@jax-data-science/api-clients 0.0.1 → 0.1.0-a.0

package/package.json

@@ -1,9 +1,9 @@
 {
   "name": "@jax-data-science/api-clients",
-  "version": "0.0.1",
+  "version": "0.1.0-a.0",
   "peerDependencies": {
-    "@angular/common": "^19.2.14",
-    "@angular/core": "^19.2.14",
+    "@angular/common": "^20.3.0",
+    "@angular/core": "^20.3.0",
     "rxjs": "^7.8.0",
     "@microsoft/fetch-event-source": "^2.0.1"
   },

package/lib/models/base-response.d.ts

@@ -1,4 +0,0 @@
-export interface BaseResponse {
-    errors?: Error[];
-    info?: Record<string, any>;
-}

package/lib/models/error.d.ts

@@ -1,5 +0,0 @@
-export interface ErrorResponse {
-    code?: string;
-    num_code?: number;
-    message: string;
-}

package/lib/models/isa-data/isa-data.model.d.ts

@@ -1,75 +0,0 @@
-/**
- * This module defines the data models for representing the Investigation-Study-Assay (ISA)
- * data model, which is a standard for describing life science experiments and their results.
- *
- * Key Concepts:
- * - Investigation: The overall research project or study.
- * - Study: A specific experimental design within an investigation.
- * - Assay: A specific test or measurement performed on samples within a study.
- *
- * Measures represent the actual data points collected from assay executions, including:
- * - Measure: a single assay results with unique identifier
- * - MeasureSeries: a collection of measures that share common metadata and characteristics
- *
- * Each measure/series contains values, metadata about the experimental conditions,
- * and characteristics that describe sample properties or experimental parameters.
- */
-export interface Measure {
-    id: string;
-    values?: MeasureValue[];
-    metadata?: MeasureMetadata;
-    characteristics?: IsaCharacteristic[];
-}
-export interface MeasureSeries {
-    id: string;
-    values?: MeasureValue[];
-    measures?: string[];
-    metadata?: MeasureSeriesMetadata;
-    characteristics?: IsaCharacteristic[];
-}
-export interface MeasureMetadata {
-    assay_id: number;
-    description: string;
-    measure_id: number;
-    method: string;
-    study_id: string;
-    units: string;
-    treatment: string;
-    variable_name: string;
-    characteristics?: Record<string, string[]>;
-}
-export interface MeasureSeriesMetadata {
-    assay_id: number;
-    description: string;
-    initiated_at_units?: string;
-    measure_ids: string[];
-    measure_series_id: string;
-    measurement_units: string;
-    method: string;
-    study_id?: number;
-    treatment: string;
-    treatment_units: string;
-    variable_name: string;
-    characteristics?: Record<string, string[]>;
-}
-export interface MeasureValue {
-    value: string | number;
-    measure_id: string;
-    measure_series_id?: string;
-    study_id?: string;
-    source_id: string;
-}
-export interface IsaCharacteristicValue {
-    value: string | number | boolean | Date;
-    label: string;
-    count?: number;
-    description?: string;
-    metadata: Record<string, string>;
-}
-export interface IsaCharacteristic {
-    name: string;
-    value: IsaCharacteristicValue | IsaCharacteristicValue[];
-    type?: string;
-    unit?: string;
-    description?: string;
-}

package/lib/models/paging.d.ts

@@ -1,13 +0,0 @@
-export interface PagingLinks {
-    first?: string;
-    previous?: string;
-    next?: string;
-    last?: string;
-}
-export interface Paging {
-    page?: number;
-    items?: number;
-    total_pages?: number;
-    total_items?: number;
-    links?: PagingLinks;
-}

package/lib/models/response.d.ts

@@ -1,9 +0,0 @@
-import { BaseResponse } from './base-response';
-import { Paging } from './paging';
-export interface Response<T> extends BaseResponse {
-    object?: T;
-}
-export interface CollectionResponse<T> extends BaseResponse {
-    data: T[];
-    paging?: Paging;
-}

