])
mock_get_store.return_value.normalize_resource.return_value = resource
mock_get_store.return_value.search.return_value = error
r = BaseResource(resource=resource)
res = r.search(query_string="name=NotFound")
assert res == error
mock_get_store.return_value.search.assert_called_once_with(
"BaseResource",
as_json=True,
params=None,
query_string="name=NotFound")
assert r.resource == resource
assert r.id == resource.id
def test_update_with_id(self, mock_get_store):
"""Test update with id.
Calls the update method of the fhirstore client
and registers the resource
"""
resource = Patient(id="test")
mock_get_store.return_value.normalize_resource.return_value = resource
mock_get_store.return_value.update.return_value = Patient(
id="test", gender="other")
update_data = {"gender": "other"}
r = BaseResource(id="test", resource=resource)
r.update(update_data)
mock_get_store.return_value.update.assert_called_once_with(
"test", update_data)
assert r.resource == Patient(id="test", gender="other")
def test_read_missing_id(self, mock_get_store):
"""Raises an error when the id was not provided at init"""
resource = Patient()
mock_get_store.return_value.normalize_resource.return_value = resource
r = BaseResource(resource=resource)
with pytest.raises(BadRequest, match="Resource ID is required"):
r.read()
assert mock_get_store.return_value.read.call_count == 0
def test_delete(self, mock_get_store):
"""Calls the delete method of the fhirstore client"""
resource = Patient(id="test")
mock_get_store.return_value.normalize_resource.return_value = resource
r = BaseResource(resource=resource)
r.delete()
mock_get_store.return_value.delete.assert_called_once_with(
"BaseResource", "test")
assert r.resource is None
assert r.id is None
def test_patch_missing_id(self, mock_get_store):
"""Raises an error when the resource id was not provided at init"""
resource = Patient(gender="test")
mock_get_store.return_value.normalize_resource.return_value = resource
r = BaseResource(resource=resource)
with pytest.raises(
BadRequest,
match="Resource ID is required to patch a resource",
):
r.patch({"some": "patch"})
assert mock_get_store.return_value.patch.call_count == 0
def test_patch_missing_data(self, mock_get_store):
"""Raises an error when the patch data is not provided"""
resource = Patient(id="test")
mock_get_store.return_value.normalize_resource.return_value = resource
r = BaseResource(id="test")
with pytest.raises(
BadRequest,
match="Patch data is required to patch a resource",
):
r.patch(None)
assert mock_get_store.return_value.patch.call_count == 0
def test_delete_missing_id(self, mock_get_store):
"""Raises an error when the patch data is not provided"""
resource = Patient()
mock_get_store.return_value.normalize_resource.return_value = resource
r = BaseResource(resource=resource)
with pytest.raises(
BadRequest,
match="Resource ID is required to delete it",
):
r = r.delete()
assert mock_get_store.return_value.update.call_count == 0
def test_create_extra_id(self, mock_get_store):
"""Accepts the resource data when an id was provided"""
resource = Patient(id="test")
mock_get_store.return_value.normalize_resource.return_value = resource
mock_get_store.return_value.create.return_value = resource
mock_get_store.return_value.read.return_value = None
r = BaseResource(resource=resource)
r.create()
assert r.id == "test"
assert r.resource == resource
async def test_create_resource(pg_connection):
""" """
db = pg_connection
resource_obj = Patient.parse_file(FHIR_EXAMPLE_RESOURCES / "Patient.json")
resource_obj.id = str(uuid.uuid4())
resource_obj.meta = {"versionId": "1", "lastUpdated": datetime.utcnow()}
res1 = await crud.create_resource(db, resource_obj, FHIR_VERSION.R4)
await tasks.add_resource_history(db, res1, first=True)
await tasks.add_resource_history(db, res1, first=False)
result = await db.fetch_all(
f"SELECT * FROM {ResourceHistoryModel.__tablename__} ORDER BY id ASC"
)
assert len(result) == 2
assert result[0]["next_id"] == result[1]["id"]
assert result[0]["id"] == result[1]["prev_id"]
def test_read(self, mock_get_store):
"""Test read method.
Calls the read method of the fhirstore client
and registers the resource.
