Merge pull request #362 from hpi-dhc/issue/343-rename-genephenotype

Rename `GenePhenotype`

annotation-server/src/app.module.ts

@@ -5,9 +5,9 @@ import { TypeOrmModule } from '@nestjs/typeorm';
 
 import { AppController } from './app.controller';
 import { AppService } from './app.service';
-import { GenePhenotypesModule } from './gene-phenotypes/gene-phenotypes.module';
 import { GuidelinesModule } from './guidelines/guidelines.module';
 import { MedicationsModule } from './medications/medications.module';
+import { PhenotypesModule } from './phenotypes/phenotypes.module';
 
 @Module({
     imports: [
@@ -32,7 +32,7 @@ import { MedicationsModule } from './medications/medications.module';
             }),
             inject: [ConfigService],
         }),
-        GenePhenotypesModule,
+        PhenotypesModule,
         GuidelinesModule,
         MedicationsModule,
         ScheduleModule.forRoot(),

annotation-server/src/app.service.ts

@@ -1,22 +1,22 @@
 import { Injectable } from '@nestjs/common';
 import { Cron } from '@nestjs/schedule';
 
-import { GenePhenotypesService } from './gene-phenotypes/gene-phenotypes.service';
 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 genephenotypeService: GenePhenotypesService,
+        private phenotypesService: PhenotypesService,
     ) {}
 
     @Cron('0 0 1 * *', { name: 'monthlyUpdates' })
     async initializeDatabase(): Promise<void> {
         await this.medicationService.fetchAllMedications();
-        await this.genephenotypeService.fetchGenePhenotypes();
+        await this.phenotypesService.fetchPhenotypes();
         await this.guidelineService.fetchGuidelines();
     }
 }

annotation-server/src/guidelines/caches/phenotype-caches.ts

@@ -0,0 +1,89 @@
+import { ILike } from 'typeorm';
+
+import { Phenotype } from '../../phenotypes/entities/phenotype.entity';
+import { PhenotypesService } from '../../phenotypes/phenotypes.service';
+import {
+    GuidelineError,
+    GuidelineErrorBlame,
+    GuidelineErrorType,
+} from '../entities/guideline-error.entity';
+import { GuidelineCacheMap } from './guideline-cache';
+
+export class PhenotypesByGeneCache extends GuidelineCacheMap<
+    Array<Set<Phenotype>>
+> {
+    private phenotypesService: PhenotypesService;
+    private spreadsheetGeneResultHeader: Set<string>[];
+
+    constructor(
+        phenotypesService: PhenotypesService,
+        spreadsheetGeneResultHeader: Set<string>[],
+    ) {
+        super();
+        this.phenotypesService = phenotypesService;
+        this.spreadsheetGeneResultHeader = spreadsheetGeneResultHeader;
+    }
+
+    protected async retrieve(
+        ...[geneSymbolName]: string[]
+    ): Promise<Set<Phenotype>[]> {
+        const geneSymbol = await this.phenotypesService.findOneGeneSymbol({
+            where: { name: ILike(geneSymbolName) },
+            relations: [
+                'phenotypes',
+                'phenotypes.geneResult',
+                'phenotypes.geneSymbol',
+            ],
+        });
+        const phenotypes = this.spreadsheetGeneResultHeader.map(
+            (geneResults) =>
+                new Set(
+                    geneSymbol.phenotypes.filter((phenotype) =>
+                        geneResults.has(
+                            phenotype.geneResult.name.toLowerCase(),
+                        ),
+                    ),
+                ),
+        );
+        return phenotypes;
+    }
+
+    protected createError(...[geneSymbolName]: string[]): GuidelineError {
+        const error = new GuidelineError();
+        error.type = GuidelineErrorType.PHENOTYPE_NOT_FOUND;
+        error.blame = GuidelineErrorBlame.CPIC;
+        error.context = geneSymbolName;
+        return error;
+    }
+}
+
+export class PhenotypesCache extends GuidelineCacheMap<Phenotype> {
+    private phenotypesService: PhenotypesService;
+
+    constructor(phenotypesService: PhenotypesService) {
+        super();
+        this.phenotypesService = phenotypesService;
+    }
+
+    protected async retrieve(
+        ...[geneSymbolName, geneResultName]: string[]
+    ): Promise<Phenotype> {
+        return this.phenotypesService.findOne({
+            where: {
+                geneSymbol: { name: ILike(geneSymbolName) },
+                geneResult: { name: geneResultName },
+            },
+            relations: ['geneResult', 'geneSymbol'],
+        });
+    }
+
+    protected createError(
+        ...[geneSymbolName, geneResultName]: string[]
+    ): GuidelineError {
+        const error = new GuidelineError();
+        error.type = GuidelineErrorType.PHENOTYPE_NOT_FOUND;
+        error.blame = GuidelineErrorBlame.CPIC;
+        error.context = `${geneSymbolName}:${geneResultName}`;
+        return error;
+    }
+}

