Merge branch 'master' into delete_gene_track

cBioPortal · Mar 26, 2024 · eeffa8f · eeffa8f
2 parents ea7279c + 88b2c64
commit eeffa8f
Show file tree

Hide file tree

Showing 126 changed files with 4,411 additions and 707 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -240,7 +240,7 @@ jobs:
     working_directory: /tmp/repo
     machine:
       enabled: true
-      image: ubuntu-2004:202201-02
+      image: default
     resource_class: large
     steps:
       - when:

diff --git a/end-to-end-test/local/docker_compose/keycloak.yml b/end-to-end-test/local/docker_compose/keycloak.yml
@@ -15,7 +15,7 @@ services:
     networks:
     - cbio-net
     container_name: keycloak
-    image: jboss/keycloak:11.0.3
+    image: quay.io/keycloak/keycloak:11.0.3
     restart: unless-stopped
     depends_on:
     - kcdb

diff --git a/end-to-end-test/local/runtime-config/portal.properties b/end-to-end-test/local/runtime-config/portal.properties
@@ -7,10 +7,6 @@ spring.datasource.username=cbio_user
 spring.datasource.password=somepassword
 spring.jpa.database-platform=org.hibernate.dialect.MySQL5InnoDBDialect
 spring.datasource.driver-class-name=com.mysql.jdbc.Driver
-db.user=cbio_user
-db.password=somepassword
-db.driver=com.mysql.jdbc.Driver
-db.connection_string=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false&allowPublicKeyRetrieval=true
 # set tomcat_resource_name when using dbconnector=jndi instead of the default
 # dbconnector=dbcp. Note that dbconnector needs to be set in CATLINA_OPTS when
 # using Tomcat (CATALINA_OPTS="-Ddbconnector=jndi"). It does not get picked up

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/end-to-end-test/local/specs/core/oncoprint.screenshot.spec.js b/end-to-end-test/local/specs/core/oncoprint.screenshot.spec.js
@@ -132,8 +132,6 @@ describe('oncoprint', function() {
             const urlWithUserConfig = createUrlWithSettingsQueryParam(
                 MANUAL_TRACK_CONFIG
             );
-            // go to home page first because navigating to same page with hash params doesn't cause change
-            goToUrlAndSetLocalStorage(CBIOPORTAL_URL, false);
             goToUrlAndSetLocalStorage(urlWithUserConfig, false);
             waitForOncoprint(ONCOPRINT_TIMEOUT);
 
@@ -172,9 +170,7 @@ describe('oncoprint', function() {
             const urlWithUserConfig = createUrlWithSettingsQueryParam(
                 customConfig
             );
-            // go to home page first because navigating to same page with hash params doesn't cause change
-            goToUrlAndSetLocalStorage(CBIOPORTAL_URL, false);
-            browser.url(urlWithUserConfig);
+            goToUrlAndSetLocalStorage(urlWithUserConfig, false);
 
             waitForOncoprint(ONCOPRINT_TIMEOUT);
 

diff --git a/end-to-end-test/local/specs/core/patientview.spec.js b/end-to-end-test/local/specs/core/patientview.spec.js
@@ -365,13 +365,13 @@ describe('patient view page', function() {
             const mutationsTable = '[data-test=patientview-mutation-table]';
             $(`${mutationsTable} button#dropdown-custom-1`).click();
             $(`${mutationsTable} ul.dropdown-menu`)
-                .$$('li label input')[19]
+                .$$('li label input')[21]
                 .click();
             $(`${mutationsTable} ul.dropdown-menu`)
-                .$$('li label input')[20]
+                .$$('li label input')[22]
                 .click();
             $(`${mutationsTable} ul.dropdown-menu`)
-                .$$('li label input')[21]
+                .$$('li label input')[23]
                 .click();
             $(`${mutationsTable} button#dropdown-custom-1`).click();
         });

