def setUp(self):
super(QuestionnaireDaoTest, self).setUp(with_data=False)
self.dao = QuestionnaireDao()
self.questionnaire_history_dao = QuestionnaireHistoryDao()
self.questionnaire_concept_dao = QuestionnaireConceptDao()
self.questionnaire_question_dao = QuestionnaireQuestionDao()
self.code_dao = CodeDao()
self.CODE_1 = Code(codeId=1,
system='a',
value='b',
display=u'c',
topic=u'd',
codeType=CodeType.MODULE,
mapped=True)
self.CODE_2 = Code(codeId=2,
system='a',
value='x',
display=u'y',
codeType=CodeType.MODULE,
mapped=False)
self.CODE_3 = Code(codeId=3,
system='a',
value='z',
display=u'y',
codeType=CodeType.MODULE,
mapped=False)
self.CODE_4 = Code(codeId=4,
system='a',
value='c',
codeType=CodeType.QUESTION,
mapped=True,
parentId=1)
self.CODE_5 = Code(codeId=5,
system='a',
value='d',
codeType=CodeType.QUESTION,
mapped=True,
parentId=2)
self.CODE_6 = Code(codeId=6,
system='a',
value='e',
codeType=CodeType.QUESTION,
mapped=True,
parentId=2)
self.CONCEPT_1 = QuestionnaireConcept(codeId=1)
self.CONCEPT_2 = QuestionnaireConcept(codeId=2)
self.QUESTION_1 = QuestionnaireQuestion(linkId='a',
codeId=4,
repeats=False)
self.QUESTION_2 = QuestionnaireQuestion(linkId='d',
codeId=5,
repeats=True)
self.insert_codes()
def insert_codes(self):
self.code_dao.insert(self.CODE_1)
self.code_dao.insert(self.CODE_2)
self.code_dao.insert(self.CODE_3)
self.code_dao.insert(self.CODE_4)
self.code_dao.insert(self.CODE_5)
self.code_dao.insert(self.CODE_6)
self.code_dao.insert(self.MODULE_CODE_7)
self.code_dao.insert(self.skip_code)
self.consent_code_id = self.code_dao.insert(consent_code()).codeId
self.first_name_code_id = self.code_dao.insert(
first_name_code()).codeId
self.last_name_code_id = self.code_dao.insert(last_name_code()).codeId
self.email_code_id = self.code_dao.insert(email_code()).codeId
self.login_phone_number_code_id = self.code_dao.insert(
login_phone_number_code()).codeId
self.FN_QUESTION = QuestionnaireQuestion(
linkId='fn', codeId=self.first_name_code_id, repeats=False)
self.LN_QUESTION = QuestionnaireQuestion(linkId='ln',
codeId=self.last_name_code_id,
repeats=False)
self.EMAIL_QUESTION = QuestionnaireQuestion(linkId='email',
codeId=self.email_code_id,
repeats=False)
self.LOGIN_PHONE_NUMBER_QUESTION = QuestionnaireQuestion(
linkId='lpn',
codeId=self.login_phone_number_code_id,
repeats=False)
self.first_name = self.fake.first_name()
self.last_name = self.fake.last_name()
self.email = self.fake.email()
self.login_phone_number = self.fake.phone_number()
self.FN_ANSWER = QuestionnaireResponseAnswer(
questionnaireResponseAnswerId=3,
questionnaireResponseId=1,
questionId=3,
valueString=self.first_name)
self.LN_ANSWER = QuestionnaireResponseAnswer(
questionnaireResponseAnswerId=4,
questionnaireResponseId=1,
questionId=4,
valueString=self.last_name)
self.EMAIL_ANSWER = QuestionnaireResponseAnswer(
questionnaireResponseAnswerId=5,
questionnaireResponseId=1,
questionId=5,
valueString=self.email)
self.LOGIN_PHONE_NUMBER_ANSWER = QuestionnaireResponseAnswer(
questionnaireResponseAnswerId=6,
questionnaireResponseId=1,
questionId=6,
valueString=self.login_phone_number)
def _add_questions(cls, q, code_id_map, questions):
for system, code, linkId, repeats in questions:
q.questions.append(
QuestionnaireQuestion(questionnaireId=q.questionnaireId,
questionnaireVersion=q.version,
