diff --git a/resources/database/data/db/.gitkeep b/resources/database/data/db/.gitkeep
old mode 100644
new mode 100755
diff --git a/src/App.js b/src/App.js
index 7a0fbe36b267e6836c3e14951b2038ea2daf3189..2f0cb6503663ee440a56def740e42eb44faf20d5 100644
--- a/src/App.js
+++ b/src/App.js
@@ -13,6 +13,7 @@ import Visualization from "./components/Visualization/Visualization";
import Comparisons from "./components/Comparisons/Comparisons";
import Comparison from "./components/Comparisons/Comparison";
import Profile from "./pages/Profile/Profile";
+import EditProfile from "./components/EditProfile/EditProfile";
import RunBoard from "./components/RunBoard/RunBoard";
import NotFound from "./pages/NotFound";
@@ -28,8 +29,8 @@ function App() {
<Route exact path="/login" component={Login} />
<PrivateRoute exact path="/newrun" component={RunBoard} />
<PrivateRoute exact path="/comparison" component={Comparisons} />
- <PrivateRoute exact path="/profile" component={Profile} />
-
+ <PrivateRoute exact path="/machines" component={Profile} />
+ <PrivateRoute exact path="/profile" component={EditProfile} />
<PrivateRoute
exact
path="/newcomparison"
diff --git a/src/backend/routes/api/userController.js b/src/backend/routes/api/userController.js
index 6ca00541d33f89e084f52eca44b7663832c71eda..90ccdc0476e4a9c30433b5d771cc3b8b1d75f89f 100644
--- a/src/backend/routes/api/userController.js
+++ b/src/backend/routes/api/userController.js
@@ -18,6 +18,7 @@ const User = require("../../models/User");
// @desc Register user
// @access Public
router.post("/register", (req, res) => {
+ console.log(req.body);
// Form validation
const { errors, isValid } = validateRegisterInput(req.body);
// Check validation
@@ -191,23 +192,85 @@ router.get("/:id", function (req, res) {
// // }
// // );
// });
-router.put("/:id", (req, res, next) => {
+router.put("/:id", (req, res) => {
+ console.log(req.body);
+ console.log(req.params);
+ const { errors, isValid } = validateRegisterInput(req.body);
+ // Check validation
+ if (!isValid) {
+ return res.status(400).json(errors);
+ }
+ let newPassword = [];
const updatedUser = new User({
_id: req.params.id,
name: req.body.name,
email: req.body.email,
machines: req.body.machines,
});
- User.updateOne({ _id: req.params.id }, updatedUser)
- .then(() => {
- res.status(201).json({
- message: "Thing updated successfully!",
- });
- })
- .catch((error) => {
- res.status(400).json({
- error: error,
- });
+ User.findOne({ _id: req.params.id }).then((user) => {
+ // Check if user exists
+ if (!user) {
+ return res
+ .status(404)
+ .json({ namenotfound: "Account name not found" });
+ }
+ // Check password
+ bcrypt.compare(req.body.oldpass, user.password).then((isMatch) => {
+ if (isMatch) {
+ bcrypt.genSalt(10, (err, salt) => {
+ bcrypt.hash(req.body.password, salt, (err, hash) => {
+ if (err) throw err;
+ newPassword = hash;
+ console.log(newPassword);
+ User.findByIdAndUpdate(
+ req.params.id,
+ {
+ $set: {
+ password: newPassword,
+ email: req.body.email,
+ },
+ },
+ {
+ safe: true,
+ useFindAndModify: false,
+ },
+ function (err, model) {
+ console.log(err);
+ }
+ );
+ });
+ });
+
+ const payload = {
+ id: user.id,
+ name: user.name,
+ jbPath: user.jbPath,
+ email: req.body.email,
+ runs: user.runs,
+ views: user.runs,
+ machines: user.machines,
+ };
+ // Sign token
+ jwt.sign(
+ payload,
+ process.env.SECRET,
+ {
+ expiresIn: 31556926, // 1 year in seconds
+ },
+ (err, token) => {
+ res.json({
+ success: true,
+ token: "Bearer " + token,
+ });
+ }
+ );
+ // });
+ } else {
+ return res
+ .status(400)
+ .json({ passwordincorrect: "Old Password incorrect" });
+ }
});
+ });
});
module.exports = router;
diff --git a/src/components/EditProfile/EditProfile.js b/src/components/EditProfile/EditProfile.js
new file mode 100644
index 0000000000000000000000000000000000000000..68ba54286111debea4a65e27231bceba8834f61a
--- /dev/null
+++ b/src/components/EditProfile/EditProfile.js
