From eb85dbb6f468448acda61306623e9512c33381b0 Mon Sep 17 00:00:00 2001
From: Skander Hatira <skander.hatira@inrae.fr>
Date: Thu, 31 Mar 2022 13:38:33 +0200
Subject: [PATCH] added notifications button for slurm mails
---
resources/biseps | 2 +-
src/backend/helpers/createProfile.js | 8 +++++---
src/backend/helpers/createProfileComparison.js | 8 +++++---
src/components/ComparisonStepper/GlobalConfig.js | 14 ++++++++++++++
src/components/Login/Login.js | 8 +++++---
src/components/Stepper/GlobalConfig.js | 14 ++++++++++++++
src/components/Table/Table.js | 1 +
src/hooks/useConfig.js | 2 ++
8 files changed, 47 insertions(+), 10 deletions(-)
diff --git a/resources/biseps b/resources/biseps
index 418fbdd..876f966 160000
--- a/resources/biseps
+++ b/resources/biseps
@@ -1 +1 @@
-Subproject commit 418fbdd0d56a33f9c48f1dcf5aa16e4f38f65009
+Subproject commit 876f966022371d2c9c0a6236bd109f851f48475f
diff --git a/src/backend/helpers/createProfile.js b/src/backend/helpers/createProfile.js
index f44f512..c7ea6e4 100644
--- a/src/backend/helpers/createProfile.js
+++ b/src/backend/helpers/createProfile.js
@@ -27,9 +27,11 @@ function createProfile(body, uniqueDir, uniqueDirRemote) {
};
const slurmProfile = {
jobs: parseInt(body.jobs),
- cluster:
- "sbatch -t {resources.time_min} --mem={resources.mem_mb} -c {resources.cpus} -o logs_slurm/{rule}_{wildcards} -e logs_slurm/{rule}_{wildcards} --mail-type=FAIL,END --mail-user=" +
- body.email,
+ cluster: body.notification
+ ? "sbatch -t {resources.time_min} --mem={resources.mem_mb} -c {resources.cpus} -o logs_slurm/{rule}_{wildcards} -e logs_slurm/{rule}_{wildcards}" +
+ "--mail-type=FAIL,END --mail-user=" +
+ body.email
+ : "sbatch -t {resources.time_min} --mem={resources.mem_mb} -c {resources.cpus} -o logs_slurm/{rule}_{wildcards} -e logs_slurm/{rule}_{wildcards}",
"default-resources": ["cpus=1", "mem_mb=10000", "time_min=5440"],
configfile: body.remote
? "config/config.yaml"
diff --git a/src/backend/helpers/createProfileComparison.js b/src/backend/helpers/createProfileComparison.js
index 01b4584..5265577 100644
--- a/src/backend/helpers/createProfileComparison.js
+++ b/src/backend/helpers/createProfileComparison.js
@@ -29,9 +29,11 @@ function createProfile(body, uniqueDir, uniqueDirRemote) {
};
const slurmProfile = {
jobs: parseInt(body.jobs),
- cluster:
- "sbatch -t {resources.time_min} --mem={resources.mem_mb} -c {resources.cpus} -o logs_slurm/{rule}_{wildcards} -e logs_slurm/{rule}_{wildcards} --mail-type=FAIL,END --mail-user=" +
- body.email,
+ cluster: body.notification
+ ? "sbatch -t {resources.time_min} --mem={resources.mem_mb} -c {resources.cpus} -o logs_slurm/{rule}_{wildcards} -e logs_slurm/{rule}_{wildcards}" +
+ "--mail-type=FAIL,END --mail-user=" +
+ body.email
+ : "sbatch -t {resources.time_min} --mem={resources.mem_mb} -c {resources.cpus} -o logs_slurm/{rule}_{wildcards} -e logs_slurm/{rule}_{wildcards}",
"default-resources": ["cpus=1", "mem_mb=10000", "time_min=5440"],
configfile: body.remote
? "config/configComparison.yaml"
diff --git a/src/components/ComparisonStepper/GlobalConfig.js b/src/components/ComparisonStepper/GlobalConfig.js