linkId=linkId,
codeId=code_id_map.get((system, code)),
repeats=repeats if repeats else False))
def _make_history(self, questionnaire, concepts, questions):
history = QuestionnaireHistory()
history.fromdict(questionnaire.asdict(), allow_pk=True)
for concept in concepts:
new_concept = QuestionnaireConcept()
new_concept.fromdict(concept.asdict())
new_concept.questionnaireId = questionnaire.questionnaireId
new_concept.questionnaireVersion = questionnaire.version
history.concepts.append(new_concept)
for question in questions:
new_question = QuestionnaireQuestion()
new_question.fromdict(question.asdict())
new_question.questionnaireId = questionnaire.questionnaireId
new_question.questionnaireVersion = questionnaire.version
history.questions.append(new_question)
return history
from unit_test_util import SqlTestBase, sort_lists
from clock import FakeClock
from werkzeug.exceptions import NotFound, PreconditionFailed
from sqlalchemy.exc import IntegrityError
EXPECTED_CONCEPT_1 = QuestionnaireConcept(questionnaireConceptId=1,
questionnaireId=1,
questionnaireVersion=1,
codeId=1)
EXPECTED_CONCEPT_2 = QuestionnaireConcept(questionnaireConceptId=2,
questionnaireId=1,
questionnaireVersion=1,
codeId=2)
EXPECTED_QUESTION_1 = QuestionnaireQuestion(questionnaireQuestionId=1,
questionnaireId=1,
questionnaireVersion=1,
linkId='a',
codeId=4,
repeats=False)
EXPECTED_QUESTION_2 = QuestionnaireQuestion(questionnaireQuestionId=2,
questionnaireId=1,
questionnaireVersion=1,
linkId='d',
codeId=5,
repeats=True)
TIME = datetime.datetime(2016, 1, 1)
TIME_2 = datetime.datetime(2016, 1, 2)
RESOURCE_1 = '{"x": "y"}'
RESOURCE_1_WITH_ID = '{"x": "y", "version": "1", "id": "1"}'
RESOURCE_2 = '{"x": "z", "version": "2"}'
RESOURCE_2_WITH_ID = '{"x": "z", "version": "2", "id": "1"}'
def test_schema(self):
session = self.database.make_session()
hpo = HPO(hpoId=1,
name='UNSET',
displayName='No organization set',
organizationType=OrganizationType.UNSET)
code_book = CodeBook(codeBookId=1,
created=datetime.datetime.now(),
latest=True,
name="pmi",
system="http://foo/bar",
version="v0.1.1")
session.add(hpo)
session.add(code_book)
session.commit()
organization = Organization(organizationId=1,
externalId='org',
displayName='Organization',
hpoId=1)
session.add(organization)
session.commit()
site = Site(siteId=1,
siteName='site',
googleGroup='*****@*****.**',
mayolinkClientNumber=12345,
organizationId=1)
code1 = Code(codeId=1,
codeBookId=1,
system="a",
value="b",
shortValue="q",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True,
created=datetime.datetime.now())
codeHistory1 = CodeHistory(codeId=1,
codeBookId=1,
system="a",
value="b",
shortValue="q",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True,
created=datetime.datetime.now())
session.add(site)
session.add(code1)
session.add(codeHistory1)
session.commit()
code2 = Code(codeId=2,
codeBookId=1,
parentId=1,
system="a",
value="c",
display=u"X",
topic=u"d",
codeType=CodeType.QUESTION,
mapped=True,
created=datetime.datetime.now())
codeHistory2 = CodeHistory(codeId=2,
codeBookId=1,
parentId=1,
system="a",
value="c",
display=u"X",
topic=u"d",
codeType=CodeType.QUESTION,
mapped=True,
created=datetime.datetime.now())
session.add(code2)
session.add(codeHistory2)
session.commit()
code3 = Code(codeId=3,
codeBookId=1,
parentId=2,
system="a",
