Add somatic/germline gene page (#1181)

- Update gene info section 
- Add external link icon
- Add InfoTile & GeneOriginTabs
- Add genomic indicators
- Add germline core proxy config


---------

Co-authored-by: John Konecny <[email protected]>

package.json

@@ -101,6 +101,7 @@
     "@types/react-select": "^3.0.21",
     "@types/react-spinkit": "^3.0.5",
     "@types/reactstrap": "^8.0.4",
+    "@types/resize-observer-browser": "^0.1.11",
     "@types/webpack-env": "1.15.2",
     "@typescript-eslint/eslint-plugin": "2.29.0",
     "@typescript-eslint/parser": "2.29.0",

src/main/java/org/mskcc/cbio/oncokb/config/application/ApplicationProperties.java

@@ -22,6 +22,7 @@ public class ApplicationProperties {
     private String name;
     private String baseUrl = "";
     private String apiProxyUrl;
+    private String apiProxyGermlineUrl;
     private SlackProperties slack;
     private ProjectProfile profile;
     private Boolean sitemapEnabled;
@@ -62,6 +63,14 @@ public void setApiProxyUrl(String apiProxyUrl) {
         this.apiProxyUrl = apiProxyUrl;
     }
 
+    public String getApiProxyGermlineUrl() {
+        return apiProxyGermlineUrl;
+    }
+
+    public void setApiProxyGermlineUrl(String apiProxyGermlineUrl) {
+        this.apiProxyGermlineUrl = apiProxyGermlineUrl;
+    }
+
     public SlackProperties getSlack() { return slack; }
 
     public void setSlack( SlackProperties slack ) { this.slack = slack; }

src/main/java/org/mskcc/cbio/oncokb/service/ApiProxyService.java

@@ -1,6 +1,8 @@
 package org.mskcc.cbio.oncokb.service;
 
+import org.apache.commons.lang3.StringUtils;
 import org.mskcc.cbio.oncokb.config.application.ApplicationProperties;
+import org.mskcc.cbio.oncokb.security.SecurityUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -27,7 +29,13 @@ public class ApiProxyService {
 
     public URI prepareURI(HttpServletRequest request) throws URISyntaxException {
         String queryString = request.getQueryString();
-        return new URI(applicationProperties.getApiProxyUrl() + request.getRequestURI() + (queryString == null ? "" : "?" + queryString));
+        String defaultApiProxyUrl = applicationProperties.getApiProxyUrl();
+        String germlineParam = request.getParameter("germline");
+        if (germlineParam != null && Boolean.TRUE.equals(Boolean.parseBoolean(germlineParam))
+            && SecurityUtils.isAuthenticated() && StringUtils.isNotEmpty(applicationProperties.getApiProxyGermlineUrl())) {
+            defaultApiProxyUrl = applicationProperties.getApiProxyGermlineUrl();
+        }
+        return new URI(defaultApiProxyUrl + request.getRequestURI() + (queryString == null ? "" : "?" + queryString));
     }
 
     public URI prepareURI(String apiRequest) throws URISyntaxException {

src/main/webapp/app/Main.tsx

@@ -2,9 +2,8 @@ import * as React from 'react';
 import Footer from './components/Footer';
 import Header from './components/Header';
 import { observer } from 'mobx-react';
-import AppRouts from 'app/routes/routes';
+import AppRoutes from 'app/routes/routes';
 import { isAuthorized } from 'app/shared/auth/AuthUtils';
-import { Container, Row, Col, Modal, Button } from 'react-bootstrap';
 import { Stores } from 'app/App';
 import { Prompt, withRouter } from 'react-router';
 import {
@@ -19,6 +18,7 @@ import { FeedbackModal } from './components/feedback/FeedbackModal';
 import { FdaModal } from 'app/components/fdaModal/FdaModal';
 import { Location } from 'history';
 import autobind from 'autobind-decorator';
+import PageContainer from 'app/components/PageContainer';
 
 export type IMainPage = Stores;
 
@@ -104,15 +104,16 @@ class Main extends React.Component<IMainPage> {
           routing={this.props.routing}
           appStore={this.props.appStore}
         />
-        <div className={'view-wrapper'}>
-          <Container fluid={!this.props.windowStore.isXLscreen}>
-            <AppRouts
-              authenticationStore={this.props.authenticationStore}
-              appStore={this.props.appStore}
-              routing={this.props.routing}
-            />
-          </Container>
-        </div>
+        <PageContainer
+          routing={this.props.routing}
+          windowStore={this.props.windowStore}
+        >
+          <AppRoutes
+            authenticationStore={this.props.authenticationStore}
+            appStore={this.props.appStore}
+            routing={this.props.routing}
+          />
+        </PageContainer>
         <FeedbackModal
           showModal={this.props.appStore.showFeedbackFormModal}
           feedback={this.feedbackAnnotation}

src/main/webapp/app/components/Footer.module.scss

@@ -18,9 +18,9 @@
 }
 
 .footerAList > a {
-  color: white;
+  line-height: 1rem;
   border-right: 0.5px solid #fff;
-  padding: 0 5px;
+  padding: 0 0.5rem;
 
