def test_get_ffq_status_by_sample(self):
session_copy = VIOSCREEN_SESSION.copy()
session_copy.username = VIOSCREEN_USERNAME1
with Transaction() as t:
r = VioscreenSessionRepo(t)
r.upsert_session(session_copy)
session = r.get_sessions_by_username(VIOSCREEN_USERNAME1)[0]
obs = r.get_ffq_status_by_sample(BARCODE_UUID_NOTIN_REGISTRY)
self.assertEqual(obs, (False, False, None))
session.status = 'Finished'
session.endDate = _to_dt(2, 1, 1970)
r.upsert_session(session)
# enumerate the empirically observed states from vioscreen
# (is_complete, has_taken, exact_status)
obs = r.get_ffq_status_by_sample(BARCODE_UUID_FOR_VIOSESSION)
self.assertEqual(obs, (True, True, 'Finished'))
session.status = 'Started'
session.endDate = None
r.upsert_session(session)
obs = r.get_ffq_status_by_sample(BARCODE_UUID_FOR_VIOSESSION)
self.assertEqual(obs, (False, True, 'Started'))
session.status = 'New'
r.upsert_session(session)
obs = r.get_ffq_status_by_sample(BARCODE_UUID_FOR_VIOSESSION)
self.assertEqual(obs, (False, False, 'New'))
session.status = 'Review'
r.upsert_session(session)
obs = r.get_ffq_status_by_sample(BARCODE_UUID_FOR_VIOSESSION)
self.assertEqual(obs, (False, True, 'Review'))
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