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Migrate sample bi ouIds to brapi ouIds #20

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Migrate sample bi ouIds to brapi ouIds #20

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27 changes: 27 additions & 0 deletions src/main/resources/db/migration/V006_002__migrate_sample_ou_ids.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,27 @@
WITH
samples_and_bi_ou_ids AS (
-- Look for samples that have obsUnitIDs and keep ids in hand for next query
SELECT
id as sample_id,
additional_info ->> 'obsUnitID' AS bi_ou_id
FROM sample
WHERE additional_info ? 'obsUnitID'
),
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
)
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