@@ -0,0 +1,9 @@
+import React from "react";
+import DashLayout from "../Tableau/DashLayout";
+import EditProfileFilling from "../EditProfileFilling/EditProfileFilling";
+
+const EditProfile = () => {
+ return <DashLayout Filling={EditProfileFilling} />;
+};
+
+export default EditProfile;
diff --git a/src/components/EditProfileFilling/EditProfileFilling.js b/src/components/EditProfileFilling/EditProfileFilling.js
new file mode 100644
index 0000000000000000000000000000000000000000..cba7de0ea8c53e7dec93f4cd20fca02427f0914f
--- /dev/null
+++ b/src/components/EditProfileFilling/EditProfileFilling.js
@@ -0,0 +1,197 @@
+import React, { useReducer, useEffect } from "react";
+import { useHistory } from "react-router-dom";
+import { Link } from "react-router-dom";
+import { UPDATE_FORM } from "../../actions/types";
+import classnames from "classnames";
+import { formReducer } from "../../reducers/formReducer";
+import { useAuth } from "../../hooks/useAuth";
+import Avatar from "@material-ui/core/Avatar";
+import Button from "@material-ui/core/Button";
+import CssBaseline from "@material-ui/core/CssBaseline";
+import TextField from "@material-ui/core/TextField";
+import FormControlLabel from "@material-ui/core/FormControlLabel";
+import Checkbox from "@material-ui/core/Checkbox";
+import Grid from "@material-ui/core/Grid";
+import Box from "@material-ui/core/Box";
+import LockOutlinedIcon from "@material-ui/icons/LockOutlined";
+import Typography from "@material-ui/core/Typography";
+import { makeStyles } from "@material-ui/core/styles";
+import Container from "@material-ui/core/Container";
+
+function Copyright() {
+ return (
+ <Typography variant="body2" color="textSecondary" align="center">
+ {"Copyright © "}
+ <Link color="inherit" to="https://material-ui.com/">
+ Your Website
+ </Link>{" "}
+ {new Date().getFullYear()}
+ {"."}
+ </Typography>
+ );
+}
+const useStyles = makeStyles((theme) => ({
+ paper: {
+ marginTop: theme.spacing(8),
+ display: "flex",
+ flexDirection: "column",
+ alignItems: "center",
+ },
+ avatar: {
+ margin: theme.spacing(1),
+ backgroundColor: theme.palette.secondary.main,
+ },
+ form: {
+ width: "100%", // Fix IE 11 issue.
+ marginTop: theme.spacing(3),
+ },
+ submit: {
+ margin: theme.spacing(3, 0, 2),
+ },
+}));
+
+const EditProfileFilling = () => {
+ const classes = useStyles();
+
+ const auth = useAuth();
+ const initialState = {
+ name: auth.user.user.name,
+ email: auth.user.user.email,
+ oldpass: "",
+ password: "",
+ password2: "",
+ errors: {},
+ };
+ console.log(auth.user.user.name);
+ const [state, dispatch] = useReducer(formReducer, initialState);
+ const history = useHistory();
+
+ const onChange = (e) => {
+ e.persist();
+ dispatch({
+ type: UPDATE_FORM,
+ payload: { ...state, [e.target.id]: e.target.value },
+ });
+ };
+ const onSubmit = (e) => {
+ e.preventDefault();
+ console.log("updating info");
+ auth.handleEditProfile(state, dispatch, history);
+ };
+ const { errors } = state;
+
+ return (
+ <Container component="main" maxWidth="md">
+ <CssBaseline />
+ <div className={classes.paper}>
+ <Avatar className={classes.avatar}>
+ <LockOutlinedIcon />
+ </Avatar>
+
+ <Typography component="h1" variant="h5">
+ Update {auth.user.user.name} Account Information
+ </Typography>
+
+ <form className={classes.form} noValidate onSubmit={onSubmit}>
+ <Grid container spacing={2}>
+ <Grid item xs={12}>
+ <TextField
+ onChange={onChange}
+ value={state.email}
+ error={errors.email === ""}
+ helperText={errors.email === "" ? "Empty!" : errors.email}
+ className={classnames("", {
+ invalid: errors.email,
+ })}
+ id="email"
+ type="email"
+ variant="outlined"
+ required
+ fullWidth
+ label="Email Address"
+ name="email"
+ autoComplete="email"
+ />
+ </Grid>
+ <Grid item xs={12} sm={12}>
+ <TextField
+ onChange={onChange}
+ value={state.oldpass}
+ error={errors.passwordincorrect === ""}
+ helperText={
+ errors.passwordincorrect === ""
+ ? "Empty!"