diff --git a/end-to-end-test/local/specs/hide-download-controls.spec.js b/end-to-end-test/local/specs/hide-download-controls.spec.js
@@ -254,6 +254,7 @@ describe('hide download controls feature', function() {
                     it('global check for icon and occurrence of "Download" as a word', () => {
                         $('.tabAnchor_clinical').click();
                         $('[data-test=ClinicalTabPlotDiv]').waitForExist();
+                        $('[data-test=LazyMobXTable]').waitForExist();
                         globalCheck();
                     });
                 });
@@ -456,6 +457,7 @@ describe('hide download controls feature', function() {
                 'Clinical Data',
                 'CN Segments',
                 'Files & Links',
+                'Plots Beta!',
                 'Study Sponsors',
             ];
             before(() => {
@@ -609,6 +611,7 @@ describe('hide download controls feature', function() {
             describe('clinical tab', () => {
                 it('global check for icon and occurrence of "Download" as a word', () => {
                     $('.tabAnchor_clinical').click();
+                    $('[data-test=LazyMobXTable]').waitForExist();
                     $('[data-test=ClinicalTabPlotDiv]').waitForExist();
                     globalCheck();
                 });

diff --git a/...reference/can_filter_a_study_by_patient_treatments_element_chrome_1600x1000.png b/...reference/can_filter_a_study_by_patient_treatments_element_chrome_1600x1000.png
diff --git a/.../reference/can_filter_a_study_by_sample_treatments_element_chrome_1600x1000.png b/.../reference/can_filter_a_study_by_sample_treatments_element_chrome_1600x1000.png
diff --git a/...ote/screenshots/reference/check_for_survival_plots_element_chrome_1600x1000.png b/...ote/screenshots/reference/check_for_survival_plots_element_chrome_1600x1000.png
diff --git a/...s/reference/excluding_unprofiled_samples_plots_tab_element_chrome_1600x1000.png b/...s/reference/excluding_unprofiled_samples_plots_tab_element_chrome_1600x1000.png
diff --git a/...remote/screenshots/reference/filter_study_from_url_element_chrome_1600x1000.png b/...remote/screenshots/reference/filter_study_from_url_element_chrome_1600x1000.png
diff --git a/...hots/reference/fusion_filter_filter_study_from_url_element_chrome_1600x1000.png b/...hots/reference/fusion_filter_filter_study_from_url_element_chrome_1600x1000.png
diff --git a/...ison_page_survival_tab_include_overlapping_samples_element_chrome_1600x1000.png b/...ison_page_survival_tab_include_overlapping_samples_element_chrome_1600x1000.png
diff --git a/...remote/screenshots/reference/loads_a_virtual_study_element_chrome_1600x1000.png b/...remote/screenshots/reference/loads_a_virtual_study_element_chrome_1600x1000.png
diff --git a/...ence/loads_multiple_studies_with_treatments_tables_element_chrome_1600x1000.png b/...ence/loads_multiple_studies_with_treatments_tables_element_chrome_1600x1000.png
diff --git a/...ference/plots_tab_with_structural_variant_coloring_element_chrome_1600x1000.png b/...ference/plots_tab_with_structural_variant_coloring_element_chrome_1600x1000.png
diff --git a/...rison_tab_survival_tab_include_overlapping_samples_element_chrome_1600x1000.png b/...rison_tab_survival_tab_include_overlapping_samples_element_chrome_1600x1000.png
diff --git a/...ference/study_view_laml_tcga_clinical_data_clicked_element_chrome_1600x1000.png b/...ference/study_view_laml_tcga_clinical_data_clicked_element_chrome_1600x1000.png
diff --git a/...te/screenshots/reference/tcga_pancancer_atlas_page_element_chrome_1600x1000.png b/...te/screenshots/reference/tcga_pancancer_atlas_page_element_chrome_1600x1000.png
diff --git a/..._adding_charts,_each_chart_should_get_proper_data._element_chrome_1600x1000.png b/..._adding_charts,_each_chart_should_get_proper_data._element_chrome_1600x1000.png
diff --git a/end-to-end-test/remote/specs/core/customTabs.spec.js b/end-to-end-test/remote/specs/core/customTabs.spec.js
@@ -106,6 +106,11 @@ function runTests(pageName, url, tabLocation) {
 
