Clinical id service integration

package.json

@@ -58,6 +58,7 @@
 		"@types/express-serve-static-core": "4.16.7",
 		"@types/jsonwebtoken": "^8.3.2",
 		"@types/lodash": "^4.14.134",
+		"@types/memoizee": "^0.4.11",
 		"@types/migrate-mongo": "^7.0.0",
 		"@types/mocha": "^9.1.1",
 		"@types/mongodb": "^3.1.28",
@@ -66,6 +67,7 @@
 		"@types/morgan": "^1.7.35",
 		"@types/multer": "^1.3.7",
 		"@types/mysql": "^2.15.9",
+		"@types/ms": "^0.7.34",
 		"@types/node": "^12.0.10",
 		"@types/node-fetch": "^2.5.0",
 		"@types/node-vault": "^0.9.0",
@@ -105,6 +107,7 @@
 		"adm-zip": "^0.4.16",
 		"apollo-server-core": "^3.12.0",
 		"async": "^3.0.1",
+		"axios": "^1.6.7",
 		"bcrypt-nodejs": "^0.0.3",
 		"bluebird": "^3.5.5",
 		"body-parser": "^1.19.0",
@@ -124,6 +127,7 @@
 		"kafkajs": "^1.12.0",
 		"kind-of": "^6.0.3",
 		"lodash": "^4.17.21",
+		"memoizee": "^0.4.17",
 		"migrate-mongo": "^8.2.3",
 		"mock-http-server": "^1.4.1",
 		"mongoose": "^5.13.14",
@@ -132,6 +136,7 @@
 		"morgan": "^1.10.0",
 		"mquery": ">=3.2.3",
 		"multer": "^1.4.2",
+		"ms": "^2.1.3",
 		"mysql": "^2.18.1",
 		"node-fetch": "^2.6.7",
 		"node-vault": "^0.9.11",

src/clinical/donor-repo.ts

@@ -24,6 +24,7 @@ import mongoose, { PaginateModel } from 'mongoose';
 import mongoosePaginate from 'mongoose-paginate-v2';
 import { DeepReadonly } from 'deep-freeze';
 import { F, MongooseUtils, notEmpty } from '../utils';
+import { setEntityIds, setEntityIdsForDonors } from './id-generator';
 
 export const SUBMITTER_ID = 'submitterId';
 export const SPECIMEN_SUBMITTER_ID = 'specimen.submitterId';
@@ -109,20 +110,22 @@ export interface DonorRepository {
 	): Promise<DeepReadonly<Donor> | undefined>;
 	iterateAllByProgramId(programId: string): AsyncIterable<DeepReadonly<Donor>>;
 	create(donor: DeepReadonly<Partial<Donor>>): Promise<DeepReadonly<Donor>>;
-	update(donor: DeepReadonly<Donor>): Promise<DeepReadonly<Donor>>;
-	updateAll(donors: DeepReadonly<Donor>[]): Promise<DeepReadonly<Donor>[]>;
+	update(donor: Donor): Promise<DeepReadonly<Donor>>;
+	updateAll(donors: Donor[]): Promise<DeepReadonly<Donor>[]>;
 	countBy(filter: any): Promise<number>;
 }
 
 // Mongoose implementation of the DonorRepository
 export const donorDao: DonorRepository = {
 	async insertDonors(donors: Donor[]) {
-		await mongoose.connection.db.collection('donors').insertMany(donors);
+		const donorsWithIds = await setEntityIdsForDonors(donors);
+		await mongoose.connection.db.collection('donors').insertMany(donorsWithIds);
 	},
 	async updateDonor(donor: Donor) {
+		const donorsWithIds = await setEntityIds(donor);
 		await mongoose.connection.db
 			.collection('donors')
-			.findOneAndUpdate({ donorId: donor.donorId }, { $set: donor });
+			.findOneAndUpdate({ donorId: donor.donorId }, { $set: donorsWithIds });
 	},
 	async countBy(filter: any) {
 		return await DonorModel.count(filter).exec();
@@ -413,27 +416,41 @@ export const donorDao: DonorRepository = {
 		return iterateAllByProgramId(programId);
 	},
 
