EDIT

<?php

// $Id$

/**

 * Copyright (C) 2007 EDIT

 * European Distributed Institute of Taxonomy

 * http://www.e-taxonomy.eu

 *

 * The contents of this file are subject to the Mozilla Public License Version 1.1

 * See http://www.mozilla.org/MPL/MPL-1.1.html for the full license terms.

 */

define(FOOTNOTE_ANNOTATIONS, 'annotations');

/**

* Get the true path to the root of the Drupal site.

* Better than using DOCUMENT_ROOT and base_path().

*/

function absolute_path_to_drupal() {

    static $absolute_path_to_drupal = NULL;

    if ($absolute_path_to_drupal === NULL) {

        // Get the absolute path to this file:

        $dir = rtrim(str_replace('\\', '/', dirname(__FILE__)), '/');

        $parts = explode('/', $dir);

        // Iterate up the directory hierarchy until we find the website root:

        $done = FALSE;

        do{

            // Check a couple of obvious things:

            $done = is_dir("$dir/sites") && is_dir("$dir/includes") && is_file("$dir/index.php");

            if (!$done) {

                // If there's no more path to examine, we didn't find the site root:

                if (empty($parts)) {

                    $absolute_path_to_drupal = FALSE;

                    break;

                }

            // Go up one level and look again:

            array_pop($parts);

            $dir = implode('/', $parts);

            }

        }while (!$done);

        $absolute_path_to_drupal = $dir;

    }

    return $absolute_path_to_drupal;

}

function taxon_in_current_tree ($taxon_uuid) {

  $taxon_nodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon_uuid);

  $taxon_in_current_tree = false;

  if(is_array($taxon_nodes)){

    foreach($taxon_nodes as $node){

      if(get_taxonomictree_uuid_selected() == $node->classification->uuid){

        $taxon_in_current_tree = true;

        break;

      }

    }

  }

  return $taxon_in_current_tree;

}

/**

 * TODO if getting fragment from request is possible remove $_REQUEST['highlite'] HACK

 * NOT WORKING since fragments are not available to the server

 function fragment(){

 global $fragment;

 if(!$fragment){

 $fragment = substr($_SERVER['REQUEST_URI'], strrpos($_SERVER['REQUEST_URI'], '#'));

 }

 return $fragment;

 }

 */

function uuid_anchor($uuid, $innerHTML){

  $highlite = $_REQUEST['highlite'] == $uuid;

  return '<a name="'.$uuid.'" ></a><span class="'.($highlite ? 'highlite' : '').'">'.$innerHTML.'</span>';

}

/**

 * Enter description here...

 *

 * @param unknown_type $name

 * @param unknown_type $numOfNameTokens

 * @return unknown

 * @deprecated looks like this is not used anymore

 */

function tagNameParts($name, $numOfNameTokens){

  $out = '<span class="name">';

  $token = strtok($name, " \n\t");

  $i = 0;

  $noSpace = true;

  while($token != false){

    if($i == $numOfNameTokens){

      $out .= '</span> <span class="authors">';

      $noSpace = true;

    }

    $out .= ($noSpace?'':' ').$token;

    $noSpace = false;

    $token = strtok(" \n\t");

    $i++;

  }

  return $out.'</span>';

}

/**

 * Converts an array of TagedText items into a sequence of corresponding html tags whereas

 * each item will provided with a class attribute which set to the key of the TaggedText item.

 *

 * @param array $taggedtxt

 * @param String $tag

 * @param String $glue the string by which the chained text tokens are concatenated together.

 *       Default is a blank character

 * @return String of HTML

 */

function theme_cdm_taggedtext2html(array &$taggedtxt, $tag = 'span', $glue = ' ', $skiptags = array()){

  $out = '';

  $i = 0;

  foreach($taggedtxt as $tt){

    if(!in_array($tt->type, $skiptags) && strlen($tt->text) > 0){

      $out .= (strlen($out) > 0 && ++$i < count($taggedtxt)? $glue : '').'<'.$tag.' class="'.$tt->type.'">'.t($tt->text).'</'.$tag.'>';

    }

  }

  return $out;

}

/* ============================ annotations ============================= */

/**

 * Almost any cdmObject may be annotated. Therefore we provide a generic way to display

 * as well as create or update annotations.

 * The following cdm classes are annotatable:

 *

 *  DescriptionElementBase

 *	EventBase

 *	HomotypicalGroup

 *	IdentifiableEntity

 *	  DescriptionBase

 *	  IdentifiableMediaEntity

 *	  Media

 *	  Sequence

 *	  TaxonBase

 *	  TaxonNameBase

 *	  TaxonomicTree

 *	  TermBase

 *	LanguageStringBase

 *	ReferencedEntityBase

 *	  NomenclaturalStatus

 *	  OriginalSourceBase

 *	  RelationshipBase

 *	  TypeDesignationBase

 *	TaxonNode

 *  WorkingSet

 *

 */

function theme_cdm_annotations_as_footnotekeys($cdmBase, $footnote_list_key = null){

  if (variable_get('cdm_dataportal_annotations_footnotes', CDM_DATAPORTAL_ALL_FOOTNOTES)){

    return '';

  }

  $footNoteKeys = cdm_annotations_as_footnotekeys($cdmBase, $footnote_list_key);

  foreach($footNoteKeys as $a){

    //$out .=  theme('cdm_footnote_key', $a, $a->footnoteListKey, (isset($out)? ',' : ''));

    $out .=  theme('cdm_footnote_key', $a, (isset($out)? ',' : ''));

  }

  return $out;

