Added core submission logic

README.md

@@ -202,6 +202,7 @@
        (user_id, authority_name)
        VALUES
        (@UserId, 'ROLE_ADMIN'),
+       (@UserId, 'ROLE_DEV'),
        (@UserId, 'ROLE_CURATOR'),
        (@UserId, 'ROLE_USER');
 

src/main/java/org/mskcc/oncokb/curation/config/application/FrontendProperties.java

@@ -21,4 +21,14 @@ public String getSentryDsn() {
     public void setSentryDsn(String sentryDsn) {
         this.sentryDsn = sentryDsn;
     }
+
+    private Boolean stopReviewIfCoreSubmissionFails;
+
+    public Boolean getStopReviewIfCoreSubmissionFails() {
+        return stopReviewIfCoreSubmissionFails;
+    }
+
+    public void setStopReviewIfCoreSubmissionFails(Boolean stopReviewIfCoreSubmissionFails) {
+        this.stopReviewIfCoreSubmissionFails = stopReviewIfCoreSubmissionFails;
+    }
 }

src/main/java/org/mskcc/oncokb/curation/security/AuthoritiesConstants.java

@@ -7,6 +7,8 @@ public final class AuthoritiesConstants {
 
     public static final String ADMIN = "ROLE_ADMIN";
 
+    public static final String DEV = "ROLE_DEV";
+
     public static final String USER = "ROLE_USER";
 
     public static final String CURATOR = "ROLE_CURATOR";

src/main/java/org/mskcc/oncokb/curation/web/filter/SpaWebFilter.java

@@ -23,6 +23,7 @@ protected void doFilterInternal(HttpServletRequest request, HttpServletResponse
             !path.startsWith("/v3/api-docs") &&
             !path.startsWith("/login") &&
             !path.startsWith("/oauth2") &&
+            !path.startsWith("/legacy-api") &&
             !path.startsWith("/websocket") &&
             !path.contains(".") &&
             path.matches("/(.*)")

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

@@ -6,14 +6,14 @@
 import java.nio.charset.StandardCharsets;
 import org.mskcc.oncokb.curation.service.ApiProxyService;
 import org.mskcc.oncokb.curation.web.rest.errors.BadRequestAlertException;
-import org.springframework.http.HttpEntity;
-import org.springframework.http.HttpHeaders;
-import org.springframework.http.HttpMethod;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
+import org.springframework.http.*;
+import org.springframework.http.converter.FormHttpMessageConverter;
 import org.springframework.http.converter.StringHttpMessageConverter;
+import org.springframework.util.LinkedMultiValueMap;
+import org.springframework.util.MultiValueMap;
 import org.springframework.web.bind.annotation.RequestBody;
 import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.RestController;
 import org.springframework.web.client.HttpClientErrorException;
 import org.springframework.web.client.RestTemplate;
@@ -29,8 +29,34 @@ public ApiProxy(ApiProxyService apiProxyService) {
         this.apiProxyService = apiProxyService;
     }
 
-    @RequestMapping("/**")
-    public ResponseEntity<String> proxy(@RequestBody(required = false) String body, HttpMethod method, HttpServletRequest request)
+    @RequestMapping(value = "/**", consumes = MediaType.APPLICATION_FORM_URLENCODED_VALUE)
+    public ResponseEntity<String> formDataProxy(
+        @RequestParam MultiValueMap<String, Object> formParams,
+        HttpMethod method,
+        HttpServletRequest request
+    ) throws URISyntaxException {
+        URI uri = apiProxyService.prepareURI(request);
+
+        HttpHeaders httpHeaders = apiProxyService.prepareHttpHeaders(request.getContentType());
+        RestTemplate restTemplate = new RestTemplate();
+        restTemplate.getMessageConverters().add(0, new FormHttpMessageConverter());
+
+        HttpEntity<MultiValueMap<String, Object>> requestEntity = new HttpEntity<>(formParams, httpHeaders);
+        try {
+            return restTemplate.exchange(uri, method, requestEntity, String.class);
+        } catch (HttpClientErrorException httpClientErrorException) {
+            if (
+                httpClientErrorException.getStatusCode() != null && httpClientErrorException.getStatusCode().equals(HttpStatus.BAD_REQUEST)
+            ) {
+                throw new BadRequestAlertException(httpClientErrorException.getMessage(), "", "");
+            } else {
+                throw new ResponseStatusException(httpClientErrorException.getStatusCode(), httpClientErrorException.getMessage());
+            }
+        }
+    }
+
+    @RequestMapping(value = "/**", consumes = MediaType.APPLICATION_JSON_VALUE)
+    public ResponseEntity<String> jsonProxy(@RequestBody(required = false) String body, HttpMethod method, HttpServletRequest request)
         throws URISyntaxException {
         URI uri = apiProxyService.prepareURI(request);
 

