@jax-data-science/api-clients 0.0.1 → 0.0.2-0

package/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 The Jackson Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

@@ -1,21 +1,133 @@
-# api-clients
+# @jax-data-science/api-clients by The Jackson Laboratory (JAX)
 
-This library was generated with [Nx](https://nx.dev).
+## Overview
+The library provides a centralized approach for frontend applications to interact with backend services across 
+the [JAX Data Science](https://www.jax.org/research-and-faculty/data-science/tools-and-databases) ecosystem. 
+It eliminates code duplication by offering reusable API clients with consistent error handling and authentication. 
+The library abstracts service communication details, allowing developers to focus on UI logic. All services are 
+configurable, handle errors uniformly, and define type-safe models for robust data handling. 
 
-## Running unit tests
+Designed primarily for component consumption but usable independently, it ensures consistency and 
+maintainability as backend services evolve.
 
-Run `nx test api-clients` to execute the unit tests.
+## Installation
 
+```bash
+npm install @jax-data-science/api-clients
+```
+
+## Available API Clients
+
+> **Note**: For a complete list of API clients, visit our [Demo Application](https://jds-apps.jax.org/echo) or check the generated documentation.
 
-## Ontology Service
+## Quick Start
 
-Ontology Service has two implementations JAXOntologyService & OLS Ontology Service. Both converge on the same model that is
-subject to change in releases.
+### 1. Set needed service configuration in your application (e.g., base URL, timeout)
 
-To use any particular implementation
+```typescript
+/**
+ * app.module.ts
+ */
 
+...
+// MY_SERVICE_CONFIG: injection token used to provide configuration values (like API urls) for MyService
+// MyServiceConfig is an interface that defines the structure of the configuration object
+import { MY_SERVICE_CONFIG, MyServiceConfig } from '@jax-data-science/api-clients';
+...
+
+...
+@NgModule({
+  declarations: [...],
+  ...
+  providers: [
+    {
+      provide(MY_SERVICE_CONFIG, {
+        useValue: {
+          baseUrl: 'https://api.example.com', // could also come from environment variables
+          timeout: 5000, // could also come from environment variables
+        } as MyServiceConfig
+      })
+    }
+  ]
+})
 ```
-    providers: [
-        {provide: OntologyService, useClass: JAXOntologyService}
-    ]
-```
+
+
+### 2. Inject and use the API client in your components or services
+
+```typescript
+
+
+/**
+ * example.component.ts
+ */
+
+import { Component, OnInit } from '@angular/core';
+
+import { MyService } from '@jax-data-science/api-clients';
+
+@Component({
+  selector: 'app-example',
+  templateUrl: './example.component.html',
+  styleUrls: ['./example.component.css']
+})
+
+export class ExampleComponent implements OnInit {
+  data: any;
+
+  // Inject MyService into the component
+  constructor(private myService: MyService) {}
+
+  ngOnInit() {
+    // Use the service to fetch data
+    this.myService.getData().subscribe(
+      (response) => {
+        this.data = response;
+      },
+      (error) => {
+        console.error('Error fetching data:', error);
+      }
+    );
+  }
+}
+```
+
+## Contributing
+The JAX Data Science team welcomes and encourages collaborations!
+
+### Ways to Contribute
+
+- API Clients Development
+
+- Testing & Quality Assurance
+
+- Documentation
+
+- Bug Fixes & Enhancements
+
+### Reporting Issues
+
+Found a bug or have a suggestion? Please email us at: npm@jax.org
+
+When reporting issues please include:
+
+- a clear description of the problem or suggestion
+- steps to reproduce (for bugs)
+- expected vs. actual behavior
+- screenshots or code examples when applicable
+- environment details (browser, framework version, etc.)
+
+
+## Changelog
+
+For detailed release notes and version history, see [CHANGELOG.md](./CHANGELOG.md).
+
+## More Information
+
+**GitHub Repo**: [jds-ui-components](https://github.com/TheJacksonLaboratory/jds-ui-components)
+
+**Maintained By**: JAX Data Science
+
+**Contact**: npm@jax.org
+
+**Demo Application**: [View JDS Components](https://jds-apps.jax.org/echo)

package/fesm2022/jax-data-science-api-clients.mjs

@@ -941,27 +941,10 @@ class SnpGridService {
     http;
     environment;
     api;
-    // default true but becomes false if any of the API calls for general information fails
-    apiAvailable = true;
-    strains = new BehaviorSubject([]);
-    strains$ = this.strains.asObservable();
     constructor(http, environment) {
         this.http = http;
         this.environment = environment;
         this.api = environment.securedURLs.genomeMUSter;
-        this.getHealthCheck().subscribe({
-            error: () => {
-                this.apiAvailable = false;
-            },
-        });
-        this.getStrains().subscribe({
-            next: (strains) => {
-                this.apiAvailable = Boolean(strains.length);
-            },
-            error: () => {
-                this.apiAvailable = false;
-            },
-        });
     }
     /**
      * Returns the result of a health check for the API
@@ -974,7 +957,6 @@ class SnpGridService {
      */
     getMusterMetadata() {
         return this.http.get(`${this.api}/db_info`).pipe(catchError((err) => {
-            this.apiAvailable = false;
             throw err;
         }));
     }
@@ -984,9 +966,7 @@ class SnpGridService {
      * @param limit - maximum number of strains to be returned
      */
     getStrains(limit = 5000) {
-        return this.http
-            .get(`${this.api}/strains/?limit=${limit}`)
-            .pipe(tap((strains) => this.strains.next(strains.filter((s) => s.mpd_strainid))));
+        return this.http.get(`${this.api}/strains/?limit=${limit}`).pipe(map((strains) => strains.filter((s) => s.mpd_strainid)));
     }
     /**
      * Returns a list of known genes whose symbols/coordinates start with the specified value.

package/fesm2022/jax-data-science-api-clients.mjs.map

@@ -1 +1 @@
-{"version":3,"file":"jax-data-science-api-clients.mjs","sources":["../../../../libs/api-clients/src/lib/services/base.service.ts","../../../../libs/api-clients/src/lib/services/asynctask/asynctask.service.ts","../../../../libs/api-clients/src/lib/services/asynctask/asynctask.model.ts","../../../../libs/api-clients/src/lib/tokens/isa-data-config.token.ts","../../../../libs/api-clients/src/lib/services/isa-data/isa-data.service.ts","../../../../libs/api-clients/src/lib/models/isa-data/isa-data.model.ts","../../../../libs/api-clients/src/lib/services/mvar/models/response/dtos.ts","../../../../libs/api-clients/src/lib/services/mvar/mvar.service.ts","../../../../libs/api-clients/src/lib/services/mvar/mvar-client.module.ts","../../../../libs/api-clients/src/lib/services/ontology/ontology.service.base.ts","../../../../libs/api-clients/src/lib/services/ontology/ontology.model.ts","../../../../libs/api-clients/src/lib/services/ontology/ontology.shared.ts","../../../../libs/api-clients/src/lib/services/ontology/ontology.service.jax.ts","../../../../libs/api-clients/src/lib/services/ontology/ontology.service.ols.ts","../../../../libs/api-clients/src/lib/services/snp-grid/snp-grid.service.ts","../../../../libs/api-clients/src/lib/services/snp-grid/snp-grid-client.module.ts","../../../../libs/api-clients/src/lib/services/snp-grid/models/response/dtos.ts","../../../../libs/api-clients/src/index.ts","../../../../libs/api-clients/src/jax-data-science-api-clients.ts"],"sourcesContent":["import { Injectable } from '@angular/core';\nimport { HttpClient, HttpErrorResponse, HttpParams } from '@angular/common/http';\nimport { catchError, map, Observable, throwError } from 'rxjs';\n\n// models\nimport { ErrorResponse } from './../models/error';\nimport { Response, CollectionResponse } from './../models/response';\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class ApiBaseServiceFactory {\n  constructor(private http: HttpClient) { }\n\n  create(baseUrl: string): ApiBaseService {\n    return new ApiBaseService(this.http, baseUrl);\n  }\n}\n\nexport class ApiBaseService {\n  constructor(\n    private http: HttpClient,\n    private baseUrl: string,\n  ) {}\n\n  /**\n   * Handles API response errors and HTTP errors\n   * @param response The API response\n   * @private\n   */\n  private handleResponse<T>(\n    response: Response<T> | CollectionResponse<T>,\n  ): Response<T> | CollectionResponse<T> {\n    if(response.errors) {\n      // TO-DO: [GIK 6/6/2025] once the API service has the capabilities to respond\n      // with meaningful validation and analytical errors, this will need to be\n      // updated to typecast these into the ErrorResponse model and rethrow the error object\n      throw new Error(response.errors.join(', '));\n    }\n    return response;\n  }\n\n  /**\n   * Handles HTTP errors by catching them and rethrowing a consistent\n   * error response that contains an error code, numeric code, and\n   * a user-friendly message.\n   * TO-DO: [GIK 6/10/2025] consider adding error logging capabilities to an external service\n   * @param error an error object, typically an HttpErrorResponse\n   * @returns an Observable that emits an ErrorResponse object\n   */\n  private handleHttpError(error: any): Observable<never> {\n    let errorResponse: ErrorResponse;\n\n    // errors returned on the Observable response stream\n    // will be wrapped in an HttpErrorResponse class\n    if(error.name === 'HttpErrorResponse') {\n      errorResponse = {\n        code: error.statusText || 'HTTP_ERROR',\n        num_code: error.status,\n        message: this.getErrorMessage(error),\n      };\n    } else {\n      errorResponse = {\n        code: 'UNKNOWN_ERROR',\n        num_code: 0,\n        message: error.message || 'An unknown error occurred',\n      }\n    }\n\n    return throwError(() => errorResponse);\n  }\n\n  /**\n   * Get a user-friendly error message based on the HTTP status code\n   *\n   * @param error\n   * @return a string containing the error message\n   */\n  getErrorMessage(error: HttpErrorResponse): string {\n    switch(error.status) {\n      case 400:\n        return 'Bad request - malformed request syntax or invalid parameters';\n        break;\n      case 401:\n        return 'Unauthorized - authentication required or invalid credentials';\n        break;\n      case 403:\n        return 'Forbidden - the authenticated user does not have permission to perform the operation';\n        break;\n      case 404:\n        return 'Not found - the requested resource does not exist';\n        break;\n      case 422:\n        return 'Unprocessable content - the request is correctly formed but contained semantic errors';\n        break;\n      case 500:\n        return 'Internal Server Error - generic server-side error';\n        break;\n      default:\n        return `Unexpected error occurred - status code: ${error.status}`;\n    }\n  }\n\n  /**\n   * Get a single resource\n   * @param url The endpoint URL\n   * @param params Optional query parameters\n   */\n  get<T>(url: string, params?: HttpParams): Observable<Response<T>> {\n    return this.http.get<Response<T>>(`${this.baseUrl}${url}`, { params }).pipe(\n      map((response) => this.handleResponse(response)),\n      catchError((error) => this.handleHttpError(error)),\n    );\n  }\n\n  /**\n   * Get a collection of resources\n   * @param url The endpoint URL\n   * @param params Optional query parameters\n   */\n  private handleCollectionResponse<T>(\n    response: CollectionResponse<T>,\n  ): CollectionResponse<T> {\n    if (response.errors) {\n      throw new Error(response.errors.join(', '));\n    }\n    return response;\n  }\n\n  getCollection<T>(\n    url: string,\n    params?: HttpParams,\n  ): Observable<CollectionResponse<T>> {\n    return this.http\n      .get<CollectionResponse<T>>(`${this.baseUrl}${url}`, { params })\n      .pipe(\n        map((response) => this.handleCollectionResponse(response)),\n        catchError((error) => this.handleHttpError(error)),\n      );\n  }\n\n  /**\n   * Create a new resource\n   * @param url The endpoint URL\n   * @param body The resource to create\n   */\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  post<T>(url: string, body: any): Observable<Response<T>> {\n    return this.http.post<Response<T>>(`${this.baseUrl}${url}`, body).pipe(\n      map((response) => this.handleResponse(response)),\n      catchError((error) => this.handleHttpError(error)),\n    );\n  }\n\n  /**\n   * Update an existing resource\n   * @param url The endpoint URL\n   * @param body The resource updates\n   */\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  put<T>(url: string, body: any): Observable<Response<T>> {\n    return this.http.put<Response<T>>(`${this.baseUrl}${url}`, body).pipe(\n      map((response) => this.handleResponse(response)),\n      catchError((error) => this.handleHttpError(error)),\n    );\n  }\n\n  /**\n   * Partially update an existing resource\n   * @param url The endpoint URL\n   * @param body The partial resource updates\n   */\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  patch<T>(url: string, body: any): Observable<Response<T>> {\n    return this.http.patch<Response<T>>(`${this.baseUrl}${url}`, body).pipe(\n      map((response) => this.handleResponse(response)),\n      catchError((error) => this.handleHttpError(error)),\n    );\n  }\n\n  /**\n   * Delete a resource\n   * @param url The endpoint URL\n   */\n  delete<T>(url: string): Observable<Response<T>> {\n    return this.http.delete<Response<T>>(`${this.baseUrl}${url}`).pipe(\n      map((response) => this.handleResponse(response)),\n      catchError((error) => this.handleHttpError(error)),\n    );\n  }\n}\n","import { Injectable, inject } from '@angular/core';\nimport { Observable, Subscriber } from 'rxjs';\nimport { fetchEventSource, EventSourceMessage } from '@microsoft/fetch-event-source';\n// services\nimport { ApiBaseService, ApiBaseServiceFactory } from '../base.service';\n// models\nimport {\n  Input,\n  InputReference,\n  InputSubmission,\n  Result,\n  ResultReference,\n  Run\n} from './asynctask.model';\nimport { CollectionResponse, Response } from '../../models/response';\nimport { ErrorResponse } from '../../models/error';\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class AsyncTaskService {\n  // TO-DO [GIK 7/9/2025]: move 'https://astra-dev.jax.org' to an environment variable\n  private apiBaseUrl = '/asynctask/api';\n\n  private apiServiceFactory: ApiBaseServiceFactory = inject(ApiBaseServiceFactory);\n\n  private apiBaseService: ApiBaseService =\n    this.apiServiceFactory.create(this.apiBaseUrl);\n\n  setApiBaseUrl(baseUrl: string): void {\n    this.apiBaseUrl = baseUrl.endsWith('/') ? baseUrl.slice(0, -1) : baseUrl;\n\n    // ensure the URL ends with '/asynctask/api'\n    if(!this.apiBaseUrl.endsWith('asynctask/api')) {\n      this.apiBaseUrl = `${this.apiBaseUrl}/asynctask/api`;\n    }\n\n    // recreate the apiService\n    this.apiBaseService = this.apiServiceFactory.create(this.apiBaseUrl);\n  }\n\n  getApiBaseUrl(): string {\n    return this.apiBaseUrl;\n  }\n\n  // INPUT\n  addInput(inputSubmission: InputSubmission): Observable<Response<Input>> {\n    return this.apiBaseService.post<Input>('/inputs', inputSubmission);\n  }\n  getInput(id: number): Observable<Response<Input>> {\n    return this.apiBaseService.get<Input>(`/inputs/${id}`);\n  }\n  getInputs(): Observable<CollectionResponse<InputReference>> {\n    return this.apiBaseService.getCollection<InputReference>('/inputs');\n  }\n\n  /**\n   * Updates an existing input - only 'name' and 'description' can be updated\n   * @param inputId\n   * @param name - (optional) name to update\n   * @param description - (optional) description to update\n   */\n  updateInput(inputId: number, name?: string, description?: string): Observable<Response<InputReference>> {\n    let url = `/inputs/${inputId}?