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 _query_and_write_reports(exporter, now, report_type, path_received, path_missing, path_modified,
path_withdrawals):
"""Runs the reconciliation MySQL queries and writes result rows to the given CSV writers.
Note that due to syntax differences, the query runs on MySQL only (not SQLite in unit tests).
"""
report_cover_range = 10
if report_type == 'monthly':
report_cover_range = 60
# Gets all sample/order pairs where everything arrived, within the past n days.
received_predicate = lambda result: (result[_RECEIVED_TEST_INDEX] and
result[_SENT_COUNT_INDEX] <= result[_RECEIVED_COUNT_INDEX]
and
in_past_n_days(result, now, report_cover_range))
# Gets samples or orders where something has gone missing within the past n days, and if an order
# was placed, it was placed at least 36 hours ago.
missing_predicate = lambda result: ((result[_SENT_COUNT_INDEX] != result[_RECEIVED_COUNT_INDEX] or
(result[_SENT_FINALIZED_INDEX] and
not result[_RECEIVED_TEST_INDEX])) and
in_past_n_days(result, now, report_cover_range,
ordered_before=now - _THIRTY_SIX_HOURS_AGO))
# Gets samples or orders where something has modified within the past n days.
modified_predicate = lambda result: (result[_EDITED_CANCELLED_RESTORED_STATUS_FLAG_INDEX] and
in_past_n_days(result, now, report_cover_range))
code_dao = CodeDao()
race_question_code = code_dao.get_code(PPI_SYSTEM, RACE_QUESTION_CODE)
native_american_race_code = code_dao.get_code(PPI_SYSTEM, RACE_AIAN_CODE)
# break into three steps to avoid OOM issue
report_paths = [path_received, path_missing, path_modified]
report_predicates = [received_predicate, missing_predicate, modified_predicate]
for report_path, report_predicate in zip(report_paths, report_predicates):
with exporter.open_writer(report_path, report_predicate) as report_writer:
exporter.run_export_with_writer(report_writer, replace_isodate(_RECONCILIATION_REPORT_SQL),
{'race_question_code_id': race_question_code.codeId,
'native_american_race_code_id':
native_american_race_code.codeId,
'biobank_id_prefix': get_biobank_id_prefix(),
'pmi_ops_system': _PMI_OPS_SYSTEM,
'kit_id_system': _KIT_ID_SYSTEM,
'tracking_number_system': _TRACKING_NUMBER_SYSTEM,
'n_days_ago': now - datetime.timedelta(
days=(report_cover_range + 1))})
# Now generate the withdrawal report, within the past n days.
exporter.run_export(path_withdrawals, replace_isodate(_WITHDRAWAL_REPORT_SQL),
{'race_question_code_id': race_question_code.codeId,
'native_american_race_code_id': native_american_race_code.codeId,
'n_days_ago': now - datetime.timedelta(days=report_cover_range),
'biobank_id_prefix': get_biobank_id_prefix()})
def test_participant_race_answers(self):
with FakeClock(TIME_1):
participant_id = self.create_participant()
self.send_consent(participant_id)
questionnaire_id = self.create_questionnaire('questionnaire_the_basics.json')
with open(data_path('questionnaire_the_basics_resp_multiple_race.json')) as f:
resource = json.load(f)
resource['subject']['reference'] = \
resource['subject']['reference'].format(participant_id=participant_id)
resource['questionnaire']['reference'] = \
resource['questionnaire']['reference'].format(questionnaire_id=questionnaire_id)
with FakeClock(TIME_2):
resource['authored'] = TIME_2.isoformat()
self.send_post(_questionnaire_response_url(participant_id), resource)
code_dao = CodeDao()
code1 = code_dao.get_code('http://terminology.pmi-ops.org/CodeSystem/ppi',
'WhatRaceEthnicity_White')
code2 = code_dao.get_code('http://terminology.pmi-ops.org/CodeSystem/ppi',
'WhatRaceEthnicity_Hispanic')
participant_race_answers_dao = ParticipantRaceAnswersDao()
answers = participant_race_answers_dao.get_all()
self.assertEqual(len(answers), 2)
for answer in answers:
self.assertIn(answer.codeId, [code1.codeId, code2.codeId])
# resubmit the answers, old value should be removed
with open(data_path('questionnaire_the_basics_resp_multiple_race_2.json')) as f:
resource = json.load(f)
resource['subject']['reference'] = \
resource['subject']['reference'].format(participant_id=participant_id)
resource['questionnaire']['reference'] = \
resource['questionnaire']['reference'].format(questionnaire_id=questionnaire_id)
with FakeClock(TIME_2):
resource['authored'] = TIME_2.isoformat()
self.send_post(_questionnaire_response_url(participant_id), resource)
code_dao = CodeDao()
code1 = code_dao.get_code('http://terminology.pmi-ops.org/CodeSystem/ppi',
'WhatRaceEthnicity_NHPI')
code2 = code_dao.get_code('http://terminology.pmi-ops.org/CodeSystem/ppi',
'PMI_PreferNotToAnswer')
answers = participant_race_answers_dao.get_all()
self.assertEqual(len(answers), 2)
for answer in answers:
self.assertIn(answer.codeId, [code1.codeId, code2.codeId])
def _query_and_write_reports(exporter, now, path_received, path_late,
path_missing, path_withdrawals):
"""Runs the reconciliation MySQL queries and writes result rows to the given CSV writers.
