Merge pull request #103 from CanDIG/stable-candidate-2.1.0

Update Stable

.env.development

@@ -3,4 +3,5 @@ REACT_APP_FEDERATION_API_SERVER=''
 REACT_APP_BASE_NAME=''
 REACT_APP_SITE_LOCATION = ''
 REACT_APP_HTSGET_SERVER = ''
-GENERATE_SOURCEMAP=false
+REACT_APP_INGEST_SERVER = ''
+GENERATE_SOURCEMAP=false

.eslintrc

@@ -44,6 +44,9 @@
         "no-unused-vars": [
             1,
             {
+                "argsIgnorePattern": "^_",
+                "varsIgnorePattern": "^_",
+                "caughtErrorsIgnorePattern": "^_",
                 "ignoreRestSiblings": false
             }
         ],

.github/pull_request_template.md

@@ -1,33 +1,41 @@
 ## Ticket(s)
 
+-
 
 ## Description
 
+-
 
 ## Expected Behaviour
 
+-
 
 ## Related Issues (if appropriate)
 
+-
 
 ## Screenshots (if appropriate)
+
 ### Before PR
 
 ### After PR
 
 ## To do/Tickets to be made before merging branch
-- 
+
+-
 
 ## Types of Change(s)
-- [ ] 🪲 Bug fix (non-breaking change that fixes an issue)
-- [ ] ✨ New feature (non-breaking change that adds functionality)
-- [ ] 💥 Breaking change (fix or feature that would cause existing functionality to change)
+
+-   [ ] 🪲 Bug fix (non-breaking change that fixes an issue)
+-   [ ] ✨ New feature (non-breaking change that adds functionality)
+-   [ ] 💥 Breaking change (fix or feature that would cause existing functionality to change)
 
 ## Has it been tested for:
-- [ ] My change requires a change to the documentation
-- [ ] I have updated the documentation accordingly
-- [ ] Prettier linter doesn't return errors
-- [ ] Production branch PR browser testing: Chrome, Firefox, Edge, etc. 
-- [ ] Locally tested
-- [ ] Dev server tested
-- [ ] Production tested when merging into stable/production branch
+
+-   [ ] My change requires a change to the documentation
+-   [ ] I have updated the documentation accordingly
+-   [ ] Prettier linter doesn't return errors
+-   [ ] Production branch PR browser testing: Chrome, Firefox, Edge, etc.
+-   [ ] Locally tested
+-   [ ] Dev server tested
+-   [ ] Production tested when merging into stable/production branch

.github/workflows/candig-dispatch.yml

@@ -0,0 +1,27 @@
+name: Dispatch
+on:
+    push:
+        branches: [develop]
+jobs:
+    CanDIG-dispatch:
+        runs-on: ubuntu-latest
+        env:
+            PARENT_REPOSITORY: 'CanDIG/CanDIGv2'
+            CHECKOUT_BRANCH: 'develop'
+            PR_AGAINST_BRANCH: 'develop'
+            OWNER: 'CanDIG'
+        steps:
+            - name: Check out repository code
+              uses: actions/checkout@v3
+            - name: Create PR in CanDIGv2
+              id: make_pr
+              uses: jman005/github-action-pr-expanded@v0
+              with:
+                  github_token: ${{ secrets.SUBMODULE_PR }}
+                  parent_repository: ${{ env.PARENT_REPOSITORY }}
+                  checkout_branch: ${{ env.CHECKOUT_BRANCH}}
+                  pr_against_branch: ${{ env.PR_AGAINST_BRANCH }}
+                  pr_description: 'PR triggered by update to develop branch on ${{ github.repository }}. Commit hash: ${{ github.sha }}'
+                  owner: ${{ env.OWNER }}
+                  submodule_path: lib/candig-data-portal/candig-data-portal
+                  label: Submodule update

