Merge branch 'develop' into feat/DEVSU-2201-SV-burden-editable

Author: bnguyen-bcgsc

.eslintrc.js

@@ -1,39 +1,45 @@
 module.exports = {
-  "extends": [
-    "airbnb",
-    "airbnb-typescript",
-    "airbnb/hooks",
-    "plugin:@typescript-eslint/recommended"
+  extends: [
+    'airbnb',
+    'airbnb-typescript',
+    'airbnb/hooks',
+    'plugin:@typescript-eslint/recommended',
   ],
-  "env": {
-    "browser": true,
-    "es6": true,
-    "node": true
+  env: {
+    browser: true,
+    es6: true,
+    node: true,
   },
-  "parser": "@typescript-eslint/parser",
-  "parserOptions": {
-    "project": "./tsconfig.json"
+  parser: '@typescript-eslint/parser',
+  parserOptions: {
+    project: './tsconfig.json',
   },
-  "rules": {
-    "react/function-component-definition": "off",
-    "import/extensions": "off",
-    "react/jsx-props-no-spreading": "off",
-    "react/require-default-props": "off",
-    "import/prefer-default-export": "warn",
-    "max-len": "off",
-    "no-param-reassign": "warn",
-    "no-underscore-dangle": ["warn", { "allow": ["_env_"] }],
-    "no-restricted-syntax": [
-      "error",
-      "ForInStatement",
-      "LabeledStatement",
-      "WithStatement"
+  rules: {
+    'react/function-component-definition': 'off',
+    'import/extensions': 'off',
+    'react/jsx-props-no-spreading': 'off',
+    'react/require-default-props': 'off',
+    'import/prefer-default-export': 'warn',
+    'max-len': 'off',
+    'no-param-reassign': 'warn',
+    'no-underscore-dangle': ['warn', { allow: ['_env_'] }],
+    'no-restricted-syntax': [
+      'error',
+      'ForInStatement',
+      'LabeledStatement',
+      'WithStatement',
     ],
-    "prefer-destructuring": ["error", { "object": true, "array": true }],
+    'prefer-destructuring': ['error', { object: true, array: true }],
   },
-  "settings": {
-    "import/resolver": {
-      typescript: {}
+  settings: {
+    'import/resolver': {
+      typescript: {},
     },
   },
-}
+  overrides: [
+    {
+      extends: ['plugin:@typescript-eslint/disable-type-checked'],
+      files: ['./*.js'],
+    },
+  ],
+};

.github/workflows/clininfoonrelease.yml

@@ -0,0 +1,31 @@
+name: Create JIRA ticket on release PR creation
+
+on:
+  pull_request:
+    types: [opened]
+    branches:
+      - master
+
+jobs:
+  create_ticket:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v4
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v3
+        with:
+          node-version: 20
+
+      - name: Run script
+        run: node ./create-jira-ticket.js
+        env:
+          JIRA_PROJECT_NAME: ${{ vars.JIRA_PROJECT_NAME }}
+          JIRA_ISSUE_TYPE: ${{ vars.JIRA_ISSUE_TYPE }}
+          JIRA_BASE_URL: ${{ vars.JIRA_BASE_URL }}
+          JIRA_PORT: ${{ vars.JIRA_PORT }}
+          JIRA_API_TOKEN: ${{ secrets.JACLI_JIRA_TOKEN }}
+          PR_TITLE: ${{ github.event.pull_request.title }}
+          PR_DESCRIPTION: ${{ github.event.pull_request.body }}

app/components/AuthenticatedRoute/index.jsx

@@ -1,12 +1,12 @@
 /* eslint-disable react/display-name */
 import { PropTypes } from 'prop-types';
-import React, { useContext, useMemo } from 'react';
+import React, { useMemo } from 'react';
 import {
   Redirect,
   Route,
 } from 'react-router-dom';
 
-import SecurityContext from '@/context/SecurityContext';
+import useSecurity from '@/hooks/useSecurity';
 import useResource from '@/hooks/useResource';
 import { isAuthorized } from '@/services/management/auth';
 
@@ -16,7 +16,7 @@ import { isAuthorized } from '@/services/management/auth';
 const AuthenticatedRoute = ({
   component: Component, adminRequired, showNav, onToggleNav, ...rest
 }) => {
-  const { authorizationToken } = useContext(SecurityContext);
+  const { authorizationToken } = useSecurity();
   const { adminAccess } = useResource();
   const authOk = isAuthorized(authorizationToken);
 

app/components/IPRWYSIWYGEditor/index.tsx

@@ -186,7 +186,7 @@ const IPRWYSIWYGEditor = ({
 
   const handleOnSave = useCallback(() => {
     if (editor) {
-      onClose(editor.getHTML());
+      onClose(editor.isEmpty ? '' : editor.getHTML());
     }
   }, [editor, onClose]);
 

app/components/NavBar/index.tsx

@@ -12,14 +12,14 @@ import MenuIcon from '@mui/icons-material/Menu';
 import PersonIcon from '@mui/icons-material/Person';
 
 import { logout } from '@/services/management/auth';
-import SecurityContext from '@/context/SecurityContext';
+import useSecurity from '@/hooks/useSecurity';
 import SidebarContext from '@/context/SidebarContext';
 import FeedbackDialog from './components/FeedbackDialog';
 
 import './index.scss';
 
 const NavBar = (): JSX.Element => {
-  const { userDetails } = useContext(SecurityContext);
+  const { userDetails } = useSecurity();
   const { sidebarMaximized, setSidebarMaximized } = useContext(SidebarContext);
 