value="d",
display=u"Y",
topic=u"d",
codeType=CodeType.ANSWER,
mapped=False,
created=datetime.datetime.now())
codeHistory3 = CodeHistory(codeId=3,
codeBookId=1,
parentId=2,
system="a",
value="d",
display=u"Y",
topic=u"d",
codeType=CodeType.ANSWER,
mapped=False,
created=datetime.datetime.now())
session.add(code3)
session.add(codeHistory3)
session.commit()
session.commit()
p = self._participant_with_defaults(
participantId=1,
version=1,
biobankId=2,
clientId='*****@*****.**',
hpoId=hpo.hpoId,
signUpTime=datetime.datetime.now(),
lastModified=datetime.datetime.now())
ps = self._participant_summary_with_defaults(
participantId=1,
biobankId=2,
lastModified=datetime.datetime.now(),
hpoId=hpo.hpoId,
firstName=self.fake.first_name(),
middleName=self.fake.first_name(),
lastName=self.fake.last_name(),
email=self.fake.email(),
zipCode='78751',
dateOfBirth=datetime.date.today(),
genderIdentityId=1,
consentForStudyEnrollment=QuestionnaireStatus.SUBMITTED,
consentForStudyEnrollmentTime=datetime.datetime.now(),
numBaselineSamplesArrived=2)
p.participantSummary = ps
session.add(p)
ph = self._participant_history_with_defaults(
participantId=1,
biobankId=2,
clientId='*****@*****.**',
hpoId=hpo.hpoId,
signUpTime=datetime.datetime.now(),
lastModified=datetime.datetime.now())
session.add(ph)
session.commit()
session.add(
BiobankStoredSample(biobankStoredSampleId='WEB1234542',
biobankId=p.biobankId,
biobankOrderIdentifier='KIT',
test='1UR10',
confirmed=datetime.datetime.utcnow()))
session.add(
BiobankStoredSample(
biobankStoredSampleId='WEB99999', # Sample ID must be unique.
biobankId=p.
biobankId, # Participant ID and test may be duplicated.
biobankOrderIdentifier='KIT',
test='1UR10',
confirmed=datetime.datetime.utcnow()))
pm = PhysicalMeasurements(physicalMeasurementsId=1,
participantId=1,
created=datetime.datetime.now(),
resource='blah',
final=False,
logPosition=LogPosition())
pm2 = PhysicalMeasurements(physicalMeasurementsId=2,
participantId=1,
created=datetime.datetime.now(),
resource='blah',
final=True,
amendedMeasurementsId=1,
logPosition=LogPosition())
session.add(pm)
session.add(pm2)
session.commit()
q1 = Measurement(measurementId=3,
physicalMeasurementsId=pm.physicalMeasurementsId,
codeSystem='codeSystem',
codeValue='codeValue',
measurementTime=datetime.datetime.now(),
valueCodeSystem='valueCodeSystem',
valueCodeValue='value3')
session.add(q1)
session.commit()
m1 = Measurement(measurementId=1,
physicalMeasurementsId=pm.physicalMeasurementsId,
codeSystem='codeSystem',
codeValue='codeValue',
measurementTime=datetime.datetime.now(),
bodySiteCodeSystem='bodySiteCodeSystem',
bodySiteCodeValue='bodySiteCodeValue',
valueString='a',
valueDecimal=1.2,
valueUnit='cm',
valueCodeSystem='valueCodeSystem',
valueCodeValue='value',
valueDateTime=datetime.datetime.now(),
qualifierId=q1.measurementId)
session.add(m1)
session.commit()
m2 = Measurement(measurementId=2,
physicalMeasurementsId=pm.physicalMeasurementsId,
codeSystem='codeSystem',
codeValue='codeValue',
measurementTime=datetime.datetime.now(),
valueCodeSystem='valueCodeSystem',
valueCodeValue='value2',
parentId=m1.measurementId,
qualifierId=q1.measurementId)
session.add(m2)
session.commit()
q = Questionnaire(questionnaireId=1,
version=1,
created=datetime.datetime.now(),
lastModified=datetime.datetime.now(),
resource='what?')
