diff --git a/src/backend/helpers/cloneBiseps.js b/src/backend/helpers/cloneBiseps.js
index 8572a659af73676244747e13387fc0b534091849..19bac9312f169c2e233556d02e50a8f0dc10a1e8 100644
--- a/src/backend/helpers/cloneBiseps.js
+++ b/src/backend/helpers/cloneBiseps.js
@@ -4,7 +4,7 @@ const cloneBiseps = (body, uniqueDir) => {
const fs = require("fs");
execSync(
- `git clone git@forgemia.inra.fr:skander.hatira/biseps.git ${uniqueDir}`,
+ `git clone https://forgemia.inra.fr/skander.hatira/biseps.git ${uniqueDir}`,
(error, stdout, stderr) => {
if (error) {
console.log(`error: ${error.message}`);
diff --git a/src/backend/helpers/createJbrowse.js b/src/backend/helpers/createJbrowse.js
index 0ce0131c46ab4e2a2db62547e1b4784c98fbb794..fce4401e421b46f09928615153ef50f6c89b05d9 100644
--- a/src/backend/helpers/createJbrowse.js
+++ b/src/backend/helpers/createJbrowse.js
@@ -11,7 +11,6 @@ const createJbrowse = (jbPath, reset) => {
return console.error(err);
}
- console.log(jbPath);
console.log("done!");
});
};
diff --git a/src/backend/helpers/createProfile.js b/src/backend/helpers/createProfile.js
index 2233faecf8ffbd512557a32e0e733dd74007ef45..07ee791896a9d2932e2eccaec02238a3b1e00119 100644
--- a/src/backend/helpers/createProfile.js
+++ b/src/backend/helpers/createProfile.js
@@ -3,7 +3,6 @@ function createProfile(body, uniqueDir, uniqueDirRemote) {
const fs = require("fs");
const path = require("path");
console.log("creating profile");
- console.log(body);
if (!fs.existsSync(path.join(uniqueDir, "config"))) {
fs.mkdirSync(path.join(uniqueDir, "config/profiles/slurm"), {
diff --git a/src/backend/helpers/createProfileComparison.js b/src/backend/helpers/createProfileComparison.js
index 508087a8845c8ac39e6f47035a2cef90f7970e37..e1c3888960f1277c1e2c960ca3288440052bbee2 100644
--- a/src/backend/helpers/createProfileComparison.js
+++ b/src/backend/helpers/createProfileComparison.js
@@ -2,8 +2,7 @@ function createProfile(body, uniqueDir, uniqueDirRemote) {
const yaml = require("js-yaml");
const fs = require("fs");
const path = require("path");
- console.log(body);
- console.log("creating profile1");
+ console.log("creating profile");
if (!fs.existsSync(path.join(uniqueDir, "config"))) {
fs.mkdirSync(path.join(uniqueDir, "config/profiles/slurmComparison"), {
diff --git a/src/backend/helpers/spawnJbrowse.js b/src/backend/helpers/spawnJbrowse.js
index 57d8a6c410a4fceab303f10a9ce1fbeb09db530e..0b655a9786bcf5ad5c5a12ec9f51310351551543 100644
--- a/src/backend/helpers/spawnJbrowse.js
+++ b/src/backend/helpers/spawnJbrowse.js
@@ -26,7 +26,6 @@ const spawnChild = (body) => {
// );
body.genomes != [] &&
body.genomes.map((genome) => {
- console.log(path.extname(genome));
console.log(`Current directory: ${process.cwd()} | ${__dirname}`);
fork(
@@ -99,10 +98,6 @@ const spawnChild = (body) => {
body.tracks != [] &&
body.tracks.map((track) => {
// import bam
- console.log(
- `${body.jbPath}/${track.associatedGenome}/${track.id}_bam.lock`
- );
-
fork(
jbrowse,
[
diff --git a/src/backend/routes/api/comparisonController.js b/src/backend/routes/api/comparisonController.js
index 7c99f865abf67ba3d2c8e8656c1a9f5fba38a1cd..b8293fa2f7d87a76deb8a0d488ff5627fe159cfa 100644
--- a/src/backend/routes/api/comparisonController.js
+++ b/src/backend/routes/api/comparisonController.js
@@ -20,7 +20,6 @@ const User = require("../../models/User");
// @access Public
router.post("/comparison", (req, res) => {
- console.log(req.body);
// Form validation
const { errors, isValid } = validateConfigurationInput(req.body);
@@ -178,8 +177,6 @@ router.get("/:userId", function (req, res) {
router.delete("/:id", function (req, res) {
const id = req.params.id;
const userId = req.user._id;
- console.log(req.outdir);
- console.log(req.user);
Comparison.deleteOne({ _id: id })
