Release/v6.7.0

IPR Client v6.7.0 Release Notes Bug - [DEVSU-1694] - Fixed AlertDialog onClose interaction Task - [DEVSU-1610] - Added tests to DataTable and its components - [DEVSU-1637] - Upgraded MUI to v5 - [DEVSU-1681] - Updated webpack to v5 Improvement - [DEVSU-1679] - make columns resizable in germline reports 'Reviews' table
bcgsc · Dec 15, 2021 · 8fadc8a · 8fadc8a
2 parents a08e27b + aac0ab6
commit 8fadc8a
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diff --git a/.babelrc b/.babelrc
@@ -1,12 +1,13 @@
 {
   "presets": [["@babel/preset-env", {
     "useBuiltIns": "usage",
-    "modules": false,
-    "corejs": 2
+    "modules": "auto",
+    "corejs": 3
   }],
   "@babel/preset-react",
   "@babel/preset-typescript"],
   "plugins": [
+    "@babel/plugin-proposal-optional-chaining",
     "@babel/plugin-syntax-dynamic-import"
   ],
   "env": {

diff --git a/.eslintrc.json b/.eslintrc.json
@@ -81,7 +81,7 @@
     "arrow-body-style": ["error", "as-needed"],
     "object-shorthand": ["error", "always"],
     "quote-props": ["error", "consistent"],
-    "no-underscore-dangle": ["warn"],
+    "no-underscore-dangle": ["warn", {"allow": ["_env_"]}],
     "no-param-reassign": "off",
     "no-restricted-globals": "warn",
     "no-alert": "off",

diff --git a/.github/workflows/npm-test.yml b/.github/workflows/npm-test.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        node: [10, 12, 14]
+        node: [12, 14, 16]
     name: node-${{ matrix.node }}
     steps:
       - uses: actions/checkout@v2

diff --git a/README.md b/README.md
@@ -1,6 +1,7 @@
 # Integrated Pipeline Reports (IPR) Client
 
-![Build Status](https://www.bcgsc.ca/bamboo/plugins/servlet/wittified/build-status/PORI-IPRCLI) ![build](https://github.com/bcgsc/pori_ipr_client/workflows/build/badge.svg?branch=master) ![node versions](https://img.shields.io/badge/node-12%20%7C%2014-blue)
+![Build Status](https://www.bcgsc.ca/bamboo/plugins/servlet/wittified/build-status/PORI-IPRCLI) ![build](https://github.com/bcgsc/pori_ipr_client/workflows/build/badge.svg?branch=master) ![node versions](https://img.shields.io/badge/node-12%20%7C%2014%20%7C%2016-blue) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5728424.svg)](https://doi.org/10.5281/zenodo.5728424)
+
 
 ## Table of Contents
 
@@ -67,4 +68,4 @@ A demo site is available at https://pori-demo.bcgsc.ca
 ## Contributing
 
 Contributions are welcome! Before doing so, please open an issue with the feature that would be added.
-In addition, make sure that the code that is being added is linted using the rules in our .eslintrc file.
+In addition, make sure that the code that is being added is linted using the rules in our .eslintrc file.
diff --git a/app/App.tsx b/app/App.tsx
@@ -2,33 +2,28 @@
  * @module /App
  */
 import { SnackbarProvider } from 'notistack';
-import CssBaseline from '@material-ui/core/CssBaseline';
-import {
-  createMuiTheme,
-  MuiThemeProvider,
-  createGenerateClassName,
-  jssPreset,
-  StylesProvider,
-} from '@material-ui/core/styles';
-import { create } from 'jss';
+import CssBaseline from '@mui/material/CssBaseline';
+import { createTheme, ThemeProvider, StyledEngineProvider } from '@mui/material/styles';
 import React from 'react';
-import { JssProvider } from 'react-jss';
 import { BrowserRouter } from 'react-router-dom';
+// eslint-disable-next-line import/no-extraneous-dependencies
 import { ModuleRegistry } from '@ag-grid-community/core';
 import { ClientSideRowModelModule } from '@ag-grid-community/client-side-row-model';
 import { CsvExportModule } from '@ag-grid-community/csv-export';
 
 import MainView from './views/MainView';
 import { SnackbarUtilsConfigurator } from './services/SnackbarUtils';
 import CacheBuster from './components/CacheBuster';
-import cssTheme from './styles/_theme.scss';
+import cssTheme from './styles/_theme.module.scss';
 
