sra_explorer_curl_wrapper

#!/bin/bash
set -euo pipefail

if [[ $# == 1 ]]; then
    script=$1
else
    echo >&2 "the wrapper requires the original SRA Explorer curl script as input file (given via command line option"
    exit 2
fi

[[ -e "$script" ]] || { echo >&2 "file does not exist: $script"; exit 2; }

declare -a urls outfiles

while read -r curl Lopt url oopt outfile; do
    [[ "$curl" == curl ]] || echo "failed parsing script, expected 'curl', got: $curl"
    [[ "$Lopt" == -L ]] || echo "failed parsing script -L option expected, got: $Lopt"
    [[ "$oopt" == -o ]] || echo "failed parsing script -o option expected, got: $oopt"
    urls+=("$url")
    outfiles+=("$outfile")
done < <(grep "^curl " "$script")

declare -i remaining=${#urls[@]}

while true; do
    declare -a badurls=() badoutfiles=()
    for ((i=0; i<${#urls[@]}; i++)); do
        url=${urls[i]}
        outfile=${outfiles[i]}
        echo >&2 -n "Trying $url "
        if [[ -e "$outfile" ]]; then
            echo >&2 "[output file exists, skipping]"
        elif curl -s -S --fail -L "$url" -o "$outfile"; then
            echo >&2 "[OK]"
        else
            errcode=$?
            echo >&2 "Download failed with error $errcode: url: $url, outfile: $outfile"
            badurls+=("$url")
            badoutfiles+=("$outfile")
            rm -f -- "$outfile"
        fi
    done
    if [[ ${#badurls[@]} -gt 0 ]]; then
        urls=("${badurls[@]}")
        outfiles=("${badoutfiles[@]}")
        remaining=${#urls[@]}
        if [[ remaining -gt 0 ]]; then
            echo >&2
            echo >&2 "Retrying $remaining downloads that have gone bad, if you see the same error happening over and over again..."
            echo >&2
        fi
    else
        echo >&2 "[ALL DONE]"
        break
    fi
done