.then((result) => {
res.json(`Deleted ${id}`);
@@ -196,7 +193,6 @@ router.delete("/:id", function (req, res) {
});
router.post("/rerun", function (req, res) {
- console.log(req.body);
const uniqueDir = req.body.outdir;
if (!req.body.remote) {
@@ -226,8 +222,6 @@ router.post("/rerun", function (req, res) {
});
router.put("/:id", (req, res, next) => {
- console.log(req.body);
- console.log(req.params);
const updatedComparison = new Comparison({
_id: req.params.id,
diff --git a/src/backend/routes/api/machineController.js b/src/backend/routes/api/machineController.js
index 4555bff9ebf9640b0b2e54b8a9e95706d4bb026f..0a679663091def482c1917d5d33deff765d2a9e0 100644
--- a/src/backend/routes/api/machineController.js
+++ b/src/backend/routes/api/machineController.js
@@ -14,7 +14,6 @@ const User = require("../../models/User");
// @desc Run
// @access Public
router.post("/machine", (req, res) => {
- console.log(req.body);
// Form validation
const { errors, isValid } = validateConfigurationInput(req.body);
// Check validation
diff --git a/src/backend/routes/api/runController.js b/src/backend/routes/api/runController.js
index f51bf20e916209ca076f2052a5eef9abf831cd12..90bbe4177ebf369985d720912113a2896ecba1b1 100644
--- a/src/backend/routes/api/runController.js
+++ b/src/backend/routes/api/runController.js
@@ -22,7 +22,6 @@ const User = require("../../models/User");
// @desc Run
// @access Public
router.post("/run", (req, res) => {
- console.log(req.body);
// Form validation
const { errors, isValid } = validateConfigurationInput(req.body);
// Check validation
@@ -159,8 +158,6 @@ router.post("/run", (req, res) => {
router.delete("/:id", function (req, res) {
const id = req.params.id;
const userId = req.user._id;
- console.log(req.outdir);
- console.log(req.user);
Run.deleteOne({ _id: id })
.then((result) => {
res.json(`Deleted ${id}`);
@@ -199,7 +196,6 @@ router.get("/:id", function (req, res) {
}).populate("createdBy");
});
router.post("/rerun", function (req, res) {
- console.log(req.body);
const uniqueDir = req.body.outdir;
if (!req.body.remote) {
@@ -222,8 +218,6 @@ router.post("/rerun", function (req, res) {
}
});
router.put("/:id", (req, res, next) => {
- console.log(req.body);
- console.log(req.params);
const updatedRun = new Run({
_id: req.params.id,
diff --git a/src/backend/routes/api/userController.js b/src/backend/routes/api/userController.js
index 8572eea530bee1e4bca26a2dff2eab17893c3377..8d7479c5db8664a1e39ba016d7b7d9d87e9093d5 100644
--- a/src/backend/routes/api/userController.js
+++ b/src/backend/routes/api/userController.js
@@ -20,7 +20,6 @@ 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
@@ -195,8 +194,6 @@ router.get("/:id", function (req, res) {
// // );
// });
router.put("/:id", (req, res) => {
- console.log(req.body);
- console.log(req.params);
const { errors, isValid } = validateEditInput(req.body);
// Check validation
if (!isValid) {
diff --git a/src/backend/routes/api/viewController.js b/src/backend/routes/api/viewController.js
index 897c8c0c5ec39111682a1ba2716df8265cac5837..3d6a0b70b84112bd9cb73633f80927c1ae053947 100644
--- a/src/backend/routes/api/viewController.js
+++ b/src/backend/routes/api/viewController.js
@@ -15,7 +15,6 @@ const User = require("../../models/User");
// @desc Run
// @access Public
router.post("/visualize", (req, res) => {
- console.log(req.body);
// Form validation
const { errors, isValid } = validateConfigurationInput(req.body);
// Check validation
@@ -29,7 +28,6 @@ router.post("/resetJB", (req, res) => {
createJB(req.body.jbPath, true);
});
router.post("/serve", (req, res) => {
- console.log(req.body);
});
router.get("/", function (req, res) {
View.find({}, function (err, views) {
diff --git a/src/backend/server.js b/src/backend/server.js
