/
questionnaire_response.py
830 lines (694 loc) · 31.1 KB
/
questionnaire_response.py
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from collections import namedtuple
from datetime import datetime
from dateutil.relativedelta import relativedelta
from html.parser import HTMLParser
import json
from flask import current_app, has_request_context, url_for
from flask_swagger import swagger
import jsonschema
from sqlalchemy import or_
from sqlalchemy.dialects.postgresql import ENUM, JSONB
from ..database import db
from ..date_tools import FHIR_datetime
from ..system_uri import (
TRUENTH_EXTERNAL_STUDY_SYSTEM,
TRUENTH_STATUS_EXTENSION,
TRUENTH_VISIT_NAME_EXTENSION,
)
from .audit import Audit
from .encounter import Encounter
from .fhir import bundle_results
from .overall_status import OverallStatus
from .qbd import QBD
from .questionnaire import Questionnaire
from .questionnaire_bank import QuestionnaireBank, trigger_date, visit_name
from .reference import Reference
from .user import User, current_user, patients_query
from .user_consent import consent_withdrawal_dates
class NoFutureDates(ValueError):
"""Raised on data validation failures where future dates are verboten"""
pass
class QuestionnaireResponse(db.Model):
def default_status(context):
return context.current_parameters['document']['status']
def default_authored(context):
# Includes a call to validate_authored - exception raised if not valid
authored = FHIR_datetime.parse(
context.current_parameters['document']['authored'])
QuestionnaireResponse.validate_authored(authored)
return authored
__tablename__ = 'questionnaire_responses'
id = db.Column(db.Integer, primary_key=True)
subject_id = db.Column(db.ForeignKey('users.id'), nullable=False)
subject = db.relationship("User", back_populates="questionnaire_responses")
document = db.Column(JSONB)
encounter_id = db.Column(
db.ForeignKey('encounters.id', name='qr_encounter_id_fk'),
nullable=False)
questionnaire_bank_id = db.Column(
db.ForeignKey('questionnaire_banks.id'), nullable=True)
qb_iteration = db.Column(db.Integer(), nullable=True)
encounter = db.relationship("Encounter", cascade='delete')
questionnaire_bank = db.relationship("QuestionnaireBank")
# Fields derived from document content
status = db.Column(
ENUM(
'in-progress',
'completed',
name='questionnaire_response_statuses'
),
default=default_status
)
authored = db.Column(
db.DateTime,
default=default_authored
)
def __str__(self):
"""Print friendly format for logging, etc."""
return "QuestionnaireResponse {0.id} for user {0.subject_id} " \
"{0.status} {0.authored}".format(self)
def assign_qb_relationship(self, acting_user_id, qbd_accessor=None):
"""Lookup and assign questionnaire bank and iteration
On submission, and subsequently when a user's state changes (such as
the criteria for trigger_date), determine the associated questionnaire
bank and iteration and assign, or clear if no match is found.
:param acting_user_id: current driver of process, for audit purposes
:param qbd_accessor: function to look up appropriate QBD for given QNR
Takes ``as_of_date`` and ``classification`` parameters
"""
authored = FHIR_datetime.parse(self.document['authored'])
if qbd_accessor is None:
from .qb_status import QB_Status # avoid cycle
qbstatus = QB_Status(self.subject, as_of_date=authored)
def qbstats_current_qbd(as_of_date, classification):
if as_of_date != authored:
raise RuntimeError(
"local QB_Status instantiated w/ wrong as_of_date")
return qbstatus.current_qbd(classification)
qbd_accessor = qbstats_current_qbd
initial_qb_id = self.questionnaire_bank_id
initial_qb_iteration = self.qb_iteration
# clear both until current values are determined
self.questionnaire_bank_id, self.qb_iteration = None, None
qn_ref = self.document.get("questionnaire").get("reference")
qn_name = qn_ref.split("/")[-1] if qn_ref else None
qn = Questionnaire.find_by_name(name=qn_name)
qbd = qbd_accessor(as_of_date=authored, classification=None)
if qbd and qn and qn.id in (
q.questionnaire.id for q in
