💊 Feat/1194 Drug Info Validation

src/common-model/entities.ts

@@ -17,8 +17,8 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-import { z as zod } from 'zod';
 import { entities as dictionaryEntities } from '@overturebio-stack/lectern-client';
+import { z as zod } from 'zod';
 
 // this is temporary to keep code compiling until surgery is ready in dictionary, to be removed in favor of
 // the surgery in ClinicalEntitySchemaNames
@@ -101,10 +101,11 @@ export type ClinicalFields =
 	| PrimaryDiagnosisFieldsEnum
 	| FamilyHistoryFieldsEnum
 	| TreatmentFieldsEnum
-	| TherapyRxNormFields
+	| TherapyRxNormFieldsEnum
+	| TherapyDrugFieldsEnum
 	| RadiationFieldsEnum
 	| SurgeryFieldsEnum
-	| CommonTherapyFields
+	| CommonTherapyFieldsEnum
 	| ExposureFieldsEnum
 	| ComorbidityFieldsEnum
 	| BiomarkerFieldsEnum;
@@ -201,12 +202,18 @@ export enum TreatmentFieldsEnum {
 	treatment_duration = 'treatment_duration',
 }
 
-export enum TherapyRxNormFields {
+export enum TherapyRxNormFieldsEnum {
 	drug_name = 'drug_name',
 	drug_rxnormid = 'drug_rxnormcui',
 }
 
-export enum CommonTherapyFields {
+export enum TherapyDrugFieldsEnum {
+	drug_database = 'drug_database',
+	drug_id = 'drug_id',
+	drug_term = 'drug_term',
+}
+
+export enum CommonTherapyFieldsEnum {
 	program_id = 'program_id',
 	submitter_donor_id = 'submitter_donor_id',
 	submitter_treatment_id = 'submitter_treatment_id',
@@ -223,7 +230,7 @@ export enum RadiationFieldsEnum {
 	reference_radiation_treatment_id = 'reference_radiation_treatment_id',
 }
 
-export enum ImmunotherapyFields {
+export enum ImmunotherapyFieldsEnum {
 	immunotherapy_type = 'immunotherapy_type',
 }
 
@@ -282,29 +289,29 @@ export const ClinicalUniqueIdentifier: TypeEntitySchemaNameToIndenfiterType = {
 	[ClinicalEntitySchemaNames.FOLLOW_UP]: FollowupFieldsEnum.submitter_follow_up_id,
 	[ClinicalEntitySchemaNames.TREATMENT]: TreatmentFieldsEnum.submitter_treatment_id,
 	[ClinicalEntitySchemaNames.CHEMOTHERAPY]: [
-		CommonTherapyFields.submitter_donor_id,
-		CommonTherapyFields.submitter_treatment_id,
-		TherapyRxNormFields.drug_rxnormid,
+		CommonTherapyFieldsEnum.submitter_donor_id,
+		CommonTherapyFieldsEnum.submitter_treatment_id,
+		TherapyRxNormFieldsEnum.drug_rxnormid,
 	],
 	[ClinicalEntitySchemaNames.IMMUNOTHERAPY]: [
-		CommonTherapyFields.submitter_donor_id,
-		CommonTherapyFields.submitter_treatment_id,
-		TherapyRxNormFields.drug_rxnormid,
+		CommonTherapyFieldsEnum.submitter_donor_id,
+		CommonTherapyFieldsEnum.submitter_treatment_id,
+		TherapyRxNormFieldsEnum.drug_rxnormid,
 	],
 	[SURGERY_SCHEMA_NAME]: [
-		CommonTherapyFields.submitter_donor_id,
-		CommonTherapyFields.submitter_treatment_id,
+		CommonTherapyFieldsEnum.submitter_donor_id,
+		CommonTherapyFieldsEnum.submitter_treatment_id,
 		SpecimenFieldsEnum.submitter_specimen_id,
 	],
 	[ClinicalEntitySchemaNames.RADIATION]: [
-		CommonTherapyFields.submitter_donor_id,
-		CommonTherapyFields.submitter_treatment_id,
+		CommonTherapyFieldsEnum.submitter_donor_id,
+		CommonTherapyFieldsEnum.submitter_treatment_id,
 		RadiationFieldsEnum.radiation_therapy_modality,
 	],
 	[ClinicalEntitySchemaNames.HORMONE_THERAPY]: [
-		CommonTherapyFields.submitter_donor_id,
-		CommonTherapyFields.submitter_treatment_id,
-		TherapyRxNormFields.drug_rxnormid,
+		CommonTherapyFieldsEnum.submitter_donor_id,
+		CommonTherapyFieldsEnum.submitter_treatment_id,
+		TherapyRxNormFieldsEnum.drug_rxnormid,
 	],
 	[ClinicalEntitySchemaNames.COMORBIDITY]: [
 		ComorbidityFieldsEnum.submitter_donor_id,

