Merge pull request #589 from biocore/csymons_sample_summary_updates

Sample Summary Report Adjustments

Author: cassidysymons

microsetta_private_api/admin/admin_impl.py

@@ -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
@@ -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)

microsetta_private_api/admin/sample_summary.py

@@ -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:
@@ -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
 
@@ -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,
@@ -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,
@@ -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",

microsetta_private_api/admin/tests/test_admin_repo.py

@@ -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)
 

microsetta_private_api/api/microsetta_private_api.yaml

@@ -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

microsetta_private_api/repo/admin_repo.py

@@ -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
@@ -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
         -------
@@ -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)
 
@@ -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
         ----------
@@ -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
         """
@@ -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
             ]