Note that due to syntax differences, the query runs on MySQL only (not SQLite in unit tests).
"""
# Gets all sample/order pairs where everything arrived, regardless of timing.
received_predicate = lambda result: (result[_RECEIVED_TEST_INDEX] and
result[_SENT_COUNT_INDEX] == result[
_RECEIVED_COUNT_INDEX])
# Gets orders for which the samples arrived, but they arrived late, within the past 7 days.
late_predicate = lambda result: (result[_ELAPSED_HOURS_INDEX] and int(
result[_ELAPSED_HOURS_INDEX]) >= 24 and in_past_week(result, now))
# Gets samples or orders where something has gone missing within the past 7 days, and if an order
# was placed, it was placed at least 36 hours ago.
missing_predicate = lambda result: (
(result[_SENT_COUNT_INDEX] != result[_RECEIVED_COUNT_INDEX] or (result[
_SENT_FINALIZED_INDEX] and not result[_RECEIVED_TEST_INDEX])) and
in_past_week(result, now, ordered_before=now - _THIRTY_SIX_HOURS_AGO))
code_dao = CodeDao()
race_question_code = code_dao.get_code(PPI_SYSTEM, RACE_QUESTION_CODE)
native_american_race_code = code_dao.get_code(PPI_SYSTEM, RACE_AIAN_CODE)
# Open three files and a database session; run the reconciliation query and pipe the output
# to the files, using per-file predicates to filter out results.
with exporter.open_writer(path_received, received_predicate) as received_writer, \
exporter.open_writer(path_late, late_predicate) as late_writer, \
exporter.open_writer(path_missing, missing_predicate) as missing_writer, \
database_factory.get_database().session() as session:
writer = CompositeSqlExportWriter(
[received_writer, late_writer, missing_writer])
exporter.run_export_with_session(
writer, session, replace_isodate(_RECONCILIATION_REPORT_SQL), {
'race_question_code_id': race_question_code.codeId,
'native_american_race_code_id':
native_american_race_code.codeId,
'biobank_id_prefix': get_biobank_id_prefix(),
'pmi_ops_system': _PMI_OPS_SYSTEM,
'kit_id_system': _KIT_ID_SYSTEM,
'tracking_number_system': _TRACKING_NUMBER_SYSTEM
})
# Now generate the withdrawal report.
exporter.run_export(
path_withdrawals, replace_isodate(_WITHDRAWAL_REPORT_SQL), {
'race_question_code_id': race_question_code.codeId,
'native_american_race_code_id': native_american_race_code.codeId,
'seven_days_ago': now - datetime.timedelta(days=7),
'biobank_id_prefix': get_biobank_id_prefix()
})
def _get_validation_result(email, codes_to_answers):
result = _ValidationResult()
summaries = ParticipantSummaryDao().get_by_email(email)
if not summaries:
result.add_error('No ParticipantSummary found for %r.' % email)
return result
if len(summaries) > 1:
result.add_error('%d ParticipantSummary values found for %r.' %
(len(summaries), email))
return result
participant_id = summaries[0].participantId
code_dao = CodeDao()
qra_dao = QuestionnaireResponseAnswerDao()
with qra_dao.session() as session:
for code_string, answer_string in codes_to_answers.iteritems():
result.tests_count += 1
question_code = code_dao.get_code(PPI_SYSTEM, code_string)
if not question_code:
result.add_error(
'Could not find question code %r, skipping answer %r.' %
(code_string, answer_string))
continue
if question_code.codeType != CodeType.QUESTION:
result.add_error(
'Code %r type is %s, not QUESTION; skipping.' %
(code_string, question_code.codeType))
continue
qras = qra_dao.get_current_answers_for_concepts(
session, participant_id, [question_code.codeId])
qra_values = set()
for qra in qras:
try:
qra_values.add(
_get_value_for_qra(qra, question_code, code_dao,
session))
except ValueError as e:
result.add_error(e.message)
continue
if answer_string:
expected_values = set(
_boolean_to_lower(v.strip())
for v in answer_string.split('|'))
else:
expected_values = set()
if expected_values != qra_values:
result.add_error(
'%s: Expected %s, found %s.' %
(question_code.value, _format_values(expected_values),
_format_values(qra_values)))
return result
def _setup_questionnaires(self):
"""Locates questionnaires and verifies that they have the appropriate questions in them."""
questionnaire_dao = QuestionnaireDao()
code_dao = CodeDao()
question_code_to_questionnaire_id = {}
self._questionnaire_to_questions = collections.defaultdict(list)
self._question_code_to_answer_codes = {}
# Populate maps of questionnaire ID/version to [(question_code, link ID)] and
# question code to answer codes.
for concept in _QUESTIONNAIRE_CONCEPTS:
code = code_dao.get_code(PPI_SYSTEM, concept)
if code is None:
raise BadRequest(
'Code missing: %s; import data and clear cache.' % concept)
questionnaire = questionnaire_dao.get_latest_questionnaire_with_concept(
code.codeId)
if questionnaire is None:
raise BadRequest(
'Questionnaire for code %s missing; import data.' %
concept)
questionnaire_id_and_version = (questionnaire.questionnaireId,
questionnaire.version)
if concept == CONSENT_FOR_STUDY_ENROLLMENT_MODULE:
self._consent_questionnaire_id_and_version = questionnaire_id_and_version
elif concept == THE_BASICS_PPI_MODULE:
self._the_basics_questionnaire_id_and_version = questionnaire_id_and_version
questions = self._questionnaire_to_questions[
questionnaire_id_and_version]
if questions:
