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 test_invalid_questionnaire(self):
participant_id = self.create_participant()
questionnaire_id = self.create_questionnaire('questionnaire1.json')
q = QuestionnaireDao()
quesstionnaire = q.get(questionnaire_id)
make_transient(quesstionnaire)
quesstionnaire.status = QuestionnaireDefinitionStatus.INVALID
q.update(quesstionnaire)
q.get(questionnaire_id)
with open(data_path('questionnaire_response3.json')) as fd:
resource = json.load(fd)
self.send_consent(participant_id)
resource['subject']['reference'] = \
resource['subject']['reference'].format(participant_id=participant_id)
# The resource gets rewritten to include the version
resource['questionnaire']['reference'] = 'Questionnaire/%s' % questionnaire_id
self.send_post(_questionnaire_response_url(participant_id), resource,
expected_status=httplib.BAD_REQUEST)
resource['questionnaire']['reference'] = 'Questionnaire/%s/_history/2' % questionnaire_id
self.send_post(_questionnaire_response_url(participant_id), resource,
expected_status=httplib.BAD_REQUEST)
def test_invalid_questionnaire_linkid(self):
"""
DA-623 - Make sure that an invalid link id in response triggers a BadRequest status.
Per a PTSC group request, only log a message for invalid link ids.
In the future if questionnaires with bad link ids trigger a BadRequest, the code below
can be uncommented.
"""
participant_id = self.create_participant()
self.send_consent(participant_id)
questionnaire_id = self.create_questionnaire(
'questionnaire_family_history.json')
with open(data_path('questionnaire_family_history_resp.json')) as fd:
resource = json.load(fd)
# update resource json to set participant and questionnaire ids.
resource['subject']['reference'] = \
resource['subject']['reference'].format(participant_id=participant_id)
resource['questionnaire']['reference'] = \
resource['questionnaire']['reference'].format(questionnaire_id=questionnaire_id)
self.send_post(_questionnaire_response_url(participant_id),
resource,
expected_status=httplib.OK)
def test_update_no_ifmatch_specified(self):
response = self.insert_questionnaire()
with open(data_path('questionnaire2.json')) as f2:
questionnaire2 = json.load(f2)
self.send_put('Questionnaire/%s' % response['id'], questionnaire2,
expected_status=httplib.BAD_REQUEST)
def test_update_wrong_ifmatch_specified(self):
response = self.insert_questionnaire()
with open(data_path('questionnaire2.json')) as f2:
questionnaire2 = json.load(f2)
self.send_put('Questionnaire/%s' % response['id'], questionnaire2,
expected_status=httplib.PRECONDITION_FAILED,
headers={ 'If-Match': 'W/"123"' })
def test_participant_gender_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_gender.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)
participant_gender_answers_dao = ParticipantGenderAnswersDao()
answers = participant_gender_answers_dao.get_all()
self.assertEqual(len(answers), 2)
for answer in answers:
self.assertIn(answer.codeId, [90, 95])
# resubmit the answers, old value should be removed
with open(data_path('questionnaire_the_basics_resp_multiple_gender_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)
answers = participant_gender_answers_dao.get_all()
self.assertEqual(len(answers), 2)
for answer in answers:
self.assertIn(answer.codeId, [100, 95])
def test_update_right_ifmatch_specified(self):
response = self.insert_questionnaire()
self.assertEquals('W/"1"', response['meta']['versionId'])
with open(data_path('questionnaire2.json')) as f2:
questionnaire2 = json.load(f2)
update_response = self.send_put('Questionnaire/%s' % response['id'], questionnaire2,
headers={ 'If-Match': response['meta']['versionId'] },
expected_response_headers = { 'ETag': 'W/"2"'})
questionnaire2['id'] = response['id']
questionnaire2['version'] = '2'
self.assertJsonResponseMatches(questionnaire2, update_response)
self.assertEquals('W/"2"', update_response['meta']['versionId'])
def test_insert(self):
questionnaire_files = (
'questionnaire1.json',
'questionnaire2.json',
'questionnaire_demographics.json',
)
for json_file in questionnaire_files:
with open(data_path(json_file)) as f:
