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Commit b514518

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shiroyukimpanik
shiroyuki
authored and
mpanik
committed
Manually merge Data Explorer module, COVID-19 app (i.e., discovery app), and beacon app; and resolved regression introduced by babel/compat-data (angular/angular-cli#17262)
Aggregated commits from 2020.03.03 to 2020.03.20 - Support for coronavirus app - Preliminary support for Google Maps - Added the condition to hide the app switcher if there is only one accessible app - Implemented the condition to hide the sidebar if there is only one submodule available - Preliminary support for Bing Maps - Moved terms into its own menu - Nextstrain integration and small style fixes - Added attribution for GISAID - Added attribution of NGDC - Parameterized COVID Beacon Url - Ensured that the first query is triggered on initialization - Preliminary UX updates - Synchronize query params with URL and initiate search automatically - Make mouse a hand over clickable rows - Fixed the error/warning on bi-directional binding, unused reference, hid the info panel by default, and make the button explicitly do something (instead of 'toggle') - Do search on enter - When the search starts, deactivate the search box - Dynamically set mobile state if necessary - Turn off pagination on mobile - Reduced self-referencing and local variables and ensure that when the row is selected, the details panel is automatically displayed. - When the user clicks on a row (cell), the info panel is auto-displayed. - Replaced how the sidebar is able from relying on the number of submodules to the property of the module metadata. - Added the test for Workflow Registry - Added the test for COVID-19 beacon - Removed the default title. (COVID-23) - Implemented Google Analytics by injecting to <head> (COVID-8) - Introduced dynamic theme (COVID-20)
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‎angular/package-lock.json

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‎angular/package.json

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},
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"private": true,
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"dependencies": {
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"@angular/animations": "^8.2.8",
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"@angular/cdk": "~8.2.1",
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"@angular/common": "^8.2.8",
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"@angular/compiler": "~8.2.8",
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"@angular/core": "^8.2.8",
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"@agm/core": "^1.1.0",
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"@angular/animations": "^8.2.14",
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"@angular/cdk": "^8.2.3",
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"@angular/common": "^8.2.14",
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"@angular/compiler": "^8.2.14",
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"@angular/core": "^8.2.14",
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"@angular/flex-layout": "^8.0.0-beta.27",
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"@angular/forms": "^8.2.8",
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"@angular/material": "^8.2.1",
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"@angular/platform-browser": "~8.2.8",
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"@angular/platform-browser-dynamic": "~8.2.8",
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"@angular/router": "~8.2.8",
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"@angular/forms": "^8.2.14",
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"@angular/material": "^8.2.3",
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"@angular/platform-browser": "^8.2.14",
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"@angular/platform-browser-dynamic": "^8.2.14",
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"@angular/router": "^8.2.14",
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"@materia-ui/ngx-monaco-editor": "4.0.1",
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"@ngx-loading-bar/core": "^4.2.0",
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"@ngx-loading-bar/http-client": "^4.2.0",
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"@types/bingmaps": "0.0.1",
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"@types/googlemaps": "^3.39.3",
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"ag-grid-angular": "^22.1.1",
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"ag-grid-community": "^22.1.1",
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"ang-jsoneditor": "1.8.3",
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"angular-maps": "^6.0.3",
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"angular-material-dynamic-themes": "^1.0.4",
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"angular7-json-schema-form": "^1.0.4",
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"bingmaps": "^2.0.3",
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"brace": "^0.11.1",
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"dayjs": "^1.8.16",
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"ddap-common-lib": "0.0.19-67-g6ac7b50",
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"ddap-common-lib": "0.0.19-72-g461e5a4",
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"hammerjs": "^2.0.8",
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"jsoneditor": "^7.0.4",
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"highlight.js": "^9.15.10",
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"jsoneditor": "^7.5.0",
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"linkifyjs": "latest",
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"lodash.clonedeep": "^4.5.0",
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"lodash.get": "^4.4.2",
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"lodash.isequal": "^4.5.0",
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"lodash.samplesize": "^4.2.0",
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"lodash.set": "^4.3.2",
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"lodash.startcase": "^4.4.0",
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"lodash.uniq": "^4.5.0",
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"monaco-editor": "~0.18.1",
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"ng2-ace-editor": "^0.3.9",
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"ngx-chips": "^2.0.2",
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"ngx-clipboard": "^12.2.0",
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"ngx-chips": "^2.1.0",
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"ngx-clipboard": "^12.3.1",
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"ngx-highlightjs": "^3.0.3",
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"ngx-webstorage-service": "^4.1.0",
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"@materia-ui/ngx-monaco-editor": "4.0.1",
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"monaco-editor": "~0.18.1",
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"rxjs": "~6.5.3",
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"rxjs": "^6.5.4",
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"showdown": "^1.9.1",
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"tslib": "^1.10.0",
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"zone.js": "~0.9.1",
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"linkifyjs": "latest"
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"tslib": "^1.11.0",
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"zone.js": "~0.9.1"
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},
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"devDependencies": {
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"@angular-devkit/build-angular": "^0.803.24",
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"@angular-devkit/build-ng-packagr": "~0.803.6",
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"@angular/cli": "^8.3.6",
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"@angular/compiler-cli": "^8.2.8",
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"@types/long": "^4.0.0",
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"@types/node": "~12.7.8",
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"codelyzer": "~5.1.0",
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"@angular-devkit/build-angular": "^0.803.25",
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"@angular-devkit/build-ng-packagr": "^0.803.25",
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"@angular/cli": "^8.3.25",
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"@angular/compiler-cli": "^8.2.14",
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"@babel/compat-data": "~7.8.0",
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"@types/long": "^4.0.1",
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"@types/node": "^12.7.12",
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"codelyzer": "^5.1.2",
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"husky": "^4.2.3",
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"lint-staged": "^10.0.7",
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"lint-staged": "^10.0.8",
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"protobufjs": "^6.8.8",
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"ts-node": "~8.3.0",
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"tslint": "~5.18.0",

