Feature/fix submit to core (#439)

* Handle when Instant json element is a json object The completedDate in the DB could be ISO 8601 string, or json object. I think this has to do with the recent spring boot upgrade, but I can't find the specific version of the change. I will handle both scenarios for now * Textarea in review mode should fit text content (#427) * Update pom version * Fix reject cancer type name review (#428) * Add reference to oncokb sop alteration nomenclature in add mutation modal helper (#432) * Update pom version * Avoid fetching management info repeatedly * Do not rerender the side bar when loading session The getSession is an async method which updates the loading status. * Fix drug code not selectable (#435) * Bump actions to latest version (#438) * resize text area when input changes (#440) * add sorting by firebase index (#443) * Delete mutation/tumor/treatment as last step to avoid stale index (#444) * Review no longer removes data for core submission * Added comments to useLastReviewOnly * Add children review paths * Fixed approve all * Fixed UI tests * Fixed UI tests * break in middle of word to fix collapsible title overlfow (#442) * Change searchEntities to readHandler instead of updateHandler (#445) * Fixed submit all * Fixed submission bug * Fixed data validation tool (#447) * Allow curating mutation summary (#433) * Fixed submit all * Fixed tests * Fixed gene type submissions * Removed last review check inside getevidences and gene type * Added mutation summary --------- Co-authored-by: Hongxin <[email protected]> Co-authored-by: Hongxin <[email protected]> Co-authored-by: Calvin Lu <[email protected]> Co-authored-by: oncokb-bot <[email protected]> Co-authored-by: bprize15 <[email protected]>
oncokb · Oct 3, 2024 · dafac59 · dafac59
1 parent 4204647
commit dafac59
Show file tree

Hide file tree

Showing 43 changed files with 849 additions and 163 deletions.
diff --git a/.github/workflows/after-branch-commit.yml b/.github/workflows/after-branch-commit.yml
@@ -91,7 +91,7 @@ jobs:
           version: ${{ steps.find_release.outputs.tag }}
 
       - name: 'Setup Java'
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v4
         with:
           java-version: 8
 

diff --git a/.github/workflows/docker-release.yml b/.github/workflows/docker-release.yml
@@ -8,11 +8,11 @@ jobs:
     name: Build and Push
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
         with:
           node-version: '20.12.2'
-      - uses: actions/setup-java@v2
+      - uses: actions/setup-java@v4
         with:
           distribution: 'adopt'
           java-version: '17'

diff --git a/.github/workflows/github-ci.yml b/.github/workflows/github-ci.yml
@@ -5,11 +5,11 @@ jobs:
     name: OncoKB Build
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
         with:
           node-version: "20.12.2"
-      - uses: actions/setup-java@v2
+      - uses: actions/setup-java@v4
         with:
           distribution: 'adopt'
           java-version: '17'

diff --git a/.github/workflows/webdriver-test.yml b/.github/workflows/webdriver-test.yml
@@ -7,7 +7,7 @@ jobs:
       runs-on: ubuntu-latest
 
       steps:
-        - uses: actions/checkout@v2
+        - uses: actions/checkout@v4
 
         - name: Build Docker images
           run: docker compose build
@@ -19,7 +19,7 @@ jobs:
 
         - name: Archive screenshots
           if: failure()
-          uses: actions/upload-artifact@v2
+          uses: actions/upload-artifact@v4
           with:
             name: visual-regression-screenshots
             path: ./src/test/javascript/screenshots
diff --git a/pom.xml b/pom.xml
@@ -7,7 +7,7 @@
 
     <groupId>org.mskcc.oncokb.curation</groupId>
     <artifactId>oncokb-curation</artifactId>
-    <version>2.0.21</version>
+    <version>2.0.23</version>
     <packaging>jar</packaging>
     <name>OncoKB Curation</name>
     <description>Description for oncokb-curation</description>

diff --git a/src/main/java/org/mskcc/oncokb/curation/config/InstantTypeAdapter.java b/src/main/java/org/mskcc/oncokb/curation/config/InstantTypeAdapter.java
@@ -8,7 +8,18 @@ public class InstantTypeAdapter implements JsonSerializer<Instant>, JsonDeserial
 
