added queries for sample summary table

microsetta_private_api/admin/admin_impl.py

@@ -29,9 +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_by_project_id,\
+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
+    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
@@ -515,10 +517,12 @@ def query_barcode_stats(body, token_info, strip_sampleid):
         barcodes = get_barcodes_by_emails(body["emails"])
     elif 'outbound_tracking_numbers' in body:
         project_id = None
-        barcodes = get_barcodes_by_outbound_tracking_numbers(body["outbound_tracking_numbers"])
+        barcodes = get_barcodes_by_outbound_tracking_numbers
+        (body["outbound_tracking_numbers"])
     elif 'inbound_tracking_numbers' in body:
         project_id = None
-        barcodes = get_barcodes_by_inbound_tracking_numbers(body["inbound_tracking_numbers"])
+        barcodes = get_barcodes_by_inbound_tracking_numbers
+        (body["inbound_tracking_numbers"])
     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

@@ -14,34 +14,40 @@ 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):
     if kit_ids is None:
         raise ValueError("kit_id must be defined.")
 
     with Transaction() as t:
         return AdminRepo(t).get_kit_barcodes(kit_ids)
-
+
+
 def get_barcodes_by_emails(emails):
     if emails is None:
         raise ValueError("email must be defined.")
 
     with Transaction() as t:
         return AdminRepo(t).get_email_barcodes(emails)
-
+
+
 def get_barcodes_by_outbound_tracking_numbers(outbound_tracking_numbers):
     if outbound_tracking_numbers is None:
         raise ValueError("outbound_tracking_numbers must be defined.")
 
     with Transaction() as t:
-        return AdminRepo(t).get_outbound_tracking_barcodes(outbound_tracking_numbers)
-
+        return AdminRepo(t).get_outbound_tracking_barcodes
+    (outbound_tracking_numbers)
+
+
 def get_barcodes_by_inbound_tracking_numbers(inbound_tracking_numbers):
     if inbound_tracking_numbers is None:
         raise ValueError("inbound_tracking_numbers must be defined.")
 
     with Transaction() as t:
-        return AdminRepo(t).get_inbound_tracking_barcodes(inbound_tracking_numbers)
+        return AdminRepo(t).get_inbound_tracking_barcodes
+    (inbound_tracking_numbers)
 
 
 def per_sample(project, barcodes, strip_sampleid):
@@ -113,10 +119,16 @@ def per_sample(project, barcodes, strip_sampleid):
                 ffq_complete, ffq_taken, _ = vs_repo.get_ffq_status_by_sample(
                     sample.id
                 )
-            
+
             kit_id_name = kit_repo.get_kit_id_name_by_barcode(barcode)
-            outbound_fedex_tracking = admin_repo.get_outbound_tracking_by_barcodes(barcode)
-            inbound_fedex_tracking = admin_repo.get_inbound_tracking_by_barcodes(barcode)
+            outbound_fedex_tracking = \
+                admin_repo.get_outbound_tracking_by_barcodes(barcode)
+            inbound_fedex_tracking = \
+                admin_repo.get_inbound_tracking_by_barcodes(barcode)
+            first_scan_timestamp_status = \
+                admin_repo.get_first_scan_timestamp_by_barcodes(barcode)
+            last_scan_timestamp_status = \
+                admin_repo.get_last_scan_timestamp_by_barcodes(barcode)
 
             summary = {
                 "sampleid": None if strip_sampleid else barcode,
@@ -133,8 +145,9 @@ def per_sample(project, barcodes, strip_sampleid):
                 "sample-received": sample_status is not None,
                 "kit-id": kit_id_name,
                 "outbound-tracking": outbound_fedex_tracking,
-                "inbound-tracking": inbound_fedex_tracking
-
+                "inbound-tracking": inbound_fedex_tracking,
+                "first-scan-timestamp-status": first_scan_timestamp_status,
+                "last-scan-timestamp-status": last_scan_timestamp_status
             }
 
             for status in ["sample-is-valid",

microsetta_private_api/repo/admin_repo.py

@@ -555,7 +555,7 @@ def get_project_barcodes(self, project_id):
             else:
                 cur.execute(query, [project_id, ])
                 return list([v[0] for v in cur.fetchall()])
-            
+
     def get_kit_barcodes(self, kit_ids):
         """Obtain the barcodes associated with a kit
 
@@ -589,7 +589,7 @@ def get_kit_barcodes(self, kit_ids):
             """
             cur.execute(query_barcodes, [tuple(ag_kit_ids)])
             return [row[0] for row in cur.fetchall()]
-        
+
     def get_email_barcodes(self, emails):
         """Obtain the barcodes associated with an email
 