index 3015846f84f7c37b97b9cf30f1bd17c2c0e808f8..912278147925a95e679ebcac332f38a72f2aaed0 100644
--- a/src/backend/server.js
+++ b/src/backend/server.js
@@ -17,8 +17,7 @@ const cors = require("cors");
require("dotenv").config({ path: path.join(__dirname, "../backend/.env") });
const sock = process.argv[2];
const unixSocket = process.argv[3];
-console.log(process.argv);
-console.log(__dirname);
+
const app = express();
app.use(cors());
app.use(
@@ -27,14 +26,7 @@ app.use(
})
);
app.use(bodyParser.json());
-console.log("where am i");
-console.log(unixSocket);
-console.log(process.argv);
-console.log("hahahahaha");
-console.log("hahahahaha");
-console.log("hahahahaha");
-console.log("hahahahaha");
-console.log(process.platform);
+
const connectWithRetry = () => {
return mongoose.connect(
process.platform == "win32" ? unixSocket : process.env.DATABASE,
@@ -42,10 +34,10 @@ const connectWithRetry = () => {
function (err) {
if (err) {
console.error(
- "Failed to connect to mongo on startup - retrying in 0,5 sec",
+ "Failed to connect to mongo on startup - retrying in 1 sec",
err
);
- setTimeout(connectWithRetry, 500);
+ setTimeout(connectWithRetry, 1000, 5);
} else {
console.log("MongoDB successfully connected");
}
diff --git a/src/backend/snakemake.js b/src/backend/snakemake.js
index 06d1954c1058a9903f4cdfd0dbe0035e602e118a..ec35b2d68c88e3b65b679bec8177fae5d4b6d694 100644
--- a/src/backend/snakemake.js
+++ b/src/backend/snakemake.js
@@ -11,7 +11,7 @@ const spawnChild = async (body, profile, uniqueDir, homeDir, unlock) => {
process.platform == "win32"
? "conda"
: `$(head -n 1 $HOME/.conda/environments.txt)`;
- const command = process.platform == "win32" ? "conda" : `${base}/bin/conda`;
+ const command = process.platform == "win32" ? "conda" : "conda";
const options = {
slient: false,
detached: false,
diff --git a/src/backend/spawnMongod.js b/src/backend/spawnMongod.js
index 4564471c5d5960647204193a6e32f69e53b91b16..174ab6eaa28f1bdec5a0ad79f2f22e34ed748f87 100644
--- a/src/backend/spawnMongod.js
+++ b/src/backend/spawnMongod.js
@@ -3,14 +3,11 @@ const spawnChild = async (unixSocket) => {
const path = require("path");
const fs = require("fs");
-
const homedir = require("os").homedir();
const logfile = path.join(homedir, "mongoWindow.txt");
const output = fs.openSync(logfile, "a");
- const command =
- process.platform == "win32"
- ? "conda"
- : `$(head -n 1 $HOME/.conda/environments.txt)/bin/conda`;
+ const command = process.platform == "win32" ? "conda" : "conda";
+ // : `$(head -n 1 $HOME/.conda/environments.txt)/bin/conda`;
const options = {
slient: false,
@@ -24,7 +21,7 @@ const spawnChild = async (unixSocket) => {
const port = 27017;
const dbpath = path.join(__dirname, "resources/database/data/db");
- const child = spawn(
+ const child = await spawn(
command,
[
"run",
diff --git a/src/backend/spawnServer.js b/src/backend/spawnServer.js
index 547c5b3d10a7937e4bd609f1000ea2e19625185a..5821c4537f0587fbdd2cc26646bb8d494071902a 100644
--- a/src/backend/spawnServer.js
+++ b/src/backend/spawnServer.js
@@ -15,7 +15,7 @@ const spawnServer = async (sock, unixSocket) => {
// options
// );
- const child = fork(
+ const child = await fork(
path.join(__dirname, "backend/server.js"),
[sock, unixSocket],
options
diff --git a/src/components/ComparisonStepper/RunForm.js b/src/components/ComparisonStepper/RunForm.js
index da4ced8a85a0be77bd7bb017263a2308ebe5626f..3276633cf89ed36c9a0dfdb5acd14ab482fd1255 100644
--- a/src/components/ComparisonStepper/RunForm.js
+++ b/src/components/ComparisonStepper/RunForm.js
@@ -180,7 +180,6 @@ export default function RunForm() {
email: user.user.email,
};
const token = sessionStorage.jwtToken;
- console.log(request);
const options = {
method: "POST",
path: "http://localhost/api/comparisons/comparison",