src/submission/submission-entities.ts

@@ -17,24 +17,24 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-import { DeepReadonly } from 'deep-freeze';
 import { entities as dictionaryEntities } from '@overturebio-stack/lectern-client';
+import { DeepReadonly } from 'deep-freeze';
 import {
+	BiomarkerFieldsEnum,
 	ClinicalEntitySchemaNames,
+	ClinicalTherapyType,
+	CommonTherapyFieldsEnum,
+	ComorbidityFieldsEnum,
 	DonorFieldsEnum,
-	SpecimenFieldsEnum,
-	PrimaryDiagnosisFieldsEnum,
+	ExposureFieldsEnum,
+	FamilyHistoryFieldsEnum,
 	FollowupFieldsEnum,
-	TreatmentFieldsEnum,
-	TherapyRxNormFields,
-	CommonTherapyFields,
+	ImmunotherapyFieldsEnum,
+	PrimaryDiagnosisFieldsEnum,
 	RadiationFieldsEnum,
-	ClinicalTherapyType,
-	ImmunotherapyFields,
-	FamilyHistoryFieldsEnum,
-	ExposureFieldsEnum,
-	ComorbidityFieldsEnum,
-	BiomarkerFieldsEnum,
+	SpecimenFieldsEnum,
+	TherapyRxNormFieldsEnum,
+	TreatmentFieldsEnum,
 } from '../common-model/entities';
 
 /**
@@ -170,6 +170,7 @@ export enum DataValidationErrors {
 	INVALID_LOST_TO_FOLLOW_UP_ID = 'INVALID_LOST_TO_FOLLOW_UP_ID',
 	INVALID_SUBMISSION_AFTER_LOST_TO_FOLLOW_UP = 'INVALID_SUBMISSION_AFTER_LOST_TO_FOLLOW_UP',
 	INVALID_DIAGNOSIS_AFTER_LOST_TO_FOLLOW_UP = 'INVALID_DIAGNOSIS_AFTER_LOST_TO_FOLLOW_UP',
+	INVALID_DRUG_INFO = 'INVALID_DRUG_INFO',
 }
 
 export type RegistrationStat = Array<{
@@ -406,19 +407,19 @@ export const ClinicalEntityToEnumFieldsMap: Record<ClinicalEntitySchemaNames, st
 	[ClinicalEntitySchemaNames.BIOMARKER]: Object.values(BiomarkerFieldsEnum),
 	[ClinicalEntitySchemaNames.FOLLOW_UP]: Object.values(FollowupFieldsEnum),
 	[ClinicalEntitySchemaNames.TREATMENT]: Object.values(TreatmentFieldsEnum),
-	[ClinicalEntitySchemaNames.CHEMOTHERAPY]: (Object.values(TherapyRxNormFields) as string[]).concat(
-		Object.values(CommonTherapyFields),
-	),
+	[ClinicalEntitySchemaNames.CHEMOTHERAPY]: (Object.values(
+		TherapyRxNormFieldsEnum,
+	) as string[]).concat(Object.values(CommonTherapyFieldsEnum)),
 	[ClinicalEntitySchemaNames.RADIATION]: (Object.values(RadiationFieldsEnum) as string[]).concat(
-		Object.values(CommonTherapyFields),
+		Object.values(CommonTherapyFieldsEnum),
 	),
 	[ClinicalEntitySchemaNames.HORMONE_THERAPY]: (Object.values(
-		TherapyRxNormFields,
-	) as string[]).concat(Object.values(CommonTherapyFields)),
-	[ClinicalEntitySchemaNames.IMMUNOTHERAPY]: (Object.values(TherapyRxNormFields) as string[])
-		.concat(Object.values(CommonTherapyFields))
-		.concat(Object.values(ImmunotherapyFields) as string[]),
-	[ClinicalEntitySchemaNames.SURGERY]: Object.values(CommonTherapyFields) as string[],
+		TherapyRxNormFieldsEnum,
+	) as string[]).concat(Object.values(CommonTherapyFieldsEnum)),
+	[ClinicalEntitySchemaNames.IMMUNOTHERAPY]: (Object.values(TherapyRxNormFieldsEnum) as string[])
+		.concat(Object.values(CommonTherapyFieldsEnum))
+		.concat(Object.values(ImmunotherapyFieldsEnum) as string[]),
+	[ClinicalEntitySchemaNames.SURGERY]: Object.values(CommonTherapyFieldsEnum) as string[],
 };
 