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

@@ -1,164 +0,0 @@
-/**
- * AsyncTask Service Models
- *
- * This module contains TypeScript interfaces for the AsyncTask service API.
- * These models are based on the OpenAPI specification and represent the
- * core entities used in the AsyncTask workflow system.
- */
-/**
- * Represents the current execution status of a workflow.
- * Based on temporalio.api.enums.v1.WorkflowExecutionStatus
- */
-export declare enum WorkflowExecutionStatus {
-    RUNNING = 1,
-    COMPLETED = 2,
-    FAILED = 3,
-    CANCELED = 4,
-    TERMINATED = 5,
-    CONTINUED_AS_NEW = 6,
-    TIMED_OUT = 7
-}
-/**
- * Represents a configuration of input parameters for a workflow run.
- */
-export interface Input {
-    /**
-     * Auto-generated primary key
-     */
-    id?: number | null;
-    /**
-     * Type of the input
-     */
-    type?: string | null;
-    /**
-     * Foreign key to the user who created this input
-     */
-    owner_id: number;
-    /**
-     * JSON dictionary containing input parameters
-     */
-    values: Record<string, any>;
-    /**
-     * Optional descriptive name
-     */
-    name?: string | null;
-    /**
-     * Optional detailed description
-     */
-    description?: string | null;
-}
-/**
- * Lightweight reference to an input configuration.
- * Used for list endpoints to minimize data transfer.
- */
-export interface InputReference {
-    /**
-     * Input identifier
-     */
-    id: number;
-    /**
-     * Optional descriptive name
-     */
-    name?: string | null;
-    /**
-     * Optional detailed description
-     */
-    description?: string | null;
-}
-/**
- * Input submission for creating a new workflow run
- */
-export interface InputSubmission {
-    /**
-     * Optional descriptive name
-     */
-    name?: string | null;
-    /**
-     * Optional detailed description
-     */
-    description?: string | null;
-    /**
-     * Type of task to execute
-     */
-    task_type: string;
-    /**
-     * Input values specific to the task type
-     */
-    values: Record<string, any> | string;
-}
-/**
- * Represents output data from a completed workflow run.
- */
-export interface Result {
-    /**
-     * Auto-generated primary key
-     */
-    id: number;
-    /**
-     * Foreign key to the associated run
-     */
-    run_id: number;
-    /**
-     * JSON dictionary containing result data
-     */
-    values: Record<string, any>;
-    /**
-     * Optional descriptive name
-     */
-    name?: string | null;
-    /**
-     * Optional detailed description
-     */
-    description?: string | null;
-}
-/**
- * Lightweight reference to a result.
- * Used for list endpoints to minimize data transfer.
- */
-export interface ResultReference {
-    /**
-     * Result identifier
-     */
-    id: number;
-    /**
-     * Associated run identifier
-     */
-    run_id: number;
-    /**
-     * Optional descriptive name
-     */
-    name?: string | null;
-    /**
-     * Optional detailed description
-     */
-    description?: string | null;
-}
-/**
- * Represents an execution instance of a workflow.
- */
-export interface Run {
-    /**
-     * Auto-generated primary key
-     */
-    id: number;
-    /**
-     * Foreign key to the input configuration
-     */
-    input_id: number;
-    /**
-     * Foreign key to the user who initiated the run
-     */
-    owner_id: number;
-    /**
-     * Temporal workflow identifier
-     */
-    workflow_id: string;
-    /**
-     * Current execution status from Temporal
-     */
-    status: WorkflowExecutionStatus;
-    /**
-     * Run start time in ISO 8601 format
-     */
-    init_time?: string | null;
-}