# We already handled this questionnaire.
continue
for question in questionnaire.questions:
question_code = code_dao.get(question.codeId)
if (question_code.value
in _QUESTION_CODES) or (question_code.value
in self._answer_specs):
question_code_to_questionnaire_id[
question_code.value] = questionnaire.questionnaireId
questions.append((question_code.value, question.linkId))
if question_code.value in _QUESTION_CODES:
answer_codes = self._get_answer_codes(question_code)
all_codes = (answer_codes + _CONSTANT_CODES
) if answer_codes else _CONSTANT_CODES
self._question_code_to_answer_codes[
question_code.value] = all_codes
# Log warnings for any question codes not found in the questionnaires.
for code_value in _QUESTION_CODES + self._answer_specs.keys():
questionnaire_id = question_code_to_questionnaire_id.get(
code_value)
if not questionnaire_id:
logging.warning(
'Question for code %s missing; import questionnaires',
code_value)
def _get_answer_sql(num_shards, shard_number):
code_dao = CodeDao()
code_ids = []
question_codes = list(ANSWER_FIELD_TO_QUESTION_CODE.values())
question_codes.append(RACE_QUESTION_CODE)
question_codes.append(EHR_CONSENT_QUESTION_CODE)
for code_value in question_codes:
code = code_dao.get_code(PPI_SYSTEM, code_value)
code_ids.append(str(code.codeId))
params = _get_params(num_shards, shard_number)
params['unmapped'] = UNMAPPED
return replace_isodate(_ANSWER_QUERY.format((','.join(code_ids)))), params
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)
def test_insert(self):
participant_id = self.create_participant()
questionnaire_id = self.create_questionnaire('questionnaire1.json')
with open(data_path('questionnaire_response3.json')) as fd:
resource = json.load(fd)
# Sending response with the dummy participant id in the file is an error
self.send_post(_questionnaire_response_url('{participant_id}'),
resource,
expected_status=httplib.NOT_FOUND)
# Fixing participant id but not the questionnaire id is also an error
resource['subject']['reference'] = \
resource['subject']['reference'].format(participant_id=participant_id)
self.send_post(_questionnaire_response_url(participant_id),
resource,
expected_status=httplib.BAD_REQUEST)
# Fix the reference
resource['questionnaire']['reference'] = \
resource['questionnaire']['reference'].format(questionnaire_id=questionnaire_id)
# Sending the response before the consent is an error.
self.send_post(_questionnaire_response_url(participant_id),
resource,
expected_status=httplib.BAD_REQUEST)
# After consent, the post succeeds
self.send_consent(participant_id)
response = self.send_post(_questionnaire_response_url(participant_id),
resource)
resource['id'] = response['id']
# The resource gets rewritten to include the version
resource['questionnaire'][
'reference'] = 'Questionnaire/%s/_history/1' % questionnaire_id
self.assertJsonResponseMatches(resource, response)
# Do a get to fetch the questionnaire
get_response = self.send_get(
_questionnaire_response_url(participant_id) + "/" + response['id'])
self.assertJsonResponseMatches(resource, get_response)
code_dao = CodeDao()
# Ensure we didn't create codes in the extra system
self.assertIsNone(code_dao.get_code(PPI_EXTRA_SYSTEM, 'IgnoreThis'))
name_of_child = code_dao.get_code("sys", "nameOfChild")
birth_weight = code_dao.get_code("sys", "birthWeight")
birth_length = code_dao.get_code("sys", "birthLength")
vitamin_k_dose_1 = code_dao.get_code("sys", "vitaminKDose1")
vitamin_k_dose_2 = code_dao.get_code("sys", "vitaminKDose2")
hep_b_given = code_dao.get_code("sys", "hepBgiven")
abnormalities_at_birth = code_dao.get_code("sys",
"abnormalitiesAtBirth")
answer_dao = QuestionnaireResponseAnswerDao()
with answer_dao.session() as session:
code_ids = [
code.codeId for code in [
name_of_child, birth_weight, birth_length,
vitamin_k_dose_1, vitamin_k_dose_2, hep_b_given,
abnormalities_at_birth
]
]
current_answers = answer_dao.get_current_answers_for_concepts(session,\
from_client_participant_id(participant_id), code_ids)
self.assertEquals(7, len(current_answers))
questionnaire = QuestionnaireDao().get_with_children(questionnaire_id)
question_id_to_answer = {
answer.questionId: answer
for answer in current_answers
}
code_id_to_answer = {
question.codeId:
question_id_to_answer.get(question.questionnaireQuestionId)
for question in questionnaire.questions
}
self.assertEquals("Cathy Jones",
code_id_to_answer[name_of_child.codeId].valueString)
self.assertEquals(3.25,
code_id_to_answer[birth_weight.codeId].valueDecimal)
self.assertEquals(44.3,
code_id_to_answer[birth_length.codeId].valueDecimal)
self.assertEquals(44,
code_id_to_answer[birth_length.codeId].valueInteger)
self.assertEquals(True,
code_id_to_answer[hep_b_given.codeId].valueBoolean)
self.assertEquals(
0, code_id_to_answer[abnormalities_at_birth.codeId].valueInteger)
self.assertEquals(datetime.date(1972, 11, 30),
code_id_to_answer[vitamin_k_dose_1.codeId].valueDate)
self.assertEquals(
datetime.datetime(1972, 11, 30, 12, 34, 42),
code_id_to_answer[vitamin_k_dose_2.codeId].valueDateTime)
class ParticipantSummaryDao(UpdatableDao):
def __init__(self):
super(ParticipantSummaryDao,
self).__init__(ParticipantSummary,
order_by_ending=_ORDER_BY_ENDING)
self.hpo_dao = HPODao()
self.code_dao = CodeDao()
def get_id(self, obj):
return obj.participantId
def get_by_email(self, email):
with self.session() as session:
return session.query(ParticipantSummary).filter(
ParticipantSummary.email == email).all()
def _validate_update(self, session, obj, existing_obj):
"""Participant summaries don't have a version value; drop it from validation logic."""
