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RADar-AZDelta / Rabbit-in-a-Blender

An ETL pipeline to transform your EMP data to OMOP.
https://radar-azdelta.github.io/Rabbit-in-a-Blender/
GNU General Public License v3.0
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Implementation of era_tables #93

Closed annabel-uzl closed 2 months ago

annabel-uzl commented 3 months ago

I looked into the implementation of the era tables and used the scripts Ohdsi defined online: https://ohdsi.github.io/CommonDataModel/sqlScripts.html#Era_Tables However, when I ran the etl (e.g. riab --run-etl ./omop-cdm --table condition_era), I got the following error:

error: argument -t/--table: invalid choice: 'condition_era' (choose from 'metadata', 'cdm_source', 'vocabulary', 'location', 'care_site', 'provider', 'person', 'observation_period', 'visit_occurrence', 'visit_detail', 'condition_occurrence', 'drug_exposure', 'procedure_occurrence', 'device_exposure', 'measurement', 'observation', 'death', 'note', 'note_nlp', 'specimen', 'fact_relationship', 'payer_plan_period', 'cost', 'episode', 'episode_event')

It seems like the _era tables are not implemented in the etl? Can they be added?

pjlammertyn commented 2 months ago

CLI aangepast, en ook de ETL flow:

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