Update .env.example with latest settings

.env.example

@@ -1,15 +1,59 @@
-NEXTAUTH_SECRET=dAbxJF2DRzqwGYn+BWKdj8o9ieMri4FWsmIRn77r2F8=
+# Please modify the following environment variables accordingly.
+
+CTIMS_ENV=development
+CTIMS_API_VERSION=2.1
+
+
+#DATABASE_URL=mysql://ctims:ctims@localhost:3306/ctims
+#AES 256 key, it can be generated using https://cloak.47ng.com/key
+#Random example key given here. Please replace this key for your install.
+#PRISMA_FIELD_ENCRYPTION_KEY=k1.aesgcm256.wPyWsb8gQ2Xn-UgiaOQRqs3nb4FWIYR01DDihQgeqBg=
+
+# command to create a new secret - openssl rand -base64 32
+# NEXTAUTH Secret is used to encrypt the NextAuth.js JWT
+#Example value QG0ip+EjLW4j9BNlXPcC5kXjXcEAW/cYP1mbZKLP1q8=
+NEXTAUTH_SECRET=secret
 REACT_APP_API_URL=http://localhost:3333/api
 NEXTAUTH_URL=http://localhost:3000
-NEXT_AUTH_API_URL=http://backend:3333/api
+NEXTAUTH_API_URL=http://backend:3333/api
+NEXT_PUBLIC_SIGNOUT_REDIRECT_URL=http://localhost:3000
+NEXT_PUBLIC_TRIAL_LOCK_PING_TIME_MS=240000
+NEXT_TRIAL_LOCK_CLEAR_TIME_MS=300000
+
+
+#keycloak settings
 KEYCLOAK_URL=<KEYCLOAK_URL>
 KEYCLOAK_CLIENT_ID=<client_id>
+# Keycloak client uuid. This is different from the id above.
+# If you cannot find it in the client settings, the URL usually includes it. Example: http://localhost:8080/admin/master/console/#/ctims/clients/3813811a-***/settings, 3813811a-*** is the uuid
 KEYCLOAK_CLIENT_UUID=<uuid>
+# We suggest creating a new realm instead of using the default master realm.
 KEYCLOAK_REALM=<realm>
+# This is the client secret that stored under the Credentials tab in the client page.
+# The realm needs to have client authentication enabled to see the Credentials tab.
 KEYCLOAK_CLIENT_SECRET=<client_secret>
-KEYCLOAK_ADMIN_CLIENT_ID=ctims-admin # a client with sevice account enabled
+# a client with sevice account enabled
+# It does not need to be a separate client. If your above client already has service account enabled, use the same ID here.
+KEYCLOAK_ADMIN_CLIENT_ID=ctims-admin 
 KEYCLOAK_ADMIN_CLIENT_SECRET=<secret>
-KEYCLOAK_TOKEN_ENDPOINT=https://cbioportal.pmgenomics.ca/newauth/realms/UHN/protocol/openid-connect/token
-NEXT_PUBLIC_ENABLE_MATCHMINER_INTEGRATION=true
-NEXT_PUBLIC_TRIAL_LOCK_PING_TIME_MS=240000
-NEXT_TRIAL_LOCK_CLEAR_TIME_MS=300000
+# This is the endpoint to get access token.
+KEYCLOAK_TOKEN_ENDPOINT=
+
+#matchminer settings - only if matchminer integration is enabled
+NEXT_PUBLIC_ENABLE_MATCHMINER_INTEGRATION = true
+MM_API_URL=<matchminer-api-url>/api
+MM_API_TOKEN=
+
+#Rabbitmq settings for MatchMiner communication
+RABBITMQ_URL=rabbitmq
+RABBITMQ_PORT=5672
+MATCHMINER_SEND_QUEUE=run_match
+MATCHMINER_RECEIVE_QUEUE=match_message
+
+# email notification settings
+#example Host name gmail.com
+MAIL_HOST=<hostname>
+MAIL_USERNAME=<userid>
+MAIL_PASSWORD=<leave_blank>
+CTIMS_SUPPORT_EMAIL=<ctims_support_email>
+CTIMS_URL=<ctims_website_url>

.gitignore

@@ -19,6 +19,8 @@
 *.sublime-workspace
 apps/api/.env
 apps/web/.env
+apps/api/prisma/.env
+.env
 