qbd.questionnaire_bank.questionnaires):
self.questionnaire_bank_id = qbd.qb_id
self.qb_iteration = qbd.iteration
# if a valid qb wasn't found, try the indefinite option
else:
qbd = qbd_accessor(
as_of_date=authored, classification='indefinite')
if qbd and qn and qn.id in (
q.questionnaire.id for q in
qbd.questionnaire_bank.questionnaires):
self.questionnaire_bank_id = qbd.qb_id
self.qb_iteration = qbd.iteration
if not self.questionnaire_bank_id:
current_app.logger.warning(
"Can't locate QB for patient {}'s questionnaire_response "
"with reference to given instrument {}".format(
self.subject_id, qn_name))
self.questionnaire_bank_id = 0 # none of the above
self.qb_iteration = None
if self.questionnaire_bank_id != initial_qb_id or (
self.qb_iteration != initial_qb_iteration):
msg = (
"Updating to qb_id ({}) and qb_iteration ({}) on"
" questionnaire_response {}".format(
self.questionnaire_bank_id, self.qb_iteration,
self.id))
audit = Audit(
subject_id=self.subject_id, user_id=acting_user_id,
context='assessment', comment=msg)
db.session.add(audit)
@staticmethod
def purge_qb_relationship(subject_id, acting_user_id):
"""Remove qb association from subject user's QuestionnaireResponses
An event such as changing consent date potentially alters the
"visit_name" (i.e. 3 month, baseline, etc.) any existing QNRs
may have been assigned. This method removes all such QNR->QB
associations that may now apply to the wrong QB, forcing subsequent
recalculation
"""
audits = []
matching = QuestionnaireResponse.query.filter(
QuestionnaireResponse.subject_id == subject_id).filter(
QuestionnaireResponse.questionnaire_bank_id.isnot(None))
for qnr in matching:
audit = Audit(
user_id=acting_user_id, subject_id=subject_id,
context='assessment',
comment="Removing qb_id:iteration {}:{} from QNR {}".format(
qnr.questionnaire_bank_id, qnr.qb_iteration, qnr.id))
audits.append(audit)
qnr.questionnaire_bank_id = None
qnr.qb_iteration = None
for audit in audits:
db.session.add(audit)
db.session.commit()
@staticmethod
def by_identifier(identifier):
"""Query for QuestionnaireResponse(s) with given identifier"""
if not any((identifier.system, identifier.value)):
raise ValueError("Can't look up null identifier")
if identifier.system is None: # FHIR allows null system
found = QuestionnaireResponse.query.filter(
QuestionnaireResponse.document['identifier']['system'].is_(
None)).filter(
QuestionnaireResponse.document['identifier']['value']
== json.dumps(identifier.value))
else:
found = QuestionnaireResponse.query.filter(
QuestionnaireResponse.document['identifier']['system']
== json.dumps(identifier.system)).filter(
QuestionnaireResponse.document['identifier']['value']
== json.dumps(identifier.value))
return found.order_by(QuestionnaireResponse.id.desc()).all()
@staticmethod
def validate_authored(authored):
"""Validate the authored value is current or in the past
Don't allow future authored dates (but allow for up to 60 second
drift from external services)
"""
if authored > datetime.utcnow() + relativedelta(seconds=60):
raise NoFutureDates("future authored dates forbidden")
@staticmethod
def validate_document(document):
"""Validate given JSON document against our swagger schema"""
swag = swagger(current_app)
draft4_schema = {
'$schema': 'http://json-schema.org/draft-04/schema#',
'type': 'object',
'definitions': swag['definitions'],
}
validation_schema = 'QuestionnaireResponse'
# Copy desired schema (to validate against) to outermost dict
draft4_schema.update(swag['definitions'][validation_schema])
jsonschema.validate(document, draft4_schema)
@property
def document_answered(self):
"""
Return a QuestionnaireResponse populated with text answers based on codes in valueCoding
"""
instrument_id = self.document['questionnaire']['reference'].split('/')[-1]
questionnaire = Questionnaire.find_by_name(name=instrument_id)
# return original document if no reference Questionnaire available
if not questionnaire:
return self.document
questionnaire_map = questionnaire.questionnaire_code_map()