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

@@ -6,7 +6,7 @@ import { Guideline } from './guideline.entity';
 export enum GuidelineErrorType {
     MEDICATION_NAME_NOT_FOUND = 'medication_name_not_found',
     MEDICATION_RXCUI_NOT_FOUND = 'medication_rxcui_not_found',
-    GENEPHENOTYPE_NOT_FOUND = 'genephenotype_not_found',
+    PHENOTYPE_NOT_FOUND = 'phenotype_not_found',
     GENE_NOT_FOUND = 'gene_not_found',
     GUIDELINE_MISSING_FROM_SHEET = 'guideline_missing_from_sheet',
     GUIDELINE_MISSING_FROM_CPIC = 'guideline_missing_from_cpic',

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

@@ -1,8 +1,8 @@
 import { Column, Entity, ManyToOne, OneToMany } from 'typeorm';
 
 import { BaseEntity } from '../../common/entities/base.entity';
-import { GenePhenotype } from '../../gene-phenotypes/entities/gene-phenotype.entity';
 import { Medication } from '../../medications/medication.entity';
+import { Phenotype } from '../../phenotypes/entities/phenotype.entity';
 import { CpicRecommendationDto } from '../dtos/cpic-recommendation.dto';
 import { GuidelineError } from './guideline-error.entity';
 
@@ -32,8 +32,8 @@ export class Guideline extends BaseEntity {
     })
     medication: Medication;
 
-    @ManyToOne(() => GenePhenotype, { onDelete: 'CASCADE' })
-    genePhenotype: GenePhenotype;
+    @ManyToOne(() => Phenotype, { onDelete: 'CASCADE' })
+    phenotype: Phenotype;
 
     @Column()
     cpicRecommendation: string;
@@ -68,18 +68,18 @@ export class Guideline extends BaseEntity {
     static fromCpicRecommendation(
         recommendation: CpicRecommendationDto,
         medication: Medication,
-        genePhenotype: GenePhenotype,
+        phenotype: Phenotype,
     ): Guideline {
         const guideline = new Guideline();
 
         guideline.medication = medication;
-        guideline.genePhenotype = genePhenotype;
+        guideline.phenotype = phenotype;
         guideline.cpicRecommendation = recommendation.drugrecommendation;
         guideline.cpicClassification = recommendation.classification;
         if (recommendation.comments.toLowerCase() !== 'n/a')
             guideline.cpicComment = recommendation.comments;
         guideline.cpicImplication =
-            recommendation.implications[genePhenotype.geneSymbol.name];
+            recommendation.implications[phenotype.geneSymbol.name];
         guideline.cpicGuidelineId = recommendation.guidelineid;
         guideline.errors = [];
 

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

@@ -2,8 +2,8 @@ import { HttpModule } from '@nestjs/axios';
 import { Module } from '@nestjs/common';
 import { TypeOrmModule } from '@nestjs/typeorm';
 
-import { GenePhenotypesModule } from '../gene-phenotypes/gene-phenotypes.module';
 import { MedicationsModule } from '../medications/medications.module';
+import { PhenotypesModule } from '../phenotypes/phenotypes.module';
 import { GuidelineError } from './entities/guideline-error.entity';
 import { Guideline } from './entities/guideline.entity';
 import { GuidelinesController } from './guidelines.controller';
@@ -12,7 +12,7 @@ import { GuidelinesService } from './guidelines.service';
 @Module({
     imports: [
         HttpModule,
-        GenePhenotypesModule,
+        PhenotypesModule,
         MedicationsModule,
         TypeOrmModule.forFeature([Guideline, GuidelineError]),
     ],