+// eslint-disable-next-line import/no-extraneous-dependencies
 import '@ag-grid-community/core/dist/styles/ag-grid.min.css';
+// eslint-disable-next-line import/no-extraneous-dependencies
 import '@ag-grid-community/core/dist/styles/ag-theme-material.min.css';
 import '@fontsource/roboto';
 import './styles/ag-grid.scss';
 
-const theme = createMuiTheme({
+const theme = createTheme({
   direction: 'ltr',
   palette: {
     primary: {
@@ -52,7 +47,6 @@ const theme = createMuiTheme({
     text: {
       primary: cssTheme.textPrimary,
       secondary: cssTheme.textSecondary,
-      hint: cssTheme.textHint,
       disabled: cssTheme.textDisabled,
     },
   },
@@ -67,38 +61,37 @@ const theme = createMuiTheme({
     h6: { fontSize: cssTheme.fontSizeH6 },
     subtitle1: { fontSize: cssTheme.fontSizeSubtitle1 },
   },
-  // Dialog title header bug: https://github.com/mui-org/material-ui/issues/16569
-  props: {
-    MuiDialogTitle: {
-      disableTypography: true,
+  components: {
+    MuiCssBaseline: {
+      styleOverrides: {
+        '@global': {
+          html: {
+            WebkitFontSmoothing: 'auto',
+          },
+        },
+      },
     },
-  },
-  overrides: {
     MuiDialogTitle: {
-      root: {
-        fontSize: cssTheme.fontSizeH3,
+      styleOverrides: {
+        root: {
+          fontSize: cssTheme.fontSizeH2,
+        },
       },
     },
-    MuiCssBaseline: {
-      '@global': {
-        html: {
-          WebkitFontSmoothing: 'auto',
-        },
+    MuiButton: {
+      defaultProps: {
+        color: 'inherit',
+      },
+    },
+    MuiTabs: {
+      defaultProps: {
+        indicatorColor: 'secondary',
+        textColor: 'secondary',
       },
     },
   },
 });
 
-const generateClassName = createGenerateClassName({
-  productionPrefix: 'ipr',
-});
-
-const jss = create({
-  ...jssPreset(),
-  // We define a custom insertion point that JSS will look for injecting the styles in the DOM.
-  insertionPoint: 'jss-insertion-point',
-});
-
 ModuleRegistry.registerModules([
   ClientSideRowModelModule,
   CsvExportModule,
@@ -116,21 +109,19 @@ const basename = window._env_.PUBLIC_PATH.endsWith('/') ? window._env_.PUBLIC_PA
  */
 function App() {
   return (
-    <StylesProvider generateClassName={generateClassName} injectFirst>
-      <JssProvider jss={jss}>
-        <MuiThemeProvider theme={theme}>
-          <SnackbarProvider anchorOrigin={{ vertical: 'bottom', horizontal: 'left' }}>
-            <SnackbarUtilsConfigurator />
-            <CssBaseline />
-            <BrowserRouter basename={basename}>
-              <CacheBuster>
-                <MainView />
-              </CacheBuster>
-            </BrowserRouter>
-          </SnackbarProvider>
-        </MuiThemeProvider>
-      </JssProvider>
-    </StylesProvider>
+    <StyledEngineProvider injectFirst>
+      <ThemeProvider theme={theme}>
+        <SnackbarProvider anchorOrigin={{ vertical: 'bottom', horizontal: 'left' }}>
+          <SnackbarUtilsConfigurator />
+          <CssBaseline />
+          <BrowserRouter basename={basename}>
+            <CacheBuster>
+              <MainView />
+            </CacheBuster>
+          </BrowserRouter>
+        </SnackbarProvider>
+      </ThemeProvider>
+    </StyledEngineProvider>
   );
 }
 

diff --git a/app/common.d.ts b/app/common.d.ts
@@ -11,6 +11,21 @@ declare let CONFIG: {
   },
 };
 
