regression_tests.sh

#!/bin/bash
set -e

THREADS=5

# https://stackoverflow.com/questions/59895/
HERE="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
VPIPEROOT=${HERE}/..

if [[ -z "${1}" ]]; then
	echo "Usage: $0 <virus>" >&2
	exit 2
elif [[ ! "${1}" =~ ^[[:alnum:]_-]+$ ]]; then
	echo "Bad virus name $1" >&2
	exit 2
elif [[ ! -f ${VPIPEROOT}/config/${1}.yaml ]]; then
	echo "Missing virus base config for ${1}" >&2
	exit 2
elif [[ ! -d ${VPIPEROOT}/tests/data/${1}/ ]]; then
	echo "Missing virus test data for ${1}" >&2
	exit 2
fi
VIRUS=$1

CWD=$(pwd)
# shellcheck disable=SC2317  # ShellCheck may incorrectly believe that code is unreachable if it's invoked in a trap
function restore_wd {
    cd "${CWD}"
}
trap restore_wd EXIT

PROJECT_DIR=/tmp/project/${VIRUS}

function setup_project {
    PROJECT_DIR=$(mktemp -d)
    pushd "${PROJECT_DIR}"
    "${VPIPEROOT}/init_project.sh"
    popd
}

# setup project files when not run on via github actions
[ -z "$CI" ] && setup_project


function run_workflow {

    pushd "${PROJECT_DIR}"
    mkdir config
    cat > config/config.yaml <<CONFIG
general:
    virus_base_config: "${VIRUS}"

output:
    snv: true
    local: true
    global: false
    visualization: true
    diversity: true
    QA: true
    upload: true

upload:
    orig_cram: true

snv:
    threads: ${THREADS}
CONFIG
    cat > config/config-trim.yaml <<CONFIG_TRIM
output:
    trim_primers: true
CONFIG_TRIM
    config_file=( "config/config.yaml" )

    data_root="${VPIPEROOT}/tests/data/${VIRUS}/"
    # does this test data provides a samples TSV?
    config_addendum=""
    if [ -e "${data_root}/samples.tsv" ]; then
        config_addendum=", samples_file: ${data_root}/samples.tsv"
        # automatically turn trimming on if 4-columns format in TSV
        # shellcheck disable=SC2162
        while read s b l p o; do
            # no proto?
            if [[ -z "${p}" ]]; then
                continue
            fi

            # proto => trim!
            config_file+=( "config/config-trim.yaml" )
            echo "with trimming"
            break

            : "${s} ${b} ${l} ${o}" are unused
        done < "${data_root}/samples.tsv"
    fi
    # does this test data provides extra configuration options
    if [ -e "${data_root}/config-extra.yaml" ]; then
        config_file+=( "${data_root}/config-extra.yaml" )
       echo "with extra config:"
       cat "${data_root}/config-extra.yaml"
       echo
    fi

    echo "config files ${config_file[*]}"
    PYTHONUNBUFFERED=1 snakemake \
        -s "${VPIPEROOT}/workflow/Snakefile" \
        --configfile "${config_file[@]}" \
        --config "input={datadir: ${data_root}${config_addendum}}" \
        --use-conda \
        --cores ${THREADS} \
        --dry-run
    echo
    if [ -e "${data_root}/samples.tsv" ]; then
        cat "${data_root}/samples.tsv"
    else
        # show file generated by dry-run
        cat config/samples.tsv
    fi
    echo
    PYTHONUNBUFFERED=1 snakemake \
        -s "${VPIPEROOT}/workflow/Snakefile" \
        --configfile "${config_file[@]}" \
        --config "input={datadir: ${data_root}${config_addendum}}" \
        --use-conda \
        --cores ${THREADS} \
        -p \
        --keep-going

    echo
    PYTHONUNBUFFERED=1 snakemake \
        -s "${VPIPEROOT}/workflow/Snakefile" \
        --configfile "${config_file[@]}" \
        --config "input={datadir: ${data_root}${config_addendum}}" \
        --lint || echo "(Linter unhappy)"

    popd
}


TEST_NAME=$(basename "${0%.*}")_${VIRUS}
EXIT_CODE=0

function check_logs {
    grep -E 'failed|for error' "${PROJECT_DIR}/.snakemake/log/"*".snakemake.log" && EXIT_CODE=1 || echo "snakemake execution successful"
}

mkdir -p /tmp/v-pipe_tests/
DIFF_FILE="/tmp/v-pipe_tests/diffs_${TEST_NAME}.txt"
LOG_FILE="/tmp/v-pipe_tests/log_${TEST_NAME}.txt"
rm -f "${DIFF_FILE}"
rm -f "${LOG_FILE}"

function compare_to_recorded_results {

    cd "${CWD}/expected_outputs/${TEST_NAME}"

    while IFS= read -r -d '' RECORDED_OUTPUT; do
        CURRENT_OUTPUT=${PROJECT_DIR}/${RECORDED_OUTPUT}
        echo "COMPARE ${RECORDED_OUTPUT} AND ${CURRENT_OUTPUT}"
        if diff -u -a -I '^#' "${RECORDED_OUTPUT}" "${CURRENT_OUTPUT}" >> "${DIFF_FILE}"; then
            :
        else
            echo
            echo "RESULTS ${RECORDED_OUTPUT} AND ${CURRENT_OUTPUT} DIFFER"
            echo
            EXIT_CODE=1;
        fi
    done < <(find . -type f -print0)
}

# setup_project
run_workflow 2>&1 | tee "${LOG_FILE}"
echo
echo
check_logs
echo
echo
compare_to_recorded_results

echo

if [ ${EXIT_CODE} = 1 ]; then
    echo "TESTS FAILED, CHECK ${DIFF_FILE} and ${LOG_FILE} FOR FUTHER INFORMATION"
else
    echo TESTS SUCEEDED
fi

exit ${EXIT_CODE}