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alismanalisman
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Merge pull request #4533 from TJMKuijpers/custom-numerical-chart
Allow numeric data type for custom data charts
2 parents 754c9cc + f5dc6d5 commit 5757156

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11 files changed

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‎end-to-end-test/local/screenshots/reference/add_custom_data_tab_should_have_numerical_and_categorical_selector_element_chrome_1600x1000.png

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‎end-to-end-test/local/specs/core/studyview.screenshot.spec.js

+42
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,7 @@ const ADD_CHART_X_VS_Y_TAB = '.addChartTabs a.tabAnchor_X_Vs_Y';
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const WAIT_FOR_VISIBLE_TIMEOUT = 30000;
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const MUTATIONS_GENES_TABLE = "[data-test='mutations-table']";
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const CANCER_GENE_FILTER_ICON = "[data-test='header-filter-icon']";
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const ADD_CUSTOM_CHART_TAB = '.addChartTabs a.tabAnchor.tabAnchor_Custom_Data';
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describe('study view generic assay categorical/binary features', function() {
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it('generic assay pie chart should be added in the summary tab', () => {
@@ -79,6 +80,47 @@ describe('study view generic assay categorical/binary features', function() {
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});
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});
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describe('Test the Custom data tab', function() {
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it('Add custom data tab should have numerical and categorical selector', () => {
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const url = `${CBIOPORTAL_URL}/study?id=lgg_ucsf_2014_test_generic_assay`;
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goToUrlAndSetLocalStorage(url, true);
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waitForNetworkQuiet();
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$(ADD_CHART_BUTTON).waitForDisplayed({
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timeout: WAIT_FOR_VISIBLE_TIMEOUT,
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});
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$(ADD_CHART_BUTTON).click();
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waitForNetworkQuiet();
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// Change to custom tab
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$(ADD_CUSTOM_CHART_TAB).waitForDisplayed({
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timeout: WAIT_FOR_VISIBLE_TIMEOUT,
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});
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$(ADD_CUSTOM_CHART_TAB).click();
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const res = browser.checkElement('div.msk-tab.custom');
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assertScreenShotMatch(res);
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});
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it('Selecting numerical for custom data should return a bar chart', () => {
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const url = `${CBIOPORTAL_URL}/study?id=lgg_ucsf_2014_test_generic_assay`;
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goToUrlAndSetLocalStorage(url, true);
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waitForNetworkQuiet();
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$(ADD_CHART_BUTTON).waitForDisplayed({
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timeout: WAIT_FOR_VISIBLE_TIMEOUT,
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});
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$(ADD_CHART_BUTTON).click();
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waitForNetworkQuiet();
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// Change to custom tab
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$(ADD_CUSTOM_CHART_TAB).waitForDisplayed({
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timeout: WAIT_FOR_VISIBLE_TIMEOUT,
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});
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$(ADD_CUSTOM_CHART_TAB).click();
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CUSTOM_CHART_TAB = $('div.msk-tab.custom');
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// Add values to the input form
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});
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});
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describe('study view x vs y charts', () => {
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const X_VS_Y_CHART = `div[data-test="chart-container-X-VS-Y-AGE-MUTATION_COUNT"]`;
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const X_VS_Y_HAMBURGER_ICON = `${X_VS_Y_CHART} [data-test="chart-header-hamburger-icon"]`;

‎env/custom.sh

+2-2
Original file line numberDiff line numberDiff line change
@@ -1,2 +1,2 @@
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#export CBIOPORTAL_URL="http://localhost:8080"
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#export GENOME_NEXUS_URL="https://www.genomenexus.org"
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export CBIOPORTAL_URL="http://localhost:8081"
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export GENOME_NEXUS_URL="https://www.genomenexus.org"

‎packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts

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Original file line numberDiff line numberDiff line change
@@ -2476,6 +2476,97 @@ export default class CBioPortalAPIInternal {
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return response.body;
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});
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};
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fetchCustomDataBinCountsUsingPOSTURL(parameters: {
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'clinicalDataBinCountFilter': ClinicalDataBinCountFilter,
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'dataBinMethod' ? : "DYNAMIC" | "STATIC",
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$queryParameters ? : any
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}): string {
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let queryParameters: any = {};
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let path = '/custom-data-bin-counts/fetch';
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if (parameters['dataBinMethod'] !== undefined) {
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queryParameters['dataBinMethod'] = parameters['dataBinMethod'];
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}
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if (parameters.$queryParameters) {
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Object.keys(parameters.$queryParameters).forEach(function(parameterName) {
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var parameter = parameters.$queryParameters[parameterName];
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queryParameters[parameterName] = parameter;
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});
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}
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let keys = Object.keys(queryParameters);
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return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : '');
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};
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/**
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* Fetch custom data bin counts by study view filter
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* @method
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* @name CBioPortalAPIInternal#fetchCustomDataBinCountsUsingPOST
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* @param {} clinicalDataBinCountFilter - Clinical data bin count filter
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* @param {string} dataBinMethod - Method for data binning
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*/
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fetchCustomDataBinCountsUsingPOSTWithHttpInfo(parameters: {
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'clinicalDataBinCountFilter': ClinicalDataBinCountFilter,
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'dataBinMethod' ? : "DYNAMIC" | "STATIC",
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$queryParameters ? : any,
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$domain ? : string
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}): Promise < request.Response > {
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const domain = parameters.$domain ? parameters.$domain : this.domain;
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const errorHandlers = this.errorHandlers;
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const request = this.request;
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let path = '/custom-data-bin-counts/fetch';
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let body: any;
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let queryParameters: any = {};
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let headers: any = {};
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let form: any = {};
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return new Promise(function(resolve, reject) {
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headers['Accept'] = 'application/json';
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headers['Content-Type'] = 'application/json';
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if (parameters['clinicalDataBinCountFilter'] !== undefined) {
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body = parameters['clinicalDataBinCountFilter'];
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}
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if (parameters['clinicalDataBinCountFilter'] === undefined) {
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reject(new Error('Missing required parameter: clinicalDataBinCountFilter'));
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return;
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}
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if (parameters['dataBinMethod'] !== undefined) {
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queryParameters['dataBinMethod'] = parameters['dataBinMethod'];
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}
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if (parameters.$queryParameters) {
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Object.keys(parameters.$queryParameters).forEach(function(parameterName) {
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var parameter = parameters.$queryParameters[parameterName];
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queryParameters[parameterName] = parameter;
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});
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}
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request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers);
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});
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};
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/**
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* Fetch custom data bin counts by study view filter
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* @method
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* @name CBioPortalAPIInternal#fetchCustomDataBinCountsUsingPOST
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* @param {} clinicalDataBinCountFilter - Clinical data bin count filter
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* @param {string} dataBinMethod - Method for data binning
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*/
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fetchCustomDataBinCountsUsingPOST(parameters: {
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'clinicalDataBinCountFilter': ClinicalDataBinCountFilter,
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'dataBinMethod' ? : "DYNAMIC" | "STATIC",
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$queryParameters ? : any,
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$domain ? : string
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}): Promise < Array < ClinicalDataBin >
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> {
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return this.fetchCustomDataBinCountsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) {
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return response.body;
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});
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};
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fetchCustomDataCountsUsingPOSTURL(parameters: {
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'clinicalDataCountFilter': ClinicalDataCountFilter,
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$queryParameters ? : any

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