Why?:
Script scripts/migrate_individuals.sh uses public.individuals.observed_features, this column cannot ever been empty, it must, at least, contains HP:0000001
Check:
select internal_id
from public.individuals i
where i.observed_features = '' ;
Solution:
Only PH00002126 failed.
update public.individuals set observed_features = (
select string_agg(DISTINCT t.hpo_id , ',' ORDER BY t.hpo_id) AS hpo_ids from hpo.term t
where t."name" = any(string_to_array((select observed_features_names from public.individuals i where i.internal_id = 'PH00002126'),';'))
),
simplified_observed_features = (
select string_agg(DISTINCT t.hpo_id , ',' ORDER BY t.hpo_id) AS hpo_ids from hpo.term t
where t."name" = any(string_to_array((select observed_features_names from public.individuals i where i.internal_id = 'PH00002126'),';'))
)
where internal_id = 'PH00002126'
;
Why?: Script
scripts/migrate_individuals.sh
usespublic.individuals.observed_features
, this column cannot ever been empty, it must, at least, containsHP:0000001
Check:
Solution: Only
PH00002126
failed.