 # IDE - VSCode
 .vscode/*

Dockerfile

@@ -42,9 +42,6 @@ COPY --from=build /app/dist/apps/web .
 RUN rm -rf /var/www/html/.next/cache
 RUN sh -c 'echo "[]" > /var/www/html/.next/server/next-font-manifest.json'
 
-ENV NEXTAUTH_SECRET=dAbxJF2DRzqwGYn+BWKdj8o9ieMri4FWsmIRn77r2F8=
-ENV REACT_APP_API_URL=http://backend:3333/api
-ENV NEXTAUTH_URL=http://localhost:3000
 
 RUN yarn install --production
 

apps/api/prisma/seed/index.js

@@ -42,7 +42,7 @@ main().then(() => {
 async function fetchHgncData() {
   try {
     const response = await get(
-      'https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/json/hgnc_complete_set.json'
+      'http://storage.googleapis.com/public-download-files/hgnc/json/json/hgnc_complete_set.json'
     );
     if (response.status != 200) {
       throw new Error('Failed to fetch data');
@@ -63,7 +63,7 @@ async function saveGenes(data) {
         hugoSymbol: x.symbol,
       };
     });
-    
+
     await prisma.gene.createMany({
       data: genesData,
       skipDuplicates: true,

apps/api/src/app/trial/trial.service.ts

@@ -134,9 +134,9 @@ export class TrialService implements OnModuleInit {
         where: { id: existing_trial.id },
         data: {
           status,
-          principal_investigator,
-          nickname,
-          nct_id,
+          principal_investigator: principal_investigator === undefined? null : principal_investigator,
+          nickname: nickname === undefined? null : nickname,
+          nct_id: nct_id === undefined? null : nct_id,
           ctml_schemas: {
             connect: {
               version: ctml_schema_version

apps/web/components/editor/EditorTopBar.tsx

@@ -18,9 +18,9 @@ import useHandleSignOut from "../../hooks/useHandleSignOut";
 import useUpdateTrialLock from "../../hooks/useUpdateTrialLock";
 
 interface EditorTopBarProps {
-    title?: string;
-    lastSaved: string;
-    setLastSaved: any;
+  title?: string;
+  lastSaved: string;
+  setLastSaved: any;
 }
 
 const EditorTopBar = (props: EditorTopBarProps) => {
@@ -264,7 +264,7 @@ const EditorTopBar = (props: EditorTopBarProps) => {
     <>
       <Toast ref={toast} position="top-center" />
       <ConfirmDialog visible={isConfirmationDialogVisible} onHide={() => setIsConfirmationDialogVisible(false)} message="Are you sure you want to leave this page? Unsaved inputs will be lost."
-          header="Confirmation" acceptLabel="Discard" rejectLabel="Cancel" accept={accept} reject={reject}
+                     header="Confirmation" acceptLabel="Discard" rejectLabel="Cancel" accept={accept} reject={reject}
       />
       <ExportCtmlDialog
         isDialogVisible={isDialogVisible}
@@ -276,33 +276,37 @@ const EditorTopBar = (props: EditorTopBarProps) => {
         sendCtmlClicked={onSendClick}
         onCTMLDialogHide={() => setIsSendDialogVisible(false)}
         onIsOKClicked={handleSendCTMLOKClicked}/>
-    <div className={styles.topBar}>
-      <div className={styles.logoContainer}>
-        <img src={'/assets/ctims-logo.svg'} alt={'logo'} className={styles.logo}/>
-      </div>
-      <div className={styles.nav}>
-        <div className={styles.btnTitleContainer}>
-          <div className={styles.backBtn} onClick={(e) => backClick(e)}>
-            <i className="pi pi-arrow-left"></i>
-          </div>
-          <div className={styles.title}>{props.title ? props.title : "New CTML"}</div>
+      <div className={styles.topBar}>
+        <div className={styles.logoContainer}>
+          <img src={'/assets/ctims-logo.svg'} alt={'logo'} className={styles.logo}/>
         </div>
-        <div className={styles.lastsaved}>Last saved: {props.lastSaved}</div>
-        <div className={styles.menuBtnGroup}>
-          {/*<Button label="Discard" className="p-button-text p-button-plain" />*/}
-          <Button label={isGroupAdmin ? 'Export' : 'Validate'}
-                  onClick={onExportClick}
-                  className="p-button-text p-button-plain" />
-          <>
+        <div className={styles.nav}>
+          <div className={styles.btnTitleContainer}>
+            <div className={styles.backBtn} onClick={(e) => backClick(e)}>
+              <i className="pi pi-arrow-left"></i>
+            </div>
+            <div className={styles.title}>{props.title ? props.title : "New CTML"}</div>
+          </div>
+          <div className={styles.lastsaved}>Last saved: {props.lastSaved}</div>
+          <div className={styles.menuBtnGroup}>
+            {/*<Button label="Discard" className="p-button-text p-button-plain" />*/}
             {isGroupAdmin &&
-              <Button disabled={isFormDisabled} label="Send CTML to Matcher" className={styles.saveBtn} onClick={onSendClick} />
+              <Button
+                label="Export"
+                onClick={onExportClick}
+                className="p-button-text p-button-plain"
+              />
             }
-          </>
-          <Button disabled={isFormDisabled} label="Save" className={styles.saveBtn} onClick={onSaveClick} />
-        </div>
+            <>
+              {isGroupAdmin &&
+                <Button disabled={isFormDisabled} label="Send CTML to Matcher" className={styles.saveBtn} onClick={onSendClick} />
+              }
+            </>
+            <Button disabled={isFormDisabled} label="Save" className={styles.saveBtn} onClick={onSaveClick} />
+          </div>
 