questionnaire = json.load(f)
response = self.send_post('Questionnaire', questionnaire)
questionnaire_id = response['id']
del response['id']
questionnaire['version'] = '1'
self.assertJsonResponseMatches(questionnaire, response)
response = self.send_get('Questionnaire/%s' % questionnaire_id)
del response['id']
self.assertJsonResponseMatches(questionnaire, response)
# Ensure we didn't create codes in the extra system
self.assertIsNone(CodeDao().get_code(PPI_EXTRA_SYSTEM, 'IgnoreThis'))
def test_column_missing(self):
with open(test_data.data_path(
'biobank_samples_missing_field.csv')) as samples_file:
reader = csv.DictReader(samples_file, delimiter='\t')
with self.assertRaises(biobank_samples_pipeline.DataError):
biobank_samples_pipeline._upsert_samples_from_csv(reader)
def create_questionnaire(self, filename):
with open(data_path(filename)) as f:
questionnaire = json.load(f)
response = self.send_post('Questionnaire', questionnaire)
return response['id']
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)
def test_demographic_questionnaire_responses(self):
with FakeClock(TIME_1):
participant_id = self.create_participant()
self.send_consent(participant_id)
questionnaire_id = self.create_questionnaire(
'questionnaire_demographics.json')
with open(data_path('questionnaire_response_demographics.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):
self.send_post(_questionnaire_response_url(participant_id),
resource)
participant = self.send_get('Participant/%s' % participant_id)
summary = self.send_get('Participant/%s/Summary' % participant_id)
expected = {
'ageRange': 'UNSET',
'genderIdentity': 'UNMAPPED',
'firstName': self.first_name,
'lastName': self.last_name,
'email': self.email,
'race': 'UNSET',
'hpoId': 'UNSET',
'awardee': 'UNSET',
'site': 'UNSET',
'organization': 'UNSET',
'education': 'UNSET',
'income': 'UNSET',
'language': 'UNSET',
'sex': 'UNSET',
'sexualOrientation': 'UNSET',
'state': 'UNSET',
'recontactMethod': 'UNSET',
'enrollmentStatus': 'INTERESTED',
'samplesToIsolateDNA': 'UNSET',
'numBaselineSamplesArrived': 0,
'numCompletedPPIModules': 1,
'numCompletedBaselinePPIModules': 1,
'biobankId': participant['biobankId'],
'participantId': participant_id,
'physicalMeasurementsStatus': 'UNSET',
'consentForElectronicHealthRecords': 'UNSET',
'consentForStudyEnrollment': 'SUBMITTED',
'consentForStudyEnrollmentTime': TIME_1.isoformat(),
'consentForCABoR': 'UNSET',
'questionnaireOnFamilyHealth': 'UNSET',
'questionnaireOnHealthcareAccess': 'UNSET',
'questionnaireOnMedicalHistory': 'UNSET',
'questionnaireOnMedications': 'UNSET',
'questionnaireOnOverallHealth': 'UNSET',
'questionnaireOnLifestyle': 'UNSET',
'questionnaireOnTheBasics': 'SUBMITTED',
'questionnaireOnTheBasicsTime': TIME_2.isoformat(),
'biospecimenCollectedSite': 'UNSET',
'biospecimenFinalizedSite': 'UNSET',
'biospecimenProcessedSite': 'UNSET',
'biospecimenSourceSite': 'UNSET',
'physicalMeasurementsCreatedSite': 'UNSET',
'physicalMeasurementsFinalizedSite': 'UNSET',
'biospecimenStatus': 'UNSET',
'sampleOrderStatus1ED04': 'UNSET',
'sampleOrderStatus1ED10': 'UNSET',
'sampleOrderStatus1HEP4': 'UNSET',
'sampleOrderStatus1PST8': 'UNSET',
'sampleOrderStatus1PS08': 'UNSET',
'sampleOrderStatus2PST8': 'UNSET',
'sampleOrderStatus1SAL': 'UNSET',
'sampleOrderStatus1SST8': 'UNSET',
'sampleOrderStatus2SST8': 'UNSET',
'sampleOrderStatus1SS08': 'UNSET',
'sampleOrderStatus1UR10': 'UNSET',
'sampleOrderStatus2ED10': 'UNSET',
'sampleStatus1ED04': 'UNSET',
'sampleStatus1ED10': 'UNSET',
'sampleStatus1HEP4': 'UNSET',
'sampleStatus1PST8': 'UNSET',
'sampleStatus2PST8': 'UNSET',
'sampleStatus1PS08': 'UNSET',
'sampleStatus1SAL': 'UNSET',
'sampleStatus1SST8': 'UNSET',
'sampleStatus2SST8': 'UNSET',
'sampleStatus1SS08': 'UNSET',
'sampleStatus1UR10': 'UNSET',
'sampleStatus2ED10': 'UNSET',
'samplesToIsolateDNA': 'UNSET',
'signUpTime': TIME_1.isoformat(),
'withdrawalStatus': 'NOT_WITHDRAWN',
'suspensionStatus': 'NOT_SUSPENDED',
}
self.assertJsonResponseMatches(expected, summary)
def test_consent_with_extension_language(self):
with FakeClock(TIME_1):
participant_id = self.create_participant()
