Update migration script with stricter matching to OU, add assertion

Author: jloux-brapi

src/main/resources/db/migration/V006_002__migrate_sample_ou_ids.sql

@@ -4,24 +4,58 @@ WITH
         SELECT
             id as sample_id,
             additional_info ->> 'obsUnitID' AS bi_ou_id
-FROM sample
-WHERE additional_info ? 'obsUnitID'
+        FROM sample
+        WHERE additional_info ? 'obsUnitID'
+    ),
+    exrefid_source_with_one_ou_connected AS (
+        SELECT ex.external_reference_id, ex.external_reference_source, (array_agg(id))[1] AS exref_pk
+        FROM external_reference ex
+        JOIN observation_unit_external_references ouex ON ex.id = ouex.external_references_id
+        WHERE ex.external_reference_source = 'breedinginsight.org/observationunits'
+        GROUP BY ex.external_reference_id, ex.external_reference_source
+        HAVING COUNT(*) = 1
     ),
     ou_ids_matched_on_samples AS (
 --      Now match the bi-generated exref ou ids to ex refs ids, and keep samples ids for matching in update
-SELECT
-    ou.id AS ou_id,
-    samples_and_bi_ou_ids.sample_id
-FROM observation_unit ou
-    JOIN observation_unit_external_references ouex ON ou.id = ouex.observation_unit_entity_id
-    JOIN external_reference ex ON ouex.external_references_id = ex.id
-    JOIN samples_and_bi_ou_ids ON ex.external_reference_id = samples_and_bi_ou_ids.bi_ou_id
+        SELECT
+            ou.id AS ou_id,
+            samples_and_bi_ou_ids.sample_id
+        FROM observation_unit ou
+        JOIN observation_unit_external_references ouex ON ou.id = ouex.observation_unit_entity_id
+        JOIN exrefid_source_with_one_ou_connected on exrefid_source_with_one_ou_connected.exref_pk = ouex.external_references_id
+        JOIN samples_and_bi_ou_ids ON exrefid_source_with_one_ou_connected.external_reference_id = samples_and_bi_ou_ids.bi_ou_id
     )
 UPDATE sample
 SET additional_info = jsonb_set(
         additional_info,
         '{obsUnitID}',
         to_jsonb(mos.ou_id)
-                      )
-    FROM ou_ids_matched_on_samples mos
-WHERE id = mos.sample_id
+)
+FROM ou_ids_matched_on_samples mos
+WHERE id = mos.sample_id;
+
+-- Assertion to ensure all samples with ou in additional info now relate to observation unit db id
+DO $$
+    DECLARE
+    samples_with_ou_count integer;
+            samples_with_ous_matched_to_ou_count integer;
+    BEGIN
+        SELECT COUNT(*)
+        INTO samples_with_ou_count
+        FROM sample
+        WHERE additional_info ? 'obsUnitID';
+
+        SELECT COUNT(*)
+        INTO samples_with_ous_matched_to_ou_count
+        FROM sample s
+                 JOIN observation_unit ou on ou.id::text = s.additional_info ->> 'obsUnitID'
+        WHERE s.additional_info ? 'obsUnitID';
+
+        IF samples_with_ou_count <> samples_with_ous_matched_to_ou_count THEN
+                    RAISE EXCEPTION
+                        'V006.002 After migration, expected all % sample.additional_info->>obsUnitID rows to match to observation_unit.id, but only % matched',
+                        samples_with_ou_count,
+                        samples_with_ous_matched_to_ou_count;
+        END IF;
+    END
+$$;