Merge pull request #416 from zhx828/minor-changs

Bug fixes

Author: zhx828

k8s/oncokb-public-local.yml

@@ -22,7 +22,7 @@ spec:
     spec:
       containers:
         - name: oncokb-public
-          image: cbioportal/oncokb-public:2.3.4
+          image: cbioportal/oncokb-public:2.3.5
           env:
             - name: SPRING_PROFILES_ACTIVE
               value: prod,no-liquibase

pom.xml

@@ -5,7 +5,7 @@
 
     <groupId>org.mskcc.cbio.oncokb</groupId>
     <artifactId>public-website</artifactId>
-    <version>2.3.4</version>
+    <version>2.3.5</version>
     <packaging>jar</packaging>
     <name>OncoKB Public Website</name>
 
@@ -621,7 +621,7 @@
                             <image>adoptopenjdk:11-jre-hotspot</image>
                         </from>
                         <to>
-                            <image>cbioportal/oncokb-public:2.3.4</image>
+                            <image>cbioportal/oncokb-public:2.3.5</image>
                         </to>
                         <container>
                             <entrypoint>

src/main/docker/app.yml

@@ -1,7 +1,7 @@
 version: '2'
 services:
   oncokb-app:
-    image: cbioportal/oncokb-public:2.3.4
+    image: cbioportal/oncokb-public:2.3.5
     environment:
       - _JAVA_OPTIONS=-Xmx512m -Xms256m
       - SPRING_PROFILES_ACTIVE=prod,swagger

src/main/webapp/app/config/constants.tsx

@@ -53,6 +53,7 @@ export const GRID_BREAKPOINTS = {
 };
 export const SOP_LINK = 'https://sop.oncokb.org';
 export const FAQ_LINK = 'https://faq.oncokb.org';
+export const DEMO_WEBSITE_LINK = 'https://demo.oncokb.org';
 
 export const REDIRECT_TIMEOUT_MILLISECONDS = 10000;
 export const NOTIFICATION_TIMEOUT_MILLISECONDS = 5000;

src/main/webapp/app/pages/APIAccessPage.tsx

@@ -6,6 +6,7 @@ import {
   DATA_RELEASES,
   DataRelease,
   DEFAULT_MARGIN_BOTTOM_LG,
+  DEMO_WEBSITE_LINK,
   DOCUMENT_TITLES,
   LicenseType,
   PAGE_ROUTE,
@@ -30,6 +31,7 @@ import { Link } from 'react-router-dom';
 import Select from 'react-select';
 import DocumentTitle from 'react-document-title';
 import AuthenticationStore from 'app/store/AuthenticationStore';
+import { Linkout } from 'app/shared/links/Linkout';
 
 type DownloadAvailabilityWithDate = DataRelease & DownloadAvailability;
 
@@ -208,6 +210,12 @@ export default class APIAccessPage extends React.Component<{
                   https://www.oncokb.org/api/v1/genes
                 </code>
               </div>
+              <div className={'mt-2'}>
+                You can also use our{' '}
+                <Linkout link={DEMO_WEBSITE_LINK}>demo website</Linkout> which
+                includes the full data of BRAF, TP53 and ROS1 before committing
+                to our license.
+              </div>
             </div>
           </div>
           {this.props.authenticationStore.account &&

src/main/webapp/app/pages/ActionableGenesPage.tsx

@@ -16,6 +16,7 @@ import { Evidence, MainType } from 'app/shared/api/generated/OncoKbPrivateAPI';
 import Select from 'react-select';
 import _ from 'lodash';
 import {
+  concatElementsByComma,
   getCancerTypeNameFromOncoTreeType,
   getDefaultColumnDefinition,
   getDrugNameFromTreatment,
@@ -436,10 +437,6 @@ export default class ActionableGenesPage extends React.Component<
     return Promise.resolve(content.join('\n'));
   }
 
-  concatElementsByComma(list: ReactNode[]) {
-    return list.reduce((prev, curr) => [prev, ', ', curr]);
-  }
-
   getAlterationCell(hugoSymbol: string, alterations: string[]) {
     const linkedAlts = alterations.map<React.ReactNode>(
       (alteration, index: number) => (
@@ -457,7 +454,7 @@ export default class ActionableGenesPage extends React.Component<
           <DefaultTooltip
             overlay={
               <div style={{ maxWidth: '400px' }}>
-                {this.concatElementsByComma(linkedAlts)}
+                {concatElementsByComma(linkedAlts)}
               </div>
             }
             overlayStyle={{
@@ -478,7 +475,7 @@ export default class ActionableGenesPage extends React.Component<
         </span>
       );
     } else {
-      return this.concatElementsByComma(linkedAlts);
+      return concatElementsByComma(linkedAlts);
     }
   }
 