   &:last-child {
     border: 0;

src/main/webapp/app/components/Footer.tsx

@@ -32,28 +32,19 @@ class Footer extends React.Component<{ lastDataUpdate: string }> {
         <div className={'mb-2'}>
           <CitationText highlightLinkout={true} boldLinkout />
         </div>
-        <div className={classnames(styles.footerAList, 'mb-2')}>
-          <a
-            href="https://www.mskcc.org"
-            target="_blank"
-            rel="noopener noreferrer"
-          >
-            MSK <ExternalLinkIcon />
-          </a>
-          <a
-            href="https://www.mskcc.org/research-areas/programs-centers/molecular-oncology"
-            target="_blank"
-            rel="noopener noreferrer"
-          >
-            CMO <ExternalLinkIcon />
-          </a>
-          <a
-            href="https://www.cbioportal.org"
-            target="_blank"
-            rel="noopener noreferrer"
-          >
-            cBioPortal <ExternalLinkIcon />
-          </a>
+        <div
+          className={classnames(
+            styles.footerAList,
+            'mb-2 d-flex justify-content-center'
+          )}
+        >
+          <ExternalLinkIcon link="https://www.mskcc.org">MSK</ExternalLinkIcon>
+          <ExternalLinkIcon link="https://www.mskcc.org/research-areas/programs-centers/molecular-oncology">
+            CMO
+          </ExternalLinkIcon>
+          <ExternalLinkIcon link="https://www.cbioportal.org">
+            cBioPortal
+          </ExternalLinkIcon>
           <OncoTreeLink />
         </div>
       </>

src/main/webapp/app/components/PageContainer.tsx

@@ -1,15 +1,44 @@
-import React from 'react';
+import React, { FunctionComponent } from 'react';
 import { Col, Row } from 'react-bootstrap';
+import WindowStore from 'app/store/WindowStore';
+import { RouterStore } from 'mobx-react-router';
+import { PAGE_ROUTE } from 'app/config/constants';
+import { GENETIC_TYPE } from 'app/components/geneticTypeTabs/GeneticTypeTabs';
+import { parseGenePagePath } from 'app/shared/utils/UrlUtils';
 
+const Container: FunctionComponent<{
+  inGenePage: boolean;
+}> = props => {
+  if (props.inGenePage) {
+    return <div>{props.children}</div>;
+  } else {
+    return (
+      <Row className={`justify-content-center`}>
+        <Col md={11}>{props.children}</Col>
+      </Row>
+    );
+  }
+};
 const PageContainer: React.FunctionComponent<{
-  className?: string;
+  routing: RouterStore;
+  windowStore: WindowStore;
 }> = props => {
+  const genePagePath = parseGenePagePath(props.routing.location.pathname);
+  const inGenePage = genePagePath.geneticType !== undefined;
   return (
-    <Row className={`justify-content-center ${props.className}`}>
-      <Col xl={10} lg={11}>
-        {props.children}
-      </Col>
-    </Row>
+    <div className={'view-wrapper'}>
+      <div
+        className={
+          inGenePage
+            ? ''
+            : props.windowStore.isXLscreen
+            ? 'container'
+            : 'container-fluid'
+        }
+      >
+        <Container inGenePage={inGenePage}>{props.children}</Container>
+      </div>
+    </div>
   );
 };
 export default PageContainer;

src/main/webapp/app/components/geneticTypeTabs/GeneticTypeTabs.tsx

@@ -0,0 +1,47 @@
+import React, { FunctionComponent, useState } from 'react';
+import styles from './genetic-type-tabs.module.scss';
+import classnames from 'classnames';
+import { RouterStore } from 'mobx-react-router';
+
+export enum GENETIC_TYPE {
+  SOMATIC = 'somatic',
+  GERMLINE = 'germline',
+}
+
+const GeneticTypeTabs: FunctionComponent<{
+  routing: RouterStore;
+  hugoSymbol: string;
+  geneticType?: GENETIC_TYPE;
+  onChange: (status: string) => void;
+}> = props => {
+  const [selected, setSelected] = useState<GENETIC_TYPE>(
+    props.geneticType || GENETIC_TYPE.SOMATIC
+  );
+
+  const ontoggle = (status: GENETIC_TYPE) => {
+    setSelected(status);
+    props.onChange(status);
+  };
+
+  return (
+    <div className={styles.tabs}>
+      {[GENETIC_TYPE.SOMATIC, GENETIC_TYPE.GERMLINE].map((geneOrigin, idx) => (
+        <div
+          key={idx}
+          style={{ width: '50%' }}
+          className={
+            selected === geneOrigin
+              ? classnames(styles.tab, styles.selectedTab, 'font-bold')
+              : classnames(styles.tab, styles.unselectedTab)
+          }
+          onClick={() => ontoggle(geneOrigin)}
+        >
+          {geneOrigin.substring(0, 1).toUpperCase()}
+          {geneOrigin.toLowerCase().slice(1)}
+        </div>
+      ))}
+    </div>
+  );
+};
+
+export default GeneticTypeTabs;

