def test_scan_barcode_success(self):
with Transaction() as t:
# TODO FIXME HACK: Need to build mock barcodes rather than using
# these fixed ones
TEST_BARCODE = '000000001'
TEST_STATUS = "sample-has-inconsistencies"
TEST_NOTES = "THIS IS A UNIT TEST"
admin_repo = AdminRepo(t)
# check that before doing a scan, no scans are recorded for this
diag = admin_repo.retrieve_diagnostics_by_barcode(TEST_BARCODE)
self.assertEqual(len(diag['scans_info']), 0)
# do a scan
admin_repo.scan_barcode(TEST_BARCODE, {
"sample_status": TEST_STATUS,
"technician_notes": TEST_NOTES
})
# show that now a scan is recorded for this barcode
diag = admin_repo.retrieve_diagnostics_by_barcode(TEST_BARCODE)
self.assertEqual(len(diag['scans_info']), 1)
first_scan = diag['scans_info'][0]
self.assertEqual(first_scan['technician_notes'], TEST_NOTES)
self.assertEqual(first_scan['sample_status'], TEST_STATUS)
def test_retrieve_diagnostics_by_barcode_nonexistent(self):
with Transaction() as t:
admin_repo = AdminRepo(t)
# Uhh, should this return a 404 not found or just an empty
# diagnostic object...?
diag = admin_repo.retrieve_diagnostics_by_barcode('NotABarcode :D')
self.assertIsNone(diag)
def search_barcode(token_info, sample_barcode):
validate_admin_access(token_info)
with Transaction() as t:
admin_repo = AdminRepo(t)
diag = admin_repo.retrieve_diagnostics_by_barcode(sample_barcode)
if diag is None:
return jsonify(code=404, message="Barcode not found"), 404
return jsonify(diag), 200
def test_retrieve_diagnostics_by_barcode_nonexistent(self):
with Transaction() as t:
# TODO FIXME HACK: Need to build mock barcodes rather than using
# these fixed ones
admin_repo = AdminRepo(t)
# Uhh, should this return a 404 not found or just an empty
# diagnostic object...?
diag = admin_repo.retrieve_diagnostics_by_barcode('NotABarcode :D')
self.assertIsNone(diag)
def test_retrieve_diagnostics_by_barcode_not_agp(self):
with Transaction() as t:
admin_repo = AdminRepo(t)
diag = admin_repo.retrieve_diagnostics_by_barcode('000044481')
self.assertIsNotNone(diag['barcode_info'])
self.assertIsNone(diag['account'])
self.assertIsNone(diag['source'])
self.assertIsNone(diag['sample'])
self.assertGreater(len(diag['scans_info']), 0)
self.assertGreater(len(diag['projects_info']), 0)
def test_retrieve_diagnostics_by_barcode_wo_extra_info(self):
with Transaction() as t:
# TODO FIXME HACK: Need to build mock barcodes rather than using
# these fixed ones
admin_repo = AdminRepo(t)
diag = admin_repo.retrieve_diagnostics_by_barcode('000033903')
self.assertIsNotNone(diag['barcode_info'])
self.assertIsNone(diag['account'])
self.assertIsNone(diag['source'])
self.assertIsNone(diag['sample'])
self.assertGreater(len(diag['projects_info']), 0)
self.assertEqual(len(diag['scans_info']), 0)
def test_retrieve_diagnostics_by_barcode_w_scans(self):
def make_tz_datetime(y, m, d):
return datetime.datetime(y,
m,
d,
0,
0,
tzinfo=psycopg2.tz.FixedOffsetTimezone(
offset=-420, name=None))
# Non-AGP barcode so no acct, source, or sample;
# also no preexisting scans in test db
test_barcode = '000004531'
first_scan_id = 'f7fd3022-3a9c-4f79-b92c-5cebd83cba38'
second_scan_id = '76aec821-aa28-4dea-a796-2cfd1276f78c'
first_scan = {
"barcode_scan_id": first_scan_id,
"barcode": test_barcode,
"scan_timestamp": make_tz_datetime(2017, 7, 16),
"sample_status": 'no-registered-account',
"technician_notes": "huh?"