if not existing_obj:
raise NotFound('%s with id %s does not exist' %
(self.model_type.__name__, id))
def _has_withdrawn_filter(self, query):
for field_filter in query.field_filters:
if (field_filter.field_name == 'withdrawalStatus'
and field_filter.value == WithdrawalStatus.NO_USE):
return True
if field_filter.field_name == 'withdrawalTime' and field_filter.value is not None:
return True
return False
def _get_non_withdrawn_filter_field(self, query):
"""Returns the first field referenced in query filters which isn't in
WITHDRAWN_PARTICIPANT_FIELDS."""
for field_filter in query.field_filters:
if not field_filter.field_name in WITHDRAWN_PARTICIPANT_FIELDS:
return field_filter.field_name
return None
def _initialize_query(self, session, query_def):
non_withdrawn_field = self._get_non_withdrawn_filter_field(query_def)
if self._has_withdrawn_filter(query_def):
if non_withdrawn_field:
raise BadRequest(
"Can't query on %s for withdrawn participants" %
non_withdrawn_field)
# When querying for withdrawn participants, ensure that the only fields being filtered on or
# ordered by are in WITHDRAWN_PARTICIPANT_FIELDS.
return super(ParticipantSummaryDao,
self)._initialize_query(session, query_def)
else:
query = super(ParticipantSummaryDao,
self)._initialize_query(session, query_def)
if non_withdrawn_field:
# When querying on fields that aren't available for withdrawn participants,
# ensure that we only return participants
# who have not withdrawn or withdrew in the past 48 hours.
withdrawn_visible_start = clock.CLOCK.now(
) - WITHDRAWN_PARTICIPANT_VISIBILITY_TIME
return query.filter(
or_(
ParticipantSummary.withdrawalStatus !=
WithdrawalStatus.NO_USE,
ParticipantSummary.withdrawalTime >=
withdrawn_visible_start))
else:
# When querying on fields that are available for withdrawn participants, return everybody;
# withdrawn participants will have all but WITHDRAWN_PARTICIPANT_FIELDS cleared out 48
# hours after withdrawing.
return query
def _get_order_by_ending(self, query):
if self._has_withdrawn_filter(query):
return _WITHDRAWN_ORDER_BY_ENDING
return self.order_by_ending
def _add_order_by(self, query, order_by, field_names, fields):
if order_by.field_name in _CODE_FILTER_FIELDS:
return super(ParticipantSummaryDao, self)._add_order_by(
query, OrderBy(order_by.field_name + 'Id', order_by.ascending),
field_names, fields)
return super(ParticipantSummaryDao,
self)._add_order_by(query, order_by, field_names, fields)
def make_query_filter(self, field_name, value):
"""Handle HPO and code values when parsing filter values."""
if field_name == 'hpoId':
hpo = self.hpo_dao.get_by_name(value)
if not hpo:
raise BadRequest('No HPO found with name %s' % value)
return super(ParticipantSummaryDao,
self).make_query_filter(field_name, hpo.hpoId)
if field_name in _CODE_FILTER_FIELDS:
if value == UNSET:
return super(ParticipantSummaryDao,
self).make_query_filter(field_name + 'Id', None)
# Note: we do not at present support querying for UNMAPPED code values.
code = self.code_dao.get_code(PPI_SYSTEM, value)
if not code:
raise BadRequest('No code found: %s' % value)
return super(ParticipantSummaryDao,
self).make_query_filter(field_name + 'Id',
code.codeId)
return super(ParticipantSummaryDao,
self).make_query_filter(field_name, value)
def update_from_biobank_stored_samples(self, participant_id=None):
"""Rewrites sample-related summary data. Call this after updating BiobankStoredSamples.
If participant_id is provided, only that participant will have their summary updated."""