document = self.document
for question in document.get('group', {}).get('question', ()):
combined_answers = consolidate_answer_pairs(question['answer'])
# Separate out text and coded answer, then override text
text_and_coded_answers = []
for answer in combined_answers:
# Add text answer before coded answer
if list(answer.keys())[0] == 'valueCoding':
# Prefer text looked up from code over sibling valueString answer
text_answer = questionnaire_map.get(
answer['valueCoding']['code'],
answer['valueCoding'].get('text')
)
text_and_coded_answers.append({'valueString': text_answer})
text_and_coded_answers.append(answer)
question['answer'] = text_and_coded_answers
return document
def extensions(self):
"""Return list of FHIR extensions
No place within the FHIR spec to associate 'visit name' nor a
'status' as per business rules (i.e. 'in-progress' becomes
'partially completed' once the associated QB expires). Use FHIR
`extension`s to pass these fields to clients like the front end
@returns list of FHIR extensions for this instance, typically one for `visit_name`
"""
from .qb_timeline import expires # avoid cycle
results = []
if self.questionnaire_bank_id is not None:
qb = QuestionnaireBank.query.get(self.questionnaire_bank_id)
recur_id = None
for r in qb.recurs:
recur_id = r.id
qbd = QBD(
relative_start=None, iteration=self.qb_iteration,
recur_id=recur_id, qb_id=self.questionnaire_bank_id)
results.append({
'visit_name': visit_name(qbd),
'url': TRUENTH_VISIT_NAME_EXTENSION})
expires_at = expires(self.subject_id, qbd)
if (expires_at and expires_at < datetime.utcnow() and
self.status == 'in-progress'):
results.append({
'status': OverallStatus.partially_completed.name,
'url': TRUENTH_STATUS_EXTENSION
})
return results
QNR = namedtuple('QNR', [
'qnr_id', 'qb_id', 'iteration', 'status', 'instrument', 'authored',
'encounter_id'])
class QNR_results(object):
"""API for QuestionnaireResponses for a user"""
def __init__(self, user, qb_id=None, qb_iteration=None):
"""Optionally include qb_id and qb_iteration to limit"""
self.user = user
self.qb_id = qb_id
self.qb_iteration = qb_iteration
self._qnrs = None
@property
def qnrs(self):
"""Return cached qnrs or query first time"""
if self._qnrs is not None:
return self._qnrs
query = QuestionnaireResponse.query.filter(
QuestionnaireResponse.subject_id == self.user.id).with_entities(
QuestionnaireResponse.id,
QuestionnaireResponse.questionnaire_bank_id,
QuestionnaireResponse.qb_iteration,
QuestionnaireResponse.status,
QuestionnaireResponse.document[
('questionnaire', 'reference')].label('instrument_id'),
QuestionnaireResponse.authored,
QuestionnaireResponse.encounter_id).order_by(
QuestionnaireResponse.authored)
if self.qb_id:
query = query.filter(
QuestionnaireResponse.questionnaire_bank_id == self.qb_id
).filter(
QuestionnaireResponse.qb_iteration == self.qb_iteration)
self._qnrs = []
requery = False
for qnr in query:
if qnr.instrument_id is None:
current_app.logger.warning(
"QNR {} query returned no instrument".format(qnr.id))
instrument = None
requery = True
else:
instrument = qnr.instrument_id.split('/')[-1]
self._qnrs.append(QNR(
qnr_id=qnr.id,
qb_id=qnr.questionnaire_bank_id,
iteration=qnr.qb_iteration,
status=qnr.status,
instrument=instrument,
authored=qnr.authored,
encounter_id=qnr.encounter_id))
if requery:
# Ugly workaround till we figure out why this is happening
# see TN-2417
for i, qnr in enumerate(self._qnrs):
if qnr.instrument is None:
doc = QuestionnaireResponse.query.filter(
QuestionnaireResponse.id == qnr.qnr_id).with_entities(
QuestionnaireResponse.document).first()
if doc is None:
current_app.logger.warning(
"doc still None on second try for "
"qnr {}".format(qnr.qnr_id))
else:
self._qnrs[i] = qnr._replace(
instrument=
doc[0]['questionnaire']['reference'].split(
'/')[-1])
return self._qnrs
def assign_qb_relationships(self, qb_generator):
"""Associate any QNRs with respective qbs
Typically, done at time of QNR POST - however occasionally events
force a renewed lookup of QNR -> QB association.