@@ -623,7 +623,7 @@ def get_email_barcodes(self, emails):
             """
             cur.execute(query_barcodes, [tuple(created_with_kit_ids)])
             return [row[0] for row in cur.fetchall()]
-        
+
     def get_outbound_tracking_barcodes(self, outbound_tracking_numbers):
         """Obtain the barcodes associated with an outbound tracking number
 
@@ -644,7 +644,8 @@ def get_outbound_tracking_barcodes(self, outbound_tracking_numbers):
         """
 
         with self._transaction.cursor() as cur:
-            cur.execute(query_outbound_tracking, [tuple(outbound_tracking_numbers)])
+            cur.execute(query_outbound_tracking,
+                        [tuple(outbound_tracking_numbers)])
             kit_ids = [row[0] for row in cur.fetchall()]
 
             if not kit_ids:
@@ -657,7 +658,7 @@ def get_outbound_tracking_barcodes(self, outbound_tracking_numbers):
             """
             cur.execute(query_barcodes, [tuple(kit_ids)])
             return [row[0] for row in cur.fetchall()]
-        
+
     def get_inbound_tracking_barcodes(self, inbound_tracking_numbers):
         """Obtain the barcodes associated with an inbound tracking number
 
@@ -678,7 +679,8 @@ def get_inbound_tracking_barcodes(self, inbound_tracking_numbers):
         """
 
         with self._transaction.cursor() as cur:
-            cur.execute(query_inbound_tracking, [tuple(inbound_tracking_numbers)])
+            cur.execute(query_inbound_tracking,
+                        [tuple(inbound_tracking_numbers)])
             kit_ids = [row[0] for row in cur.fetchall()]
 
             if not kit_ids:
@@ -721,7 +723,7 @@ def get_outbound_tracking_by_barcodes(self, barcodes):
                 return None
 
             return [row[0] for row in rows]
-        
+
     def get_inbound_tracking_by_barcodes(self, barcodes):
         """Obtain the inbound tracking numbers associated with a barcode
 
@@ -752,6 +754,80 @@ def get_inbound_tracking_by_barcodes(self, barcodes):
 
             return [row[0] for row in rows]
 
+    def get_first_scan_timestamp_by_barcodes(self, barcodes):
+        """Obtain the first scan timestamp and
+           sample status associated with a barcode
+
+        Parameters
+        ----------
+        barcodes : list
+            The list of barcodes to obtain first
+            scan timestamps and sample statuses for
+
+        Returns
+        -------
+        list
+            A list of tuples where each tuple contains
+            the first scan timestamp and sample status
+        """
+
+        if isinstance(barcodes, str):
+            barcodes = [barcodes]
+
+        query = """
+            SELECT MIN(scan_timestamp), sample_status
+            FROM barcodes.barcode_scans
+            WHERE barcode = %s
+            GROUP BY sample_status
+            ORDER BY MIN(scan_timestamp)
+            LIMIT 1
+        """
+
+        with self._transaction.cursor() as cur:
+            for barcode in barcodes:
+                cur.execute(query, [barcode])
+                result = cur.fetchone()
+                results = result[0], result[1]
+
+            return results
+
+    def get_last_scan_timestamp_by_barcodes(self, barcodes):
+        """Obtain the last scan timestamp and
+           sample status associated with a barcode
+
+        Parameters
+        ----------
+        barcodes : list
+            The list of barcodes to obtain last
+            scan timestamps and sample statuses for
+
+        Returns
+        -------
+        list
+            A list of tuples where each tuple contains
+            the last scan timestamp and sample status
+        """
+
+        if isinstance(barcodes, str):
+            barcodes = [barcodes]
+
+        query = """
+            SELECT MAX(scan_timestamp), sample_status
+            FROM barcodes.barcode_scans
+            WHERE barcode = %s
+            GROUP BY sample_status
+            ORDER BY MAX(scan_timestamp) DESC
+            LIMIT 1
+        """
+
+        with self._transaction.cursor() as cur:
+            for barcode in barcodes:
+                cur.execute(query, [barcode])
+                result = cur.fetchone()
+                results = result[0], result[1]
+
+            return results
+
     def create_project(self, project):
         """Create a project entry in the database
 

microsetta_private_api/repo/kit_repo.py

@@ -67,12 +67,12 @@ def get_kit_unused_samples(self, supplied_kit_id):
             else:
                 samples = [sample_repo._get_sample_by_id(r[1]) for r in rows]
                 return Kit(rows[0][0], samples)
-            
+
     def get_kit_id_name_by_barcode(self, barcode):
         with self._transaction.cursor() as cur:
             cur.execute("""
-                        SELECT kit_id 
-                        FROM barcodes.barcode 
+                        SELECT kit_id
+                        FROM barcodes.barcode
                         WHERE barcode = %s
                         """, (barcode,))