baseline_tests_sql, baseline_tests_params = get_sql_and_params_for_array(
config.getSettingList(config.BASELINE_SAMPLE_TEST_CODES),
'baseline')
dna_tests_sql, dna_tests_params = get_sql_and_params_for_array(
config.getSettingList(config.DNA_SAMPLE_TEST_CODES), 'dna')
sample_sql, sample_params = _get_sample_sql_and_params()
sql = """
UPDATE
participant_summary
SET
num_baseline_samples_arrived = (
SELECT
COUNT(*)
FROM
biobank_stored_sample
WHERE
biobank_stored_sample.biobank_id = participant_summary.biobank_id
AND biobank_stored_sample.test IN %s
),
samples_to_isolate_dna = (
CASE WHEN EXISTS(SELECT * FROM biobank_stored_sample
WHERE biobank_stored_sample.biobank_id = participant_summary.biobank_id
AND biobank_stored_sample.test IN %s)
THEN :received ELSE :unset END
) %s""" % (baseline_tests_sql, dna_tests_sql, sample_sql)
params = {
'received': int(SampleStatus.RECEIVED),
'unset': int(SampleStatus.UNSET)
}
params.update(baseline_tests_params)
params.update(dna_tests_params)
params.update(sample_params)
enrollment_status_params = {
'submitted': int(QuestionnaireStatus.SUBMITTED),
'num_baseline_ppi_modules': self._get_num_baseline_ppi_modules(),
'completed': int(PhysicalMeasurementsStatus.COMPLETED),
'received': int(SampleStatus.RECEIVED),
'full_participant': int(EnrollmentStatus.FULL_PARTICIPANT),
'member': int(EnrollmentStatus.MEMBER),
'interested': int(EnrollmentStatus.INTERESTED)
}
enrollment_status_sql = _ENROLLMENT_STATUS_SQL
# If participant_id is provided, add the participant ID filter to both update statements.
if participant_id:
sql += _PARTICIPANT_ID_FILTER
params['participant_id'] = participant_id
enrollment_status_sql += _PARTICIPANT_ID_FILTER
enrollment_status_params['participant_id'] = participant_id
with self.session() as session:
session.execute(sql, params)
session.execute(enrollment_status_sql, enrollment_status_params)
def _get_num_baseline_ppi_modules(self):
return len(
config.getSettingList(config.BASELINE_PPI_QUESTIONNAIRE_FIELDS))
def update_enrollment_status(self, summary):
"""Updates the enrollment status field on the provided participant summary to
the correct value based on the other fields on it. Called after
a questionnaire response or physical measurements are submitted."""
consent = (summary.consentForStudyEnrollment
== QuestionnaireStatus.SUBMITTED
and summary.consentForElectronicHealthRecords
== QuestionnaireStatus.SUBMITTED)
enrollment_status = self.calculate_enrollment_status(
consent, summary.numCompletedBaselinePPIModules,
summary.physicalMeasurementsStatus, summary.samplesToIsolateDNA)
summary.enrollment_status = enrollment_status
def calculate_enrollment_status(self, consent_for_study_enrollment_and_ehr,
num_completed_baseline_ppi_modules,
physical_measurements_status,
samples_to_isolate_dna):
if consent_for_study_enrollment_and_ehr:
if (num_completed_baseline_ppi_modules
== self._get_num_baseline_ppi_modules()
and physical_measurements_status
== PhysicalMeasurementsStatus.COMPLETED
and samples_to_isolate_dna == SampleStatus.RECEIVED):
return EnrollmentStatus.FULL_PARTICIPANT
return EnrollmentStatus.MEMBER
return EnrollmentStatus.INTERESTED
def to_client_json(self, model):
result = model.asdict()
# Participants that withdrew more than 48 hours ago should have fields other than
# WITHDRAWN_PARTICIPANT_FIELDS cleared.
if (model.withdrawalStatus == WithdrawalStatus.NO_USE
and model.withdrawalTime <
clock.CLOCK.now() - WITHDRAWN_PARTICIPANT_VISIBILITY_TIME):
result = {k: result.get(k) for k in WITHDRAWN_PARTICIPANT_FIELDS}
result['participantId'] = to_client_participant_id(model.participantId)
biobank_id = result.get('biobankId')
if biobank_id:
result['biobankId'] = to_client_biobank_id(biobank_id)
date_of_birth = result.get('dateOfBirth')
if date_of_birth:
result['ageRange'] = get_bucketed_age(date_of_birth,
clock.CLOCK.now())
else:
result['ageRange'] = UNSET
format_json_hpo(result, self.hpo_dao, 'hpoId')
_initialize_field_type_sets()
for fieldname in _DATE_FIELDS:
format_json_date(result, fieldname)
for fieldname in _CODE_FIELDS:
format_json_code(result, self.code_dao, fieldname)
for fieldname in _ENUM_FIELDS:
format_json_enum(result, fieldname)
if (model.withdrawalStatus == WithdrawalStatus.NO_USE
or model.suspensionStatus == SuspensionStatus.NO_CONTACT):
result['recontactMethod'] = 'NO_CONTACT'
# Strip None values.
result = {k: v for k, v in result.iteritems() if v is not None}
return result
class ParticipantSummaryDao(UpdatableDao):
def __init__(self):
super(ParticipantSummaryDao,
self).__init__(ParticipantSummary,
order_by_ending=_ORDER_BY_ENDING)
self.hpo_dao = HPODao()
self.code_dao = CodeDao()
self.site_dao = SiteDao()
self.organization_dao = OrganizationDao()
def get_id(self, obj):
return obj.participantId
def _validate_update(self, session, obj, existing_obj): # pylint: disable=unused-argument
"""Participant summaries don't have a version value; drop it from validation logic."""
if not existing_obj:
raise NotFound('%s with id %s does not exist' %
(self.model_type.__name__, id))
def _has_withdrawn_filter(self, query):
for field_filter in query.field_filters:
if (field_filter.field_name == 'withdrawalStatus'
and field_filter.value == WithdrawalStatus.NO_USE):
return True
if field_filter.field_name == 'withdrawalTime' and field_filter.value is not None:
return True
return False
def _get_non_withdrawn_filter_field(self, query):
"""Returns the first field referenced in query filters which isn't in
WITHDRAWN_PARTICIPANT_FIELDS."""
