From 916c07b247b88144eb40e0a29da9229224a8e48a Mon Sep 17 00:00:00 2001
From: Skander Hatira <skander.hatira@inrae.fr>
Date: Wed, 18 Aug 2021 11:31:10 +0200
Subject: [PATCH] working in dev
---
resources/biseps | 2 +-
.../Visualization/VisualizationFill.js | 20 +++++++++----------
2 files changed, 11 insertions(+), 11 deletions(-)
diff --git a/resources/biseps b/resources/biseps
index 6e471e8..288f26b 160000
--- a/resources/biseps
+++ b/resources/biseps
@@ -1 +1 @@
-Subproject commit 6e471e82b11342bf39d0516f7a10ede827dcdf30
+Subproject commit 288f26b082865e7c2904ab458372574c6c926eb5
diff --git a/src/components/Visualization/VisualizationFill.js b/src/components/Visualization/VisualizationFill.js
index b17ae5a..7a47c49 100644
--- a/src/components/Visualization/VisualizationFill.js
+++ b/src/components/Visualization/VisualizationFill.js
@@ -357,8 +357,8 @@ export default function VisualizationFill() {
const handleServe = () => {
try {
- const server = http.createServer((request, response) => {
- return handler(request, response, {
+ const server = http.createServer(async (request, response) => {
+ await handler(request, response, {
public: user.user.jbPath,
});
});
@@ -372,8 +372,8 @@ export default function VisualizationFill() {
retrieve: 1,
})
.then(function (port) {
- const server = http.createServer((request, response) => {
- return handler(request, response, {
+ const server = http.createServer(async (request, response) => {
+ await handler(request, response, {
public: user.user.jbPath,
});
});
@@ -486,12 +486,12 @@ export default function VisualizationFill() {
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`;
const chhBW = `${outdir}/results/${sample.samplePath}/methylation_extraction_bismark/${sample.samplePath}.deduplicated.CX_report.txt.sorted.chh.bw`;
- const samplePath = `${outdir}/results/${sample.samplePath}/alignment_bismark/${sample.samplePath}.deduplicated.bam`;
+ const samplePath = `${outdir}/results/${sample.samplePath}/alignment_bismark/${sample.samplePath}.deduplicated.bw`;
const bedGraphLocal = path.join(
bisepsTemp,
path.basename(bedGraph)
);
- const samplePathBai = `${outdir}/results/${sample.samplePath}/alignment_bismark/${sample.samplePath}.deduplicated.bam.bai`;
+ // const samplePathBai = `${outdir}/results/${sample.samplePath}/alignment_bismark/${sample.samplePath}.deduplicated.bam.bai`;
const cgBWLocal = path.join(bisepsTemp, path.basename(cgBW));
const chgBWLocal = path.join(bisepsTemp, path.basename(chgBW));
const chhBWLocal = path.join(bisepsTemp, path.basename(chhBW));
@@ -507,7 +507,7 @@ export default function VisualizationFill() {
cgBW,
chgBW,
chhBW,
- samplePathBai,
+ // samplePathBai,
];
const associatedGenomePath = row.genome.replace(
/^.*[\\\/]/,
@@ -518,7 +518,7 @@ export default function VisualizationFill() {
console.log(
path.join(
user.user.jbPath,
- `${associatedGenomePath}/${sample.samplePath}.deduplicated.bam`
+ `${associatedGenomePath}/${sample.samplePath}.deduplicated.bw`
)
);
console.log(associatedGenomePath);
@@ -532,7 +532,7 @@ export default function VisualizationFill() {
!fileExist(
path.join(
user.user.jbPath,
- `${associatedGenome}/${sample.samplePath}.deduplicated.bam`
+ `${associatedGenome}/${sample.samplePath}.deduplicated.bw`
)
) &&
fileExist(
@@ -577,7 +577,7 @@ export default function VisualizationFill() {
fileExist(
path.join(
user.user.jbPath,
- `${associatedGenome}/${sample.samplePath}.deduplicated.bam`
+ `${associatedGenome}/${sample.samplePath}.deduplicated.bw`
)
) &&
fileExist(
--
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