Update visit_source_value JOINs to only use hadm_id
#61
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etl/etl/cdm_drug_exposure.sql
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| src.source_concept_id AS drug_source_concept_id, | ||
| src.route_source_code AS route_source_value, | ||
| src.dose_unit_source_code AS dose_unit_source_value, | ||
| `@etl_project.@etl_dataset`.obf_id_str(src.trace_id, 32) AS drug_exposure_id, |
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I'm a little bit worried about uniqueness of drug_exposure_id when the generated value is based on src.trace_id only: drug_exposure source rows can be multiplied due to multiple mapping of drug_source_value (for example, when a drug mapped to ingredients concepts). Maybe src.trace_id + drug_concept_id would be a safer choice?
atsvetkova-ody
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I looked through the changes, and I have only two notes:
- about drug_exposure_id: I expect some risk of generating duplicated values when only src.trace_id is passed to the obfuscating function. May be src.trace_id + drug_concept_id could be a safer option.
- about visit_source_value, just an idea probably to think it over later: we used to populate visit_source_value with the source visit_id to track original visits. But having trace_id field or with adding another non-OMOP field dedicated to source visit_id, it can be safe to return initial role to visit_source_value, i. e. to populate it with the values used to find visit_concept_id.
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Thanks for the feedback @atsvetkova-ody !
I've updated this to combine
I don't think I understand what you are suggesting here. Looking at the old code, on main, Can I ask if you've reviewed all of the open PR commits (most of which are in this PR since I've been building on top of PRs to avoid merge conflicts)? I ask so I can decide what to merge. |
This PR should be merged after the PRs ahead of it.
In #57 , we updated
visit_source_valueto simply behadm_idinstead of a concatenation ofhadm_idand other variables. This PR updates theJOINstatements which usevisit_source_valueto simplyJOINagainsthadm_id, see 225c79c.