<?php
// $Revision: 1.2.2.1.2.5 $
// ------------------------------------------------------------------------- //
//  XooNIps - Neuroinformatics Base Platform System                          //
//  Copyright (C) 2005-2011 RIKEN, Japan All rights reserved.                //
//  http://xoonips.sourceforge.jp/                                           //
// ------------------------------------------------------------------------- //
//  This program is free software; you can redistribute it and/or modify     //
//  it under the terms of the GNU General Public License as published by     //
//  the Free Software Foundation; either version 2 of the License, or        //
//  (at your option) any later version.                                      //
//                                                                           //
//  You may not change or alter any portion of this comment or credits       //
//  of supporting developers from this source code or any supporting         //
//  source code which is considered copyrighted (c) material of the          //
//  original comment or credit authors.                                      //
//                                                                           //
//  This program is distributed in the hope that it will be useful,          //
//  but WITHOUT ANY WARRANTY; without even the implied warranty of           //
//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the            //
//  GNU General Public License for more details.                             //
//                                                                           //
//  You should have received a copy of the GNU General Public License        //
//  along with this program; if not, write to the Free Software              //
//  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 USA //
// ------------------------------------------------------------------------- //
if ( ! defined( 'XOONIPS_PATH' ) ) {
  exit();
}

// class file
require_once XOONIPS_PATH.'/class/base/JSON.php';
require_once dirname( dirname( __FILE__ ) ).'/class/pubmed.class.php';

// change internal encoding to UTF-8
if ( extension_loaded( 'mbstring' ) ) {
  mb_language( 'uni' );
  mb_internal_encoding( 'UTF-8' );
  mb_http_output( 'pass' );
}

$is_error = false;
$error_message = '';
// if ( ! isset( $_SERVER['HTTP_REFERER'] ) || strpos( $_SERVER['HTTP_REFERER'], XOOPS_URL.'/modules/xoonips/' ) !== 0 ) {
if ( ! isset( $_SERVER['HTTP_REFERER'] ) || preg_match( '/\\/modules\\/xoonips\\//', $_SERVER['HTTP_REFERER'] ) == 0 ) {
  $is_error = true;
  $error_message = 'Turn REFERER on';
}

if ( ! $is_error && ! isset( $_GET['pmid'] ) ) {
  $is_error = true;
  $error_message = 'pmid required';
}

if ( ! $is_error ) {
  $pmid = trim( $_GET['pmid'] );
  if ( ! is_numeric( $pmid ) ) {
    $is_error = true;
    $error_message = 'pmid has to be numeric character';
  }
  $pmid = intval( $pmid );
}

function &get_pubmed_data( $pmid ) {
  $ret = array();
  $pubmed = new XooNIps_PubMed_ArticleSet();
  if ( ! $pubmed->set_pmid( $pmid ) ) {
    return $ret;
  }
  if ( ! $pubmed->fetch() ) {
    return $ret;
  }
  if ( ! $pubmed->parse() ) {
    return $ret;
  }
  if ( ! isset( $pubmed->_data[$pmid] ) ) {
    return $ret;
  }
  $article =& $pubmed->_data[$pmid];
  // pubmed id
  $ret['pmid'] = $article['PMID'];
  // title
  $ret['title'] = $article['ArticleTitle'];
  if ( preg_match( '/^\\[(.*)\\]$/', $ret['title'], $matches ) ) {
    $ret['title'] = $matches[1];
  }
  // volume
  $ret['volume'] = ( $article['Journal_Volume'] != '' ) ? $article['Journal_Volume'] : '';
  // issue
  $ret['issue'] = ( $article['Journal_Issue'] != '' ) ? $article['Journal_Issue'] : '';
  // publication_year
  if ( $article['Journal_PubDate_Year'] != '' ) {
    $ret['year'] = $article['Journal_PubDate_Year'];
  } else {
    if ( preg_match( '/(\\d\\d\\d\\d)\\s.*/', $article['Journal_MedlineDate'], $matches ) ) {
      $ret['year'] = $matches[1];
    } else {
      $ret['year'] = '';
    }
  }
  // journal
  if ( $article['Journal_Title'] != '' ) {
    $ret['journal'] = $article['Journal_Title'];
  } else if ( $article['MedlineTA'] != '' ) {
    $journal_esearch = new XooNIps_PubMed_JournalEsearch();
    if ( $journal_esearch->set_journal_ta( $article['MedlineTA'] ) ) {
      if ( $journal_esearch->fetch() ) {
        if ( $journal_esearch->parse() ) {
          if ( isset( $journal_esearch->_data['id'] ) ) {
            $jids =& $journal_esearch->_data['id'];
            $journal_esummary = new XooNIps_PubMed_JournalEsummary();
            foreach ( $jids as $jid ) {
              $journal_esummary->set_journal_id( $jid );
            }
            if ( $journal_esummary->fetch() ) {
              if ( $journal_esummary->parse() ) {
                foreach ( $jids as $jid ) {
                  if ( isset( $journal_esummary->_data[$jid] ) ) {
                    $docsum =& $journal_esummary->_data[$jid];
                    if ( $docsum['MedAbbr'] == $article['MedlineTA'] ) {
                      $ret['journal'] = $docsum['Title'];
                    }
                  }
                }
              }
            }
          }
        }
      }
    }
  } else {
    $ret['journal'] = '';
  }
  // page
  $ret['page'] = ( $article['MedlinePgn'] != '' ) ? $article['MedlinePgn'] : '';
  // abstract
  $ret['abst'] = ( $article['AbstractText'] != '' ) ? $article['AbstractText'] : '';
  if ( empty( $ret['abst'] ) ) {
    if ( $article['OtherAbstractText'] != '' ) {
      $ret['abst'] = $article['OtherAbstractText'];
    }
  }
  // author
  $ret['author'] = array();
  if ( ! empty( $article['AuthorList'] ) ) {
    foreach ( $article['AuthorList'] as $author ) {
      $str = $author['LastName'].' ';
      if ( $author['Initials'] != '' ) {
        $str .= $author['Initials'];
      } else if ( $author['ForeName'] != '' ) {
        $str .= $author['ForeName'];
      } else {
        if ( $author['MiddleName'] != '' ) {
          $str .= $author['MiddleName'].' ';
        }
        $str .= $author['FirstName'];
      }
      $ret['author'][] = $str;
    }
  }
  // keywords
  $ret['keywords'] = array();
  if ( ! empty( $article['MeshHeadingList'] ) ) {
    foreach ( $article['MeshHeadingList'] as $meshheading ) {
      $str = $meshheading['DescriptorName'];
      if ( count( $meshheading['QualifierName'] ) > 0 ) {
        $tmpstr = implode( ',', $meshheading['QualifierName'] );
        $str .= ','.$tmpstr;
      }
      $ret['keywords'][] = $str;
    }
  }
  return $ret;
}

if ( ! $is_error ) {
  $data =& get_pubmed_data( $pmid );
  if ( empty( $data ) ) {
    $data['error'] = 'failed to get pubmed resources';
  }
} else {
  $data = array();
  $data['error'] = $error_message;
}

// json
$json = new Services_JSON();
$encode = $json->encode( $data );

// output
header( 'Content-Type: text/javascript+json; charset=utf-8' );
echo $encode;

?>
