#!/bin/bash
#
# A simple script which would establish a folder with entry points to the tools
# from a folder where a specific tool is found under for a given image.
# ATM hardcoded for neurodesk images of FSL.

# Should be made as parameters, hardcoded for now
image=neurodesk/neurodesk-fsl--6.0.7.4.simg
image_path="$(dirname "$0" | xargs readlink -f)/../images/$image"
tool=bet
# That was not good enough
#toolkit_pattern='\(\<FSL\>\|fsl-.*python\|fslmaths\)'
toolkit_pattern='.'

set -eu
out_path="$1"

function sing_exec() {
    singularity exec "$image_path" "$@"
}

set -eu
tool_path=$(sing_exec which "$tool")
tool_binpath=$(dirname "$tool_path")

mkdir -p "$out_path"
echo "INFO: Creating wrapper ._exec"
echo "#\!/bin/sh

img='$image_path'
bindir='$tool_binpath'

toolname=\"\$(basename \"\$0\")\"
singularity exec \"\$img\" \"\$toolname\" \"\$@\""  > "$out_path/._exec"
chmod a+x "$out_path/._exec"

echo "INFO: Populating shim symlinks - "
sing_exec bash -c "find '$tool_binpath' -maxdepth 1 -type f -perm /+x -print0  |  xargs -0 grep -l '$toolkit_pattern'" \
| while read -r tool_to_link_path; do
    tool_to_link="$(basename "$tool_to_link_path")"
    echo -n " $tool_to_link"
    ln -s ._exec "$out_path/$tool_to_link"
done
echo

nf=$(find "$out_path" -type l -lname ._exec | wc -l)
echo "INFO: Seeing $nf symlinks under '$out_path' now."
if echo "$PATH" | grep -q "$out_path:"; then
    echo "INFO: It seems that PATH already contains $out_path"
else
    echo "INFO: Do  export PATH=\"$out_path:\$PATH\""
fi