diff --git a/src/components/Comparisons/ComparisonTable.js b/src/components/Comparisons/ComparisonTable.js
index afd068cc248edb20861895647edae2c091e51637..7eed90b25bc2b56354aebf93266d0522bd4e9650 100644
--- a/src/components/Comparisons/ComparisonTable.js
+++ b/src/components/Comparisons/ComparisonTable.js
@@ -126,7 +126,6 @@ export default function InteractiveList() {
});
});
req.on("error", (err) => console.log(err));
- console.log(request);
req.end();
if (remote) {
let client = new Client();
@@ -223,7 +222,6 @@ export default function InteractiveList() {
...selectedRow,
public: !selectedRow.public,
};
- console.log(request);
const token = sessionStorage.jwtToken;
const options = {
method: "PUT",
diff --git a/src/components/Stepper/GlobalConfig.js b/src/components/Stepper/GlobalConfig.js
index bf9536450c99d021a9a2765e7e09e46101f1a9dc..b554de4bb2a2aa2b5b3aab62144942c08ec8bc03 100644
--- a/src/components/Stepper/GlobalConfig.js
+++ b/src/components/Stepper/GlobalConfig.js
@@ -97,7 +97,6 @@ export default function GlobalConfig() {
fetchData();
}, []);
- console.log(data);
const handleRunState = (e) => {
setRunState({
...runState,
@@ -111,16 +110,12 @@ export default function GlobalConfig() {
});
};
const handleSlider = (e, newValue) => {
- console.log(e.target);
setRunState({
...runState,
[e.target.id]: newValue,
});
};
- console.log(runState.remoteDir);
- console.log(value);
- console.log(runState);
return (
<React.Fragment>
<Typography variant="h6" gutterBottom>
@@ -369,7 +364,6 @@ export default function GlobalConfig() {
value={runState.remoteDir}
onChange={(event, newValue) => {
if (typeof newValue === "string") {
- console.log(newValue);
setRunState({
...runState,
remoteDir: newValue,
diff --git a/src/components/Table/NewTable.js b/src/components/Table/NewTable.js
index a5cd988b23048afad5d25652894db4c9c9ee4549..800ea3367d07fc5e957b78ff0d4846aba0cf2d2f 100644
--- a/src/components/Table/NewTable.js
+++ b/src/components/Table/NewTable.js
@@ -296,29 +296,23 @@ export default function NewTable() {
const updatedSelected = [...selected];
const sorted = updatedSelected.sort((a, b) => a - b);
while (sorted.length) {
- console.log(sorted);
updatedUnits.splice(sorted.pop(), 1);
}
setUnits(updatedUnits);
setSelected([]);
};
- console.log(selected);
- console.log(units);
const handleUnitChange = (e) => {
const updatedRemoteUnits = [...remoteunits];
- console.log(e.target.dataset.idx);
updatedRemoteUnits[e.target.dataset.idx][e.target.id] = e.target.value;
setRemoteUnits(updatedRemoteUnits);
const updatedUnits = [...units];
- console.log(e.target.dataset.idx);
updatedUnits[e.target.dataset.idx][e.target.id] = e.target.value;
setUnits(updatedUnits);
};
const handleUnitFiles = (e) => {
const updatedUnits = [...units];
- console.log(e.target.dataset.idx);
const updatedRemoteUnits = [...remoteunits];
updatedRemoteUnits[e.target.dataset.idx][e.target.id] = path
@@ -348,7 +342,6 @@ export default function NewTable() {
const handleClick = (event, index) => {
const selectedIndex = selected.indexOf(index);
let newSelected = [];
- console.log(index);
if (selectedIndex === -1) {
newSelected = newSelected.concat(selected, index);
} else if (selectedIndex === 0) {
@@ -364,7 +357,6 @@ export default function NewTable() {
setSelected(newSelected);
};
- console.log(selected);
const handleChangePage = (event, newPage) => {
setPage(newPage);
diff --git a/src/components/Table/Table.js b/src/components/Table/Table.js
index 035f3dd41568ff39817fcdadfd58ed8c3e34c864..c0188f9d62f5855ebaaa030672348e3fc51e8fb5 100644
--- a/src/components/Table/Table.js
+++ b/src/components/Table/Table.js
@@ -92,7 +92,6 @@ export default function InteractiveList() {
const handleChange = (e) => {
setDeleted(e.target.value);
};
