harvest

#!/bin/bash
source commons.bash

export FILTER_DATASETS=""
export TAGS="latest"
export SYMLINK="NO"

# Parse args
POSITIONAL=()
while [[ $# -gt 0 ]]
do
key="$1"
case $key in
    --datasets)
	# Split string using ',' separator
	IFS=',' read -ra DST <<< "$2"
    export FILTER_DATASETS=("${DST[@]}")
    shift # past argument
    shift # past value
    ;;
    --tags)
	# Split string using ',' separator
	IFS=',' read -ra DST <<< "$2"
    export TAGS=("${DST[@]}")
    shift # past argument
    shift # past value
    ;;
    --symlink)
    export SYMLINK=YES
    shift # past argument
    ;;
    --help)
    export HELP=YES
    shift # past argument
    ;;
    *)    # unknown option
    POSITIONAL+=("$1") # save it in an array for later
    shift # past argument
    ;;
esac
done
set -- "${POSITIONAL[@]}" # restore positional parameter

usage(){
  echo "Usage: $0 [options] <group> <odm_orthophoto.tif,\"*.laz\",...> <destination directory>"
  echo
  echo "Copy test results to a folder."
  echo
  echo "Group:"
  for group in groups/*.bash; do
  	source $group
  	echo "	$(basename $group .bash)	${DATASETS[@]}"
  done
  echo
  echo "Options:"
  echo "	--datasets <dataset1,dataset2,...>	Copy only the specified datasets from the group"
  echo "	--tags	<tag1,tag2,...>	Copy only results from these tags. (default: latest)"
  echo "	--symlink	Use symlinks instead of file copies (to save space and for speed)."
  exit
}

environment_check(){
	check_command "find" "Run \033[1msudo apt install -y findutils\033[0m" "sudo apt install -y findutils"
	check_command "sed" "Run \033[1msudo apt install -y sed\033[0m" "sudo apt install -y sed"
}

environment_check

group=${POSITIONAL[0]}
pattern=${POSITIONAL[1]}
destination=${POSITIONAL[2]}

if [ "$HELP" == "YES" ] || [ -z "$pattern" ] || [ -z "$destination" ]; then
	usage
fi

if [ -e "groups/$group.bash" ]; then
	get_datasets_for_group "$group" "${FILTER_DATASETS[@]}"

	for dataset in "${datasets[@]}"; do
		for tag in "${TAGS[@]}"; do
			files=()
			while IFS=  read -r -d $'\0'; do
			    files+=("$REPLY")
			done < <(cd results && find $tag/$dataset/ -name "$pattern" 2>/dev/null -print0)

			if [ ! -z "$files" ]; then
				if [ ! -e "$destination" ]; then
					mkdir -p "$destination"
					echo "Created directory $destination"
				fi
			fi

			if [ ! -z "$files" ]; then
				echo $files
				for file in "${files[@]}"; do
					dst_filename=$(sed "s/\//-/g" <<< $file)

					if [ "$SYMLINK" == "YES" ]; then
						if [ -L "$destination/$dst_filename" ]; then
							rm "$destination/$dst_filename"
						fi

						ln -sv "$(pwd)/""results/$file" "$destination/$dst_filename"
					else
						cp -v "results/$file" "$destination/$dst_filename"
					fi
				done
			fi
		done
	done
else
	usage
fi