SSH in Bash Script Messing Up File Read [duplicate]

Question

I have a script that reads a file line by line and does stuff based on what it reads. One of the things it does is ssh to a remote server and gets some information. For some reason that's completely beyond me, this stops the reading of lines from the file.

The script is essentially (I've cut out a lot of it to simplify the question, so don't worry if it looks like it doesn't really do anything):

cat $csv | while read line; do
   shopt -s nocasematch
   for j in "${file_list[@]}"; do
      found=0;
      for i in $(ssh some_server "ls /some_path/${line:0:1}/${line:1:1}/$line*"); do
         if [[ $i =~ .*$j$ ]]; then
            echo "do something";
            found=1;
            break;
         fi;
      done;
      if [[ $found -ne 1 ]]; then
         echo "don't have $j";
      fi;
      if [[ $found -ne 1 && $j == '\.pdf' ]]; then
         getPDF $line ${dest};
      fi;
   done;
   shopt -u nocasematch
done

This script winds up only running on the first line of the csv. If I replace the "ssh" part of the script with anything else though, it runs all the way through on all lines of the file. What gives?

Is ssh eating your stdin (here, your useless use of cat is stdin) ? Try ssh -n and see what happens ... — Useless
– Useless, Commented Jul 5, 2011 at 15:30
I strongly recommend you always use read -r when doing line by line reading of a file, and you probably want while IFS=$'\n' read -r at that if whitespace is important to you. — sorpigal
– sorpigal, Commented Jul 5, 2011 at 16:43

Ignacio Vazquez-Abrams · Accepted Answer · 2011-07-05 15:25:55Z

10

ssh is consuming stdin. Pass -n.

answered Jul 5, 2011 at 15:25

Ignacio Vazquez-Abrams

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1 Comment

Eli Over a year ago

That did it. Thanks! For those of you looking at this in the future who want more explanation, look up the -n option by running "man ssh." The final working version of the script is the same as above, except that the ssh part reads "ssh -n some_server..."

Charles Duffy · Accepted Answer · 2013-09-12 00:29:53Z

1

If you run commands which read from stdin (such as ssh) inside a loop, you need to ensure that either:

Your loop isn't iterating over stdin
Your command has had its stdin redirected:

The former:

while read -u 5 -r; do
  ssh "$REPLY" ...
done 5<file

...which, using bash 4.1 or newer, can be rewritten with automatic file descriptor assignment as so:

while read -u "$file_fd" -r; do
  ssh "$REPLY" ...
done {file_fd}<file

The latter:

while read -r; do
  ssh "$REPLY" ... </dev/null
done <file

answered Sep 12, 2013 at 0:29

Charles Duffy

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