Merge pull request #403 from hpi-dhc/issue/258-validate-dtos

Validate DTOs

.markdownlint.yml

@@ -4,6 +4,9 @@ default: true
 # Allow inline html by disabling rule MD033
 MD033: false
 
+# Allow bare urls
+MD034: false
+
 # Allow other elements but h1 in first line
 MD041: false
 

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;
+        });
+    }
+}

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

@@ -1,4 +1,30 @@
-import { BaseEntity } from '../entities/base.entity';
+import { ParseArrayOptions, ParseArrayPipe } from '@nestjs/common';
+import {
+    IntersectionType,
+    OmitType,
+    PartialType,
+    PickType,
+} from '@nestjs/mapped-types';
 
-export type PatchBodyDto<T extends BaseEntity> = (Pick<T, 'id'> &
-    Partial<Omit<T, 'id'>>)[];
+import { Guideline } from '../../guidelines/entities/guideline.entity';
+import { Medication } from '../../medications/medication.entity';
+
+export class PatchMedicationDto extends IntersectionType(
+    PickType(Medication, ['id'] as const),
+    PartialType(Medication),
+) {}
+
+export class PatchGuidelineDto extends IntersectionType(
+    PickType(Guideline, ['id'] as const),
+    OmitType(PartialType(Guideline), ['id'] as const),
+) {}
+
+export function getPatchArrayPipe(
+    items: ParseArrayOptions['items'],
+): ParseArrayPipe {
+    return new ParseArrayPipe({
+        items,
+        whitelist: true,
+        forbidNonWhitelisted: true,
+    });
+}

annotation-server/src/common/entities/base.entity.ts

@@ -1,6 +1,8 @@
+import { IsNumber } from 'class-validator';
 import { PrimaryGeneratedColumn } from 'typeorm';
 
 export abstract class BaseEntity {
     @PrimaryGeneratedColumn()
+    @IsNumber()
     id: number;
 }

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;

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;

annotation-server/src/guidelines/entities/guideline.entity.ts

@@ -1,3 +1,4 @@
+import { IsEnum, IsString } from 'class-validator';
 import { Column, Entity, ManyToOne, OneToMany } from 'typeorm';
 
 import { BaseEntity } from '../../common/entities/base.entity';
@@ -15,16 +16,19 @@ export enum WarningLevel {
 @Entity()
 export class Guideline extends BaseEntity {
     @Column({ nullable: true })
+    @IsString()
     implication: string;
 
     @Column({ nullable: true })
+    @IsString()
     recommendation: string;
 
     @Column({
         type: 'enum',
         enum: WarningLevel,
         nullable: true,
     })
+    @IsEnum(WarningLevel)
     warningLevel: WarningLevel;
 
     @ManyToOne(() => Medication, (medication) => medication.guidelines, {

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

@@ -11,7 +11,10 @@ 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 {
+    getPatchArrayPipe,
+    PatchGuidelineDto,
+} from '../common/dtos/patch-body.dto';
 import {
     ApiFindGuidelineErrorsQueries,
     FindGuidelineErrorQueryDto,
@@ -53,9 +56,10 @@ export class GuidelinesController {
     @ApiBodyPatch('guideline')
     @Patch()
     async patchGuidelines(
-        @Body() patch: PatchBodyDto<Guideline>,
+        @Body(getPatchArrayPipe(PatchGuidelineDto))
+        patches: PatchGuidelineDto[],
     ): Promise<void> {
-        return this.guidelinesService.patch(patch);
+        return this.guidelinesService.patch(patches);
     }
 
     @ApiOperation({ summary: 'Fetch all guidelines' })

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

@@ -3,10 +3,11 @@ 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';
 
-import { PatchBodyDto } from '../common/dtos/patch-body.dto';
+import { PatchGuidelineDto } 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';
@@ -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),
@@ -405,11 +414,13 @@ export class GuidelinesService {
         return guidelinesForPhenotype;
     }
 