+ : errors.passwordincorrect
+ }
+ className={classnames("", {
+ invalid: errors.passwordincorrect,
+ })}
+ id="oldpass"
+ type="password"
+ variant="outlined"
+ required
+ fullWidth
+ name="oldpass"
+ label="Old Password"
+ type="password"
+ autoComplete="current-password"
+ />
+ </Grid>
+ <Grid item xs={12} sm={6}>
+ <TextField
+ onChange={onChange}
+ value={state.password}
+ error={errors.password === ""}
+ helperText={errors.password === "" ? "Empty!" : errors.password}
+ className={classnames("", {
+ invalid: errors.password,
+ })}
+ id="password"
+ type="password"
+ variant="outlined"
+ required
+ fullWidth
+ name="password"
+ label="New Password"
+ autoComplete="current-password"
+ />
+ </Grid>
+ <Grid item xs={12} sm={6}>
+ <TextField
+ onChange={onChange}
+ value={state.password2}
+ error={errors.password2 === ""}
+ helperText={
+ errors.password2 === "" ? "Empty!" : errors.password2
+ }
+ className={classnames("", {
+ invalid: errors.password2,
+ })}
+ id="password2"
+ type="password"
+ variant="outlined"
+ required
+ fullWidth
+ name="password2"
+ label="Confirm New Password"
+ type="password"
+ autoComplete="current-password"
+ />
+ </Grid>
+ </Grid>
+ <Button
+ type="submit"
+ fullWidth
+ variant="contained"
+ color="primary"
+ className={classes.submit}
+ >
+ Update{" "}
+ </Button>
+ </form>
+ </div>
+ </Container>
+ );
+};
+
+export default EditProfileFilling;
diff --git a/src/components/Login/Login.js b/src/components/Login/Login.js
index e62a80b6380b04eabc2742a01f8f6eb1efd63489..5c8e9446b1ec9b9c9b34f11fb8feecaac39b3d7d 100644
--- a/src/components/Login/Login.js
+++ b/src/components/Login/Login.js
@@ -85,7 +85,7 @@ const Login = () => {
const { errors } = state;
return (
- <Container component="main" maxWidth="xs">
+ <Container component="main" maxWidth="md">
<CssBaseline />
<div className={classes.paper}>
<Avatar className={classes.avatar}>
diff --git a/src/components/Navbar/Navbar.js b/src/components/Navbar/Navbar.js
deleted file mode 100644
index e8ebecb6ce0e8f2d6b0798f856a1bf5b9c5cf77f..0000000000000000000000000000000000000000
--- a/src/components/Navbar/Navbar.js
+++ /dev/null
@@ -1,47 +0,0 @@
-import React from "react";
-import { Link } from "react-router-dom";
-import { useAuth } from "../../hooks/useAuth";
-const Navbar = () => {
- const auth = useAuth();
- return (
- <div>
- <nav
- className={`${
- auth.user.isAuthenticated
- ? "#00acc1 cyan darken-1"
- : "#00897b teal darken-1"
- }`}
- >
- <div className="nav-wrapper container">
- <Link to="/" className="brand-logo">
- BiSSProP
- </Link>
- <ul id="nav-mobile" className="right hide-on-med-and-down">
- <li>
- <Link to="/docs">Docs</Link>
- </li>
- <li>
- <Link to="/examples">Examples</Link>
- </li>
- {auth.user.isAuthenticated ? (
- <>
- <li>
- <Link to="/newrun">Runs</Link>
- </li>
- <li>
- <Link onClick={auth.signout}>Logout</Link>
- </li>
- </>
- ) : (
- <li>
- <Link to="/login">Login</Link>
- </li>
- )}
- </ul>
- </div>
- </nav>
- </div>
- );
-};
-
-export default Navbar;
diff --git a/src/components/Register/Register.js b/src/components/Register/Register.js
index 8ab15dfaba86bb25d276b1ea563a072598a3931f..0dff51797a376b827c5d1f6c54b39a1bf572ba11 100644
--- a/src/components/Register/Register.js
+++ b/src/components/Register/Register.js
@@ -80,7 +80,7 @@ const Register = () => {
const { errors } = state;
return (
