From 583fd63a36a20185473a31e7a0b389e912a6c366 Mon Sep 17 00:00:00 2001
From: Skander Hatira <skander.hatira@inrae.fr>
Date: Fri, 1 Oct 2021 15:06:01 +0200
Subject: [PATCH] posix file path style
---
resources/mongodbMac.yaml | 1 -
src/backend/helpers/createUnits.js | 1 +
.../routes/api/comparisonController.js | 25 +++++++-----
src/backend/routes/api/runController.js | 39 +++++++++++++------
src/components/Comparisons/ComparisonForm.js | 7 +++-
src/components/Table/NewTable.js | 8 ++--
src/components/Table/Table.js | 6 ++-
7 files changed, 59 insertions(+), 28 deletions(-)
diff --git a/resources/mongodbMac.yaml b/resources/mongodbMac.yaml
index d82a2bd..81c9171 100755
--- a/resources/mongodbMac.yaml
+++ b/resources/mongodbMac.yaml
@@ -13,4 +13,3 @@ dependencies:
- ncurses=6.2=h0a44026_1
- openssl=1.1.1h=haf1e3a3_0
- zlib=1.2.11=h1de35cc_3
-prefix: /Users/shatira/miniconda3/envs/mongodb
diff --git a/src/backend/helpers/createUnits.js b/src/backend/helpers/createUnits.js
index bda48e7..df77e48 100644
--- a/src/backend/helpers/createUnits.js
+++ b/src/backend/helpers/createUnits.js
@@ -3,6 +3,7 @@ const createUnits = (body, uniqueDir) => {
const fs = require("fs");
const path = require("path");
const fields = ["sample", "lane", "techrep", "biorep", "fq1", "fq2"];
+
const opts = { fields, delimiter: "\t" };
console.log("creating units");
if (body.remote) {
diff --git a/src/backend/routes/api/comparisonController.js b/src/backend/routes/api/comparisonController.js
index e7b4063..ff251dd 100644
--- a/src/backend/routes/api/comparisonController.js
+++ b/src/backend/routes/api/comparisonController.js
@@ -31,7 +31,6 @@ router.post("/comparison", (req, res) => {
} else {
console.log("made validation");
if (!req.body.remote) {
- const date = new Date().getTime().toString();
const uniqueDir = path.join(
req.body.outdir,
new Date().getTime().toString()
@@ -100,15 +99,23 @@ router.post("/comparison", (req, res) => {
// "../../../bisepsComparison/",
// date
// );
- const uniqueDir = path.join(
- req.body.outdir,
- new Date().getTime().toString()
- );
- const uniqueDirRemote = path.join(req.body.remoteDir, date);
+ const uniqueDir = path
+ .join(req.body.outdir, new Date().getTime().toString())
+ .split(path.sep)
+ .join(path.posix.sep);
+ const uniqueDirRemote = path
+ .join(req.body.remoteDir, date)
+ .split(path.sep)
+ .join(path.posix.sep);
const profile = req.body.cluster
- ? path.join(uniqueDir, "config/profiles/slurmComparison")
- : path.join(uniqueDir, "config/profiles/localComparison");
- const homeDir = path.join(req.body.remoteDir, date);
+ ? path
+ .join(uniqueDir, "config/profiles/slurmComparison")
+ .split(path.sep)
+ .join(path.posix.sep)
+ : path
+ .join(uniqueDir, "config/profiles/localComparison")
+ .split(path.sep)
+ .join(path.posix.sep);
const newComparison = new Comparison({
outdir: uniqueDir,
diff --git a/src/backend/routes/api/runController.js b/src/backend/routes/api/runController.js
index c971caf..9e1f2a4 100644
--- a/src/backend/routes/api/runController.js
+++ b/src/backend/routes/api/runController.js
@@ -30,11 +30,14 @@ router.post("/run", (req, res) => {
return res.status(400).json(errors);
} else {
if (!req.body.remote) {
- const uniqueDir = path.join(
- req.body.outdir,
- new Date().getTime().toString()
- );
- const profile = path.join(uniqueDir, "config/profiles/local");
+ const uniqueDir = path
+ .join(req.body.outdir, new Date().getTime().toString())
+ .split(path.sep)
+ .join(path.posix.sep);
+ const profile = path
+ .join(uniqueDir, "config/profiles/local")
+ .split(path.sep)
+ .join(path.posix.sep);