package/lib/services/asynctask/asynctask.service.d.ts

@@ -1,60 +0,0 @@
-import { Observable } from 'rxjs';
-import { Input, InputReference, InputSubmission, Result, ResultReference, Run } from './asynctask.model';
-import { CollectionResponse, Response } from '../../models/response';
-import * as i0 from "@angular/core";
-export declare class AsyncTaskService {
-    private apiBaseUrl;
-    private apiServiceFactory;
-    private apiBaseService;
-    setApiBaseUrl(baseUrl: string): void;
-    getApiBaseUrl(): string;
-    addInput(inputSubmission: InputSubmission): Observable<Response<Input>>;
-    getInput(id: number): Observable<Response<Input>>;
-    getInputs(): Observable<CollectionResponse<InputReference>>;
-    /**
-     * Updates an existing input - only 'name' and 'description' can be updated
-     * @param inputId
-     * @param name - (optional) name to update
-     * @param description - (optional) description to update
-     */
-    updateInput(inputId: number, name?: string, description?: string): Observable<Response<InputReference>>;
-    createRun(inputId?: number, inputSubmission?: InputSubmission): Observable<Response<Run>>;
-    getRun(id: number): Observable<Response<Run>>;
-    /**
-     *
-     * @param workflowId - (optional) workflow identifier
-     */
-    getRuns(workflowId?: string): Observable<CollectionResponse<Run>>;
-    /**
-     * Gets the input associated with the specific run ID. One run is associated
-     * with only one input, so this function returns a single input object.
-     * @param runId
-     */
-    getRunInput(runId: number): Observable<Response<Input>>;
-    /**
-     * Gets the result associated with the specific run ID. One run is associated
-     * with only one result, so this function returns a single result object.
-     * @param runId
-     */
-    getRunResult(runId: number): Observable<Response<Result>>;
-    /**
-     * Calls the fetchEventSource() function, which is a wrapper around the native
-     * EventSource API. This function is used to establish connection to an API
-     * endpoint and listen to event streaming data associated with task runs.
-     * TO-DO [GIK 7/9/2025]: needs to add a reconnect logic
-     * @return an observable that emits run events
-     */
-    getRunEvents(accessToken: string): Observable<Run>;
-    getResult(resId: number): Observable<Response<Result>>;
-    getResults(): Observable<CollectionResponse<ResultReference>>;
-    /**
-     * Updates an existing result record - 'name' and 'description' can be updated
-     * @param resId
-     * @param name - (optional) result's name to update
-     * @param description - (optional) result's description to update
-     */
-    updateResult(resId: number, name?: string, description?: string): Observable<Response<ResultReference>>;
-    getHealthCheck(): Observable<any>;
-    static ɵfac: i0.ɵɵFactoryDeclaration<AsyncTaskService, never>;
-    static ɵprov: i0.ɵɵInjectableDeclaration<AsyncTaskService>;
-}

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

@@ -1,74 +0,0 @@
-import { HttpClient, HttpErrorResponse, HttpParams } from '@angular/common/http';
-import { Observable } from 'rxjs';
-import { Response, CollectionResponse } from './../models/response';
-import * as i0 from "@angular/core";
-export declare class ApiBaseServiceFactory {
-    private http;
-    constructor(http: HttpClient);
-    create(baseUrl: string): ApiBaseService;
-    static ɵfac: i0.ɵɵFactoryDeclaration<ApiBaseServiceFactory, never>;
-    static ɵprov: i0.ɵɵInjectableDeclaration<ApiBaseServiceFactory>;
-}
-export declare class ApiBaseService {
-    private http;
-    private baseUrl;
-    constructor(http: HttpClient, baseUrl: string);
-    /**
-     * Handles API response errors and HTTP errors
-     * @param response The API response
-     * @private
-     */
-    private handleResponse;
-    /**
-     * Handles HTTP errors by catching them and rethrowing a consistent
-     * error response that contains an error code, numeric code, and
-     * a user-friendly message.
-     * TO-DO: [GIK 6/10/2025] consider adding error logging capabilities to an external service
-     * @param error an error object, typically an HttpErrorResponse
-     * @returns an Observable that emits an ErrorResponse object
-     */
-    private handleHttpError;
-    /**
-     * Get a user-friendly error message based on the HTTP status code
-     *
-     * @param error
-     * @return a string containing the error message
-     */
-    getErrorMessage(error: HttpErrorResponse): string;
-    /**
-     * Get a single resource
-     * @param url The endpoint URL
-     * @param params Optional query parameters
-     */
-    get<T>(url: string, params?: HttpParams): Observable<Response<T>>;
-    /**
-     * Get a collection of resources
-     * @param url The endpoint URL
-     * @param params Optional query parameters
-     */
-    private handleCollectionResponse;
-    getCollection<T>(url: string, params?: HttpParams): Observable<CollectionResponse<T>>;
-    /**
-     * Create a new resource
-     * @param url The endpoint URL
-     * @param body The resource to create
-     */
-    post<T>(url: string, body: any): Observable<Response<T>>;
-    /**
-     * Update an existing resource
-     * @param url The endpoint URL
-     * @param body The resource updates
-     */
-    put<T>(url: string, body: any): Observable<Response<T>>;
-    /**
-     * Partially update an existing resource
-     * @param url The endpoint URL
-     * @param body The partial resource updates
-     */
-    patch<T>(url: string, body: any): Observable<Response<T>>;
-    /**
-     * Delete a resource
-     * @param url The endpoint URL
-     */
-    delete<T>(url: string): Observable<Response<T>>;
-}