     @Override
     public Instant deserialize(JsonElement json, Type typeOfT, JsonDeserializationContext context) {
-        return Instant.parse(json.getAsString());
+        if (json.isJsonPrimitive()) {
+            // Handle the ISO 8601 string format
+            return Instant.parse(json.getAsString());
+        } else if (json.isJsonObject()) {
+            // Handle the {"seconds":..., "nanos":...} object format
+            JsonObject jsonObject = json.getAsJsonObject();
+            long seconds = jsonObject.get("seconds").getAsLong();
+            int nanos = jsonObject.get("nanos").getAsInt();
+            return Instant.ofEpochSecond(seconds, nanos);
+        } else {
+            throw new JsonParseException("Unexpected JSON type: " + json.getClass().getSimpleName());
+        }
     }
 
     @Override

diff --git a/src/main/java/org/mskcc/oncokb/curation/web/filter/SpaWebFilter.java b/src/main/java/org/mskcc/oncokb/curation/web/filter/SpaWebFilter.java
@@ -24,6 +24,7 @@ protected void doFilterInternal(HttpServletRequest request, HttpServletResponse
             !path.startsWith("/login") &&
             !path.startsWith("/oauth2") &&
             !path.startsWith("/legacy-api") &&
+            !path.startsWith("/websocket") &&
             !path.contains(".") &&
             path.matches("/(.*)")
         ) {

diff --git a/src/main/java/org/mskcc/oncokb/curation/web/websocket/ProxyWebSocketHandler.java b/src/main/java/org/mskcc/oncokb/curation/web/websocket/ProxyWebSocketHandler.java
@@ -25,7 +25,7 @@ public ProxyWebSocketHandler(ApplicationProperties applicationProperties) {
     @Override
     public void afterConnectionEstablished(WebSocketSession session) throws Exception {
         try {
-            String incomingUri = session.getUri().toString();
+            String incomingUri = session.getUri().getPath();
             StandardWebSocketClient client = new StandardWebSocketClient();
             OncoCoreWebSocketHandler handler = new OncoCoreWebSocketHandler(session);
             client.doHandshake(handler, this.baseUrl + "/api" + incomingUri);

diff --git a/src/main/webapp/app/app.tsx b/src/main/webapp/app/app.tsx
@@ -42,9 +42,8 @@ const App: React.FunctionComponent<IAppProps> = (props: IAppProps) => {
             pauseOnFocusLoss
           />
           <BetaSiteMessage />
-          {props.loadingAuth ? (
-            <LoadingIndicator isLoading size={LoaderSize.LARGE} center={true} />
-          ) : (
+          {props.loadingAuth && <LoadingIndicator isLoading size={LoaderSize.LARGE} center={true} />}
+          {props.authAccount && (
             <div>
               {props.isAuthorized && <NavigationSidebar />}
               <div className="app-center-content-wrapper" style={{ margin: props.centerContentMargin }}>
@@ -63,6 +62,7 @@ const mapStoreToProps = ({ authStore, layoutStore, firebaseAppStore }: IRootStor
   authorities: authStore.account.authorities,
   isCurator: hasAnyAuthority(authStore.account.authorities ?? [], [AUTHORITIES.CURATOR]),
   loadingAuth: authStore.loading,
+  authAccount: authStore.account,
   navigationSidebarWidth: layoutStore.navigationSidebarWidth,
   toggleNavSidebar: layoutStore.toggleNavigationSidebar,
   centerContentMargin: layoutStore.centerContentMargin,

diff --git a/src/main/webapp/app/components/sidebar/NavigationSidebar.tsx b/src/main/webapp/app/components/sidebar/NavigationSidebar.tsx
@@ -210,9 +210,9 @@ export const NavigationSidebar: React.FunctionComponent<StoreProps> = ({ isNavSi
       .value();
 
     setEntityMenuOrder(order);
-  }, []);
 