`;\n    if(name !== undefined) {\n      url += `name=${name}&`;\n    }\n    if(description !== undefined) {\n      url += `description=${description}`;\n    }\n\n    return this.apiBaseService.patch<InputReference>(url, null);\n  }\n\n  // RUN\n  createRun(inputId?: number, inputSubmission?: InputSubmission): Observable<Response<Run>> {\n    const url = inputId ? `/runs?input_id=${inputId}` : '/runs';\n\n    return this.apiBaseService.post<Run>(url, inputSubmission || null);\n  }\n\n  getRun(id: number): Observable<Response<Run>> {\n    return this.apiBaseService.get<Run>(`/runs/${id}`);\n  }\n\n  /**\n   *\n   * @param workflowId - (optional) workflow identifier\n   */\n  getRuns(workflowId?: string): Observable<CollectionResponse<Run>> {\n    const url = (workflowId ? `/runs?workflow_id=${workflowId}` : '/runs');\n\n    return this.apiBaseService.getCollection<Run>(url);\n  }\n\n  /**\n   * Gets the input associated with the specific run ID. One run is associated\n   * with only one input, so this function returns a single input object.\n   * @param runId\n   */\n  getRunInput(runId: number): Observable<Response<Input>> {\n    return this.apiBaseService.get<Input>(`/runs/${runId}/inputs`);\n  }\n\n  /**\n   * Gets the result associated with the specific run ID. One run is associated\n   * with only one result, so this function returns a single result object.\n   * @param runId\n   */\n  getRunResult(runId: number): Observable<Response<Result>> {\n    return this.apiBaseService.get<Result>(`/runs/${runId}/results`);\n  }\n\n  /**\n   * Calls the fetchEventSource() function, which is a wrapper around the native\n   * EventSource API. This function is used to establish connection to an API\n   * endpoint and listen to event streaming data associated with task runs.\n   * TO-DO [GIK 7/9/2025]: needs to add a reconnect logic\n   * @return an observable that emits run events\n   */\n  getRunEvents(accessToken: string): Observable<Run> {\n    const api = this.apiBaseService\n    // observable constructor argument is 'subscribe()' method implementation\n    return new Observable<Run>(\n      (subscriber: Subscriber<Run>) => {\n        // abort controller to cancel the request (on component destroy)\n        const abortController = new AbortController();\n\n        fetchEventSource(`${this.apiBaseUrl}/runs/events`, {\n          method: 'GET',\n          headers: {\n            'Content-Type': 'text/event-stream',\n            'Cache-Control': 'no-cache',\n            'Authorization': `Bearer ${accessToken}`\n          },\n\n          async onopen(response): Promise<void> {\n            // SSE media type must be 'text/event-stream'\n            const contentType = response.headers.get('content-type');\n\n            if(!contentType?.startsWith('text/event-stream')) {\n              const errorResponse: ErrorResponse = {\n                code: 'INVALID_CONTENT_TYPE',\n                num_code: response.status,\n                message: `Expected content-type to be text/event-stream, but got: ${contentType}`\n              };\n              throw errorResponse;\n            }\n\n            // resolve promise (without returning anything), which indicates that the connection is open\n            if(response.ok && response.status === 200)  return;\n\n            // opening SSE connection failed\n            if(response.status >= 400 && response.status < 500 && response.status !== 429) {\n              const errorResponse: ErrorResponse = {\n                code: 'RESOURCE_NOT_FOUND',\n                num_code: response.status,\n                message: 'Resource not found or access denied'\n              }\n              throw errorResponse;\n            }\n          },\n          onmessage(event: EventSourceMessage) {\n            try {\n              const run: Run = JSON.parse(event.data) as Run;\n              subscriber.next(run);\n            } catch(error) {\n              const errorResponse: ErrorResponse = {\n                code: 'PARSE_ERROR',\n                num_code: 0,\n                message: `Failed to parse event data: ${event.data}`\n              }\n              throw errorResponse;\n            }\n          },\n          onclose(): void {\n            subscriber.complete();\n          },\n          onerror(errorRes: ErrorResponse): void {\n            // send an error message to subscriber's error handler\n            subscriber.error(errorRes);\n            // rethrow the error to stop the operation\n            throw errorRes;\n          },\n          signal: abortController.signal\n        });\n\n        return () => {\n          abortController.abort(); // close connection on unsubscribe\n        }\n      });\n  }\n\n  // RESULT\n  getResult(resId: number): Observable<Response<Result>> {\n    return this.apiBaseService.get<Result>(`/results/${resId}`);\n  }\n\n  getResults(): Observable<CollectionResponse<ResultReference>> {\n    return this.apiBaseService.getCollection<ResultReference>('/results');\n  }\n\n  /**\n   * Updates an existing result record - 'name' and 'description' can be updated\n   * @param resId\n   * @param name - (optional) result's name to update\n   * @param description - (optional) result's description to update\n   */\n  updateResult(resId: number, name?: string, description?: string): Observable<Response<ResultReference>> {\n    let url = `/results/${resId}?`;\n    if(name !== undefined) {\n      url += `name=${name}&`;\n    }\n    if(description !== undefined) {\n      url += `description=${description}`;\n    }\n    \n    return this.apiBaseService.patch<ResultReference>(url, null);\n  }\n\n  // HEALTH CHECK\n  // TO-DO [GIK 05/30/2025]: should be moved outside this service\n  getHealthCheck(): Observable<any> {\n    return this.apiBaseService.get<any>('/monitors/servers/health');\n  }\n}\n","/**\n * AsyncTask Service Models\n * \n * This module contains TypeScript interfaces for the AsyncTask service API.\n * These models are based on the OpenAPI specification and represent the\n * core entities used in the AsyncTask workflow system.\n */\n\n/**\n * Represents the current execution status of a workflow.\n * Based on temporalio.api.enums.v1.WorkflowExecutionStatus\n */\nexport enum WorkflowExecutionStatus {\n  RUNNING = 1,\n  COMPLETED = 2,\n  FAILED = 3,\n  CANCELED = 4,\n  TERMINATED = 5,\n  CONTINUED_AS_NEW = 6,\n  TIMED_OUT = 7\n}\n\n/**\n * Represents a configuration of input parameters for a workflow run.\n */\nexport interface Input {\n  /**\n   * Auto-generated primary key\n   */\n  id?: number | null;\n  \n  /**\n   * Type of the input\n   */\n  type?: string | null;\n  \n  /**\n   * Foreign key to the user who created this input\n   */\n  owner_id: number;\n  \n  /**\n   * JSON dictionary containing input parameters\n   */\n  values: Record<string, any>;\n  \n  /**\n   * Optional descriptive name\n   */\n  name?: string | null;\n  \n  /**\n   * Optional detailed description\n   */\n  description?: string | null;\n}\n\n/**\n * Lightweight reference to an input configuration.\n * Used for list endpoints to minimize data transfer.\n */\nexport interface InputReference {\n  /**\n   * Input identifier\n   */\n  id: number;\n  \n  /**\n   * Optional descriptive name\n   */\n  name?: string | null;\n  \n  /**\n   * Optional detailed description\n   */\n  description?: string | null;\n}\n\n/**\n * Input submission for creating a new workflow run\n */\nexport interface InputSubmission {\n    /**\n     * Optional descriptive name\n     */\n    name?: string | null;\n    \n    /**\n     * Optional detailed description\n     */\n    description?: string | null;\n    \n    /**\n     * Type of task to execute\n     */\n    task_type: string;\n    \n    /**\n     * Input values specific to the task type\n     */\n    values: Record<string, any> | string;\n  }\n  \n\n/**\n * Represents output data from a completed workflow run.\n */\nexport interface Result {\n  /**\n   * Auto-generated primary key\n   */\n  id: number;\n  \n  /**\n   * Foreign key to the associated run\n   */\n  run_id: number;\n  \n  /**\n   * JSON dictionary containing result data\n   */\n  values: Record<string, any>;\n  \n  /**\n   * Optional descriptive name\n   */\n  name?: string | null;\n  \n  /**\n   * Optional detailed description\n   */\n  description?: string | null;\n}\n\n/**\n * Lightweight reference to a result.\n * Used for list endpoints to minimize data transfer.\n */\nexport interface ResultReference {\n  /**\n   * Result identifier\n   */\n  id: number;\n  \n  /**\n   * Associated run identifier\n   */\n  run_id: number;\n  \n  /**\n   * Optional descriptive name\n   */\n  name?: string | null;\n  \n  /**\n   * Optional detailed description\n   */\n  description?: string | null;\n}\n\n/**\n * Represents an execution instance of a workflow.\n */\nexport interface Run {\n  /**\n   * Auto-generated primary key\n   */\n  id: number;\n  \n  /**\n   * Foreign key to the input configuration\n   */\n  input_id: number;\n  \n  /**\n   * Foreign key to the user who initiated the run\n   */\n  owner_id: number;\n  \n  /**\n   * Temporal workflow identifier\n   */\n  workflow_id: string;\n  \n  /**\n   * Current execution status from Temporal\n   */\n  status: WorkflowExecutionStatus;\n\n  /**\n   * Run start time in ISO 8601 format\n   */\n  init_time?: string | null; // ISO 8601 format\n}\n","import { InjectionToken } from '@angular/core';\n\nexport interface IsaDataServiceConfig {\n  baseUrl: string;\n}\n\nexport const ISA_DATA_SERVICE_CONFIG = new InjectionToken<IsaDataServiceConfig>(\n  'ISA_DATA_SERVICE_CONFIG'\n);","import { Injectable, inject } from '@angular/core';\nimport { Observable } from 'rxjs';\n// services\nimport { ApiBaseService, ApiBaseServiceFactory } from '../base.service';\n// models\nimport { Response } from '../../models/response';\nimport { ErrorResponse } from '../../models/error';\nimport {\n  MeasureSeriesMetadata,\n  MeasureMetadata,\n  IsaCharacteristic\n} from '../../models/isa-data/isa-data.model';\n// tokens\nimport {\n  ISA_DATA_SERVICE_CONFIG,\n  IsaDataServiceConfig\n} from '../../tokens/isa-data-config.token';\n\n/**\n * service for interacting with ISA (Investigation-Study-Assay) data model API.\n */\n@Injectable({\n  providedIn: 'root'\n})\nexport class ISADataService {\n  private readonly apiConfig: IsaDataServiceConfig = inject(ISA_DATA_SERVICE_CONFIG);\n  private readonly apiServiceFactory: ApiBaseServiceFactory = inject(ApiBaseServiceFactory);\n  private readonly apiBaseService: ApiBaseService;\n\n  constructor() {\n    this.apiBaseService = this.apiServiceFactory.create(this.apiConfig.baseUrl);\n  }\n\n  getApiBaseUrl(): string {\n    return this.apiConfig.baseUrl;\n  }\n\n  // measure operations\n\n  /**\n   * Fetches measure series metadata for the given measure series IDs and study IDs.\n   *\n   * @param measureSeriesIds - measure series identifiers to fetch metadata for. ONLY ONE ID IS SUPPORTED.\n   * @param studyIds - ONLY ONE ID IS SUPPORTED. REQUIRED!! WILL BE REMOVED IN THE FUTURE.\n   *\n   * @return Observable<Response<MeasureSeriesMetadata>> - an observable containing the measure series metadata.\n   */\n  getMeasureSeriesMetadata(measureSeriesIds: string[], studyIds: string[]) :\n    Observable<Response<MeasureSeriesMetadata>> {\n    if(!measureSeriesIds?.length) {\n      const errorResponse: ErrorResponse = {\n        code: 'BAD_REQUEST',\n        num_code: 400,\n        message: 'missing required parameter: measureSeriesIds',\n      };\n\n      throw errorResponse;\n    }\n\n\n    const url = this.buildUrl('/visualization/measures/metadata', {\n      measureSeriesIds: measureSeriesIds.join(','),\n      studyId: studyIds.join(',')\n    });\n\n\n    return this.apiBaseService.get<MeasureSeriesMetadata>(url);\n  }\n\n  /**\n   * THIS METHOD SHOULD NOT BE USED. PLACEHOLDER FOR FUTURE IMPLEMENTATION ONCE THE API GROWS.\n   */\n  getMeasuresMetadata(measureIds: string[], studyIds: string[]) :\n    Observable<Response<MeasureMetadata>>  {\n    const reqUrl = '';\n    return this.apiBaseService.get<MeasureMetadata>(reqUrl);\n  }\n\n  /**\n   * Fetches measure series characteristics for the given measure series IDs and study IDs.\n   *\n   * @param measureSeriesIds - measure series identifiers to fetch metadata for. ONLY ONE ID IS SUPPORTED.\n   * @param studyIds - ONLY ONE ID IS SUPPORTED. REQUIRED!! WILL BE REMOVED IN THE FUTURE.\n   *\n   * @return Observable<Response<MeasureSeriesMetadata>> - an observable containing the measure series metadata.\n   */\n  getMeasureSeriesCharacteristics(measureSeriesIds: string[], studyIds: string[]) :\n    Observable<Response<IsaCharacteristic>> {\n    if(!measureSeriesIds?.length) {\n      const errorResponse: ErrorResponse = {\n        code: 'BAD_REQUEST',\n        num_code: 400,\n        message: 'missing required parameter: measureSeriesIds',\n      };\n\n      throw errorResponse;\n    }\n\n    const url = this.buildUrl('/visualization/measures/characteristics', {\n      measureSeriesIds: measureSeriesIds.join(','),\n      studyIds: studyIds.join(',')\n    });\n\n\n    return this.apiBaseService.get(url);\n  }\n\n  // ASSAYS: to-be-implemented\n\n  /**\n   * Placeholder for assay operations\n   * TODO: Implement assay-related methods\n   */\n\n  // STUDIES: to-be-implemented\n\n  /**\n   * Placeholder for study operations\n   * TODO: Implement study-related methods\n   */\n\n  // INVESTIGATIONS: to-be-implemented\n\n  /**\n   * Placeholder for investigation operations\n   * TODO: Implement investigation-related methods\n   */\n\n  /**\n   * Builds the URL for the ISA data service.\n   *\n   * @param endpoint - the API endpoint path.\n   * @param params - optional query parameters as key-value pairs.\n   *\n   * @return complete URL with query string parameters.\n   */\n  private buildUrl(endpoint: string, params: Record<string, string>) {\n    const queryParams = new URLSearchParams(params).toString();\n\n    return queryParams ? `${endpoint}?${queryParams}` : endpoint;\n  }\n\n  // HEALTH CHECK\n  // TO-DO [GIK 05/30/2025]: should be moved outside this service\n  getHealthCheck(): Observable<any> {\n    return this.apiBaseService!.get<any>('/monitors/servers/health');\n  }\n}\n","/**\n * This module defines the data models for representing the Investigation-Study-Assay (ISA)\n * data model, which is a standard for describing life science experiments and their results.\n *\n * Key Concepts:\n * - Investigation: The overall research project or study.\n * - Study: A specific experimental design within an investigation.\n * - Assay: A specific test or measurement performed on samples within a study.\n *\n * Measures represent the actual data points collected from assay executions, including:\n * - Measure: a single assay results with unique identifier\n * - MeasureSeries: a collection of measures that share common metadata and characteristics\n *\n * Each measure/series contains values, metadata about the experimental conditions,\n * and characteristics that describe sample properties or experimental parameters.