 export const TreatmentTypeValuesMappedByTherapy: Record<ClinicalTherapyType, string> = {

src/submission/submission-error-messages.ts

@@ -17,8 +17,8 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-import { SubmissionBatchErrorTypes } from './submission-entities';
 import _ from 'lodash';
+import { SubmissionBatchErrorTypes } from './submission-entities';
 
 const ERROR_MESSAGES: { [key: string]: (errorData: any) => string } = {
 	/* ***************** *
@@ -140,6 +140,7 @@ const ERROR_MESSAGES: { [key: string]: (errorData: any) => string } = {
 		info: { lost_to_followup_diagnosis_id, lost_to_followup_age, submitter_primary_diagnosis_id },
 	}) =>
 		`A clinical event that occurs after the donor was lost to follow up cannot be submitted. The donor was indicated to be lost to follow up at age ${lost_to_followup_age} after their primary diagnosis ("submitter_primary_diagnosis_id" = "${lost_to_followup_diagnosis_id}"), but a new primary diagnosis ("${submitter_primary_diagnosis_id}") that started after the donor was lost to follow up has been submitted. If the donor was found later on, then update the "lost_to_followup_after_clinical_event_id" field to be empty.`,
+	INVALID_DRUG_INFO: () => 'Please provide the missing drug information.',
 };
 
 const BATCH_ERROR_MESSAGES: Record<SubmissionBatchErrorTypes, (errorData: any) => string> = {

