Merge branch 'master' into study-plots-tab

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);

package.json

@@ -1,7 +1,7 @@
 {
   "name": "cbioportal-frontend",
   "private": true,
-  "version": "3.3.273",
+  "version": "3.3.274",
   "workspaces": {
     "packages": [
       ".",
@@ -160,7 +160,7 @@
     "bundle-loader": "^0.5.4",
     "cbioportal-clinical-timeline": "^0.3.79",
     "cbioportal-frontend-commons": "^0.5.63",
-    "cbioportal-ts-api-client": "^0.9.67",
+    "cbioportal-ts-api-client": "^0.9.68",
     "cbioportal-utils": "^0.3.39",
     "chart.js": "^2.6.0",
     "classnames": "^2.2.5",

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",

packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json

@@ -5423,7 +5423,7 @@
         "categorization": {
           "enum": [
             "MUTATED",
-            "EVENT"
+            "MUTATION_TYPE"
           ],
           "type": "string"
         },

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
 

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

@@ -5233,7 +5233,7 @@
         "categorization": {
           "enum": [
             "MUTATED",
-            "EVENT"
+            "MUTATION_TYPE"
           ],
           "type": "string"
         },

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
 

src/pages/studyView/addChartButton/customCaseSelection/CustomCaseSelectionUtils.tsx

@@ -1,4 +1,4 @@
-import _ from 'lodash';
+import _, { uniq } from 'lodash';
 import { Sample } from 'cbioportal-ts-api-client';
 import { ClinicalDataType, ClinicalDataTypeEnum } from '../../StudyViewUtils';
 import Pluralize from 'pluralize';
@@ -132,6 +132,7 @@ export function validateLines(
 
     let occurrence: { [key: string]: number } = {};
     let validLines: { [key: string]: InputLine } = {};
+    let multiStudyCases: string[] = [];
 
     // Remove all dups, not necessary to mention in the message
     _.reduce(
@@ -140,27 +141,34 @@ export function validateLines(
         }),
         (acc, line) => {
             let _case = '';
-            let validLine = true;
+            let validLine = false;
+            let newLines: InputLine[] = [];
             if (line.studyId === undefined || line.studyId === '') {
-                if (!isSingleStudy) {
-                    warningMessages.push({
-                        code: CodeEnum.INVALID_CASE_ID,
-                        message: new Error(
-                            `No study specified for ${caseType} id: ${line.caseId}, and more than one study selected for query. The case will be ignored.`
-                        ),
-                    });
-                    validLine = false;
-                } else {
-                    _case = getUniqueCaseId(selectedStudies[0], line.caseId);
-                    if (!validPair[_case]) {
-                        invalidCases.push(line.caseId);
-                        validLine = false;
-                    } else {
+                let validCaseCount = 0;
+                selectedStudies.map(studyId => {
+                    _case = getUniqueCaseId(studyId, line.caseId);
+                    if (validPair[_case]) {
                         if (occurrence[_case] === undefined) {
                             occurrence[_case] = 0;
                         }
                         occurrence[_case]++;
+
+                        let newLine = _.cloneDeep(line);
+                        newLine.studyId = studyId;
+                        newLines.push(newLine);
+
+                        validCaseCount += 1;
+                        validLine = true;
                     }
+                });
+
+                if (validCaseCount === 0) {
+                    invalidCases.push(line.caseId);
+                }
+
+                // case where it belongs to multiple studies
+                if (validCaseCount > 1) {
+                    multiStudyCases.push(line.caseId);
                 }
             } else {
                 if (!_.includes(selectedStudies, line.studyId)) {
@@ -170,28 +178,42 @@ export function validateLines(
                             `Incorrect study id: ${line.studyId}`
                         ),
                     });
-                    validLine = false;
                 } else {
                     _case = getUniqueCaseId(line.studyId, line.caseId);
                     if (validPair[_case] !== undefined) {
                         if (occurrence[_case] === undefined) {
                             occurrence[_case] = 0;
                         }
                         occurrence[_case]++;
+                        validLine = true;
                     } else {
                         invalidCases.push(line.caseId);
-                        validLine = false;
                     }
+                    newLines.push(_.cloneDeep(line));
                 }
             }
+
             if (validLine) {
-                acc[getInputLineKey(line)] = line;
+                _.forEach(newLines, newLine => {
+                    acc[getInputLineKey(newLine)] = newLine;
+                });
             }
             return acc;
         },
         validLines
     );
 
+    if (!isSingleStudy && !_.isEmpty(multiStudyCases)) {
+        warningMessages.push({
+            code: CodeEnum.INVALID_CASE_ID,
+            message: new Error(
+                `The ${caseType} ID's below belong to multiple studies. All of them in the different studies will be selected. 
+                To select specific ${caseType}, pelase specify study_id, Example: study_id:sample_id. 
+                ${caseType} ID's: ${multiStudyCases.join(', ')}`
+            ),
+        });
+    }
+
     // Find duplication cases
     const dups = _.reduce(
         occurrence,

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}