-  props.fetchManagementInfo!();
+    props.getManagementInfo!();
+  }, []);
 
   return (
     <Sidebar
@@ -318,7 +318,7 @@ const mapStoreToProps = ({ layoutStore, authStore, managementStore }: IRootStore
   account: authStore.account,
   managementVersion: managementStore.version,
   managementCommit: managementStore.commit,
-  fetchManagementInfo: flow(managementStore.fetchManagementInfo),
+  getManagementInfo: managementStore.getManagementInfo,
 });
 
 type StoreProps = Partial<ReturnType<typeof mapStoreToProps>>;

diff --git a/src/main/webapp/app/entities/drug/drug-update.tsx b/src/main/webapp/app/entities/drug/drug-update.tsx
@@ -7,7 +7,7 @@ import { IRootStore } from 'app/stores';
 import { SaveButton } from 'app/shared/button/SaveButton';
 import { getEntityActionRoute } from 'app/shared/util/RouteUtils';
 import { ENTITY_ACTION, ENTITY_TYPE } from 'app/config/constants/constants';
-import NcitCodeSelect, { parseNcitUniqId } from 'app/shared/select/NcitCodeSelect';
+import NcitCodeSelect from 'app/shared/select/NcitCodeSelect';
 import { mapIdList } from 'app/shared/util/entity-utils';
 import { IDrug } from 'app/shared/model/drug.model';
 import { INciThesaurus } from 'app/shared/model/nci-thesaurus.model';
@@ -46,7 +46,6 @@ export const DrugUpdate = (props: IDrugUpdateProps) => {
       props.getEntity(props.match.params.id);
     }
 
-    props.getNciThesauruses({});
     props.getFlags({});
     props.getAssociations({});
   }, []);
@@ -148,9 +147,9 @@ export const DrugUpdate = (props: IDrugUpdateProps) => {
               <FormGroup>
                 <Label>Code</Label>
                 <NcitCodeSelect
-                  ncit={drugEntity.nciThesaurus}
+                  ncit={drugEntity.nciThesaurus ?? selectedNcit}
                   onChange={selectedOption => {
-                    setSelectedNcit(selectedOption ? parseNcitUniqId(selectedOption.value) : undefined);
+                    setSelectedNcit(selectedOption ? selectedOption.ncit : undefined);
                   }}
                 />
               </FormGroup>
@@ -164,14 +163,12 @@ export const DrugUpdate = (props: IDrugUpdateProps) => {
 };
 
 const mapStoreToProps = (storeState: IRootStore) => ({
-  nciThesauruses: storeState.nciThesaurusStore.entities,
   flags: storeState.flagStore.entities,
   associations: storeState.associationStore.entities,
   drugEntity: storeState.drugStore.entity,
   loading: storeState.drugStore.loading,
   updating: storeState.drugStore.updating,
   updateSuccess: storeState.drugStore.updateSuccess,
-  getNciThesauruses: storeState.nciThesaurusStore.getEntities,
   getFlags: storeState.flagStore.getEntities,
   getAssociations: storeState.associationStore.getEntities,
   getEntity: storeState.drugStore.getEntity,

diff --git a/src/main/webapp/app/pages/curation/collapsible/CancerTypeCollapsible.tsx b/src/main/webapp/app/pages/curation/collapsible/CancerTypeCollapsible.tsx
@@ -10,7 +10,6 @@ import { isSectionRemovableWithoutReview } from 'app/shared/util/firebase/fireba
 import EditIcon from 'app/shared/icons/EditIcon';
 import ModifyCancerTypeModal from 'app/shared/modal/ModifyCancerTypeModal';
 import { notifyError } from 'app/oncokb-commons/components/util/NotificationUtils';
-import _ from 'lodash';
 import { getLevelDropdownOptions } from 'app/shared/util/firebase/firebase-level-utils';
 import { DIAGNOSTIC_LEVELS_ORDERING, READABLE_FIELD, PROGNOSTIC_LEVELS_ORDERING } from 'app/config/constants/firebase';
 import { RealtimeTextAreaInput } from 'app/shared/firebase/input/RealtimeInputs';