- console.log(deleted);
const handleClickOpen = (row) => {
setSelectedRow(row);
setOpen(true);
@@ -103,15 +102,12 @@ export default function InteractiveList() {
newSelected[idx] = !selected[idx];
setSelected(newSelected);
- console.log(selected);
};
- console.log(selected);
const handleLog = (row, filePath) => {
let sftp = new Client();
if (!fs.existsSync(bisepsTemp)) {
fs.mkdirSync(bisepsTemp);
}
- console.log(row);
let remotePath = `${row.remoteDir}/${filePath}`;
let localPath = row.date + filePath;
sftp
@@ -125,9 +121,7 @@ export default function InteractiveList() {
password: row.machine.password,
})
.then(() => {
- console.log(remotePath);
- console.log(localPath);
- console.log("made it all the way here?");
+
return sftp.fastGet(
remotePath.split(path.sep).join(path.posix.sep),
@@ -135,8 +129,6 @@ export default function InteractiveList() {
);
})
.then((data) => {
- console.log(data);
- console.log("done done done");
createBrowserWindow(path.join(bisepsTemp, localPath));
sftp.end();
})
@@ -160,7 +152,6 @@ export default function InteractiveList() {
password: row.machine.password,
})
.then(async () => {
- console.log("made it all the way here?");
if (!fs.existsSync(path.join(bisepsTemp, path.basename(cx)))) {
return sftp.fastGet(cx, path.join(bisepsTemp, path.basename(cx)));
}
@@ -169,13 +160,7 @@ export default function InteractiveList() {
const downloadFiles = (row, sample, tracks) => {
let sftp = new Client();
- console.log(tracks);
- console.log(row, sample);
- console.log("download files");
- console.log(homedir);
- console.log(row.machine);
- console.log(sample);
if (!fs.existsSync(bisepsTemp)) {
fs.mkdirSync(bisepsTemp);
@@ -192,7 +177,6 @@ export default function InteractiveList() {
password: row.machine.password,
})
.then(async () => {
- console.log("made it all the way here?");
// return sftp.fastGet(remotePath, path.join(bisepsTemp, localPath));
// tracks.map((track) => {
// console.log(track);
@@ -200,7 +184,6 @@ export default function InteractiveList() {
if (
!fs.existsSync(path.join(bisepsTemp, path.basename(tracks[track])))
) {
- console.log(path.join(bisepsTemp, path.basename(tracks[track])));
try {
await sftp.fastGet(
tracks[track],
@@ -221,7 +204,6 @@ export default function InteractiveList() {
path.join(`${sample.samplePath}-multiqc_report.html`)
)
);
- console.log("done done done");
sftp.end();
})
.catch((err) => {
@@ -247,7 +229,6 @@ export default function InteractiveList() {
unlock: selected || false,
...row,
};
- console.log(request);
const token = sessionStorage.jwtToken;
const options = {
method: "POST",
@@ -290,9 +271,6 @@ export default function InteractiveList() {
handleOpenAlert();
};
const handleDelete = (user, row, deleted) => {
- console.log(row);
- console.log(row);
- console.log(deleted);
if (deleted === "DELETE") {
const request = {
user: user.user,
@@ -330,7 +308,6 @@ export default function InteractiveList() {
});
});
req.on("error", (err) => console.log(err));
- console.log(request);
req.end();
if (row.remote) {
let client = new Client();
@@ -373,7 +350,6 @@ export default function InteractiveList() {
...selectedRow,
public: !selectedRow.public,
};
- console.log(request);
const token = sessionStorage.jwtToken;
const options = {
method: "PUT",
@@ -462,16 +438,13 @@ export default function InteractiveList() {
height: 720,
width: 1080,
});
- console.log("here");
win.loadURL(`file://${path}`);
};
- console.log(data);
const openInFolder = (path) => {
shell.showItemInFolder(path);
};
- console.log(data);
return (
<Container maxWidth="lg" className={classes.container}>
@@ -746,9 +719,7 @@ export default function InteractiveList() {
// handleRemoteFiles(row, sample);
downloadFiles(row, sample, tracks)
: () => {
- console.log(sample);
