slideSQLheader

#!/bin/bash
#
# Description: Extract SQL-file column headers created by cellprofiler
#
# The MIT License (MIT)
# Copyright (c) 2014-2016, Bas G.L. Nelissen, UMC Utrecht, the Netherlands.
# 
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, modify, merge, publish,
# distribute, sublicense, and/or sell copies of the Software, and to
# permit persons to whom the Software is furnished to do so, subject to
# the following conditions:
# 
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
# 
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
# CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#

#Variables
SCRIPTNAME=$(basename $0)
DESCRIPTIONSHORT="Extract SQL-file column names created by cellprofiler"
DEPENDENCIES=("perl")
SUFFIX=".head"

# usage message
usage() {
cat <<- EOF
$SCRIPTNAME --help for more information.
EOF
}

# version info
version() {
cat << EOF
slideToolkit 0.1 beta
($SCRIPTNAME is part of the slideToolkit)

The MIT License (MIT) <http://opensource.org/licenses/MIT>
Copyright (c) 2014-2016, Bas G.L. Nelissen, UMC Utrecht, the Netherlands.

Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:

The above copyright notice and this permission notice shall be included
in all copies or substantial portions of the Software.

There is NO WARRANTY, to the extent permitted by law.

Written by Bas G.L. Nelissen | https://github.com/bglnelissen.
EOF
}


# Errors go to stderr
err() {
  echo "${SCRIPTNAME} ERROR: $@" >&2
}

#help message
helpMessage() {
cat <<- EOF
${SCRIPTNAME}: ${DESCRIPTIONSHORT}

usage:
  $SCRIPTNAME [options] -f <filename>

options:
  -f, --file <filename>     "SQL_SETUP.SQL" file 
  
  [--add-head] <filename>   "file.csv" file 
  [--ignore-dependencies]   ignores all dependencies, but gives warning

  --help                    display this help
  --version                 display version and license information


examples:
  $SCRIPTNAME "SQL_SETUP.SQL"
  $SCRIPTNAME  --file="SQL_SETUP.SQL" --add-head="file.csv"

dependencies: ${DEPENDENCIES[@]}

Extract SQL-file column names created by cellprofiler. These headers
can be added to a .csv file using the --add-head option, a copy
(.head.csv) will be created

The slideToolkit and all its tools are released under the terms of the MIT license.
The slideToolkit (C) 2014-2016, Bas G.L. Nelissen, UMC Utrecht, the Netherlands.
Report issues at https://github.com/bglnelissen/slideToolkit/issues.

EOF
}
#Menu
#Empty variables
FILE=""
ADDHEAD=""
#illegal option
illegalOption() {
cat <<- EOF
$SCRIPTNAME: illegal option $1
$(usage)
EOF
exit 1
}
#loop through options
while :
do
  case $1 in
    -h)
      usage
      exit 0 ;;
    --help | -\?)
      helpMessage
      exit 0 ;;
    --version )
      version
      exit 0 ;;
    -f | --file)
      FILE=$2
      shift 2 ;;
    --file=*)
      FILE=${1#*=}
      shift ;;
    --add-head)
      ADDHEAD=$2
      shift 2 ;;
    --add-head=*)
      ADDHEAD=${1#*=}
      shift ;;
     --ignore-dependencies)
      IGNOREDEPENDENCIES=TRUE
      shift ;;
    --) # End of all options
      shift
      break ;;
    -*)
      illegalOption "$1"
      shift ;;
    *)  # no more options. Stop while loop
      break ;;
  esac
done
#DEFAULTS
#set FILE
if [ "$FILE" != "" ]; then
  FILE="$FILE"
else
  FILE="$1"
fi
# set IGNOREDEPENDENCIES
if [[ "$IGNOREDEPENDENCIES" =~ (true|TRUE|YES|yes) ]] ; then
  IGNOREDEPENDENCIES=true
else
  IGNOREDEPENDENCIES=false
fi

#requirements
checkRequirements() {
  if ! [[ -f "$FILE" ]] ; then
    err "No such file: $FILE">&2;
    usage
    exit 1
  fi
  if ! [[ -z "$ADDHEAD" ]]; then
    if ! [[ -f "$ADDHEAD" ]] ; then
      err "No such file: $ADDHEAD">&2;
      usage
      exit 1
    fi  
  fi
}

# Dependencies
checkDependencies(){
  DEPS=""
  DEPS_FAIL="0"
  for DEP in ${DEPENDENCIES[@]}; do
    if [[ 0 != "$(command -v "$DEP" >/dev/null ;echo "$?")" ]]; then
       err "Missing dependency: $DEP"
       DEPS_FAIL=$(($DEPS_FAIL + 1))
    fi
  done
  if [[ "$DEPS_FAIL" > 0 ]]; then
    # only warning when --ignore-dependencies is set.
    if [[ "$IGNOREDEPENDENCIES" == "true" ]]; then
      err "Ignoring missing dependencies (${DEPS_FAIL}), continue..."
    else
      err "Fix missing dependencies (${DEPS_FAIL}), exit."
      usage
      exit 1
    fi
  fi
}

# actual program
programOutput(){
  # Find line with "CREATE TABLE Per_Image (" and print this and '9999' lines after)
  # Find line with "PRIMARY KEY (ImageNumber) )" and print this and '9999' lines before)
  # Remove First and last line, fetch 1st column only, replace newlines with comma's.
  # Remove trailing comma
  HEAD=$(cat "$FILE" | \
      grep -A 9999 -w "CREATE TABLE Per_Image (" | \
      grep -B 9999 -w "PRIMARY KEY (ImageNumber) )" | \
      tail -n+2 | head -n-1 | awk '{print $1}' | tr '\n' ',' | \
      perl -p -e 's/^(.*).$/\1/')
  # add head, yes -> do it, no -> echo head to stdout
  if ! [[ -z "$ADDHEAD" ]]; then
    echo "$(echo $HEAD; cat $ADDHEAD)" > "${ADDHEAD%.*}${SUFFIX}.${ADDHEAD##*.}"
  else
    echo "$HEAD"
  fi
}
#all check?
checkRequirements
checkDependencies

#lets go!
programOutput