for field_filter in query.field_filters:
if not field_filter.field_name in WITHDRAWN_PARTICIPANT_FIELDS:
return field_filter.field_name
return None
def _initialize_query(self, session, query_def):
non_withdrawn_field = self._get_non_withdrawn_filter_field(query_def)
if self._has_withdrawn_filter(query_def):
if non_withdrawn_field:
raise BadRequest(
"Can't query on %s for withdrawn participants" %
non_withdrawn_field)
# When querying for withdrawn participants, ensure that the only fields being filtered on or
# ordered by are in WITHDRAWN_PARTICIPANT_FIELDS.
return super(ParticipantSummaryDao,
self)._initialize_query(session, query_def)
else:
query = super(ParticipantSummaryDao,
self)._initialize_query(session, query_def)
if non_withdrawn_field:
# When querying on fields that aren't available for withdrawn participants,
# ensure that we only return participants
# who have not withdrawn or withdrew in the past 48 hours.
withdrawn_visible_start = clock.CLOCK.now(
) - WITHDRAWN_PARTICIPANT_VISIBILITY_TIME
return query.filter(
or_(
ParticipantSummary.withdrawalStatus !=
WithdrawalStatus.NO_USE,
ParticipantSummary.withdrawalTime >=
withdrawn_visible_start))
else:
# When querying on fields that are available for withdrawn participants, return everybody;
# withdrawn participants will have all but WITHDRAWN_PARTICIPANT_FIELDS cleared out 48
# hours after withdrawing.
return query
def _get_order_by_ending(self, query):
if self._has_withdrawn_filter(query):
return _WITHDRAWN_ORDER_BY_ENDING
return self.order_by_ending
def _add_order_by(self, query, order_by, field_names, fields):
if order_by.field_name in _CODE_FILTER_FIELDS:
return super(ParticipantSummaryDao, self)._add_order_by(
query, OrderBy(order_by.field_name + 'Id', order_by.ascending),
field_names, fields)
return super(ParticipantSummaryDao,
self)._add_order_by(query, order_by, field_names, fields)
def make_query_filter(self, field_name, value):
"""Handle HPO and code values when parsing filter values."""
if field_name == 'biobankId':
value = from_client_biobank_id(value, log_exception=True)
if field_name == 'hpoId' or field_name == 'awardee':
hpo = self.hpo_dao.get_by_name(value)
if not hpo:
raise BadRequest('No HPO found with name %s' % value)
if field_name == 'awardee':
field_name = 'hpoId'
return super(ParticipantSummaryDao,
self).make_query_filter(field_name, hpo.hpoId)
if field_name == 'organization':
organization = self.organization_dao.get_by_external_id(value)
if not organization:
raise BadRequest('No organization found with name %s' % value)
return super(ParticipantSummaryDao,
self).make_query_filter(field_name + 'Id',
organization.organizationId)
if field_name in _SITE_FIELDS:
if value == UNSET:
return super(ParticipantSummaryDao,
self).make_query_filter(field_name + 'Id', None)
site = self.site_dao.get_by_google_group(value)
if not site:
raise BadRequest('No site found with google group %s' % value)
return super(ParticipantSummaryDao,
self).make_query_filter(field_name + 'Id',
site.siteId)
if field_name in _CODE_FILTER_FIELDS:
if value == UNSET:
return super(ParticipantSummaryDao,
self).make_query_filter(field_name + 'Id', None)
# Note: we do not at present support querying for UNMAPPED code values.
code = self.code_dao.get_code(PPI_SYSTEM, value)
if not code:
raise BadRequest('No code found: %s' % value)
return super(ParticipantSummaryDao,
self).make_query_filter(field_name + 'Id',
code.codeId)
return super(ParticipantSummaryDao,
self).make_query_filter(field_name, value)
def update_from_biobank_stored_samples(self, participant_id=None):
"""Rewrites sample-related summary data. Call this after updating BiobankStoredSamples.
If participant_id is provided, only that participant will have their summary updated."""
now = clock.CLOCK.now()
sample_sql, sample_params = _get_sample_sql_and_params(now)
baseline_tests_sql, baseline_tests_params = _get_baseline_sql_and_params(
)
dna_tests_sql, dna_tests_params = _get_dna_isolates_sql_and_params()
sample_status_time_sql = _get_sample_status_time_sql_and_params()
sample_status_time_params = {}
counts_sql = """
UPDATE
participant_summary
SET
num_baseline_samples_arrived = {baseline_tests_sql},
samples_to_isolate_dna = {dna_tests_sql},
last_modified = :now
WHERE
num_baseline_samples_arrived != {baseline_tests_sql} OR
samples_to_isolate_dna != {dna_tests_sql}
""".format(baseline_tests_sql=baseline_tests_sql,
dna_tests_sql=dna_tests_sql)
counts_params = {'now': now}
counts_params.update(baseline_tests_params)
counts_params.update(dna_tests_params)