             $('.mainTabs').waitForDisplayed();
 
+            if (tabLocation === 'STUDY_PAGE') {
+                $('i.fa-chevron-right').waitForDisplayed();
+                $('i.fa-chevron-right').click();
+            }
+
             assert.equal(
                 $('=Patient Tab').isDisplayed(),
                 false,
@@ -143,6 +148,11 @@ function runTests(pageName, url, tabLocation) {
 
             $('.mainTabs').waitForDisplayed();
 
+            if (tabLocation === 'STUDY_PAGE') {
+                $('i.fa-chevron-right').waitForDisplayed();
+                $('i.fa-chevron-right').click();
+            }
+
             assert.equal(
                 $('=Hidden Tab').isDisplayed(),
                 false,
@@ -235,7 +245,8 @@ function runTests(pageName, url, tabLocation) {
                 };
             });
 
-            $('=Async Tab').click();
+            // offset to avoid overlapping elements
+            $('=Async Tab').click({ x: -10 });
 
             browser.pause(1000);
 

diff --git a/end-to-end-test/shared/specUtils.js b/end-to-end-test/shared/specUtils.js
@@ -209,6 +209,8 @@ function goToUrlAndSetLocalStorage(url, authenticated = false) {
     const currentUrl = browser.getUrl();
     const needToLogin =
         authenticated && (!currentUrl || !currentUrl.includes('http'));
+    // navigate to blank page first to prevent issues with url hash params
+    browser.url('about:blank');
     if (!useExternalFrontend) {
         browser.url(url);
         console.log('Connecting to: ' + url);

diff --git a/package.json b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "cbioportal-frontend",
   "private": true,
-  "version": "3.3.271",
+  "version": "3.3.274",
   "workspaces": {
     "packages": [
       ".",
@@ -158,10 +158,10 @@
     "bootstrap-sass": "3.4.1",
     "bowser": "^1.7.1",
     "bundle-loader": "^0.5.4",
-    "cbioportal-clinical-timeline": "^0.3.77",
-    "cbioportal-frontend-commons": "^0.5.61",
-    "cbioportal-ts-api-client": "^0.9.67",
-    "cbioportal-utils": "^0.3.38",
+    "cbioportal-clinical-timeline": "^0.3.79",
+    "cbioportal-frontend-commons": "^0.5.63",
+    "cbioportal-ts-api-client": "^0.9.68",
+    "cbioportal-utils": "^0.3.39",
     "chart.js": "^2.6.0",
     "classnames": "^2.2.5",
     "clinical-timeline": "0.0.30",
@@ -226,9 +226,9 @@
     "mobx-utils": "6.0.1",
     "numeral": "^2.0.6",
     "object-sizeof": "^1.2.0",
-    "oncokb-frontend-commons": "^0.0.22",
+    "oncokb-frontend-commons": "^0.0.23",
     "oncokb-styles": "~1.4.2",
-    "oncokb-ts-api-client": "^1.3.3",
+    "oncokb-ts-api-client": "^1.3.4",
     "oncoprintjs": "^6.0.5",
     "pako": "2.0.2",
     "parameter-validator": "^1.0.2",
@@ -271,7 +271,7 @@
     "react-markdown": "^7.0.1",
     "react-mfb": "^0.6.0",
     "react-motion": "^0.4.7",
-    "react-mutation-mapper": "^0.8.104",
+    "react-mutation-mapper": "^0.8.106",
     "react-overlays": "0.7.4",
     "react-portal": "^4.2.0",
     "react-rangeslider": "^2.1.0",

diff --git a/packages/cbioportal-clinical-timeline/package.json b/packages/cbioportal-clinical-timeline/package.json
@@ -1,7 +1,7 @@
 {
   "name": "cbioportal-clinical-timeline",
   "description": "cBioPortal Clinical Timeline",
-  "version": "0.3.77",
+  "version": "0.3.79",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
   "jsnext:main": "dist/index.es.js",
@@ -39,7 +39,7 @@
   },
   "dependencies": {
     "autobind-decorator": "^2.1.0",
-    "cbioportal-frontend-commons": "^0.5.61",
+    "cbioportal-frontend-commons": "^0.5.63",
     "lodash": "^4.17.11",
     "react-bootstrap": "^0.31.5",
     "react-overlays": "0.7.4",