+declare global {
+  interface Window {
+    _env_: {
+      KEYCLOAK_CLIENT_ID: string;
+      KEYCLOAK_REALM: string;
+      KEYCLOAK_URL: string;
+      GRAPHKB_URL: string;
+      API_BASE_URL: string;
+      CONTACT_EMAIL: string;
+      CONTACT_TICKET_URL: string;
+      IS_DEMO: boolean;
+    };
+  }
+}
+
 type RecordDefaults = {
   ident: string;
   updatedAt: string | null;
@@ -83,6 +98,96 @@ type KbMatchType = {
   category: string;
 };
 
+type CopyNumberType = {
+  chromosomeBand: string | null;
+  cna: string | null;
+  cnvState: string | null;
+  copyChange: number | null;
+  end: number | null;
+  gene: GeneType | null;
+  kbCategory: string | null;
+  kbMatches: KbMatchType[];
+  log2Cna: string | null;
+  lohState: string | null;
+  size: number | null;
+  start: number | null;
+} & RecordDefaults;
+
+type StructuralVariantType = {
+  breakpoint: string | null;
+  conventionalName: string | null;
+  ctermGene: string | null;
+  ctermTranscript: string | null;
+  detectedIn: string | null;
+  eventType: string | null;
+  exon1: string | null;
+  exon2: string | null;
+  frame: string | null;
+  gene1: Record<string, unknown> | null;
+  gene2: Record<string, unknown> | null;
+  highQuality: boolean;
+  kbMatches: null | KbMatchType[];
+  mavis_product_id: number | null;
+  name: string | null;
+  ntermGene: string | null;
+  ntermTranscript: string | null;
+  omicSupport: boolean;
+  svg: string | null;
+  svgTitle: string | null;
+} & RecordDefaults;
+
+type SmallMutationType = {
+  altSeq: string | null;
+  chromosome: number | null;
+  endPosition: number | null;
+  gene: Record<string, unknown>;
+  germline: string | null;
+  hgvsCds: string | null;
+  hgvsProtein: string | null;
+  kbMatches: KbMatchType[];
+  ncbiBuild: string | null;
+  normalAltCount: number | null;
+  normalDepth: number | null;
+  normalRefCount: number | null;
+  proteinChange: string | null;
+  refSeq: string | null;
+  rnaAltCount: number | null;
+  rnaDepth: number | null;
+  rnaRefCount: number | null;
+  startPosition: number | null;
+  transcript: string | null;
+  tumourAltCount: number | null;
+  tumourDepth: number | null;
+  tumourRefCount: number | null;
+  zygosity: string | null;
+} & RecordDefaults;
+
+type ExpOutliersType = {
+  biopsySiteFoldChange: number | null;
+  biopsySitePercentile: number | null;
+  biopsySiteQC: number | null;
+  biopsySiteZScore: number | null;
+  biopsySitekIQR: number | null;
+  diseaseFoldChange: number | null;
+  diseasePercentile: number | null;
+  diseaseQC: number | null;
+  diseaseZScore: number | null;
+  diseasekIQR: number | null;
+  expressionState: string | null;
+  gene: GeneType;
+  kbCategory: string | null;
+  kbMatches: KbMatchType[];
+  location: number | null;
+  primarySiteFoldChange: number | null;
+  primarySitePercentile: number | null;
+  primarySiteQC: number | null;
+  primarySiteZScore: number | null;
+  primarySitekIQR: number | null;
+  rnaReads: number | null;
+  rpkm: number | null;
+  tpm: number | null;
+} & RecordDefaults;
+
 export {
   RecordDefaults,
   UserType,
@@ -92,4 +197,8 @@ export {
   ImageType,
   GeneType,
   KbMatchType,
+  CopyNumberType,
+  StructuralVariantType,
+  SmallMutationType,
+  ExpOutliersType,
 };