def test_update_from_samples_changed_tests(self):
baseline_tests = ["1PST8", "2PST8"]
config.override_setting(config.BASELINE_SAMPLE_TEST_CODES, baseline_tests)
self.dao.update_from_biobank_stored_samples() # safe noop
participant = self._insert(Participant(participantId=1, biobankId=11))
self.assertEquals(self.dao.get(participant.participantId).numBaselineSamplesArrived, 0)
sample_dao = BiobankStoredSampleDao()
def add_sample(test_code, sample_id):
TIME = datetime.datetime(2018, 3, 2)
sample_dao.insert(BiobankStoredSample(
biobankStoredSampleId=sample_id, biobankId=participant.biobankId,
biobankOrderIdentifier='KIT', test=test_code, confirmed=TIME))
add_sample(baseline_tests[0], '11111')
add_sample(baseline_tests[1], '22223')
self.dao.update_from_biobank_stored_samples()
summary = self.dao.get(participant.participantId)
init_last_modified = summary.lastModified
self.assertEquals(summary.numBaselineSamplesArrived, 2)
# sleep 1 sec to make lastModified different
time.sleep(1)
# Simulate removal of one of the baseline tests from config.json.
baseline_tests.pop()
config.override_setting(config.BASELINE_SAMPLE_TEST_CODES, baseline_tests)
self.dao.update_from_biobank_stored_samples()
summary = self.dao.get(participant.participantId)
self.assertEquals(summary.numBaselineSamplesArrived, 1)
self.assertNotEqual(init_last_modified, summary.lastModified)
def test_only_update_dna_sample(self):
dna_tests = ["1ED10", "1SAL2"]
config.override_setting(config.DNA_SAMPLE_TEST_CODES, dna_tests)
self.dao.update_from_biobank_stored_samples() # safe noop
p_dna_samples = self._insert(Participant(participantId=1, biobankId=11))
self.assertEquals(self.dao.get(p_dna_samples.participantId).samplesToIsolateDNA, None)
self.assertEquals(
self.dao.get(p_dna_samples.participantId).enrollmentStatusCoreStoredSampleTime, None)
self.assertEquals(
self.dao.get(p_dna_samples.participantId).enrollmentStatusCoreOrderedSampleTime, None)
sample_dao = BiobankStoredSampleDao()
def add_sample(participant, test_code, sample_id, confirmed_time):
sample_dao.insert(BiobankStoredSample(
biobankStoredSampleId=sample_id, biobankId=participant.biobankId,
biobankOrderIdentifier='KIT', test=test_code, confirmed=confirmed_time))
confirmed_time_0 = datetime.datetime(2018, 3, 1)
add_sample(p_dna_samples, dna_tests[0], '11111', confirmed_time_0)
self.dao.update_from_biobank_stored_samples()
self.assertEquals(self.dao.get(p_dna_samples.participantId).samplesToIsolateDNA,
SampleStatus.RECEIVED)
# only update dna sample will not update enrollmentStatusCoreStoredSampleTime
self.assertEquals(
self.dao.get(p_dna_samples.participantId).enrollmentStatusCoreStoredSampleTime, None)
self.assertEquals(
self.dao.get(p_dna_samples.participantId).enrollmentStatusCoreOrderedSampleTime, None)
def setUp(self):
super(MarkGhostParticipantsTest, self).setUp(use_mysql=True)
NdbTestBase.doSetUp(self)
TestBase.setup_fake(self)
config.override_setting(config.GHOST_ID_BUCKET, [_FAKE_BUCKET])
self.participant_dao = ParticipantDao()
self.p_history = ParticipantHistoryDao()
def test_update_from_samples(self):
# baseline_tests = ['BASELINE1', 'BASELINE2']
baseline_tests = ["1PST8", "2PST8"]
config.override_setting(config.BASELINE_SAMPLE_TEST_CODES, baseline_tests)
self.dao.update_from_biobank_stored_samples() # safe noop
p_baseline_samples = self._insert(Participant(participantId=1, biobankId=11))
p_mixed_samples = self._insert(Participant(participantId=2, biobankId=22))
p_no_samples = self._insert(Participant(participantId=3, biobankId=33))
p_unconfirmed = self._insert(Participant(participantId=4, biobankId=44))
self.assertEquals(self.dao.get(p_baseline_samples.participantId).numBaselineSamplesArrived, 0)
def get_p_baseline_last_modified():
return self.dao.get(p_baseline_samples.participantId).lastModified
p_baseline_last_modified1 = get_p_baseline_last_modified()
sample_dao = BiobankStoredSampleDao()
def add_sample(participant, test_code, sample_id):
TIME = datetime.datetime(2018, 3, 2)
sample_dao.insert(BiobankStoredSample(