diff --git a/packages/cbioportal-frontend-commons/package.json b/packages/cbioportal-frontend-commons/package.json
@@ -1,7 +1,7 @@
 {
   "name": "cbioportal-frontend-commons",
   "description": "cBioPortal Frontend Modules",
-  "version": "0.5.61",
+  "version": "0.5.63",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
   "jsnext:main": "dist/index.es.js",
@@ -38,14 +38,14 @@
   },
   "dependencies": {
     "autobind-decorator": "^2.1.0",
-    "cbioportal-utils": "^0.3.38",
+    "cbioportal-utils": "^0.3.39",
     "classnames": "^2.2.5",
     "jquery": "^3.2.1",
     "lodash": "^4.17.15",
     "measure-text": "0.0.4",
     "numeral": "^2.0.6",
     "object-sizeof": "^1.2.0",
-    "oncokb-ts-api-client": "^1.3.3",
+    "oncokb-ts-api-client": "^1.3.4",
     "rc-tooltip": "^5.0.2",
     "rc-trigger": "^5.2.1",
     "rc-util": "^5.8.0",

diff --git a/packages/cbioportal-frontend-commons/src/components/appContext/AppContext.tsx b/packages/cbioportal-frontend-commons/src/components/appContext/AppContext.tsx
@@ -1,17 +1,7 @@
 import React, { Context } from 'react';
 
-export enum DownloadControlOption {
-    SHOW_ALL = 'show',
-    HIDE_DATA = 'data',
-    HIDE_ALL = 'hide',
-}
-
-export interface IAppContext {
-    showDownloadControls: DownloadControlOption;
-}
+export interface IAppContext {}
 
 export const AppContext: Context<IAppContext> = React.createContext<
     IAppContext
->({
-    showDownloadControls: DownloadControlOption.SHOW_ALL,
-});
+>({});
diff --git a/packages/cbioportal-frontend-commons/src/components/downloadControls/DownloadControls.tsx b/packages/cbioportal-frontend-commons/src/components/downloadControls/DownloadControls.tsx
@@ -11,7 +11,6 @@ import { saveSvg, saveSvgAsPng } from 'save-svg-as-png';
 import svgToPdfDownload from '../../lib/svgToPdfDownload';
 import { CSSProperties } from 'react';
 import { isPromiseLike } from 'cbioportal-utils';
-import { AppContext, DownloadControlOption } from '../appContext/AppContext';
 
 type ButtonSpec = {
     key: string;
@@ -30,6 +29,12 @@ export type DownloadControlsButton =
 
 export type DataType = 'summary' | 'full';
 
+export enum DownloadControlOption {
+    SHOW_ALL = 'show',
+    HIDE_DATA = 'data',
+    HIDE_ALL = 'hide',
+}
+
 interface IDownloadControlsProps {
     getSvg?: () => SVGElement | null | PromiseLike<SVGElement | null>;
     getData?: (
@@ -306,9 +311,7 @@ export default class DownloadControls extends React.Component<
     }
 
     render() {
-        if (
-            this.context.showDownloadControls === DownloadControlOption.HIDE_ALL
-        ) {
+        if (this.showDownload === false) {
             return null;
         }
 
