Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

sample summary report expansion #585

Merged
merged 13 commits into from
Oct 29, 2024
24 changes: 21 additions & 3 deletions microsetta_private_api/admin/admin_impl.py
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,11 @@
post_daklapack_orders
from microsetta_private_api import localization
from microsetta_private_api.admin.sample_summary import per_sample
from microsetta_private_api.admin.sample_summary import get_barcodes_for
from microsetta_private_api.admin.sample_summary import \
get_barcodes_by_project_id,\
get_barcodes_by_kit_ids, get_barcodes_by_emails,\
get_barcodes_by_outbound_tracking_numbers,\
get_barcodes_by_inbound_tracking_numbers
from microsetta_private_api.util.melissa import verify_address
from microsetta_private_api.util.query_builder_to_sql import build_condition
from werkzeug.exceptions import Unauthorized
Expand Down Expand Up @@ -500,12 +504,26 @@ def query_project_barcode_stats(body, token_info, strip_sampleid):

def query_barcode_stats(body, token_info, strip_sampleid):
validate_admin_access(token_info)

project_id = None

if 'sample_barcodes' in body:
project_id = None
barcodes = body["sample_barcodes"]
elif 'kit_ids' in body:
barcodes = get_barcodes_by_kit_ids(body["kit_ids"])
elif 'emails' in body:
barcodes = get_barcodes_by_emails(body["emails"])
elif 'outbound_tracking_numbers' in body:
barcodes = get_barcodes_by_outbound_tracking_numbers(
body["outbound_tracking_numbers"]
)
elif 'inbound_tracking_numbers' in body:
barcodes = get_barcodes_by_inbound_tracking_numbers(
body["inbound_tracking_numbers"]
)
elif 'project_id' in body:
project_id = body["project_id"]
barcodes = get_barcodes_for(project_id)
barcodes = get_barcodes_by_project_id(project_id)

unprocessed_barcodes = None

Expand Down
63 changes: 58 additions & 5 deletions microsetta_private_api/admin/sample_summary.py
Original file line number Diff line number Diff line change
Expand Up @@ -7,14 +7,33 @@
from werkzeug.exceptions import NotFound


def get_barcodes_for(project_id):
if project_id is None:
raise ValueError("project_id must be defined.")

def get_barcodes_by_project_id(project_id):
with Transaction() as t:
return AdminRepo(t).get_project_barcodes(project_id)


def get_barcodes_by_kit_ids(kit_ids):
with Transaction() as t:
return AdminRepo(t).get_barcodes_filter(kit_ids=kit_ids)


def get_barcodes_by_emails(emails):
with Transaction() as t:
return AdminRepo(t).get_barcodes_filter(emails=emails)


def get_barcodes_by_outbound_tracking_numbers(outbound_tracking_numbers):
with Transaction() as t:
return AdminRepo(t).get_barcodes_filter(
outbound_tracking_numbers=outbound_tracking_numbers)


def get_barcodes_by_inbound_tracking_numbers(inbound_tracking_numbers):
with Transaction() as t:
return AdminRepo(t).get_barcodes_filter(
inbound_tracking_numbers=inbound_tracking_numbers)


def per_sample(project, barcodes, strip_sampleid):
summaries = []
with Transaction() as t:
Expand All @@ -38,6 +57,20 @@ def per_sample(project, barcodes, strip_sampleid):
sample = diag['sample']
account = diag['account']
source = diag['source']
first_scans_info = diag['scans_info']
last_scans_info = diag['latest_scan']
if first_scans_info:
first_scan_timestamp = first_scans_info[0]['scan_timestamp']
first_scan_status = first_scans_info[0]['sample_status']
else:
first_scan_timestamp = None
first_scan_status = None
if last_scans_info:
latest_scan_timestamp = last_scans_info['scan_timestamp']
latest_scan_status = last_scans_info['sample_status']
else:
latest_scan_timestamp = None
latest_scan_status = None

account_email = None if account is None else account.email
source_type = None if source is None else source.source_type
Expand Down Expand Up @@ -94,6 +127,19 @@ def per_sample(project, barcodes, strip_sampleid):
sample_date = None
sample_time = None

kit_by_barcode = admin_repo.get_kit_by_barcode([barcode])

if kit_by_barcode and len(kit_by_barcode) > 0:
info = kit_by_barcode[0]

kit_id_name = info['kit_id']
outbound_fedex_tracking = info['outbound_tracking']
inbound_fedex_tracking = info['inbound_tracking']
else:
kit_id_name = None
outbound_fedex_tracking = None
inbound_fedex_tracking = None

summary = {
"sampleid": None if strip_sampleid else barcode,
"project": barcode_project,
Expand All @@ -106,7 +152,14 @@ def per_sample(project, barcodes, strip_sampleid):
"ffq-taken": ffq_taken,
"ffq-complete": ffq_complete,
"sample-status": sample_status,
"sample-received": sample_status is not None
"sample-received": sample_status is not None,
"first-scan-timestamp": first_scan_timestamp,
"first-scan-status": first_scan_status,
"latest-scan-timestamp": latest_scan_timestamp,
"latest-scan-status": latest_scan_status,
"kit-id": kit_id_name,
"outbound-tracking": outbound_fedex_tracking,
"inbound-tracking": inbound_fedex_tracking,
}

for status in ["sample-is-valid",
Expand Down
134 changes: 134 additions & 0 deletions microsetta_private_api/admin/tests/test_admin_repo.py
Original file line number Diff line number Diff line change
Expand Up @@ -1487,3 +1487,137 @@ def test_update_perk_fulfillment_state(self):
)
obs = cur.fetchone()
self.assertFalse(obs[0])

def test_get_barcodes_filter_kit_ids_success(self):
with Transaction() as t:
setup_sql = """
INSERT INTO barcodes.kit (kit_id, box_id)
VALUES ('test1', '0001e15f-4170-4b28-b111-191cd567c347');