src/main/resources/config/liquibase/data/authority.csv

@@ -1,4 +1,5 @@
 name
 ROLE_ADMIN
+ROLE_DEV
 ROLE_USER
 ROLE_CURATOR

src/main/webapp/app/appConfig.ts

@@ -1,6 +1,7 @@
 type FrontendProperties = {
   firebase?: FirebaseProperties;
   sentryDsn?: string;
+  stopReviewIfCoreSubmissionFails?: boolean;
 };
 
 export type FirebaseProperties = {

src/main/webapp/app/components/diff-viewer/DiffViewer.tsx

@@ -19,7 +19,7 @@ type DiffViewerProps = {
   className?: string;
 };
 
-const getMergedDiff = (newContent='', oldContent='') => {
+const getMergedDiff = (newContent = '', oldContent = '') => {
   const dmp = new DiffMatchPatch();
   const diff = dmp.diff_main(oldContent, newContent);
   dmp.diff_cleanupSemantic(diff);

src/main/webapp/app/components/tabs/CurationToolsTab.tsx

@@ -1,18 +1,21 @@
 import { componentInject } from 'app/shared/util/typed-inject';
-import { IRootStore } from 'app/stores';
+import { IRootStore, hasAnyAuthority } from 'app/stores';
 import React, { useEffect, useRef, useState } from 'react';
 import { Button, Col, Row } from 'reactstrap';
 import { FaRegCheckCircle } from 'react-icons/fa';
-import { FaRegCircleXmark } from 'react-icons/fa6';
-import { notifyError } from 'app/oncokb-commons/components/util/NotificationUtils';
+import { FaRegCircleXmark, FaArrowRotateLeft } from 'react-icons/fa6';
+import { notifyError, notifySuccess } from 'app/oncokb-commons/components/util/NotificationUtils';
 import { IGene } from 'app/shared/model/gene.model';
 import _ from 'lodash';
 import { IFlag } from 'app/shared/model/flag.model';
-import { CURRENT_REVIEWER } from 'app/config/constants/constants';
+import { AUTHORITIES, CURRENT_REVIEWER } from 'app/config/constants/constants';
 import { GeneType } from 'app/shared/model/firebase/firebase.model';
 import { onValue, ref } from 'firebase/database';
 import { FB_COLLECTION } from 'app/config/constants/firebase';
+import SaveGeneButton from 'app/shared/button/SaveGeneButton';
 import { Unsubscribe } from 'firebase/database';
+import { geneIsReleased } from 'app/shared/util/entity-utils/gene-entity-utils';
+import Tooltip from 'rc-tooltip';
 
 export type ReleaseGeneTestData = {
   passed: boolean;
@@ -22,6 +25,8 @@ export type ReleaseGeneTestData = {
 
 export interface ICurationToolsTabProps extends StoreProps {
   genePath: string;
+  isGermline: boolean;
+  hugoSymbol: string;
 }
 
 export function CurationToolsTab({
@@ -33,6 +38,11 @@ export function CurationToolsTab({
   searchGenes,
   updateGene,
   searchFlags,
+  isGermline,
+  hugoSymbol,
+  isDev,
+  firebaseGeneService,
+  geneLegacyApi,
 }: ICurationToolsTabProps) {
   const [geneName, setGeneName] = useState<string>();
   const [geneSummary, setGeneSummary] = useState<string>();
@@ -114,7 +124,7 @@ export function CurationToolsTab({
 
   useEffect(() => {
     const geneData = geneEntities?.find(entity => entity.hugoSymbol === geneName);
-    setIsReleased(geneData?.flags?.some(flag => isReleasedFlag(flag)) || false);
+    setIsReleased(geneData === undefined ? false : geneIsReleased(geneData));
     geneToUpdate.current = geneData;
   }, [geneEntities, geneName]);
 