const path = `${row.outdir}/results/${sample.samplePath}/${sample.samplePath}-multiqc_report.html`;
- console.log(path);
createBrowserWindow(path);
}
}
diff --git a/src/components/Visualization/VisualizationFill.js b/src/components/Visualization/VisualizationFill.js
index dd4a85f82418483d7a0c5cf910c5c21a17f12894..1d23348a980140dab32fb31b1f5c82488b3e0151 100644
--- a/src/components/Visualization/VisualizationFill.js
+++ b/src/components/Visualization/VisualizationFill.js
@@ -51,7 +51,6 @@ export default function VisualizationFill() {
const handleToggle = (genome) => () => {
const currentIndex = checked.indexOf(genome);
- console.log(currentIndex);
const newChecked = [...checked];
if (currentIndex === -1) {
@@ -66,7 +65,6 @@ export default function VisualizationFill() {
const handleToggleTrack =
(track, associatedGenome, id, name, cgbw, chgbw, chhbw, bedbw) => () => {
const currentIndex = checkedTrack.findIndex((x) => x.id === id);
- console.log(currentIndex);
const newChecked = [...checkedTrack];
if (currentIndex === -1) {
@@ -89,7 +87,6 @@ export default function VisualizationFill() {
const handleToggleComp = (bed, bedtbi, associatedGenome, id) => () => {
const currentIndex = checkedComp.findIndex((x) => x.id === id);
- console.log(currentIndex);
const newChecked = [...checkedComp];
if (currentIndex === -1) {
@@ -178,7 +175,6 @@ export default function VisualizationFill() {
fetchData();
fetchComparisons();
}, [refresh]);
- console.log(comp);
const fileExist = (path) => {
try {
if (fs.existsSync(path)) {
@@ -188,14 +184,11 @@ export default function VisualizationFill() {
return false;
}
};
- console.log(comp);
const downloadFiles = (row, tracks) => {
let sftp = new Client();
- console.log(tracks);
console.log("download files");
- console.log(homedir);
if (!fs.existsSync(bisepsTemp)) {
fs.mkdirSync(bisepsTemp);
@@ -220,7 +213,6 @@ export default function VisualizationFill() {
if (
!fs.existsSync(path.join(bisepsTemp, path.basename(tracks[track])))
) {
- console.log(path.join(bisepsTemp, path.basename(tracks[track])));
try {
await sftp.fastGet(
tracks[track].split(path.sep).join(path.posix.sep),
@@ -333,11 +325,8 @@ export default function VisualizationFill() {
const blankSample = {};
const helper = {};
const mix = data.concat(comp);
- console.log(mix);
const result = mix.reduce(function (r, o) {
- console.log(r);
const key = o.genome;
- console.log(o.genome);
const genome = path.basename(o.genome);
const genomePath = o.genome;
if (!helper[key]) {
@@ -347,7 +336,6 @@ export default function VisualizationFill() {
return r;
}, []);
- console.log(result);
const handleServe = () => {
// const server = http.createServer(async (request, response) => {
@@ -377,9 +365,7 @@ export default function VisualizationFill() {
public: user.user.jbPath,
});
});
- console.log(user.user.jbPath);
server.listen(port[0], () => {
- console.log(server.listening);
shell.openExternal(`http://localhost:${port[0]}`);
});
@@ -434,7 +420,6 @@ export default function VisualizationFill() {
>
{result.map((genome, idx) => {
const labelId = `checkbox-list-label-${genome}`;
- console.log(idx);
return (
<ListItem
@@ -493,8 +478,6 @@ export default function VisualizationFill() {
<div>
{row.samples.map((sample, idx) => {
const outdir = row.remote ? `${row.remoteDir}` : row.outdir;
- console.log(row);
- console.log(outdir);
const bedGraph = `${outdir}/results/${sample.samplePath}/methylation_extraction_bismark/${sample.samplePath}.deduplicated.sorted.bedGraph.bw`;
const cgBW = `${outdir}/results/${sample.samplePath}/methylation_extraction_bismark/${sample.samplePath}.deduplicated.CX_report.txt.sorted.cg.bw`;
const chgBW = `${outdir}/results/${sample.samplePath}/methylation_extraction_bismark/${sample.samplePath}.deduplicated.CX_report.txt.sorted.chg.bw`;
