Feature/v4.24 (#1194)

* v4.24

* Update src/main/webapp/app/pages/genePage/SomaticGermlineGenePage.tsx

Co-authored-by: Calvin Lu <[email protected]>

* Update src/main/webapp/app/components/userMessager/UserMessage.tsx

Co-authored-by: Calvin Lu <[email protected]>

* Fixed screenshot

* Addressed Comments

---------

Co-authored-by: Calvin Lu <[email protected]>

src/main/java/org/mskcc/cbio/oncokb/web/rest/ApiProxy.java

@@ -94,7 +94,7 @@ public ResponseEntity<String> proxy(@RequestBody(required = false) String body,
         }
     }
 
-    @RequestMapping("/private/utils/data/sqlDump")
+    @RequestMapping(path = {"/private/utils/data/sqlDump", "/private/utils/data/transcriptSqlDump"})
     public ResponseEntity<byte[]> proxyDataReleaseDownload(@RequestBody(required = false) String body, HttpMethod method, HttpServletRequest request)
         throws URISyntaxException {
         URI uri = apiProxyService.prepareURI(request);

src/main/java/org/mskcc/cbio/oncokb/web/rest/errors/ExceptionTranslator.java

@@ -13,6 +13,7 @@
 import org.springframework.web.bind.MethodArgumentNotValidException;
 import org.springframework.web.bind.annotation.ControllerAdvice;
 import org.springframework.web.bind.annotation.ExceptionHandler;
+import org.springframework.web.client.HttpClientErrorException;
 import org.springframework.web.context.request.NativeWebRequest;
 import org.springframework.web.context.request.WebRequest;
 import org.springframework.core.env.Environment;
@@ -56,6 +57,20 @@ public ExceptionTranslator(Environment env) {
         this.env = env;
     }
 
+    @ExceptionHandler
+    public ResponseEntity<Problem> handleHttpClientErrorException(HttpClientErrorException ex, NativeWebRequest request) {
+        Problem problem = Problem.builder()
+            .withType(ErrorConstants.DEFAULT_TYPE)
+            .withTitle("HTTP Error")
+            .withStatus(Status.valueOf(ex.getStatusCode().value()))
+            .with(MESSAGE_KEY, "error.http." + ex.getStatusCode().value())
+            .withDetail(ex.getResponseBodyAsString())
+            .with(PATH_KEY, request.getNativeRequest(HttpServletRequest.class).getRequestURI())
+            .build();
+
+        return create(ex, problem, request);
+    }
+
     /**
      * Post-process the Problem payload to add the message key for the front-end if needed.
      */
@@ -146,7 +161,6 @@ public ResponseEntity<Problem> handleDatabaseReadOnlyException(DatabaseReadOnlyE
 
     @Override
     public ProblemBuilder prepare(final Throwable throwable, final StatusType status, final URI type) {
-
         Collection<String> activeProfiles = Arrays.asList(env.getActiveProfiles());
 
         if (activeProfiles.contains(JHipsterConstants.SPRING_PROFILE_PRODUCTION)) {
@@ -161,7 +175,6 @@ public ProblemBuilder prepare(final Throwable throwable, final StatusType status
                         .map(this::toProblem)
                         .orElse(null));
             }
-
             if (throwable instanceof DataAccessException) {
                 return Problem.builder()
                     .withType(type)
@@ -173,7 +186,6 @@ public ProblemBuilder prepare(final Throwable throwable, final StatusType status
                         .map(this::toProblem)
                         .orElse(null));
             }
-
             if (containsPackageName(throwable.getMessage())) {
                 return Problem.builder()
                     .withType(type)

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

@@ -14,7 +14,6 @@ import ExternalLinkIcon from 'app/shared/icons/ExternalLinkIcon';
 import { OncoTreeLink } from 'app/shared/utils/UrlUtils';
 import {
   LinkedInLink,
-  TwitterLink,
   UserGoogleGroupLink,
 } from 'app/shared/links/SocialMediaLinks';
 
