If no files were produced and a sleep occurred, then exit loop in bash script-CodePudding

I have a bash script that does stuff with files that are outputted by a GUI. I have it sleep for some time and if it finds files then it goes back through the loop. However, I want the script to exit if it doesn't find any files after the sleep period but if files are generated during the sleep period then to go back through the loop. But the script gets stuck in the loop to keep sleeping if it doesn't detect any files. My script looks like this:

#!/bin/bash

current_directory=$(pwd)
folder=1
while [ $folder -le 100 ]; do
fast5files=$(ls $current_directory/fast5/ | grep ".fast5" | wc -l)      
if [ $fast5files -ge 1 ]    
then
   mkdir $current_directory/fast5/$folder
   mv $current_directory/fast5/*.fast5 $current_directory/fast5/$folder/
   program does something to fast5files here
   another program does something to fast5files here
     sleep $1         #variable set by user
   ((folder  ))
elif [ $fast5files -eq 0 ]
then
    echo "Couldn't find enough fast5 files. Waiting for 15 seconds"
    sleep 15
        elif [ $fast5files -eq 0 ]
        then
            echo "Exiting script due to not enough fast5 files"
            exit 1
fi
done

CodePudding user response：

You set folder and check it, but never modify it.

folder=1
while [ $folder -le 100 ]; do ...

If it never gets modified, the loop will never end without a manual break or exit or something like that.

Maybe something like -

countFiles() { local lst=( fast5/*.fast5* );
  if [[ -e $lst ]]; then cnt=${#lst[@]}; else return 1; fi;
  return $((!cnt)); 
}

while true; do
  if countFiles
  then echo doing stuff :$cnt:
       flag=0
  elif (( flag > 0 ))
  then echo "Exiting script due to not enough fast5 files"
       exit 1
  else ((  flag))
       echo "Couldn't find enough fast5 files. Waiting for 15 seconds"
       sleep 15
  fi
done

This is quick and sloppy, setting a global from inside a function, etc., but should give you some ideas.

CodePudding user response：

you need to add the exit after the sleep statment. you have created a new elif branch that will never match as it is already matched earlier

#/bin/bash

current_directory=$(pwd)
folder=1
while [ $folder -le 100 ]; do
fast5files=$(ls $current_directory/fast5/ | grep ".fast5" | wc -l)      
if [ $fast5files -ge 1 ]    
then
   # do something here
   return 1
elif [ $fast5files -eq 0 ]
then
    echo "Couldn't find enough fast5 files. Waiting for 15 seconds"
    sleep 15
    echo "now exiting"
    exit 1
fi

That said i don't know why you still want to sleep, and not just exit, you can also just update the loop statement to exit when fast5files is 0 i.e.

#/bin/bash

current_directory=$(pwd)
folder=1
fast5files=1
while [ $folder -le 100 -o $fast5files -ge 0 ]; do
  # do stuff
  sleep 15
  fast5files=$(find -type f -printf '.' -name '*.fast5' | wc -l)
done

fyi nothing in the current script updates the folder parameter so that part of the statement will always be true

CodePudding user response：

You don't need to check if *.fast5 files exist before mving them. Just attempt to mv them and check the exit status of mv. Probably this is what you're looking for:

#!/bin/bash

slept=0
n=1
while ((n <= 100))
do
    mkdir -p fast5/$n || exit
    if mv fast5/*.fast5 fast5/$n 2>/dev/null
    then
        ((  n))
        slept=0
    elif ((!slept))
    then
        sleep 15
        slept=1
    else
        break
    fi
done