diff --git a/src/main/webapp/app/pages/curation/collapsible/MutationCollapsible.tsx b/src/main/webapp/app/pages/curation/collapsible/MutationCollapsible.tsx
@@ -35,7 +35,7 @@ import { IRootStore } from 'app/stores';
 import { get, onValue, ref } from 'firebase/database';
 import _ from 'lodash';
 import { observer } from 'mobx-react';
-import React, { useCallback, useEffect, useMemo, useState } from 'react';
+import React, { useCallback, useEffect, useMemo, useRef, useState } from 'react';
 import { Button } from 'reactstrap';
 import BadgeGroup from '../BadgeGroup';
 import { DeleteSectionButton } from '../button/DeleteSectionButton';
@@ -49,6 +49,7 @@ import { NestLevelColor, NestLevelMapping, NestLevelType } from './NestLevel';
 import { RemovableCollapsible } from './RemovableCollapsible';
 import { Unsubscribe } from 'firebase/database';
 import { getLocationIdentifier } from 'app/components/geneHistoryTooltip/gene-history-tooltip-utils';
+import { SimpleConfirmModal } from 'app/shared/modal/SimpleConfirmModal';
 
 export interface IMutationCollapsibleProps extends StoreProps {
   mutationPath: string;
@@ -77,15 +78,21 @@ const MutationCollapsible = ({
   annotatedAltsCache,
   genomicIndicators,
   showLastModified,
+  handleFirebaseUpdate,
 }: IMutationCollapsibleProps) => {
   const firebaseMutationsPath = `${getFirebaseGenePath(isGermline, hugoSymbol)}/mutations`;
 
   const [mutationUuid, setMutationUuid] = useState<string>('');
   const [mutationName, setMutationName] = useState<string>('');
   const [mutationNameReview, setMutationNameReview] = useState<Review | null>(null);
+  const [mutationSummary, setMutationSummary] = useState<string>('');
   const [mutationAlterations, setMutationAlterations] = useState<Alteration[] | null>(null);
   const [isRemovableWithoutReview, setIsRemovableWithoutReview] = useState(false);
   const [relatedAnnotationResult, setRelatedAnnotationResult] = useState<AlterationAnnotationStatus[]>([]);
+  const [oncogenicity, setOncogenicity] = useState<string>('');
+  const [showSimpleConfirmModal, setShowSimpleConfirmModal] = useState<boolean>(false);
+  const [simpleConfirmModalBody, setSimpleConfirmModalBody] = useState<string | undefined>(undefined);
+  const [mutationSummaryRef, setMutationSummaryRef] = useState<HTMLElement | null>(null);
 
   useEffect(() => {
     const arr = annotatedAltsCache?.get(hugoSymbol ?? '', [{ name: mutationName, alterations: mutationAlterations }]) ?? [];
@@ -157,6 +164,11 @@ const MutationCollapsible = ({
         setMutationName(snapshot.val());
       }),
     );
+    callbacks.push(
+      onValue(ref(firebaseDb, `${mutationPath}/summary`), snapshot => {
+        setMutationSummary(snapshot.val());
+      }),
+    );
     callbacks.push(
       onValue(ref(firebaseDb, `${mutationPath}/alterations`), snapshot => {
         setMutationAlterations(snapshot.val());
@@ -169,6 +181,11 @@ const MutationCollapsible = ({
         setIsRemovableWithoutReview(isSectionRemovableWithoutReview(review));
       }),
     );
+    callbacks.push(
+      onValue(ref(firebaseDb, `${mutationPath}/mutation_effect/oncogenic`), snapshot => {
+        setOncogenicity(snapshot.val());
+      }),
+    );
 
     onValue(
       ref(firebaseDb, `${mutationPath}/name_uuid`),
@@ -197,6 +214,34 @@ const MutationCollapsible = ({
     [mutationPath, mutationName, parsedHistoryList],
   );
 