@@ -146,6 +156,28 @@ export function CurationToolsTab({
       }
       await updateGene?.(newGene);
       await searchGenes?.({ query: geneName, exact: true }); // repopulate gene store entities
+      await firebaseGeneService?.saveGene(isGermline, hugoSymbol);
+    } catch (error) {
+      notifyError(error);
+    }
+  }
+
+  async function handleUndoReleaseGeneConfirmClick() {
+    const newGene = _.cloneDeep(geneToUpdate.current);
+
+    try {
+      if (!newGene) {
+        throw new Error('Error retrieving gene');
+      }
+
+      if (newGene.flags) {
+        newGene.flags = newGene.flags.filter(flag => !isReleasedFlag(flag));
+      } else {
+        newGene.flags = [];
+      }
+      await updateGene?.(newGene);
+      await searchGenes?.({ query: geneName, exact: true }); // repopulate gene store entities
+      geneLegacyApi!.removeGene(newGene);
     } catch (error) {
       notifyError(error);
     }
@@ -159,12 +191,26 @@ export function CurationToolsTab({
 
     if (isReleased) {
       return (
-        <Row>
-          <Col className={'d-flex align-items-center'}>
-            <FaRegCheckCircle className="text-success me-2" />
-            <span>Gene is released</span>
-          </Col>
-        </Row>
+        <>
+          <Row className="mb-3">
+            <Col className={'d-flex align-items-center'}>
+              <FaRegCheckCircle className="text-success me-2" />
+              <span>Gene is released</span>
+              <Tooltip overlay={'Undo Release'}>
+                <Button size={'sm'} onClick={handleUndoReleaseGeneConfirmClick} className={'ms-2'} color="danger" outline>
+                  <FaArrowRotateLeft />
+                </Button>
+              </Tooltip>
+            </Col>
+          </Row>
+          {!isGermline && isDev && (
+            <Row className="border-top pt-3">
+              <Col>
+                <SaveGeneButton hugoSymbol={hugoSymbol} />
+              </Col>
+            </Row>
+          )}
+        </>
       );
     }
 
@@ -192,23 +238,36 @@ export function CurationToolsTab({
     }
 
     return (
-      <Button color="primary" onClick={() => setReleaseGeneClicked(clicked => !clicked)}>
-        Release Gene
-      </Button>
+      <div>
+        <Button color="primary" onClick={() => setReleaseGeneClicked(clicked => !clicked)}>
+          Release Gene
+        </Button>
+      </div>
     );
   }
 
   return getContent();
 }
 
-const mapStoreToProps = ({ firebaseAppStore, firebaseMetaStore, geneStore, flagStore }: IRootStore) => ({
+const mapStoreToProps = ({
+  firebaseAppStore,
+  firebaseMetaStore,
+  geneStore,
+  flagStore,
+  authStore,
+  firebaseGeneService,
+  geneLegacyApi,
+}: IRootStore) => ({
   firebaseDb: firebaseAppStore.firebaseDb,
   metaList: firebaseMetaStore.data,
   addMetaListListener: firebaseMetaStore.addListener,
   geneEntities: geneStore.entities,
   searchGenes: geneStore.searchEntities,
   updateGene: geneStore.updateEntity,
   searchFlags: flagStore.searchEntities,
+  isDev: hasAnyAuthority(authStore.account.authorities, [AUTHORITIES.DEV]),
+  firebaseGeneService,
+  geneLegacyApi,
 });
 
 type StoreProps = Partial<ReturnType<typeof mapStoreToProps>>;

src/main/webapp/app/components/tabs/GeneListPageToolsTab.tsx

@@ -1,19 +1,21 @@
-import { CURATE_NEW_GENE_TEXT, DEFAULT_ICON_SIZE, PAGE_ROUTE } from 'app/config/constants/constants';
+import { AUTHORITIES, CURATE_NEW_GENE_TEXT, DEFAULT_ICON_SIZE, PAGE_ROUTE } from 'app/config/constants/constants';
 import GeneSelect from 'app/shared/select/GeneSelect';
 import { componentInject } from 'app/shared/util/typed-inject';
-import { IRootStore } from 'app/stores';
+import { IRootStore, hasAnyAuthority } from 'app/stores';
 import { observer } from 'mobx-react';
 import React, { useRef, useState } from 'react';
 import { FaExclamationCircle } from 'react-icons/fa';
-import { Button } from 'reactstrap';
+import { Button, Col, Row } from 'reactstrap';
 import './curation-tools-tab.scss';
 import { MetaCollection } from 'app/shared/model/firebase/firebase.model';
+import SaveGeneButton from 'app/shared/button/SaveGeneButton';
 
 export interface IGeneListPageToolsTab extends StoreProps {
   metaData: MetaCollection | null;
+  isGermline: boolean;
 }
 