src/main/webapp/app/components/geneticTypeTabs/genetic-type-tabs.module.scss

@@ -0,0 +1,33 @@
+@import '../../variables';
+
+.tabs {
+  display: flex;
+  margin: 1.5rem 0 0 0;
+}
+
+.tab {
+  text-align: center;
+  padding: 0.75rem 0;
+  border: 1px solid $oncokb-darker-blue;
+  cursor: pointer;
+}
+
+.tab:first-child {
+  border-left: 0;
+  border-top-right-radius: 3px;
+}
+
+.tab:last-child {
+  border-right: 0;
+  border-top-left-radius: 3px;
+}
+
+.selectedTab {
+  padding-top: 0.5rem;
+  border-width: 3px 1px 0 1px;
+}
+
+.unselectedTab {
+  background-color: $inactive;
+  border-width: 0 0 1px 0;
+}

src/main/webapp/app/components/geneticTypeTag/GeneticTypeTag.tsx

@@ -0,0 +1,25 @@
+import React, { FunctionComponent } from 'react';
+import { GENETIC_TYPE } from 'app/components/geneticTypeTabs/GeneticTypeTabs';
+import classnames from 'classnames';
+import styles from './genetic-type-tag.module.scss';
+import { capitalize } from 'cbioportal-frontend-commons';
+
+const GeneticTypeTag: FunctionComponent<{
+  geneticType: GENETIC_TYPE;
+  className?: string;
+}> = props => {
+  return (
+    <span
+      className={classnames(
+        props.className,
+        props.geneticType === GENETIC_TYPE.GERMLINE
+          ? styles.germlineTag
+          : styles.somaticTag
+      )}
+    >
+      {capitalize(props.geneticType)}
+    </span>
+  );
+};
+
+export default GeneticTypeTag;

src/main/webapp/app/components/geneticTypeTag/genetic-type-tag.module.scss

@@ -0,0 +1,25 @@
+@import '../../variables';
+
+.geneticTypeTag {
+  font-weight: 500 !important;
+  font-family: "Gotham Book";
+  display: inline-flex;
+  padding: 0 var(--radius-8, 8px);
+  justify-content: center;
+  align-items: center;
+  gap: var(--radius-8, 8px);
+  border-radius: 56px;
+}
+
+.germlineTag {
+  @extend .geneticTypeTag;
+  color: $primary;
+  border: var(--radius-2, 2px) solid var(--Color-11, $primary);
+  background: #F0F5FF;
+}
+
+.somaticTag {
+  @extend .geneticTypeTag;
+  color: #FFFFFF;
+  background: $primary;
+}

src/main/webapp/app/components/infoTile/InfoTile.tsx

@@ -0,0 +1,52 @@
+import React, { CSSProperties } from 'react';
+import styles from './info-tile.module.scss';
+import { COLOR_GREY } from 'app/config/theme';
+import classnames from 'classnames';
+
+export type Category = {
+  title: string;
+  content?: JSX.Element | string;
+  className?: string;
+};
+export type InfoTile = {
+  title: string;
+  categories: Category[];
+  className?: string;
+};
+
+const Category: React.FunctionComponent<Category> = props => {
+  const isNa = props.content === undefined || props.content === null;
+  const isText = isNa || typeof props.content === 'string';
+  const style: CSSProperties = { height: '3rem' };
+  if (isText) {
+    style.fontSize = '1.5rem';
+    style.fontFamily = 'Gotham Bold';
+  }
+  return (
+    <div className={classnames(props.className, 'flex-grow-1')}>
+      <div style={{ color: COLOR_GREY }} className={'mb-1'}>
+        {props.title}
+      </div>
+      <div className={classnames('d-flex align-items-center')} style={style}>
+        {props.content}
+      </div>
+    </div>
+  );
+};
+
+const InfoTile: React.FunctionComponent<InfoTile> = props => {
+  return props.categories.length > 0 ? (
+    <div className={classnames(styles.tile, 'mr-2', props.className)}>
+      <div className={'h6 font-bold mb-2'}>{props.title}</div>
+      <div className={'d-flex'}>
+        {props.categories.map((category, idx) => (
+          <Category key={idx} {...category} className={styles.category} />
+        ))}
+      </div>
+    </div>
+  ) : (
+    <></>
+  );
+};
+
+export default InfoTile;