Good, that’s progress. Scanning the source is working and we entered the actual Java code.
Now it seem the target file is not properly set.
You could add echos to the loop body:
To see how the variables are set
sourceFile="$(realpath "$F")"
echo ${sourceFile}
targetFile="${targetDirectory}/${targetFilePrefix}_$(removeExtension "$(basename ${F})").dim"
echo ${targetFile}
echo "${gptPath} ${graphXmlPath} -e -p ${parameterFilePath} -t ${targetFile} ${sourceFile}"
Hi Marco,
his problem is the parameters part. I sent to him new bash file before with echo in RUS Support chat room but I don’t know why he still uses the last one
his bash file must be like this:
#!/bin/bash
############################################
############################################
#export PATH=~/Research/Checking_Bulk_GPT/output:$PATH
#gptPath="~/snap.bak/bin/gpt"
export PATH=~/progs/snap/bin:$PATH
gptPath="/home/shosseini/snap.bak/bin/gpt"
#gptPath=“gpt”
############################################
############################################
graphXmlPath="$1"
#graphXmlPath="/home/shosseini/Research/Checking_Bulk_GPT/outout/spk.xml"
#parameterFilePath="$2"
sourceDirectory="$2"
#sourceDirectory="/home/shosseini/Research/Checking_Bulk_GPT"
targetDirectory="$3"
#targetDirectory="/home/shosseini/Research/Checking_Bulk_GPT/output"
targetFilePrefix="$4"
#targetFilePrefix=“spk”
############################################
############################################
removeExtension() {
file="1"
echo "(echo “file" | sed -r 's/\.[^\.]*//’)”
}
############################################
############################################
mkdir -p “${targetDirectory}”
for F in (ls -1d "{sourceDirectory}"/S1*.SAFE); do
sourceFile="$(realpath “F")"
targetFile="{targetDirectory}/{targetFilePrefix}_(removeExtension “(basename {F})”).dim”
echo “Executing :” “{gptPath} {graphXmlPath} -e -t {targetFile} {sourceFile}”
#echo “===============”
#{gptPath} {graphXmlPath} -e -p {parameterFilePath} -t {targetFile} {sourceFile}
{gptPath} {graphXmlPath} -e -t {targetFile} ${sourceFile}
done
Hi Samira, I tried the last one you sent, but it has problem, also as I edit up the file, it is not necessary to unzip the files because the code could read the zip, I’ll give this try, of @marpet
Hi Falah, the one that you use is not last version.
in the last version there is echo to show the path and I removed the parameters part…
Yes you’re totally right, but I meant that I tried the last one you sent with echo correction, it gave error, but might be the capital letter ZIP, was used, your comment is important 
, so now the one I used is available here, anything else to edit or add up,
processDataset.bash (2.0 KB)
why you have this part in your bash file: -p ${parameterFilePath}
I added up the echo, as the last version here,
but still gives error,
in this line:
{gptPath} {graphXmlPath} -e -p {parameterFilePath} -t {targetFile} ${sourceFile}
remove -p ${parameterFilePath}
that’s why i tell you it is not last version
I just now added it up according to @marpet suggestion,
OK you must remove -p {parameterFilePath} because in your bash (upper parts) it is uncommented. you didn't introduce parametes file to it. then remove this part(-p {parameterFilePath} ) in your bash file.
the whole statement should be removed, or only the -p
only -p ${parameterFilePath}
It’ll be in this form, right?
echo “{gptPath} {graphXmlPath} -e -t {targetFile} {sourceFile}”
it must be like this: {gptPath} {graphXmlPath} -e -t {targetFile} {sourceFile}
with out echo
in the for loop must be wrriten:
sourceFile="$(realpath “F")" targetFile="{targetDirectory}/{targetFilePrefix}_(removeExtension “(basename {F})”).dim”
echo “Executing :” “{gptPath} {graphXmlPath} -e -t {targetFile} {sourceFile}”
#echo “===============”
#{gptPath} {graphXmlPath} -e -p {parameterFilePath} -t {targetFile} {sourceFile}
{gptPath} {graphXmlPath} -e -t {targetFile} ${sourceFile}
sourceFile="$(realpath “F")"
echo {sourceFile}
targetFile=”{targetDirectory}/{targetFilePrefix}_(removeExtension "(basename {F})").dim"
echo “Executing :” “gptPath{graphXmlPath} -e -t targetFile{sourceFile}”
#echo “===============”
#gptPath{graphXmlPath} -e -p parameterFilePath−t{targetFile} sourceFile{gptPath} graphXmlPath−e−t{targetFile} {sourceFile}
yes.I think it is right…
