def handle_item(item, env, context):
root = {"linkId": item["linkId"]}
if "text" in item:
root["text"] = item["text"]
if "itemContext" in item:
data = fhirpath(context, item["itemContext"]["expression"], env)
context = data
if (context and "initialExpression" in item and "repeats" in item
and item["repeats"] is True):
answers = []
root["answer"] = answers
for index, _item in enumerate(context):
type = get_type(item)
data = fhirpath(
context,
"%context[{}].{}".format(
index, item["initialExpression"]["expression"]),
env,
)
answers.append({"value": {item["type"]: data[0]}})
elif "initialExpression" in item:
data = fhirpath(context, item["initialExpression"]["expression"], env)
if data and len(data):
type = get_type(item)
if item.get("repeats") is True:
root["answer"] = [{"value": {type: d}} for d in data]
else:
root["answer"] = [{"value": {type: data[0]}}]
elif "initial" in item:
root["answer"] = item["initial"]
if (item["type"] == "group" and "repeats" in item
and item["repeats"] is True and is_list(context)):
answer = []
for c in context:
q = []
for i in item["item"]:
q.append(handle_item(i, env, c))
answer.append({"item": q})
root["answer"] = answer
elif "item" in item:
root["item"] = []
for i in item["item"]:
root["item"].append(handle_item(i, env, context))
return root
def pp(i):
if not isinstance(i, str):
return i
exprs = re_all(r"(?P<var>{{[\S\s]+}})", i)
vs = {}
for exp in exprs:
data = fhirpath({}, exp["var"][2:-2], env)
if len(data) > 0:
vs[exp["var"]] = data[0]
res = i
for k, v in vs.items():
res = res.replace(k, v)
return res
def constraint_check_for_item(errors, questionnaire_item, env):
for constraint in questionnaire_item.get("constraint", []):
expression = constraint["expression"]["expression"]
result = fhirpath({}, expression, env)
import logging
logging.debug("expression %s", expression)
logging.debug("result %s", result)
logging.debug("env %s", env)
if result == [True]:
# TODO: calculate error location path
errors.append(constraint)
for item in questionnaire_item.get("item", []):
constraint_check_for_item(errors, item, env)
def resolve_string_template(i, env, encode_result=False):
if not isinstance(i, str):
return i
exprs = re_all(r"(?P<var>{{[\S\s]+?}})", i)
vs = {}
for exp in exprs:
data = fhirpath({}, exp["var"][2:-2], env)
if len(data) > 0:
# TODO: pass comma separated values for x-fhir-query
vs[exp["var"]] = quote(data[0]) if encode_result else data[0]
else:
vs[exp["var"]] = ""
res = i
for k, v in vs.items():
res = res.replace(k, v)
return res
def prepare_variables(item):
variables = {}
for var in item.get("variable", []):
variables[var["name"]] = fhirpath({}, var["expression"])
return variables
def handle_item(item, env, context):
def init_item():
new_item = {"linkId": item["linkId"]}
if "text" in item:
new_item["text"] = item["text"]
return new_item
if "itemContext" in item:
context = fhirpath(context, item["itemContext"]["expression"], env)
if "itemPopulationContext" in item:
context = fhirpath(context,
item["itemPopulationContext"]["expression"], env)
if (item["type"] == "group" and item.get("repeats", False) is True
and is_list(context)):
root_items = []
for c in context:
populated_items = []
for i in item["item"]:
populated_items.extend(handle_item(i, env, c))
root_item = init_item()
root_item["item"] = populated_items
root_items.append(root_item)
return root_items
root_item = init_item()
if context and "initialExpression" in item and item.get("repeats",
False) is True:
answers = []
for index, _item in enumerate(context):
data = fhirpath(
context,
"%context[{}].{}".format(
index, item["initialExpression"]["expression"]),
env,
)
if data and len(data):
type = get_type(item, data)
answers.extend([{"value": {type: d}} for d in data])
if answers:
root_item["answer"] = answers
elif "initialExpression" in item:
answers = []
data = fhirpath(context, item["initialExpression"]["expression"], env)
if data and len(data):
type = get_type(item, data)
if item.get("repeats") is True:
answers = [{"value": {type: d}} for d in data]
else:
answers = [{"value": {type: data[0]}}]
if answers:
root_item["answer"] = answers
elif "initial" in item:
root_item["answer"] = item["initial"]
if "item" in item:
populated_items = []
for i in item["item"]:
populated_items.extend(handle_item(i, env, context))
root_item["item"] = populated_items
return [root_item]
async def test_populate_nutritio_order(sdk, safe_db):
"""
TODO think how this kind of error may be handled
Shown typo (missing bracket) causes an empty bundle response
The system should check such cases an fire warnings
"""
q = sdk.client.resource(
"Questionnaire",
**{
"status": "active",
"launchContext": [{"name": "LaunchPatient", "type": "Patient"}],
"sourceQueries": [{"localRef": "Bundle#DietAndNutrition"}],
"contained": [
{
"id": "DietAndNutrition",
"type": "batch",
"entry": [
{
"request": { # -------second bracket is missing here \/
"url": "/NutritionOrder?patient={{%LaunchPatient.id}&status=active",
"method": "GET",
}
}
],
"resourceType": "Bundle",
}
],
"item": [
{
"text": "Diet and Nutrition",
"type": "choice",
"linkId": "diet",
"repeats": True,
"answerValueSet": "diet",
"initialExpression": {
"language": "text/fhirpath",
"expression": "%DietAndNutrition.entry[0].resource.entry.resource.oralDiet.type.coding.where(system = 'http://snomed.info/sct')",
},
}
],
},
)
await q.save()
assert q.id is not None
launch_patient = sdk.client.resource("Patient")
await launch_patient.save()
assert launch_patient.id is not None
n = sdk.client.resource(
"NutritionOrder",
**{
"intent": "plan",
"status": "active",
"patient": {
"id": launch_patient.id,
"resourceType": "Patient"
},
"dateTime": "2020-01-01T00:00",
"oralDiet": {
"type": [{
"coding": [{
"code": "437091000124100",
"system": "http://snomed.info/sct",
"display": "Calcium modified diet",
}]
}]
},
},
)
await n.save()
assert n.id is not None
p = await q.execute("$populate",
data=create_parameters(LaunchPatient=launch_patient))
populated_answer = fhirpath(
p,
"QuestionnaireResponse.item.where(linkId='diet').answer.value.Coding")
assert populated_answer == []