Provide a hot fix to address OMOP Vocab bug for COVID Visit(HCPCS code 704057 ) mapped to COVID dx in condition

[stephanieshong]

detail description about this bug is reported in the OMOP vocabulary issue GitHub page, link is here: OHDSI/Vocabulary-v5.0#697
Basically a COVID test clinic visit is mapped to COVID dx without valid test result indicating that the test result was positive.

• TriNetX

• PCORnet

• ACT

OMOP - site will have to apply the new release of the OMOP vocab tables and apply the corrected map for the HCPCS code = 704057.

[stephanieshong]

Code fix has been implemented in the pipeline. But not yet deployed.

[stephanieshong]

Due to the amount of time it will take to create a new version of the pipeline template and deployment of the new template versions across 80+ site's pipeline, we may take less time intensive path to complete this hot fix. Was informed that the new vocabulary update will be provided to us soon. When the new OMOP vocabulary tables becomes available we would also need to UNDO the hot fix patch fairly quickly. Will update when the hot patch fix is applied to LDS.

[stephanieshong]

-Added a filter to unioned_condition_occurrence which removes rows where condition_concept_id is 37311061 AND condition_source_concept_id is 704057 (as discussed this morning)
-Create a dataset called computed_condition_era which is based on unioned_condition_occurrence but uses the same code as condition_era in pre-union
-Run pre_clean_condition_era on computed_condition_era
-Rest of pipeline proceeds as usual
-hot fix complete for the build.

[stephanieshong]

The latest update of OMOP vocabulary files takes care of the covid19 test visit procedure code incorrectly mapping over to the condition domain. Build v.100 contains the fix.