\n */\n\nexport interface Measure {\n  id: string;\n  values?: MeasureValue[];\n  metadata?: MeasureMetadata;\n  characteristics?: IsaCharacteristic[];\n}\n\nexport interface MeasureSeries {\n  id: string;\n  values?: MeasureValue[];\n  measures?: string[];\n  metadata?: MeasureSeriesMetadata;\n  characteristics?: IsaCharacteristic[];\n}\n\nexport interface MeasureMetadata {\n  assay_id: number;\n  description: string;\n  measure_id: number;\n  method: string;\n  study_id: string;\n  units: string;\n  treatment: string;\n  variable_name: string;\n\n  characteristics?: Record<string, string[]>\n}\n\nexport interface MeasureSeriesMetadata {\n  assay_id: number;\n  description: string;\n  initiated_at_units?: string;\n  measure_ids: string[];\n  measure_series_id: string;\n  measurement_units: string;\n  method: string;\n  study_id?: number;\n  treatment: string;\n  treatment_units: string;\n  variable_name: string;\n\n  characteristics?: Record<string, string[]>;\n};\n\nexport interface MeasureValue {\n  value: string | number;\n  measure_id: string;\n  measure_series_id?: string;\n  study_id?: string;\n  source_id: string;\n}\n\nexport interface IsaCharacteristicValue {\n  value: string | number | boolean | Date;\n  label: string; // e.g., 'High', 'Low', 'Positive', '2023-10-01'\n  count?: number;\n  description?: string; // optional description of the characteristic value\n  metadata: Record<string, string>; // additional metadata about the characteristic value\n}\n\nexport interface IsaCharacteristic {\n  name: string;\n  value: IsaCharacteristicValue | IsaCharacteristicValue[];\n  type?: string; // e.g., 'text', 'numeric', 'date'\n  unit?: string; // e.g., 'mg/L', 'Celsius'\n  description?: string; // optional description of the characteristic\n}\n","export interface VariantResults {\n  variantCount: number;\n  variants: Variant[];\n}\n\nexport interface Variant {\n  accession: string;\n  alt: string;\n  aminoAcidChange: string;\n  assembly: string;\n  canonVarIdentifier: {\n    caID: string;\n    id: number;\n    variantRefTxt: string;\n  };\n  chr: string;\n  dnaHgvsNotation: string;\n  functionalClassCode: string;\n  functionalClasses: SequenceOntologyTerm[]; // added artificially\n  gene: {\n    chr: string;\n    description: string;\n    ensemblGeneId: string;\n    entrezGeneId: string;\n    id: number;\n    mgiId: string;\n    name: string;\n    symbol: string;\n    synonyms: {\n      id: number;\n    }[];\n    transcripts: {\n      id: number;\n    }[];\n    type: string;\n  };\n  id: number;\n  impact: string;\n  parentRefInd: boolean;\n  position: number;\n  proteinHgvsNotation: string;\n  proteinPosition: string;\n  ref: string;\n  sources: {\n    id: number;\n    name: string;\n    sourceVersion: string;\n    url: string;\n  }[];\n  transcripts: {\n    description: string;\n    geneSymbol: string;\n    id: number;\n    mRnaId: string;\n    primaryIdentifier: string;\n  }[];\n  type: string;\n  variantHgvsNotation: string;\n  variantRefTxt: string;\n}\n\nexport interface SequenceOntologyTerm {\n  definition: string;\n  id: number;\n  label: string;\n  soId: string;\n  subClassOf: string;\n  mpdTerm: string;\n}\n\n\nexport interface SNP {\n  alternate_bases: string;\n  calls: Call[];\n  chr: string;\n  observed: string;\n  reference_base: string;\n  rs: string;\n  start_position: number | null; // allow for null value for gutter row\n  annotation?: Variant | null;\n}\n\nexport interface Call {\n  strain_name: string;\n  sample_id: number;\n  genotype: string;\n  prob: number;\n  base: string;\n}\n\nexport interface SNPSearchRegion {\n  chromosome: string;\n  start_position: number;\n  end_position: number;\n  reference_base?: string;\n  alternate_base?: string;\n}\n\n// TODO - move to constants file/library\nexport const MUS_CHRS = [\n  '1',\n  '2',\n  '3',\n  '4',\n  '5',\n  '6',\n  '7',\n  '8',\n  '9',\n  '10',\n  '11',\n  '12',\n  '13',\n  '14',\n  '15',\n  '16',\n  '17',\n  '18',\n  '19',\n  'X',\n  'Y',\n];\n","import { Inject, Injectable } from '@angular/core';\nimport { HttpClient } from '@angular/common/http';\nimport { BehaviorSubject, combineLatest, map, Observable, tap } from \"rxjs\";\n\nimport { MUS_CHRS, SequenceOntologyTerm, SNP, SNPSearchRegion, Variant, VariantResults } from './models/response/dtos';\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class MVarService {\n\n  private api;\n\n  sequenceOntologyMapping: Record<string, SequenceOntologyTerm> = {};\n\n  private soTerms: BehaviorSubject<SequenceOntologyTerm[]> = new BehaviorSubject(<SequenceOntologyTerm[]>[]);\n  soTerms$: Observable<SequenceOntologyTerm[]> = this.soTerms.asObservable();\n\n  constructor(private http: HttpClient, @Inject('environment') private environment: any) {\n    this.api = environment.unsecuredURLs.mvar;\n\n    // create a sequence ontology lookup\n    this.getSequenceOntologyTerms().subscribe((terms) => {\n      terms.forEach((t) => {\n        if (t.label) {\n          this.sequenceOntologyMapping[t.label] = t;\n        }\n      });\n    });\n  }\n\n  /**\n   * Gets Variants from mvar for a given set snp regions\n   * @param regions Array of snp regions\n   * @param pageStart snp start location\n   * @param pageEnd snp end location\n   * @param assembly Desired assembly version. Acceptable values are 'mm10' (GRCm38) and 'mm39' (GRCm39)\n   */\n  getVariants(regions: SNPSearchRegion[], pageStart: SNP, pageEnd: SNP, assembly: string): Observable<Variant[]> {\n    return combineLatest(\n      this.getRegionsToRequestVariantsFor(regions, pageStart, pageEnd).map((r) => {\n        return this.http.get<VariantResults>(\n          `${this.api}/variant/query?chr=${r.chromosome}&startPos=${r.start_position}&endPos=${r.end_position}&max=8000&assembly=${assembly}`,\n        );\n      }),\n    ).pipe(\n      map((variants: VariantResults[]) => {\n        const allVariants = variants.map((v) => v.variants).flat();\n        allVariants.forEach((variant: Variant) => {\n          const classCodes = variant.functionalClassCode.split(',')[0];\n          // add the ontology term\n          variant.functionalClasses = classCodes.split('&').map((c) => this.sequenceOntologyMapping[c]);\n        });\n        return allVariants;\n      }),\n    );\n  }\n\n  /**\n   * Returns all sequence ontology terms in MVAR\n   */\n  getSequenceOntologyTerms(): Observable<SequenceOntologyTerm[]> {\n    return this.http\n      .get<SequenceOntologyTerm[]>(`${this.api}/sequenceOntology/query?max=3000`)\n      .pipe(tap((terms) => this.soTerms.next(terms)));\n  }\n\n  /**\n   * Translates the regions requested from MUSter and the regions actually displayed on the current page into\n   * regions to request from MVAR\n   * @param requestedRegions - regions included in the request to MUSter\n   * @param pageStart - first SNP from the sorted results from MUSter to display in the table\n   * @param pageEnd - last SNP from the sorted results from MUSter to display in the table\n   */\n  getRegionsToRequestVariantsFor(\n    requestedRegions: SNPSearchRegion[],\n    pageStart: SNP,\n    pageEnd: SNP,\n  ): SNPSearchRegion[] {\n    const displayStartBP = pageStart.start_position || 0;\n    const displayEndBP = pageEnd.start_position || 0;\n    const regionsByChr: Record<string, SNPSearchRegion[]> = {};\n    requestedRegions.forEach((r) => {\n      if (regionsByChr[r.chromosome]) {\n        regionsByChr[r.chromosome].push(r);\n      } else {\n        regionsByChr[r.chromosome] = [r];\n      }\n    });\n\n    const displayedRegions: SNPSearchRegion[] = [];\n    if (pageStart.chr === pageEnd.chr) {\n      regionsByChr[pageStart.chr].forEach((r) => {\n        if (r.start_position <= displayEndBP && r.end_position >= displayStartBP) {\n          displayedRegions.push({\n            chromosome: r.chromosome,\n            start_position: Math.max(r.start_position, displayStartBP),\n            end_position: Math.min(r.end_position, displayEndBP),\n          });\n        }\n      });\n    } else {\n      const displayedChrs = Object.keys(regionsByChr).filter(\n        (r) =>\n          MUS_CHRS.indexOf(r) >= MUS_CHRS.indexOf(pageStart.chr) &&\n          MUS_CHRS.indexOf(r) <= MUS_CHRS.indexOf(pageEnd.chr),\n      );\n\n      displayedChrs.forEach((chr) => {\n        regionsByChr[chr].forEach((r) => {\n          if (r.end_position >= displayStartBP && chr === pageStart.chr) {\n            displayedRegions.push({\n              chromosome: r.chromosome,\n              start_position: Math.max(r.start_position, displayStartBP),\n              end_position: r.end_position,\n            });\n          } else if (r.start_position <= displayEndBP && chr === pageEnd.chr) {\n            displayedRegions.push({\n              chromosome: r.chromosome,\n              start_position: r.start_position,\n              end_position: Math.min(r.end_position, displayEndBP),\n            });\n          } else if (chr !== pageStart.chr && chr !== pageEnd.chr) {\n            displayedRegions.push({\n              chromosome: r.chromosome,\n              start_position: r.start_position,\n              end_position: r.end_position,\n            });\n          }\n        });\n      });\n    }\n\n    return displayedRegions;\n  }\n}\n","import { ModuleWithProviders, NgModule } from '@angular/core';\nimport { CommonModule } from '@angular/common';\nimport { MVarService } from \"./mvar.service\";\n\n@NgModule({\n  imports: [CommonModule],\n})\nexport class MvarClientModule {\n\n  public static forRoot(environment: any): ModuleWithProviders<MvarClientModule> {\n    return {\n      ngModule: MvarClientModule,\n      providers: [\n        MVarService,\n        {\n          provide: 'environment', // you can also use InjectionToken\n          useValue: environment\n        }\n      ]\n    };\n  }\n\n}\n","import { Observable } from 'rxjs';\nimport { Ontology, OntologyTerm } from './ontology.model';\nimport { CollectionResponse, Response } from '../../models/response';\n\nexport abstract class OntologyService {\n  abstract search(query: string, limit: number, ontology: Ontology): Observable<CollectionResponse<OntologyTerm>>;\n  abstract term(id: string): Observable<Response<OntologyTerm>>;\n  abstract parents(id: string): Observable<CollectionResponse<OntologyTerm>>;\n  abstract children(id: string): Observable<CollectionResponse<OntologyTerm>>;\n  abstract ancestors(id: string): Observable<CollectionResponse<OntologyTerm>>;\n  abstract descendants(id: string): Observable<CollectionResponse<OntologyTerm>>;\n}","export interface OntologyConfig {\n  name: string;\n  prefix: string;\n  github: {\n    api: string;\n    home: string;\n  };\n  home: string;\n  api: {\n    docs: string;\n    base: string;\n  };\n  base_file: string;\n  international: boolean;\n  description: string;\n}\n\nexport enum Ontology {\n  HP = 'HP',\n  MONDO = 'MONDO',\n  MP = 'MP',\n  CL = 'CL',\n  MAXO = 'MAXO'\n}\n\nexport interface OntologyTerm {\n  id: string;\n  name: string;\n}\n\n// OLS Term interface based on provided JSON\nexport interface OLSTerm {\n  appearsIn: string[];\n  curie: string;\n  definedBy: string[];\n  definition?: Array<{\n    type: string[];\n    value: string;\n    axioms?: Array<{ [key: string]: string }>\n  }>;\n  definitionProperty?: string;\n  directAncestor?: string[];\n  directParent?: Array<string>;\n  hasDirectChildren?: boolean;\n  hasDirectParents?: boolean;\n  hasHierarchicalChildren?: boolean;\n  hasHierarchicalParents?: boolean;\n  hierarchicalAncestor?: string[];\n  hierarchicalParent?: Array<string | {\n    type: string[];\n    value: string;\n    axioms?: Array<{ [key: string]: string }>\n  }>;\n  hierarchicalProperty?: string;\n  imported?: boolean;\n  iri: string;\n  isDefiningOntology?: boolean;\n  isObsolete?: boolean;\n  isPreferredRoot?: boolean;\n  label?: string[];\n  linkedEntities?: Record<string, any>;\n  linksTo?: string[];\n  numDescendants?: number;\n  numHierarchicalDescendants?: number;\n  ontologyId?: string;\n  ontologyIri?: string;\n  ontologyPreferredPrefix?: string;\n  searchableAnnotationValues?: any[];\n  shortForm?: string;\n  type?: string[];\n  [key: string]: any;\n}\n\n// OLS Response interface\nexport interface OLSResponse {\n  page: number;\n  numElements: number;\n  totalPages: number;\n  totalElements: number;\n  elements: OLSTerm[];\n  facetFieldsToCounts?: Record<string, any>;\n}","import { Ontology } from \"./ontology.model\";\n\n/**\n   * Get the ontology from curie\n   */\nexport function ontologyFromCurie(curie: string): Ontology {\n    return Ontology[curie.split(':')[0] as keyof typeof Ontology];\n}","import { HttpClient } from '@angular/common/http';\nimport { Injectable } from '@angular/core';\nimport { Observable, throwError } from 'rxjs';\nimport { Ontology, OntologyConfig, OntologyTerm } from './ontology.model';\n\nimport { CollectionResponse, Response } from '../../models/response';\nimport { ontologyFromCurie } from './ontology.shared';\nimport { OntologyService } from './ontology.service.base';\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class JaxOntologyService extends OntologyService {\n  config_location = 'https://raw.githubusercontent.com/TheJacksonLaboratory/ontology-service/refs/heads/main/config/ontologies-internal.json'\n  private config!: OntologyConfig[];\n\n  /**\n   * Get the configuration file from the source for the backend api service\n   */\n  constructor(private httpClient: HttpClient) {\n    super();\n    this.httpClient.get<OntologyConfig[]>(this.config_location).subscribe({\n      next: (config) => this.config = config,\n      error: () => {\n        this.config = [];\n      }\n    });\n  }\n\n  /**\n   * Search for terms in an ontology\n   * @param query - the search query\n   * @param limit - the number of results to return\n   * @param ontology - the ontology to search\n   */\n  search(query: string, limit: number, ontology: Ontology): Observable<CollectionResponse<OntologyTerm>> {\n    return this.httpClient.get<CollectionResponse<OntologyTerm>>(`${this.ontologyBaseResolver(ontology)}/search?q=${query}&limit=${limit}`);\n  }\n\n  /**\n   * Get a term by its ID\n   * @param id - the term ID\n   */\n  term(id: string): Observable<Response<OntologyTerm>>  {\n    try {\n      const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}`;\n      return this.httpClient.get<Response<OntologyTerm>>(url);\n    } catch (error) {\n      return throwError(() => error);\n    }\n  }\n\n  /**\n   * Get the parents of a term\n   * @param id - the term ID\n   */\n  parents(id: string): Observable<CollectionResponse<OntologyTerm>> {\n    try {\n      const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}/parents`;\n      return this.httpClient.get<CollectionResponse<OntologyTerm>>(url);\n    } catch (error) {\n      return throwError(() => error);\n    }\n  }\n\n  /**\n   * Get the children of a term\n   * @param id - the term ID\n   */\n  children(id: string): Observable<CollectionResponse<OntologyTerm>> {\n    try {\n      const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}/children`;\n      return this.httpClient.get<CollectionResponse<OntologyTerm>>(url);\n    } catch (error: any) {\n      return throwError(() => error);\n    }\n  }\n\n  /**\n   * Get the ancestors of a term\n   * @param id - the term ID\n   */\n  ancestors(id: string): Observable<CollectionResponse<OntologyTerm>> {\n    try {\n      const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}/ancestors`;\n      return this.httpClient.get<CollectionResponse<OntologyTerm>>(url);\n    } catch (error) {\n       return throwError(() => error);\n    }\n  }\n\n  /**\n   * Get the descendants of a term\n   * @param id - the term ID\n   */\n  descendants(id: string): Observable<CollectionResponse<OntologyTerm>> {\n    try {\n      const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}/descendants`;\n      return this.httpClient.get<CollectionResponse<OntologyTerm>>(url);\n    } catch (error) {\n       return throwError(() => error);\n    }\n  }\n\n  /**\n   * Get the ontology api base url configuration\n   **/\n  ontologyBaseResolver(ontology: Ontology): string {\n    if (!this.config || this.config.length === 0) {\n      throw new Error('No ontology configuration found.');\n    }\n    const ontology_config = this.config.find((config) => config.prefix.toUpperCase() === ontology);\n\n    if(!ontology_config) {\n      throw new Error('Ontology not found in configuration.');\n    }\n    return ontology_config.api.base;\n  }\n}\n","// ols-ontology.service.ts\nimport { Injectable } from '@angular/core';\nimport { HttpClient } from '@angular/common/http';\nimport { OntologyService } from './ontology.service.base';\nimport { Observable, map, pipe } from 'rxjs';\nimport { OLSResponse, OLSTerm, Ontology, OntologyTerm } from './ontology.model';\nimport { CollectionResponse, Response } from '../../models/response';\nimport { ontologyFromCurie } from './ontology.shared';\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class OLSOntologyService extends OntologyService {\n\n    private OLS_SEARCH_BASE = 'https://www.ebi.ac.uk/ols4/api/v2/entities';\n    private OLS_ENTITY_BASE = 'https://www.ebi.ac.uk/ols4/api/v2/ontologies';\n    private PURL_BASE = 'http://purl.obolibrary.org/obo';\n    constructor(private httpClient: HttpClient) {\n        super();\n    }\n\n    term(id: string): Observable<Response<OntologyTerm>> {\n        const ontology = ontologyFromCurie(id);\n        const params = new URLSearchParams;\n        params.set('includeObsoleteEntities', 'false');\n        return this.httpClient.get<OLSTerm>(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}?