badA2increment.sh

#!/bin/bash
# Script to deal with improperly incremented subsurface modules from Atlas

if [ -z "$1" ] && [ -z "$2" ] && [ -z "$3" ]; then
  echo '
  badA2increment copies and processes the bad file in a new directory.

  Use: badA2increment [Serial #] [increm] [Deploy ID] [Type]

        Serial #  = ONLY the serial number of the improperly deployed module
        increm    = the increment OF the instrument (120, 180, etc)
        Deploy ID = the id of the deployment, [ra|pi]###[a|b]
        Type      = type of files [ temp | sal | pres ]
        Cond #    = serial of the conductivity/pressure sensor, required for merging.

  Examples:
  badA2increment 11212 120 ra121a temp
  badA2increment 11212 120 ra121a sal 1211
  badA2increment 11212 120 ra121a pres 234882
  '
  exit 1
fi

if [ -z "$1" ]; then
  echo 'Need the serial number!'
  exit
elif [ -z "$2" ]; then
  echo 'Need the increment!'
  exit
elif [ -z "$3" ]; then
  echo 'Need the deployment!'
  exit
elif [[ $3 =~ ..\d\d\d[a-c] ]]; then
  echo 'Need the deployment leg please'
  printf 'Did you mean?\n %sa' "$3"
  exit
elif [[ $1 =~ [A-Za-z] ]]; then
  echo 'No letters in the serial number please'
  exit
elif [[ $2 =~ [0-9]{2,3}\b ]]; then
  printf 'Did you mean %s increment?' "$2"
  exit
elif [ "$4" == 'temp' ]; then
  file=$(find "*$1.*")
  calfile=$(find "*".cal)
  id=${3: -4}
  echo 'Creating directory...'
  mkdir "$1"
  mv "$file" "$1"/
  echo 'Moving files, running processing programs...'
  processA2Mod "$3" ./ --cal "$calfile"
  cd "$1"/ || exit 5
  cp "$file" "${file}"_orig
  processA2Mod "$3" "$file" --cal ../"$calfile" --inc "$2"
  echo 'Cleaning files, moving up for merging...'
  find "${4}""${id}".ram | while read -r file; do
    (
      head -n 5 "$file"
      tail -n +6 "$file" | grep -e '\d\d\d\d\d\d\d\d\d\d000'
    ) >"${file}"_"${2}"
    mv "${file}"_"${2}" ../
  done
  cd ..
  echo 'Merging files...'
  find "${4}""${id}".ram | while read -r file; do
    mv "$file" "${file}"_orig
    mergeA2ram "$1" "${file}"_orig "${file}"_"${2}" >"${file}"
    mv "${file}"_"${2}" "$1"/
  done
  echo 'Done.'
elif [ "$4" == 'pres' ]; then
  if [ -z "$5" ]; then
    echo 'Need the pressure sensor serial'
    exit
  fi
  file=$(find "*$1.*")
  calfile=$(find "*".cal)
  id=${3: -4}
  echo 'Creating directory...'
  mkdir "$1"
  mv "$file" "$1"/
  echo 'Moving files, running processing programs...'
  processA2Mod "$3" ./ --cal "$calfile"
  cd "$1"/ || exit 6
  cp "$file" "${file}"_orig
  processA2Mod "$3" "$file" --cal ../"$calfile" --inc "$2"
  echo 'Cleaning files, moving up for merging...'
  find "${4}""${id}".ram | while read -r file; do
    (
      head -n 5 "$file"
      tail -n +6 "$file" | grep -e '\d\d\d\d\d\d\d\d\d\d000'
    ) >"${file}"_"${2}"
    mv "${file}"_"${2}" ../
  done
  cd ..
  echo 'Merging files...'
  find "${4}""${id}".ram | while read -r file; do
    mv "$file" "${file}"_orig
    mergeA2ram "$5" "${file}"_orig "${file}"_"${2}" >"${file}"
    mv "${file}"_"${2}" "$1"/
  done
  echo 'Done.'
elif [ "$4" == 'sal' ]; then
  if [ -z "$5" ]; then
    echo 'Need the conductivity cell number'
    exit
  fi
  file=$(find "*$1.*")
  calfile=$(find "*".cal)
  id=${3: -4}
  echo 'Creating directory...'
  mkdir "$1"
  mv "$file" "$1"/
  echo 'Moving files, running processing programs...'
  processA2Mod "$3" ./ --cal "$calfile"
  cd "$1"/ || exit 8
  cp "$file" "${file}"_orig
  processA2Mod "$3" "$file" --cal ../"$calfile" --inc "$2"
  echo 'Cleaning files, moving up for merging...'
  find {cond"${id}".ram,dens"${id}".ram,sal"${id}".ram,temp"${id}".ram} | while read -r file; do
    (
      head -n 5 "$file"
      tail -n +6 "$file" | grep -e '\d\d\d\d\d\d\d\d\d\d000'
    ) >"${file}"_"${2}"
    mv "${file}"_"${2}" ../
  done
  cd .. || exit 7
  echo 'Merging salinity files...'
  find {cond"${id}".ram,dens"${id}".ram,sal"${id}".ram} | while read -r file; do
    mv "$file" "${file}"_orig
    mergeA2ram "$5" "${file}"_orig "${file}"_"${2}" >"${file}"
    mv "${file}"_"${2}" "$1"/
  done
  echo 'Merging temperature file...'
  find temp"${id}".ram | while read -r file; do
    mv "$file" "${file}"_orig
    mergeA2ram "$1" "${file}"_orig "${file}"_"${2}" >"${file}"
    mv "${file}"_"${2}" "$1"/
  done
  echo 'Done.'
else
  echo 'No direction given. Gotta feed the beast.'
  exit
fi