feat(annotation-server): validate internal dtos

Co-authored-by: Matti Schmidt <contact@schmidtchen.me>
hpi-dhc · Jul 18, 2022 · 3a15341 · 3a15341
1 parent f11f9c1
commit 3a15341
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Showing 6 changed files with 34 additions and 9 deletions.
diff --git a/annotation-server/src/common/dtos/instantiable.dto.ts b/annotation-server/src/common/dtos/instantiable.dto.ts
@@ -0,0 +1,7 @@
+export class InstantiableDto<T> {
+    constructor(dto: T) {
+        Object.entries(dto).forEach(([key, value]) => {
+            this[key] = value;
+        });
+    }
+}
diff --git a/annotation-server/src/guidelines/dtos/cpic-guideline.dto.ts b/annotation-server/src/guidelines/dtos/cpic-guideline.dto.ts
@@ -1,6 +1,8 @@
 import { IsNotEmpty, IsNumber, IsString, IsUrl } from 'class-validator';
 
-export class CpicGuidelineDto {
+import { InstantiableDto } from '../../common/dtos/instantiable.dto';
+
+export class CpicGuidelineDto extends InstantiableDto<CpicGuidelineDto> {
     @IsNumber()
     @IsNotEmpty()
     id: number;

diff --git a/annotation-server/src/guidelines/dtos/cpic-recommendation.dto.ts b/annotation-server/src/guidelines/dtos/cpic-recommendation.dto.ts
@@ -1,6 +1,8 @@
 import { IsNotEmpty, IsNumber, IsObject, IsString } from 'class-validator';
 
-export class CpicRecommendationDto {
+import { InstantiableDto } from '../../common/dtos/instantiable.dto';
+
+export class CpicRecommendationDto extends InstantiableDto<CpicRecommendationDto> {
     @IsString()
     @IsNotEmpty()
     drugid: string;

diff --git a/annotation-server/src/guidelines/guidelines.service.ts b/annotation-server/src/guidelines/guidelines.service.ts
@@ -3,6 +3,7 @@ import { HttpService } from '@nestjs/axios';
 import { HttpException, HttpStatus, Injectable, Logger } from '@nestjs/common';
 import { ConfigService } from '@nestjs/config';
 import { InjectRepository } from '@nestjs/typeorm';
+import { validateOrReject } from 'class-validator';
 import { lastValueFrom } from 'rxjs';
 import { FindOptionsOrder, FindOptionsOrderValue, Repository } from 'typeorm';
 
@@ -167,7 +168,13 @@ export class GuidelinesService {
         );
         const recommendationDtos: CpicRecommendationDto[] = (
             await lastValueFrom(response)
-        ).data;
+        ).data.map(
+            (response: CpicRecommendationDto) =>
+                new CpicRecommendationDto(response),
+        );
+        await Promise.all(
+            recommendationDtos.map((dto) => validateOrReject(dto)),
+        );
 
         const guidelinesByMeds: Map<string, Guideline[]> = new Map();
         const guidelineErrors: Set<GuidelineError> = new Set();
@@ -234,7 +241,9 @@ export class GuidelinesService {
         );
         const guidelineDtos: CpicGuidelineDto[] = (
             await lastValueFrom(response)
-        ).data;
+        ).data.map((data: CpicGuidelineDto) => new CpicGuidelineDto(data));
+        await Promise.all(guidelineDtos.map((dto) => validateOrReject(dto)));
+
         const guidelineDtoById: Map<number, CpicGuidelineDto> = new Map();
         guidelineDtos.forEach((guidelineDto) =>
             guidelineDtoById.set(guidelineDto.id, guidelineDto),

diff --git a/annotation-server/src/phenotypes/dtos/diplotype.dto.ts b/annotation-server/src/phenotypes/dtos/diplotype.dto.ts
@@ -1,6 +1,8 @@
-import { IsNotEmpty, IsString } from 'class-validator';
+import { IsNotEmpty, IsOptional, IsString } from 'class-validator';
 
-export class DiplotypeDto {
+import { InstantiableDto } from '../../common/dtos/instantiable.dto';
+
+export class DiplotypeDto extends InstantiableDto<DiplotypeDto> {
     @IsString()
     @IsNotEmpty()
     genesymbol: string;
@@ -10,6 +12,6 @@ export class DiplotypeDto {
     generesult: string;
 
     @IsString()
-    @IsNotEmpty()
+    @IsOptional()
     consultationtext: string;
 }
diff --git a/annotation-server/src/phenotypes/phenotypes.service.ts b/annotation-server/src/phenotypes/phenotypes.service.ts
@@ -1,6 +1,7 @@
 import { HttpService } from '@nestjs/axios';
 import { Injectable, Logger } from '@nestjs/common';
 import { InjectRepository } from '@nestjs/typeorm';
+import { validateOrReject } from 'class-validator';
 import { lastValueFrom } from 'rxjs';
 import { FindOneOptions, Repository } from 'typeorm';
 
@@ -40,8 +41,10 @@ export class PhenotypesService {
             },
         );
 
-        const diplotypeDtos: DiplotypeDto[] = (await lastValueFrom(response))
-            .data;
+        const diplotypeDtos: DiplotypeDto[] = (
+            await lastValueFrom(response)
+        ).data.map((data: DiplotypeDto) => new DiplotypeDto(data));
+        await Promise.all(diplotypeDtos.map((dto) => validateOrReject(dto)));
 
         this.savePhenotypes(diplotypeDtos);