package/lib/services/isa-data/isa-data.service.d.ts

@@ -1,60 +0,0 @@
-import { Observable } from 'rxjs';
-import { Response } from '../../models/response';
-import { MeasureSeriesMetadata, MeasureMetadata, IsaCharacteristic } from '../../models/isa-data/isa-data.model';
-import * as i0 from "@angular/core";
-/**
- * service for interacting with ISA (Investigation-Study-Assay) data model API.
- */
-export declare class ISADataService {
-    private readonly apiConfig;
-    private readonly apiServiceFactory;
-    private readonly apiBaseService;
-    constructor();
-    getApiBaseUrl(): string;
-    /**
-     * Fetches measure series metadata for the given measure series IDs and study IDs.
-     *
-     * @param measureSeriesIds - measure series identifiers to fetch metadata for. ONLY ONE ID IS SUPPORTED.
-     * @param studyIds - ONLY ONE ID IS SUPPORTED. REQUIRED!! WILL BE REMOVED IN THE FUTURE.
-     *
-     * @return Observable<Response<MeasureSeriesMetadata>> - an observable containing the measure series metadata.
-     */
-    getMeasureSeriesMetadata(measureSeriesIds: string[], studyIds: string[]): Observable<Response<MeasureSeriesMetadata>>;
-    /**
-     * THIS METHOD SHOULD NOT BE USED. PLACEHOLDER FOR FUTURE IMPLEMENTATION ONCE THE API GROWS.
-     */
-    getMeasuresMetadata(measureIds: string[], studyIds: string[]): Observable<Response<MeasureMetadata>>;
-    /**
-     * Fetches measure series characteristics for the given measure series IDs and study IDs.
-     *
-     * @param measureSeriesIds - measure series identifiers to fetch metadata for. ONLY ONE ID IS SUPPORTED.
-     * @param studyIds - ONLY ONE ID IS SUPPORTED. REQUIRED!! WILL BE REMOVED IN THE FUTURE.
-     *
-     * @return Observable<Response<MeasureSeriesMetadata>> - an observable containing the measure series metadata.
-     */
-    getMeasureSeriesCharacteristics(measureSeriesIds: string[], studyIds: string[]): Observable<Response<IsaCharacteristic>>;
-    /**
-     * Placeholder for assay operations
-     * TODO: Implement assay-related methods
-     */
-    /**
-     * Placeholder for study operations
-     * TODO: Implement study-related methods
-     */
-    /**
-     * Placeholder for investigation operations
-     * TODO: Implement investigation-related methods
-     */
-    /**
-     * Builds the URL for the ISA data service.
-     *
-     * @param endpoint - the API endpoint path.
-     * @param params - optional query parameters as key-value pairs.
-     *
-     * @return complete URL with query string parameters.
-     */
-    private buildUrl;
-    getHealthCheck(): Observable<any>;
-    static ɵfac: i0.ɵɵFactoryDeclaration<ISADataService, never>;
-    static ɵprov: i0.ɵɵInjectableDeclaration<ISADataService>;
-}