.github/workflows/lint.yml

@@ -0,0 +1,39 @@
+name: Lint
+
+on:
+    # Trigger the workflow on push or pull request,
+    # but only for the develop branch
+    push:
+        branches:
+            - develop
+    pull_request:
+        branches:
+            - develop
+
+# Down scope as necessary via https://docs.github.com/en/actions/security-guides/automatic-token-authentication#modifying-the-permissions-for-the-github_token
+permissions:
+    checks: write
+    contents: write
+
+jobs:
+    run-linters:
+        name: Run linters
+        runs-on: ubuntu-latest
+
+        steps:
+            - name: Check out Git repository
+              uses: actions/checkout@v3
+
+            - name: Set up Node.js
+              uses: actions/setup-node@v1
+              with:
+                  node-version: 12
+
+            - name: Install Node.js dependencies
+              run: npm ci
+
+            - name: Run linters
+              uses: wearerequired/lint-action@v2
+              with:
+                  eslint: true
+                  prettier: true

.prettierrc

@@ -5,6 +5,5 @@
     "trailingComma": "none",
     "tabWidth": 4,
     "useTabs": false,
-    "endOfLine": "auto",
-    "camelcase": "off"
+    "endOfLine": "auto"
 }

PULL_REQUEST_TEMPLATE/stable_pr_template.md

@@ -1,6 +1,7 @@
 ## vX.X.X: Description
+
 Add a summary description of the main user-facing changes made in this release, relative to the last stable release.
 
-- [] Tagged as a release in this repo
-- [] Passes integration tests on a development instance
-- [] Images pushed to Dockerhub
+-   [ ] Tagged as a release in this repo
+-   [ ] Passes integration tests on a development instance
+-   [ ] Images pushed to Dockerhub

package.json

@@ -2,6 +2,7 @@
     "name": "candig-data-portal",
     "version": "0.1.0",
     "private": true,
+    "homepage": "/portal",
     "dependencies": {
         "@candig/igv": "^2.10.5-c.1",
         "@emotion/cache": "^11.4.0",
@@ -30,7 +31,6 @@
         "highcharts": "^10.0.0",
         "highcharts-react-official": "^3.1.0",
         "history": "^5.0.0",
-        "js-cookie": "^3.0.5",
         "material-ui-popup-state": "^1.8.0",
         "npm": "^8.6.0",
         "papaparse": "^5.3.2",
@@ -97,4 +97,3 @@
         "webpack-cli": "^4.9.2"
     }
 }
-

public/index.html

@@ -22,7 +22,7 @@
 
         <link rel="preconnect" href="https://fonts.gstatic.com" />
         <link
-            href="https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700&family=Poppins:wght@400;500;600;700&family=Roboto:wght@400;500;700&display=swap"
+            href="https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700&family=Poppins:wght@400;500;600;700&family=Roboto:wght@400;500;700&display=swap&family=Catamaran:wght@400&display=swap"
             rel="stylesheet"
         />
     </head>

src/layout/MainLayout/Header/NotificationSection/NotificationList.js

@@ -1,5 +1,3 @@
-import React from 'react';
-
 import { makeStyles } from '@mui/styles';
 import {
     Avatar,

src/layout/MainLayout/Header/ProfileSection/UpgradePlanCard.js

@@ -1,5 +1,3 @@
-import React from 'react';
-
 import { makeStyles } from '@mui/styles';
 import { Button, Card, CardContent, Grid, Stack, Typography } from '@mui/material';
 

src/layout/MainLayout/Header/ProfileSection/index.js

@@ -9,11 +9,9 @@ import {
     ClickAwayListener,
     Divider,
     Grid,
-    InputAdornment,
     List,
     ListItemIcon,
     ListItemText,
-    OutlinedInput,
     Paper,
     Popper,
     Typography
@@ -29,7 +27,7 @@ import Transitions from 'ui-component/extended/Transitions';
 import { SITE } from 'store/constant';
 
 // assets
-import { IconLogout, IconSearch, IconSettings } from '@tabler/icons';
+import { IconLogout, IconSettings } from '@tabler/icons';
 import User1 from 'assets/images/users/user-round.svg';
 import BCGSC from 'assets/images/users/bcgsc.svg';
 import UHN from 'assets/images/users/UHN.svg';
@@ -77,6 +75,9 @@ const useStyles = makeStyles((theme) => ({
     cardContent: {
         padding: '16px !important'
     },
+    showOnTop: {
+        zIndex: 11001
+    },
     card: {
         backgroundColor: theme.palette.primary.light,
         marginBottom: '16px',
@@ -108,6 +109,9 @@ const useStyles = makeStyles((theme) => ({
     badgeWarning: {
         backgroundColor: theme.palette.warning.dark,
         color: '#fff'
+    },
+    usernamePadding: {
+        paddingBottom: '1em'
     }
 }));
 
