upload_and_post_vcf

#! /bin/sh

SCRIPT_NAME=$(basename $0)

short_usage()
{
  echo "Cf :  $SCRIPT_NAME  [--help]"
}
long_usage()
{
  echo "Post VCFs to Cycledash"
  echo "  Description   :  "
  echo "Usage :"
  echo "-----"
  echo "       $SCRIPT_NAME {--help,-h,}"
  echo ""
  echo "Options :"
  echo "-------"
  echo ""
}


if [ "$1" = "--help" ]
then
  long_usage ;
  exit
fi
if [ $# -eq 0 ]
then
  short_usage ;
  exit
fi
while getopts hv:V:U:t:n:N:P:w: option
do
  case $option in
    h ) long_usage ; exit ;;
    V ) export VCF_PATH=$OPTARG ;;
    v ) export VARIANT_CALLER_NAME=$OPTARG ;;
    U ) export CYCLEDASH_URL=$OPTARG ;;
    t ) export TUMOR_BAM_URI=$OPTARG ;;
    n ) export NORMAL_BAM_URI=$OPTARG ;;
    N ) export NOTES=$OPTARG ;;
    P ) export PROJECT_NAME=$OPTARG ;;
    w ) export WITNESS=$OPTARG ;;
    \?) short_usage ;  exit 2 ;;
  esac
done

curl=curl

tmp_file=`mktemp /tmp/bbXXX`
$curl -f -F file=@$VCF_PATH $CYCLEDASH_URL/upload > $tmp_file

if [ `cat $tmp_file | wc -l` -lt 2 ] ; then
    tmp_json=`mktemp /tmp/bbXXX`
    cat <<EOF > $tmp_json
{
"uri": "`cat $tmp_file`",
"callerName": "$VARIANT_CALLER_NAME",
"tumorBamUri": "$TUMOR_BAM_URI",
"normalBamUri": "$NORMAL_BAM_URI",
"projectName": "$PROJECT_NAME",
"notes": "
EOF
echo ${NOTES} | sed 's/"/\\"/g' >> $tmp_json
echo '" }' >> $tmp_json
    $curl -H 'Content-Type: application/json' -f  $CYCLEDASH_URL/runs --data @$tmp_json -o $WITNESS
else
    exit 3
fi

shift `expr $OPTIND - 1`

if [ $# -ne 0 ] ; then
    for arg in $*; do
        echo "Don't know what to do with: $arg"
    done
fi