@jax-data-science/api-clients 0.0.2-0 → 0.1.0-a.0

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

@@ -1,80 +0,0 @@
-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;
-}
-export interface OLSTerm {
-    appearsIn: string[];
-    curie: string;
-    definedBy: string[];
-    definition?: Array<{
-        type: string[];
-        value: string;
-        axioms?: Array<{
-            [key: string]: string;
-        }>;
-    }>;
-    definitionProperty?: string;
-    directAncestor?: string[];
-    directParent?: Array<string>;
-    hasDirectChildren?: boolean;
-    hasDirectParents?: boolean;
-    hasHierarchicalChildren?: boolean;
-    hasHierarchicalParents?: boolean;
-    hierarchicalAncestor?: string[];
-    hierarchicalParent?: Array<string | {
-        type: string[];
-        value: string;
-        axioms?: Array<{
-            [key: string]: string;
-        }>;
-    }>;
-    hierarchicalProperty?: string;
-    imported?: boolean;
-    iri: string;
-    isDefiningOntology?: boolean;
-    isObsolete?: boolean;
-    isPreferredRoot?: boolean;
-    label?: string[];
-    linkedEntities?: Record<string, any>;
-    linksTo?: string[];
-    numDescendants?: number;
-    numHierarchicalDescendants?: number;
-    ontologyId?: string;
-    ontologyIri?: string;
-    ontologyPreferredPrefix?: string;
-    searchableAnnotationValues?: any[];
-    shortForm?: string;
-    type?: string[];
-    [key: string]: any;
-}
-export interface OLSResponse {
-    page: number;
-    numElements: number;
-    totalPages: number;
-    totalElements: number;
-    elements: OLSTerm[];
-    facetFieldsToCounts?: Record<string, any>;
-}

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

@@ -1,11 +0,0 @@
-import { Observable } from 'rxjs';
-import { Ontology, OntologyTerm } from './ontology.model';
-import { CollectionResponse, Response } from '../../models/response';
-export declare abstract class OntologyService {
-    abstract search(query: string, limit: number, ontology: Ontology): Observable<CollectionResponse<OntologyTerm>>;
-    abstract term(id: string): Observable<Response<OntologyTerm>>;
-    abstract parents(id: string): Observable<CollectionResponse<OntologyTerm>>;
-    abstract children(id: string): Observable<CollectionResponse<OntologyTerm>>;
-    abstract ancestors(id: string): Observable<CollectionResponse<OntologyTerm>>;
-    abstract descendants(id: string): Observable<CollectionResponse<OntologyTerm>>;
-}

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

@@ -1,53 +0,0 @@
-import { HttpClient } from '@angular/common/http';
-import { Observable } from 'rxjs';
-import { Ontology, OntologyTerm } from './ontology.model';
-import { CollectionResponse, Response } from '../../models/response';
-import { OntologyService } from './ontology.service.base';
-import * as i0 from "@angular/core";
-export declare class JaxOntologyService extends 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 api base url configuration
-     **/
-    ontologyBaseResolver(ontology: Ontology): string;
-    static ɵfac: i0.ɵɵFactoryDeclaration<JaxOntologyService, never>;
-    static ɵprov: i0.ɵɵInjectableDeclaration<JaxOntologyService>;
-}

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

@@ -1,22 +0,0 @@
-import { HttpClient } from '@angular/common/http';
-import { OntologyService } from './ontology.service.base';
-import { Observable } from 'rxjs';
-import { OLSTerm, Ontology, OntologyTerm } from './ontology.model';
-import { CollectionResponse, Response } from '../../models/response';
-import * as i0 from "@angular/core";
-export declare class OLSOntologyService extends OntologyService {
-    private httpClient;
-    private OLS_SEARCH_BASE;
-    private OLS_ENTITY_BASE;
-    private PURL_BASE;
-    constructor(httpClient: HttpClient);
-    term(id: string): Observable<Response<OntologyTerm>>;
-    search(query: string, limit: number, ontology: Ontology): Observable<CollectionResponse<OntologyTerm>>;
-    parents(id: string): Observable<CollectionResponse<OntologyTerm>>;
-    children(id: string): Observable<CollectionResponse<OntologyTerm>>;
-    ancestors(id: string): Observable<CollectionResponse<OntologyTerm>>;
-    descendants(id: string): Observable<CollectionResponse<OntologyTerm>>;
-    mapOLSTermToOntologyTerm(olsTerm: OLSTerm): OntologyTerm;
-    static ɵfac: i0.ɵɵFactoryDeclaration<OLSOntologyService, never>;
-    static ɵprov: i0.ɵɵInjectableDeclaration<OLSOntologyService>;
-}

package/lib/services/ontology/ontology.shared.d.ts

@@ -1,5 +0,0 @@
-import { Ontology } from "./ontology.model";
-/**
-   * Get the ontology from curie
-   */
-export declare function ontologyFromCurie(curie: string): Ontology;

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

@@ -1,95 +0,0 @@
-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/services/snp-grid/snp-grid-client.module.d.ts

@@ -1,9 +0,0 @@
-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/services/snp-grid/snp-grid.service.d.ts

@@ -1,94 +0,0 @@
-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;
-    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/lib/tokens/isa-data-config.token.d.ts

@@ -1,5 +0,0 @@
-import { InjectionToken } from '@angular/core';
-export interface IsaDataServiceConfig {
-    baseUrl: string;
-}
-export declare const ISA_DATA_SERVICE_CONFIG: InjectionToken<IsaDataServiceConfig>;