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Deterministic Sample ID assignments [VS-371] #7770

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merged 7 commits into from
Apr 13, 2022
Merged

Deterministic Sample ID assignments [VS-371] #7770

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wip
mcovarr Apr 9, 2022
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wip
mcovarr Apr 9, 2022
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mcovarr Apr 9, 2022
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Add branch to Dockstore
mcovarr Apr 11, 2022
0d619af
different approach
mcovarr Apr 11, 2022
ef35d1f
take three
mcovarr Apr 11, 2022
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tidy
mcovarr Apr 12, 2022
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsAssignIds.wdl
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Expand Up @@ -141,7 +141,7 @@ task AssignIds {

# perform actual id assignment
bq --project_id=~{project_id} query --format=csv --use_legacy_sql=false --parameter=offset:INTEGER:$offset \
'UPDATE `~{dataset_name}.~{sample_info_table}` m SET m.sample_id = id_assign.id FROM (SELECT sample_name, @offset + ROW_NUMBER() OVER() as id FROM `~{dataset_name}.~{sample_info_table}` WHERE sample_id IS NULL) id_assign WHERE m.sample_name = id_assign.sample_name;'
'UPDATE `~{dataset_name}.~{sample_info_table}` m SET m.sample_id = id_assign.id FROM (SELECT sample_name, @offset + ROW_NUMBER() OVER(order by sample_name) as id FROM `~{dataset_name}.~{sample_info_table}` WHERE sample_id IS NULL) id_assign WHERE m.sample_name = id_assign.sample_name;'

# retrieve the list of assigned ids and samples to update the datamodel
echo "entity:sample_id,gvs_id" > update.tsv
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