@@ -58,7 +57,6 @@ class Footer extends React.Component<{ lastDataUpdate: string }> {
           <Link to={PAGE_ROUTE.TERMS}>Terms of Use</Link>
           <ContactLink emailSubject={'Contact us'}>Contact Us</ContactLink>
           <LinkedInLink short />
-          <TwitterLink short />
           <Linkout link={API_DOCUMENT_LINK}>API</Linkout>
         </div>
         <div className={classnames(styles.footerAList)}>

src/main/webapp/app/components/authDownloadButton/AuthDownloadButton.tsx

@@ -8,6 +8,7 @@ import { observer, inject } from 'mobx-react';
 import { observable, action } from 'mobx';
 import { LoadingButton } from 'app/shared/button/LoadingButton';
 import { IDownloadButtonWithPromise } from 'app/components/downloadButtonWithPromise/DownloadButtonWithPromise';
+import { notifyError } from 'app/shared/utils/NotificationUtils';
 
 interface IAuthDownloadButton extends IDownloadButtonWithPromise {
   routing?: RouterStore;
@@ -28,10 +29,19 @@ export class AuthDownloadButton extends React.Component<IAuthDownloadButton> {
         .then(data => {
           if (Array.isArray(data)) {
             data = data.join('');
+          } else if (data === undefined || data === null) {
+            return;
           }
           fileDownload(data, this.props.fileName, this.props.mime);
         })
-        .catch(error => {})
+        .catch(error => {
+          console.error(error);
+          notifyError(
+            new Error(
+              `There was an error fetching the file "${this.props.fileName}"`
+            )
+          );
+        })
         .finally(() => {
           this.downloading = false;
         });

src/main/webapp/app/components/downloadButtonWithPromise/DownloadButtonWithPromise.tsx

@@ -4,9 +4,10 @@ import fileDownload from 'js-file-download';
 import { observer, inject } from 'mobx-react';
 import { observable, action } from 'mobx';
 import { LoadingButton } from 'app/shared/button/LoadingButton';
+import { notifyError } from 'app/shared/utils/NotificationUtils';
 
 export interface IDownloadButtonWithPromise extends ButtonProps {
-  getDownloadData: () => Promise<string | Blob | string[]>;
+  getDownloadData: () => Promise<string | Blob | string[] | null | undefined>;
   fileName: string;
   mime?: string;
   buttonText: string;
@@ -27,10 +28,19 @@ export class DownloadButtonWithPromise extends React.Component<
       .then(data => {
         if (Array.isArray(data)) {
           data = data.join('');
+        } else if (data === undefined || data === null) {
+          return;
         }
         fileDownload(data, this.props.fileName, this.props.mime);
       })
-      .catch(error => {})
+      .catch(error => {
+        console.error(error);
+        notifyError(
+          new Error(
+            `There was an error fetching the file "${this.props.fileName}"`
+          )
+        );
+      })
       .finally(() => {
         this.downloading = false;
       });

src/main/webapp/app/components/userMessager/UserMessage.tsx

@@ -23,7 +23,6 @@ import { Linkout } from 'app/shared/links/Linkout';
 import { COLOR_BLACK, COLOR_DARK_BLUE, COLOR_WARNING } from 'app/config/theme';
 import {
   LinkedInLink,
-  TwitterLink,
   UserGoogleGroupLink,
 } from 'app/shared/links/SocialMediaLinks';
 
@@ -60,8 +59,7 @@ if (
         <div>
           <div>
             <span>
-              Follow us on <LinkedInLink /> and <TwitterLink />, or subscribe to
-              our{' '}
+              Follow us on <LinkedInLink /> or subscribe to our{' '}
               <UserGoogleGroupLink>low-volume email list</UserGoogleGroupLink>,
               to stay updated on our latest data releases and new features!
             </span>

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

@@ -864,6 +864,7 @@ export type DataRelease = {
 };
 
 export const DATA_RELEASES: DataRelease[] = [
+  { date: '12192024', version: 'v4.24' },
   { date: '11262024', version: 'v4.23' },
   { date: '10242024', version: 'v4.22' },
   { date: '09252024', version: 'v4.21' },

src/main/webapp/app/index.tsx

@@ -42,7 +42,10 @@ superagent.Request.prototype.query = function (queryParameters: any) {
   const token = getStoredToken();
   if (token) {
     this.set('Authorization', `Bearer ${token}`);
-    if (this.url.endsWith('sqlDump')) {
+    if (
+      this.url.endsWith('sqlDump') ||
+      this.url.endsWith('transcriptSqlDump')
+    ) {
       this.responseType('blob');
     }
   }

