def map_answers(reader):
"""Emit (participantId, date|<metric>.<answer>) for each answer.
Metric names are taken from the field name in code_constants.
Code and string answers are accepted.
Incoming rows are expected to be sorted by participant ID, start time, and question code,
such that repeated answers for the same question are next to each other.
"""
last_participant_id = None
last_start_time = None
race_code_values = []
code_dao = CodeDao()
for participant_id, start_time, question_code, answer_code, answer_string in reader:
# Multiple race answer values for the participant at a single time
# are combined into a single race enum.
if race_code_values and (last_participant_id != participant_id or
last_start_time != start_time or
question_code != RACE_QUESTION_CODE):
race_codes = [code_dao.get_code(PPI_SYSTEM, value) for value in race_code_values]
race = get_race(race_codes)
yield(last_participant_id, make_tuple(last_start_time,
make_metric(RACE_METRIC, str(race))))
race_code_values = []
last_participant_id = participant_id
last_start_time = start_time
if question_code == RACE_QUESTION_CODE:
race_code_values.append(answer_code)
continue
if question_code == EHR_CONSENT_QUESTION_CODE:
metric = EHR_CONSENT_ANSWER_METRIC
answer_value = answer_code
else:
question_field = QUESTION_CODE_TO_FIELD[question_code]
metric = transform_participant_summary_field(question_field[0])
if question_field[1] == FieldType.CODE:
answer_value = answer_code
if metric == 'state':
state_val = answer_code[len(answer_code) - 2:]
census_region = census_regions.get(state_val) or UNSET
yield(participant_id, make_tuple(start_time, make_metric(CENSUS_REGION_METRIC,
census_region)))
elif question_field[1] == FieldType.STRING:
answer_value = answer_string
else:
raise AssertionError("Invalid field type: %s" % question_field[1])
yield(participant_id, make_tuple(start_time, make_metric(metric, answer_value)))
# Emit race for the last participant if we saved some values for it.
if race_code_values:
race_codes = [code_dao.get_code(PPI_SYSTEM, value) for value in race_code_values]
race = get_race(race_codes)
yield(last_participant_id, make_tuple(last_start_time,
make_metric(RACE_METRIC, str(race))))
def _update_participant_summary(self, session, questionnaire_response,
code_ids, questions, questionnaire_history,
resource_json):
"""Updates the participant summary based on questions answered and modules completed
in the questionnaire response.
If no participant summary exists already, only a response to the study enrollment consent
questionnaire can be submitted, and it must include first and last name and e-mail address.
"""
# Block on other threads modifying the participant or participant summary.
participant = ParticipantDao().get_for_update(
session, questionnaire_response.participantId)
if participant is None:
raise BadRequest('Participant with ID %d is not found.' %
questionnaire_response.participantId)
participant_summary = participant.participantSummary
code_ids.extend(
[concept.codeId for concept in questionnaire_history.concepts])
code_dao = CodeDao()
something_changed = False
# If no participant summary exists, make sure this is the study enrollment consent.
if not participant_summary:
consent_code = code_dao.get_code(
PPI_SYSTEM, CONSENT_FOR_STUDY_ENROLLMENT_MODULE)
if not consent_code:
raise BadRequest(
'No study enrollment consent code found; import codebook.')