self.send_consent(participant_id, language='es')
participant = self.send_get('Participant/%s' % participant_id)
summary = self.send_get('Participant/%s/Summary' % participant_id)
expected = {
'ageRange': 'UNSET',
'genderIdentity': 'UNSET',
'firstName': self.first_name,
'lastName': self.last_name,
'email': self.email,
'streetAddress': self.streetAddress,
'streetAddress2': self.streetAddress2,
'race': 'UNSET',
'hpoId': 'UNSET',
'awardee': 'UNSET',
'site': 'UNSET',
'organization': 'UNSET',
'education': 'UNSET',
'income': 'UNSET',
"language": "UNSET",
'sex': 'UNSET',
'sexualOrientation': 'UNSET',
'state': 'UNSET',
'recontactMethod': 'UNSET',
'enrollmentStatus': 'INTERESTED',
'samplesToIsolateDNA': 'UNSET',
'numBaselineSamplesArrived': 0,
'numCompletedPPIModules': 0,
'numCompletedBaselinePPIModules': 0,
'biobankId': participant['biobankId'],
'participantId': participant_id,
'physicalMeasurementsStatus': 'UNSET',
'consentForDvElectronicHealthRecordsSharing': 'UNSET',
'consentForElectronicHealthRecords': 'UNSET',
'consentForStudyEnrollment': 'SUBMITTED',
'consentForStudyEnrollmentTime': TIME_1.isoformat(),
'consentForStudyEnrollmentAuthored': TIME_1.isoformat(),
'consentForCABoR': 'UNSET',
'primaryLanguage': 'es',
'questionnaireOnFamilyHealth': 'UNSET',
'questionnaireOnHealthcareAccess': 'UNSET',
'questionnaireOnMedicalHistory': 'UNSET',
'questionnaireOnMedications': 'UNSET',
'questionnaireOnOverallHealth': 'UNSET',
'questionnaireOnLifestyle': 'UNSET',
'questionnaireOnTheBasics': 'UNSET',
'biospecimenCollectedSite': 'UNSET',
'biospecimenFinalizedSite': 'UNSET',
'biospecimenProcessedSite': 'UNSET',
'biospecimenSourceSite': 'UNSET',
'physicalMeasurementsCreatedSite': 'UNSET',
'physicalMeasurementsFinalizedSite': 'UNSET',
'biospecimenStatus': 'UNSET',
'sampleOrderStatus1ED04': 'UNSET',
'sampleOrderStatus1ED10': 'UNSET',
'sampleOrderStatus1HEP4': 'UNSET',
'sampleOrderStatus1PST8': 'UNSET',
'sampleOrderStatus1PS08': 'UNSET',
'sampleOrderStatus2PST8': 'UNSET',
'sampleOrderStatus1SAL': 'UNSET',
'sampleOrderStatus1SAL2': 'UNSET',
'sampleOrderStatus1SST8': 'UNSET',
'sampleOrderStatus2SST8': 'UNSET',
'sampleOrderStatus1SS08': 'UNSET',
'sampleOrderStatus1UR10': 'UNSET',
'sampleOrderStatus1UR90': 'UNSET',
'sampleOrderStatus2ED10': 'UNSET',
'sampleOrderStatus1CFD9': 'UNSET',
'sampleOrderStatus1PXR2': 'UNSET',
'sampleOrderStatus1ED02': 'UNSET',
'sampleOrderStatusDV1SAL2': 'UNSET',
'sampleStatus1ED04': 'UNSET',
'sampleStatus1ED10': 'UNSET',
'sampleStatus1HEP4': 'UNSET',
'sampleStatus1PST8': 'UNSET',
'sampleStatus2PST8': 'UNSET',
'sampleStatus1PS08': 'UNSET',
'sampleStatus1SAL': 'UNSET',
'sampleStatus1SAL2': 'UNSET',
'sampleStatus1SST8': 'UNSET',
'sampleStatus2SST8': 'UNSET',
'sampleStatus1SS08': 'UNSET',
'sampleStatus1UR10': 'UNSET',
'sampleStatus1UR90': 'UNSET',
'sampleStatus2ED10': 'UNSET',
'sampleStatus1CFD9': 'UNSET',
'sampleStatus1ED02': 'UNSET',
'sampleStatus1PXR2': 'UNSET',
'sampleStatusDV1SAL2': 'UNSET',
'signUpTime': TIME_1.isoformat(),
'withdrawalStatus': 'NOT_WITHDRAWN',
'withdrawalReason': 'UNSET',
'suspensionStatus': 'NOT_SUSPENDED',
'numberDistinctVisits': 0,
'ehrStatus': 'UNSET',
}
self.assertJsonResponseMatches(expected, summary)
# verify if the response is not consent, the primary language will not change
questionnaire_id = self.create_questionnaire(
'questionnaire_family_history.json')
with open(data_path('questionnaire_family_history_resp.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):
self.send_post(_questionnaire_response_url(participant_id),
resource)
summary = self.send_get('Participant/%s/Summary' % participant_id)
self.assertEqual(expected['primaryLanguage'],
summary['primaryLanguage'])
def test_update_before_insert(self):
with open(data_path('questionnaire1.json')) as f:
questionnaire = json.load(f)
self.send_put('Questionnaire/1', questionnaire, expected_status=httplib.BAD_REQUEST)
def insert_questionnaire(self):
with open(data_path('questionnaire1.json')) as f:
questionnaire = json.load(f)
return self.send_post('Questionnaire', questionnaire,
expected_response_headers = { 'ETag': 'W/"1"'})
