diff --git a/microsetta_private_api/admin/admin_impl.py b/microsetta_private_api/admin/admin_impl.py
index b52975852..46af6143c 100644
--- a/microsetta_private_api/admin/admin_impl.py
+++ b/microsetta_private_api/admin/admin_impl.py
@@ -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
@@ -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
diff --git a/microsetta_private_api/admin/sample_summary.py b/microsetta_private_api/admin/sample_summary.py
index 5b3312571..4c22bcb57 100644
--- a/microsetta_private_api/admin/sample_summary.py
+++ b/microsetta_private_api/admin/sample_summary.py
@@ -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:
@@ -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
@@ -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,
@@ -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",
diff --git a/microsetta_private_api/admin/tests/test_admin_repo.py b/microsetta_private_api/admin/tests/test_admin_repo.py
index 40da36a7a..89f5b7bb3 100644
--- a/microsetta_private_api/admin/tests/test_admin_repo.py
+++ b/microsetta_private_api/admin/tests/test_admin_repo.py
@@ -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)
diff --git a/microsetta_private_api/api/microsetta_private_api.yaml b/microsetta_private_api/api/microsetta_private_api.yaml
index 88c96e8dc..ac3b36ea2 100644
--- a/microsetta_private_api/api/microsetta_private_api.yaml
+++ b/microsetta_private_api/api/microsetta_private_api.yaml
@@ -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
diff --git a/microsetta_private_api/repo/admin_repo.py b/microsetta_private_api/repo/admin_repo.py
index ab032ea19..800815257 100644
--- a/microsetta_private_api/repo/admin_repo.py
+++ b/microsetta_private_api/repo/admin_repo.py
@@ -553,6 +553,115 @@ def get_project_barcodes(self, project_id):
cur.execute(query, [project_id, ])
return list([v[0] for v in cur.fetchall()])
+ def get_barcodes_filter(self, kit_ids=None, emails=None,
+ outbound_tracking_numbers=None,
+ inbound_tracking_numbers=None):
+ """Obtain the barcodes based on different filtering criteria.
+
+ Parameters
+ ----------
+ kit_ids : list, optional
+ List of kit IDs to obtain barcodes for.
+ emails : list, optional
+ List of emails to obtain barcodes for.
+ outbound_tracking_numbers : list, optional
+ List of outbound tracking numbers to obtain barcodes for.
+ inbound_tracking_numbers : list, optional
+ List of inbound tracking numbers to obtain barcodes for.
+
+ Returns
+ -------
+ list
+ The list of observed barcodes based on the provided criteria.
+ """
+ query = """
+ SELECT b.barcode
+ FROM barcodes.barcode AS b
+ JOIN barcodes.kit AS k ON b.kit_id = k.kit_id
+ """
+
+ conditions = []
+ params = []
+
+ if kit_ids:
+ conditions.append("k.kit_id IN %s")
+ params.append(tuple(kit_ids))
+
+ if emails:
+ query += """
+ JOIN ag.ag_kit_barcodes AS akb ON akb.barcode = b.barcode
+ JOIN ag.source AS s ON s.id = akb.source_id
+ JOIN ag.account AS a ON s.account_id = a.id
+ """
+ conditions.append("a.email IN %s")
+ params.append(tuple(emails))
+
+ if outbound_tracking_numbers:
+ conditions.append("k.outbound_fedex_tracking IN %s")
+ params.append(tuple(outbound_tracking_numbers))
+
+ if inbound_tracking_numbers:
+ conditions.append("k.inbound_fedex_tracking IN %s")
+ params.append(tuple(inbound_tracking_numbers))
+
+ if conditions:
+ query += " WHERE " + " AND ".join(conditions)
+
+ with self._transaction.cursor() as cur:
+ cur.execute(query, params)
+ barcodes = [row[0] for row in cur.fetchall()]
+
+ return barcodes
+
+ def get_kit_by_barcode(self, barcodes):
+ """Obtain the outbound tracking, inbound tracking numbers,
+ and kit ID associated with a list of barcodes.
+
+ Parameters
+ ----------
+ barcodes : list
+ The list of barcodes to obtain information for.
+
+ Returns
+ -------
+ list of dict
+ A list of dictionaries with outbound tracking,
+ inbound tracking, and kit ID for each barcode.
+ """
+ query = """
+ SELECT
+ b.barcode,
+ k.outbound_fedex_tracking,
+ k.inbound_fedex_tracking,
+ k.kit_id
+ FROM
+ barcodes.barcode b
+ JOIN
+ barcodes.kit k
+ ON
+ b.kit_id = k.kit_id
+ WHERE
+ b.barcode IN %s
+ """
+
+ with self._transaction.cursor() as cur:
+ cur.execute(query, [tuple(barcodes)])
+
+ rows = cur.fetchall()
+
+ if len(rows) == 0:
+ return None
+
+ return [
+ {
+ "barcode": row[0],
+ "outbound_tracking": row[1],
+ "inbound_tracking": row[2],
+ "kit_id": row[3]
+ }
+ for row in rows
+ ]
+
def create_project(self, project):
"""Create a project entry in the database