${params.toString()}`).pipe(map(olsResponse => {\n            return {\n                object: this.mapOLSTermToOntologyTerm(olsResponse)\n            };\n        }));\n    }\n\n    search(query: string, limit: number, ontology: Ontology): Observable<CollectionResponse<OntologyTerm>> {\n\n        const params = new URLSearchParams\n        params.set('search', query);\n        params.set('size', limit.toString());\n        params.set('ontologyId', ontology.toLowerCase());\n        params.set('includeObsoleteEntities', 'false');\n        return this.httpClient.get<OLSResponse>(`${this.OLS_SEARCH_BASE}?${params.toString()}`).pipe(map(olsResponse => {\n            const collectionResponse: CollectionResponse<OntologyTerm> = {\n                data: olsResponse.elements.filter((olsTerm: OLSTerm) => olsTerm.definedBy.includes(ontology.toLowerCase())).map(olsTerm => this.mapOLSTermToOntologyTerm(olsTerm)),\n                paging: {\n                    page: olsResponse.page,\n                    total_pages: olsResponse.totalPages,\n                    total_items: olsResponse.totalElements\n                }\n            };\n            return collectionResponse;\n        }));\n    }\n\n    parents(id: string): Observable<CollectionResponse<OntologyTerm>> {\n        const ontology = ontologyFromCurie(id);\n        const params = new URLSearchParams;\n        params.set('includeObsoleteEntities', 'false');\n        return this.httpClient.get<OLSTerm>(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}?${params.toString()}`).pipe(map(olsTerm => {\n            const data =  olsTerm.directParent\n                    ? olsTerm.directParent\n                        .map(parent =>\n                            olsTerm.linkedEntities && olsTerm.linkedEntities[parent]\n                                ? this.mapOLSTermToOntologyTerm(olsTerm.linkedEntities[parent])\n                                : \"\"\n                        ).filter(parent => parent !== \"\")\n                    : []\n            return {\n                data: data,\n                paging: {\n                    page: 1,\n                    total_pages: 1,\n                    total_items: data.length\n                }\n            };\n        }));\n    }\n\n    children(id: string): Observable<CollectionResponse<OntologyTerm>> {\n        const ontology = ontologyFromCurie(id);\n        const params = new URLSearchParams;\n        params.set('includeObsoleteEntities', 'false');\n        params.set('size', '100');\n        params.set('lang', 'en');\n        return this.httpClient.get<OLSResponse>(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}/children?${params.toString()}`).pipe(map(childrenResponse => {\n            const data =  childrenResponse.elements.map(olsTerm => this.mapOLSTermToOntologyTerm(olsTerm));\n            return {\n                data: data,\n                paging: {\n                    page: childrenResponse.page,\n                    total_pages: childrenResponse.totalPages,\n                    total_items: data.length\n                }\n            };\n        }));\n    }\n\n    ancestors(id: string): Observable<CollectionResponse<OntologyTerm>> {\n        const ontology = ontologyFromCurie(id);\n        const params = new URLSearchParams;\n        params.set('includeObsoleteEntities', 'false');\n        return this.httpClient.get<OLSTerm>(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}?${params.toString()}`).pipe(map(olsTerm => {\n            const data =  olsTerm.directAncestor\n                    ? olsTerm.directAncestor\n                        .map(ancestor =>\n                            olsTerm.linkedEntities && olsTerm.linkedEntities[ancestor]\n                                ? this.mapOLSTermToOntologyTerm(olsTerm.linkedEntities[ancestor])\n                                : \"\"\n                        ).filter(ancestor => ancestor !== \"\")\n                    : []\n            return {\n                data: data,\n                paging: {\n                    page: 1,\n                    total_pages: 1,\n                    total_items: data.length\n                }\n            };\n        }));\n    }\n\n    // finish testing this method\n    descendants(id: string): Observable<CollectionResponse<OntologyTerm>> {\n        const ontology = ontologyFromCurie(id);\n        const params = new URLSearchParams;\n        params.set('includeObsoleteEntities', 'false');\n        params.set('size', '100'); // max size for children endpoint\n        params.set('lang', 'en');\n        return this.httpClient.get<OLSResponse>(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}/hierarchicalChildren?${params.toString()}`).pipe(map(childrenResponse => {\n            const data =  childrenResponse.elements.map(olsTerm => this.mapOLSTermToOntologyTerm(olsTerm));\n            return {\n                data: data,\n                paging: {\n                    page: childrenResponse.page,\n                    total_pages: childrenResponse.totalPages,\n                    total_items: data.length\n                }\n            };\n        }));\n    }\n\n    mapOLSTermToOntologyTerm(olsTerm: OLSTerm): OntologyTerm {\n        return {\n            id: olsTerm.curie,\n            name: olsTerm.label && olsTerm.label.length > 0 ? olsTerm.label[0] : 'No label'\n        };\n    }\n}","import { Inject, Injectable } from '@angular/core';\nimport { HttpClient } from \"@angular/common/http\";\nimport { BehaviorSubject, catchError, map, Observable, tap } from \"rxjs\";\n\nimport {\n  Dataset, DatasetStatus,\n  Gene, GenotypeResults,\n  MusterHealthCheck,\n  MusterMetadata,\n  ReferenceSNP,\n  SNPSearchProperties,\n  Strain\n} from './models/response/dtos';\nimport { SNPSearchRegion } from '../mvar/models/response/dtos';\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class SnpGridService {\n  private api;\n\n  // default true but becomes false if any of the API calls for general information fails\n  apiAvailable = true;\n\n  private strains: BehaviorSubject<Strain[]> = new BehaviorSubject(<Strain[]>[]);\n  strains$: Observable<Strain[]> = this.strains.asObservable();\n\n  constructor(private http: HttpClient, @Inject('environment') private environment: any) {\n    this.api = environment.securedURLs.genomeMUSter;\n\n    this.getHealthCheck().subscribe({\n      error: () => {\n        this.apiAvailable = false;\n      },\n    });\n    this.getStrains().subscribe({\n      next: (strains) => {\n        this.apiAvailable = Boolean(strains.length);\n      },\n      error: () => {\n        this.apiAvailable = false;\n      },\n    });\n  }\n\n  /**\n   * Returns the result of a health check for the API\n   */\n  getHealthCheck(): Observable<MusterHealthCheck> {\n    return this.http.get<MusterHealthCheck>(`${this.api}/healthcheck`);\n  }\n\n  /**\n   * Returns the metadata on the MUSter DB\n   */\n  getMusterMetadata(): Observable<MusterMetadata> {\n    return this.http.get<MusterMetadata>(`${this.api}/db_info`).pipe(\n      catchError((err) => {\n        this.apiAvailable = false;\n        throw err;\n      }),\n    );\n  }\n\n  /**\n   * Returns strains available in the API and takes an optional limit; by default the limit is set\n   * to 5000 to get all strains\n   * @param limit - maximum number of strains to be returned\n   */\n  getStrains(limit = 5000): Observable<Strain[]> {\n    return this.http\n      .get<Strain[]>(`${this.api}/strains/?limit=${limit}`)\n      .pipe(tap((strains) => this.strains.next(strains.filter((s) => s.mpd_strainid))));\n  }\n\n  /**\n   * Returns a list of known genes whose symbols/coordinates start with the specified value.\n   * @param searchValue - value to use for the \"starts with\" filter\n   * @param limit - maximum number of genes to return, default is 20\n   */\n  getGenes(searchValue: string, limit = 20): Observable<Gene[]> {\n    return this.http.get<Gene[]>(`${this.api}/genes/?symbol=${searchValue}%&limit=${limit}`);\n  }\n\n  /**\n   * Returns the gene that matches the specified gene symbol\n   * @param geneSymbol - symbol to use to get the associated gene info\n   */\n  getGene(geneSymbol: string): Observable<Gene | null> {\n    return this.http\n      .get<Gene[]>(`${this.api}/genes/?symbol=${geneSymbol}`)\n      .pipe(map((genes) => (genes.length ? genes[0] : null)));\n  }\n\n  /**\n   * Returns true if the specified gene symbol is valid from the perspective of MUSter\n   * @param geneSymbol - symbol to use to check the validity of\n   */\n  isGeneSymbolValid(geneSymbol: string): Observable<boolean> {\n    return this.getGene(geneSymbol).pipe(\n      map((g: Gene | null) => g !== null && geneSymbol.toLowerCase() === g.symbol.toLowerCase()),\n    );\n  }\n\n  /**\n   * Returns list of known reference SNP (RS) data which includes IDs and coordinates\n   * @param searchValue - value to use to filter the search results\n   * @param limit - maximum number of results to return, default is 20\n   */\n  getReferenceSNPs(searchValue: string, limit = 20): Observable<ReferenceSNP[]> {\n    return this.http.get<ReferenceSNP[]>(`${this.api}/rsids/?rsid=${searchValue}%&limit=${limit}`);\n  }\n\n  /**\n   * Returns the RS info that matches the specified rsID\n   * @param rsid - the RSID to use to get the associated RS info\n   */\n  getReferenceSNP(rsid: string): Observable<ReferenceSNP | null> {\n    return this.http\n      .get<ReferenceSNP[]>(`${this.api}/rsids/?rsid=${rsid}`)\n      .pipe(map((rsids) => (rsids.length ? { ...rsids[0], end_position: rsids[0].start_position } : null)));\n  }\n\n  /**\n   * Returns true if the specified rsID is valid from the perspective of MUSter\n   * @param rsid - rsID to use to check the validity of\n   */\n  isRSIDValid(rsid: string): Observable<boolean> {\n    return this.getReferenceSNP(rsid).pipe(\n      map((rs: ReferenceSNP | null) => rs !== null && rsid.toLowerCase() === rs.rsid.toLowerCase()),\n    );\n  }\n\n  /**\n   * Returns the SNP results generated from the query constructed from the specified parameters and page\n   * @param parameters - search properties (strain IDs, regions, assembly version, etc.)\n   * @param page - requested page, which is 0-indexed. The 0th page is the initial page\n   * @param pageSize - number of records to show per page. Default of 5000\n   */\n  getGenotypes(parameters: SNPSearchProperties, page = 0, pageSize = 5000): Observable<GenotypeResults> {\n    let constructedURL =\n      `${this.api}/snps/?` +\n      `assembly=${parameters.assembly}&` +\n      `mpd_strain_ids=${parameters.strains.join(',')}&` +\n      `limit=${pageSize}`;\n\n    if (parameters.strains_b?.length) {\n      constructedURL += `&mpd_strain_ids_b=${parameters.strains_b.join(',')}&strain_limit=${parameters.strains.length + parameters.strains_b.length}`;\n    } else {\n      constructedURL += `&strain_limit=${parameters.strains.length}`\n    }\n\n    if (parameters.rsids?.length) {\n      constructedURL += `&rsids=${parameters.rsids.join(',')}`;\n    }\n\n    if (parameters.genes?.length) {\n      constructedURL += `&genes=${parameters.genes.join(',')}`;\n    }\n\n    if (parameters.regions?.length) {\n      constructedURL += `&regions=${parameters.regions.join(',')}`;\n    }\n\n    if (parameters.dataset_id) {\n      constructedURL += `&dataset_id=${parameters.dataset_id}`;\n    }\n\n    if (parameters.is_unique_row) {\n      constructedURL += `&is_unique_row=${parameters.is_unique_row}`;\n    }\n\n    if (page) {\n      constructedURL += `&offset=${pageSize * page}`;\n    }\n\n    return this.http.get<GenotypeResults>(constructedURL);\n  }\n\n  /**\n   * Returns the URL that will generate a download (in file form) for the specified strain IDs and regions\n   * @param strains - list of mpd_strain_ids to query SNPs for\n   * @param regions - list of SNPSearchRegions to query SNPs for (chromosome, start and end)\n   * @param dataset_id - ID of the dataset to query SNPs for\n   * @param is_unique_row - boolean for polymorphism filtering - true for only rows with polymorphism, false for all\n   * @param limit - the limit of the number of result rows to include in the download - you're likely to\n   *                prefer to pass the total number of rows generated by the query itself, which is included\n   *                as part of the GenotypeResults returned by getGenotypes()\n   */\n  getGenotypeDownloadURLForCurrentData(strains: number[], regions: SNPSearchRegion[], dataset_id: number | undefined, is_unique_row = false,  limit: number): string {\n    if (!dataset_id) {\n      // default to the GenomeMuster dataset id\n      dataset_id = 2;\n    }\n    const stringifiedRegions = `regions=${regions\n      .map((reg) => `${reg.chromosome}:${reg.start_position}-${reg.end_position}`)\n      .join(',')}`;\n    const stringifiedStrains = `mpd_strain_ids=${strains.join(',')}`;\n    return `${this.api}/snps/download?dataset_id=${dataset_id}&${stringifiedStrains}&${stringifiedRegions}&limit=${limit}&is_unique_row=${is_unique_row}`;\n  }\n\n  /**\n   * Returns the dataset with the given ID\n   * @param id\n   */\n  getDataset(id: number): Observable<Dataset> {\n    return this.http.get<Dataset>(`${this.api}/datasets/${id}`)\n  }\n\n  /**\n   * Returns a list of Datasets that match the given criteria\n   * @param status  The value of the status to be used for filtering\n   * @param limit   The maximum number of records to return\n   */\n  findDatasets(status: DatasetStatus, limit = 50): Observable<Dataset[]> {\n    let url = `${this.api}/datasets`;\n    url += `/?limit=${limit}`;\n    if (status) {\n      url += `&status=${status}`;\n    }\n    return this.http.get<Dataset[]>(url);\n  }\n\n  /**\n   * Return a list of strains that match the given criteria\n   * @param datasetId  The ID of the dataset from which to fetch the strains\n   * @param limit      The maximum number of records to return\n   */\n  datasetStrains(datasetId: number, limit = 5000): Observable<Strain[]> {\n    const url = `${this.api}/dataset_strain/?dataset_id=${datasetId}&limit=${limit}`;\n    return this.http.get<Strain[]>(url);\n  }\n\n}\n","import { ModuleWithProviders, NgModule } from '@angular/core';\nimport { CommonModule } from '@angular/common';\nimport { SnpGridService } from \"./snp-grid.service\";\n\n@NgModule({\n  imports: [CommonModule],\n})\nexport class SnpGridClientModule {\n\n  public static forRoot(environment: any): ModuleWithProviders<SnpGridClientModule> {\n    return {\n      ngModule: SnpGridClientModule,\n      providers: [\n        SnpGridService,\n        {\n          provide: 'environment', // you can also use InjectionToken\n          useValue: environment\n        }\n      ]\n    };\n  }\n\n}\n","import { SNP, SNPSearchRegion } from \"../../../mvar/models/response/dtos\";\n\nexport interface MusterHealthCheck {\n  status: string;\n  timestamp: string;\n}\n\nexport interface MusterMetadata {\n  total_number_of_SNPs: number;\n  last_updated: string;\n  version: string;\n  total_number_of_strains: number;\n}\n\nexport interface Strain {\n  bq_sample_id: number;\n  mpd_strainid: number;\n  strainname: string;\n  straintype: string;\n}\n\nexport interface Gene {\n  symbol: string;\n  chr: string;\n  start_position: number;\n  end_position: number;\n  strand: string;\n  description: string;\n  mginum: string;\n  markertype: string;\n  centimorgan: number;\n  featuretype: string;\n}\n\nexport interface ReferenceSNP {\n  chr: string;\n  start_position: number;\n  end_position?: number; // added later\n  rsid: string;\n}\n\nexport interface MusterSearchParameters {\n  bq_sample_ids: null;\n  genes: string | null; // stringified array\n  genes_data: Gene[];\n  limit: number;\n  mpd_strain_ids: string; // stringified array\n  next_region: string | null;\n  offset: number;\n  query_regions: {\n    chromosome: string;\n    regions: SNPSearchRegion[];\n  }[];\n  regions: SNPSearchRegion[];\n  rsids: string | null; //stringified array\n  rsids_data: ReferenceSNP[];\n  strain_limit: number;\n  strain_names: null;\n  dataset: Dataset;\n}\n\nexport interface SNPSearchProperties {\n  strains: number[];\n  strains_b?: number[];\n  rsids?: string[];\n  regions?: string[];\n  assembly: string;\n  genes?: string[];\n  offset?: number;\n  dataset_id?: number;\n  is_unique_row?: boolean;\n}\n\nexport interface GenotypeResults {\n  message: string | null;\n  next_region: string;\n  parameter: MusterSearchParameters;\n  snps: SNP[];\n  status: string;\n  total_rows: number;\n}\n\nexport enum DatasetStatus {\n  Queued = 'queued',\n  Loading = 'loading',\n  Done = 'done',\n  Archived = 'archived',\n}\n\nexport interface Dataset {\n  id: number,\n  display_name: string,\n  sort_by: number,\n  year: string,\n  procedure: string,\n  panel: string,\n  sex: string,\n  dataset_name: string,\n  source: string,\n  status: DatasetStatus,\n  num_of_strains: number,\n  pubmed: string,\n  description: string,\n  assembly_version: string,\n}\n","// AsyncTask API client\nexport * from './lib/services/asynctask/asynctask.service';\nexport * from './lib/services/asynctask/asynctask.model';\n\n// ISA Data API client\nexport * from './lib/services/isa-data/isa-data.service';\nexport * from './lib/models/isa-data/isa-data.model';\nexport * from './lib/tokens/isa-data-config.token';\n\n// MVAR API client\nexport * from './lib/services/mvar/mvar.service';\nexport * from './lib/services/mvar/models/response/dtos';\nexport * from './lib/services/mvar/mvar-client.module';\n\n// Ontology API client\nexport * from './lib/services/ontology/ontology.service.base';\nexport * from './lib/services/ontology/ontology.service.jax';\nexport * from './lib/services/ontology/ontology.service.ols';\n\n// MVar API client\nexport * from './lib/services/mvar/mvar.service';\nexport * from './lib/services/mvar/models/response/dtos';\nexport * from './lib/services/mvar/mvar-client.module';\n\n// SNP Grid API client\nexport * from './lib/services/snp-grid/snp-grid-client.module';\nexport * from './lib/services/snp-grid/models/response/dtos';\nexport * from './lib/services/snp-grid/snp-grid.service';\n","/**\n * Generated bundle index. Do not edit.\n */\n\nexport * from 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{ Injectable } from '@angular/core';\nimport { HttpClient, HttpErrorResponse, HttpParams } from '@angular/common/http';\nimport { catchError, map, Observable, throwError } from 'rxjs';\n\n// models\nimport { ErrorResponse } from './../models/error';\nimport { Response, CollectionResponse } from './../models/response';\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class ApiBaseServiceFactory {\n  constructor(private http: HttpClient) { }\n\n  create(baseUrl: string): ApiBaseService {\n    return new ApiBaseService(this.http, baseUrl);\n  }\n}\n\nexport class ApiBaseService {\n  constructor(\n    private http: HttpClient,\n    private baseUrl: string,\n  ) {}\n\n  /**\n   * Handles API response errors and HTTP errors\n   * @param response The API response\n   * @private\n   */\n  private handleResponse<T>(\n    response: Response<T> | CollectionResponse<T>,\n  ): Response<T> | CollectionResponse<T> {\n    if(response.errors) {\n      // TO-DO: [GIK 6/6/2025] once the API service has the capabilities to respond\n      // with meaningful validation and analytical errors, this will need to be\n      // updated to typecast these into the ErrorResponse model and rethrow the error object\n      throw new Error(response.errors.join(', '));\n    }\n    return response;\n  }\n\n  /**\n   * Handles HTTP errors by catching them and rethrowing a consistent\n   * error response that contains an error code, numeric code, and\n   * a user-friendly message.\n   * TO-DO: [GIK 6/10/2025] consider adding error logging capabilities to an external service\n   * @param error an error object, typically an HttpErrorResponse\n   * @returns an Observable that emits an ErrorResponse object\n   */\n  private handleHttpError(error: any): Observable<never> {\n    let errorResponse: ErrorResponse;\n\n    // errors returned on the Observable response stream\n    // will be wrapped in an HttpErrorResponse class\n    if(error.name === 'HttpErrorResponse') {\n      errorResponse = {\n        code: error.statusText || 'HTTP_ERROR',\n        num_code: error.status,\n        message: this.getErrorMessage(error),\n      };\n    } else {\n      errorResponse = {\n        code: 'UNKNOWN_ERROR',\n        num_code: 0,\n        message: error.message || 'An unknown error occurred',\n      }\n    }\n\n    return throwError(() => errorResponse);\n  }\n\n  /**\n   * Get a user-friendly error message based on the HTTP status code\n   *\n   * @param error\n   * @return a string containing the error message\n   */\n  getErrorMessage(error: HttpErrorResponse): string {\n    switch(error.status) {\n      case 400:\n        return 'Bad request - malformed request syntax or invalid parameters';\n        break;\n      case 401:\n        return 'Unauthorized - authentication required or invalid credentials';\n        break;\n      case 403:\n        return 'Forbidden - the authenticated user does not have permission to perform the operation';\n        break;\n      case 404:\n        return 'Not found - the requested resource does not exist';\n        break;\n      case 422:\n        return 'Unprocessable content - the request is correctly formed but contained semantic errors';\n        break;\n      case 500:\n        return 'Internal Server Error - generic server-side error';\n        break;\n      default:\n        return `Unexpected error occurred - status code: ${error.status}`;\n    }\n  }\n\n  /**\n   * Get a single resource\n   * @param url The endpoint URL\n   * @param params Optional query parameters\n   */\n  get<T>(url: string, params?: HttpParams): Observable<Response<T>> {\n    return this.http.get<Response<T>>(`${this.baseUrl}${url}`, { params }).pipe(\n      map((response) => this.handleResponse(response)),\n      catchError((error) => this.handleHttpError(error)),\n    );\n  }\n\n  /**\n   * Get a collection of resources\n   * @param url The endpoint URL\n   * @param params Optional query parameters\n   */\n  private handleCollectionResponse<T>(\n    response: CollectionResponse<T>,\n  ): CollectionResponse<T> {\n    if (response.errors) {\n      throw new Error(response.errors.join(', '));\n    }\n    return response;\n  }\n\n  getCollection<T>(\n    url: string,\n    params?: HttpParams,\n  ): Observable<CollectionResponse<T>> {\n    return this.http\n      .get<CollectionResponse<T>>(`${this.baseUrl}${url}`, { params })\n      .pipe(\n        map((response) => this.handleCollectionResponse(response)),\n        catchError((error) => this.handleHttpError(error)),\n      );\n  }\n\n  /**\n   * Create a new resource\n   * @param url The endpoint URL\n   * @param body The resource to create\n   */\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  post<T>(url: string, body: any): Observable<Response<T>> {\n    return this.http.post<Response<T>>(`${this.baseUrl}${url}`, body).pipe(\n      map((response) => this.handleResponse(response)),\n      catchError((error) => this.handleHttpError(error)),\n    );\n  }\n\n  /**\n   * Update an existing resource\n   * @param url The endpoint URL\n   * @param body The resource updates\n   */\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  put<T>(url: string, body: any): Observable<Response<T>> {\n    return this.http.put<Response<T>>(`${this.baseUrl}${url}`, body).pipe(\n      map((response) => this.handleResponse(response)),\n      catchError((error) => this.handleHttpError(error)),\n    );\n  }\n\n  /**\n   * Partially update an existing resource\n   * @param url The endpoint URL\n   * @param body The partial resource updates\n   */\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  patch<T>(url: string, body: any): Observable<Response<T>> {\n    return this.http.patch<Response<T>>(`${this.baseUrl}${url}`, body).pipe(\n      map((response) => this.handleResponse(response)),\n      catchError((error) => this.handleHttpError(error)),\n    );\n  }\n\n  /**\n   * Delete a resource\n   * @param url The endpoint URL\n   */\n  delete<T>(url: string): Observable<Response<T>> {\n    return this.http.delete<Response<T>>(`${this.baseUrl}${url}`).pipe(\n      map((response) => this.handleResponse(response)),\n      catchError((error) => this.handleHttpError(error)),\n    );\n  }\n}\n","import { Injectable, inject } from '@angular/core';\nimport { Observable, Subscriber } from 'rxjs';\nimport { fetchEventSource, EventSourceMessage } from '@microsoft/fetch-event-source';\n// services\nimport { ApiBaseService, ApiBaseServiceFactory } from '../base.service';\n// models\nimport {\n  Input,\n  InputReference,\n  InputSubmission,\n  Result,\n  ResultReference,\n  Run\n} from './asynctask.model';\nimport { CollectionResponse, Response } from '../../models/response';\nimport { ErrorResponse } from '../../models/error';\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class AsyncTaskService {\n  // TO-DO [GIK 7/9/2025]: move 'https://astra-dev.jax.org' to an environment variable\n  private apiBaseUrl = '/asynctask/api';\n\n  private apiServiceFactory: ApiBaseServiceFactory = inject(ApiBaseServiceFactory);\n\n  private apiBaseService: ApiBaseService =\n    this.apiServiceFactory.create(this.apiBaseUrl);\n\n  setApiBaseUrl(baseUrl: string): void {\n    this.apiBaseUrl = baseUrl.endsWith('/') ? baseUrl.slice(0, -1) : baseUrl;\n\n    // ensure the URL ends with '/asynctask/api'\n    if(!this.apiBaseUrl.endsWith('asynctask/api')) {\n      this.apiBaseUrl = `${this.apiBaseUrl}/asynctask/api`;\n    }\n\n    // recreate the apiService\n    this.apiBaseService = this.apiServiceFactory.create(this.apiBaseUrl);\n  }\n\n  getApiBaseUrl(): string {\n    return this.apiBaseUrl;\n  }\n\n  // INPUT\n  addInput(inputSubmission: InputSubmission): Observable<Response<Input>> {\n    return this.apiBaseService.post<Input>('/inputs', inputSubmission);\n  }\n  getInput(id: number): Observable<Response<Input>> {\n    return this.apiBaseService.get<Input>(`/inputs/${id}`);\n  }\n  getInputs(): Observable<CollectionResponse<InputReference>> {\n    return this.apiBaseService.getCollection<InputReference>('/inputs');\n  }\n\n  /**\n   * Updates an existing input - only 'name' and 'description' can be updated\n   * @param inputId\n   * @param name - (optional) name to update\n   * @param description - (optional) description to update\n   */\n  updateInput(inputId: number, name?: string, description?: string): Observable<Response<InputReference>> {\n    let url = `/inputs/${inputId}?`;\n    if(name !== undefined) {\n      url += `name=${name}&`;\n    }\n    if(description !== undefined) {\n      url += `description=${description}`;\n    }\n\n    return this.apiBaseService.patch<InputReference>(url, null);\n  }\n\n  // RUN\n  createRun(inputId?: number, inputSubmission?: InputSubmission): Observable<Response<Run>> {\n    const url = inputId ? `/runs?input_id=${inputId}` : '/runs';\n\n    return this.apiBaseService.post<Run>(url, inputSubmission || null);\n  }\n\n  getRun(id: number): Observable<Response<Run>> {\n    return this.apiBaseService.get<Run>(`/runs/${id}`);\n  }\n\n  /**\n   *\n   * @param workflowId - (optional) workflow identifier\n   */\n  getRuns(workflowId?: string): Observable<CollectionResponse<Run>> {\n    const url = (workflowId ? `/runs?workflow_id=${workflowId}` : '/runs');\n\n    return this.apiBaseService.getCollection<Run>(url);\n  }\n\n  /**\n   * Gets the input associated with the specific run ID. One run is associated\n   * with only one input, so this function returns a single input object.\n   * @param runId\n   */\n  getRunInput(runId: number): Observable<Response<Input>> {\n    return this.apiBaseService.get<Input>(`/runs/${runId}/inputs`);\n  }\n\n  /**\n   * Gets the result associated with the specific run ID. One run is associated\n   * with only one result, so this function returns a single result object.\n   * @param runId\n   */\n  getRunResult(runId: number): Observable<Response<Result>> {\n    return this.apiBaseService.get<Result>(`/runs/${runId}/results`);\n  }\n\n  /**\n   * Calls the fetchEventSource() function, which is a wrapper around the native\n   * EventSource API. This function is used to establish connection to an API\n   * endpoint and listen to event streaming data associated with task runs.\n   * TO-DO [GIK 7/9/2025]: needs to add a reconnect logic\n   * @return an observable that emits run events\n   */\n  getRunEvents(accessToken: string): Observable<Run> {\n    const api = this.apiBaseService\n    // observable constructor argument is 'subscribe()' method implementation\n    return new Observable<Run>(\n      (subscriber: Subscriber<Run>) => {\n        // abort controller to cancel the request (on component destroy)\n        const abortController = new AbortController();\n\n        fetchEventSource(`${this.apiBaseUrl}/runs/events`, {\n          method: 'GET',\n          headers: {\n            'Content-Type': 'text/event-stream',\n            'Cache-Control': 'no-cache',\n            'Authorization': `Bearer ${accessToken}`\n          },\n\n          async onopen(response): Promise<void> {\n            // SSE media type must be 'text/event-stream'\n            const contentType = response.headers.get('content-type');\n\n            if(!contentType?.startsWith('text/event-stream')) {\n              const errorResponse: ErrorResponse = {\n                code: 'INVALID_CONTENT_TYPE',\n                num_code: response.status,\n                message: `Expected content-type to be text/event-stream, but got: ${contentType}`\n              };\n              throw errorResponse;\n            }\n\n            // resolve promise (without returning anything), which indicates that the connection is open\n            if(response.ok && response.status === 200)  return;\n\n            // opening SSE connection failed\n            if(response.status >= 400 && response.status < 500 && response.status !