if not consent_code.codeId in code_ids:
raise BadRequest(
"Can't submit order for participant %s without consent" %
questionnaire_response.participantId)
raise_if_withdrawn(participant)
participant_summary = ParticipantDao.create_summary_for_participant(
participant)
something_changed = True
else:
raise_if_withdrawn(participant_summary)
# Fetch the codes for all questions and concepts
codes = code_dao.get_with_ids(code_ids)
code_map = {
code.codeId: code
for code in codes if code.system == PPI_SYSTEM
}
question_map = {
question.questionnaireQuestionId: question
for question in questions
}
race_code_ids = []
ehr_consent = False
dvehr_consent = QuestionnaireStatus.SUBMITTED_NO_CONSENT
# Set summary fields for answers that have questions with codes found in QUESTION_CODE_TO_FIELD
for answer in questionnaire_response.answers:
question = question_map.get(answer.questionId)
if question:
code = code_map.get(question.codeId)
if code:
summary_field = QUESTION_CODE_TO_FIELD.get(code.value)
if summary_field:
if something_changed:
self._update_field(participant_summary,
summary_field[0],
summary_field[1], answer)
else:
something_changed = self._update_field(
participant_summary, summary_field[0],
summary_field[1], answer)
elif code.value == RACE_QUESTION_CODE:
race_code_ids.append(answer.valueCodeId)
elif code.value == DVEHR_SHARING_QUESTION_CODE:
code = code_dao.get(answer.valueCodeId)
if code and code.value == DVEHRSHARING_CONSENT_CODE_YES:
dvehr_consent = QuestionnaireStatus.SUBMITTED
elif code and code.value == DVEHRSHARING_CONSENT_CODE_NOT_SURE:
dvehr_consent = QuestionnaireStatus.SUBMITTED_NOT_SURE
elif code.value == EHR_CONSENT_QUESTION_CODE:
code = code_dao.get(answer.valueCodeId)
if code and code.value == CONSENT_PERMISSION_YES_CODE:
ehr_consent = True
elif code.value == CABOR_SIGNATURE_QUESTION_CODE:
if answer.valueUri or answer.valueString:
# TODO: validate the URI? [DA-326]
if not participant_summary.consentForCABoR:
participant_summary.consentForCABoR = True
participant_summary.consentForCABoRTime = questionnaire_response.created
something_changed = True
# If race was provided in the response in one or more answers, set the new value.
if race_code_ids:
race_codes = [code_dao.get(code_id) for code_id in race_code_ids]
race = get_race(race_codes)
if race != participant_summary.race:
participant_summary.race = race
something_changed = True
# Set summary fields to SUBMITTED for questionnaire concepts that are found in
# QUESTIONNAIRE_MODULE_CODE_TO_FIELD
module_changed = False
for concept in questionnaire_history.concepts:
code = code_map.get(concept.codeId)
if code:
summary_field = QUESTIONNAIRE_MODULE_CODE_TO_FIELD.get(
code.value)
if summary_field:
new_status = QuestionnaireStatus.SUBMITTED
if code.value == CONSENT_FOR_ELECTRONIC_HEALTH_RECORDS_MODULE and not ehr_consent:
new_status = QuestionnaireStatus.SUBMITTED_NO_CONSENT
elif code.value == CONSENT_FOR_DVEHR_MODULE:
new_status = dvehr_consent
elif code.value == CONSENT_FOR_STUDY_ENROLLMENT_MODULE:
# set language of consent to participant summary
for extension in resource_json.get('extension', []):
if extension.get('url') == _LANGUAGE_EXTENSION and \
extension.get('valueCode') in LANGUAGE_OF_CONSENT:
if participant_summary.primaryLanguage != extension.get(
'valueCode'):
participant_summary.primaryLanguage = extension.get(
'valueCode')
something_changed = True
break
elif extension.get('url') == _LANGUAGE_EXTENSION and \
extension.get('valueCode') not in LANGUAGE_OF_CONSENT:
logging.warn(
'consent language %s not recognized.' %
extension.get('valueCode'))
if getattr(participant_summary,
summary_field) != new_status:
setattr(participant_summary, summary_field, new_status)
setattr(participant_summary, summary_field + 'Time',
questionnaire_response.created)
something_changed = True
module_changed = True
if module_changed:
participant_summary.numCompletedBaselinePPIModules = \
count_completed_baseline_ppi_modules(participant_summary)
participant_summary.numCompletedPPIModules = \
count_completed_ppi_modules(participant_summary)
if something_changed:
first_last = (participant_summary.firstName,
participant_summary.lastName)
email_phone = (participant_summary.email,
participant_summary.loginPhoneNumber)
if not all(first_last):
raise BadRequest(
'First name (%s), and last name (%s) required for consenting.'
% tuple([
'present' if part else 'missing' for part in first_last
]))
if not any(email_phone):
raise BadRequest(
'Email address (%s), or phone number (%s) required for consenting.'
% tuple([
'present' if part else 'missing'
for part in email_phone
]))
ParticipantSummaryDao().update_enrollment_status(
participant_summary)
participant_summary.lastModified = clock.CLOCK.now()
session.merge(participant_summary)
# switch account to test account if the phone number is start with 444
# this is a requirement from PTSC
if participant_summary.loginPhoneNumber is not None and \
participant_summary.loginPhoneNumber.startswith(TEST_LOGIN_PHONE_NUMBER_PREFIX):
ParticipantDao().switch_to_test_account(
session, participant_summary.participantId)
def _update_participant_summary(
self, session, questionnaire_response, code_ids, questions, questionnaire_history):
"""Updates the participant summary based on questions answered and modules completed
in the questionnaire response.