}
second_scan = {
"barcode_scan_id": second_scan_id,
"barcode": test_barcode,
"scan_timestamp": make_tz_datetime(2020, 12, 4),
"sample_status": 'sample-is-valid',
"technician_notes": None
}
try:
add_dummy_scan(first_scan)
add_dummy_scan(second_scan)
with Transaction() as t:
admin_repo = AdminRepo(t)
diag = admin_repo.retrieve_diagnostics_by_barcode(test_barcode)
self.assertIsNotNone(diag['barcode_info'])
self.assertIsNone(diag['account'])
self.assertIsNone(diag['source'])
self.assertIsNone(diag['sample'])
self.assertGreater(len(diag['projects_info']), 0)
self.assertEqual(len(diag['scans_info']), 2)
# order matters in the returned vals, so test that
self.assertEqual(diag['scans_info'][0], first_scan)
self.assertEqual(diag['scans_info'][1], second_scan)
self.assertEqual(diag['latest_scan'], second_scan)
finally:
delete_test_scan(first_scan_id)
delete_test_scan(second_scan_id)
def test_scan_barcode(self):
with Transaction() as t:
# TODO FIXME HACK: Need to build mock barcodes rather than using
# these fixed ones
TEST_BARCODE = '000000001'
TEST_STATUS = "sample-has-inconsistencies"
TEST_NOTES = "THIS IS A UNIT TEST"
admin_repo = AdminRepo(t)
diag = admin_repo.retrieve_diagnostics_by_barcode(TEST_BARCODE)
prestatus = diag['barcode_info']['status']
admin_repo.scan_barcode(
TEST_BARCODE,
{
"sample_status": TEST_STATUS,
"technician_notes": TEST_NOTES
}
)
diag = admin_repo.retrieve_diagnostics_by_barcode(TEST_BARCODE)
self.assertEqual(diag['barcode_info']['technician_notes'],
TEST_NOTES)
self.assertEqual(diag['barcode_info']['sample_status'],
TEST_STATUS)
self.assertEqual(diag['barcode_info']['status'],
prestatus)
with self.assertRaises(NotFound):
admin_repo.scan_barcode(
"THIZIZNOTAREALBARCODEISWARE",
{
"sample_status": "Abc",
"technician_notes": "123"
}
)
self.fail("Shouldn't get here")
def test_search_barcode(self):
with Transaction() as t:
# TODO FIXME HACK: Need to build mock barcodes rather than using
# these fixed ones
admin_repo = AdminRepo(t)
diag = admin_repo.retrieve_diagnostics_by_barcode('000038448')
self.assertIsNotNone(diag['barcode'])
self.assertIsNone(diag['account'])
self.assertIsNone(diag['source'])
self.assertIsNotNone(diag['sample'])
self.assertGreater(len(diag['barcode_info']['projects']), 0)
diag = admin_repo.retrieve_diagnostics_by_barcode('000033903')
self.assertIsNotNone(diag['barcode'])
self.assertIsNone(diag['account'])
self.assertIsNone(diag['source'])
self.assertIsNone(diag['sample'])
self.assertGreater(len(diag['barcode_info']['projects']), 0)
# Uhh, should this return a 404 not found or just an empty
# diagnostic object...?
diag = admin_repo.retrieve_diagnostics_by_barcode('NotABarcode :D')
self.assertIsNone(diag)
def per_sample(project, barcodes, strip_sampleid):
summaries = []
with Transaction() as t:
admin_repo = AdminRepo(t)
sample_repo = SampleRepo(t)
template_repo = SurveyTemplateRepo(t)
vs_repo = VioscreenSessionRepo(t)
if project is not None:
project_barcodes = admin_repo.get_project_barcodes(project)
else:
project = 'Unspecified'
if barcodes is None:
barcodes = project_barcodes
for barcode in barcodes:
diag = admin_repo.retrieve_diagnostics_by_barcode(barcode)
if diag is None:
raise NotFound(f"Barcode not found: {barcode}")
sample = diag['sample']
account = diag['account']
source = diag['source']
account_email = None if account is None else account.email
source_email = None
source_type = None if source is None else source.source_type
vio_id = None
if source is not None and source_type == Source.SOURCE_TYPE_HUMAN:
source_email = source.source_data.email
vio_id = template_repo.get_vioscreen_id_if_exists(account.id,
source.id,
sample.id)
# at least one sample has been observed that "is_microsetta",
# described in the barcodes.project_barcode table, but which is
# unexpectedly not present in ag.ag_kit_barcodes
if sample is None:
sample_status = None
sample_site = None
ffq_complete = None
ffq_taken = None
else:
sample_status = sample_repo.get_sample_status(
sample.barcode,
sample._latest_scan_timestamp
)
sample_site = sample.site
ffq_complete, ffq_taken, _ = vs_repo.get_ffq_status_by_sample(
sample.id
)
summary = {
"sampleid": None if strip_sampleid else barcode,
"project": project,
"source-type": source_type,
"site-sampled": sample_site,
"source-email": source_email,
"account-email": account_email,
"vioscreen_username": vio_id,
"ffq-taken": ffq_taken,
"ffq-complete": ffq_complete,
"sample-status": sample_status,
"sample-received": sample_status is not None
}
for status in ["sample-is-valid",
"no-associated-source",
"no-registered-account",
"no-collection-info",
"sample-has-inconsistencies",
"received-unknown-validity"]:
summary[status] = sample_status == status
summaries.append(summary)
return summaries