src/submission/submission-service.ts

@@ -30,14 +30,14 @@ import {
 	Specimen,
 } from '../clinical/clinical-entities';
 import {
-	donorDao,
 	DONOR_DOCUMENT_FIELDS,
 	FindByProgramAndSubmitterFilter,
+	donorDao,
 } from '../clinical/donor-repo';
 import {
 	ClinicalEntitySchemaNames,
 	DonorFieldsEnum,
-	TherapyRxNormFields,
+	TherapyRxNormFieldsEnum,
 } from '../common-model/entities';
 import * as dictionaryManager from '../dictionary/manager';
 import { schemaFilter } from '../exception/property-exceptions/validation';
@@ -79,12 +79,12 @@ import {
 	RegistrationStat,
 	RegistrationStats,
 	RevalidateClinicalSubmissionCommand,
+	SUBMISSION_STATE,
 	SampleRegistrationFieldsEnum,
 	SubmissionBatchError,
 	SubmissionBatchErrorTypes,
 	SubmissionValidationError,
 	SubmissionValidationUpdate,
-	SUBMISSION_STATE,
 	SubmittedRegistrationRecord,
 	ValidateSubmissionResult,
 } from './submission-entities';
@@ -971,9 +971,9 @@ export namespace operations {
 		}
 		const recordWithRxNormPopulated = _.cloneDeep(r) as Record<string, any>;
 		// we replace the drug name to normalize the case
-		recordWithRxNormPopulated[TherapyRxNormFields.drug_name] =
+		recordWithRxNormPopulated[TherapyRxNormFieldsEnum.drug_name] =
 			rxnormConceptLookupResult.rxNormRecord.str;
-		recordWithRxNormPopulated[TherapyRxNormFields.drug_rxnormid] =
+		recordWithRxNormPopulated[TherapyRxNormFieldsEnum.drug_rxnormid] =
 			rxnormConceptLookupResult.rxNormRecord.rxcui;
 		return {
 			record: recordWithRxNormPopulated as dictionaryEntities.TypedDataRecord,
@@ -989,12 +989,12 @@ export namespace operations {
 		error: SubmissionValidationError | undefined;
 	}> {
 		// if the id is provided we do a look up and double check against the name (if provided)
-		if (isNotAbsent(therapyRecord[TherapyRxNormFields.drug_rxnormid] as string)) {
-			const rxcui = therapyRecord[TherapyRxNormFields.drug_rxnormid] as string;
+		if (isNotAbsent(therapyRecord[TherapyRxNormFieldsEnum.drug_rxnormid] as string)) {
+			const rxcui = therapyRecord[TherapyRxNormFieldsEnum.drug_rxnormid] as string;
 			const rxRecords = await dbRxNormService.lookupByRxcui(rxcui.trim());
 			if (_.isEmpty(rxRecords)) {
 				const error: SubmissionValidationError = {
-					fieldName: TherapyRxNormFields.drug_rxnormid,
+					fieldName: TherapyRxNormFieldsEnum.drug_rxnormid,
 					index: index,
 					info: {},
 					message: validationErrorMessage(DataValidationErrors.THERAPY_RXNORM_RXCUI_NOT_FOUND),
@@ -1009,7 +1009,7 @@ export namespace operations {
 			const matchingRecord = rxRecords.find(
 				(rx) =>
 					rx.str.toLowerCase().trim() ==
-					(therapyRecord[TherapyRxNormFields.drug_name] as string).toLowerCase().trim(),
+					(therapyRecord[TherapyRxNormFieldsEnum.drug_name] as string).toLowerCase().trim(),
 			);
 
 			if (matchingRecord != undefined) {
@@ -1021,7 +1021,7 @@ export namespace operations {
 
 			const foundNames = rxRecords.map((r) => r.str);
 			const error: SubmissionValidationError = {
-				fieldName: TherapyRxNormFields.drug_rxnormid,
+				fieldName: TherapyRxNormFieldsEnum.drug_rxnormid,
 				index: index,
 				info: {},
 				message: validationErrorMessage(DataValidationErrors.THERAPY_RXNORM_DRUG_NAME_INVALID, {
@@ -1038,7 +1038,7 @@ export namespace operations {
 		// nothing was provided
 		// this shouldn't happen unless the schema is not validating correctly
 		const error: SubmissionValidationError = {
-			fieldName: TherapyRxNormFields.drug_rxnormid,
+			fieldName: TherapyRxNormFieldsEnum.drug_rxnormid,
 			index: index,
 			info: {},
 			message: `an rxcui id or drug name is required`,

src/submission/validation-clinical/surgery.ts

@@ -22,21 +22,21 @@ import { isEqual, omit } from 'lodash';
 import _ from 'mongoose-sequence';
 import { Donor, Therapy } from '../../clinical/clinical-entities';
 import {
-	DataValidationErrors,
-	SubmissionValidationError,
-	SubmissionValidationOutput,
-	SubmittedClinicalRecord,
-} from '../submission-entities';
+	ClinicalEntitySchemaNames,
+	CommonTherapyFieldsEnum,
+	DonorFieldsEnum,
+	SurgeryFieldsEnum,
+} from '../../common-model/entities';
 import {
 	findClinicalObjects,
 	getSingleClinicalObjectFromDonor,
 } from '../../common-model/functions';
 import {
-	ClinicalEntitySchemaNames,
-	CommonTherapyFields,
-	DonorFieldsEnum,
-	SurgeryFieldsEnum,
-} from '../../common-model/entities';
+	DataValidationErrors,
+	SubmissionValidationError,
+	SubmissionValidationOutput,
+	SubmittedClinicalRecord,
+} from '../submission-entities';
 import { checkTreatmentHasCorrectTypeForTherapy, getTreatment } from './therapy';
 import * as utils from './utils';
 