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

@@ -449,10 +449,10 @@ export default class CancerGenesPage extends React.Component<{
             </Col>
             <Col className="col-auto">
               <DownloadButtonWithPromise
-                fileName="cancerGeneList.tsv"
-                getDownloadData={() =>
-                  oncokbClient.utilsCancerGeneListTxtGetUsingGET({})
-                }
+                fileName={'cancerGeneList.tsv'}
+                getDownloadData={() => {
+                  return oncokbClient.utilsCancerGeneListTxtGetUsingGET({});
+                }}
                 buttonText="Cancer Gene List"
               />
             </Col>

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

@@ -38,48 +38,92 @@ const getDataTitle = (date: string, version: string) => {
   return `${getNewsTitle(date)} (${version})`;
 };
 
+function getMajorVersion(versionString: string): number | undefined {
+  const match = versionString.match(/^v(\d+)\./);
+
+  return match ? parseInt(match[1], 10) : undefined;
+}
+function getMinorVersion(versionString: string): number | undefined {
+  const match = versionString.match(/^v(\d+)\.(\d+)/);
+
+  return match ? parseInt(match[2], 10) : undefined;
+}
+
 const BUTTON_CLASS_NAME = 'mr-2 my-1';
 const DownloadButtonGroups: React.FunctionComponent<{
   data: DownloadAvailabilityWithDate;
 }> = props => {
+  const majorVersion = getMajorVersion(props.data.version) ?? 0;
+  const minorVersion = getMinorVersion(props.data.version) ?? 0;
+  const versionIsLessThan4 = majorVersion < 4;
   return (
     <>
       {props.data.hasAllCuratedGenes ? (
         <AuthDownloadButton
           className={BUTTON_CLASS_NAME}
           fileName={`all_curated_genes_${props.data.version}.tsv`}
-          getDownloadData={() =>
-            oncokbClient.utilsAllCuratedGenesTxtGetUsingGET({
+          getDownloadData={() => {
+            return oncokbClient.utilsAllCuratedGenesTxtGetUsingGET({
               version: props.data.version,
-            })
-          }
+            });
+          }}
           buttonText="All Curated Genes"
         />
       ) : null}
       {props.data.hasCancerGeneList ? (
         <AuthDownloadButton
           className={BUTTON_CLASS_NAME}
           fileName={`cancer_gene_list_${props.data.version}.tsv`}
-          getDownloadData={() =>
-            oncokbClient.utilsCancerGeneListTxtGetUsingGET({
+          getDownloadData={() => {
+            return oncokbClient.utilsCancerGeneListTxtGetUsingGET({
               version: props.data.version,
-            })
-          }
+            });
+          }}
           buttonText="Cancer Gene List"
         />
       ) : null}
       {props.data.hasAllActionableVariants ? (
-        <AuthDownloadButton
-          className={BUTTON_CLASS_NAME}
-          fileName={`oncokb_${props.data.version.replace('.', '_')}.sql.gz`}
-          getDownloadData={async () => {
-            const data = await oncokbPrivateClient.utilDataSqlDumpGetUsingGET({
-              version: props.data.version,
-            });
-            return data;
-          }}
-          buttonText="Data Dump"
-        />
+        <>
+          <AuthDownloadButton
+            className={BUTTON_CLASS_NAME}
+            fileName={`oncokb_${props.data.version.replace('.', '_')}.sql.gz`}
+            getDownloadData={async () => {
+              const data = await oncokbPrivateClient.utilDataSqlDumpGetUsingGET(
+                {
+                  version: props.data.version,
+                }
+              );
+              return data;
+            }}
+            buttonText="Data Dump"
+          />
+          <AuthDownloadButton
+            disabled={versionIsLessThan4}
+            title={
+              versionIsLessThan4
+                ? 'Not available for versions below 4.0'
+                : undefined
+            }
+            className={BUTTON_CLASS_NAME}
+            fileName={`oncokb_transcript_${props.data.version.replace(
+              '.',
+              '_'
+            )}.sql.gz`}
+            getDownloadData={async () => {
+              const version =
+                majorVersion === 4 && minorVersion < 23
+                  ? 'v4.23'
+                  : props.data.version;
+              const data = await oncokbPrivateClient.utilDataTranscriptSqlDumpUsingGET(
+                {
+                  version,
+                }
+              );
+              return data;
+            }}
+            buttonText="Transcript Data"
+          />
+        </>
       ) : null}
     </>
   );
@@ -224,6 +268,12 @@ export default class APIAccessPage extends React.Component<{
                           )}
                           , the latest
                         </h6>
+                        <p className="rounded">
+                          The transcript database serves OncoKB metadata
+                          included gene, transcript, sequence, etc. Only
+                          required for local installations that will utilize the
+                          /byGenomicChange and /byHGVSg endpoints
+                        </p>
                         <DownloadButtonGroups
                           data={this.dataAvailability.result[0]}
                         />