   const [anchorEl, setAnchorEl] = useState<HTMLElement | null>();

app/components/TumourSummaryEdit/index.tsx

@@ -140,25 +140,26 @@ const TumourSummaryEdit = ({
 
       if (reportDirty && newReportData) {
         apiCalls.push(api.put(`/reports/${report.ident}`, newReportData, {}));
-      } else {
-        apiCalls.push({ request: () => null });
       }
 
       if (mutationBurdenDirty && newMutationBurdenData) {
         if (mutationBurden?.ident) {
           apiCalls.push(api.put(`/reports/${report.ident}/mutation-burden/${mutationBurden.ident}`, newMutationBurdenData, {}));
         } else {
-          // Default role of new mutation burden data for reports with no existing analysis per ClinInfo team
-          apiCalls.push(api.post(`/reports/${report.ident}/mutation-burden`, { ...newMutationBurdenData, role: 'primary' }, {}));
+          apiCalls.push(api.post(
+            `/reports/${report.ident}/mutation-burden`,
+            { ...newMutationBurdenData, role: 'primary' },
+            {},
+          ));
         }
-      } else {
-        apiCalls.push({ request: () => null });
       }
 
-      if (tmburMutDirty && newTmburMutData && tmburMutBur?.ident) {
-        apiCalls.push(api.put(`/reports/${report.ident}/tmbur-mutation-burden`, newTmburMutData, {}));
-      } else {
-        apiCalls.push({ request: () => null });
+      if (tmburMutDirty && newTmburMutData) {
+        if (tmburMutBur?.ident) {
+          apiCalls.push(api.put(`/reports/${report.ident}/tmbur-mutation-burden`, newTmburMutData, {}));
+        } else {
+          apiCalls.push(api.post(`/reports/${report.ident}/tmbur-mutation-burden`, newTmburMutData, {}));
+        }
       }
 
       callSet = new ApiCallSet(apiCalls);
@@ -168,19 +169,33 @@ const TumourSummaryEdit = ({
         setIsApiCalling(false);
       } else {
         try {
-          const resp = await callSet.request();
-          const tmburMutResp = resp.pop();
-          const primaryBurdenResp = resp.pop();
-          const reportResp = resp.pop();
+          await callSet.request();
+
+          let microbialResp = null;
+          let tmburMutResp = null;
+          let mutationBurdenResp = null;
+          let reportResp = null;
 
           // Too complicated between delete/update/new, might as well grab updated micb species for report again
-          const microbialResp = await api.get(`/reports/${report.ident}/summary/microbial`).request();
+          if (microbialDirty) {
+            microbialResp = await api.get(`/reports/${report.ident}/summary/microbial`).request();
+          }
+          if (tmburMutDirty) {
+            tmburMutResp = await api.get(`/reports/${report.ident}/tmbur-mutation-burden`).request();
+          }
+          if (mutationBurdenDirty) {
+            mutationBurdenResp = await api.get(`/reports/${report.ident}/mutation-burden/`).request();
+          }
+          if (reportDirty) {
+            reportResp = await api.get(`/reports/${report.ident}`).request();
+          }
+
           snackbar.success('Successfully updated Tumour Summary');
           onClose(
             true,
             microbialDirty ? microbialResp : null,
             reportDirty ? reportResp : null,
-            mutationBurdenDirty ? primaryBurdenResp : null,
+            mutationBurdenDirty ? mutationBurdenResp.find((mb) => mb.role === 'primary') : null,
             tmburMutDirty ? tmburMutResp : null,
           );
         } catch (callSetError) {
@@ -365,31 +380,29 @@ const TumourSummaryEdit = ({
   }, [newMutationBurdenData, handleMutationBurdenChange]);
 
   const tmburMutBurSection = useMemo(() => {
-    return (
-      <>
-        <TextField
-          className="tumour-dialog__text-field"
-          label="genomeSnvTmb"
-          value={newTmburMutData?.genomeSnvTmb ?? null}
-          name="genomeSnvTmb"
-          onChange={handleTmburChange}
-          variant="outlined"
-          fullWidth
-          type="number"
-        />
-        <TextField
-          className="tumour-dialog__text-field"
-          label="genomeIndelTmb"
-          value={newTmburMutData?.genomeIndelTmb ?? null}
-          name="genomeIndelTmb"
-          onChange={handleTmburChange}
-          variant="outlined"
-          fullWidth
-          type="number"
-        />
-      </>
-    );
-  }, [newTmburMutData, handleTmburChange]);
+    <>
+      <TextField
+        className="tumour-dialog__text-field"
+        label="genomeSnvTmb"
+        value={newTmburMutData?.genomeSnvTmb ?? 0}
+        name="genomeSnvTmb"
+        onChange={handleTmburChange}
+        variant="outlined"
+        fullWidth
+        type="number"
+      />
+      <TextField
+        className="tumour-dialog__text-field"
+        label="genomeIndelTmb"
+        value={newTmburMutData?.genomeIndelTmb ?? 0}
+        name="genomeIndelTmb"
+        onChange={handleTmburChange}
+        variant="outlined"
+        fullWidth
+        type="number"
+      />
+    </>;
+  }, [newTmburMutData?.genomeSnvTmb, newTmburMutData?.genomeIndelTmb, handleTmburChange]);
 
   return (
     <Dialog open={isOpen}>

app/context/ReportContext/types.d.ts

@@ -55,6 +55,7 @@ type ReportType = {
   kbDiseaseMatch: string;
   m1m2Score: number;
   captiv8Score: number;
+  appendix?: string;
 } & RecordDefaults;
 
 type ReportContextType = {