INSERT INTO barcodes.barcode (barcode, kit_id)
VALUES ('00001234', 'test1');
"""
with t.cursor() as cur:
cur.execute(setup_sql)

admin_repo = AdminRepo(t)

barcodes = admin_repo.get_barcodes_filter(kit_ids=['test1'])
self.assertEqual(barcodes, ['00001234'])

def test_get_barcodes_filter_kit_ids_failure(self):
with Transaction() as t:
admin_repo = AdminRepo(t)
barcodes = admin_repo.get_barcodes_filter(kit_ids=['notarealkit'])
self.assertEqual(barcodes, [])

def test_get_barcodes_filter_emails_success(self):
with Transaction() as t:
setup_sql = """
INSERT INTO ag.source (id, account_id,
source_type, source_name)
VALUES ('0003ddfd-4949-4105-90a9-1b1530af5352', %s,
'Human', 'Test Source');
INSERT INTO barcodes.kit (kit_id, box_id)
VALUES ('test1', '0001e15f-4170-4b28-b111-191cd567c347');
INSERT INTO barcodes.barcode (barcode, kit_id)
VALUES ('00001234', 'test1');
INSERT INTO ag.ag_kit_barcodes (barcode, source_id)
VALUES ('00001234', '0003ddfd-4949-4105-90a9-1b1530af5352');
"""
with t.cursor() as cur:
cur.execute(setup_sql, (STANDARD_ACCT_ID,))

admin_repo = AdminRepo(t)

barcodes = admin_repo.get_barcodes_filter(emails=['foo@baz.com'])
self.assertEqual(barcodes, ['00001234'])

def test_get_barcodes_filter_emails_failure(self):
with Transaction() as t:
admin_repo = AdminRepo(t)
barcodes = admin_repo.get_barcodes_filter(
emails=['notarealemail@example.com'])
self.assertEqual(barcodes, [])

def test_get_barcodes_filter_outbound_tracking_success(self):
with Transaction() as t:
setup_sql = """
INSERT INTO barcodes.kit (kit_id, box_id,
outbound_fedex_tracking)
VALUES ('test1', '0001e15f-4170-4b28-b111-191cd567c347',
'12345');
INSERT INTO barcodes.barcode (barcode, kit_id)
VALUES ('00001234', 'test1');
"""
with t.cursor() as cur:
cur.execute(setup_sql)

admin_repo = AdminRepo(t)

barcodes = \
admin_repo.get_barcodes_filter(
outbound_tracking_numbers=['12345'])
self.assertEqual(barcodes, ['00001234'])

def test_get_barcodes_filter_outbound_tracking_failure(self):
with Transaction() as t:
admin_repo = AdminRepo(t)
barcodes = admin_repo.get_barcodes_filter(
outbound_tracking_numbers=['99999'])
self.assertEqual(barcodes, [])

def test_get_barcodes_filter_inbound_tracking_success(self):
with Transaction() as t:
setup_sql = """
INSERT INTO barcodes.kit (kit_id, box_id,
inbound_fedex_tracking)
VALUES ('test1', '0001e15f-4170-4b28-b111-191cd567c347',
'67890');
INSERT INTO barcodes.barcode (barcode, kit_id)
VALUES ('00001234', 'test1');
"""
with t.cursor() as cur:
cur.execute(setup_sql)

admin_repo = AdminRepo(t)

barcodes = admin_repo.get_barcodes_filter(
inbound_tracking_numbers=['67890'])
self.assertEqual(barcodes, ['00001234'])

def test_get_barcodes_filter_inbound_tracking_failure(self):
with Transaction() as t:
admin_repo = AdminRepo(t)
barcodes = admin_repo.get_barcodes_filter(
inbound_tracking_numbers=['99999'])
self.assertEqual(barcodes, [])

def test_get_kit_by_barcode_success(self):
with Transaction() as t:
setup_sql = """
INSERT INTO barcodes.kit (kit_id, box_id)
VALUES ('test1', '0001e15f-4170-4b28-b111-191cd567c348');

INSERT INTO barcodes.barcode (barcode, kit_id)
VALUES ('00001234', 'test1');
"""
with t.cursor() as cur:
cur.execute(setup_sql)

admin_repo = AdminRepo(t)

kit_info = admin_repo.get_kit_by_barcode(['00001234'])
expected = [{
'barcode': '00001234',
'outbound_tracking': None,
'inbound_tracking': None,
'kit_id': 'test1'
}]
self.assertEqual(kit_info, expected)

def test_get_kit_by_barcode_failure(self):
with Transaction() as t:
admin_repo = AdminRepo(t)
kit_info = admin_repo.get_kit_by_barcode(['nonexistent_barcode'])
self.assertIsNone(kit_info)
16 changes: 16 additions & 0 deletions microsetta_private_api/api/microsetta_private_api.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -2998,6 +2998,22 @@ paths:
# not using the defined schema for sample_barcode as it is
# readOnly
type: string
'kit_ids':
type: array
items:
type: string
'emails':
type: array
items:
type: string
'outbound_tracking_numbers':
type: array
items:
type: string
'inbound_tracking_numbers':
type: array
items:
type: string
responses:
'200':
description: Return an object containing a list of dictionaries of sample status for requested accounts
Expand Down
Loading
Loading