megdb

#!/bin/bash


# Exit immediately if a command exits with a non-zero status.
# this might cause problems e.g. using read to read a heredoc cause read to always return non-zero
# set -o errexit
# Treat unset variables as an error when substituting.
set -o nounset

# 1. section: global constants (all words upper case separated by underscore)

declare TMP_DIR=${TMPDIR:-/tmp}/prog.$$.d
declare TMP_FILE_PREFIX=${TMPDIR:-/tmp}/prog.$$
# 1 = do clean else don't
declare -r DO_CLEAN=0

function cleanup() {
  
  [[ "${DO_CLEAN}" -eq 1 ]] && {
    echo "cleaning";
    rm -f ${TMP_FILE_PREFIX}.* ;
  }
}

function check_file() {
  
  local file;
  
  if [ -z "${1}" ]; then
     echo "ERROR: empty argument to ${FUNCNAME}" >&2
     return 100
    else
      file="$1"
  fi
    
  if [ ! -r ${file} ]; then
    _exit "Error: File ${file} does not exist or is not readable." 100
  fi

}



function _check_required_programs() {

  # Required program(s)
  req_progs=(readlink)
  for p in ${req_progs[@]}; do
    hash "${p}" 2>&- || \	    
    { echo >&2 " Required program \"${p}\" not installed or in search PATH.";
      exit 1; 
    }
  done
}

function render_template() {
  eval "echo \"$(<$1)\""
}


# Single function
function main() {
  #the optional paramters string 
  local -r OPTS=':f:'
  
  while builtin getopts ${OPTS} opt "${@}"; do
    
    case $opt in
      f) declare -rg TEMPLATE_FILE=$(readlink -f ${OPTARG} ) 
         check_file ${TEMPLATE_FILE}
      ;;
      
      
      \?)
	  
	  echo ${opt} ${OPTIND} 'is an invalid option'; usage; exit ${INVALID_OPTION}
	  ;;
      
      
      :)
	  echo 'required argument not found for option -'${OPTARG}; usage; exit ${INVALID_OPTION}
	  ;;
      *) echo "Too many options. Can not happen actually :)"
         ;;
      
    esac
  done

  shift $((OPTIND-1))
  
  local -r OUTPUT_DIR=${1:-${TMP_DIR}}

  mkdir -pv ${OUTPUT_DIR} || {
    echo "Could not create ${OUTPUT_DIR}";
    exit 10;
  }
  
  echo "Writing results to ${OUTPUT_DIR}"
  

  # depending on what files get generatetd by the template sql declare
  # all but only cp the real generated one
  local sample_file=${OUTPUT_DIR}/ena_sample.xml
  local experiment_file=${OUTPUT_DIR}/ena_experiment.xml
  local run_file=${OUTPUT_DIR}/ena_run.xml
  local analysis_file=${OUTPUT_DIR}/ena_analysis.xml
  
  PSQL_SOURCE_FILE=${TMP_FILE_PREFIX}.generated.sql
  render_template ${TEMPLATE_FILE} > ${PSQL_SOURCE_FILE}
  
  psql \
      -e \
      --set ON_ERROR_STOP=true \
      --no-align \
      --tuples-only \
      -h localhost -U renzo -p 5491 -d megdb_r8 \
      -f ${PSQL_SOURCE_FILE} || exit 10

  cleanup

  exit 0
}


# Always check return values and give informative return values. 
# see https://google-styleguide.googlecode.com/svn/trunk/shell.xml?showone=Checking_Return_Values#Checking_Return_Values
trap "cleanup; exit 1"  1 2 3 13 15
# this is the main executable function at end of script
main "$@"