Merge branch 'master' into improve-custom-selections

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

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

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);
 

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);

src/shared/components/columnVisibilityControls/ColumnVisibilityControls.tsx

@@ -3,6 +3,7 @@ import _ from 'lodash';
 import { Dropdown, Checkbox } from 'react-bootstrap';
 import { DropdownToggleProps } from 'react-bootstrap/lib/DropdownToggle';
 import { DropdownMenuProps } from 'react-bootstrap/lib/DropdownMenu';
+import { action, computed } from 'mobx';
 
 export interface IColumnVisibilityDef {
     id: string;
@@ -40,6 +41,8 @@ export class ColumnVisibilityControls extends React.Component<
     constructor(props: IColumnVisibilityControlsProps) {
         super(props);
         this.handleSelect = this.handleSelect.bind(this);
+        this.selectAll = this.selectAll.bind(this);
+        this.deselectAll = this.deselectAll.bind(this);
     }
 
     public render() {
@@ -52,6 +55,59 @@ export class ColumnVisibilityControls extends React.Component<
         );
     }
 
+    private toggleAllColumns(select: boolean) {
+        if (!this.props.columnVisibility) return;
+
+        const toggledColumns = new Set<string>();
+        this.props.columnVisibility.forEach(column => {
+            if (column.visible !== select) {
+                toggledColumns.add(column.id);
+            }
+        });
+
+        toggledColumns.forEach(columnId => {
+            if (this.props.onColumnToggled && columnId) {
+                this.props.onColumnToggled(
+                    columnId,
+                    this.props.columnVisibility
+                );
+            }
+        });
+    }
+
+    private selectAll() {
+        this.toggleAllColumns(true);
+    }
+
+    private deselectAll() {
+        this.toggleAllColumns(false);
+    }
+
+    get selectDeselectAllButtons() {
+        return (
+            <div
+                style={{
+                    display: 'flex',
+                    alignItems: 'baseline',
+                    gap: '3px',
+                }}
+            >
+                <button
+                    className="btn btn-default btn-xs"
+                    onClick={this.selectAll}
+                >
+                    {`Select all`}
+                </button>
+                <button
+                    className="btn btn-default btn-xs"
+                    onClick={this.deselectAll}
+                >
+                    {'Deselect all'}
+                </button>
+            </div>
+        );
+    }
+
     private get defaultDropdown() {
         return (
             <Dropdown className={this.props.className} id="dropdown-custom-1">
@@ -70,6 +126,9 @@ export class ColumnVisibilityControls extends React.Component<
                         whiteSpace: 'nowrap',
                     }}
                 >
+                    <div style={{ marginTop: 10, marginBottom: 10 }}>
+                        {this.selectDeselectAllButtons}
+                    </div>
                     <ul className="list-unstyled">
                         {this.props.columnVisibility &&
                             _.map(

src/shared/components/iframeLoader/IFrameLoader.tsx

@@ -4,6 +4,7 @@ import LoadingIndicator from '../loadingIndicator/LoadingIndicator';
 import { observer } from 'mobx-react';
 import { makeObservable, observable } from 'mobx';
 import autobind from 'autobind-decorator';
+import FontAwesome from 'react-fontawesome';
 interface FrameLoaderProps {
     url: string;
     className?: string;
@@ -35,12 +36,30 @@ export default class IFrameLoader extends React.Component<
     //NOTE: we need zindex to be higher than that of global loader
     render() {
         return (
-            <div style={{ position: 'relative', width: this.props.width }}>
+            <div
+                style={{
+                    position: 'relative',
+                    width: this.props.width,
+                    marginTop: 5,
+                }}
+            >
                 <LoadingIndicator
                     center={true}
                     size={'big'}
                     isLoading={!this.iframeLoaded}
                 />
+                <a
+                    href={this.props.url}
+                    target="_blank"
+                    style={{
+                        position: 'absolute',
+                        fontSize: 12,
+                        right: 0,
+                        top: -18,
+                    }}
+                >
+                    Open in new window <FontAwesome name="external-link" />
+                </a>
                 <iframe
                     id={this.props.iframeId || ''}
                     className={this.props.className || ''}
@@ -50,6 +69,7 @@ export default class IFrameLoader extends React.Component<
                         zIndex: 100,
                         height: this.props.height,
                         border: 'none',
+                        marginTop: 5,
                     }}
                     src={this.props.url}
                     onLoad={this.onLoad}