Update species migration to work with new uuids

[nickpalladino]

Description

Story: B-2622

This migration change assumes you're starting with a database that has no entries in the crop table or data has been migrated using this:

-- cleanup duplicate Strawberry crop record on qa test
delete from crop where id = '30';

-- define utility function to update all user references
CREATE OR REPLACE FUNCTION public.replace_anonymous_user()
    RETURNS void LANGUAGE plpgsql AS $$
DECLARE
    r  record;
    tgt uuid := 'AAAAAAAA-AAAA-AAAA-AAAA-AAAAAAAAAAAA'::uuid;
    src text := 'anonymousUser';
BEGIN
    FOR r IN
        SELECT table_schema, table_name, column_name
        FROM   information_schema.columns
        WHERE  table_schema = 'public'
          AND  column_name  = 'auth_user_id'
          AND  data_type IN ('uuid','text','character varying')
        LOOP
            RAISE NOTICE 'Updating %.% -> %', r.table_schema, r.table_name, r.column_name;
            EXECUTE format('UPDATE %I.%I SET %I = $1 WHERE %I = $2',
                           r.table_schema, r.table_name, r.column_name, r.column_name)
                USING tgt, src;
        END LOOP;
END $$;

-- run function
SELECT public.replace_anonymous_user();

-- create table of crop foreign keys
CREATE TEMP TABLE crop_fk_columns AS
SELECT
    tc.table_schema,
    tc.table_name,
    kcu.column_name,
    tc.constraint_name
FROM   information_schema.table_constraints tc
           JOIN   information_schema.key_column_usage  kcu
                  ON tc.constraint_name = kcu.constraint_name
WHERE  tc.constraint_type = 'FOREIGN KEY'
  AND  tc.table_schema = 'public'
  AND  tc.constraint_schema = 'public'
  AND  tc.constraint_name IN (
    SELECT conname
    FROM   pg_constraint
    WHERE  confrelid = 'public.crop'::regclass
);

-- verify this matches migrate_crops.sql
select * from crop_fk_columns;


CREATE EXTENSION IF NOT EXISTS "uuid-ossp";

-- migrate old crop id references to new uuids
BEGIN;

-- 2.1  Add a uuid column to public.crop
ALTER TABLE public.crop ADD COLUMN new_id uuid;

-- 2.2  Fill new_id with a generated UUID for each row
-- The namespace in the seeding script
DO $$
DECLARE
    ns  constant uuid := '9a4deca9-4068-46a3-9efe-db0c181f491a';
BEGIN
    /* -----------------------------------------------------------
       Normalise names exactly the same way the seeder does:
       1. lower‑case                → lower()
       2. trim leading/trailing     → trim()
       3. remove ALL whitespace     → regexp_replace(...,'\s','','g')
    ----------------------------------------------------------- */
    UPDATE public.crop c
    SET    new_id =
               uuid_generate_v5(
                       ns,
                       regexp_replace(lower(trim(c.crop_name)), '\s', '', 'g')
               )
    WHERE  c.new_id IS NULL;        -- just in case you run it twice
END $$;

-- 2.3  Build a mapping table for easy joins (optional to keep)
CREATE TEMP TABLE crop_id_map AS
SELECT id         AS old_id,
       new_id     AS new_id
FROM   public.crop;

-- 2.4  Drop FK constraints so we can rewrite ids in child tables
DO $drop_fks$
    DECLARE
        r record;
    BEGIN
        FOR r IN SELECT * FROM crop_fk_columns LOOP
                EXECUTE format(
                        'ALTER TABLE %I.%I DROP CONSTRAINT %I;',
                        r.table_schema, r.table_name, r.constraint_name);
            END LOOP;
    END $drop_fks$;

-- 2.5  Rewrite crop_id in every child table
DO $update_children$
    DECLARE
        r record;
    BEGIN
        FOR r IN SELECT * FROM crop_fk_columns LOOP
                RAISE NOTICE 'Updating %.% → %', r.table_schema, r.table_name, r.column_name;
                EXECUTE format(
                        'UPDATE %I.%I AS t
                           SET %I = m.new_id
                          FROM crop_id_map m
                         WHERE t.%I = m.old_id;',
                        r.table_schema, r.table_name, r.column_name, r.column_name);
                -- Change column type to uuid
                EXECUTE format(
                        'ALTER TABLE %I.%I
                           ALTER COLUMN %I TYPE uuid USING %I::uuid;',
                        r.table_schema, r.table_name, r.column_name, r.column_name);
            END LOOP;
    END $update_children$;

-- 2.6  Swap primary key in public.crop
ALTER TABLE public.crop
    DROP CONSTRAINT crop_pkey,
    ALTER COLUMN id DROP DEFAULT,
    ALTER COLUMN id TYPE uuid USING new_id,
    ADD PRIMARY KEY (id);

ALTER TABLE public.crop DROP COLUMN new_id;

-- 2.7  Re‑create FK constraints
DO $add_fks$
DECLARE
    r record;
BEGIN
    FOR r IN SELECT * FROM crop_fk_columns LOOP
            EXECUTE format(
                    'ALTER TABLE %I.%I
                       ADD CONSTRAINT %I
                       FOREIGN KEY (%I) REFERENCES public.crop(id);',
                    r.table_schema, r.table_name, r.constraint_name,
                    r.column_name);
        END LOOP;
END $add_fks$;

-- if looks good
COMMIT;

-- if problems
ROLLBACK;

select * from program;

-- verify there are no duplicates
WITH norm AS (
    SELECT id,
           crop_name,
           regexp_replace(lower(trim(crop_name)), '\s', '', 'g') AS normalised
    FROM   public.crop
)
SELECT normalised, array_agg(id) AS dupe_ids
FROM   norm
GROUP  BY normalised
HAVING count(*) > 1;

Dependencies

• brapi server latest develop

Testing

• Can create and update species list

Checklist:

• I have performed a self-review of my own code
• I have tested my code and ensured it meets the acceptance criteria of the story
• I have tested that my code works with both the brapi-java-server and BreedBase
• I have create/modified unit tests to cover this change
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to documentation
• I have run TAF: <please include a link to TAF run>