"""
resource = Patient(id="test")
mock_get_store.return_value.normalize_resource.return_value = resource
mock_get_store.return_value.read.return_value = resource
r = BaseResource(id="test")
r.read()
mock_get_store.return_value.read.assert_called_once_with(
"BaseResource", "test")
assert r.resource == resource
def test_create(self, mock_uuid, mock_get_store):
"""Test create method.
Calls the create method of the fhirstore client
and registers the ID
"""
resource = Patient(gender="male")
mock_get_store.return_value.normalize_resource.return_value = resource
mock_get_store.return_value.create.return_value = resource
mock_get_store.return_value.read.return_value = None
r = BaseResource(resource=resource)
r.create()
mock_get_store.return_value.create.assert_called_once_with(resource)
assert r.id == "uuid"
assert r.resource == resource
def test_search_params(self, mock_get_store):
"""
Calls the search method of the fhirstore client using `params`
"""
resource = Patient(id="test")
mock_get_store.return_value.normalize_resource.return_value = resource
mock_get_store.return_value.search.return_value = resource
r = BaseResource(resource=resource)
params = MultiDict((("name", "Vincent"), ))
res = r.search(params=params)
assert res == resource
mock_get_store.return_value.search.assert_called_once_with(
"BaseResource", as_json=True, params=params, query_string=None)
assert r.resource == resource
assert r.id == resource.id
def test_search_qs(self, mock_get_store):
"""
Calls the search method of the fhirstore client using `query_string`
"""
resource = Patient(id="test")
mock_get_store.return_value.normalize_resource.return_value = resource
mock_get_store.return_value.search.return_value = resource
r = BaseResource(resource=resource)
res = r.search(query_string="name=Vincent")
assert res == resource
mock_get_store.return_value.search.assert_called_once_with(
"BaseResource",
as_json=True,
params=None,
query_string="name=Vincent")
assert r.resource == resource
assert r.id == resource.id
from fhirpy import SyncFHIRClient
from fhir.resources.patient import Patient
from fhir.resources.observation import Observation
from fhir.resources.humanname import HumanName
from fhir.resources.contactpoint import ContactPoint
import json
client = SyncFHIRClient(
url='https://dh9fytkn0e.execute-api.eu-west-2.amazonaws.com/dev',
extra_headers={
"x-api-key":
"EzAVxFOjEqagIbYVHK2Mz7RUp1GOpRHMVTTxVQk9",
"Authorization":
"eyJraWQiOiJ2ZXZ0cUNYZitiUzNBM3hNWm5IVFhRbDlucTFZaDloRzJZNkxVXC94bTd0ST0iLCJhbGciOiJSUzI1NiJ9.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.XxflQNEL_N8XWut2MxGNTZfnjei4qCsbvEBs31n1RMemY9DneEU1haYGGaHp4T3CyBy2-eLeaDbfI16dhEnh_5D6qSgRoMPWv5ScZop2uvoqujkufsp-C6lZsRtetyowETrcaSs46jvumqzpONUO5F5i7UdEg2lh9N0iKfUi67MepgMy9gBJMZkKQhTl6S0BRNHfyGhUT5kbN2EeFeDltiSOaDZKk7IbRoUO0OnZYNFcqmDNAjPYzLFKNnYyGcsMlPSKZaULHt3P7EhAS-e5EOG5c8-Sqp7fPOZ3cpq2QHr5RF4hZcyZiUwoyYoeW4_MDvhkdew2tdnyEsFQHwuO2g"
})
patients_resources = client.resources('Patient')
patient0 = Patient.parse_obj(
patients_resources.search(family='Jameson',
given='Matt').first().serialize())
print("Our paitent:", patient0.name)
# page_file = "temp/pg"+str(count)+".png"
# page.save(page_file, "PNG")
# count = count+1
# for page_num in range(count):
# page_file = "temp/pg"+str(page_num)+".png"
# score_assessment_form(page_file, page_num,
# wThresh=W_THRESH, hThresh=H_THRESH)
# print("Raw Score:", subtotal)
# creating FHIR resource for patient record
pat = Patient({
"id": "1",
"name": [{
"given": ["John"],
"family": "Doe"
}],
"birthDate": "2019-01-24"
})
print(pat)
enc = Encounter()
enc.subject = pat
docref_json = {
"resourceType": "DocumentReference",
}
doc = DocumentReference()
obs = Observation()
print("--finish--")