+  async function simpleConfirmModalOnConfirm() {
+    await handleFirebaseUpdate?.(mutationPath, { summary: '' });
+    if (mutationSummaryRef) {
+      mutationSummaryRef.click();
+    }
+    setShowSimpleConfirmModal(false);
+    setSimpleConfirmModalBody(undefined);
+  }
+
+  function oncogenicityRadioOnClick(
+    event: React.MouseEvent<HTMLInputElement> | React.MouseEvent<HTMLLabelElement> | React.MouseEvent<HTMLDivElement>,
+  ) {
+    if (mutationSummary && event.target) {
+      let newOncogenicityVal;
+      if (event.target instanceof HTMLInputElement) {
+        newOncogenicityVal = event.target.value;
+      } else if (event.target instanceof HTMLDivElement || event.target instanceof HTMLLabelElement) {
+        newOncogenicityVal = event.target.innerText;
+      }
+      if (newOncogenicityVal === RADIO_OPTION_NONE) {
+        event.preventDefault();
+        setMutationSummaryRef(event.target as HTMLElement);
+        setShowSimpleConfirmModal(true);
+        setSimpleConfirmModalBody(`Mutation summary will be removed after removing oncogenicity.`);
+      }
+    }
+  }
+
   async function handleDeleteMutation(toVus = false) {
     if (!firebaseDb) {
       return;
@@ -308,6 +353,25 @@ const MutationCollapsible = ({
         }
         isPendingDelete={isMutationPendingDelete}
       >
+        <RealtimeTextAreaInput
+          firebasePath={`${mutationPath}/summary`}
+          inputClass={styles.summaryTextarea}
+          label="Mutation Summary (Optional)"
+          labelIcon={
+            <GeneHistoryTooltip
+              historyData={parsedHistoryList}
+              location={`${getMutationName(mutationName, mutationAlterations)}, ${READABLE_FIELD.SUMMARY}`}
+              locationIdentifier={getLocationIdentifier({
+                mutationUuid,
+                fields: [READABLE_FIELD.SUMMARY],
+              })}
+            />
+          }
+          name="mutationSummary"
+          parseRefs
+          disabled={oncogenicity === ''}
+          disabledMessage={'Not curatable: mutation summary is only curatable when oncogenicity is specified.'}
+        />
         <Collapsible
           idPrefix={`${mutationName}-mutation-effect`}
           title="Mutation Effect"
@@ -369,6 +433,10 @@ const MutationCollapsible = ({
                     }
                   </>
                 }
+                /** Radio a bit tricky. Have to use onMouseDown event to cancel the default event.
+                 * The onclick event does not like to be overwritten **/
+                onMouseDown={oncogenicityRadioOnClick}
+                labelOnClick={oncogenicityRadioOnClick}
                 isRadio
                 options={[...ONCOGENICITY_OPTIONS, RADIO_OPTION_NONE].map(label => ({
                   label,
@@ -598,6 +666,12 @@ const MutationCollapsible = ({
           }}
         />
       ) : undefined}
+      <SimpleConfirmModal
+        show={showSimpleConfirmModal}
+        body={simpleConfirmModalBody}
+        onConfirm={simpleConfirmModalOnConfirm}
+        onCancel={() => setShowSimpleConfirmModal(false)}
+      />
     </>
   );
 };
@@ -623,6 +697,7 @@ const mapStoreToProps = ({
   firebaseDb: firebaseAppStore.firebaseDb,
   annotatedAltsCache: curationPageStore.annotatedAltsCache,
   genomicIndicators: firebaseGenomicIndicatorsStore.data,
+  handleFirebaseUpdate: firebaseGeneService.updateObject,
 });
 
 type StoreProps = Partial<ReturnType<typeof mapStoreToProps>>;

diff --git a/src/main/webapp/app/pages/curation/collapsible/styles.module.scss b/src/main/webapp/app/pages/curation/collapsible/styles.module.scss
@@ -40,6 +40,7 @@
 
 .collapsibleTitleWrapper {
   display: flex;
+  word-break: break-word;
   align-items: center;
   :hover {
     cursor: pointer;

diff --git a/src/main/webapp/app/pages/curation/header/MutationsSectionHeader.tsx b/src/main/webapp/app/pages/curation/header/MutationsSectionHeader.tsx
@@ -46,6 +46,7 @@ export enum SortOptions {
   LAST_MODIFIED = 'Last Modified',
   POSITION_INCREASING = 'Position Increasing',
   POSITION_DECREASING = 'Position Decreasing',
+  FIREBASE = 'Firebase',
 }
 
 const YES = 'Yes';