Bug/#413 exception fail (#1131)

* remove formatting data function

* add default properties in document for new saves

* make comment more clear

* cleanup

* add migration

---------

Co-authored-by: Ciaran Schutte <[email protected]>

migrations/20240209102734-413-add-default-exception-properties.js

@@ -0,0 +1,38 @@
+/**
+ * ensure that all property entity exceptions are defined with default values ie. []
+ */
+const defaults = {
+	follow_up: [],
+	treatment: [],
+	specimen: [],
+};
+
+module.exports = {
+	async up(db, client) {
+		try {
+			const exceptions = await db
+				.collection('entityexceptions')
+				.find()
+				.toArray();
+
+			exceptions.forEach((exception) => {
+				const _id = exception._id;
+				const update = { ...defaults, ...exception };
+
+				db.collection('entityexceptions').updateOne(
+					{ _id },
+					{
+						$set: update,
+					},
+				);
+			});
+		} catch (e) {
+			console.error('migration up failed', err);
+			throw err;
+		}
+	},
+
+	async down(db, client) {
+		// no action needed
+	},
+};

src/exception/property-exceptions/property-exception-service.ts

@@ -42,35 +42,6 @@ import {
 	validateRecords,
 } from './validation';
 
-/**
- * creates exception object with tsv style records
- * @param programId
- * @param records
- * @param schema
- * @returns valid EntityException array
- */
-const recordsToEntityException = ({
-	programId,
-	records,
-	schema,
-}: {
-	programId: string;
-	records: ReadonlyArray<EntityExceptionRecord>;
-	schema: ClinicalEntitySchemaNames;
-}) => {
-	const exception: OnlyRequired<EntityException, 'programId'> = { programId };
-
-	if (schema === ClinicalEntitySchemaNames.SPECIMEN) {
-		exception.specimen = records as SpecimenExceptionRecord[];
-	} else if (schema === ClinicalEntitySchemaNames.FOLLOW_UP) {
-		exception.follow_up = records as FollowUpExceptionRecord[];
-	} else if (schema === ClinicalEntitySchemaNames.TREATMENT) {
-		exception.treatment = records as TreatmentExceptionRecord[];
-	}
-
-	return exception;
-};
-
 /**
  * normalize before schema validation
  * tsv record values may contain different casing, validation needs normalized casing
@@ -190,8 +161,7 @@ export const createEntityException = async ({
 		throw new ValidationError(errors);
 	}
 
-	const exceptionToSave = recordsToEntityException({ programId, records, schema });
-	const doc = await entityExceptionRepository.save(exceptionToSave);
+	const doc = await entityExceptionRepository.save(programId, records, schema);
 	return success(doc);
 };
 

src/exception/property-exceptions/repo/entity.ts

@@ -24,9 +24,10 @@ import {
 	BaseEntityExceptionRecord,
 	Entity,
 	EntityException,
+	EntityExceptionRecord,
 	ExceptionValue,
-	OnlyRequired,
 } from '../types';
+import { ClinicalEntitySchemaNames } from '../../../common-model/entities';
 
 const L = loggerFor(__filename);
 
@@ -66,17 +67,26 @@ const EntityExceptionModel =
 	mongoose.model<EntityException>('EntityException', entityExceptionSchema);
 
 const entityExceptionRepository = {
-	async save(exception: OnlyRequired<EntityException, 'programId'>): Promise<EntityException> {
-		L.debug(`Creating new donor exception with: ${JSON.stringify(exception)}`);
+	async save(
+		programId: string,
+		records: ReadonlyArray<EntityExceptionRecord>,
+		entity: ClinicalEntitySchemaNames,
+	): Promise<EntityException> {
+		const entities: Record<Entity, typeof records> = {
+			follow_up: [],
+			treatment: [],
+			specimen: [],
+		};
+		const update = { ...entities, ...{ [entity]: records } };
 
-		const update = { $set: exception };
+		L.debug(`Creating new donor exception for program: ${programId}, entity: ${entity}`);
 
 		try {
-			const doc = await EntityExceptionModel.findOneAndUpdate(
-				{ programId: exception.programId },
-				update,
-				{ upsert: true, new: true, returnDocument: 'after' },
-			).lean(true);
+			const doc = await EntityExceptionModel.findOneAndUpdate({ programId }, update, {
+				upsert: true,
+				new: true,
+				returnDocument: 'after',
+			}).lean(true);
 			return doc;
 		} catch (e) {
 			L.error('Failed to create entity exception: ', e);

src/submission/exceptions/exceptions.ts

@@ -123,7 +123,7 @@ const validateFieldValueWithExceptions = ({
 					.forEach((exception) => exceptions.push(exception));
 				break;
 			default:
-				// schema is neither specimen nor followup, do not filter for entity exceptions
+				// schema is NOT specimen || follow_up || treatment, do not filter for entity exceptions
 				break;
 		}