@jax-data-science/api-clients 0.0.1-0

package/lib/ontology/ontology.model.d.ts

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+export interface OntologyConfig {
+    name: string;
+    prefix: string;
+    github: {
+        api: string;
+        home: string;
+    };
+    home: string;
+    api: {
+        docs: string;
+        base: string;
+    };
+    base_file: string;
+    international: boolean;
+    description: string;
+}
+export declare enum Ontology {
+    HP = "HP",
+    MONDO = "MONDO",
+    MP = "MP",
+    CL = "CL",
+    MAXO = "MAXO"
+}
+export interface OntologyTerm {
+    id: string;
+    name: string;
+}

package/lib/ontology/ontology.service.d.ts

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+import { HttpClient } from '@angular/common/http';
+import { Observable } from 'rxjs';
+import { Ontology, OntologyTerm } from './ontology.model';
+import { CollectionResponse, Response } from '../models/response';
+import * as i0 from "@angular/core";
+export declare class OntologyService {
+    private httpClient;
+    config_location: string;
+    private config;
+    /**
+     * Get the configuration file from the source for the backend api service
+     */
+    constructor(httpClient: HttpClient);
+    /**
+     * Search for terms in an ontology
+     * @param query - the search query
+     * @param limit - the number of results to return
+     * @param ontology - the ontology to search
+     */
+    search(query: string, limit: number, ontology: Ontology): Observable<CollectionResponse<OntologyTerm>>;
+    /**
+     * Get a term by its ID
+     * @param id - the term ID
+     */
+    term(id: string): Observable<Response<OntologyTerm>>;
+    /**
+     * Get the parents of a term
+     * @param id - the term ID
+     */
+    parents(id: string): Observable<CollectionResponse<OntologyTerm>>;
+    /**
+     * Get the children of a term
+     * @param id - the term ID
+     */
+    children(id: string): Observable<CollectionResponse<OntologyTerm>>;
+    /**
+     * Get the ancestors of a term
+     * @param id - the term ID
+     */
+    ancestors(id: string): Observable<CollectionResponse<OntologyTerm>>;
+    /**
+     * Get the descendants of a term
+     * @param id - the term ID
+     */
+    descendants(id: string): Observable<CollectionResponse<OntologyTerm>>;
+    /**
+     * Get the ontology from curie
+     */
+    ontologyFromCurie(curie: string): Ontology;
+    /**
+     * Get the ontology api base url configuration
+     **/
+    ontologyBaseResolver(ontology: Ontology): string;
+    static ɵfac: i0.ɵɵFactoryDeclaration<OntologyService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<OntologyService>;
+}

package/lib/snp-grid/models/response/dtos.d.ts

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+import { SNP, SNPSearchRegion } from "../../../mvar/models/response/dtos";
+export interface MusterHealthCheck {
+    status: string;
+    timestamp: string;
+}
+export interface MusterMetadata {
+    total_number_of_SNPs: number;
+    last_updated: string;
+    version: string;
+    total_number_of_strains: number;
+}
+export interface Strain {
+    bq_sample_id: number;
+    mpd_strainid: number;
+    strainname: string;
+    straintype: string;
+}
+export interface Gene {
+    symbol: string;
+    chr: string;
+    start_position: number;
+    end_position: number;
+    strand: string;
+    description: string;
+    mginum: string;
+    markertype: string;
+    centimorgan: number;
+    featuretype: string;
+}
+export interface ReferenceSNP {
+    chr: string;
+    start_position: number;
+    end_position?: number;
+    rsid: string;
+}
+export interface MusterSearchParameters {
+    bq_sample_ids: null;
+    genes: string | null;
+    genes_data: Gene[];
+    limit: number;
+    mpd_strain_ids: string;
+    next_region: string | null;
+    offset: number;
+    query_regions: {
+        chromosome: string;
+        regions: SNPSearchRegion[];
+    }[];
+    regions: SNPSearchRegion[];
+    rsids: string | null;
+    rsids_data: ReferenceSNP[];
+    strain_limit: number;
+    strain_names: null;
+    dataset: Dataset;
+}
+export interface SNPSearchProperties {
+    strains: number[];
+    strains_b?: number[];
+    rsids?: string[];
+    regions?: string[];
+    assembly: string;
+    genes?: string[];
+    offset?: number;
+    dataset_id?: number;
+    is_unique_row?: boolean;
+}
+export interface GenotypeResults {
+    message: string | null;
+    next_region: string;
+    parameter: MusterSearchParameters;
+    snps: SNP[];
+    status: string;
+    total_rows: number;
+}
+export declare enum DatasetStatus {
+    Queued = "queued",
+    Loading = "loading",
+    Done = "done",
+    Archived = "archived"
+}
+export interface Dataset {
+    id: number;
+    display_name: string;
+    sort_by: number;
+    year: string;
+    procedure: string;
+    panel: string;
+    sex: string;
+    dataset_name: string;
+    source: string;
+    status: DatasetStatus;
+    num_of_strains: number;
+    pubmed: string;
+    description: string;
+    assembly_version: string;
+}

package/lib/snp-grid/snp-grid-client.module.d.ts

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+import { ModuleWithProviders } from '@angular/core';
+import * as i0 from "@angular/core";
+import * as i1 from "@angular/common";
+export declare class SnpGridClientModule {
+    static forRoot(environment: any): ModuleWithProviders<SnpGridClientModule>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<SnpGridClientModule, never>;
+    static ɵmod: i0.ɵɵNgModuleDeclaration<SnpGridClientModule, never, [typeof i1.CommonModule], never>;
+    static ɵinj: i0.ɵɵInjectorDeclaration<SnpGridClientModule>;
+}