- <Container component="main" maxWidth="xs">
+ <Container component="main" maxWidth="md">
<CssBaseline />
<div className={classes.paper}>
<Avatar className={classes.avatar}>
diff --git a/src/components/Table/Table.js b/src/components/Table/Table.js
index cce1d8baa9ed03e31b78929b1dbc2725533507b5..19646a97a1ea75b9f72d8758293f2026ee2e2c73 100644
--- a/src/components/Table/Table.js
+++ b/src/components/Table/Table.js
@@ -706,17 +706,18 @@ export default function InteractiveList() {
: true
}
key={sample._id}
- onClick={() => {
- if (row.remote) {
- // handleRemoteFiles(row, sample);
- downloadFiles(row, sample, tracks);
- } else {
- console.log(sample);
- const path = `${row.outdir}/results/${sample.samplePath}/${sample.samplePath}-multiqc_report.html`;
- console.log(path);
- createBrowserWindow(path);
- }
- }}
+ onClick={
+ row.remote
+ ? () =>
+ // handleRemoteFiles(row, sample);
+ downloadFiles(row, sample, tracks)
+ : () => {
+ console.log(sample);
+ const path = `${row.outdir}/results/${sample.samplePath}/${sample.samplePath}-multiqc_report.html`;
+ console.log(path);
+ createBrowserWindow(path);
+ }
+ }
>
<ListItemAvatar>
<Avatar>
diff --git a/src/components/Tableau/DashLayout.js b/src/components/Tableau/DashLayout.js
index b8fe628a03d05cfbc158396f1dfbfa87f499a5b2..b415e9cd2f66c12d8437e71df2b437c39f97b95f 100644
--- a/src/components/Tableau/DashLayout.js
+++ b/src/components/Tableau/DashLayout.js
@@ -19,7 +19,12 @@ import SettingsIcon from "@material-ui/icons/Settings";
import LibraryBooksIcon from "@material-ui/icons/LibraryBooks";
import { useConfig } from "../../hooks/useConfig";
import Alert from "@material-ui/lab/Alert";
-
+import Menu from "@material-ui/core/Menu";
+import MenuItem from "@material-ui/core/MenuItem";
+import Fade from "@material-ui/core/Fade";
+import ListItemIcon from "@material-ui/core/ListItemIcon";
+import AccountCircleIcon from "@material-ui/icons/AccountCircle";
+import EditIcon from "@material-ui/icons/Edit";
const drawerWidth = 240;
const useStyles = makeStyles((theme) => ({
@@ -131,7 +136,16 @@ const DashLayout = ({ Filling }) => {
const handleDrawerClose = () => {
setOpenDrawer(false);
};
+ const [anchorEl, setAnchorEl] = React.useState(null);
+ const open = Boolean(anchorEl);
+
+ const handleClick = (event) => {
+ setAnchorEl(event.currentTarget);
+ };
+ const handleClose = () => {
+ setAnchorEl(null);
+ };
return (
<div className={classes.root}>
<CssBaseline />
@@ -159,24 +173,12 @@ const DashLayout = ({ Filling }) => {
noWrap
className={classes.title}
>
- {auth.user.user.name} Dashboard
+ Dashboard
</Typography>
{auth.user.isAuthenticated ? (
<>
- <IconButton component={Link} to="/profile" color="inherit">
- <Typography
- component="h1"
- variant="h6"
- color="inherit"
- noWrap
- className={classes.title}
- >
- Manage Remote Machines
- </Typography>{" "}
- <SettingsIcon />
- </IconButton>
- <IconButton component={Link} to="/profile" color="inherit">
+ {/* <IconButton component={Link} to="/docs" color="inherit">
<Typography
component="h1"
variant="h6"
@@ -188,8 +190,9 @@ const DashLayout = ({ Filling }) => {
</Typography>
<LibraryBooksIcon />
- </IconButton>
- <IconButton onClick={auth.signout} color="inherit">
+ </IconButton> */}
+
+ <IconButton onClick={handleClick} color="inherit">
<Typography
component="h1"
variant="h6"
@@ -197,10 +200,41 @@ const DashLayout = ({ Filling }) => {
