mjhjmtu

I need two make a new bash array, not including elements which are in second one. And then use this array in while loop:

while [ -n "$ids_toproc[0]" ] ; do

Here is a code a implemented:

all_ids=( /input/sub-* )
all_ids=( "$all_ids[@]#/input/sub-" )
all_ids=( "$all_ids[@]%/" )

exist_ids=( /output/fmriprep/sub-*.html )
exist_ids=( "$exist_ids[@]#/output/fmriprep/sub-" )
exist_ids=( "$exist_ids[@]%/" )
exist_ids=( "$exist_ids[@]%%.*" ) # delete extention

ids_toproc=( `echo $all_ids[@] $exist_ids[@] | tr ' ' 'n' | sort | uniq -u` )

Is code is ok? is it right way to do compare?

This is a follow-up question to "shell script inside docker". Thanks for posting it as a separate issue!

What I would probably have done here, since the creation of your all_ids array needs to be slightly more complicated than just parsing the ID out from directory names, is to use a loop in which each ID is checked against the filenames the /output/fmriprep directory. If no output file is found for a given ID, then the ID is added to the all_ids list.

all_ids=()
for dirname in /input/sub-*/; do
 id=$dirname#/input/sub- # remove "/input/sub-"
 id=$id%/ # remove trailing "/"

 if [ ! -e "/output/fmriprep/sub-$id.html" ]; then
 # no output file corresponding to this ID found,
 # add it to he list
 all_ids+=( "$id" )
 fi
done