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

@@ -76,7 +76,7 @@ import GeneticTypeTabs, {
 } from 'app/components/geneticTypeTabs/GeneticTypeTabs';
 import InfoTile from 'app/components/infoTile/InfoTile';
 import AnnotatedAlterations from 'app/pages/annotationPage/AnnotatedAlterations';
-import { LinkedInLink, TwitterLink } from 'app/shared/links/SocialMediaLinks';
+import { LinkedInLink } from 'app/shared/links/SocialMediaLinks';
 import styles from './GenePage.module.scss';
 import StickyMiniNavBar from 'app/shared/nav/StickyMiniNavBar';
 import MiniNavBarHeader from 'app/shared/nav/MiniNavBarHeader';
@@ -106,8 +106,8 @@ const NoContent: FunctionComponent<{
       <p className={'d-flex flex-column'}>
         <div>Don’t miss out on the latest data releases and new features.</div>
         <div>
-          Follow us on <LinkedInLink /> and <TwitterLink />, or subscribe to our
-          low-volume email list!
+          Follow us on <LinkedInLink /> or subscribe to our low-volume email
+          list!
         </div>
       </p>
       <Button

src/main/webapp/app/pages/newsPage/Links.tsx

@@ -5,12 +5,16 @@ export const FdaApprovalLink: React.FunctionComponent<{
   link: string;
   approval: string;
   year?: string;
+  for?: string;
 }> = props => {
   let linkText = 'FDA approval ';
   if (props.year) {
     linkText += `(${props.year}) `;
   }
   linkText += `of ${props.approval}`;
+  if (props.for) {
+    linkText += ` for ${props.for}`;
+  }
   return <Linkout link={props.link}>{linkText}</Linkout>;
 };
 export const FdaWithdrawalLink: React.FunctionComponent<{

src/main/webapp/app/pages/newsPage/NewsPage.tsx

@@ -34,7 +34,6 @@ import { FdaApprovalLink } from 'app/pages/newsPage/Links';
 import { LevelOfEvidencePageLink } from 'app/shared/links/LevelOfEvidencePageLink';
 import {
   LinkedInLink,
-  TwitterLink,
   UserGoogleGroupLink,
 } from 'app/shared/links/SocialMediaLinks';
 import { Helmet } from 'react-helmet-async';
@@ -80,13 +79,14 @@ export default class NewsPage extends React.Component<{
           <p>
             <b>Stay tuned</b> for future data updates (improved annotations, new
             alterations), as well as new features. You can follow us on{' '}
-            <LinkedInLink /> and <TwitterLink />, or subscribe to our{' '}
+            <LinkedInLink />, or subscribe to our{' '}
             <UserGoogleGroupLink>low-volume email list</UserGoogleGroupLink> for
             updates.
           </p>
           <CitationText />
         </div>
         <div className="mt-2">
+          <NewsList date={'12192024'} />
           <NewsList date={'11262024'} />
           <NewsList date={'10242024'} />
           <NewsList date={'09252024'} />