.circ

# Print usage information
_ci_usage() {
	cat <<-MSG
		Run CI tests

		Commands:
		run          run the pipeline in '\$CI_DIR'
		check        compute checksums and validate results
		clean        remove the temporary directory used for vaildation

		Notes:
		If '\$CI_DIR' is in the Nextflow asset folder the pipeline is run using the GitHub repository
		to allow to change revision from the comand line, e.g.:

		CI_DIR=~/.nextflow/assets/guigolab/grape-nf ci test -r v0.4.1
	MSG
}

# Get canonical path of either a directory or a file
_ci_canonicalize_path() {
    if [ -d "$1" ]; then
        _ci_canonicalize_dir_path "$1"
    else
        _ci_canonicalize_file_path "$1"
    fi
}

# Get canonical path of a directory
_ci_canonicalize_dir_path() {
    (cd "$1" 2>/dev/null && pwd -P)
}

# Get canonical path of a file
_ci_canonicalize_file_path() {
    local dir file
    dir=$(dirname -- "$1")
    file=$(basename -- "$1")
    (cd "$dir" 2>/dev/null && printf '%s/%s\n' "$(pwd -P)" "$file")
}

# Check that Nextflow is installed and download it to the current
# folder otherwise
_ci_setup_nxf() {
	if ! nextflow &>/dev/null; then
		export PATH=$PWD:$PATH
		if [ ! -x nextflow ]; then
			curl -fsSL get.nextflow.io | bash && chmod +x nextflow
		fi
	fi
}

# Get the content of a BAM file for checksum
_ci_normalize_bam() {
	docker run --rm -v $CI_DIR:$CI_DIR -v $1:$1 -w $PWD grapenf/samtools:1.3.1 bash -c "samtools view -h $2 | grep -v '@CO\|@PG' | LC_ALL=C sort > $(basename $2) 2>/dev/null"
}

# Get file to the CI output directory either by creating a symlink
# or normalizing a BAM file
_ci_get_file() {
	local baseDir=$1
	local filename=$2
	case "$filename" in
		*.bam)
			_ci_normalize_bam "$baseDir" "$filename" ;;
		*.bed|*.bw|*.results|*.json|*.g[tf]f)
			ln -fs "$filename";;
		*)
			echo "'${filename##*.}' extension not supported";;
	esac
}

# Get current script being sourced
_ci_get_script_dir() {
	local CI_SCRIPT="$1"
	if [ ! -z "$BASH_SOURCE" ]
	then
		CI_SCRIPT=${BASH_SOURCE[0]}
	fi
	echo $(_ci_canonicalize_path $(dirname ${CI_SCRIPT}))
}

# Run the pipeline for CI
_ci_run() {
	local WF=${CI_DIR}
	if [[ "$CI_DIR" =~ "$HOME/.nextflow/asset" ]]; then
		local ORG=$(basename $(dirname $CI_DIR))
		local REPO=$(basename $CI_DIR)
		WF="${ORG}/${REPO}"
	fi
	_ci_setup_nxf && nextflow run ${WF} -profile $CI_PROFILE "${CI_RUNOPTS[@]}" "$@"
}

# Check pipeline results for CI
_ci_check() {
	(mkdir -p $CI_OUTDIR && cd $CI_OUTDIR
	echo $CI_PROFILE > .ci_profile
	cut -f 3 ../pipeline.db | while read f
	do
		_ci_get_file $(_ci_canonicalize_path ..) $f
	done
	md5sum -c ${CI_DIR}/data/$CI_PROFILE.md5)
}

# Cleanup CI result directory
_ci_clean() {
	rm --interactive=never -r $CI_OUTDIR
}

# Perform a ful CI test
_ci_test() {
	# Define colors
	local RED="\033[1;31m"
	local GREEN="\033[1;32m"
	local YELLOW="\033[1;33m"
	local BLUE="\033[1;34m"
	local NORMAL="\033[0m"

	echo -e "==$YELLOW Running with profile -> $BLUE${CI_PROFILE}$NORMAL" \
	&& _ci_run "$@" \
	&& echo -e "==$YELLOW Compute MD5 checksums$NORMAL" \
	&& _ci_check \
	&& echo -e "==$GREEN SUCCESS$NORMAL" \
	&& echo -e "==$YELLOW Cleaning up$NORMAL" \
	&& _ci_clean \
	&& echo -e "==$YELLOW DONE$NORMAL" && exit 0 \
	|| echo -e "==$RED FAILED$NORMAL" && exit 1
}

# Main command
ci() {
	case $1 in
		run)
			shift
			(_ci_run "$@");;
		check)
			shift
			(_ci_check);;
		clean)
			shift
			(_ci_clean);;
		test)
			shift
			(_ci_test "$@");;
		*)
			_ci_usage;;
	esac
}

# Define CI environment variables
CI_DIR=$(_ci_get_script_dir $0)
CI_LOG=pipeline-ci.log
CI_PROFILE="starrsem"
CI_OUTDIR="checksum"
CI_RUNOPTS=("-process.errorStrategy=terminate" "-with-docker")