biobankStoredSampleId=sample_id, biobankId=participant.biobankId,
biobankOrderIdentifier='KIT', test=test_code, confirmed=TIME))
add_sample(p_baseline_samples, baseline_tests[0], '11111')
add_sample(p_baseline_samples, baseline_tests[1], '22223')
add_sample(p_mixed_samples, baseline_tests[0], '11112')
add_sample(p_mixed_samples, 'NOT1', '44441')
# add unconfirmed sample
sample_dao.insert(BiobankStoredSample(biobankStoredSampleId=55555,
biobankId=p_unconfirmed.biobankId,
biobankOrderIdentifier='KIT', test=baseline_tests[1],
confirmed=None))
# sleep 1 sec to make lastModified different
time.sleep(1)
self.dao.update_from_biobank_stored_samples()
p_baseline_last_modified2 = get_p_baseline_last_modified()
self.assertNotEquals(p_baseline_last_modified2, p_baseline_last_modified1)
self.assertEquals(self.dao.get(p_baseline_samples.participantId).numBaselineSamplesArrived, 2)
self.assertEquals(self.dao.get(p_mixed_samples.participantId).numBaselineSamplesArrived, 1)
self.assertEquals(self.dao.get(p_no_samples.participantId).numBaselineSamplesArrived, 0)
self.assertEquals(self.dao.get(p_unconfirmed.participantId).numBaselineSamplesArrived, 0)
M_baseline_samples = self._insert(Participant(participantId=9, biobankId=99))
add_sample(M_baseline_samples, baseline_tests[0], '999')
M_first_update = self.dao.get(M_baseline_samples.participantId)
# sleep 1 sec to make lastModified different
time.sleep(1)
self.dao.update_from_biobank_stored_samples()
add_sample(M_baseline_samples, baseline_tests[1], '9999')
M_second_update = self.dao.get(M_baseline_samples.participantId)
# sleep 1 sec to make lastModified different
time.sleep(1)
self.dao.update_from_biobank_stored_samples()
self.assertNotEqual(M_first_update.lastModified, M_second_update.lastModified)
self.assertEquals(get_p_baseline_last_modified(), p_baseline_last_modified2)
def test_update_from_samples(self):
# baseline_tests = ['BASELINE1', 'BASELINE2']
baseline_tests = ["1PST8", "2PST8"]
config.override_setting(config.BASELINE_SAMPLE_TEST_CODES,
baseline_tests)
self.dao.update_from_biobank_stored_samples() # safe noop
p_baseline_samples = self._insert(
Participant(participantId=1, biobankId=11))
p_mixed_samples = self._insert(
Participant(participantId=2, biobankId=22))
p_no_samples = self._insert(Participant(participantId=3, biobankId=33))
self.assertEquals(
self.dao.get(
p_baseline_samples.participantId).numBaselineSamplesArrived, 0)
sample_dao = BiobankStoredSampleDao()
def add_sample(participant, test_code, sample_id):
TIME = datetime.datetime(2018, 3, 2)
sample_dao.insert(
BiobankStoredSample(biobankStoredSampleId=sample_id,
biobankId=participant.biobankId,
biobankOrderIdentifier='KIT',
test=test_code,
confirmed=TIME))
add_sample(p_baseline_samples, baseline_tests[0], '11111')
add_sample(p_baseline_samples, baseline_tests[1], '22223')
add_sample(p_mixed_samples, baseline_tests[0], '11112')
add_sample(p_mixed_samples, 'NOT1', '44441')
self.dao.update_from_biobank_stored_samples()
test_last_modified_doesnt_change_below = self.dao.get(1).lastModified
self.assertEquals(
self.dao.get(
p_baseline_samples.participantId).numBaselineSamplesArrived, 2)
self.assertEquals(
self.dao.get(
p_mixed_samples.participantId).numBaselineSamplesArrived, 1)
self.assertEquals(
self.dao.get(p_no_samples.participantId).numBaselineSamplesArrived,
0)
M_baseline_samples = self._insert(
Participant(participantId=9, biobankId=99))
add_sample(M_baseline_samples, baseline_tests[0], '999')
M_first_update = self.dao.get(M_baseline_samples.participantId)
self.dao.update_from_biobank_stored_samples()
add_sample(M_baseline_samples, baseline_tests[1], '9999')
M_second_update = self.dao.get(M_baseline_samples.participantId)
self.dao.update_from_biobank_stored_samples()
p_baseline_update = self.dao.get(p_baseline_samples.participantId)
self.assertNotEqual(M_first_update.lastModified,
M_second_update.lastModified)
self.assertEquals(p_baseline_update.lastModified,
test_last_modified_doesnt_change_below)
def test_nonprod(self):
