feat(annotation-server): guidelines only init endpoint

annotation-server/package.json

@@ -55,7 +55,6 @@
     "@nestjs/cli": "^8.0.0",
     "@nestjs/schematics": "^8.0.0",
     "@nestjs/testing": "^8.0.0",
-    "@types/cron": "^1.7.3",
     "@types/express": "^4.17.13",
     "@types/jest": "27.4.1",
     "@types/jsonstream": "^0.8.30",

annotation-server/src/app.module.ts

@@ -1,6 +1,5 @@
 import { Module } from '@nestjs/common';
 import { ConfigModule, ConfigService } from '@nestjs/config';
-import { ScheduleModule } from '@nestjs/schedule';
 import { TypeOrmModule } from '@nestjs/typeorm';
 
 import { AppController } from './app.controller';
@@ -35,7 +34,6 @@ import { PhenotypesModule } from './phenotypes/phenotypes.module';
         PhenotypesModule,
         GuidelinesModule,
         MedicationsModule,
-        ScheduleModule.forRoot(),
     ],
     controllers: [AppController],
     providers: [AppService],

annotation-server/src/app.service.ts

@@ -1,22 +1,17 @@
 import { Injectable } from '@nestjs/common';
-import { Cron } from '@nestjs/schedule';
 
 import { GuidelinesService } from './guidelines/guidelines.service';
 import { MedicationsService } from './medications/medications.service';
-import { PhenotypesService } from './phenotypes/phenotypes.service';
 
 @Injectable()
 export class AppService {
     constructor(
         private medicationService: MedicationsService,
         private guidelineService: GuidelinesService,
-        private phenotypesService: PhenotypesService,
     ) {}
 
-    @Cron('0 0 1 * *', { name: 'monthlyUpdates' })
     async initializeDatabase(): Promise<void> {
         await this.medicationService.fetchAllMedications();
-        await this.phenotypesService.fetchPhenotypes();
         await this.guidelineService.fetchGuidelines();
     }
 }

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

@@ -1,4 +1,4 @@
-import { Controller, Get, Param, Query } from '@nestjs/common';
+import { Controller, Get, Param, Post, Query } from '@nestjs/common';
 import { ApiOperation, ApiParam, ApiTags } from '@nestjs/swagger';
 
 import {
@@ -18,6 +18,12 @@ import { GuidelinesService } from './guidelines.service';
 export class GuidelinesController {
     constructor(private guidelinesService: GuidelinesService) {}
 
+    @ApiOperation({ summary: 'Clear and update all data from CPIC' })
+    @Post()
+    initializeDatabase(): Promise<void> {
+        return this.guidelinesService.fetchGuidelines();
+    }
+
     @ApiOperation({ summary: 'Fetch all guidelines' })
     @ApiFindGuidelinesQueries()
     @Get()

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

@@ -1,6 +1,6 @@
 import { sheets_v4 } from '@googleapis/sheets';
 import { HttpService } from '@nestjs/axios';
-import { Injectable, Logger } from '@nestjs/common';
+import { HttpException, HttpStatus, Injectable, Logger } from '@nestjs/common';
 import { ConfigService } from '@nestjs/config';
 import { InjectRepository } from '@nestjs/typeorm';
 import { lastValueFrom } from 'rxjs';
@@ -120,6 +120,16 @@ export class GuidelinesService {
     }
 
     async fetchGuidelines(): Promise<void> {
+        if (!(await this.medicationsService.hasData())) {
+            throw new HttpException(
+                {
+                    status: HttpStatus.BAD_REQUEST,
+                    error: 'Medication data has to be initialized.',
+                },
+                HttpStatus.BAD_REQUEST,
+            );
+        }
+        await this.phenotypesService.fetchPhenotypes();
         await this.clearAllData();
         const guidelines = await this.fetchCpicGuidelines();
         await this.addGuidelineURLS(guidelines);

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

@@ -155,6 +155,10 @@ export class MedicationsService {
         await this.medicationRepository.delete({});
     }
 
+    async hasData(): Promise<boolean> {
+        return (await this.medicationRepository.count()) > 0;
+    }
+
     getJSONfromZip(): Promise<string> {
         const jsonPath = path.join(os.tmpdir(), 'drugbank-data.json');
         const proc = getOsSpecificPyProcess(this.configService);

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

@@ -26,10 +26,19 @@ describe('App (e2e)', () => {
         medicationService.clearAllMedicationData();
     });
 
+    describe('Pre-initialization', () => {
+        it('should fail to load guidelines without medications', async () => {
+            const createResponse = await request(app.getHttpServer()).post(
+                '/guidelines',
+            );
+            expect(createResponse.status).toEqual(400);
+        });
+    });
+
     describe('Initialization', () => {
         it('should load all data', async () => {
             const createResponse = await request(app.getHttpServer()).post(
-                '/init/',
+                '/init',
             );
             expect(createResponse.status).toEqual(201);
         }, 30000);

yarn.lock

@@ -1146,14 +1146,6 @@
   resolved "https://registry.yarnpkg.com/@types/cookiejar/-/cookiejar-2.1.2.tgz#66ad9331f63fe8a3d3d9d8c6e3906dd10f6446e8"
   integrity sha512-t73xJJrvdTjXrn4jLS9VSGRbz0nUY3cl2DMGDU48lKl+HR9dbbjW2A9r3g40VA++mQpy6uuHg33gy7du2BKpog==
 
-"@types/cron@^1.7.3":
-  version "1.7.3"
-  resolved "https://registry.yarnpkg.com/@types/cron/-/cron-1.7.3.tgz#993db7d54646f61128c851607b64ba4495deae93"
-  integrity sha512-iPmUXyIJG1Js+ldPYhOQcYU3kCAQ2FWrSkm1FJPoii2eYSn6wEW6onPukNTT0bfiflexNSRPl6KWmAIqS+36YA==
-  dependencies:
-    "@types/node" "*"
-    moment ">=2.14.0"
-
 "@types/eslint-scope@^3.7.3":
   version "3.7.3"
   resolved "https://registry.yarnpkg.com/@types/eslint-scope/-/eslint-scope-3.7.3.tgz#125b88504b61e3c8bc6f870882003253005c3224"
@@ -5741,7 +5733,7 @@ moment-timezone@^0.5.x:
   dependencies:
     moment ">= 2.9.0"
 
-"moment@>= 2.9.0", moment@>=2.14.0, moment@^2.29.1:
+"moment@>= 2.9.0", moment@^2.29.1:
   version "2.29.3"
   resolved "https://registry.yarnpkg.com/moment/-/moment-2.29.3.tgz#edd47411c322413999f7a5940d526de183c031f3"
   integrity sha512-c6YRvhEo//6T2Jz/vVtYzqBzwvPT95JBQ+smCytzf7c50oMZRsR/a4w88aD34I+/QVSfnoAnSBFPJHItlOMJVw==