feat(annotation-server): patch medications

annotation-server/src/common/api/bodies.ts

@@ -0,0 +1,9 @@
+import { ApiBody } from '@nestjs/swagger';
+
+export function ApiBodyPatch(resourceName: string): MethodDecorator {
+    return ApiBody({
+        description: `An array of partial ${resourceName} entities. Note that the ID is required.`,
+        required: true,
+        isArray: true,
+    });
+}

annotation-server/src/common/dtos/patch-body.dto.ts

@@ -0,0 +1,4 @@
+import { BaseEntity } from '../entities/base.entity';
+
+export type PatchBodyDto<T extends BaseEntity> = (Pick<T, 'id'> &
+    Partial<Omit<T, 'id'>>)[];

annotation-server/src/guidelines/guidelines.controller.ts

@@ -34,7 +34,7 @@ export class GuidelinesController {
     @ApiOperation({
         summary: 'Supplement matching guideline data from a Google Sheet',
     })
-    @Patch()
+    @Patch('sheet')
     async supplementSheetData(): Promise<void> {
         return this.guidelinesService.supplementSheetData();
     }

annotation-server/src/medications/medications.controller.ts

@@ -1,7 +1,9 @@
-import { Controller, Get, Param, Patch, Query } from '@nestjs/common';
+import { Body, Controller, Get, Param, Patch, Query } from '@nestjs/common';
 import { ApiOperation, ApiTags } from '@nestjs/swagger';
 
+import { ApiBodyPatch } from '../common/api/bodies';
 import { ApiParamGetById } from '../common/api/params';
+import { PatchBodyDto } from '../common/dtos/patch-body.dto';
 import {
     ApiFindMedicationsQueries,
     ApiFindMedicationQueries,
@@ -24,11 +26,20 @@ export class MedicationsController {
     @ApiOperation({
         summary: 'Supplement matching medication data from a Google Sheet',
     })
-    @Patch()
+    @Patch('sheet')
     async supplementSheetData(): Promise<void> {
         return this.medicationsService.supplementSheetData();
     }
 
+    @ApiOperation({ summary: 'Patch medications' })
+    @ApiBodyPatch('medication')
+    @Patch()
+    async patchMedications(
+        @Body() patch: PatchBodyDto<Medication>,
+    ): Promise<void> {
+        return this.medicationsService.patch(patch);
+    }
+
     @ApiOperation({ summary: 'Fetch all medications' })
     @ApiFindMedicationsQueries()
     @Get()

annotation-server/src/medications/medications.service.ts

@@ -18,6 +18,7 @@ import {
     FindOptionsOrderValue,
 } from 'typeorm';
 
+import { PatchBodyDto } from '../common/dtos/patch-body.dto';
 import { fetchSpreadsheetCells } from '../common/utils/google-sheets';
 import { FetchTarget } from '../fetch-dates/fetch-date.entity';
 import { FetchDatesService } from '../fetch-dates/fetch-dates.service';
@@ -162,6 +163,14 @@ export class MedicationsService {
         return (await this.medicationRepository.count()) > 0;
     }
 
+    async patch(patch: PatchBodyDto<Medication>): Promise<void> {
+        await Promise.all(
+            patch.map(({ id, ...update }) =>
+                this.medicationRepository.update(id, update),
+            ),
+        );
+    }
+
     getJSONfromZip(): Promise<string> {
         const jsonPath = path.join(os.tmpdir(), 'drugbank-data.json');
         const proc = getOsSpecificPyProcess(this.configService);

annotation-server/test/app.e2e-spec.ts

@@ -63,14 +63,14 @@ describe('App (e2e)', () => {
     describe('Add sheet data', () => {
         it('should supplement medication data', async () => {
             const patchResponse = await request(app.getHttpServer()).patch(
-                `/medications`,
+                `/medications/sheet`,
             );
             expect(patchResponse.status).toEqual(200);
         }, 30000);
 
         it('should supplement guideline data', async () => {
             const patchResponse = await request(app.getHttpServer()).patch(
-                `/guidelines`,
+                `/guidelines/sheet`,
             );
             expect(patchResponse.status).toEqual(200);
         }, 30000);
@@ -211,6 +211,26 @@ describe('App (e2e)', () => {
         });
     });
 
+    describe('Modify data', () => {
+        it('should patch details of one medication', async () => {
+            const patchResponse = await request(app.getHttpServer())
+                .patch('/medications/')
+                .send([{ id: codeineId, drugclass: 'Not a pain killer' }]);
+            expect(patchResponse.status).toEqual(200);
+        });
+    });
+
+    describe('Verify modified data', () => {
+        it('should verify details for one medication', async () => {
+            const getResponse = await request(app.getHttpServer()).get(
+                '/medications/' + codeineId,
+            );
+            expect(getResponse.status).toEqual(200);
+            expect(getResponse.body.drugclass).toEqual('Not a pain killer');
+            expect(getResponse.body.indication).toEqual('Codeine/indication');
+        });
+    });
+
     afterAll(async () => {
         await medicationService.clearAllMedicationData();
         await app.close();