nfn_export.bash

#!/bin/bash

USAGE=$(cat <<'USAGE_END'

  Usage: nfn_export.bash -v RECONCILER-VERSION -w WORKFLOW-ID -r RENAME-TO -a ARGS -c COPY-TO -e EXPORT-FILE-NAME

  -h
      Print this message and exit.

  -v RECONCILER-VERSION
      The version of reconcile.py. This gets inserted into output file names.

  -w WORKFLOW-ID
      The expedition's workflow ID. This will be prepended to output file names.

  -r RENAME-TO
      The output file names without the RECONCILER-VERSION or WORKFLOW-ID.

  -a ARGS
      Any extra arguments to pass to reconcile.py. If you have many, quote them.

  -c COPY-TO
      Copy the output files to this directory.

  -e EXPORT-FILE-NAME
      The raw input file that reconcile.py uses as input.
.
USAGE_END
)

while getopts "a:v:w:r:e:c:h" option; do
  case "${option}" in
    e) EXPORT=${OPTARG};;
    r) RENAME=${OPTARG};;
    v) VERSION=${OPTARG};;
    w) WORKFLOW=${OPTARG};;
    c) COPY_TO=${OPTARG};;
    a) X_ARGS=${OPTARG};;
    h) echo "${USAGE}"
       exit 1
  esac
done

if [ -z ${EXPORT} ] || [ -z ${RENAME} ] || [ -z ${VERSION} ] || [ -z ${WORKFLOW} ]
then
  echo "Arguments: -v, -w, -r, & -e are required."
  echo "$USAGE"
  exit 1
fi

PREFIX="${WORKFLOW}_${RENAME}"
DIR="output/${PREFIX}"

RAW="${DIR}/${PREFIX}.raw_transcripts.${VERSION}.csv"
RECONCILED="${DIR}/${PREFIX}.reconciled.${VERSION}.csv"
SUMMARY="${DIR}/${PREFIX}.summary.${VERSION}.html"
UNRECONCILED="${DIR}/${PREFIX}.unreconciled.${VERSION}.csv"

echo ""
echo "Workflow:           ${WORKFLOW}"
echo "Version:            v${VERSION}"
echo "Name of Folder:     ${PREFIX}"
# echo "Unreconciled file   ${UNRECONCILED}"
# echo "Reconciled file     ${RECONCILED}"
# echo "Summary file        ${SUMMARY}"
# echo "Raw file            ${RAW}"
# echo "Copy to:            ${COPY_TO}"
echo ""

mkdir -p ${DIR}

cp ${EXPORT} ${RAW}
cp data/NfN_Reconciliation_HelpV1.0.pdf ${DIR}

python3 reconcile.py ${X_ARGS} -w ${WORKFLOW} -u ${UNRECONCILED} -r ${RECONCILED} -s ${SUMMARY} ${RAW}


if [ -n "$COPY_TO" ]
then
  cp -r ${DIR} ${COPY_TO}
fi