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Bug: Handle Empty RxNorm fields #1199

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merged 2 commits into from
Sep 30, 2024
Merged

Bug: Handle Empty RxNorm fields #1199

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f210d58
First scenario
demariadaniel Sep 30, 2024
1e9f5dc
Remove export
demariadaniel Sep 30, 2024
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15 changes: 12 additions & 3 deletions src/submission/submission-service.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -918,9 +918,18 @@ export namespace operations {
);
errorsAccumulator = errorsAccumulator.concat(programIdError);

// special case for therapies where we need to populate the rxnorm Ids, only do this step
// if the record is valid so far to avoid spending alot of time here
if (errorsAccumulator.length == 0 && isRxNormTherapy(command.clinicalType)) {
// Records using alternate Drug DB fields should skip RxNorm validation
// Drug DB field validation is handled downstream in validation-clinical/therapy.ts
const { drug_database, drug_term, drug_id } = processedRecord;
const hasDrugDbFields = Boolean(drug_database || drug_id || drug_term);
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This allows me to skip rxNormDB validation if I provide any one of these three properties.

Do you have a check elsewhere that ensures if I have one of these fields that i have all of these and none of the rxnorm fields?

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This is handled by a mix of Dictionary and Clinical validations

Dictionary enforces that either RxNorm or Drug Db are submitted:
https://github.com/icgc-argo/argo-dictionary/pull/437/files#diff-893b20bc0b00b45e9cb1df1d1a13b5cba5dcf4627f2f182f345762618077ac54

Clinical enforces that all 3 Drug Db fields are submitted when RxNorm is blank:
https://github.com/icgc-argo/argo-clinical/pull/1195/files#diff-57392d148ba45d8530fa1789680e51f9398e3b20e910bccf1fa0e95b78445a08R297


// Special case for therapies where we need to populate the rxnorm Ids
// Only do this step if the record is valid so far to avoid spending alot of time here
if (
errorsAccumulator.length == 0 &&
isRxNormTherapy(command.clinicalType) &&
!hasDrugDbFields
) {
const result = await validateRxNormFields(processedRecord, index, schemaName);
if (result.error != undefined) {
errorsAccumulator = errorsAccumulator.concat([result.error]);
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