@@ -512,7 +495,6 @@ export default function VisualizationFill() {
bisepsTemp,
path.basename(samplePath)
);
- console.log(samplePathLocal);
const tracks = [
samplePath,
@@ -527,12 +509,7 @@ export default function VisualizationFill() {
""
);
const associatedGenome = path.parse(associatedGenomePath).name;
- console.log(
- path.join(
- user.user.jbPath,
- `${associatedGenomePath}/${sample.samplePath}.deduplicated.bw`
- )
- );
+
const sampleExist = fileExist(
row.remote ? samplePathLocal : samplePath
@@ -640,8 +617,6 @@ export default function VisualizationFill() {
return (
<>
{row.contexts.map((context) => {
- console.log(context);
- console.log(comparison);
const outdir = row.remote
? `${row.remoteDir}`
: row.outdir;
@@ -668,7 +643,6 @@ export default function VisualizationFill() {
`${associatedGenome}/${comparison.id}-${context}.bed.gz`
)
);
- console.log(checkedComp);
const tracks = [bed, bedtbi];
return (
<ListItem
diff --git a/src/hooks/useAuth.js b/src/hooks/useAuth.js
index 1b42966bfa89c38a58dd352b47ec959a5ed2e3cb..243727371ca9561010a6cefc26233db218dbfb01 100644
--- a/src/hooks/useAuth.js
+++ b/src/hooks/useAuth.js
@@ -84,7 +84,6 @@ const useProvideAuth = () => {
type: GET_ERRORS,
payload: jsbody,
});
- console.log(jsbody);
} else {
// Save to localStorage
// Set token to localStorage
@@ -107,7 +106,6 @@ const useProvideAuth = () => {
req.end();
};
const handleEditProfile = async (userData, dispatch, history) => {
- console.log(userData);
const options = {
method: "PUT",
path: `http://localhost/api/users/${user.user.id}`,
@@ -129,7 +127,6 @@ const useProvideAuth = () => {
res.on("end", function () {
const body = Buffer.concat(chunks).toString();
const jsbody = JSON.parse(body);
- console.log(jsbody);
if ("success" in jsbody) {
// Save to localStorage
@@ -163,18 +160,13 @@ const useProvideAuth = () => {
if (await sessionStorage.jwtToken) {
// Set auth token header auth
const token = sessionStorage.jwtToken;
- console.log(token);
// setAuthToken(token);
// Decode token and get user info and exp
const decoded = jwt_decode(token);
- console.log(decoded);
// Check for expired token
const currentTime = Date.now() / 1000; // to get in milliseconds
if (decoded.exp < currentTime) {
- console.log("yes");
// Remove token from local storage
- console.log(currentTime);
- console.log(decoded.exp);
sessionStorage.removeItem("jwtToken");
// setAuthToken(false);
dispatchUser({
@@ -189,8 +181,6 @@ const useProvideAuth = () => {
type: SET_CURRENT_USER,
payload: decoded,
});
- console.log(decoded);
- console.log(user);
history.push(`${path}`);
}
};
diff --git a/src/index.js b/src/index.js
index fb0579895a28c941159cf4d6615e122336e788c7..e5418ec772d63e68ff0513a1ffbec3896bb0784e 100644
--- a/src/index.js
+++ b/src/index.js
@@ -9,7 +9,6 @@ sessionStorage.setItem("Sock", remote.getGlobal("sharedObj").prop1);
sessionStorage.setItem("Conda", remote.getGlobal("sharedObj").conda);
sessionStorage.setItem("Platform", remote.getGlobal("sharedObj").platform);
-console.log(sessionStorage);
function render() {
ReactDOM.render(
<React.Fragment>
diff --git a/src/main.js b/src/main.js
index e73fe18f895a7d7fc5fbac3d6825fca2d39bfe96..74f9d5828ab8b8618feef1068a1bd58e1e346b59 100644
--- a/src/main.js
+++ b/src/main.js
@@ -11,7 +11,6 @@ const mongod = require("./backend/spawnMongod.js");
const os = require("os");
const path = require("path");
const fs = require("fs");
-console.log(os.tmpdir());
const sock =
process.platform == "win32"
? path.join("\\\\?\\pipe", `biseps${uid}`)
@@ -34,10 +33,7 @@ const mongodLock = path.join(
const homedir = require("os").homedir();
const bisepsTemp = path.join(homedir, ".bisepsTemp/");
-console.log(bisepsTemp);
-console.log(unixSocket);
-console.log(sock);
-console.log(process.platform);
+
exec(
`${