-    async patch(patch: PatchBodyDto<Guideline>): Promise<void> {
+    async patch(patches: PatchGuidelineDto[]): Promise<void> {
         await Promise.all(
-            patch.map(({ id, ...update }) =>
-                this.guidelinesRepository.update(id, update),
-            ),
+            patches
+                .filter((patch) => Object.keys(patch).length > 1)
+                .map(({ id, ...update }) =>
+                    this.guidelinesRepository.update(id, update),
+                ),
         );
     }
 

annotation-server/src/main.ts

@@ -1,3 +1,4 @@
+import { ValidationPipe } from '@nestjs/common';
 import { ConfigService } from '@nestjs/config';
 import { NestFactory } from '@nestjs/core';
 import { NestExpressApplication } from '@nestjs/platform-express';
@@ -11,6 +12,7 @@ async function bootstrap() {
     const configService = app.get(ConfigService);
 
     app.setGlobalPrefix('/api/v1');
+    app.useGlobalPipes(new ValidationPipe());
     app.useGlobalInterceptors(new TypeormErrorInterceptor());
 
     const config = new DocumentBuilder()

annotation-server/src/medications/dtos/find-medication-query-dto.ts

@@ -1,6 +1,6 @@
 import { applyDecorators } from '@nestjs/common';
 import { ApiQuery } from '@nestjs/swagger';
-import { IsBooleanString, IsIn } from 'class-validator';
+import { IsBooleanString, IsIn, IsOptional } from 'class-validator';
 
 import {
     ApiQueryLimit,
@@ -16,13 +16,16 @@ export class FindMedicationQueryDto extends SearchableFindQueryDto {
     sortby: string;
 
     @IsBooleanString()
-    withGuidelines: string;
+    @IsOptional()
+    withGuidelines?: string;
 
     @IsBooleanString()
-    getGuidelines: string;
+    @IsOptional()
+    getGuidelines?: string;
 
     @IsBooleanString()
-    onlyIds: string;
+    @IsOptional()
+    onlyIds?: string;
 }
 
 export function ApiFindMedicationsQueries(): MethodDecorator {

annotation-server/src/medications/medication.entity.ts

@@ -1,3 +1,4 @@
+import { IsString } from 'class-validator';
 import { Entity, Column, OneToMany, ViewEntity, ViewColumn } from 'typeorm';
 
 import { BaseEntity } from '../common/entities/base.entity';
@@ -22,9 +23,11 @@ export class Medication extends BaseEntity {
     synonyms: string[];
 
     @Column({ nullable: true })
+    @IsString()
     drugclass: string;
 
     @Column({ nullable: true })
+    @IsString()
     indication: string;
 
     @OneToMany(() => Guideline, (guideline) => guideline.medication)

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

@@ -3,7 +3,10 @@ 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 {
+    getPatchArrayPipe,
+    PatchMedicationDto,
+} from '../common/dtos/patch-body.dto';
 import {
     ApiFindMedicationsQueries,
     ApiFindMedicationQueries,
@@ -35,9 +38,10 @@ export class MedicationsController {
     @ApiBodyPatch('medication')
     @Patch()
     async patchMedications(
-        @Body() patch: PatchBodyDto<Medication>,
+        @Body(getPatchArrayPipe(PatchMedicationDto))
+        patches: PatchMedicationDto[],
     ): Promise<void> {
-        return this.medicationsService.patch(patch);
+        return this.medicationsService.patch(patches);
     }
 
     @ApiOperation({ summary: 'Fetch all medications' })

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

@@ -9,7 +9,7 @@ import { InjectRepository } from '@nestjs/typeorm';
 import * as JSONStream from 'JSONStream';
 import { FindOneOptions, Repository } from 'typeorm';
 
-import { PatchBodyDto } from '../common/dtos/patch-body.dto';
+import { PatchMedicationDto } 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';
@@ -166,11 +166,13 @@ export class MedicationsService {
         return (await this.medicationRepository.count()) > 0;
     }
 
-    async patch(patch: PatchBodyDto<Medication>): Promise<void> {
+    async patch(patches: PatchMedicationDto[]): Promise<void> {
         await Promise.all(
-            patch.map(({ id, ...update }) =>
-                this.medicationRepository.update(id, update),
-            ),
+            patches
+                .filter((patch) => Object.keys(patch).length > 1)
+                .map(({ id, ...update }) =>
+                    this.medicationRepository.update(id, update),
+                ),
         );
     }
 

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;
 }

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);