qh = QuestionnaireHistory(questionnaireId=1,
version=1,
created=datetime.datetime.now(),
lastModified=datetime.datetime.now(),
resource='what?')
qh.questions.append(
QuestionnaireQuestion(questionnaireQuestionId=1,
questionnaireId=1,
questionnaireVersion=1,
linkId="1.2.3",
codeId=2,
repeats=True))
qh.concepts.append(
QuestionnaireConcept(questionnaireConceptId=1,
questionnaireId=1,
questionnaireVersion=1,
codeId=1))
session.add(q)
session.add(qh)
session.commit()
qr = QuestionnaireResponse(questionnaireResponseId=1,
questionnaireId=1,
questionnaireVersion=1,
participantId=1,
created=datetime.datetime.now(),
resource='blah')
qr.answers.append(
QuestionnaireResponseAnswer(questionnaireResponseAnswerId=1,
questionnaireResponseId=1,
questionId=1,
endTime=datetime.datetime.now(),
valueSystem='a',
valueCodeId=3,
valueDecimal=123,
valueString=self.fake.first_name(),
valueDate=datetime.date.today()))
session.add(qr)
session.commit()
mv = MetricsVersion(metricsVersionId=1,
inProgress=False,
complete=True,
date=datetime.datetime.utcnow(),
dataVersion=1)
session.add(mv)
session.commit()
mb = MetricsBucket(metricsVersionId=1,
date=datetime.date.today(),
hpoId='PITT',
metrics='blah')
session.add(mb)
session.commit()
def setUp(self):
super(QuestionnaireResponseDaoTest, self).setUp()
self.code_dao = CodeDao()
self.participant_dao = ParticipantDao()
self.questionnaire_dao = QuestionnaireDao()
self.questionnaire_response_dao = QuestionnaireResponseDao()
self.questionnaire_response_answer_dao = QuestionnaireResponseAnswerDao(
)
self.participant_summary_dao = ParticipantSummaryDao()
self.CODE_1 = Code(codeId=1,
system=PPI_SYSTEM,
value=GENDER_IDENTITY_QUESTION_CODE,
display=u'c',
topic=u'd',
codeType=CodeType.QUESTION,
mapped=True)
self.CODE_2 = Code(codeId=2,
system='a',
value='x',
display=u'y',
codeType=CodeType.QUESTION,
mapped=False)
self.CODE_3 = Code(codeId=3,
system='a',
value='c',
codeType=CodeType.ANSWER,
mapped=True,
parentId=1)
self.CODE_4 = Code(codeId=4,
system='a',
value='d',
codeType=CodeType.ANSWER,
mapped=True,
parentId=2)
self.CODE_5 = Code(codeId=5,
system='a',
value='e',
codeType=CodeType.ANSWER,
mapped=False,
parentId=1)
self.CODE_6 = Code(codeId=6,
system='a',
value='f',
codeType=CodeType.ANSWER,
mapped=True,
parentId=1)
self.MODULE_CODE_7 = Code(codeId=7,
system=PPI_SYSTEM,
value=THE_BASICS_PPI_MODULE,
codeType=CodeType.MODULE,
mapped=True)
self.CONCEPT_1 = QuestionnaireConcept(codeId=7)
self.CODE_1_QUESTION_1 = QuestionnaireQuestion(linkId='a',
codeId=1,
repeats=False)
self.CODE_2_QUESTION = QuestionnaireQuestion(linkId='d',
codeId=2,
repeats=True)
# Same code as question 1
self.CODE_1_QUESTION_2 = QuestionnaireQuestion(linkId='x',
codeId=1,
repeats=False)
self.skip_code = Code(codeId=8,
system=PPI_SYSTEM,
value=PMI_SKIP_CODE,
mapped=True,
codeType=CodeType.ANSWER)
config.override_setting(config.CONSENT_PDF_BUCKET, [_FAKE_BUCKET])