You didn't make all of the changes I suggested and you made some changes I didn't suggest. Let's analyze the commands being run inside the for loop. (I've removed the semicolons and split the commands onto separate lines to make it easier to read.) With the reformatting, you have:

Code:

$(grep -i "^..............ASPRODUCTSUMMARY"< "$i" > "newtemp.csv")
$(mv -v newtemp.csv "$i")

Since you have $(...) around both of these commands, the shell executes the grep (which succeeded the first time) and then tried to execute the output produced by the grep. I assume this gave you the first command not found error.

Then the mv command executes producing output that looks something like and then tries to execute that string (which I assume gave you a error message.) Remove the $( and the matching ) from both of these commands and you should make some progress.

Then you have a for loop starting with:

Code:

for file in $(ls -l)

this executes the loop nine times for every file found in the directory. The first time through the loop, $file will be something like -rw-r--r--; the second time through the loop, $file will be the number of links to the file; ...; and the ninth time through the loop for each file, $file will be set to the name of a file. I had suggested that you change your original '$(ls -l $FOLDERDIR)' to '$(ls)'. I made a mistake leaving in the single quotes (and you corrected that. Thank you. But leaving $(ls -l) instead of $(ls) gives you a big problem.

Then in the final while loop you have another mv -v command inside $(...) which I assume is giving you several more command not found errors. Get rid of the $( and the matching ) again here.

Please also reformat this. It has been noted (and you agreed) that this code is a disaster. It looks like you are trying to minimize the number of lines of code in your script instead of trying to make it easy to understand. This may make sense when you have a simple program that can be written as a single line; but in a case like this it just makes your script unreadable. Don't you agree that:

Code:

for i in $(ls -l | grep '^-' | awk '{print $9}')
do 
        grep -i "^..............ASPRODUCTSUMMARY" < "$i" > "newtemp.csv"        mv -v newtemp.csv "$i"
done
for file in $(ls)
do
        caseid=$(echo "$file" | cut -c1-10)
        studytype=$(echo "$file" | cut -c12-15)
        prefix="$caseid,$studytype,"
        while read -r line
        do      echo "$prefix$line"
        done < "$file" > temp.CSV
        mv -v temp.CSV "$i"
done
exit 0

is a lot easier to read and understand than:

Code:

for i in $(ls -l | grep '^-' | awk '{print $9}');do  
grep -i "^..............ASPRODUCTSUMMARY"< "$i" > "newtemp.csv"
mv -v newtemp.csv "$i";done;for file in $(ls);do
caseid=$(echo "$file" | cut -c1-10);studytype=$(echo "$file" | cut -c12-15)
prefix="$caseid,$studytype,";while read -r line;do;echo "$prefix$line"
done < "$file" > temp.CSV;mv -v temp.CSV "$i";done;exit 0

The code above is an exaggeration of the formatting you're using, but not by much.

There are some problems that will arise even with this if any of the file names encountered while running ls contain any spaces, tabs, or newlines. I will assume for now that these directories are always being updated programmatically and that other users don't have permission to create any files in these directories.