Fix screenshots. Update test. Update api clients (#5081)

* Update screenshots * Fix quick search test * Update api clients and fix typing of new Clickhouse dependent code * Add a wait for bin screenshot test
cBioPortal · Jan 9, 2025 · cf407de · cf407de
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Showing 12 changed files with 78 additions and 387 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/.../breadcrumbs_are_editable_for_mutation_count_chart_element_chrome_1600x1000.png b/.../breadcrumbs_are_editable_for_mutation_count_chart_element_chrome_1600x1000.png
diff --git a/...shots/reference/show_binary_vs_mutation_count_plot_element_chrome_1600x1000.png b/...shots/reference/show_binary_vs_mutation_count_plot_element_chrome_1600x1000.png
diff --git a/...ots/reference/show_category_vs_mutation_count_plot_element_chrome_1600x1000.png b/...ots/reference/show_category_vs_mutation_count_plot_element_chrome_1600x1000.png
diff --git a/...nshots/reference/shows_box_plot_for_numerical_data_element_chrome_1600x1000.png b/...nshots/reference/shows_box_plot_for_numerical_data_element_chrome_1600x1000.png
diff --git a/end-to-end-test/local/specs/study-view-custom-bins.screenshot.spec.js b/end-to-end-test/local/specs/study-view-custom-bins.screenshot.spec.js
@@ -35,6 +35,7 @@ describe('Custom Bins menu in study view chart header', function() {
         selectMenuOption('label=Median split');
         clickUpdate();
         $('body').moveTo();
+        browser.pause(2000);
         const res = checkElementWithMouseDisabled(MUTATION_COUNT_CHART);
         assertScreenShotMatch(res);
     });

diff --git a/end-to-end-test/remote/specs/core/quickSearch.spec.js b/end-to-end-test/remote/specs/core/quickSearch.spec.js
@@ -55,7 +55,8 @@ describe('Quick Search', () => {
     });
 
     it('should give results for genes', async () => {
-        await clickElement('strong=454 more genes (click to load 20 more)');
+        //browser.debug();
+        await clickElement('strong=458 more genes (click to load 20 more)');
         await (await getElement('strong=ADAM12')).waitForExist();
         await clickElement('strong=ADAM15');
         await (await getElement('a=ADAM15')).waitForExist({ timeout: 60000 });

diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json
@@ -628,93 +628,6 @@
         "operationId": "fetchCNAGenesUsingPOST"
       }
     },
-    "/api/column-store/treatments/patient-counts/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "Agent",
-            "enum": [
-              "Agent",
-              "AgentClass",
-              "AgentTarget"
-            ],
-            "in": "query",
-            "name": "tier",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "studyViewFilter",
-            "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/PatientTreatmentReport"
-            }
-          }
-        },
-        "tags": [
-          "study-view-column-store-controller"
-        ],
-        "description": "Get all patient level treatments",
-        "operationId": "fetchPatientTreatmentCountsUsingPOST"
-      }
-    },
-    "/api/column-store/treatments/sample-counts/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "Agent",
-            "enum": [
-              "Agent",
-              "AgentClass",
-              "AgentTarget"
-            ],
-            "in": "query",
-            "name": "tier",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "studyViewFilter",
-            "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/SampleTreatmentReport"
-            }
-          }
-        },
-        "tags": [
-          "study-view-column-store-controller"
-        ],
-        "operationId": "fetchSampleTreatmentCountsUsingPOST"
-      }
-    },
     "/api/cosmic-counts/fetch": {
       "post": {
         "consumes": [
@@ -5791,18 +5704,6 @@
       },
       "type": "object"
     },
-    "PatientTreatment": {
-      "properties": {
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "treatment": {
-          "type": "string"
-        }
-      },
-      "type": "object"
-    },
     "PatientTreatmentFilter": {
       "properties": {
         "treatment": {
@@ -5811,25 +5712,6 @@
       },
       "type": "object"
     },
-    "PatientTreatmentReport": {
-      "properties": {
-        "patientTreatments": {
-          "items": {
-            "$ref": "#/definitions/PatientTreatment"
-          },
-          "type": "array"
-        },
-        "totalPatients": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "totalSamples": {
-          "format": "int32",
-          "type": "integer"
-        }
-      },
-      "type": "object"
-    },
     "PatientTreatmentRow": {
       "properties": {
         "count": {
@@ -6048,21 +5930,6 @@
       },
       "type": "object"
     },
-    "SampleTreatmentReport": {
-      "properties": {
-        "totalSamples": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "treatments": {
-          "items": {
-            "$ref": "#/definitions/SampleTreatmentRow"
-          },
-          "type": "array"
-        }
-      },
-      "type": "object"
-    },
     "SampleTreatmentRow": {
       "properties": {
         "count": {

diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts
@@ -920,24 +920,10 @@ export type PatientIdentifier = {
 
         'studyId': string
 
-};
-export type PatientTreatment = {
-    'count': number
-
-        'treatment': string
-
 };
 export type PatientTreatmentFilter = {
     'treatment': string
 
-};
-export type PatientTreatmentReport = {
-    'patientTreatments': Array < PatientTreatment >
-
-        'totalPatients': number
-
-        'totalSamples': number
-
 };
 export type PatientTreatmentRow = {
     'count': number
@@ -1036,12 +1022,6 @@ export type SampleTreatmentFilter = {
 