"""
from .qb_timeline import calc_and_adjust_expired, calc_and_adjust_start
if self.qb_id:
raise ValueError(
"Can't associate results when restricted to single QB")
qbs = [qb for qb in qb_generator(self.user)]
indef_qbs = [qb for qb in qb_generator(
self.user, classification="indefinite")]
td = trigger_date(user=self.user)
old_td, withdrawal_date = consent_withdrawal_dates(self.user)
if not td and old_td:
td = old_td
def qbd_accessor(as_of_date, classification):
"""Simplified qbd lookup consults only assigned qbs"""
if classification == 'indefinite':
container = indef_qbs
else:
container = qbs
# Loop until date matching qb found, break if beyond
for qbd in container:
qb_start = calc_and_adjust_start(
user=self.user, qbd=qbd, initial_trigger=td)
qb_expired = calc_and_adjust_expired(
user=self.user, qbd=qbd, initial_trigger=td)
if as_of_date < qb_start:
continue
if qb_start <= as_of_date < qb_expired:
return qbd
if qb_expired > as_of_date:
break
# typically triggered from updating task job - use system
# as acting user in audits, if no current user is available
acting_user = None
if has_request_context():
acting_user = current_user()
if not acting_user:
acting_user = User.query.filter_by(email='__system__').first()
for qnr in self.qnrs:
QuestionnaireResponse.query.get(
qnr.qnr_id).assign_qb_relationship(
acting_user_id=acting_user.id, qbd_accessor=qbd_accessor)
db.session.commit()
# Force fresh lookup on next access
self._qnrs = None
def qnrs_missing_qb_association(self):
"""Returns true if any QNRs exist without qb associations
Business rules mandate purging qnr->qb association following
events such as a change of consent date. This method can be
used to determine if qnr->qb association lookup may be required.
NB - it can be legitimate for QNRs to never have a QB association,
such as systems that don't define QBs for all assessments or those
taken prior to a new trigger date.
:returns: True if at least one QNR exists for the user missing qb_id
"""
associated = [qnr for qnr in self.qnrs if qnr.qb_id is not None]
return len(self.qnrs) != len(associated)
def earliest_result(self, qb_id, iteration):
"""Returns timestamp of earliest result for given params, or None"""
for qnr in self.qnrs:
if (qnr.qb_id == qb_id and
qnr.iteration == iteration):
return qnr.authored
def entry_method(self):
"""Returns first entry method found in results, or None"""
for qnr in self.qnrs:
if qnr.encounter_id is not None:
encounter = Encounter.query.get(qnr.encounter_id)
if encounter.type and len(encounter.type):
return encounter.type[0].code
def required_qs(self, qb_id):
"""Return required list (order counts) of Questionnaires for QB"""
from .questionnaire_bank import QuestionnaireBank # avoid import cyc.
qb = QuestionnaireBank.query.get(qb_id)
return [q.name for q in qb.questionnaires]
def completed_qs(self, qb_id, iteration):
"""Return set of completed Questionnaire results for given QB"""
return {qnr.instrument for qnr in self.qnrs if
qnr.qb_id == qb_id
and qnr.iteration == iteration
and qnr.status == "completed"}
def partial_qs(self, qb_id, iteration):
"""Return set of partial Questionnaire results for given QB"""
return {qnr.instrument for qnr in self.qnrs if
qnr.qb_id == qb_id
and qnr.iteration == iteration
and qnr.status == "in-progress"}
def completed_date(self, qb_id, iteration):
"""Returns timestamp when named QB was completed, or None"""
required = set(self.required_qs(qb_id))
have = self.completed_qs(qb_id=qb_id, iteration=iteration)
if required - have:
# incomplete set
return None
# Return time when last completed in required came in
germane = [qnr for qnr in self.qnrs if
qnr.qb_id == qb_id
and qnr.iteration == iteration
and qnr.status == "completed"]
for item in germane:
if item.instrument in required:
required.remove(item.instrument)
if not required:
return item.authored