enrollment_status_sql = _ENROLLMENT_STATUS_SQL
enrollment_status_params = {
'submitted': int(QuestionnaireStatus.SUBMITTED),
'unset': int(QuestionnaireStatus.UNSET),
'num_baseline_ppi_modules': self._get_num_baseline_ppi_modules(),
'completed': int(PhysicalMeasurementsStatus.COMPLETED),
'received': int(SampleStatus.RECEIVED),
'full_participant': int(EnrollmentStatus.FULL_PARTICIPANT),
'member': int(EnrollmentStatus.MEMBER),
'interested': int(EnrollmentStatus.INTERESTED),
'now': now
}
# If participant_id is provided, add the participant ID filter to all update statements.
if participant_id:
sample_sql += ' AND participant_id = :participant_id'
sample_params['participant_id'] = participant_id
counts_sql += ' AND participant_id = :participant_id'
counts_params['participant_id'] = participant_id
enrollment_status_sql += ' AND participant_id = :participant_id'
enrollment_status_params['participant_id'] = participant_id
sample_status_time_sql += ' AND a.participant_id = :participant_id'
sample_status_time_params['participant_id'] = participant_id
sample_sql = replace_null_safe_equals(sample_sql)
counts_sql = replace_null_safe_equals(counts_sql)
with self.session() as session:
session.execute(sample_sql, sample_params)
session.execute(counts_sql, counts_params)
session.execute(enrollment_status_sql, enrollment_status_params)
# TODO: Change this to the optimized sql in _update_dv_stored_samples()
session.execute(sample_status_time_sql, sample_status_time_params)
def _get_num_baseline_ppi_modules(self):
return len(
config.getSettingList(config.BASELINE_PPI_QUESTIONNAIRE_FIELDS))
def update_enrollment_status(self, summary):
"""Updates the enrollment status field on the provided participant summary to
the correct value based on the other fields on it. Called after
a questionnaire response or physical measurements are submitted."""
consent = (summary.consentForStudyEnrollment == QuestionnaireStatus.SUBMITTED and
summary.consentForElectronicHealthRecords == QuestionnaireStatus.SUBMITTED) or \
(summary.consentForStudyEnrollment == QuestionnaireStatus.SUBMITTED and
summary.consentForElectronicHealthRecords is None and
summary.consentForDvElectronicHealthRecordsSharing == QuestionnaireStatus.SUBMITTED)
enrollment_status = self.calculate_enrollment_status(
consent, summary.numCompletedBaselinePPIModules,
summary.physicalMeasurementsStatus, summary.samplesToIsolateDNA)
summary.enrollmentStatusMemberTime = self.calculate_member_time(
consent, summary)
summary.enrollmentStatusCoreOrderedSampleTime = self.calculate_core_ordered_sample_time(
consent, summary)
summary.enrollmentStatusCoreStoredSampleTime = self.calculate_core_stored_sample_time(
consent, summary)
# Update last modified date if status changes
if summary.enrollmentStatus != enrollment_status:
summary.lastModified = clock.CLOCK.now()
summary.enrollmentStatus = enrollment_status
def calculate_enrollment_status(self, consent,
num_completed_baseline_ppi_modules,
physical_measurements_status,
samples_to_isolate_dna):
if consent:
if (num_completed_baseline_ppi_modules
== self._get_num_baseline_ppi_modules()
and physical_measurements_status
== PhysicalMeasurementsStatus.COMPLETED
and samples_to_isolate_dna == SampleStatus.RECEIVED):
return EnrollmentStatus.FULL_PARTICIPANT
return EnrollmentStatus.MEMBER
return EnrollmentStatus.INTERESTED
def calculate_member_time(self, consent, participant_summary):
if consent and participant_summary.enrollmentStatusMemberTime is not None:
return participant_summary.enrollmentStatusMemberTime
elif consent:
if participant_summary.consentForElectronicHealthRecords is None and \
participant_summary.consentForDvElectronicHealthRecordsSharing == \
QuestionnaireStatus.SUBMITTED:
return participant_summary.consentForDvElectronicHealthRecordsSharingTime
return participant_summary.consentForElectronicHealthRecordsTime
else:
return None
def calculate_core_stored_sample_time(self, consent, participant_summary):
if consent and \
participant_summary.numCompletedBaselinePPIModules == \
self._get_num_baseline_ppi_modules() and \
participant_summary.physicalMeasurementsStatus == PhysicalMeasurementsStatus.COMPLETED and \
participant_summary.samplesToIsolateDNA == SampleStatus.RECEIVED:
max_core_sample_time = self.calculate_max_core_sample_time(
participant_summary, field_name_prefix='sampleStatus')
if max_core_sample_time and participant_summary.enrollmentStatusCoreStoredSampleTime:
return participant_summary.enrollmentStatusCoreStoredSampleTime
else:
return max_core_sample_time
else:
return None
def calculate_core_ordered_sample_time(self, consent, participant_summary):
if consent and \
participant_summary.numCompletedBaselinePPIModules == \
self._get_num_baseline_ppi_modules() and \
participant_summary.physicalMeasurementsStatus == PhysicalMeasurementsStatus.COMPLETED:
max_core_sample_time = self.calculate_max_core_sample_time(
participant_summary, field_name_prefix='sampleOrderStatus')
if max_core_sample_time and participant_summary.enrollmentStatusCoreOrderedSampleTime:
return participant_summary.enrollmentStatusCoreOrderedSampleTime
else:
return max_core_sample_time
else:
return None
def calculate_max_core_sample_time(self,
participant_summary,
field_name_prefix='sampleStatus'):
keys = [
field_name_prefix + '%sTime' % test
for test in config.getSettingList(config.DNA_SAMPLE_TEST_CODES)
]
sample_time_list = \
[v for k, v in participant_summary if k in keys and v is not None]
sample_time = min(sample_time_list) if sample_time_list else None
if sample_time is not None:
return max([
sample_time, participant_summary.enrollmentStatusMemberTime,
participant_summary.questionnaireOnTheBasicsTime,
participant_summary.questionnaireOnLifestyleTime,
participant_summary.questionnaireOnOverallHealthTime,
participant_summary.physicalMeasurementsFinalizedTime
])
else:
return None
def calculate_distinct_visits(self,
pid,
finalized_time,
id_,
amendment=False):
""" Participants may get PM or biobank samples on same day. This should be considered as
a single visit in terms of program payment to participant.