         'treatment': string
 
-};
-export type SampleTreatmentReport = {
-    'totalSamples': number
-
-        'treatments': Array < SampleTreatmentRow >
-
 };
 export type SampleTreatmentRow = {
     'count': number
@@ -2539,172 +2519,6 @@ export default class CBioPortalAPIInternal {
                 return response.body;
             });
         };
-    fetchPatientTreatmentCountsUsingPOSTURL(parameters: {
-        'tier' ? : "Agent" | "AgentClass" | "AgentTarget",
-        'studyViewFilter' ? : StudyViewFilter,
-        $queryParameters ? : any
-    }): string {
-        let queryParameters: any = {};
-        let path = '/api/column-store/treatments/patient-counts/fetch';
-        if (parameters['tier'] !== undefined) {
-            queryParameters['tier'] = parameters['tier'];
-        }
-
-        if (parameters.$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('&')) : '');
-    };
-
-    /**
-     * Get all patient level treatments
-     * @method
-     * @name CBioPortalAPIInternal#fetchPatientTreatmentCountsUsingPOST
-     * @param {string} tier - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.
-     * @param {} studyViewFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.
-     */
-    fetchPatientTreatmentCountsUsingPOSTWithHttpInfo(parameters: {
-        'tier' ? : "Agent" | "AgentClass" | "AgentTarget",
-        'studyViewFilter' ? : StudyViewFilter,
-        $queryParameters ? : any,
-            $domain ? : string
-    }): Promise < request.Response > {
-        const domain = parameters.$domain ? parameters.$domain : this.domain;
-        const errorHandlers = this.errorHandlers;
-        const request = this.request;
-        let path = '/api/column-store/treatments/patient-counts/fetch';
-        let body: any;
-        let queryParameters: any = {};
-        let headers: any = {};
-        let form: any = {};
-        return new Promise(function(resolve, reject) {
-            headers['Accept'] = 'application/json';
-            headers['Content-Type'] = 'application/json';
-
-            if (parameters['tier'] !== undefined) {
-                queryParameters['tier'] = parameters['tier'];
-            }
-
-            if (parameters['studyViewFilter'] !== undefined) {
-                body = parameters['studyViewFilter'];
-            }
-
-            if (parameters.$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);
-
-        });
-    };
-
-    /**
-     * Get all patient level treatments
-     * @method
-     * @name CBioPortalAPIInternal#fetchPatientTreatmentCountsUsingPOST
-     * @param {string} tier - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.
-     * @param {} studyViewFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.
-     */
-    fetchPatientTreatmentCountsUsingPOST(parameters: {
-        'tier' ? : "Agent" | "AgentClass" | "AgentTarget",
-        'studyViewFilter' ? : StudyViewFilter,
-        $queryParameters ? : any,
-            $domain ? : string
-    }): Promise < PatientTreatmentReport > {
-        return this.fetchPatientTreatmentCountsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) {
-            return response.body;
-        });
-    };
-    fetchSampleTreatmentCountsUsingPOSTURL(parameters: {
-        'tier' ? : "Agent" | "AgentClass" | "AgentTarget",
-        'studyViewFilter' ? : StudyViewFilter,
-        $queryParameters ? : any
-    }): string {
-        let queryParameters: any = {};
-        let path = '/api/column-store/treatments/sample-counts/fetch';
-        if (parameters['tier'] !== undefined) {
-            queryParameters['tier'] = parameters['tier'];
-        }
-
-        if (parameters.$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('&')) : '');
-    };
-
-    /**
-     * 
-     * @method
-     * @name CBioPortalAPIInternal#fetchSampleTreatmentCountsUsingPOST
-     * @param {string} tier - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.
-     * @param {} studyViewFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.
-     */
-    fetchSampleTreatmentCountsUsingPOSTWithHttpInfo(parameters: {
-        'tier' ? : "Agent" | "AgentClass" | "AgentTarget",
-        'studyViewFilter' ? : StudyViewFilter,
-        $queryParameters ? : any,
-            $domain ? : string
-    }): Promise < request.Response > {
-        const domain = parameters.$domain ? parameters.$domain : this.domain;
-        const errorHandlers = this.errorHandlers;
-        const request = this.request;
-        let path = '/api/column-store/treatments/sample-counts/fetch';
-        let body: any;
-        let queryParameters: any = {};
-        let headers: any = {};
-        let form: any = {};
-        return new Promise(function(resolve, reject) {
-            headers['Accept'] = 'application/json';
-            headers['Content-Type'] = 'application/json';
-
-            if (parameters['tier'] !== undefined) {
-                queryParameters['tier'] = parameters['tier'];
-            }
-
-            if (parameters['studyViewFilter'] !== undefined) {
-                body = parameters['studyViewFilter'];
-            }
-
-            if (parameters.$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);
-
-        });
-    };
-
-    /**
-     * 
-     * @method
-     * @name CBioPortalAPIInternal#fetchSampleTreatmentCountsUsingPOST
-     * @param {string} tier - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.
-     * @param {} studyViewFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.
-     */
-    fetchSampleTreatmentCountsUsingPOST(parameters: {
-        'tier' ? : "Agent" | "AgentClass" | "AgentTarget",
-        'studyViewFilter' ? : StudyViewFilter,
-        $queryParameters ? : any,
-            $domain ? : string
-    }): Promise < SampleTreatmentReport > {
-        return this.fetchSampleTreatmentCountsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) {
-            return response.body;
-        });
-    };
     fetchCosmicCountsUsingPOSTURL(parameters: {
         'keywords': Array < string > ,
         $queryParameters ? : any