noWrap
className={classes.title}
>
- Logout
+ Account
</Typography>
- <ExitToAppIcon />
+ <AccountCircleIcon />
</IconButton>
+
+ <Menu
+ id="fade-menu"
+ anchorEl={anchorEl}
+ keepMounted
+ open={open}
+ onClose={handleClose}
+ TransitionComponent={Fade}
+ >
+ <MenuItem component={Link} to="/profile">
+ <ListItemIcon>
+ <EditIcon />
+ </ListItemIcon>
+ <Typography variant="inherit">Edit Profile </Typography>
+ </MenuItem>
+ <MenuItem component={Link} to="/machines">
+ <ListItemIcon>
+ <SettingsIcon />
+ </ListItemIcon>
+ <Typography variant="inherit">
+ Manage Remote Machines
+ </Typography>
+ </MenuItem>
+
+ <MenuItem onClick={auth.signout}>
+ <ListItemIcon>
+ <ExitToAppIcon />
+ </ListItemIcon>
+ <Typography variant="inherit">Logout </Typography>
+ </MenuItem>
+ </Menu>
</>
) : (
""
diff --git a/src/components/Visualization/VisualizationFill.js b/src/components/Visualization/VisualizationFill.js
index a2f50d07bf89f8fc3e5011c8fde90f1c2780cc3a..edbd1a477161f57dbb723fa5d2a6c8b0673218df 100644
--- a/src/components/Visualization/VisualizationFill.js
+++ b/src/components/Visualization/VisualizationFill.js
@@ -188,16 +188,13 @@ export default function VisualizationFill() {
return false;
}
};
- const downloadFiles = (row, sample, tracks) => {
+ const downloadFiles = (row, tracks) => {
let sftp = new Client();
console.log(tracks);
- console.log(row, sample);
console.log("download files");
console.log(homedir);
- console.log(row.machine);
- console.log(sample);
if (!fs.existsSync(bisepsTemp)) {
fs.mkdirSync(bisepsTemp);
@@ -600,7 +597,7 @@ export default function VisualizationFill() {
edge="end"
disabled={sampleExist}
aria-label="files"
- onClick={() => downloadFiles(row, sample, tracks)}
+ onClick={() => downloadFiles(row, tracks)}
>
<GetAppIcon
style={{
@@ -661,6 +658,7 @@ export default function VisualizationFill() {
path.basename(bed)
);
console.log(checkedComp);
+ const tracks = [bed, bedtbi];
return (
<ListItem
key={`${comparison._id}-${idx}-${context}`}
@@ -735,9 +733,7 @@ export default function VisualizationFill() {
<IconButton
edge="end"
aria-label="files"
- onClick={() =>
- downloadFiles(row, sample, tracks)
- }
+ onClick={() => downloadFiles(row, tracks)}
>
<GetAppIcon />
</IconButton>
diff --git a/src/hooks/useAuth.js b/src/hooks/useAuth.js
index 9981ceed3da2c3f2ab46a223ab33e3d896e74c50..6f0d9760e6f6d63e13f34f2e938cdb80f75f70a6 100644
--- a/src/hooks/useAuth.js
+++ b/src/hooks/useAuth.js
@@ -107,6 +107,7 @@ const useProvideAuth = () => {
req.end();
};
const handleEditProfile = async (userData, dispatch, history) => {
+ console.log(userData);
const options = {
method: "PUT",
path: `http://localhost/api/users/${user.user.id}`,
@@ -128,14 +129,9 @@ const useProvideAuth = () => {
res.on("end", function () {
const body = Buffer.concat(chunks).toString();
const jsbody = JSON.parse(body);
- if (!jsbody.token) {
- dispatch({
- type: GET_ERRORS,
- payload: jsbody,
- });
- console.log(jsbody);
- history.push("/alignment");
- } else {
+ console.log(jsbody);
+
+ if ("success" in jsbody) {
// Save to localStorage
// Set token to localStorage
const { token } = jsbody;
@@ -148,7 +144,13 @@ const useProvideAuth = () => {
type: SET_CURRENT_USER,
payload: decoded,
});
+ console.log("successful put request");
history.push("/alignment");
+ } else {
+ dispatch({
+ type: GET_ERRORS,
+ payload: jsbody,
+ });
}
});
});