If no participant summary exists already, only a response to the study enrollment consent
questionnaire can be submitted, and it must include first and last name and e-mail address.
"""
# Block on other threads modifying the participant or participant summary.
participant = ParticipantDao().get_for_update(session, questionnaire_response.participantId)
if participant is None:
raise BadRequest('Participant with ID %d is not found.' %
questionnaire_response.participantId)
participant_summary = participant.participantSummary
code_ids.extend([concept.codeId for concept in questionnaire_history.concepts])
code_dao = CodeDao()
something_changed = False
# If no participant summary exists, make sure this is the study enrollment consent.
if not participant_summary:
consent_code = code_dao.get_code(PPI_SYSTEM, CONSENT_FOR_STUDY_ENROLLMENT_MODULE)
if not consent_code:
raise BadRequest('No study enrollment consent code found; import codebook.')
if not consent_code.codeId in code_ids:
raise BadRequest("Can't submit order for participant %s without consent" %
questionnaire_response.participantId)
raise_if_withdrawn(participant)
participant_summary = ParticipantDao.create_summary_for_participant(participant)
something_changed = True
else:
raise_if_withdrawn(participant_summary)
# Fetch the codes for all questions and concepts
codes = code_dao.get_with_ids(code_ids)
code_map = {code.codeId: code for code in codes if code.system == PPI_SYSTEM}
question_map = {question.questionnaireQuestionId: question for question in questions}
race_code_ids = []
ehr_consent = False
# Set summary fields for answers that have questions with codes found in QUESTION_CODE_TO_FIELD
for answer in questionnaire_response.answers:
question = question_map.get(answer.questionId)
if question:
code = code_map.get(question.codeId)
if code:
summary_field = QUESTION_CODE_TO_FIELD.get(code.value)
if summary_field:
something_changed = self._update_field(participant_summary, summary_field[0],
summary_field[1], answer)
elif code.value == RACE_QUESTION_CODE:
race_code_ids.append(answer.valueCodeId)
elif code.value == EHR_CONSENT_QUESTION_CODE:
code = code_dao.get(answer.valueCodeId)
if code and code.value == CONSENT_PERMISSION_YES_CODE:
ehr_consent = True
elif code.value == CABOR_SIGNATURE_QUESTION_CODE:
if answer.valueUri or answer.valueString:
# TODO: validate the URI? [DA-326]
if not participant_summary.consentForCABoR:
participant_summary.consentForCABoR = True
participant_summary.consentForCABoRTime = questionnaire_response.created
something_changed = True
# If race was provided in the response in one or more answers, set the new value.
if race_code_ids:
race_codes = [code_dao.get(code_id) for code_id in race_code_ids]
race = get_race(race_codes)
if race != participant_summary.race:
participant_summary.race = race
something_changed = True
# Set summary fields to SUBMITTED for questionnaire concepts that are found in
# QUESTIONNAIRE_MODULE_CODE_TO_FIELD
module_changed = False
for concept in questionnaire_history.concepts:
code = code_map.get(concept.codeId)
if code:
summary_field = QUESTIONNAIRE_MODULE_CODE_TO_FIELD.get(code.value)
if summary_field:
new_status = QuestionnaireStatus.SUBMITTED
if code.value == CONSENT_FOR_ELECTRONIC_HEALTH_RECORDS_MODULE and not ehr_consent:
new_status = QuestionnaireStatus.SUBMITTED_NO_CONSENT
if getattr(participant_summary, summary_field) != new_status:
setattr(participant_summary, summary_field, new_status)
setattr(participant_summary, summary_field + 'Time', questionnaire_response.created)
something_changed = True
module_changed = True
if module_changed:
participant_summary.numCompletedBaselinePPIModules = \
count_completed_baseline_ppi_modules(participant_summary)
participant_summary.numCompletedPPIModules = \
count_completed_ppi_modules(participant_summary)
if something_changed:
first_last_email = (
participant_summary.firstName, participant_summary.lastName, participant_summary.email)
if not all(first_last_email):
raise BadRequest(
'First name (%s), last name (%s), and email address (%s) required for consenting.'
% tuple(['present' if part else 'missing' for part in first_last_email]))
ParticipantSummaryDao().update_enrollment_status(participant_summary)
participant_summary.lastModified = clock.CLOCK.now()
session.merge(participant_summary)