#!/bin/sh

# ===========================================================================
#
#                            PUBLIC DOMAIN NOTICE
#            National Center for Biotechnology Information (NCBI)
#
#  This software/database is a "United States Government Work" under the
#  terms of the United States Copyright Act.  It was written as part of
#  the author's official duties as a United States Government employee and
#  thus cannot be copyrighted.  This software/database is freely available
#  to the public for use. The National Library of Medicine and the U.S.
#  Government do not place any restriction on its use or reproduction.
#  We would, however, appreciate having the NCBI and the author cited in
#  any work or product based on this material.
#
#  Although all reasonable efforts have been taken to ensure the accuracy
#  and reliability of the software and data, the NLM and the U.S.
#  Government do not and cannot warrant the performance or results that
#  may be obtained by using this software or data. The NLM and the U.S.
#  Government disclaim all warranties, express or implied, including
#  warranties of performance, merchantability or fitness for any particular
#  purpose.
#
# ===========================================================================
#
# File Name:  xtract
#
# Author:  Jonathan Kans, Aaron Ucko
#
# Version Creation Date:   11/01/2016
#
# ==========================================================================

pth=$( dirname "$0" )

case "$pth" in
  /* )
    ;; # already absolute
  *  )
    pth=$(cd "$pth" && pwd)
    ;;
esac

case ":$PATH:" in
  *:"$pth":* )
    ;;
  * )
    PATH="$PATH:$pth"
    export PATH
    ;;
esac

# read command-line arguments to intercept certain commands

for arg in "$@"
do
  case "$arg" in
    -format | -filter | -normalize | -outline | -contour | -synopsis | -tokens )
      # front-ends to functions implemented in transmute
      transmute "$@"
      exit
      ;;
    -j2x | -a2x | -t2x | -c2x | -g2x )
      # front-ends to functions implemented in transmute
      transmute "$@"
      exit
      ;;
    -e2index | -e2invert | -e2join | -e2delete )
      # front-ends to functions implemented in rchive
      rchive "$@"
      exit
      ;;
    -insdx )
      while [ $# -gt 0 ]
      do
        case "$1" in
          -insdx )
            shift
            if [ -t 0 ]
            then
              xtract -insd-xml "$@"
            else
              xtract -insd-xml "$@" |
              transmute -t2x -set Set -rec Rec -insdx "$@"
            fi
            exit
            ;;
          * )
            shift
            ;;
        esac
      done
      exit
      ;;
    * )
      continue
      ;;
  esac
done

# pass remaining commands to precompiled xtract executable
exec /usr/lib/ncbi-entrez-direct/xtract "$@"