return Boolean: true if there has not been an order on same date."""
from dao.biobank_order_dao import BiobankOrderDao
from dao.physical_measurements_dao import PhysicalMeasurementsDao
day_has_order, day_has_measurement = False, False
existing_orders = BiobankOrderDao().get_biobank_orders_for_participant(
pid)
ordered_samples = BiobankOrderDao(
).get_ordered_samples_for_participant(pid)
existing_measurements = PhysicalMeasurementsDao(
).get_measuremnets_for_participant(pid)
order_id_to_finalized_date = {
sample.biobankOrderId: sample.finalized.date()
for sample in ordered_samples if sample.finalized
}
if existing_orders and finalized_time:
for order in existing_orders:
order_finalized_date = order_id_to_finalized_date.get(
order.biobankOrderId)
if order_finalized_date == finalized_time.date() and order.biobankOrderId != id_ and \
order.orderStatus != BiobankOrderStatus.CANCELLED:
day_has_order = True
elif order.biobankOrderId == id_ and order.orderStatus == BiobankOrderStatus.AMENDED:
day_has_order = True
elif not finalized_time and amendment:
day_has_order = True
if existing_measurements and finalized_time:
for measurement in existing_measurements:
if not measurement.finalized:
continue
if measurement.finalized.date() == finalized_time.date() and measurement.physicalMeasurementsId\
!= id_:
day_has_measurement = True
is_distinct_visit = not (day_has_order or day_has_measurement)
return is_distinct_visit
def to_client_json(self, model):
result = model.asdict()
# Participants that withdrew more than 48 hours ago should have fields other than
# WITHDRAWN_PARTICIPANT_FIELDS cleared.
if (model.withdrawalStatus == WithdrawalStatus.NO_USE and
(model.withdrawalTime is None or model.withdrawalTime <
clock.CLOCK.now() - WITHDRAWN_PARTICIPANT_VISIBILITY_TIME)):
result = {k: result.get(k) for k in WITHDRAWN_PARTICIPANT_FIELDS}
elif model.withdrawalStatus != WithdrawalStatus.NO_USE and \
model.suspensionStatus == SuspensionStatus.NO_CONTACT:
for i in SUSPENDED_PARTICIPANT_FIELDS:
result[i] = UNSET
result['participantId'] = to_client_participant_id(model.participantId)
biobank_id = result.get('biobankId')
if biobank_id:
result['biobankId'] = to_client_biobank_id(biobank_id)
date_of_birth = result.get('dateOfBirth')
if date_of_birth:
result['ageRange'] = get_bucketed_age(date_of_birth,
clock.CLOCK.now())
else:
result['ageRange'] = UNSET
if result.get('primaryLanguage') is None:
result['primaryLanguage'] = UNSET
if 'organizationId' in result:
result['organization'] = result['organizationId']
del result['organizationId']
format_json_org(result, self.organization_dao, 'organization')
format_json_hpo(result, self.hpo_dao, 'hpoId')
result['awardee'] = result['hpoId']
_initialize_field_type_sets()
for fieldname in _DATE_FIELDS:
format_json_date(result, fieldname)
for fieldname in _CODE_FIELDS:
format_json_code(result, self.code_dao, fieldname)
for fieldname in _ENUM_FIELDS:
format_json_enum(result, fieldname)
for fieldname in _SITE_FIELDS:
format_json_site(result, self.site_dao, fieldname)
if (model.withdrawalStatus == WithdrawalStatus.NO_USE
or model.suspensionStatus == SuspensionStatus.NO_CONTACT):
result['recontactMethod'] = 'NO_CONTACT'
# Strip None values.
result = {k: v for k, v in result.iteritems() if v is not None}
return result
def _decode_token(self, query_def, fields):
""" If token exists in participant_summary api, decode and use lastModified to add a buffer
of 60 seconds. This ensures when a _sync link is used no one is missed. This will return
at a minimum, the last participant and any more that have been modified in the previous 60
seconds. Duplicate participants returned should be handled on the client side."""
decoded_vals = super(ParticipantSummaryDao,
self)._decode_token(query_def, fields)
if query_def.order_by and (query_def.order_by.field_name
== 'lastModified'
and query_def.always_return_token is True
and query_def.backfill_sync is True):
decoded_vals[0] = decoded_vals[0] - datetime.timedelta(
seconds=config.LAST_MODIFIED_BUFFER_SECONDS)
return decoded_vals
@staticmethod
def update_ehr_status(summary, update_time):
summary.ehrStatus = EhrStatus.PRESENT
if not summary.ehrReceiptTime:
summary.ehrReceiptTime = update_time
summary.ehrUpdateTime = update_time
return summary