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
def query_email_stats(body, token_info):
validate_admin_access(token_info)
email_list = body.get("emails", [])
project = body.get("project")
results = []
with Transaction() as t:
account_repo = AccountRepo(t)
kit_repo = KitRepo(t)
source_repo = SourceRepo(t)
sample_repo = SampleRepo(t)
for email in email_list:
result = {'email': email, 'project': project}
results.append(result)
# can use internal lookup by email, because we have admin access
account = account_repo._find_account_by_email(email) # noqa
if account is None:
result['summary'] = "No Account"
continue
else:
result['account_id'] = account.id
result['creation_time'] = account.creation_time
result['kit_name'] = account.created_with_kit_id
if account.created_with_kit_id is not None:
unused = kit_repo.get_kit_unused_samples(
account.created_with_kit_id
)
if unused is None:
result['unclaimed-samples-in-kit'] = 0
else:
result['unclaimed-samples-in-kit'] = len(unused.samples)
sample_statuses = defaultdict(int)
sources = source_repo.get_sources_in_account(account.id)
samples_in_project = 0
for source in sources:
samples = sample_repo.get_samples_by_source(account.id,
source.id)
for sample in samples:
if project is not None and \
project != "" and \
project not in sample.sample_projects:
continue
samples_in_project += 1
sample_status = sample_repo.get_sample_status(
sample.barcode,
sample._latest_scan_timestamp # noqa
)
if sample_status is None:
sample_status = "never-scanned"
sample_statuses[sample_status] += 1
result.update(sample_statuses)
if result.get('unclaimed-samples-in-kit', 0) > 0:
result['summary'] = 'Possible Unreturned Samples'
elif samples_in_project == 0:
result['summary'] = "No Samples In Specified Project"
elif result.get('sample-is-valid') == samples_in_project:
result['summary'] = 'All Samples Valid'
else:
result['summary'] = 'May Require User Interaction'
return jsonify(results), 200