+        </div>
       </div>
-    </div>
     </>
   )
 }

apps/web/components/trials/Results.module.scss

@@ -4,6 +4,9 @@
   width: 100%;
   box-shadow: 0px 1px 4px rgba(0, 0, 0, 0.25);
   border-radius: 8px;
+  overflow: hidden;
+
+
 }
 
 .titleText {

apps/web/components/trials/Results.tsx

@@ -4,9 +4,10 @@ import useGetMatchResults from '../../hooks/useGetMatchResults';
 import useDownloadResults from '../../hooks/useDownloadResults';
 import { classNames } from 'primereact/utils';
 import styles from './Results.module.scss';
-import { DataTable } from 'primereact/datatable';
+import {DataTable, DataTableSortMeta} from 'primereact/datatable';
 import { Column } from 'primereact/column';
 import { CSVLink } from "react-csv";
+import {MULTI_SORT_META_RESULTS} from "../../constants/appConstants";
 import {TrialStatusEnum} from "../../../../libs/types/src/trial-status.enum";
 import { setIsLongOperation } from 'apps/web/store/slices/contextSlice';
 import { useDispatch } from 'react-redux';
@@ -48,6 +49,10 @@ const Results = (props: {trials: [], getTrialsForUsersInGroupLoading: boolean})
   useEffect(() => {
     if (getMatchResultsResponse) {
       const processedData = postProcess(getMatchResultsResponse);
+
+      // Sort by 'updatedAt' in descending order BEFORE rendering
+      processedData.sort((a, b) => new Date(b.updatedAt).getTime() - new Date(a.updatedAt).getTime());
+
       setResults(processedData);
     }
   }, [getMatchResultsResponse])
@@ -75,6 +80,10 @@ const Results = (props: {trials: [], getTrialsForUsersInGroupLoading: boolean})
   // result download file name
   const [resultFileName, setResultFileName] = useState<string>('');
 
+
+  const DEFAULT_SORT: DataTableSortMeta[] = [{ field: 'updatedAt', order: -1 }];
+  const [multiSortMeta, setMultiSortMeta] = useState<DataTableSortMeta[]>(DEFAULT_SORT);
+
   const headers = [
     {label: "Trial Id", key: "trialId"},
     {label: "Nickname", key: "nickname"},
@@ -114,6 +123,43 @@ const Results = (props: {trials: [], getTrialsForUsersInGroupLoading: boolean})
   // don't have global const state for csvLink as it can be null as component is mounted/unmounted when datatable is changed
   let csvLink: React.MutableRefObject<any> = useRef(null);
 
