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[GH-ISSUE #93] Implementation of era_tables #55

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opened 2026-03-23 20:28:45 +00:00 by mirror · 1 comment
mirror commented 2026-03-23 20:28:45 +00:00
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Originally created by @annabel-uzl on GitHub (Aug 12, 2024).
Original GitHub issue: https://github.com/RADar-AZDelta/Rabbit-in-a-Blender/issues/93

Originally assigned to: @pjlammertyn on GitHub.

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?

Originally created by @annabel-uzl on GitHub (Aug 12, 2024). Original GitHub issue: https://github.com/RADar-AZDelta/Rabbit-in-a-Blender/issues/93 Originally assigned to: @pjlammertyn on GitHub. 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?
mirror commented 2026-03-23 20:28:46 +00:00
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@pjlammertyn commented on GitHub (Sep 18, 2024):

CLI aangepast, en ook de ETL flow:

image

<!-- gh-comment-id:2357879488 --> @pjlammertyn commented on GitHub (Sep 18, 2024): CLI aangepast, en ook de ETL flow: ![image](https://github.com/user-attachments/assets/0b26d3ca-cb8b-424b-a833-9c4bb3889cc6)
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