== 429) {\n              const errorResponse: ErrorResponse = {\n                code: 'RESOURCE_NOT_FOUND',\n                num_code: response.status,\n                message: 'Resource not found or access denied'\n              }\n              throw errorResponse;\n            }\n          },\n          onmessage(event: EventSourceMessage) {\n            try {\n              const run: Run = JSON.parse(event.data) as Run;\n              subscriber.next(run);\n            } catch(error) {\n              const errorResponse: ErrorResponse = {\n                code: 'PARSE_ERROR',\n                num_code: 0,\n                message: `Failed to parse event data: ${event.data}`\n              }\n              throw errorResponse;\n            }\n          },\n          onclose(): void {\n            subscriber.complete();\n          },\n          onerror(errorRes: ErrorResponse): void {\n            // send an error message to subscriber's error handler\n            subscriber.error(errorRes);\n            // rethrow the error to stop the operation\n            throw errorRes;\n          },\n          signal: abortController.signal\n        });\n\n        return () => {\n          abortController.abort(); // close connection on unsubscribe\n        }\n      });\n  }\n\n  // RESULT\n  getResult(resId: number): Observable<Response<Result>> {\n    return this.apiBaseService.get<Result>(`/results/${resId}`);\n  }\n\n  getResults(): Observable<CollectionResponse<ResultReference>> {\n    return this.apiBaseService.getCollection<ResultReference>('/results');\n  }\n\n  /**\n   * Updates an existing result record - 'name' and 'description' can be updated\n   * @param resId\n   * @param name - (optional) result's name to update\n   * @param description - (optional) result's description to update\n   */\n  updateResult(resId: number, name?: string, description?: string): Observable<Response<ResultReference>> {\n    let url = `/results/${resId}?`;\n    if(name !== undefined) {\n      url += `name=${name}&`;\n    }\n    if(description !== undefined) {\n      url += `description=${description}`;\n    }\n    \n    return this.apiBaseService.patch<ResultReference>(url, null);\n  }\n\n  // HEALTH CHECK\n  // TO-DO [GIK 05/30/2025]: should be moved outside this service\n  getHealthCheck(): Observable<any> {\n    return this.apiBaseService.get<any>('/monitors/servers/health');\n  }\n}\n","/**\n * AsyncTask Service Models\n * \n * This module contains TypeScript interfaces for the AsyncTask service API.\n * These models are based on the OpenAPI specification and represent the\n * core entities used in the AsyncTask workflow system.\n */\n\n/**\n * Represents the current execution status of a workflow.\n * Based on temporalio.api.enums.v1.WorkflowExecutionStatus\n */\nexport enum WorkflowExecutionStatus {\n  RUNNING = 1,\n  COMPLETED = 2,\n  FAILED = 3,\n  CANCELED = 4,\n  TERMINATED = 5,\n  CONTINUED_AS_NEW = 6,\n  TIMED_OUT = 7\n}\n\n/**\n * Represents a configuration of input parameters for a workflow run.\n */\nexport interface Input {\n  /**\n   * Auto-generated primary key\n   */\n  id?: number | null;\n  \n  /**\n   * Type of the input\n   */\n  type?: string | null;\n  \n  /**\n   * Foreign key to the user who created this input\n   */\n  owner_id: number;\n  \n  /**\n   * JSON dictionary containing input parameters\n   */\n  values: Record<string, any>;\n  \n  /**\n   * Optional descriptive name\n   */\n  name?: string | null;\n  \n  /**\n   * Optional detailed description\n   */\n  description?: string | null;\n}\n\n/**\n * Lightweight reference to an input configuration.\n * Used for list endpoints to minimize data transfer.\n */\nexport interface InputReference {\n  /**\n   * Input identifier\n   */\n  id: number;\n  \n  /**\n   * Optional descriptive name\n   */\n  name?: string | null;\n  \n  /**\n   * Optional detailed description\n   */\n  description?: string | null;\n}\n\n/**\n * Input submission for creating a new workflow run\n */\nexport interface InputSubmission {\n    /**\n     * Optional descriptive name\n     */\n    name?: string | null;\n    \n    /**\n     * Optional detailed description\n     */\n    description?: string | null;\n    \n    /**\n     * Type of task to execute\n     */\n    task_type: string;\n    \n    /**\n     * Input values specific to the task type\n     */\n    values: Record<string, any> | string;\n  }\n  \n\n/**\n * Represents output data from a completed workflow run.\n */\nexport interface Result {\n  /**\n   * Auto-generated primary key\n   */\n  id: number;\n  \n  /**\n   * Foreign key to the associated run\n   */\n  run_id: number;\n  \n  /**\n   * JSON dictionary containing result data\n   */\n  values: Record<string, any>;\n  \n  /**\n   * Optional descriptive name\n   */\n  name?: string | null;\n  \n  /**\n   * Optional detailed description\n   */\n  description?: string | null;\n}\n\n/**\n * Lightweight reference to a result.\n * Used for list endpoints to minimize data transfer.\n */\nexport interface ResultReference {\n  /**\n   * Result identifier\n   */\n  id: number;\n  \n  /**\n   * Associated run identifier\n   */\n  run_id: number;\n  \n  /**\n   * Optional descriptive name\n   */\n  name?: string | null;\n  \n  /**\n   * Optional detailed description\n   */\n  description?: string | null;\n}\n\n/**\n * Represents an execution instance of a workflow.\n */\nexport interface Run {\n  /**\n   * Auto-generated primary key\n   */\n  id: number;\n  \n  /**\n   * Foreign key to the input configuration\n   */\n  input_id: number;\n  \n  /**\n   * Foreign key to the user who initiated the run\n   */\n  owner_id: number;\n  \n  /**\n   * Temporal workflow identifier\n   */\n  workflow_id: string;\n  \n  /**\n   * Current execution status from Temporal\n   */\n  status: WorkflowExecutionStatus;\n\n  /**\n   * Run start time in ISO 8601 format\n   */\n  init_time?: string | null; // ISO 8601 format\n}\n","import { InjectionToken } from '@angular/core';\n\nexport interface IsaDataServiceConfig {\n  baseUrl: string;\n}\n\nexport const ISA_DATA_SERVICE_CONFIG = new InjectionToken<IsaDataServiceConfig>(\n  'ISA_DATA_SERVICE_CONFIG'\n);","import { Injectable, inject } from '@angular/core';\nimport { Observable } from 'rxjs';\n// services\nimport { ApiBaseService, ApiBaseServiceFactory } from '../base.service';\n// models\nimport { Response } from '../../models/response';\nimport { ErrorResponse } from '../../models/error';\nimport {\n  MeasureSeriesMetadata,\n  MeasureMetadata,\n  IsaCharacteristic\n} from '../../models/isa-data/isa-data.model';\n// tokens\nimport {\n  ISA_DATA_SERVICE_CONFIG,\n  IsaDataServiceConfig\n} from '../../tokens/isa-data-config.token';\n\n/**\n * service for interacting with ISA (Investigation-Study-Assay) data model API.\n */\n@Injectable({\n  providedIn: 'root'\n})\nexport class ISADataService {\n  private readonly apiConfig: IsaDataServiceConfig = inject(ISA_DATA_SERVICE_CONFIG);\n  private readonly apiServiceFactory: ApiBaseServiceFactory = inject(ApiBaseServiceFactory);\n  private readonly apiBaseService: ApiBaseService;\n\n  constructor() {\n    this.apiBaseService = this.apiServiceFactory.create(this.apiConfig.baseUrl);\n  }\n\n  getApiBaseUrl(): string {\n    return this.apiConfig.baseUrl;\n  }\n\n  // measure operations\n\n  /**\n   * Fetches measure series metadata for the given measure series IDs and study IDs.\n   *\n   * @param measureSeriesIds - measure series identifiers to fetch metadata for. ONLY ONE ID IS SUPPORTED.\n   * @param studyIds - ONLY ONE ID IS SUPPORTED. REQUIRED!! WILL BE REMOVED IN THE FUTURE.\n   *\n   * @return Observable<Response<MeasureSeriesMetadata>> - an observable containing the measure series metadata.\n   */\n  getMeasureSeriesMetadata(measureSeriesIds: string[], studyIds: string[]) :\n    Observable<Response<MeasureSeriesMetadata>> {\n    if(!measureSeriesIds?.length) {\n      const errorResponse: ErrorResponse = {\n        code: 'BAD_REQUEST',\n        num_code: 400,\n        message: 'missing required parameter: measureSeriesIds',\n      };\n\n      throw errorResponse;\n    }\n\n\n    const url = this.buildUrl('/visualization/measures/metadata', {\n      measureSeriesIds: measureSeriesIds.join(','),\n      studyId: studyIds.join(',')\n    });\n\n\n    return this.apiBaseService.get<MeasureSeriesMetadata>(url);\n  }\n\n  /**\n   * THIS METHOD SHOULD NOT BE USED. PLACEHOLDER FOR FUTURE IMPLEMENTATION ONCE THE API GROWS.\n   */\n  getMeasuresMetadata(measureIds: string[], studyIds: string[]) :\n    Observable<Response<MeasureMetadata>>  {\n    const reqUrl = '';\n    return this.apiBaseService.get<MeasureMetadata>(reqUrl);\n  }\n\n  /**\n   * Fetches measure series characteristics for the given measure series IDs and study IDs.\n   *\n   * @param measureSeriesIds - measure series identifiers to fetch metadata for. ONLY ONE ID IS SUPPORTED.\n   * @param studyIds - ONLY ONE ID IS SUPPORTED. REQUIRED!! WILL BE REMOVED IN THE FUTURE.\n   *\n   * @return Observable<Response<MeasureSeriesMetadata>> - an observable containing the measure series metadata.\n   */\n  getMeasureSeriesCharacteristics(measureSeriesIds: string[], studyIds: string[]) :\n    Observable<Response<IsaCharacteristic>> {\n    if(!measureSeriesIds?.length) {\n      const errorResponse: ErrorResponse = {\n        code: 'BAD_REQUEST',\n        num_code: 400,\n        message: 'missing required parameter: measureSeriesIds',\n      };\n\n      throw errorResponse;\n    }\n\n    const url = this.buildUrl('/visualization/measures/characteristics', {\n      measureSeriesIds: measureSeriesIds.join(','),\n      studyIds: studyIds.join(',')\n    });\n\n\n    return this.apiBaseService.get(url);\n  }\n\n  // ASSAYS: to-be-implemented\n\n  /**\n   * Placeholder for assay operations\n   * TODO: Implement assay-related methods\n   */\n\n  // STUDIES: to-be-implemented\n\n  /**\n   * Placeholder for study operations\n   * TODO: Implement study-related methods\n   */\n\n  // INVESTIGATIONS: to-be-implemented\n\n  /**\n   * Placeholder for investigation operations\n   * TODO: Implement investigation-related methods\n   */\n\n  /**\n   * Builds the URL for the ISA data service.\n   *\n   * @param endpoint - the API endpoint path.\n   * @param params - optional query parameters as key-value pairs.\n   *\n   * @return complete URL with query string parameters.\n   */\n  private buildUrl(endpoint: string, params: Record<string, string>) {\n    const queryParams = new URLSearchParams(params).toString();\n\n    return queryParams ? `${endpoint}?${queryParams}` : endpoint;\n  }\n\n  // HEALTH CHECK\n  // TO-DO [GIK 05/30/2025]: should be moved outside this service\n  getHealthCheck(): Observable<any> {\n    return this.apiBaseService!.get<any>('/monitors/servers/health');\n  }\n}\n","/**\n * This module defines the data models for representing the Investigation-Study-Assay (ISA)\n * data model, which is a standard for describing life science experiments and their results.\n *\n * Key Concepts:\n * - Investigation: The overall research project or study.\n * - Study: A specific experimental design within an investigation.\n * - Assay: A specific test or measurement performed on samples within a study.\n *\n * Measures represent the actual data points collected from assay executions, including:\n * - Measure: a single assay results with unique identifier\n * - MeasureSeries: a collection of measures that share common metadata and characteristics\n *\n * Each measure/series contains values, metadata about the experimental conditions,\n * and characteristics that describe sample properties or experimental parameters.\n */\n\nexport interface Measure {\n  id: string;\n  values?: MeasureValue[];\n  metadata?: MeasureMetadata;\n  characteristics?: IsaCharacteristic[];\n}\n\nexport interface MeasureSeries {\n  id: string;\n  values?: MeasureValue[];\n  measures?: string[];\n  metadata?: MeasureSeriesMetadata;\n  characteristics?: IsaCharacteristic[];\n}\n\nexport interface MeasureMetadata {\n  assay_id: number;\n  description: string;\n  measure_id: number;\n  method: string;\n  study_id: string;\n  units: string;\n  treatment: string;\n  variable_name: string;\n\n  characteristics?: Record<string, string[]>\n}\n\nexport interface MeasureSeriesMetadata {\n  assay_id: number;\n  description: string;\n  initiated_at_units?: string;\n  measure_ids: string[];\n  measure_series_id: string;\n  measurement_units: string;\n  method: string;\n  study_id?: number;\n  treatment: string;\n  treatment_units: string;\n  variable_name: string;\n\n  characteristics?: Record<string, string[]>;\n};\n\nexport interface MeasureValue {\n  value: string | number;\n  measure_id: string;\n  measure_series_id?: string;\n  study_id?: string;\n  source_id: string;\n}\n\nexport interface IsaCharacteristicValue {\n  value: string | number | boolean | Date;\n  label: string; // e.g., 'High', 'Low', 'Positive', '2023-10-01'\n  count?: number;\n  description?: string; // optional description of the characteristic value\n  metadata: Record<string, string>; // additional metadata about the characteristic value\n}\n\nexport interface IsaCharacteristic {\n  name: string;\n  value: IsaCharacteristicValue | IsaCharacteristicValue[];\n  type?: string; // e.g., 'text', 'numeric', 'date'\n  unit?: string; // e.g., 'mg/L', 'Celsius'\n  description?: string; // optional description of the characteristic\n}\n","export interface VariantResults {\n  variantCount: number;\n  variants: Variant[];\n}\n\nexport interface Variant {\n  accession: string;\n  alt: string;\n  aminoAcidChange: string;\n  assembly: string;\n  canonVarIdentifier: {\n    caID: string;\n    id: number;\n    variantRefTxt: string;\n  };\n  chr: string;\n  dnaHgvsNotation: string;\n  functionalClassCode: string;\n  functionalClasses: SequenceOntologyTerm[]; // added artificially\n  gene: {\n    chr: string;\n    description: string;\n    ensemblGeneId: string;\n    entrezGeneId: string;\n    id: number;\n    mgiId: string;\n    name: string;\n    symbol: string;\n    synonyms: {\n      id: number;\n    }[];\n    transcripts: {\n      id: number;\n    }[];\n    type: string;\n  };\n  id: number;\n  impact: string;\n  parentRefInd: boolean;\n  position: number;\n  proteinHgvsNotation: string;\n  proteinPosition: string;\n  ref: string;\n  sources: {\n    id: number;\n    name: string;\n    sourceVersion: string;\n    url: string;\n  }[];\n  transcripts: {\n    description: string;\n    geneSymbol: string;\n    id: number;\n    mRnaId: string;\n    primaryIdentifier: string;\n  }[];\n  type: string;\n  variantHgvsNotation: string;\n  variantRefTxt: string;\n}\n\nexport interface SequenceOntologyTerm {\n  definition: string;\n  id: number;\n  label: string;\n  soId: string;\n  subClassOf: string;\n  mpdTerm: string;\n}\n\n\nexport interface SNP {\n  alternate_bases: string;\n  calls: Call[];\n  chr: string;\n  observed: string;\n  reference_base: string;\n  rs: string;\n  start_position: number | null; // allow for null value for gutter row\n  annotation?: Variant | null;\n}\n\nexport interface Call {\n  strain_name: string;\n  sample_id: number;\n  genotype: string;\n  prob: number;\n  base: string;\n}\n\nexport interface SNPSearchRegion {\n  chromosome: string;\n  start_position: number;\n  end_position: number;\n  reference_base?: string;\n  alternate_base?: string;\n}\n\n// TODO - move to constants file/library\nexport const MUS_CHRS = [\n  '1',\n  '2',\n  '3',\n  '4',\n  '5',\n  '6',\n  '7',\n  '8',\n  '9',\n  '10',\n  '11',\n  '12',\n  '13',\n  '14',\n  '15',\n  '16',\n  '17',\n  '18',\n  '19',\n  'X',\n  'Y',\n];\n","import { Inject, Injectable } from '@angular/core';\nimport { HttpClient } from '@angular/common/http';\nimport { BehaviorSubject, combineLatest, map, Observable, tap } from \"rxjs\";\n\nimport { MUS_CHRS, SequenceOntologyTerm, SNP, SNPSearchRegion, Variant, VariantResults } from './models/response/dtos';\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class MVarService {\n\n  private api;\n\n  sequenceOntologyMapping: Record<string, SequenceOntologyTerm> = {};\n\n  private soTerms: BehaviorSubject<SequenceOntologyTerm[]> = new BehaviorSubject(<SequenceOntologyTerm[]>[]);\n  soTerms$: Observable<SequenceOntologyTerm[]> = this.soTerms.asObservable();\n\n  constructor(private http: HttpClient, @Inject('environment') private environment: any) {\n    this.api = environment.unsecuredURLs.mvar;\n\n    // create a sequence ontology lookup\n    this.getSequenceOntologyTerms().subscribe((terms) => {\n      terms.forEach((t) => {\n        if (t.label) {\n          this.sequenceOntologyMapping[t.label] = t;\n        }\n      });\n    });\n  }\n\n  /**\n   * Gets Variants from mvar for a given set snp regions\n   * @param regions Array of snp regions\n   * @param pageStart snp start location\n   * @param pageEnd snp end location\n   * @param assembly Desired assembly version. Acceptable values are 'mm10' (GRCm38) and 'mm39' (GRCm39)\n   */\n  getVariants(regions: SNPSearchRegion[], pageStart: SNP, pageEnd: SNP, assembly: string): Observable<Variant[]> {\n    return combineLatest(\n      this.getRegionsToRequestVariantsFor(regions, pageStart, pageEnd).map((r) => {\n        return this.http.get<VariantResults>(\n          `${this.api}/variant/query?chr=${r.chromosome}&startPos=${r.start_position}&endPos=${r.end_position}&max=8000&assembly=${assembly}`,\n        );\n      }),\n    ).pipe(\n      map((variants: VariantResults[]) => {\n        const allVariants = variants.map((v) => v.variants).flat();\n        allVariants.forEach((variant: Variant) => {\n          const classCodes = variant.functionalClassCode.split(',')[0];\n          // add the ontology term\n          variant.functionalClasses = classCodes.split('&').map((c) => this.sequenceOntologyMapping[c]);\n        });\n        return allVariants;\n      }),\n    );\n  }\n\n  /**\n   * Returns all sequence ontology terms in MVAR\n   */\n  getSequenceOntologyTerms(): Observable<SequenceOntologyTerm[]> {\n    return this.http\n      .get<SequenceOntologyTerm[]>(`${this.api}/sequenceOntology/query?max=3000`)\n      .pipe(tap((terms) => this.soTerms.next(terms)));\n  }\n\n  /**\n   * Translates the regions requested from MUSter and the regions actually displayed on the current page into\n   * regions to request from MVAR\n   * @param requestedRegions - regions included in the request to MUSter\n   * @param pageStart - first SNP from the sorted results from MUSter to display in the table\n   * @param pageEnd - last SNP from the sorted results from MUSter to display in the table\n   */\n  getRegionsToRequestVariantsFor(\n    requestedRegions: SNPSearchRegion[],\n    pageStart: SNP,\n    pageEnd: SNP,\n  ): SNPSearchRegion[] {\n    const displayStartBP = pageStart.start_position || 0;\n    const displayEndBP = pageEnd.start_position || 0;\n    const regionsByChr: Record<string, SNPSearchRegion[]> = {};\n    requestedRegions.forEach((r) => {\n      if (regionsByChr[r.chromosome]) {\n        regionsByChr[r.chromosome].push(r);\n      } else {\n        regionsByChr[r.chromosome] = [r];\n      }\n    });\n\n    const displayedRegions: SNPSearchRegion[] = [];\n    if (pageStart.chr === pageEnd.chr) {\n      regionsByChr[pageStart.chr].forEach((r) => {\n        if (r.start_position <= displayEndBP && r.end_position >= displayStartBP) {\n          displayedRegions.push({\n            chromosome: r.chromosome,\n            start_position: Math.max(r.start_position, displayStartBP),\n            end_position: Math.min(r.end_position, displayEndBP),\n          });\n        }\n      });\n    } else {\n      const displayedChrs = Object.keys(regionsByChr).filter(\n        (r) =>\n          MUS_CHRS.indexOf(r) >= MUS_CHRS.indexOf(pageStart.chr) &&\n          MUS_CHRS.indexOf(r) <= MUS_CHRS.indexOf(pageEnd.chr),\n      );\n\n      displayedChrs.forEach((chr) => {\n        regionsByChr[chr].forEach((r) => {\n          if (r.end_position >= displayStartBP && chr === pageStart.chr) {\n            displayedRegions.push({\n              chromosome: r.chromosome,\n              start_position: Math.max(r.start_position, displayStartBP),\n              end_position: r.end_position,\n            });\n          } else if (r.start_position <= displayEndBP && chr === pageEnd.chr) {\n            displayedRegions.push({\n              chromosome: r.chromosome,\n              start_position: r.start_position,\n              end_position: Math.min(r.end_position, displayEndBP),\n            });\n          } else if (chr !== pageStart.chr && chr !== pageEnd.chr) {\n            displayedRegions.push({\n              chromosome: r.chromosome,\n              start_position: r.start_position,\n              end_position: r.end_position,\n            });\n          }\n        });\n      });\n    }\n\n    return displayedRegions;\n  }\n}\n","import { ModuleWithProviders, NgModule } from '@angular/core';\nimport { CommonModule } from '@angular/common';\nimport { MVarService } from \"./mvar.service\";\n\n@NgModule({\n  imports: [CommonModule],\n})\nexport class MvarClientModule {\n\n  public static forRoot(environment: any): ModuleWithProviders<MvarClientModule> {\n    return {\n      ngModule: MvarClientModule,\n      providers: [\n        MVarService,\n        {\n          provide: 'environment', // you can also use InjectionToken\n          useValue: environment\n        }\n      ]\n    };\n  }\n\n}\n","import { Observable } from 'rxjs';\nimport { Ontology, OntologyTerm } from './ontology.model';\nimport { CollectionResponse, Response } from '../../models/response';\n\nexport abstract class OntologyService {\n  abstract search(query: string, limit: number, ontology: Ontology): Observable<CollectionResponse<OntologyTerm>>;\n  abstract term(id: string): Observable<Response<OntologyTerm>>;\n  abstract parents(id: string): Observable<CollectionResponse<OntologyTerm>>;\n  abstract children(id: string): Observable<CollectionResponse<OntologyTerm>>;\n  abstract ancestors(id: string): Observable<CollectionResponse<OntologyTerm>>;\n  abstract descendants(id: string): Observable<CollectionResponse<OntologyTerm>>;\n}","export interface OntologyConfig {\n  name: string;\n  prefix: string;\n  github: {\n    api: string;\n    home: string;\n  };\n  home: string;\n  api: {\n    docs: string;\n    base: string;\n  };\n  base_file: string;\n  international: boolean;\n  description: string;\n}\n\nexport enum Ontology {\n  HP = 'HP',\n  MONDO = 'MONDO',\n  MP = 'MP',\n  CL = 'CL',\n  MAXO = 'MAXO'\n}\n\nexport interface OntologyTerm {\n  id: string;\n  name: string;\n}\n\n// OLS Term interface based on provided JSON\nexport interface OLSTerm {\n  appearsIn: string[];\n  curie: string;\n  definedBy: string[];\n  definition?: Array<{\n    type: string[];\n    value: string;\n    axioms?: Array<{ [key: string]: string }>\n  }>;\n  definitionProperty?: string;\n  directAncestor?: string[];\n  directParent?: Array<string>;\n  hasDirectChildren?: boolean;\n  hasDirectParents?: boolean;\n  hasHierarchicalChildren?: boolean;\n  hasHierarchicalParents?: boolean;\n  hierarchicalAncestor?: string[];\n  hierarchicalParent?: Array<string | {\n    type: string[];\n    value: string;\n    axioms?: Array<{ [key: string]: string }>\n  }>;\n  hierarchicalProperty?: string;\n  imported?: boolean;\n  iri: string;\n  isDefiningOntology?: boolean;\n  isObsolete?: boolean;\n  isPreferredRoot?: boolean;\n  label?: string[];\n  linkedEntities?: Record<string, any>;\n  linksTo?: string[];\n  numDescendants?: number;\n  numHierarchicalDescendants?: number;\n  ontologyId?: string;\n  ontologyIri?: string;\n  ontologyPreferredPrefix?: string;\n  searchableAnnotationValues?: any[];\n  shortForm?: string;\n  type?: string[];\n  [key: string]: any;\n}\n\n// OLS Response interface\nexport interface OLSResponse {\n  page: number;\n  numElements: number;\n  totalPages: number;\n  totalElements: number;\n  elements: OLSTerm[];\n  facetFieldsToCounts?: Record<string, any>;\n}","import { Ontology } from \"./ontology.model\";\n\n/**\n   * Get the ontology from curie\n   */\nexport function ontologyFromCurie(curie: string): Ontology {\n    return Ontology[curie.split(':')[0] as keyof typeof Ontology];\n}","import { HttpClient } from '@angular/common/http';\nimport { Injectable } from '@angular/core';\nimport { Observable, throwError } from 'rxjs';\nimport { Ontology, OntologyConfig, OntologyTerm } from './ontology.model';\n\nimport { CollectionResponse, Response } from '../../models/response';\nimport { ontologyFromCurie } from './ontology.shared';\nimport { OntologyService } from './ontology.service.base';\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class JaxOntologyService extends OntologyService {\n  config_location = 'https://raw.githubusercontent.com/TheJacksonLaboratory/ontology-service/refs/heads/main/config/ontologies-internal.json'\n  private config!: OntologyConfig[];\n\n  /**\n   * Get the configuration file from the source for the backend api service\n   */\n  constructor(private httpClient: HttpClient) {\n    super();\n    this.httpClient.get<OntologyConfig[]>(this.config_location).subscribe({\n      next: (config) => this.config = config,\n      error: () => {\n        this.config = [];\n      }\n    });\n  }\n\n  /**\n   * Search for terms in an ontology\n   * @param query - the search query\n   * @param limit - the number of results to return\n   * @param ontology - the ontology to search\n   */\n  search(query: string, limit: number, ontology: Ontology): Observable<CollectionResponse<OntologyTerm>> {\n    return this.httpClient.get<CollectionResponse<OntologyTerm>>(`${this.ontologyBaseResolver(ontology)}/search?q=${query}&limit=${limit}`);\n  }\n\n  /**\n   * Get a term by its ID\n   * @param id - the term ID\n   */\n  term(id: string): Observable<Response<OntologyTerm>>  {\n    try {\n      const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}`;\n      return this.httpClient.get<Response<OntologyTerm>>(url);\n    } catch (error) {\n      return throwError(() => error);\n    }\n  }\n\n  /**\n   * Get the parents of a term\n   * @param id - the term ID\n   */\n  parents(id: string): Observable<CollectionResponse<OntologyTerm>> {\n    try {\n      const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}/parents`;\n      return this.httpClient.get<CollectionResponse<OntologyTerm>>(url);\n    } catch (error) {\n      return throwError(() => error);\n    }\n  }\n\n  /**\n   * Get the children of a term\n   * @param id - the term ID\n   */\n  children(id: string): Observable<CollectionResponse<OntologyTerm>> {\n    try {\n      const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}/children`;\n      return this.httpClient.get<CollectionResponse<OntologyTerm>>(url);\n    } catch (error: any) {\n      return throwError(() => error);\n    }\n  }\n\n  /**\n   * Get the ancestors of a term\n   * @param id - the term ID\n   */\n  ancestors(id: string): Observable<CollectionResponse<OntologyTerm>> {\n    try {\n      const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}/ancestors`;\n      return this.httpClient.get<CollectionResponse<OntologyTerm>>(url);\n    } catch (error) {\n       return throwError(() => error);\n    }\n  }\n\n  /**\n   * Get the descendants of a term\n   * @param id - the term ID\n   */\n  descendants(id: string): Observable<CollectionResponse<OntologyTerm>> {\n    try {\n      const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}/descendants`;\n      return this.httpClient.get<CollectionResponse<OntologyTerm>>(url);\n    } catch (error) {\n       return throwError(() => error);\n    }\n  }\n\n  /**\n   * Get the ontology api base url configuration\n   **/\n  ontologyBaseResolver(ontology: Ontology): string {\n    if (!this.config || this.config.length === 0) {\n      throw new Error('No ontology configuration found.');\n    }\n    const ontology_config = this.config.find((config) => config.prefix.toUpperCase() === ontology);\n\n    if(!ontology_config) {\n      throw new Error('Ontology not found in configuration.');\n    }\n    return ontology_config.api.base;\n  }\n}\n","// ols-ontology.service.ts\nimport { Injectable } from '@angular/core';\nimport { HttpClient } from '@angular/common/http';\nimport { OntologyService } from './ontology.service.base';\nimport { Observable, map, pipe } from 'rxjs';\nimport { OLSResponse, OLSTerm, Ontology, OntologyTerm } from './ontology.model';\nimport { CollectionResponse, Response } from '../../models/response';\nimport { ontologyFromCurie } from './ontology.shared';\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class OLSOntologyService extends OntologyService {\n\n    private OLS_SEARCH_BASE = 'https://www.ebi.ac.uk/ols4/api/v2/entities';\n    private OLS_ENTITY_BASE = 'https://www.ebi.ac.uk/ols4/api/v2/ontologies';\n    private PURL_BASE = 'http://purl.obolibrary.org/obo';\n    constructor(private httpClient: HttpClient) {\n        super();\n    }\n\n    term(id: string): Observable<Response<OntologyTerm>> {\n        const ontology = ontologyFromCurie(id);\n        const params = new URLSearchParams;\n        params.set('includeObsoleteEntities', 'false');\n        return this.httpClient.get<OLSTerm>(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}?${params.toString()}`).pipe(map(olsResponse => {\n            return {\n                object: this.mapOLSTermToOntologyTerm(olsResponse)\n            };\n        }));\n    }\n\n    search(query: string, limit: number, ontology: Ontology): Observable<CollectionResponse<OntologyTerm>> {\n\n        const params = new URLSearchParams\n        params.set('search', query);\n        params.set('size', limit.toString());\n        params.set('ontologyId', ontology.toLowerCase());\n        params.set('includeObsoleteEntities', 'false');\n        return this.httpClient.get<OLSResponse>(`${this.OLS_SEARCH_BASE}?${params.toString()}`).pipe(map(olsResponse => {\n            const collectionResponse: CollectionResponse<OntologyTerm> = {\n                data: olsResponse.elements.filter((olsTerm: OLSTerm) => olsTerm.definedBy.includes(ontology.toLowerCase())).map(olsTerm => this.mapOLSTermToOntologyTerm(olsTerm)),\n                paging: {\n                    page: olsResponse.page,\n                    total_pages: olsResponse.totalPages,\n                    total_items: olsResponse.totalElements\n                }\n            };\n            return collectionResponse;\n        }));\n    }\n\n    parents(id: string): Observable<CollectionResponse<OntologyTerm>> {\n        const ontology = ontologyFromCurie(id);\n        const params = new URLSearchParams;\n        params.set('includeObsoleteEntities', 'false');\n        return this.httpClient.get<OLSTerm>(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}?${params.toString()}`).pipe(map(olsTerm => {\n            const data =  olsTerm.directParent\n                    ? olsTerm.directParent\n                        .map(parent =>\n                            olsTerm.linkedEntities && olsTerm.linkedEntities[parent]\n                                ? this.mapOLSTermToOntologyTerm(olsTerm.linkedEntities[parent])\n                                : \"\"\n                        ).filter(parent => parent !