update sql tables as per data freeze 12

shanmukhasampath commented 1 year ago

DF12 SQL fixes

[x] Setting up environment - minimum_extended table has column with changed names. Update to account these changes.
[x] Visit Occurrence - SOURCE BIOBANK needs to make the change to include missing BL_AGE
[x] BIRTH_MOTHER stem - Birth mother now have APPROX_DELIVERY_DATE column which conflicts with calculated APPROX_DELIVERY_DATE
[x] cdm source - Change it to DF12
[x] Update export_tables.sh to change the storage bucket
[x] Update config_template.yml to account for DF12 changes

javier-gracia-tabuenca-tuni commented 9 months ago

is this completed ?

shanmukhasampath commented 9 months ago

Hi @javier-gracia-tabuenca-tuni, yes this is completed.

FINNGEN / ETL