-function GeneListPageToolsTab({ metaData, createGene }: IGeneListPageToolsTab) {
+function GeneListPageToolsTab({ metaData, isDev, createGene, isGermline }: IGeneListPageToolsTab) {
   const selectedGene = useRef<string>();
   const [createButtonDisabled, setCreateButtonDisabled] = useState(true);
   const [showGeneExistsWarning, setShowGeneExistsWarning] = useState(false);
@@ -41,28 +43,42 @@ function GeneListPageToolsTab({ metaData, createGene }: IGeneListPageToolsTab) {
   }
 
   return (
-    <div>
-      <h6 className="mb-2">{CURATE_NEW_GENE_TEXT}</h6>
-      <div className="mb-2">
-        <GeneSelect onChange={handleChangeSelectedGene} />
-      </div>
-      <div className={`d-flex align-items-center ${showGeneExistsWarning ? 'justify-content-between' : 'justify-content-end'}`}>
-        {showGeneExistsWarning && (
-          <div className="error-message me-2">
-            <FaExclamationCircle className="me-2" size={DEFAULT_ICON_SIZE} color="danger" />
-            <span>Gene already exists</span>
+    <>
+      <Row>
+        <Col className="mb-3">
+          <div>
+            <h6 className="mb-2">{CURATE_NEW_GENE_TEXT}</h6>
+            <div className="mb-2">
+              <GeneSelect onChange={handleChangeSelectedGene} />
+            </div>
+            <div className={`d-flex align-items-center ${showGeneExistsWarning ? 'justify-content-between' : 'justify-content-end'}`}>
+              {showGeneExistsWarning && (
+                <div className="error-message me-2">
+                  <FaExclamationCircle className="me-2" size={DEFAULT_ICON_SIZE} color="danger" />
+                  <span>Gene already exists</span>
+                </div>
+              )}
+              <Button color="primary" disabled={createButtonDisabled} onClick={handleCreateGene}>
+                Create
+              </Button>
+            </div>
           </div>
-        )}
-        <Button color="primary" disabled={createButtonDisabled} onClick={handleCreateGene}>
-          Create
-        </Button>
-      </div>
-    </div>
+        </Col>
+      </Row>
+      {!isGermline && isDev && (
+        <Row className="pt-3 border-top">
+          <div>
+            <SaveGeneButton />
+          </div>
+        </Row>
+      )}
+    </>
   );
 }
 
-const mapStoreToProps = ({ firebaseGeneService }: IRootStore) => ({
+const mapStoreToProps = ({ firebaseGeneService, authStore }: IRootStore) => ({
   createGene: firebaseGeneService.createGene,
+  isDev: hasAnyAuthority(authStore.account.authorities, [AUTHORITIES.DEV]),
 });
 
 type StoreProps = Partial<ReturnType<typeof mapStoreToProps>>;

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

@@ -4,6 +4,7 @@ import { ToastOptions } from 'react-toastify';
 
 export const AUTHORITIES = {
   ADMIN: 'ROLE_ADMIN',
+  DEV: 'ROLE_DEV',
   USER: 'ROLE_USER',
   CURATOR: 'ROLE_CURATOR',
 };
@@ -336,6 +337,7 @@ export enum SearchOptionType {
 export enum USER_AUTHORITY {
   ROLE_USER = 'ROLE_USER',
   ROLE_ADMIN = 'ROLE_ADMIN',
+  ROLE_DEV = 'ROLE_DEV',
   ROLE_CURATOR = 'ROLE_CURATOR',
 }
 

src/main/webapp/app/entities/drug/drug-update.tsx

@@ -139,7 +139,7 @@ export const DrugUpdate = (props: IDrugUpdateProps) => {
                 {flags
                   ? flags.map(otherEntity => (
                       <option value={otherEntity.id} key={otherEntity.id}>
-                        {otherEntity.id}
+                        Type: {otherEntity.type}, Flag: {otherEntity.name}
                       </option>
                     ))
                   : null}

src/main/webapp/app/pages/curation/CurationPage.tsx

@@ -250,7 +250,7 @@ export const CurationPage = (props: ICurationPageProps) => {
             tabs={[
               {
                 title: 'Tools',
-                content: <CurationToolsTab genePath={firebaseGenePath} />,
+                content: <CurationToolsTab genePath={firebaseGenePath} isGermline={isGermline} hugoSymbol={hugoSymbol ?? ''} />,
               },
               {
                 title: 'History',