Merge pull request #129 from pughlab/qa

Qa

Dockerfile

@@ -21,12 +21,14 @@ ARG NEXTAUTH_SECRET
 ARG REACT_APP_API_URL
 ARG NEXTAUTH_URL
 ARG NEXTAUTH_API_URL
+ARG NEXT_PUBLIC_SIGNOUT_REDIRECT_URL
 
 ENV NODE_ENV=production
 ENV NEXTAUTH_SECRET=$NEXTAUTH_SECRET
 ENV REACT_APP_API_URL=$REACT_APP_API_URL
 ENV NEXTAUTH_URL=$NEXTAUTH_URL
 ENV NEXTAUTH_API_URL=$NEXTAUTH_API_URL
+ENV NEXT_PUBLIC_SIGNOUT_REDIRECT_URL=$NEXT_PUBLIC_SIGNOUT_REDIRECT_URL
 
 #RUN npx nx run-many --target=build --all
 RUN npx nx build web

apps/api/.env.example

@@ -25,3 +25,4 @@ KEYCLOAK_TOKEN_ENDPOINT=https://cbioportal.pmgenomics.ca/newauth/realms/UHN/prot
 MM_API_URL=<matchminer-api-url>/api
 PRISMA_FIELD_ENCRYPTION_KEY=<prisma_field_encryption_key>
 CTIMS_ENV=production | development
+CTIMS_API_VERSION=2.1

apps/api/Dockerfile

@@ -36,6 +36,7 @@ ARG PRISMA_FIELD_ENCRYPTION_KEY
 ARG MM_API_URL
 ARG CTIMS_ENV
 ARG MM_API_TOKEN
+ARG CTIMS_API_VERSION
 
 ENV KEYCLOAK_REALM=$KEYCLOAK_REALM
 ENV KEYCLOAK_URL=$KEYCLOAK_URL
@@ -49,6 +50,7 @@ ENV PRISMA_FIELD_ENCRYPTION_KEY=$PRISMA_FIELD_ENCRYPTION_KEY
 ENV MM_API_URL=$MM_API_URL
 ENV CTIMS_ENV=$CTIMS_ENV
 ENV MM_API_TOKEN=$MM_API_TOKEN
+ENV CTIMS_API_VERSION=$CTIMS_API_VERSION
 
 RUN yarn generate:build
 #RUN yarn start:prod

apps/api/src/app/app.module.ts

@@ -10,6 +10,7 @@ import { UserModule } from './user/user.module';
 import {AuthModule} from "./auth/auth.module";
 import { EventModule } from "./event/event.module";
 import { MatchminerModule } from './matchminer/matchminer.module';
+import { InfoModule } from './info/info.module';
 
 @Global()
 @Module({
@@ -21,6 +22,7 @@ import { MatchminerModule } from './matchminer/matchminer.module';
     UserModule,
     MatchminerModule,
     EventModule,
+    InfoModule,
   ],
   controllers: [AppController],
   providers: [AppService, PrismaService],

apps/api/src/app/info/info.controller.ts

@@ -0,0 +1,20 @@
+import { Controller, Get } from '@nestjs/common';
+import { InfoService } from './info.service';
+import { ApiOperation, ApiTags } from '@nestjs/swagger';
+
+
+@Controller('info')
+@ApiTags('info')
+export class InfoController {
+
+  constructor(private infoService: InfoService) {
+
+  }
+
+  @Get()
+  @ApiOperation({summary: "Get app info"})
+  getAppInfo() {
+    return this.infoService.getAppInfo();
+  }
+
+}

apps/api/src/app/info/info.module.ts

@@ -0,0 +1,9 @@
+import { Module } from '@nestjs/common';
+import { InfoService } from './info.service';
+import { InfoController } from './info.controller';
+
+@Module({
+  controllers: [InfoController],
+  providers: [InfoService],
+})
+export class InfoModule {}

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

@@ -0,0 +1,16 @@
+import { Injectable, Logger } from '@nestjs/common';
+
+@Injectable()
+export class InfoService {
+
+    private CTIMS_API_VERSION = process.env.CTIMS_API_VERSION;
+
+    private readonly logger = new Logger(InfoService.name, { timestamp: true });
+
+    getAppInfo() {
+        let info = {
+            'version': this.CTIMS_API_VERSION,
+        }
+        return info;
+    }
+}

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

@@ -122,7 +122,8 @@ export class TrialService implements OnModuleInit {
               }
             }
           },
-          protocol_no: (typeof protocol_no === 'string') ? protocol_no : protocol_no.toString()
+          protocol_no: protocol_no === undefined ? '' :
+            (typeof protocol_no !== 'string' ? protocol_no.toString() : protocol_no)
         }
       });
 