== \"\")\n                    : []\n            return {\n                data: data,\n                paging: {\n                    page: 1,\n                    total_pages: 1,\n                    total_items: data.length\n                }\n            };\n        }));\n    }\n\n    children(id: string): Observable<CollectionResponse<OntologyTerm>> {\n        const ontology = ontologyFromCurie(id);\n        const params = new URLSearchParams;\n        params.set('includeObsoleteEntities', 'false');\n        params.set('size', '100');\n        params.set('lang', 'en');\n        return this.httpClient.get<OLSResponse>(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}/children?${params.toString()}`).pipe(map(childrenResponse => {\n            const data =  childrenResponse.elements.map(olsTerm => this.mapOLSTermToOntologyTerm(olsTerm));\n            return {\n                data: data,\n                paging: {\n                    page: childrenResponse.page,\n                    total_pages: childrenResponse.totalPages,\n                    total_items: data.length\n                }\n            };\n        }));\n    }\n\n    ancestors(id: string): Observable<CollectionResponse<OntologyTerm>> {\n        const ontology = ontologyFromCurie(id);\n        const params = new URLSearchParams;\n        params.set('includeObsoleteEntities', 'false');\n        return this.httpClient.get<OLSTerm>(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}?${params.toString()}`).pipe(map(olsTerm => {\n            const data =  olsTerm.directAncestor\n                    ? olsTerm.directAncestor\n                        .map(ancestor =>\n                            olsTerm.linkedEntities && olsTerm.linkedEntities[ancestor]\n                                ? this.mapOLSTermToOntologyTerm(olsTerm.linkedEntities[ancestor])\n                                : \"\"\n                        ).filter(ancestor => ancestor !== \"\")\n                    : []\n            return {\n                data: data,\n                paging: {\n                    page: 1,\n                    total_pages: 1,\n                    total_items: data.length\n                }\n            };\n        }));\n    }\n\n    // finish testing this method\n    descendants(id: string): Observable<CollectionResponse<OntologyTerm>> {\n        const ontology = ontologyFromCurie(id);\n        const params = new URLSearchParams;\n        params.set('includeObsoleteEntities', 'false');\n        params.set('size', '100'); // max size for children endpoint\n        params.set('lang', 'en');\n        return this.httpClient.get<OLSResponse>(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}/hierarchicalChildren?${params.toString()}`).pipe(map(childrenResponse => {\n            const data =  childrenResponse.elements.map(olsTerm => this.mapOLSTermToOntologyTerm(olsTerm));\n            return {\n                data: data,\n                paging: {\n                    page: childrenResponse.page,\n                    total_pages: childrenResponse.totalPages,\n                    total_items: data.length\n                }\n            };\n        }));\n    }\n\n    mapOLSTermToOntologyTerm(olsTerm: OLSTerm): OntologyTerm {\n        return {\n            id: olsTerm.curie,\n            name: olsTerm.label && olsTerm.label.length > 0 ? olsTerm.label[0] : 'No label'\n        };\n    }\n}","import { Inject, Injectable } from '@angular/core';\nimport { HttpClient } from \"@angular/common/http\";\nimport { catchError, map, Observable } from \"rxjs\";\n\nimport {\n  Dataset, DatasetStatus,\n  Gene, GenotypeResults,\n  MusterHealthCheck,\n  MusterMetadata,\n  ReferenceSNP,\n  SNPSearchProperties,\n  Strain\n} from './models/response/dtos';\nimport { SNPSearchRegion } from '../mvar/models/response/dtos';\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class SnpGridService {\n  private api;\n\n  constructor(private http: HttpClient, @Inject('environment') private environment: any) {\n    this.api = environment.securedURLs.genomeMUSter;\n  }\n\n  /**\n   * Returns the result of a health check for the API\n   */\n  getHealthCheck(): Observable<MusterHealthCheck> {\n    return this.http.get<MusterHealthCheck>(`${this.api}/healthcheck`);\n  }\n\n  /**\n   * Returns the metadata on the MUSter DB\n   */\n  getMusterMetadata(): Observable<MusterMetadata> {\n    return this.http.get<MusterMetadata>(`${this.api}/db_info`).pipe(\n      catchError((err) => {\n        throw err;\n      }),\n    );\n  }\n\n  /**\n   * Returns strains available in the API and takes an optional limit; by default the limit is set\n   * to 5000 to get all strains\n   * @param limit - maximum number of strains to be returned\n   */\n  getStrains(limit = 5000): Observable<Strain[]> {\n    return this.http.get<Strain[]>(`${this.api}/strains/?limit=${limit}`).pipe(\n      map((strains) => strains.filter((s) => s.mpd_strainid))\n    );\n  }\n\n  /**\n   * Returns a list of known genes whose symbols/coordinates start with the specified value.\n   * @param searchValue - value to use for the \"starts with\" filter\n   * @param limit - maximum number of genes to return, default is 20\n   */\n  getGenes(searchValue: string, limit = 20): Observable<Gene[]> {\n    return this.http.get<Gene[]>(`${this.api}/genes/?symbol=${searchValue}%&limit=${limit}`);\n  }\n\n  /**\n   * Returns the gene that matches the specified gene symbol\n   * @param geneSymbol - symbol to use to get the associated gene info\n   */\n  getGene(geneSymbol: string): Observable<Gene | null> {\n    return this.http\n      .get<Gene[]>(`${this.api}/genes/?symbol=${geneSymbol}`)\n      .pipe(map((genes) => (genes.length ? genes[0] : null)));\n  }\n\n  /**\n   * Returns true if the specified gene symbol is valid from the perspective of MUSter\n   * @param geneSymbol - symbol to use to check the validity of\n   */\n  isGeneSymbolValid(geneSymbol: string): Observable<boolean> {\n    return this.getGene(geneSymbol).pipe(\n      map((g: Gene | null) => g !== null && geneSymbol.toLowerCase() === g.symbol.toLowerCase()),\n    );\n  }\n\n  /**\n   * Returns list of known reference SNP (RS) data which includes IDs and coordinates\n   * @param searchValue - value to use to filter the search results\n   * @param limit - maximum number of results to return, default is 20\n   */\n  getReferenceSNPs(searchValue: string, limit = 20): Observable<ReferenceSNP[]> {\n    return this.http.get<ReferenceSNP[]>(`${this.api}/rsids/?rsid=${searchValue}%&limit=${limit}`);\n  }\n\n  /**\n   * Returns the RS info that matches the specified rsID\n   * @param rsid - the RSID to use to get the associated RS info\n   */\n  getReferenceSNP(rsid: string): Observable<ReferenceSNP | null> {\n    return this.http\n      .get<ReferenceSNP[]>(`${this.api}/rsids/?rsid=${rsid}`)\n      .pipe(map((rsids) => (rsids.length ? { ...rsids[0], end_position: rsids[0].start_position } : null)));\n  }\n\n  /**\n   * Returns true if the specified rsID is valid from the perspective of MUSter\n   * @param rsid - rsID to use to check the validity of\n   */\n  isRSIDValid(rsid: string): Observable<boolean> {\n    return this.getReferenceSNP(rsid).pipe(\n      map((rs: ReferenceSNP | null) => rs !== null && rsid.toLowerCase() === rs.rsid.toLowerCase()),\n    );\n  }\n\n  /**\n   * Returns the SNP results generated from the query constructed from the specified parameters and page\n   * @param parameters - search properties (strain IDs, regions, assembly version, etc.)\n   * @param page - requested page, which is 0-indexed. The 0th page is the initial page\n   * @param pageSize - number of records to show per page. Default of 5000\n   */\n  getGenotypes(parameters: SNPSearchProperties, page = 0, pageSize = 5000): Observable<GenotypeResults> {\n    let constructedURL =\n      `${this.api}/snps/?` +\n      `assembly=${parameters.assembly}&` +\n      `mpd_strain_ids=${parameters.strains.join(',')}&` +\n      `limit=${pageSize}`;\n\n    if (parameters.strains_b?.length) {\n      constructedURL += `&mpd_strain_ids_b=${parameters.strains_b.join(',')}&strain_limit=${parameters.strains.length + parameters.strains_b.length}`;\n    } else {\n      constructedURL += `&strain_limit=${parameters.strains.length}`\n    }\n\n    if (parameters.rsids?.length) {\n      constructedURL += `&rsids=${parameters.rsids.join(',')}`;\n    }\n\n    if (parameters.genes?.length) {\n      constructedURL += `&genes=${parameters.genes.join(',')}`;\n    }\n\n    if (parameters.regions?.length) {\n      constructedURL += `&regions=${parameters.regions.join(',')}`;\n    }\n\n    if (parameters.dataset_id) {\n      constructedURL += `&dataset_id=${parameters.dataset_id}`;\n    }\n\n    if (parameters.is_unique_row) {\n      constructedURL += `&is_unique_row=${parameters.is_unique_row}`;\n    }\n\n    if (page) {\n      constructedURL += `&offset=${pageSize * page}`;\n    }\n\n    return this.http.get<GenotypeResults>(constructedURL);\n  }\n\n  /**\n   * Returns the URL that will generate a download (in file form) for the specified strain IDs and regions\n   * @param strains - list of mpd_strain_ids to query SNPs for\n   * @param regions - list of SNPSearchRegions to query SNPs for (chromosome, start and end)\n   * @param dataset_id - ID of the dataset to query SNPs for\n   * @param is_unique_row - boolean for polymorphism filtering - true for only rows with polymorphism, false for all\n   * @param limit - the limit of the number of result rows to include in the download - you're likely to\n   *                prefer to pass the total number of rows generated by the query itself, which is included\n   *                as part of the GenotypeResults returned by getGenotypes()\n   */\n  getGenotypeDownloadURLForCurrentData(strains: number[], regions: SNPSearchRegion[], dataset_id: number | undefined, is_unique_row = false,  limit: number): string {\n    if (!dataset_id) {\n      // default to the GenomeMuster dataset id\n      dataset_id = 2;\n    }\n    const stringifiedRegions = `regions=${regions\n      .map((reg) => `${reg.chromosome}:${reg.start_position}-${reg.end_position}`)\n      .join(',')}`;\n    const stringifiedStrains = `mpd_strain_ids=${strains.join(',')}`;\n    return `${this.api}/snps/download?dataset_id=${dataset_id}&${stringifiedStrains}&${stringifiedRegions}&limit=${limit}&is_unique_row=${is_unique_row}`;\n  }\n\n  /**\n   * Returns the dataset with the given ID\n   * @param id\n   */\n  getDataset(id: number): Observable<Dataset> {\n    return this.http.get<Dataset>(`${this.api}/datasets/${id}`)\n  }\n\n  /**\n   * Returns a list of Datasets that match the given criteria\n   * @param status  The value of the status to be used for filtering\n   * @param limit   The maximum number of records to return\n   */\n  findDatasets(status: DatasetStatus, limit = 50): Observable<Dataset[]> {\n    let url = `${this.api}/datasets`;\n    url += `/?limit=${limit}`;\n    if (status) {\n      url += `&status=${status}`;\n    }\n    return this.http.get<Dataset[]>(url);\n  }\n\n  /**\n   * Return a list of strains that match the given criteria\n   * @param datasetId  The ID of the dataset from which to fetch the strains\n   * @param limit      The maximum number of records to return\n   */\n  datasetStrains(datasetId: number, limit = 5000): Observable<Strain[]> {\n    const url = `${this.api}/dataset_strain/?dataset_id=${datasetId}&limit=${limit}`;\n    return this.http.get<Strain[]>(url);\n  }\n\n}\n","import { ModuleWithProviders, NgModule } from '@angular/core';\nimport { CommonModule } from '@angular/common';\nimport { SnpGridService } from \"./snp-grid.service\";\n\n@NgModule({\n  imports: [CommonModule],\n})\nexport class SnpGridClientModule {\n\n  public static forRoot(environment: any): ModuleWithProviders<SnpGridClientModule> {\n    return {\n      ngModule: SnpGridClientModule,\n      providers: [\n        SnpGridService,\n        {\n          provide: 'environment', // you can also use InjectionToken\n          useValue: environment\n        }\n      ]\n    };\n  }\n\n}\n","import { SNP, SNPSearchRegion } from \"../../../mvar/models/response/dtos\";\n\nexport interface MusterHealthCheck {\n  status: string;\n  timestamp: string;\n}\n\nexport interface MusterMetadata {\n  total_number_of_SNPs: number;\n  last_updated: string;\n  version: string;\n  total_number_of_strains: number;\n}\n\nexport interface Strain {\n  bq_sample_id: number;\n  mpd_strainid: number;\n  strainname: string;\n  straintype: string;\n}\n\nexport interface Gene {\n  symbol: string;\n  chr: string;\n  start_position: number;\n  end_position: number;\n  strand: string;\n  description: string;\n  mginum: string;\n  markertype: string;\n  centimorgan: number;\n  featuretype: string;\n}\n\nexport interface ReferenceSNP {\n  chr: string;\n  start_position: number;\n  end_position?: number; // added later\n  rsid: string;\n}\n\nexport interface MusterSearchParameters {\n  bq_sample_ids: null;\n  genes: string | null; // stringified array\n  genes_data: Gene[];\n  limit: number;\n  mpd_strain_ids: string; // stringified array\n  next_region: string | null;\n  offset: number;\n  query_regions: {\n    chromosome: string;\n    regions: SNPSearchRegion[];\n  }[];\n  regions: SNPSearchRegion[];\n  rsids: string | null; //stringified array\n  rsids_data: ReferenceSNP[];\n  strain_limit: number;\n  strain_names: null;\n  dataset: Dataset;\n}\n\nexport interface SNPSearchProperties {\n  strains: number[];\n  strains_b?: number[];\n  rsids?: string[];\n  regions?: string[];\n  assembly: string;\n  genes?: string[];\n  offset?: number;\n  dataset_id?: number;\n  is_unique_row?: boolean;\n}\n\nexport interface GenotypeResults {\n  message: string | null;\n  next_region: string;\n  parameter: MusterSearchParameters;\n  snps: SNP[];\n  status: string;\n  total_rows: number;\n}\n\nexport enum DatasetStatus {\n  Queued = 'queued',\n  Loading = 'loading',\n  Done = 'done',\n  Archived = 'archived',\n}\n\nexport interface Dataset {\n  id: number,\n  display_name: string,\n  sort_by: number,\n  year: string,\n  procedure: string,\n  panel: string,\n  sex: string,\n  dataset_name: string,\n  source: string,\n  status: DatasetStatus,\n  num_of_strains: number,\n  pubmed: string,\n  description: string,\n  assembly_version: string,\n}\n","// AsyncTask API client\nexport * from './lib/services/asynctask/asynctask.service';\nexport * from './lib/services/asynctask/asynctask.model';\n\n// ISA Data API client\nexport * from './lib/services/isa-data/isa-data.service';\nexport * from './lib/models/isa-data/isa-data.model';\nexport * from './lib/tokens/isa-data-config.token';\n\n// MVAR API client\nexport * from './lib/services/mvar/mvar.service';\nexport * from './lib/services/mvar/models/response/dtos';\nexport * from './lib/services/mvar/mvar-client.module';\n\n// Ontology API client\nexport * from './lib/services/ontology/ontology.service.base';\nexport * from './lib/services/ontology/ontology.service.jax';\nexport * from './lib/services/ontology/ontology.service.ols';\n\n// MVar API client\nexport * from './lib/services/mvar/mvar.service';\nexport * from './lib/services/mvar/models/response/dtos';\nexport * from './lib/services/mvar/mvar-client.module';\n\n// SNP Grid API client\nexport * from './lib/services/snp-grid/snp-grid-client.module';\nexport * from './lib/services/snp-grid/models/response/dtos';\nexport * from './lib/services/snp-grid/snp-grid.service';\n","/**\n * Generated bundle index. Do not edit.\n */\n\nexport * from 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package/lib/services/snp-grid/snp-grid.service.d.ts

@@ -7,9 +7,6 @@ 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

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jax-data-science/api-clients",
-  "version": "0.0.1",
+  "version": "0.0.2-0",
   "peerDependencies": {
     "@angular/common": "^19.2.14",
     "@angular/core": "^19.2.14",