package/lib/services/mvar/models/response/dtos.d.ts

@@ -1,92 +0,0 @@
-export interface VariantResults {
-    variantCount: number;
-    variants: Variant[];
-}
-export interface Variant {
-    accession: string;
-    alt: string;
-    aminoAcidChange: string;
-    assembly: string;
-    canonVarIdentifier: {
-        caID: string;
-        id: number;
-        variantRefTxt: string;
-    };
-    chr: string;
-    dnaHgvsNotation: string;
-    functionalClassCode: string;
-    functionalClasses: SequenceOntologyTerm[];
-    gene: {
-        chr: string;
-        description: string;
-        ensemblGeneId: string;
-        entrezGeneId: string;
-        id: number;
-        mgiId: string;
-        name: string;
-        symbol: string;
-        synonyms: {
-            id: number;
-        }[];
-        transcripts: {
-            id: number;
-        }[];
-        type: string;
-    };
-    id: number;
-    impact: string;
-    parentRefInd: boolean;
-    position: number;
-    proteinHgvsNotation: string;
-    proteinPosition: string;
-    ref: string;
-    sources: {
-        id: number;
-        name: string;
-        sourceVersion: string;
-        url: string;
-    }[];
-    transcripts: {
-        description: string;
-        geneSymbol: string;
-        id: number;
-        mRnaId: string;
-        primaryIdentifier: string;
-    }[];
-    type: string;
-    variantHgvsNotation: string;
-    variantRefTxt: string;
-}
-export interface SequenceOntologyTerm {
-    definition: string;
-    id: number;
-    label: string;
-    soId: string;
-    subClassOf: string;
-    mpdTerm: string;
-}
-export interface SNP {
-    alternate_bases: string;
-    calls: Call[];
-    chr: string;
-    observed: string;
-    reference_base: string;
-    rs: string;
-    start_position: number | null;
-    annotation?: Variant | null;
-}
-export interface Call {
-    strain_name: string;
-    sample_id: number;
-    genotype: string;
-    prob: number;
-    base: string;
-}
-export interface SNPSearchRegion {
-    chromosome: string;
-    start_position: number;
-    end_position: number;
-    reference_base?: string;
-    alternate_base?: string;
-}
-export declare const MUS_CHRS: string[];

package/lib/services/mvar/mvar-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 MvarClientModule {
-    static forRoot(environment: any): ModuleWithProviders<MvarClientModule>;
-    static ɵfac: i0.ɵɵFactoryDeclaration<MvarClientModule, never>;
-    static ɵmod: i0.ɵɵNgModuleDeclaration<MvarClientModule, never, [typeof i1.CommonModule], never>;
-    static ɵinj: i0.ɵɵInjectorDeclaration<MvarClientModule>;
-}

package/lib/services/mvar/mvar.service.d.ts

@@ -1,35 +0,0 @@
-import { HttpClient } from '@angular/common/http';
-import { Observable } from "rxjs";
-import { SequenceOntologyTerm, SNP, SNPSearchRegion, Variant } from './models/response/dtos';
-import * as i0 from "@angular/core";
-export declare class MVarService {
-    private http;
-    private environment;
-    private api;
-    sequenceOntologyMapping: Record<string, SequenceOntologyTerm>;
-    private soTerms;
-    soTerms$: Observable<SequenceOntologyTerm[]>;
-    constructor(http: HttpClient, environment: any);
-    /**
-     * Gets Variants from mvar for a given set snp regions
-     * @param regions Array of snp regions
-     * @param pageStart snp start location
-     * @param pageEnd snp end location
-     * @param assembly Desired assembly version. Acceptable values are 'mm10' (GRCm38) and 'mm39' (GRCm39)
-     */
-    getVariants(regions: SNPSearchRegion[], pageStart: SNP, pageEnd: SNP, assembly: string): Observable<Variant[]>;
-    /**
-     * Returns all sequence ontology terms in MVAR
-     */
-    getSequenceOntologyTerms(): Observable<SequenceOntologyTerm[]>;
-    /**
-     * Translates the regions requested from MUSter and the regions actually displayed on the current page into
-     * regions to request from MVAR
-     * @param requestedRegions - regions included in the request to MUSter
-     * @param pageStart - first SNP from the sorted results from MUSter to display in the table
-     * @param pageEnd - last SNP from the sorted results from MUSter to display in the table
-     */
-    getRegionsToRequestVariantsFor(requestedRegions: SNPSearchRegion[], pageStart: SNP, pageEnd: SNP): SNPSearchRegion[];
-    static ɵfac: i0.ɵɵFactoryDeclaration<MVarService, never>;
-    static ɵprov: i0.ɵɵInjectableDeclaration<MVarService>;
-}