@@ -516,6 +513,7 @@ export default class ActionableGenesPage extends React.Component<
     {
       ...getDefaultColumnDefinition(TABLE_COLUMN_KEY.TUMOR_TYPE),
       minWidth: 300,
+      accessor: 'tumorType',
       Cell(props: { original: Treatment }) {
         return <span>{props.original.tumorType}</span>;
       }

src/main/webapp/app/pages/alterationPage/AlterationPage.tsx

@@ -5,7 +5,7 @@ import {
   TherapeuticImplication
 } from 'app/store/AnnotationStore';
 import { computed, action, IReactionDisposer, reaction } from 'mobx';
-import { Col, Row } from 'react-bootstrap';
+import { Col, Row, Button } from 'react-bootstrap';
 import AppStore from 'app/store/AppStore';
 import _ from 'lodash';
 import Select from 'react-select';
@@ -21,11 +21,16 @@ import OncoKBTable, {
 } from 'app/components/oncokbTable/OncoKBTable';
 import {
   citationsHasInfo,
+  concatElementsByComma,
   getDefaultColumnDefinition,
   OncoKBOncogenicityIcon,
   reduceJoin
 } from 'app/shared/utils/Utils';
-import { GenePageLink } from 'app/shared/utils/UrlUtils';
+import {
+  AlterationPageLink,
+  GenePageLink,
+  TumorTypePageLink
+} from 'app/shared/utils/UrlUtils';
 import { CitationTooltip } from 'app/components/CitationTooltip';
 import { DefaultTooltip } from 'cbioportal-frontend-commons';
 import { RouterStore } from 'mobx-react-router';
@@ -247,7 +252,19 @@ export default class GenePage extends React.Component<
         ...getDefaultColumnDefinition(TABLE_COLUMN_KEY.DRUGS)
       },
       {
-        ...getDefaultColumnDefinition(TABLE_COLUMN_KEY.EVIDENCE_CANCER_TYPE)
+        ...getDefaultColumnDefinition(TABLE_COLUMN_KEY.EVIDENCE_CANCER_TYPE),
+        Cell: (props: { original: any }) => {
+          return (
+            <Button
+              variant={'link'}
+              onClick={() =>
+                (this.store.tumorTypeQuery = props.original.cancerTypes)
+              }
+            >
+              {props.original.cancerTypes}
+            </Button>
+          );
+        }
       },
       {
         ...getDefaultColumnDefinition(TABLE_COLUMN_KEY.CITATIONS),

src/main/webapp/app/pages/genePage/GenePage.tsx

@@ -32,7 +32,11 @@ import {
   BiologicalVariant,
   ClinicalVariant
 } from 'app/shared/api/generated/OncoKbPrivateAPI';
-import { AlterationPageLink, CitationLink } from 'app/shared/utils/UrlUtils';
+import {
+  AlterationPageLink,
+  CitationLink,
+  TumorTypePageLink
+} from 'app/shared/utils/UrlUtils';
 import AppStore from 'app/store/AppStore';
 import OncoKBTable, {
   SearchColumn
@@ -261,11 +265,16 @@ export default class GenePage extends React.Component<
             getCancerTypeNameFromOncoTreeType(data.cancerType),
             keyword
           ),
-        Cell(props: { original: ClinicalVariant }) {
+        Cell: (props: { original: ClinicalVariant }) => {
+          const tumorType = getCancerTypeNameFromOncoTreeType(
+            props.original.cancerType
+          );
           return (
-            <span>
-              {getCancerTypeNameFromOncoTreeType(props.original.cancerType)}
-            </span>
+            <TumorTypePageLink
+              hugoSymbol={this.store.hugoSymbol}
+              alteration={props.original.variant.name}
+              tumorType={tumorType}
+            />
           );
         }
       },
@@ -626,6 +635,7 @@ export default class GenePage extends React.Component<
                           {...this.store.mutationMapperProps.result}
                           store={this.store.mutationMapperStore.result}
                           oncogenicities={this.store.uniqOncogenicity}
+                          showTrackSelector={false}
                           windowWrapper={this.windowWrapper}
                         />
                       </Col>

src/main/webapp/app/shared/utils/Utils.tsx

@@ -6,7 +6,7 @@ import {
   Article
 } from 'app/shared/api/generated/OncoKbAPI';
 import _ from 'lodash';
-import React from 'react';
+import React, { ReactNode } from 'react';
 import {
   APP_LOCAL_DATE_FORMAT,
   APP_LOCAL_DATETIME_FORMAT_Z,
@@ -428,3 +428,7 @@ export const scrollWidthOffsetInNews = (el?: any) => {
   const yOffset = -80;
   window.scrollTo({ top: yCoordinate + yOffset, behavior: 'smooth' });
 };
+
+export const concatElementsByComma = (list: ReactNode[]) => {
+  return list.reduce((prev, curr) => [prev, ', ', curr]);
+};