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.

Sign up for GitHub

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 Adjustments #589

Merged
merged 1 commit into from
Dec 2, 2024
Merged

Sample Summary Report Adjustments #589

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 5 additions & 1 deletion microsetta_private_api/admin/admin_impl.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
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
get_barcodes_by_inbound_tracking_numbers, get_barcodes_by_dak_order_ids
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 @@ -521,6 +521,10 @@ def query_barcode_stats(body, token_info, strip_sampleid):
barcodes = get_barcodes_by_inbound_tracking_numbers(
body["inbound_tracking_numbers"]
)
elif 'dak_order_ids' in body:
barcodes = get_barcodes_by_dak_order_ids(
body['dak_order_ids']
)
elif 'project_id' in body:
project_id = body["project_id"]
barcodes = get_barcodes_by_project_id(project_id)
Expand Down
14 changes: 14 additions & 0 deletions microsetta_private_api/admin/sample_summary.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,13 @@ def get_barcodes_by_inbound_tracking_numbers(inbound_tracking_numbers):
inbound_tracking_numbers=inbound_tracking_numbers)


def get_barcodes_by_dak_order_ids(dak_order_ids):
with Transaction() as t:
return AdminRepo(t).get_barcodes_filter(
dak_order_ids=dak_order_ids
)


def per_sample(project, barcodes, strip_sampleid):
summaries = []
with Transaction() as t:
Expand Down Expand Up @@ -73,6 +80,8 @@ def per_sample(project, barcodes, strip_sampleid):
latest_scan_status = None

account_email = None if account is None else account.email
account_fname = None if account is None else account.first_name
account_lname = None if account is None else account.last_name
source_type = None if source is None else source.source_type
vio_id = None

Expand Down Expand Up @@ -135,10 +144,12 @@ def per_sample(project, barcodes, strip_sampleid):
kit_id_name = info['kit_id']
outbound_fedex_tracking = info['outbound_tracking']
inbound_fedex_tracking = info['inbound_tracking']
daklapack_order_id = info['dak_order_id']
else:
kit_id_name = None
outbound_fedex_tracking = None
inbound_fedex_tracking = None
daklapack_order_id = None

summary = {
"sampleid": None if strip_sampleid else barcode,
Expand All @@ -148,6 +159,8 @@ def per_sample(project, barcodes, strip_sampleid):
"sample-date": sample_date,
"sample-time": sample_time,
"account-email": account_email,
"account-first-name": account_fname,
"account-last-name": account_lname,
"vioscreen_username": vio_id,
"ffq-taken": ffq_taken,
"ffq-complete": ffq_complete,
Expand All @@ -160,6 +173,7 @@ def per_sample(project, barcodes, strip_sampleid):
"kit-id": kit_id_name,
"outbound-tracking": outbound_fedex_tracking,
"inbound-tracking": inbound_fedex_tracking,
"daklapack-order-id": daklapack_order_id
}

for status in ["sample-is-valid",
Expand Down
116 changes: 103 additions & 13 deletions microsetta_private_api/admin/tests/test_admin_repo.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1593,26 +1593,116 @@ def test_get_barcodes_filter_inbound_tracking_failure(self):
inbound_tracking_numbers=['99999'])
self.assertEqual(barcodes, [])

def test_get_kit_by_barcode_success(self):
def test_get_barcodes_filter_dak_order_ids_success(self):
dak_order_id = 'd77e111e-ded2-4817-9240-7e94c6712102'
kit_id = 'test1'
kit_uuid = '2fd79f11-f377-4fa8-99f3-cc184192180b'
outbound_tracking = 'FEDEX_OUT_1234'
inbound_tracking = 'FEDEX_IN_5678'
barcode = '00001234'

with Transaction() as t:
setup_sql = """
INSERT INTO barcodes.kit (kit_id, box_id)
VALUES ('test1', '0001e15f-4170-4b28-b111-191cd567c348');
with t.cursor() as cur:
# Insert Daklapack order
cur.execute(
"INSERT INTO barcodes.daklapack_order "
"(dak_order_id, submitter_acct_id, order_json) "
"VALUES (%s, %s, '{}')",
(dak_order_id, ADMIN_ACCT_ID)
)

INSERT INTO barcodes.barcode (barcode, kit_id)
VALUES ('00001234', 'test1');
"""
# Insert Kit
cur.execute(
"INSERT INTO barcodes.kit "
"(kit_uuid, kit_id, box_id, outbound_fedex_tracking, "
"inbound_fedex_tracking) "
"VALUES (%s, %s, '0001e15f-4170-4b28-b111-191cd567c348', "
"%s, %s)",
(kit_uuid, kit_id, outbound_tracking, inbound_tracking)
)

# Insert Daklapack order to kit record
cur.execute(
"INSERT INTO barcodes.daklapack_order_to_kit "
"(dak_order_id, kit_uuid) "
"VALUES (%s, %s)",
(dak_order_id, kit_uuid)
)