raise RuntimeError("should have found authored for all required")
class QNR_indef_results(QNR_results):
"""Specialized for indefinite QB"""
def __init__(self, user, qb_id):
self.user = user
query = QuestionnaireResponse.query.filter(
QuestionnaireResponse.subject_id == user.id).filter(
QuestionnaireResponse.questionnaire_bank_id == qb_id
).with_entities(
QuestionnaireResponse.questionnaire_bank_id,
QuestionnaireResponse.qb_iteration,
QuestionnaireResponse.status,
QuestionnaireResponse.document[
('questionnaire', 'reference')].label('instrument_id'),
QuestionnaireResponse.authored,
QuestionnaireResponse.encounter_id).order_by(
QuestionnaireResponse.authored)
self.qnrs = []
for qnr in query:
self.qnrs.append(QNR(
qb_id=qnr.questionnaire_bank_id,
iteration=qnr.qb_iteration,
status=qnr.status,
instrument=qnr.instrument_id.split('/')[-1],
authored=qnr.authored,
encounter_id=qnr.encounter_id))
def aggregate_responses(
instrument_ids, current_user, patch_dstu2=False, celery_task=None):
"""Build a bundle of QuestionnaireResponses
:param instrument_ids: list of instrument_ids to restrict results to
:param current_user: user making request, necessary to restrict results
to list of patients the current_user has permission to see
:param patch_dstu2: set to make bundle DSTU2 compliant
:param celery_task: if defined, send occasional progress updates
"""
from .qb_timeline import qb_status_visit_name # avoid cycle
# Gather up the patient IDs for whom current user has 'view' permission
user_ids = patients_query(
current_user, include_test_role=False).with_entities(User.id)
annotated_questionnaire_responses = []
questionnaire_responses = QuestionnaireResponse.query.filter(
QuestionnaireResponse.subject_id.in_(user_ids)).order_by(
QuestionnaireResponse.authored.desc())
if instrument_ids:
instrument_filters = (
QuestionnaireResponse.document[
("questionnaire", "reference")
].astext.endswith(instrument_id)
for instrument_id in instrument_ids
)
questionnaire_responses = questionnaire_responses.filter(
or_(*instrument_filters))
patient_fields = ("careProvider", "identifier")
system_filter = current_app.config.get('REPORTING_IDENTIFIER_SYSTEMS')
if celery_task:
current, total = 0, questionnaire_responses.count()
for questionnaire_response in questionnaire_responses:
document = questionnaire_response.document_answered.copy()
subject = questionnaire_response.subject
encounter = questionnaire_response.encounter
encounter_fhir = encounter.as_fhir()
document["encounter"] = encounter_fhir
document["subject"] = {
k: v for k, v in subject.as_fhir().items() if k in patient_fields
}
if subject.organizations:
providers = []
for org in subject.organizations:
org_ref = Reference.organization(org.id).as_fhir()
identifiers = [i.as_fhir() for i in org.identifiers if
i.system in system_filter]
if identifiers:
org_ref['identifier'] = identifiers
providers.append(org_ref)
document["subject"]["careProvider"] = providers
_, timepoint = qb_status_visit_name(
subject.id, questionnaire_response.authored)
document["timepoint"] = timepoint
# Hack: add missing "resource" wrapper for DTSU2 compliance
# Remove when all interventions compliant
if patch_dstu2:
document = {
'resource': document,
# Todo: return URL to individual QuestionnaireResponse resource
'fullUrl': url_for(
'.assessment',
patient_id=subject.id,
_external=True,
),
}
annotated_questionnaire_responses.append(document)
if celery_task:
current += 1
if current % 25 == 0:
celery_task.update_state(
state='PROGRESS',
meta={'current': current, 'total': total})
return bundle_results(elements=annotated_questionnaire_responses)
def qnr_document_id(
subject_id, questionnaire_bank_id, questionnaire_name, iteration,
status):
"""Return document['identifier'] for matching QuestionnaireResponse
Using the given filter data to look for a matching QuestionnaireResponse.