@@ -421,5 +424,3 @@ export default class DownloadControls extends React.Component<
         }
     }
 }
-
-DownloadControls.contextType = AppContext;
diff --git a/packages/cbioportal-frontend-commons/src/index.tsx b/packages/cbioportal-frontend-commons/src/index.tsx
@@ -13,6 +13,7 @@ export {
     default as DownloadControls,
     DataType,
     DownloadControlsButton,
+    DownloadControlOption,
 } from './components/downloadControls/DownloadControls';
 export { default as EditableSpan } from './components/editableSpan/EditableSpan';
 export { default as EllipsisTextTooltip } from './components/ellipsisTextTooltip/EllipsisTextTooltip';

diff --git a/packages/cbioportal-ts-api-client/package.json b/packages/cbioportal-ts-api-client/package.json
@@ -1,7 +1,7 @@
 {
   "name": "cbioportal-ts-api-client",
   "description": "cBioPortal API Client for TypeScript",
-  "version": "0.9.67",
+  "version": "0.9.68",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
   "jsnext:main": "dist/index.es.js",

diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json
@@ -5423,7 +5423,7 @@
         "categorization": {
           "enum": [
             "MUTATED",
-            "EVENT"
+            "MUTATION_TYPE"
           ],
           "type": "string"
         },

diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI.ts b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI.ts
@@ -553,7 +553,7 @@ export type Mutation = {
 
 };
 export type MutationDataFilter = {
-    'categorization': "MUTATED" | "EVENT"
+    'categorization': "MUTATED" | "MUTATION_TYPE"
 
         'hugoGeneSymbol': string
 

diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json
@@ -5233,7 +5233,7 @@
         "categorization": {
           "enum": [
             "MUTATED",
-            "EVENT"
+            "MUTATION_TYPE"
           ],
           "type": "string"
         },

diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts
@@ -901,7 +901,7 @@ export type MutationCountByPosition = {
 
 };
 export type MutationDataFilter = {
-    'categorization': "MUTATED" | "EVENT"
+    'categorization': "MUTATED" | "MUTATION_TYPE"
 
         'hugoGeneSymbol': string
 

diff --git a/packages/cbioportal-utils/package.json b/packages/cbioportal-utils/package.json
@@ -1,7 +1,7 @@
 {
   "name": "cbioportal-utils",
   "description": "cBioPortal Utilities",
-  "version": "0.3.38",
+  "version": "0.3.39",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
   "jsnext:main": "dist/index.es.js",
@@ -32,7 +32,7 @@
     "buffer": "^6.0.3",
     "genome-nexus-ts-api-client": "^1.1.31",
     "lodash": "^4.17.15",
-    "oncokb-ts-api-client": "^1.3.3",
+    "oncokb-ts-api-client": "^1.3.4",
     "superagent": "^3.8.3",
     "typescript": "4.0.3"
   }

diff --git a/packages/oncokb-frontend-commons/package.json b/packages/oncokb-frontend-commons/package.json
@@ -1,6 +1,6 @@
 {
   "name": "oncokb-frontend-commons",
-  "version": "0.0.22",
+  "version": "0.0.23",
   "description": "OncoKB Frontend Modules",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
@@ -35,11 +35,11 @@
     "react-dom": "^15.0.0 || ^16.0.0"
   },
   "dependencies": {
-    "cbioportal-utils": "^0.3.38",
+    "cbioportal-utils": "^0.3.39",
     "classnames": "^2.2.5",
     "lodash": "^4.17.15",
     "oncokb-styles": "~1.4.2",
-    "oncokb-ts-api-client": "^1.3.2",
+    "oncokb-ts-api-client": "^1.3.4",
     "rc-tooltip": "^5.0.2",
     "react-bootstrap": "^0.31.5",
     "react-collapse": "^4.0.3",

diff --git a/packages/oncokb-ts-api-client/package.json b/packages/oncokb-ts-api-client/package.json
@@ -1,7 +1,7 @@
 {
   "name": "oncokb-ts-api-client",
   "description": "OncoKB API Client for TypeScript",
-  "version": "1.3.3",
+  "version": "1.3.4",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
   "jsnext:main": "dist/index.es.js",

diff --git a/packages/oncokb-ts-api-client/src/generated/OncoKbAPI-docs.json b/packages/oncokb-ts-api-client/src/generated/OncoKbAPI-docs.json
@@ -1015,15 +1015,6 @@
         },
         "ncitCode": {
           "type": "string"
-        },
-        "synonyms": {
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "uuid": {
-          "type": "string"
         }
       }
     },