index af9f7d5..304c4cb 100644
--- a/src/components/ComparisonStepper/GlobalConfig.js
+++ b/src/components/ComparisonStepper/GlobalConfig.js
@@ -609,6 +609,20 @@ export default function GlobalConfig() {
label="SLURM Cluster"
></FormControlLabel>
</Grid>
+ <Grid item xs={12} sm={4}>
+ <FormControlLabel
+ className={classes.formControl}
+ control={
+ <Checkbox
+ onChange={handleCheckBox}
+ color="secondary"
+ name="notification"
+ checked={compState.notification}
+ />
+ }
+ label="Send Email Notification"
+ ></FormControlLabel>
+ </Grid>
</Grid>
) : (
<Grid item xs={12} sm={4}>
diff --git a/src/components/Login/Login.js b/src/components/Login/Login.js
index 9ac0d51..b1b7815 100644
--- a/src/components/Login/Login.js
+++ b/src/components/Login/Login.js
@@ -83,7 +83,7 @@ const Login = () => {
signup(userData, dispatch, history);
};
const { errors } = state;
-
+ console.log(errors);
return (
<Container component="main" maxWidth="md">
<CssBaseline />
@@ -99,7 +99,7 @@ const Login = () => {
onChange={onChange}
value={state.name}
error={errors.name === ""}
- helperText={errors.name === "" ? "Empty!" : errors.name}
+ helperText={errors.name === "" ? "Empty!" : errors.namenotfound}
className={classnames("", {
invalid: errors.name || errors.namenotfound,
})}
@@ -118,7 +118,9 @@ const Login = () => {
onChange={onChange}
value={state.password}
error={errors.password === ""}
- helperText={errors.password === "" ? "Empty!" : errors.password}
+ helperText={
+ errors.password === "" ? "Empty!" : errors.passwordincorrect
+ }
className={classnames("", {
invalid: errors.password || errors.passwordincorrect,
})}
diff --git a/src/components/Stepper/GlobalConfig.js b/src/components/Stepper/GlobalConfig.js
index bb70b33..295117d 100644
--- a/src/components/Stepper/GlobalConfig.js
+++ b/src/components/Stepper/GlobalConfig.js
@@ -441,6 +441,20 @@ export default function GlobalConfig() {
label="SLURM Cluster"
></FormControlLabel>
</Grid>
+ <Grid item xs={12} sm={4}>
+ <FormControlLabel
+ className={classes.formControl}
+ control={
+ <Checkbox
+ onChange={handleCheckBox}
+ color="secondary"
+ name="notification"
+ checked={runState.notification}
+ />
+ }
+ label="Send Email Notification"
+ ></FormControlLabel>
+ </Grid>
</Grid>
) : (
<Grid item xs={12} sm={4}>
diff --git a/src/components/Table/Table.js b/src/components/Table/Table.js
index 346a06a..8d762a4 100644
--- a/src/components/Table/Table.js
+++ b/src/components/Table/Table.js
@@ -172,6 +172,7 @@ export default function InteractiveList() {
sftp.end();
})
.catch((err) => {
+ setLoading((prevState) => ({ ...prevState, [idx]: false }));
console.error(err.message);
sftp.end();
});
diff --git a/src/hooks/useConfig.js b/src/hooks/useConfig.js
index aa10df8..fdfc0d7 100644
--- a/src/hooks/useConfig.js
+++ b/src/hooks/useConfig.js
@@ -35,6 +35,7 @@ const useProvideConfig = () => {
l: 20,
n: 0,
subsample: false,
+ notification: true,
cluster: false,
remote: false,
cpu: "1",
@@ -63,6 +64,7 @@ const useProvideConfig = () => {
contexts: ["CpG"],
genome: "",
species: "",
+ notification: true,
annot: "",
remoteDir: "",
outdir: "",
--
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