@@ -112,8 +112,8 @@ export const validate = async (
 					DataValidationErrors.DUPLICATE_SURGERY_WHEN_SPECIMEN_NOT_SUBMITTED,
 					DonorFieldsEnum.submitter_donor_id,
 					{
-						submitter_donor_id: therapyRecord[CommonTherapyFields.submitter_donor_id],
-						submitter_treatment_id: therapyRecord[CommonTherapyFields.submitter_treatment_id],
+						submitter_donor_id: therapyRecord[CommonTherapyFieldsEnum.submitter_donor_id],
+						submitter_treatment_id: therapyRecord[CommonTherapyFieldsEnum.submitter_treatment_id],
 					},
 				),
 			);
@@ -147,8 +147,8 @@ function validateSurgeryByDonorAndTreatment(
 				DataValidationErrors.SURGERY_TYPES_NOT_EQUAL,
 				SurgeryFieldsEnum.submitter_specimen_id,
 				{
-					submitter_donor_id: therapyRecord[CommonTherapyFields.submitter_donor_id],
-					submitter_treatment_id: therapyRecord[CommonTherapyFields.submitter_treatment_id],
+					submitter_donor_id: therapyRecord[CommonTherapyFieldsEnum.submitter_donor_id],
+					submitter_treatment_id: therapyRecord[CommonTherapyFieldsEnum.submitter_treatment_id],
 					surgery_type: therapyRecord[SurgeryFieldsEnum.surgery_type],
 				},
 			);
@@ -160,12 +160,12 @@ function findSubmittedSurgeryByDonorAndTreatment(
 	existenDonor: DeepReadonly<Donor>,
 	therapyRecord: DeepReadonly<SubmittedClinicalRecord>,
 ) {
-	const submitterDonorId = therapyRecord[CommonTherapyFields.submitter_donor_id];
-	const sumitterTreatmentId = therapyRecord[CommonTherapyFields.submitter_treatment_id];
+	const submitterDonorId = therapyRecord[CommonTherapyFieldsEnum.submitter_donor_id];
+	const sumitterTreatmentId = therapyRecord[CommonTherapyFieldsEnum.submitter_treatment_id];
 	return getSingleClinicalObjectFromDonor(existenDonor, ClinicalEntitySchemaNames.SURGERY, {
 		clinicalInfo: {
-			[CommonTherapyFields.submitter_donor_id]: submitterDonorId as string,
-			[CommonTherapyFields.submitter_treatment_id]: sumitterTreatmentId as string,
+			[CommonTherapyFieldsEnum.submitter_donor_id]: submitterDonorId as string,
+			[CommonTherapyFieldsEnum.submitter_treatment_id]: sumitterTreatmentId as string,
 		},
 	}) as DeepReadonly<Therapy>;
 }
@@ -174,12 +174,12 @@ function findSurgeryInCurrentSubmission(
 	mergedDonor: Donor,
 	therapyRecord: DeepReadonly<SubmittedClinicalRecord>,
 ) {
-	const submitterDonorId = therapyRecord[CommonTherapyFields.submitter_donor_id];
-	const sumitterTreatmentId = therapyRecord[CommonTherapyFields.submitter_treatment_id];
+	const submitterDonorId = therapyRecord[CommonTherapyFieldsEnum.submitter_donor_id];
+	const sumitterTreatmentId = therapyRecord[CommonTherapyFieldsEnum.submitter_treatment_id];
 	const sugeries = findClinicalObjects(mergedDonor, ClinicalEntitySchemaNames.SURGERY, {
 		clinicalInfo: {
-			[CommonTherapyFields.submitter_donor_id]: submitterDonorId as string,
-			[CommonTherapyFields.submitter_treatment_id]: sumitterTreatmentId as string,
+			[CommonTherapyFieldsEnum.submitter_donor_id]: submitterDonorId as string,
+			[CommonTherapyFieldsEnum.submitter_treatment_id]: sumitterTreatmentId as string,
 		},
 	}) as DeepReadonly<Therapy>[];