Merge branch 'develop' into feat/DEVSU-2213-CD8T-score-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

@@ -162,8 +162,6 @@ const TumourSummaryEdit = ({
 
       if (reportDirty && newReportData) {
         apiCalls.push(api.put(`/reports/${report.ident}`, newReportData, {}));
-      } else {
-        apiCalls.push({ request: () => null });
       }
 
       if (tCellCd8Dirty && newTCellCd8Data) {
@@ -180,17 +178,20 @@ const TumourSummaryEdit = ({
         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);
@@ -462,8 +463,8 @@ const TumourSummaryEdit = ({
         fullWidth
         type="number"
       />
-    </>
-  ), [newTmburMutData, handleTmburChange]);
+    </>;
+  ), [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 = {

app/context/ResourceContext/index.tsx

@@ -1,10 +1,10 @@
 import React, {
-  createContext, ReactChild, useContext, useState, useEffect, useMemo,
+  createContext, ReactChild, useState, useEffect, useMemo, useContext,
 } from 'react';
-import SecurityContext from '@/context/SecurityContext';
-
 import { checkAccess, ALL_ROLES } from '@/utils/checkAccess';
+import useSecurity from '@/hooks/useSecurity';
 import ResourceContextType from './types';
+import ReportContext from '../ReportContext';
 
 const GERMLINE_ACCESS = ['admin', 'analyst', 'bioinformatician', 'projects', 'manager'];
 const GERMLINE_BLOCK = ALL_ROLES;
@@ -13,42 +13,57 @@ const REPORTS_BLOCK = [];
 const ADMIN_ACCESS = ['admin'];
 const ADMIN_BLOCK = ALL_ROLES;
 
-type UseResourcesReturnType = {
-  germlineAccess: boolean;
-  reportsAccess: boolean;
-  adminAccess: boolean;
-  reportSettingAccess: boolean;
-};
-
-const useResources = (): UseResourcesReturnType => {
-  const { userDetails } = useContext(SecurityContext);
+const useResources = (): ResourceContextType => {
+  const { userDetails: { groups, ident: userIdent } } = useSecurity();
+  const { report } = useContext(ReportContext);
 
   const [germlineAccess, setGermlineAccess] = useState(false);
   const [reportsAccess, setReportsAccess] = useState(false);
+  const [reportEditAccess, setReportEditAccess] = useState(false);
   const [adminAccess, setAdminAccess] = useState(false);
   const [reportSettingAccess, setReportSettingAccess] = useState(false);
 
+  // Check user group first to see which resources they can access
   useEffect(() => {
-    if (userDetails?.groups) {
-      if (checkAccess(userDetails.groups, GERMLINE_ACCESS, GERMLINE_BLOCK)) {
+    if (groups) {
+      if (checkAccess(groups, GERMLINE_ACCESS, GERMLINE_BLOCK)) {
         setGermlineAccess(true);
       }
 
-      if (checkAccess(userDetails.groups, REPORTS_ACCESS, REPORTS_BLOCK)) {
+      if (checkAccess(groups, REPORTS_ACCESS, REPORTS_BLOCK)) {
         setReportsAccess(true);
       }
 
-      if (checkAccess(userDetails.groups, ADMIN_ACCESS, ADMIN_BLOCK)) {
+      if (checkAccess(groups, ADMIN_ACCESS, ADMIN_BLOCK)) {
         setAdminAccess(true);
       }
-      if (checkAccess(userDetails.groups, [...ADMIN_ACCESS, 'manager'], ADMIN_BLOCK)) {
+
+      if (checkAccess(groups, [...ADMIN_ACCESS, 'manager'], ADMIN_BLOCK)) {
         setReportSettingAccess(true);
+        setReportEditAccess(true);
+      }
+    }
+  }, [groups]);
+
+  /**
+   * Check report specific permissions if user isn't admin
+   */
+  useEffect(() => {
+    if (!adminAccess) {
+      if (report && report.users.some(({ ident: i }) => i === userIdent)) {
+        setReportEditAccess(true);
+      } else {
+        setReportEditAccess(false);
       }
     }
-  }, [userDetails?.groups]);
+  }, [report, userIdent, adminAccess]);
 
   return {
-    germlineAccess, reportsAccess, adminAccess, reportSettingAccess,
+    germlineAccess,
+    reportsAccess,
+    adminAccess,
+    reportSettingAccess,
+    reportEditAccess,
   };
 };
 
@@ -57,6 +72,7 @@ const ResourceContext = createContext<ResourceContextType>({
   reportsAccess: false,
   adminAccess: false,
   reportSettingAccess: false,
+  reportEditAccess: false,
 });
 
 type ResourceContextProviderProps = {
@@ -65,19 +81,21 @@ type ResourceContextProviderProps = {
 
 const ResourceContextProvider = ({ children }: ResourceContextProviderProps): JSX.Element => {
   const {
-    germlineAccess, reportsAccess, adminAccess, reportSettingAccess,
+    germlineAccess, reportsAccess, adminAccess, reportSettingAccess, reportEditAccess,
   } = useResources();
 
   const providerValue = useMemo(() => ({
     germlineAccess,
     reportsAccess,
     adminAccess,
     reportSettingAccess,
+    reportEditAccess,
   }), [
     germlineAccess,
     reportsAccess,
     adminAccess,
     reportSettingAccess,
+    reportEditAccess,
   ]);
 
   return (

app/context/ResourceContext/types.d.ts

@@ -3,6 +3,7 @@ type ResourceContextType = {
   reportsAccess: boolean;
   adminAccess: boolean;
   reportSettingAccess: boolean;
+  reportEditAccess: boolean;
 };
 
 export default ResourceContextType;

app/context/SecurityContext/index.js

@@ -0,0 +1,23 @@
+import { UserType } from '@/common';
+import React from 'react';
+
+type SecurityContextType = {
+  authorizationToken: string;
+  setAuthorizationToken: (token: string) => void;
+  userDetails: Partial<UserType>;
+  setUserDetails: (userDetails: UserType) => void;
+};
+
+const SecurityContext = React.createContext<SecurityContextType>({
+  authorizationToken: '',
+  setAuthorizationToken: () => {},
+  userDetails: {},
+  setUserDetails: () => {},
+});
+
+export default SecurityContext;
+
+export {
+  SecurityContextType,
+  SecurityContext,
+};

app/context/SecurityContext/index.tsx

@@ -1,7 +1,7 @@
 import React, {
   createContext, ReactChild, useMemo, useContext,
 } from 'react';
-import SecurityContext from '@/context/SecurityContext';
+import useSecurity from '@/hooks/useSecurity';
 import { checkAccess } from '@/utils/checkAccess';
 import UserContextInterface from './interfaces';
 
@@ -18,7 +18,7 @@ type UserContextProviderProps = {
 };
 
 const UserContextProvider = ({ children }: UserContextProviderProps): JSX.Element => {
-  const { userDetails } = useContext(SecurityContext);
+  const { userDetails } = useSecurity();
 
   const canEdit = useMemo(() => {
     if (userDetails && checkAccess(userDetails.groups, EDIT_ACCESS, EDIT_BLOCK)) {