Merge pull request #114 from wasade/patch_patch_0055

Revise patch 0055, create pg93 compatible query
biocore · Apr 21, 2020 · 151c051 · 151c051
2 parents a8718d1 + cb53330
commit 151c051
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Showing 2 changed files with 26 additions and 13 deletions.
diff --git a/microsetta_private_api/db/patches/0055.sql b/microsetta_private_api/db/patches/0055.sql
@@ -19,22 +19,33 @@ CREATE TABLE barcodes.kit (
 
 -- Now lets make sure the barcodes are associated to the kits
 ALTER TABLE barcodes.barcode ADD COLUMN kit_id VARCHAR;
-ALTER TABLE barcodes.barcode ADD CONSTRAINT fk_barcode_kit_id
-    FOREIGN KEY (kit_id) REFERENCES barcodes.kit (kit_id);
 
 -- Let's make sure all existing kits are reflected in this 
 -- table
+INSERT INTO barcodes.kit (kit_id) 
+    SELECT supplied_kit_id 
+    FROM ag.ag_kit;
+
+-- and we need to also set the kit_id reference in the barcodes.barcode
+-- table
 DO $do$
 DECLARE
-    k varchar;
+    rec RECORD;
 BEGIN
-    FOR k IN
-        SELECT supplied_kit_id FROM ag.ag_kit
+    FOR rec IN
+        SELECT supplied_kit_id, barcode
+            FROM ag.ag_kit
+            JOIN ag.ag_kit_barcodes USING(ag_kit_id)
     LOOP
-        INSERT INTO barcodes.kit (kit_id) VALUES (k);
+        UPDATE barcodes.barcode
+            SET kit_id = rec.supplied_kit_id
+            WHERE barcode=rec.barcode;
     END LOOP;
 END $do$;
 
+
 -- And finally, let's establish FK relationships
 ALTER TABLE ag.ag_kit ADD CONSTRAINT fk_barcode_schema_kit_id
     FOREIGN KEY (supplied_kit_id) REFERENCES barcodes.kit (kit_id);
+ALTER TABLE barcodes.barcode ADD CONSTRAINT fk_barcode_kit_id
+    FOREIGN KEY (kit_id) REFERENCES barcodes.kit (kit_id);
diff --git a/microsetta_private_api/repo/admin_repo.py b/microsetta_private_api/repo/admin_repo.py
@@ -224,13 +224,15 @@ def create_kits(self, number_of_kits, number_of_samples, kit_prefix,
                                 kit_barcodes_insert)
 
         with self._transaction.dict_cursor() as cur:
-            cur.execute("SELECT kit_id, "
-                        "       kit_uuid, "
-                        "       array_agg(barcode) as sample_barcodes "
-                        "FROM barcodes.kit "
-                        "LEFT JOIN barcodes.barcode USING (kit_id)"
-                        "WHERE kit_id IN %s "
-                        "GROUP BY (kit_id, kit_uuid)", (tuple(names), ))
+            cur.execute("SELECT i.kit_id, o.kit_uuid, i.sample_barcodes "
+                        "FROM (SELECT kit_id, "
+                        "             array_agg(barcode) as sample_barcodes "
+                        "      FROM barcodes.kit "
+                        "      JOIN barcodes.barcode USING (kit_id) "
+                        "      WHERE kit_id IN %s "
+                        "      GROUP BY kit_id) i "
+                        "JOIN barcodes.kit o USING (kit_id)", (tuple(names), ))
+
             created = [{'kit_id': k, 'kit_uuid': u, 'sample_barcodes': b}
                        for k, u, b in cur.fetchall()]