# Insert barcode
cur.execute(
"INSERT INTO barcodes.barcode (barcode, kit_id) "
"VALUES (%s, %s)",
(barcode, kit_id)
)

admin_repo = AdminRepo(t)
barcodes = admin_repo.get_barcodes_filter(
dak_order_ids=[dak_order_id]
)
self.assertEqual(barcodes, [barcode])

def test_get_barcodes_filter_dak_order_ids_failure(self):
dak_order_id = 'd77e111e-ded2-4817-9240-7e94c6712102'
with Transaction() as t:
admin_repo = AdminRepo(t)
barcodes = admin_repo.get_barcodes_filter(
dak_order_ids=[dak_order_id]
)
self.assertEqual(barcodes, [])

def test_get_kit_by_barcode_success(self):
dak_order_id = 'd77e111e-ded2-4817-9240-7e94c6712102'
kit_id = 'test1'
kit_uuid = '2fd79f11-f377-4fa8-99f3-cc184192180b'
outbound_tracking = 'FEDEX_OUT_1234'
inbound_tracking = 'FEDEX_IN_5678'
barcode = '00001234'

with Transaction() as t:
with t.cursor() as cur:
cur.execute(setup_sql)
# Insert Daklapack order
cur.execute(
"INSERT INTO barcodes.daklapack_order "
"(dak_order_id, submitter_acct_id, order_json) "
"VALUES (%s, %s, '{}')",
(dak_order_id, ADMIN_ACCT_ID)
)

# Insert Kit
cur.execute(
"INSERT INTO barcodes.kit "
"(kit_uuid, kit_id, box_id, outbound_fedex_tracking, "
"inbound_fedex_tracking) "
"VALUES (%s, %s, '0001e15f-4170-4b28-b111-191cd567c348', "
"%s, %s)",
(kit_uuid, kit_id, outbound_tracking, inbound_tracking)
)

# Insert Daklapack order to kit record
cur.execute(
"INSERT INTO barcodes.daklapack_order_to_kit "
"(dak_order_id, kit_uuid) "
"VALUES (%s, %s)",
(dak_order_id, kit_uuid)
)

# Insert barcode
cur.execute(
"INSERT INTO barcodes.barcode (barcode, kit_id) "
"VALUES (%s, %s)",
(barcode, kit_id)
)

admin_repo = AdminRepo(t)

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

Expand Down
4 changes: 4 additions & 0 deletions microsetta_private_api/api/microsetta_private_api.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3014,6 +3014,10 @@ paths:
type: array
items:
type: string
'dak_order_ids':
type: array
items:
type: string
responses:
'200':
description: Return an object containing a list of dictionaries of sample status for requested accounts
Expand Down
25 changes: 21 additions & 4 deletions microsetta_private_api/repo/admin_repo.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -555,7 +555,8 @@ def get_project_barcodes(self, project_id):

def get_barcodes_filter(self, kit_ids=None, emails=None,
outbound_tracking_numbers=None,
inbound_tracking_numbers=None):
inbound_tracking_numbers=None,
dak_order_ids=None):
"""Obtain the barcodes based on different filtering criteria.

Parameters
Expand All @@ -568,6 +569,8 @@ def get_barcodes_filter(self, kit_ids=None, emails=None,
List of outbound tracking numbers to obtain barcodes for.
inbound_tracking_numbers : list, optional
List of inbound tracking numbers to obtain barcodes for.
dak_order_ids : list, optional
List of Daklapack order IDs to obtain barcodes for

Returns
-------
Expand Down Expand Up @@ -604,6 +607,14 @@ def get_barcodes_filter(self, kit_ids=None, emails=None,
conditions.append("k.inbound_fedex_tracking IN %s")
params.append(tuple(inbound_tracking_numbers))

if dak_order_ids:
query += """
JOIN barcodes.daklapack_order_to_kit dotk
ON dotk.kit_uuid = k.kit_uuid
"""
conditions.append("dotk.dak_order_id IN %s")
params.append(tuple(dak_order_ids))

if conditions:
query += " WHERE " + " AND ".join(conditions)

Expand All @@ -615,7 +626,7 @@ def get_barcodes_filter(self, kit_ids=None, emails=None,

def get_kit_by_barcode(self, barcodes):
"""Obtain the outbound tracking, inbound tracking numbers,
and kit ID associated with a list of barcodes.
kit ID, and Daklapack order ID associated with a list of barcodes.

Parameters
----------
Expand All @@ -633,13 +644,18 @@ def get_kit_by_barcode(self, barcodes):
b.barcode,
k.outbound_fedex_tracking,
k.inbound_fedex_tracking,
k.kit_id
k.kit_id,
dotk.dak_order_id
FROM
barcodes.barcode b
JOIN
barcodes.kit k
ON
b.kit_id = k.kit_id
LEFT JOIN
barcodes.daklapack_order_to_kit dotk
ON
dotk.kit_uuid = k.kit_uuid
WHERE
b.barcode IN %s
"""
Expand All @@ -657,7 +673,8 @@ def get_kit_by_barcode(self, barcodes):
"barcode": row[0],
"outbound_tracking": row[1],
"inbound_tracking": row[2],
"kit_id": row[3]
"kit_id": row[3],
"dak_order_id": row[4]
}
for row in rows
]
Expand Down
Loading