‎angular/src/app/app-routing.module.ts

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.then(mod => mod.WorkflowsModule),
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},
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{
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path: 'search',
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loadChildren: () => import('./search/search.module')
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.then(mod => mod.SearchModule),
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path: 'discovery',
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loadChildren: () => import('./discovery/discovery.module')
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.then(mod => mod.DiscoveryModule),
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},
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],
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},

‎angular/src/app/data/data.module.ts

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import { NgModule } from '@angular/core';
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import { MatGridListModule } from '@angular/material/grid-list';
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import { MatToolbarModule } from '@angular/material/toolbar';
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import { DdapLayoutModule } from 'ddap-common-lib';
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import { AceEditorModule } from 'ng2-ace-editor';
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import { SharedModule } from '../shared/shared.module';
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import { DataRoutingModule } from './data-routing.module';
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import { DataSearchComponent } from './data-search/data-search.component';
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@NgModule({
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declarations: [
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DataListComponent,
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imports: [
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SharedModule,
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DataRoutingModule,
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MatGridListModule,
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MatToolbarModule,
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AceEditorModule,
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DdapLayoutModule,
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],
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})
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export class DataModule {

‎angular/src/app/discovery/beacon-service/beacon.model.ts

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export class BeaconRequest {
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referenceName: string;
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referenceBases: string;
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alternateBases: string;
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assemblyId: string;
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start: number;
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}
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export class BeaconResponse {
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datasetId: string;
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exists: boolean;
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info: any[];
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}
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export interface BeaconAPIResponse {
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beaconId: string;
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alleleRequest: {
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referenceName: string,
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referenceBases: string,
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alternateBases: string,
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assemblyId: string,
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start: number,
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};
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datasetAlleleResponses: BeaconResponse[];
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}

‎angular/src/app/discovery/beacon-service/beacon.service.ts

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import { HttpClient, HttpHeaders, HttpParams } from '@angular/common/http';
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import { Injectable } from '@angular/core';
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import { BeaconResponse } from './beacon.model';
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@Injectable({
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providedIn: 'root',
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})
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export class BeaconService {
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apiUrl: String;
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constructor(
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private httpClient: HttpClient
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) {}
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setApiUrl (url: String) {
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this.apiUrl = url;
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}
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getApiUrl() {
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return this.apiUrl;
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}
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searchBeacon(
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assembly: string,
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referenceName: string,
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start: number,
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referenceBases: string,
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alternateBases: string,
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headers?: HttpHeaders)
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: Promise<BeaconResponse[]> { // FIXME This is an incorrect response type. Need to use BeaconAPIResponse instead.
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return this.searchBeacons(
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assembly,
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referenceName,
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start,
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referenceBases,
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alternateBases,
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headers);
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}
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searchBeacons(
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assembly: string,
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referenceName: string,
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start: number,
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referenceBases: string,
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alternateBases: string,
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headers?: HttpHeaders)
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: Promise<BeaconResponse[]> {
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const params = new HttpParams()
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.set('assemblyId', assembly)
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.set('referenceName', referenceName)
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.set('start', start + '')
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.set('referenceBases', referenceBases)
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.set('alternateBases', alternateBases)
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;
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// /query?referenceName=1&start=9924&referenceBases=C&alternateBases=T&assemblyId=GRCh38
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return this.httpClient.get<BeaconResponse[]>(`${this.apiUrl}`
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+ '/query', { 'params': params, 'headers' : headers }).toPromise();
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}
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}

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