# The dev config is isntalled by default for tests, reset.
config.override_setting(config.ALLOW_NONPROD_REQUESTS, False)
with self.assertRaises(Forbidden):
not_in_prod()
config.override_setting(config.ALLOW_NONPROD_REQUESTS, True)
not_in_prod()
def setUp(self):
super(BiobankSamplesPipelineTest, self).setUp(use_mysql=True)
NdbTestBase.doSetUp(self)
TestBase.setup_fake(self)
config.override_setting(config.BASELINE_SAMPLE_TEST_CODES,
_BASELINE_TESTS)
# Everything is stored as a list, so override bucket name as a 1-element list.
config.override_setting(config.BIOBANK_SAMPLES_BUCKET_NAME,
[_FAKE_BUCKET])
self.participant_dao = ParticipantDao()
def setUp(self):
super(MainTest, self).setUp()
config.override_setting(config.INTERNAL_STATUS_MAIL_SENDER,
['*****@*****.**'])
config.override_setting(config.INTERNAL_STATUS_MAIL_RECIPIENTS,
['*****@*****.**'])
config.override_setting(config.BIOBANK_STATUS_MAIL_RECIPIENTS,
['*****@*****.**'])
def test_update_from_samples(self):
baseline_tests = ['BASELINE1', 'BASELINE2']
config.override_setting(config.BASELINE_SAMPLE_TEST_CODES,
baseline_tests)
self.dao.update_from_biobank_stored_samples() # safe noop
p_baseline_samples = self._insert(
Participant(participantId=1, biobankId=11))
p_mixed_samples = self._insert(
Participant(participantId=2, biobankId=22))
p_no_samples = self._insert(Participant(participantId=3, biobankId=33))
self.assertEquals(
self.dao.get(
p_baseline_samples.participantId).numBaselineSamplesArrived, 0)
sample_dao = BiobankStoredSampleDao()
def add_sample(participant, test_code, sample_id):
sample_dao.insert(
BiobankStoredSample(biobankStoredSampleId=sample_id,
biobankId=participant.biobankId,
test=test_code))
add_sample(p_baseline_samples, baseline_tests[0], '11111')
add_sample(p_baseline_samples, baseline_tests[1], '22223')
add_sample(p_mixed_samples, baseline_tests[0], '11112')
add_sample(p_mixed_samples, 'NOT1', '44441')
self.dao.update_from_biobank_stored_samples()
self.assertEquals(
self.dao.get(
p_baseline_samples.participantId).numBaselineSamplesArrived, 2)
self.assertEquals(
self.dao.get(
p_mixed_samples.participantId).numBaselineSamplesArrived, 1)
self.assertEquals(
self.dao.get(p_no_samples.participantId).numBaselineSamplesArrived,
0)
def setUp(self):
super(GenomicPipelineTest, self).setUp(use_mysql=True)
NdbTestBase.doSetUp(self)
TestBase.setup_fake(self)
# Everything is stored as a list, so override bucket name as a 1-element list.
config.override_setting(config.GENOMIC_SET_BUCKET_NAME, [_FAKE_BUCKET])
config.override_setting(config.BIOBANK_SAMPLES_BUCKET_NAME,
[_FAKE_BIOBANK_SAMPLE_BUCKET])
config.override_setting(config.GENOMIC_BIOBANK_MANIFEST_FOLDER_NAME,
[_FAKE_BUCKET_FOLDER])
config.override_setting(
config.GENOMIC_BIOBANK_MANIFEST_RESULT_FOLDER_NAME,
[_FAKE_BUCKET_RESULT_FOLDER])
self.participant_dao = ParticipantDao()
self.summary_dao = ParticipantSummaryDao()
self._participant_i = 1
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])
def test_make_update_organizations_job(self, mock_build,
mock_get_application_id):
mock_build.return_value = 'foo'
mock_get_application_id.return_value = 'app_id'
config.override_setting(config.EHR_STATUS_BIGQUERY_VIEW_ORGANIZATION,
['some_view'])
job = offline.update_ehr_status.make_update_organizations_job()
self.assertNotEqual(job, None)
config.override_setting(config.EHR_STATUS_BIGQUERY_VIEW_ORGANIZATION,
['a', 'b'])
job = offline.update_ehr_status.make_update_organizations_job()
self.assertEqual(job, None)
config.override_setting(config.EHR_STATUS_BIGQUERY_VIEW_ORGANIZATION,
[''])
job = offline.update_ehr_status.make_update_organizations_job()
self.assertEqual(job, None)
config.override_setting(config.EHR_STATUS_BIGQUERY_VIEW_ORGANIZATION,
[None])
job = offline.update_ehr_status.make_update_organizations_job()
self.assertEqual(job, None)
config.override_setting(config.EHR_STATUS_BIGQUERY_VIEW_PARTICIPANT,
[])
job = offline.update_ehr_status.make_update_participant_summaries_job()
self.assertEqual(job, None)
config.override_setting(config.EHR_STATUS_BIGQUERY_VIEW_PARTICIPANT,
None)
job = offline.update_ehr_status.make_update_participant_summaries_job()
self.assertEqual(job, None)
