Allow numeric data type for custom data charts

cBioPortal · Mar 28, 2023 · 9239879 · 9239879
1 parent 7ced3b6
commit 9239879
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Showing 11 changed files with 675 additions and 72 deletions.
diff --git a/...tab_should_have_numerical_and_categorical_selector_element_chrome_1600x1000.png b/...tab_should_have_numerical_and_categorical_selector_element_chrome_1600x1000.png
diff --git a/end-to-end-test/local/specs/core/studyview.screenshot.spec.js b/end-to-end-test/local/specs/core/studyview.screenshot.spec.js
@@ -22,6 +22,7 @@ const ADD_CHART_X_VS_Y_TAB = '.addChartTabs a.tabAnchor_X_Vs_Y';
 const WAIT_FOR_VISIBLE_TIMEOUT = 30000;
 const MUTATIONS_GENES_TABLE = "[data-test='mutations-table']";
 const CANCER_GENE_FILTER_ICON = "[data-test='header-filter-icon']";
+const ADD_CUSTOM_CHART_TAB = '.addChartTabs a.tabAnchor.tabAnchor_Custom_Data';
 
 describe('study view generic assay categorical/binary features', function() {
     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() {
     });
 });
 
+describe('Test the Custom data tab', function() {
+    it('Add custom data tab should have numerical and categorical selector', () => {
+        const url = `${CBIOPORTAL_URL}/study?id=lgg_ucsf_2014_test_generic_assay`;
+        goToUrlAndSetLocalStorage(url, true);
+        waitForNetworkQuiet();
+
+        $(ADD_CHART_BUTTON).waitForDisplayed({
+            timeout: WAIT_FOR_VISIBLE_TIMEOUT,
+        });
+        $(ADD_CHART_BUTTON).click();
+
+        waitForNetworkQuiet();
+        // Change to custom tab
+        $(ADD_CUSTOM_CHART_TAB).waitForDisplayed({
+            timeout: WAIT_FOR_VISIBLE_TIMEOUT,
+        });
+        $(ADD_CUSTOM_CHART_TAB).click();
+        const res = browser.checkElement('div.msk-tab.custom');
+        assertScreenShotMatch(res);
+    });
+    it('Selecting numerical for custom data should return a bar chart', () => {
+        const url = `${CBIOPORTAL_URL}/study?id=lgg_ucsf_2014_test_generic_assay`;
+        goToUrlAndSetLocalStorage(url, true);
+        waitForNetworkQuiet();
+
+        $(ADD_CHART_BUTTON).waitForDisplayed({
+            timeout: WAIT_FOR_VISIBLE_TIMEOUT,
+        });
+        $(ADD_CHART_BUTTON).click();
+
+        waitForNetworkQuiet();
+        // Change to custom tab
+        $(ADD_CUSTOM_CHART_TAB).waitForDisplayed({
+            timeout: WAIT_FOR_VISIBLE_TIMEOUT,
+        });
+        $(ADD_CUSTOM_CHART_TAB).click();
+        CUSTOM_CHART_TAB = $('div.msk-tab.custom');
+        // Add values to the input form
+    });
+});
+
 describe('study view x vs y charts', () => {
     const X_VS_Y_CHART = `div[data-test="chart-container-X-VS-Y-AGE-MUTATION_COUNT"]`;
     const X_VS_Y_HAMBURGER_ICON = `${X_VS_Y_CHART} [data-test="chart-header-hamburger-icon"]`;

diff --git a/env/custom.sh b/env/custom.sh
@@ -1,2 +1,2 @@
-#export CBIOPORTAL_URL="http://localhost:8080"
-#export GENOME_NEXUS_URL="https://www.genomenexus.org"
+export CBIOPORTAL_URL="http://localhost:8081"
+export GENOME_NEXUS_URL="https://www.genomenexus.org"
diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts
@@ -2476,6 +2476,97 @@ export default class CBioPortalAPIInternal {
                 return response.body;
             });
         };
+
+    fetchCustomDataBinCountsUsingPOSTURL(parameters: {
+        'clinicalDataBinCountFilter': ClinicalDataBinCountFilter,
+        'dataBinMethod' ? : "DYNAMIC" | "STATIC",
+        $queryParameters ? : any
+    }): string {
+        let queryParameters: any = {};
+        let path = '/custom-data-bin-counts/fetch';
+
+        if (parameters['dataBinMethod'] !== undefined) {
+            queryParameters['dataBinMethod'] = parameters['dataBinMethod'];
+        }
+
+        if (parameters.$queryParameters) {
+            Object.keys(parameters.$queryParameters).forEach(function(parameterName) {
+                var parameter = parameters.$queryParameters[parameterName];
+                queryParameters[parameterName] = parameter;
+            });
+        }
+        let keys = Object.keys(queryParameters);
+        return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : '');
+    };
+
+    /**
+     * Fetch custom data bin counts by study view filter
+     * @method
+     * @name CBioPortalAPIInternal#fetchCustomDataBinCountsUsingPOST
+     * @param {} clinicalDataBinCountFilter - Clinical data bin count filter
+     * @param {string} dataBinMethod - Method for data binning
+     */
+    fetchCustomDataBinCountsUsingPOSTWithHttpInfo(parameters: {
+        'clinicalDataBinCountFilter': ClinicalDataBinCountFilter,
+        'dataBinMethod' ? : "DYNAMIC" | "STATIC",
+        $queryParameters ? : any,
+        $domain ? : string
+    }): Promise < request.Response > {
+        const domain = parameters.$domain ? parameters.$domain : this.domain;
+        const errorHandlers = this.errorHandlers;
+        const request = this.request;
+        let path = '/custom-data-bin-counts/fetch';
+        let body: any;
+        let queryParameters: any = {};
+        let headers: any = {};
+        let form: any = {};
+        return new Promise(function(resolve, reject) {
+            headers['Accept'] = 'application/json';
+            headers['Content-Type'] = 'application/json';
+
+            if (parameters['clinicalDataBinCountFilter'] !== undefined) {
+                body = parameters['clinicalDataBinCountFilter'];
+            }
+
+            if (parameters['clinicalDataBinCountFilter'] === undefined) {
+                reject(new Error('Missing required  parameter: clinicalDataBinCountFilter'));
+                return;
+            }
+
+            if (parameters['dataBinMethod'] !== undefined) {
+                queryParameters['dataBinMethod'] = parameters['dataBinMethod'];
+            }
+
+            if (parameters.$queryParameters) {
+                Object.keys(parameters.$queryParameters).forEach(function(parameterName) {
+                    var parameter = parameters.$queryParameters[parameterName];
+                    queryParameters[parameterName] = parameter;
+                });
+            }
+
+            request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers);
+
+        });
+    };
+
+    /**
+     * Fetch custom data bin counts by study view filter
+     * @method
+     * @name CBioPortalAPIInternal#fetchCustomDataBinCountsUsingPOST
+     * @param {} clinicalDataBinCountFilter - Clinical data bin count filter
+     * @param {string} dataBinMethod - Method for data binning
+     */
+    fetchCustomDataBinCountsUsingPOST(parameters: {
+            'clinicalDataBinCountFilter': ClinicalDataBinCountFilter,
+            'dataBinMethod' ? : "DYNAMIC" | "STATIC",
+            $queryParameters ? : any,
+            $domain ? : string
+        }): Promise < Array < ClinicalDataBin >
+        > {
+            return this.fetchCustomDataBinCountsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) {
+                return response.body;
+            });
+        };
     fetchCustomDataCountsUsingPOSTURL(parameters: {
         'clinicalDataCountFilter': ClinicalDataCountFilter,
         $queryParameters ? : any