react-mutation-mapper/dist/store/DefaultMutationMapperDataFetcher.d.ts

Generic Mutation Mapper

import _ from 'lodash';
import { AggregatedHotspots, EvidenceType, IOncoKbData, Mutation, UniprotFeature } from 'cbioportal-utils';
import { CancerGene, OncoKbAPI, OncoKBInfo } from 'oncokb-ts-api-client';
import { EnsemblFilter, EnsemblTranscript, GenomeNexusAPI, GenomeNexusAPIInternal, Hotspot, PfamDomain, PostTranslationalModification, VariantAnnotation, MyVariantInfo } from 'genome-nexus-ts-api-client';
import { MutationMapperDataFetcher } from '../model/MutationMapperDataFetcher';
export interface MutationMapperDataFetcherConfig {
    myGeneUrlTemplate?: string;
    uniprotIdUrlTemplate?: string;
    mutationAlignerUrlTemplate?: string;
    cachePostMethodsOnClients?: boolean;
    apiCacheLimit?: number;
    genomeNexusUrl?: string;
    oncoKbUrl?: string;
}
export declare class DefaultMutationMapperDataFetcher implements MutationMapperDataFetcher {
    private config;
    oncoKbClient: OncoKbAPI;
    genomeNexusClient: GenomeNexusAPI;
    genomeNexusInternalClient: GenomeNexusAPIInternal;
    constructor(config: MutationMapperDataFetcherConfig, genomeNexusClient?: Partial<GenomeNexusAPI>, genomeNexusInternalClient?: Partial<GenomeNexusAPIInternal>, oncoKbClient?: Partial<OncoKbAPI>);
    fetchSwissProtAccession(entrezGeneId: number): Promise<any>;
    fetchUniprotId(swissProtAccession: string): Promise<string>;
    fetchPfamDomainData(pfamAccessions: string[], client?: GenomeNexusAPI): Promise<PfamDomain[]>;
    fetchVariantAnnotationsIndexedByGenomicLocation(mutations: Partial<Mutation>[], fields?: string[], isoformOverrideSource?: string, client?: GenomeNexusAPI): Promise<{
        [genomicLocation: string]: VariantAnnotation;
    }>;
    fetchMyVariantInfoAnnotationsIndexedByGenomicLocation(mutations: Partial<Mutation>[], isoformOverrideSource?: string, client?: GenomeNexusAPI): Promise<{
        [genomicLocation: string]: MyVariantInfo;
    }>;
    fetchCanonicalTranscriptWithFallback(hugoSymbol: string, isoformOverrideSource: string, allTranscripts: EnsemblTranscript[] | undefined, client?: GenomeNexusAPI): Promise<EnsemblTranscript | undefined>;
    fetchCanonicalTranscript(hugoSymbol: string, isoformOverrideSource: string, client?: GenomeNexusAPI): Promise<EnsemblTranscript>;
    fetchEnsemblTranscriptsByEnsemblFilter(ensemblFilter: Partial<EnsemblFilter>, client?: GenomeNexusAPI): Promise<EnsemblTranscript[] | undefined>;
    fetchPtmData(ensemblId: string, client?: GenomeNexusAPI): Promise<PostTranslationalModification[]>;
    fetchUniprotFeatures(swissProtId: string, category: string[], client?: GenomeNexusAPI): Promise<UniprotFeature[]>;
    fetchCancerHotspotData(ensemblId: string, client?: GenomeNexusAPIInternal): Promise<Hotspot[]>;
    fetchAggregatedHotspotsData(mutations: Mutation[], client?: GenomeNexusAPIInternal): Promise<AggregatedHotspots[]>;
    fetchOncoKbCancerGenes(client?: OncoKbAPI): Promise<CancerGene[]>;
    fetchOncoKbInfo(client?: OncoKbAPI): Promise<OncoKBInfo>;
    fetchOncoKbData(mutations: Mutation[], annotatedGenes: {
        [entrezGeneId: number]: boolean;
    } | Error, getTumorType: (mutation: Mutation) => string, getEntrezGeneId: (mutation: Mutation) => number, evidenceTypes?: EvidenceType[], client?: OncoKbAPI): Promise<IOncoKbData | Error>;
    queryOncoKbData(queryVariants: Mutation[], getTumorType: (mutation: Mutation) => string, getEntrezGeneId: (mutation: Mutation) => number, client?: OncoKbAPI, evidenceTypes?: EvidenceType[]): Promise<{
        indicatorMap: _.Dictionary<import("oncokb-ts-api-client").IndicatorQueryResp>;
    }>;
}
export default DefaultMutationMapperDataFetcher;