+  const onSort = (event: any) => {
+    if (event.multiSortMeta?.length) {
+      setMultiSortMeta(event.multiSortMeta);
+      sessionStorage.setItem(MULTI_SORT_META_RESULTS, JSON.stringify(event.multiSortMeta));
+    } else {
+      setMultiSortMeta(DEFAULT_SORT);
+      sessionStorage.removeItem(MULTI_SORT_META_RESULTS);
+    }
+  };
+
+  // Restore sorting when the component mounts
+  useEffect(() => {
+    const savedSortMeta = sessionStorage.getItem(MULTI_SORT_META_RESULTS);
+    if (savedSortMeta) {
+      setMultiSortMeta(JSON.parse(savedSortMeta));
+    }
+  }, []);
+
+  const extractDateTime = (dateStr) => {
+    if (!dateStr || typeof dateStr !== 'string') {
+      return ''; // Return an empty string to prevent crashes
+    }
+
+    // Extract date and time before "by" in the string
+    const match = dateStr.match(/(.*?)(?=\s+by\s+|$)/);
+    return match ? match[1] : dateStr;
+  };
+
+  const customDateSort = (event) => {
+    const { data, order, field } = event;
+    return [...data].sort((a, b) => {
+      const dateA = new Date(extractDateTime(a[field])).getTime();
+      const dateB = new Date(extractDateTime(b[field])).getTime();
+      return order * (dateA - dateB);
+    });
+  };
+
   const downloadBodyTemplate = (rowData) => {
     // set the ref in body template so we know it's mounted
     csvLink = React.useRef<CSVLink & HTMLAnchorElement & { link: HTMLAnchorElement }>();
@@ -183,20 +229,36 @@ const Results = (props: {trials: [], getTrialsForUsersInGroupLoading: boolean})
         <span className={styles.titleText}>Match Results</span>
 
         <div className={styles.tableContainer}>
-          <DataTable value={results} rowHover={true}
+          <DataTable value={results} rowHover={true} paginator rows={10}
+                     rowsPerPageOptions={[5, 10, 25, 50]}
                      loading={props.getTrialsForUsersInGroupLoading || getMatchResultsLoading}
-                     sortField="createdOn" sortOrder={-1}
                      emptyMessage={'No match results.'}
+                     sortMode="multiple"
+                     multiSortMeta={multiSortMeta}
+                     onSort={onSort}
+                     removableSort
+                     sortField="updatedAt"  // Force 'Modified on' column to sort
+                     defaultSortOrder={-1}  // Enforce descending order
           >
-            <Column field="trialId" header="ID"></Column>
-            <Column field="nickname" header="Nickname"></Column>
-            <Column field="principal_investigator" header="Principal Investigator"></Column>
-            <Column field="createdAt" header="Created on" dataType="date"></Column>
-            <Column field="updatedAt" header="Modified on" dataType="date"></Column>
-            <Column field="trialStatus" header="Match Status" sortable></Column>
-            <Column field="trialRetCount" header="Match Results"></Column>
-            <Column field="matchSentDate" header="Last Matched" dataType="date"></Column>
-            <Column field="matchedDate" header="Last New Result" dataType="date"></Column>
+            <Column field="trialId" header="ID" sortable></Column>
+            <Column field="nickname" header="Nickname" sortable></Column>
+            <Column field="principal_investigator" header="Principal Investigator" sortable></Column>
+            <Column
+              field="createdAt"
+              header="Created on"
+              sortable
+              sortFunction={customDateSort}
+            />
+            <Column
+              field="updatedAt"
+              header="Modified on"
+              sortable
+              sortFunction={customDateSort}
+            />
+            <Column field="trialStatus" header="Match Status" sortable ></Column>
+            <Column field="trialRetCount" header="Match Results" sortable></Column>
+            <Column field="matchSentDate" header="Last Matched" dataType="date" sortable></Column>
+            <Column field="matchedDate" header="Last New Result" dataType="date" sortable></Column>
             <Column field="download" header="Download" dataType="boolean" style={{minWidth: '6rem'}}
                     body={downloadBodyTemplate}></Column>
           </DataTable>
@@ -205,4 +267,5 @@ const Results = (props: {trials: [], getTrialsForUsersInGroupLoading: boolean})
     </>
   )
 }
+
 export default Results;

apps/web/components/trials/Trials.module.scss

@@ -46,6 +46,8 @@
   width: 100%;
   box-shadow: 0px 1px 4px rgba(0, 0, 0, 0.25);
   border-radius: 8px;
+  overflow: hidden; // Add this to contain the table
+
 }
 
 .trailsEllipseBtn {