#!/bin/bash

# Parse the positional arguments
# from Method #1 in https://stackoverflow.com/a/14203146
POSITIONAL=()
while [[ $# -gt 0 ]]
do
key="$1"

case $key in
    -f|--filepath)
    FILEPATH="$2"
    shift # past argument
    shift # past value
    ;;
    *)    # unknown option
    POSITIONAL+=("$1") # save it in an array for later
    shift # past argument
    ;;
esac
done
set -- "${POSITIONAL[@]}" # restore positional parameters

# Check to see if the filepath argument was provided
if [ -z "${FILEPATH}" ]
then
      echo Please provide the path to the FTIR files on your USB key e.g. "${HOME}"/LANG/FTIR
      exit
else
      # Ensure that the filepath is valid
      PARENTDIR="$(dirname "${FILEPATH}")"
      if [ ! -d "${FILEPATH}" ] 
      then
          echo "Directory "${FILEPATH}" DOES NOT exist!" 
          exit
      # Check to see if the required .XLSX file is present
      else
          if [ -f "${FILEPATH}"/*.XLSX ]; then
		EXCELPATH="${FILEPATH}"
		
          elif [ -f "${PARENTDIR}"/*.XLSX ]; then
		EXCELPATH="${PARENTDIR}"
	  else
              echo "Cannot locate .XLSX file in "${FILEPATH}" or "${PARENTDIR}"!" 
              exit
          fi
          # Check to see if .spc files are present in the supplied path
          SPCFILES=`ls "${FILEPATH}"/*.spc 2> /dev/null`
          if [ -z "${SPCFILES}" ]
          then
              echo "Cannot locate .spc files in "${FILEPATH}"!" 
              exit
          else
              echo "Using FTIR file path: "${FILEPATH}""
          fi
      fi
fi

# Copy Files USB to /mnt/nas2/raw_sequence_data/ftir
echo "Copying files from USB to /mnt/nas2/raw_sequence_data/ftir/working_dir"
# Make the working directory on the NAS (if necessary)
mkdir -p /mnt/nas2/raw_sequence_data/ftir/working_dir/
cp -r "${FILEPATH}"/*.spc /mnt/nas2/raw_sequence_data/ftir/working_dir/
cp -r "${EXCELPATH}"/*.XLSX /mnt/nas2/raw_sequence_data/ftir/working_dir/
sleep 10

# Run Renamer
echo "Running renamer.py"
renamer.py -s /mnt/nas2/raw_sequence_data/ftir/working_dir -f /mnt/nas2/raw_sequence_data/ftir/working_dir/FTIR.XLSX -o /mnt/nas2/raw_sequence_data/ftir/working_dir/renamedfiles
sleep 5

# Compress Files
echo "Compressing files"
zip -j /mnt/nas2/raw_sequence_data/ftir/working_dir/renamedfiles/FTIR.zip /mnt/nas2/raw_sequence_data/ftir/working_dir/renamedfiles/*.spc
sleep 5

# Move Zip to USB
echo "Moving archive to USB"
mv /mnt/nas2/raw_sequence_data/ftir/working_dir/renamedfiles/FTIR.zip "$(dirname "${FILEPATH}")"
sleep 2

# Move raw files from working_dir to raw_files
echo "Moving raw files to storage"
mv /mnt/nas2/raw_sequence_data/ftir/working_dir/*.spc /mnt/nas2/raw_sequence_data/ftir/raw_files/

# Move renamed files from working_dir/renamed to renamedfiles
echo "Moving renamed files to storage"
mv /mnt/nas2/raw_sequence_data/ftir/working_dir/renamedfiles/* /mnt/nas2/raw_sequence_data/ftir/renamedfiles/

#Delete Old FTIR
echo "Removing FTIR.XLSX from NAS"
rm /mnt/nas2/raw_sequence_data/ftir/working_dir/FTIR.XLSX

# Delete original files from USB
echo "Removing original files from USB"
rm "${FILEPATH}"/*.spc

echo "Complete!"