@@ -118,7 +122,6 @@ const ProfileSection = () => {
     const theme = useTheme();
     const customization = useSelector((state) => state.customization);
 
-    const [value, setValue] = React.useState('');
     const [selectedIndex] = React.useState(1);
 
     const [open, setOpen] = React.useState(false);
@@ -185,7 +188,7 @@ const ProfileSection = () => {
                 anchorEl={anchorRef.current}
                 role={undefined}
                 transition
-                disablePortal
+                className={classes.showOnTop}
                 popperOptions={{
                     modifiers: [
                         {
@@ -210,26 +213,10 @@ const ProfileSection = () => {
                                                     First Name Last Name
                                                 </Typography> */}
                                             </Grid>
-                                            <Grid item>
+                                            <Grid item className={classes.usernamePadding}>
                                                 <Typography variant="subtitle2">{SITE}</Typography>
                                             </Grid>
                                         </Grid>
-                                        <OutlinedInput
-                                            className={classes.searchControl}
-                                            id="input-search-profile"
-                                            value={value}
-                                            onChange={(e) => setValue(e.target.value)}
-                                            placeholder="Search profile options"
-                                            startAdornment={
-                                                <InputAdornment position="start">
-                                                    <IconSearch stroke={1.5} size="1.3rem" className={classes.startAdornment} />
-                                                </InputAdornment>
-                                            }
-                                            aria-describedby="search-helper-text"
-                                            inputProps={{
-                                                'aria-label': 'weight'
-                                            }}
-                                        />
                                         <Divider />
                                         <PerfectScrollbar className={classes.ScrollHeight}>
                                             <Divider />

src/layout/MainLayout/Header/SearchSection/index.js

@@ -1,4 +1,4 @@
-import React, { useState } from 'react';
+import { useState } from 'react';
 
 // material-ui
 import { makeStyles } from '@mui/styles';

src/layout/MainLayout/Sidebar/SidebarContext.js

@@ -1,5 +1,7 @@
 import React from 'react';
 
+import PropTypes from 'prop-types';
+
 const DEFAULT_STATE = false;
 
 const SidebarReaderContext = React.createContext(DEFAULT_STATE);
@@ -20,6 +22,11 @@ export function SidebarProvider(props) {
     );
 }
 
+SidebarProvider.propTypes = {
+    data: PropTypes.object,
+    setData: PropTypes.func
+};
+
 /**
  * Obtain the context reader of the federation sites query.
  * @returns {Object} a React context of the sidebar DOM component

src/layout/MainLayout/index.js

@@ -91,8 +91,6 @@ const MainLayout = () => {
         // eslint-disable-next-line react-hooks/exhaustive-deps
     }, [matchDownMd]);
 
-    console.log(leftDrawerOpened);
-
     return (
         <div className={classes.root}>
             <SidebarProvider data={sidebarContent} setData={setSidebarContent}>

src/layout/NavMotion.js

@@ -1,5 +1,4 @@
 import PropTypes from 'prop-types';
-import React from 'react';
 
 // third-party
 import { motion } from 'framer-motion';

src/menu-items/index.js

@@ -1,5 +1,6 @@
 import clinicalGenomicSearch from './clinicalGenomicSearch';
 import summary from './summary';
+// import ingest from './ingest';
 
 // import pages from './pages';
 // import utilities from './utilities';
@@ -8,7 +9,7 @@ import summary from './summary';
 // ===========================|| MENU ITEMS ||=========================== //
 
 const menuItems = {
-    items: [summary, clinicalGenomicSearch /* pages, utilities, other */]
+    items: [summary, clinicalGenomicSearch /* , ingest, pages, utilities, other */]
 };
 
 export default menuItems;