Expecting to find exactly one, or raises NoResultFound
:return: the document identifier value, typically a string
"""
qnr = QuestionnaireResponse.query.filter(
QuestionnaireResponse.status == status).filter(
QuestionnaireResponse.subject_id == subject_id).filter(
QuestionnaireResponse.document[
('questionnaire', 'reference')
].astext.endswith(questionnaire_name)).filter(
QuestionnaireResponse.questionnaire_bank_id ==
questionnaire_bank_id).with_entities(
QuestionnaireResponse.document[(
'identifier', 'value')])
if iteration is not None:
qnr = qnr.filter(QuestionnaireResponse.qb_iteration == iteration)
else:
qnr = qnr.filter(QuestionnaireResponse.qb_iteration.is_(None))
return qnr.one()[0]
def consolidate_answer_pairs(answers):
"""
Merge paired answers (code and corresponding text) into single
row/answer
Codes are the preferred way of referring to options but option text
(at the time of administration) may be submitted alongside coded
answers for ease of display
"""
answer_types = [list(a.keys())[0] for a in answers]
# Exit early if assumptions not met
if (
len(answers) % 2 or
answer_types.count('valueCoding') != answer_types.count('valueString')
):
return answers
filtered_answers = []
for pair in zip(*[iter(answers)] * 2):
# Sort so first pair is always valueCoding
pair = sorted(pair, key=lambda k: list(k.keys())[0])
coded_answer, string_answer = pair
coded_answer['valueCoding']['text'] = string_answer['valueString']
filtered_answers.append(coded_answer)
return filtered_answers
qnr_csv_column_headers = (
'identifier',
'status',
'study_id',
'site_id',
'site_name',
'truenth_subject_id',
'author_id',
'author_role',
'entry_method',
'authored',
'timepoint',
'instrument',
'question_code',
'answer_code',
'option_text',
'other_text',
)
def generate_qnr_csv(qnr_bundle):
"""Generate a CSV from a bundle of QuestionnaireResponses"""
class HTMLStripper(HTMLParser):
"""Subclass of HTMLParser for stripping HTML tags"""
def __init__(self):
self.reset()
self.strict = False
self.convert_charrefs = True
self.fed = []
def handle_data(self, data):
self.fed.append(data)
def get_data(self):
return ' '.join(self.fed)
def strip_tags(html):
"""Strip HTML tags from strings. Inserts whitespace if necessary."""
if html is None:
return
s = HTMLStripper()
s.feed(html)
stripped = s.get_data()
# Remove extra spaces
return ' '.join(filter(None, stripped.split(' ')))
def get_identifier(id_list, **kwargs):
"""Return first identifier object matching kwargs"""
for identifier in id_list:
for k, v in kwargs.items():
if identifier.get(k) != v:
break
else:
return identifier['value']
return None
def get_site(qnr_data):
"""Return (external id, name) of first organization, else Nones"""
try:
provider = qnr_data['subject']['careProvider'][0]
org_name = provider['display']
if 'identifier' in provider:
id_value = provider['identifier'][0]['value']
else:
id_value = None
return id_value, org_name
except (KeyError, IndexError):
return None, None
def entry_method(row_data, qnr_data):
# Todo: replace with EC.PAPER CodeableConcept
if (
'type' in qnr_data['encounter'] and
'paper' in (c.get('code') for c in
qnr_data['encounter']['type'])
):
return 'enter manually - paper'
if row_data.get('truenth_subject_id') == row_data.get('author_id'):
return 'online'
else:
return 'enter manually - interview assisted'
def author_role(row_data, qnr_data):
if row_data.get('truenth_subject_id') == row_data.get('author_id'):
return 'Subject'
else:
return 'Site Resource'
for qnr in qnr_bundle['entry']:
site_id, site_name = get_site(qnr)
row_data = {
'identifier': (
qnr['identifier']['value'] if 'identifier' in qnr else None),
'status': qnr['status'],
'truenth_subject_id': get_identifier(
qnr['subject']['identifier'],
use='official'
),
'author_id': (
qnr['author']['reference'].split('/')[-1]
if 'author' in qnr else None),
'site_id': site_id,
'site_name': site_name,
# Todo: correctly pick external study of interest
'study_id': get_identifier(
qnr['subject']['identifier'],
system=TRUENTH_EXTERNAL_STUDY_SYSTEM
),
'authored': qnr['authored'],
'timepoint': qnr['timepoint'],
'instrument': qnr['questionnaire']['reference'].split('/')[-1],
}
row_data.update({
'entry_method': entry_method(row_data, qnr),
'author_role': author_role(row_data, qnr),
})
for question in qnr['group']['question']:
row_data['question_code'] = question['linkId']
for answer in consolidate_answer_pairs(
question['answer']) or ({},):
# Clear keys potentially added on previous loop
row_data.pop('answer_code', None)
row_data.pop('option_text', None)
row_data.pop('other_text', None)
if answer:
# Use first value of answer (most are single-entry dicts)
if list(answer.keys())[0] != 'valueCoding':
row_data['other_text'] = list(answer.values())[0]
# ...unless nested code (ie valueCode)
else:
row_data['answer_code'] = answer['valueCoding']['code']
# Add supplementary text added earlier
# Todo: lookup option text in stored Questionnaire
row_data['option_text'] = strip_tags(
answer['valueCoding'].get('text', None))
yield {k: v for k, v in row_data.items() if v is not None}