const newRun = new Run({
params: {
@@ -90,13 +93,28 @@ router.post("/run", (req, res) => {
spawnChild(req.body, profile, uniqueDir, "", false);
} else {
const date = new Date().getTime().toString();
- const uniqueDir = path.join(req.body.outdir, date);
- const uniqueDirRemote = path.join(req.body.remoteDir, date);
- const homeDir = path.join(req.body.remoteDir, date);
+ const uniqueDir = path
+ .join(req.body.outdir, date)
+ .split(path.sep)
+ .join(path.posix.sep);
+ const uniqueDirRemote = path
+ .join(req.body.remoteDir, date)
+ .split(path.sep)
+ .join(path.posix.sep);
+ const homeDir = path
+ .join(req.body.remoteDir, date)
+ .split(path.sep)
+ .join(path.posix.sep);
console.log(homeDir);
const profile = req.body.cluster
- ? path.join(uniqueDir, "config/profiles/slurm")
- : path.join(uniqueDir, "config/profiles/local");
+ ? path
+ .join(uniqueDir, "config/profiles/slurm")
+ .split(path.sep)
+ .join(path.posix.sep)
+ : path
+ .join(uniqueDir, "config/profiles/local")
+ .split(path.sep)
+ .join(path.posix.sep);
const newRun = new Run({
outdir: uniqueDir,
@@ -214,7 +232,6 @@ router.post("/rerun", function (req, res) {
req.body.cluster ? "config/profiles/slurm" : "config/profiles/local"
);
const uniqueDirRemote = req.body.remoteDir;
- const homeDir = path.join(req.body.remoteDir, uniqueDirRemote);
spawnChild(
req.body,
profile,
diff --git a/src/components/Comparisons/ComparisonForm.js b/src/components/Comparisons/ComparisonForm.js
index ef0f70e..b124ae3 100644
--- a/src/components/Comparisons/ComparisonForm.js
+++ b/src/components/Comparisons/ComparisonForm.js
@@ -300,7 +300,12 @@ export default function ComparisonForm() {
console.log(e.target.value);
const newFiles = [];
for (const file in e.target.value) {
- newFiles.push(path.join("data/", path.basename(e.target.value[file])));
+ newFiles.push(
+ path
+ .join("data/", path.basename(e.target.value[file]))
+ .split(path.sep)
+ .join(path.posix.sep)
+ );
console.log(e.target.value);
console.log(newFiles);
diff --git a/src/components/Table/NewTable.js b/src/components/Table/NewTable.js
index c02386d..a5cd988 100644
--- a/src/components/Table/NewTable.js
+++ b/src/components/Table/NewTable.js
@@ -321,10 +321,10 @@ export default function NewTable() {
console.log(e.target.dataset.idx);
const updatedRemoteUnits = [...remoteunits];
- updatedRemoteUnits[e.target.dataset.idx][e.target.id] = path.join(
- "data",
- path.basename(e.target.files[0].path)
- );
+ updatedRemoteUnits[e.target.dataset.idx][e.target.id] = path
+ .join("data", path.basename(e.target.files[0].path))
+ .split(path.sep)
+ .join(path.posix.sep);
setRemoteUnits(updatedRemoteUnits);
updatedUnits[e.target.dataset.idx][e.target.id] = e.target.files[0].path;
diff --git a/src/components/Table/Table.js b/src/components/Table/Table.js
index 6c58a9e..499f44c 100644
--- a/src/components/Table/Table.js
+++ b/src/components/Table/Table.js
@@ -111,7 +111,6 @@ export default function InteractiveList() {
console.log(row);
let remotePath = `${row.remoteDir}/${filePath}`;
let localPath = row.date + filePath;
- console.log(path.join(bisepsTemp, localPath));
sftp
.connect({
host: row.machine.hostname,
@@ -127,7 +126,10 @@ export default function InteractiveList() {
console.log(localPath);
console.log("made it all the way here?");
- return sftp.fastGet(remotePath, path.join(bisepsTemp, localPath));
+ return sftp.fastGet(
+ remotePath,
+ path.join(bisepsTemp, localPath).split(path.sep).join(path.posix.sep)
+ );
})
.then((data) => {
console.log(data);
--
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