Add bi specific migrations back in

Author: nickpalladino

src/main/resources/db/migration/V001.001__datasets_array.sql

@@ -0,0 +1,39 @@
+-- See the NOTICE file distributed with this work for additional information
+-- regarding copyright ownership.
+--
+-- Licensed under the Apache License, Version 2.0 (the "License");
+-- you may not use this file except in compliance with the License.
+-- You may obtain a copy of the License at
+--
+--     http://www.apache.org/licenses/LICENSE-2.0
+--
+-- Unless required by applicable law or agreed to in writing, software
+-- distributed under the License is distributed on an "AS IS" BASIS,
+-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+-- See the License for the specific language governing permissions and
+-- limitations under the License.
+
+-- Updates trial.additional_info to have a datasets array instead of just observationDatasetId.
+-- Leaves observationDatasetId in place out of an abundance of caution.
+-- Only updates rows that don't already have datasets key (just in case the code was updated prematurely).
+DO
+$$
+BEGIN
+    UPDATE
+        trial
+    SET
+        additional_info = additional_info
+            || JSONB_BUILD_OBJECT(
+                'datasets',
+                JSONB_BUILD_ARRAY(
+                    JSONB_BUILD_OBJECT(
+                        'id', additional_info->'observationDatasetId',
+                        'name', additional_info->'defaultObservationLevel',
+                        'level', '0'
+                    )
+                )
+            )
+    WHERE
+        additional_info->'datasets' IS NULL;
+END
+$$;

src/main/resources/db/migration/V002.001__update_list_positions.sql

@@ -0,0 +1,68 @@
+
+-- This migration updates existing list_item records based on DeltaBreed (Breeding Insight) specific fields.
+--
+-- These are the list types, the BJTS uses Java enums and stores ints in the database.
+-- 0: germplasm
+-- 1: markers
+-- 2: programs
+-- 3: trials
+-- 4: studies
+-- 5: observationUnits
+-- 6: observations
+-- 7: observationVariables
+-- 8: samples
+
+DO
+$$
+BEGIN
+    -- Update germplasm list items, the goal is to use the order defined by the listEntryNumbers.
+    UPDATE
+        list_item
+    SET
+        position = subquery.position
+    FROM
+        (
+            SELECT
+                -- Subtract 1 from row_number to get zero indexing.
+                row_number() OVER (PARTITION BY li.list_id ORDER BY (g.additional_info->'listEntryNumbers'->>xr.external_reference_id::text)::int) - 1 AS position,
+                li.id AS list_item_id
+            FROM
+                list_item li
+                    JOIN list l ON li.list_id = l.id
+                    JOIN list_external_references ler ON l.id = ler.list_entity_id
+                    JOIN external_reference xr ON xr.id = ler.external_references_id AND xr.external_reference_source = 'breedinginsight.org/lists'
+                    JOIN germplasm g ON li.item = g.germplasm_name
+            WHERE
+                l.list_type = 0  -- 0 is germplasm
+            ORDER BY
+                l.id
+        ) AS subquery
+    WHERE
+        list_item.id = subquery.list_item_id
+    ;
+
+    -- Update all non-germplasm list items. There is no existing order to preserve, assign sequential position values arbitrarily.
+    UPDATE
+        list_item
+    SET
+        position = subquery.position
+    FROM
+        (
+            SELECT
+                -- Subtract 1 from row_number to get zero indexing.
+                row_number() OVER (PARTITION BY li.list_id) - 1 AS position,
+                li.id AS list_item_id
+            FROM
+                list_item li
+                JOIN list l ON li.list_id = l.id
+            WHERE
+                l.list_type != 0  -- 0 is germplasm, here we are addressing non-germplasm lists.
+            ORDER BY
+                l.id
+        ) AS subquery
+    WHERE
+        list_item.id = subquery.list_item_id
+    ;
+
+END;
+$$;