@@ -164,7 +165,7 @@ export class TrialService implements OnModuleInit {
             }
           }
         },
-        protocol_no: (typeof protocol_no === 'string') ? protocol_no : protocol_no.toString()
+        protocol_no: (typeof protocol_no === 'string') ? protocol_no : protocol_no?.toString()
       },
     });
 

apps/web/.env.local.example

@@ -2,3 +2,4 @@ NEXTAUTH_SECRET=dAbxJF2DRzqwGYn+BWKdj8o9ieMri4FWsmIRn77r2F8=
 REACT_APP_API_URL=http://localhost:3333/api
 NEXTAUTH_URL=http://localhost:3000
 NEXTAUTH_API_URL=http://localhost:3333/api
+NEXT_PUBLIC_SIGNOUT_REDIRECT_URL=http://localhost:3000

apps/web/components/Footer.module.scss

@@ -0,0 +1,19 @@
+.versionContainer {
+    display: flex;
+    flex-direction: column;
+    align-self: stretch;
+    position: relative;
+    left: 0;
+    right: 0;
+    bottom: 0;
+
+    color: var(--text-subdued, rgba(0, 0, 0, 0.60));
+    text-align: center;
+    font-family: 'Inter', sans-serif;
+    font-size: 12px;
+    font-style: normal;
+    font-weight: 400;
+    line-height: 16px; /* 133.333% */
+    margin-top: 20px;
+    margin-bottom: 20px;
+  }

apps/web/components/FooterComponent.tsx

@@ -0,0 +1,22 @@
+import { useEffect } from 'react';
+import useGetApiInfo from '../hooks/useGetApiInfo';
+import styles from "./Footer.module.scss"
+const FooterComponent = () => {
+
+  const { 
+    error: getApiInfoError,
+    response: getApiInfoResponse,
+    loading: getApiInfoLoading, 
+    operation: getApiInfoOperation
+  } = useGetApiInfo();
+
+  useEffect(() => {
+    getApiInfoOperation();
+  }, [])
+
+  return (
+    <div className={styles.versionContainer}>CTIMS version {getApiInfoResponse}</div>
+  );
+};
+
+export default FooterComponent;

apps/web/components/IdleComponent.tsx

@@ -3,6 +3,8 @@ import useIdle, { IdleState } from "../hooks/useIdle";
 import { Dialog } from 'primereact/dialog';
 import {useRouter} from "next/router";
 import useRefreshToken from "../hooks/useRefreshToken";
+import useSaveTrial from "../hooks/useSaveTrial";
+import {RootState, store} from "../store/store";
 
 const IdleComponent = () => {
   const { state: idleState, remaining, count } = useIdle(); // Get the idle state, remaining time, and count from the useIdle hook
@@ -11,6 +13,13 @@ const IdleComponent = () => {
 
   const { error, response, loading, refreshTokenOperation } = useRefreshToken(); // Get the error, response, loading, and refreshTokenOperation from the useRefreshToken hook
 
+  const {
+    response: saveTrialResponse,
+    error: saveTrialError,
+    loading: saveTrialLoading,
+    saveTrialOperation
+  } = useSaveTrial();
+
   const router = useRouter(); // Get the router object from the useRouter hook
 
   const IDLE_TIMEOUT = 60; // Set the idle timeout to 60 seconds
@@ -43,8 +52,14 @@ const IdleComponent = () => {
       if (interval) {
         clearInterval(interval); // Clear the interval
       }
-      localStorage.removeItem('ctims-accessToken') // Remove the access token from local storage
-      router.push('/'); // Redirect to the home page
+
+      // Auto save before timeout and logout
+      const currentState = store.getState();
+      const {trialModel, ctmlJson} = saveToServer(currentState)
+      saveTrialOperation(trialModel, ctmlJson).then(() => {
+        localStorage.removeItem('ctims-accessToken') // Remove the access token from local storage
+        router.push('/'); // Redirect to the home page
+      });
     }
 
     return () => {
@@ -55,6 +70,50 @@ const IdleComponent = () => {
     };
   }, [showDialog, remainingTime]); // Run the effect whenever the dialog visibility or remaining time changes
 
+  const saveToServer = (state: RootState) => {
+    const ctmlModel = state.finalModelAndErrors.ctmlModel;
+    if (!ctmlModel.trialInformation.trial_id) {
+      // @ts-ignore
+      toast.current.show({
+        severity:
+          'error',
+        summary: 'Error Saving',
+        detail: 'Trial ID is required',
+      });
+      return;
+    }
+
+    const getCtmlJsonOnly = () => {
+      let ctmlModelCopy;
+      const age_group = ctmlModel.age_group;
+      const trialInformation = ctmlModel.trialInformation;
+      ctmlModelCopy = {...ctmlModel, ...trialInformation, ...age_group};
+      delete ctmlModelCopy.age_group;
+      delete ctmlModelCopy.trialInformation;
+      delete ctmlModelCopy.ctml_status;
+      delete ctmlModelCopy.nickname;
+      return ctmlModelCopy;
+    }
+
+    const getTrialModelOnly = () => {
+      return {
+        nct_id: ctmlModel.trialInformation.trial_id,
+        nickname: ctmlModel.trialInformation.nickname,
+        principal_investigator: ctmlModel.trialInformation.principal_investigator,
+        status: ctmlModel.trialInformation.ctml_status,
+        protocol_no: ctmlModel.trialInformation.protocol_no,
+      }
+    }
+
+
+
+    const trialModel = getTrialModelOnly();
+    const ctmlJson = getCtmlJsonOnly();
+
+    return { trialModel, ctmlJson };
+
+  }
+
   return (
     <div>
       <Dialog data-testid="dialog" header="Idle Warning" visible={showDialog} onHide={onHide} closable={false}>