package/lib/snp-grid/snp-grid.service.d.ts

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+import { HttpClient } from "@angular/common/http";
+import { Observable } from "rxjs";
+import { Dataset, DatasetStatus, Gene, GenotypeResults, MusterHealthCheck, MusterMetadata, ReferenceSNP, SNPSearchProperties, Strain } from './models/response/dtos';
+import { SNPSearchRegion } from '../mvar/models/response/dtos';
+import * as i0 from "@angular/core";
+export declare class SnpGridService {
+    private http;
+    private environment;
+    private api;
+    apiAvailable: boolean;
+    private strains;
+    strains$: Observable<Strain[]>;
+    constructor(http: HttpClient, environment: any);
+    /**
+     * Returns the result of a health check for the API
+     */
+    getHealthCheck(): Observable<MusterHealthCheck>;
+    /**
+     * Returns the metadata on the MUSter DB
+     */
+    getMusterMetadata(): Observable<MusterMetadata>;
+    /**
+     * Returns strains available in the API and takes an optional limit; by default the limit is set
+     * to 5000 to get all strains
+     * @param limit - maximum number of strains to be returned
+     */
+    getStrains(limit?: number): Observable<Strain[]>;
+    /**
+     * Returns a list of known genes whose symbols/coordinates start with the specified value.
+     * @param searchValue - value to use for the "starts with" filter
+     * @param limit - maximum number of genes to return, default is 20
+     */
+    getGenes(searchValue: string, limit?: number): Observable<Gene[]>;
+    /**
+     * Returns the gene that matches the specified gene symbol
+     * @param geneSymbol - symbol to use to get the associated gene info
+     */
+    getGene(geneSymbol: string): Observable<Gene | null>;
+    /**
+     * Returns true if the specified gene symbol is valid from the perspective of MUSter
+     * @param geneSymbol - symbol to use to check the validity of
+     */
+    isGeneSymbolValid(geneSymbol: string): Observable<boolean>;
+    /**
+     * Returns list of known reference SNP (RS) data which includes IDs and coordinates
+     * @param searchValue - value to use to filter the search results
+     * @param limit - maximum number of results to return, default is 20
+     */
+    getReferenceSNPs(searchValue: string, limit?: number): Observable<ReferenceSNP[]>;
+    /**
+     * Returns the RS info that matches the specified rsID
+     * @param rsid - the RSID to use to get the associated RS info
+     */
+    getReferenceSNP(rsid: string): Observable<ReferenceSNP | null>;
+    /**
+     * Returns true if the specified rsID is valid from the perspective of MUSter
+     * @param rsid - rsID to use to check the validity of
+     */
+    isRSIDValid(rsid: string): Observable<boolean>;
+    /**
+     * Returns the SNP results generated from the query constructed from the specified parameters and page
+     * @param parameters - search properties (strain IDs, regions, assembly version, etc.)
+     * @param page - requested page, which is 0-indexed. The 0th page is the initial page
+     * @param pageSize - number of records to show per page. Default of 5000
+     */
+    getGenotypes(parameters: SNPSearchProperties, page?: number, pageSize?: number): Observable<GenotypeResults>;
+    /**
+     * Returns the URL that will generate a download (in file form) for the specified strain IDs and regions
+     * @param strains - list of mpd_strain_ids to query SNPs for
+     * @param regions - list of SNPSearchRegions to query SNPs for (chromosome, start and end)
+     * @param dataset_id - ID of the dataset to query SNPs for
+     * @param is_unique_row - boolean for polymorphism filtering - true for only rows with polymorphism, false for all
+     * @param limit - the limit of the number of result rows to include in the download - you're likely to
+     *                prefer to pass the total number of rows generated by the query itself, which is included
+     *                as part of the GenotypeResults returned by getGenotypes()
+     */
+    getGenotypeDownloadURLForCurrentData(strains: number[], regions: SNPSearchRegion[], dataset_id: number | undefined, is_unique_row: boolean | undefined, limit: number): string;
+    /**
+     * Returns the dataset with the given ID
+     * @param id
+     */
+    getDataset(id: number): Observable<Dataset>;
+    /**
+     * Returns a list of Datasets that match the given criteria
+     * @param status  The value of the status to be used for filtering
+     * @param limit   The maximum number of records to return
+     */
+    findDatasets(status: DatasetStatus, limit?: number): Observable<Dataset[]>;
+    /**
+     * Return a list of strains that match the given criteria
+     * @param datasetId  The ID of the dataset from which to fetch the strains
+     * @param limit      The maximum number of records to return
+     */
+    datasetStrains(datasetId: number, limit?: number): Observable<Strain[]>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<SnpGridService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<SnpGridService>;
+}

package/package.json

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+{
+  "name": "@jax-data-science/api-clients",
+  "version": "0.0.1-0",
+  "dependencies": {
+    "@microsoft/fetch-event-source": "^2.0.1",
+    "rxjs": "^7.8.0",
+    "tslib": "^2.3.0"
+  },
+  "peerDependencies": {
+    "@angular/common": "^19.1.0",
+    "@angular/core": "^19.1.0"
+  },
+  "sideEffects": false,
+  "publishConfig": {
+    "access": "public"
+  },
+  "module": "fesm2022/jax-data-science-api-clients.mjs",
+  "typings": "index.d.ts",
+  "exports": {
+    "./package.json": {
+      "default": "./package.json"
+    },
+    ".": {
+      "types": "./index.d.ts",
+      "default": "./fesm2022/jax-data-science-api-clients.mjs"
+    }
+  }
+}