-	async update(donor: DeepReadonly<Donor>) {
-		const newDonor = new DonorModel(donor);
+	async update(donor: Donor) {
+		const dnr = await setEntityIds(donor);
+		const newDonor = new DonorModel(await setEntityIds(donor));
 		unsetIsNewFlagForUpdate(newDonor);
-
 		await newDonor.save();
 		return F(MongooseUtils.toPojo(newDonor) as Donor);
 	},
 
-	async updateAll(donors: DeepReadonly<Donor>[]) {
-		const newDonors = donors.map((donor) => {
-			const newDonor = new DonorModel(donor);
+	async updateAll(donors: Donor[]) {
+		const newDonors = donors.map(async (donor) => {
+			const newDonor = new DonorModel(await setEntityIds(donor));
 			unsetIsNewFlagForUpdate(newDonor);
 			return newDonor;
 		});
 
-		const results = await Promise.all(newDonors.map((donor) => donor.save()));
-		return newDonors.map((donor) => F(MongooseUtils.toPojo(donor) as Donor));
+		await Promise.all(
+			newDonors.map((donor) => {
+				donor.then(async (d) => {
+					await d.save();
+				});
+			}),
+		);
+		const result = await Promise.all(
+			newDonors.map((donor) =>
+				donor.then((d) => {
+					return F(MongooseUtils.toPojo(d) as Donor);
+				}),
+			),
+		);
+
+		return result;
 	},
 
-	async create(donor: DeepReadonly<Donor>) {
-		const newDonor = new DonorModel(donor);
+	async create(donor: Partial<Donor>) {
+		const newDonor = new DonorModel(await setEntityIds(donor));
 		const doc = await newDonor.save();
 		return F(MongooseUtils.toPojo(newDonor) as Donor);
 	},
@@ -656,58 +673,9 @@ DonorSchema.index({ 'specimens.samples.submitterId': 1, programId: 1 }, { unique
  * multiple times, and that makes them hard to test because tests depend
  * on resetting the config and bootstraping but global variables keep their state.
  */
-DonorSchema.plugin(AutoIncrement, {
-	inc_field: 'donorId',
-	start_seq: process.env.DONOR_ID_SEED || 250000,
-});
 
 DonorSchema.plugin(mongoosePaginate);
 
-SpecimenSchema.plugin(AutoIncrement, {
-	inc_field: 'specimenId',
-	start_seq: process.env.SPECIMEN_ID_SEED || 210000,
-});
-
-SampleSchema.plugin(AutoIncrement, {
-	inc_field: 'sampleId',
-	start_seq: process.env.SAMPLE_ID_SEED || 610000,
-});
-
-FollowUpSchema.plugin(AutoIncrement, {
-	inc_field: 'followUpId',
-	start_seq: 1,
-});
-
-PrimaryDiagnosisSchema.plugin(AutoIncrement, {
-	inc_field: 'primaryDiagnosisId',
-	start_seq: 1,
-});
-
-FamilyHistorySchema.plugin(AutoIncrement, {
-	inc_field: 'familyHistoryId',
-	start_seq: 1,
-});
-
-ExposureSchema.plugin(AutoIncrement, {
-	inc_field: 'exposureId',
-	start_seq: 1,
-});
-
-BiomarkerSchema.plugin(AutoIncrement, {
-	inc_field: 'biomarkerId',
-	start_seq: 1,
-});
-
-ComorbiditySchema.plugin(AutoIncrement, {
-	inc_field: 'comorbidityId',
-	start_seq: 1,
-});
-
-TreatmentSchema.plugin(AutoIncrement, {
-	inc_field: 'treatmentId',
-	start_seq: 1,
-});
-
 export let DonorModel = mongoose.model<DonorDocument>('Donor', DonorSchema) as PaginateModel<
 	DonorDocument
 >;