apps/web/components/Login.module.scss

@@ -369,6 +369,29 @@
 
     }
   }
+
+  .version {
+    display: flex;
+    flex-direction: column;
+    align-items: center;
+    padding: 0px;
+
+    position: absolute;
+    width: 1280px;
+    height: 18px;
+    left: 50%;
+    top: 95%;
+    transform: translate(-50%, -50%);
+
+
+    color: rgba(255, 255, 255, 0.65);
+    text-align: center;
+    font-family: 'Inter', sans-serif;
+    font-size: 12px;
+    font-style: normal;
+    font-weight: 400;
+    line-height: 16px; /* 133.333% */
+  }
 }
 
 

apps/web/components/Login.tsx

@@ -1,6 +1,6 @@
 import styles from './Login.module.scss';
 import { InputText } from "primereact/inputtext";
-import React, { useState, useRef } from "react";
+import React, { useState, useRef, useEffect } from "react";
 import {NextRouter, useRouter} from "next/router";
 import useHasMounted from "../hooks/useHasMounted";
 import Layout from "./Layout";
@@ -12,6 +12,7 @@ import {Password} from "primereact/password";
 import { Toast } from "primereact/toast";
 import { Dialog } from "primereact/dialog";
 import strings from "../data/strings.json";
+import useGetApiInfo from '../hooks/useGetApiInfo';
 
 const Login = () => {
   const hasMounted = useHasMounted();
@@ -28,6 +29,13 @@ const Login = () => {
 
   const [dialogVisible, setDialogVisible] = useState(false);
 
+  const { error, response, loading, operation} = useGetApiInfo();
+
+  useEffect(() => {
+    operation();
+  }, [])
+
+
   const componentStrings = strings.components.Login;
 
   const showDialog = () => {
@@ -139,9 +147,10 @@ const Login = () => {
               <Button label="Sign In" onClick={(e) => handleLogin(e)} />
             <div className={styles.forgotPassword} onClick={handleForgotPassword}>Forgot Password</div>
           </form>
-
         </div>
+
       </div>
+      <div className={styles.version}>CTIMS version {response}</div>
     </div>
     </Layout>
   );

apps/web/components/editor/ExportCtmlDialog.tsx

@@ -42,7 +42,9 @@ const ExportCtmlDialog = (props: ExportCtmlDialogProps) => {
     let errorObjList: RJSFValidationError[] = errorSchema.errors;
     const filteredErrorObjList = errorObjList.filter((errorObj: RJSFValidationError) => {
       return errorObj.message !== 'must be object';
-    })
+    }).filter((err_two: RJSFValidationError) => {
+      return err_two.property !== '.trialInformation.phase';
+    });
     if (!isObjectEmpty(errorSchema)) {
       const viewModelErrors = extractErrors(filteredErrorObjList);
       setErrors(viewModelErrors)

apps/web/components/trials/Results.tsx

@@ -90,6 +90,7 @@ const Results = () => {
     {label: "Left Partner Gene", key: "left_partner_gene"},
     {label: "Right Partner Gene", key: "right_partner_gene"},
     {label: "CNV Call", key: "cnv_call"},
+    {label: "MS Status", key: "ms_status"},
   ];
   // csv download link ref
   const csvLink = useRef()

apps/web/components/trials/TopBar.tsx

@@ -2,10 +2,13 @@ import {Menu} from "primereact/menu";
 import {useRef} from "react";
 import styles from './TopBar.module.scss';
 import {signOut, useSession} from "next-auth/react";
+import * as process from "process";
+import {useRouter} from "next/router";
 
 const TopBar = () => {
 
   const menu = useRef(null);
+  const router = useRouter();
 
   const {data} = useSession();
 
@@ -14,9 +17,12 @@ const TopBar = () => {
       label: 'Sign Out',
       icon: 'pi pi-sign-out',
       command: () => {
-        signOut({callbackUrl: '/', redirect: true}).then(() => {
+        // signOut({callbackUrl: '/', redirect: true}).then(() => {
+        signOut({redirect: false}).then(() => {
           localStorage.removeItem('ctims-accessToken');
+          router.push(process.env.NEXT_PUBLIC_SIGNOUT_REDIRECT_URL)
         });
+
       }
     }
   ]