SQL script to update BLSample.subLocation via a cursor to remove duplicate rows

Author: KarlLevik

schemas/ispyb/scripts/BLSample_update_subLocation.sql

@@ -0,0 +1,49 @@
+-- Use a curson to hold the result set from a complex SELECT query to get the
+-- blSampleIds of rows that duplicate the combination of (containerId, location, subLocation).
+-- Then get the rows one by one and run an UPDATE statement against each row in
+-- an effort to make the combination of (containerId, location, subLocation) unique.
+
+DELIMITER //
+
+BEGIN NOT ATOMIC
+
+  DECLARE done INT DEFAULT FALSE;
+  DECLARE ids, jpath TEXT;
+  DECLARE i, id INT;
+  DECLARE cur CURSOR FOR
+    SELECT q.blSampleIds
+    FROM (
+        SELECT containerId, location, subLocation, count(*) cnt, JSON_ARRAYAGG(blSampleId) blSampleIds
+        FROM BLSample
+        WHERE location IS NOT NULL
+        GROUP BY containerId, location, subLocation
+        HAVING cnt > 1
+        ORDER BY containerId, location, subLocation
+    ) q;
+
+  DECLARE CONTINUE HANDLER FOR NOT FOUND SET done = TRUE;
+
+  OPEN cur;
+
+  read_loop: LOOP
+    FETCH cur INTO ids;
+    IF done THEN
+      LEAVE read_loop;
+    END IF;
+
+    FOR i IN 0..JSON_LENGTH(ids)-1
+    DO
+
+      SET jpath := CONCAT('$[', i, ']');
+      SET id := CAST(JSON_EXTRACT(ids, jpath) AS INT);
+
+      UPDATE BLSample SET subLocation = i+1 WHERE blSampleId = id; -- AND subLocation IS NULL;
+
+    END FOR;
+
+  END LOOP;
+
+  CLOSE cur;
+END; //
+
+DELIMITER ;