}

function theme_cdm_annotation_footnotes($footnoteListKey, $enclosingTag = 'span'){

  if (variable_get('cdm_dataportal_annotations_footnotes', CDM_DATAPORTAL_ALL_FOOTNOTES)){

    return '';

  }

  return theme('cdm_footnotes', $footnoteListKey . '-annotations', $enclosingTag);

}

function theme_cdm_annotation_content($AnnotationTO){

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/cdm_annotations.js');

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/jquery.form.js');

  $out .= theme('cdm_list_of_annotations', $AnnotationTO->annotationElements);

  $annotationUrl = cdm_compose_url(CDM_WS_ANNOTATIONS, array($AnnotationTO->uuid));

  $annotationProxyUrl = url('cdm_api/proxy/'. urlencode($annotationUrl).'/cdm_annotation_post');

  // TODO users have to be authenticated to the dataportal to be able to write annotations

  $out .= '

        <div class="annotation_create">

          <form action="'.$annotationProxyUrl.'" method="POST">

            <textarea name="annotation"></textarea>

            <input type="hidden" name="commentator" value="">

            <input type="submit" value="'.t('Save annotation').'" />

          </form>

       </div>

  ';

  return $out;

}

function theme_cdm_list_of_annotations($annotationElements){

  $out = '<ul class="annotation_list">';

  foreach ($annotationElements as $key => $row){

    $created[$key] = $row;

  }

  array_multisort($created, SORT_ASC, $annotationElements);

  foreach ($annotationElements as $annotation){

    $out .= '<li>' . $annotation->text . '</li>';

  }

  $out .= '</ul>';

  return $out;

}

/* ============================ footnotes ============================= */

function theme_cdm_footnote_key($footnoteKey, $separator = '', $highlightable=true, $separator_off = false){

  if (!$footnoteKey->footnoteListKey){

    return '';

  }

  if (variable_get('cdm_dataportal_all_footnotes', CDM_DATAPORTAL_ALL_FOOTNOTES)){

    return '';

  }

  if ($separator_off){

    $separator = '';

  }

  $out = '<span class="footnote-key footnote-key-'.$footnoteKey->keyStr.' member-of-footnotes-'.$footnoteKey->footnoteListKey.'">'.$separator

  .'<a href="#footnote-'.$footnoteKey->keyStr.'">'.$footnoteKey->keyStr.'</a>'

  .'</span>';

  return $out;

}

function theme_cdm_footnote($footnoteKey, $footnoteText){

  _add_js_footnotes();

  $out = '<span class="footnote footnote-'.$footnoteKey.'"><a name="footnote-'.$footnoteKey.'"></a><span class="footnote-anchor">'.$footnoteKey.'.</span>&nbsp;'.$footnoteText.'</span>';

  return $out;

}

function theme_cdm_footnotes($footnoteListKey, $enclosingTag = 'span'){

  if (variable_get('cdm_dataportal_all_footnotes', CDM_DATAPORTAL_ALL_FOOTNOTES)){

    return '';

  }

  $out = '<'.$enclosingTag.' class="footnotes footnotes-'.$footnoteListKey.' ">' . FootnoteManager::renderFootnoteList($footnoteListKey) . '</'.$enclosingTag.'>';

  FootnoteManager::removeFootnoteList($footnoteListKey);

  return $out;

}

function theme_cdm_annotations($annotations, $enclosingTag = 'span'){

  if(!is_array($annotations)){

    return;

  }

  $out = '<'.$enclosingTag.' class="annotations">';

  $i = 0;

  foreach($annotations as $annotation){

    $out .= ($i++ > 0 ? ', ' : '') . $annotation->text;

  }

  $out .= '</'.$enclosingTag.'>';

  return $out;

}

function cdm_exist_footnote($footnote_list, $footnote){

  $result = false;

  if (is_array($footnote_list)){

    foreach ($footnote_list as $element){

      if ($element == $footnote){

        $result = true;

      }

    }

  }

  return $result;

}

function cdm_add_footnote_to_array(&$footnote_list, $footnote){

  if(!cdm_exist_footnote($footnote_list, $footnote)){

    $footnote_list[] = $footnote;

  }

}

/* ============================ pager ============================= */

function theme_cdm_pager(&$pager, $path, $parameters){

  $out = '';

  if ($pager->pagesAvailable > 1) {

    $out .= '<div class="pager">';

    if($pager->currentIndex > 0){

      $out .= theme('cdm_pager_link', t('« first'), 0,  $pager, $path, $parameters, array('class' => 'pager-first'));

      $out .= theme('cdm_pager_link', t('‹ previous'), $pager->currentIndex - 1, $pager, $path, $parameters, array('class' => 'pager-previous'));

    }

    if($pager->indices[0] > 0){

      $out .= '<div class="pager-list-dots-left">...</div>';

    }

    foreach($pager->indices as $index){

      $label = $index + 1;

      $out .= theme('cdm_pager_link', $label, $index,  $pager, $path, $parameters, array('class' => 'pager-first'));

    }

    if($pager->indices[count($pager->indices) - 1] < $pager->pagesAvailable - 1){

      $out .= '<div class="pager-list-dots-right">...</div>';

    }

    if($pager->nextIndex){

      $out .= theme('cdm_pager_link', t('next ›'), $pager->nextIndex, $pager, $path, $parameters, array('class' => 'pager-next'));

      $out .= theme('cdm_pager_link', t('last »'), $pager->pagesAvailable - 1, $pager, $path, $parameters, array('class' => 'pager-last'));

    }

    $out .= '</div>';

    return $out;

  }

}

function theme_cdm_pager_link($text, $linkIndex, &$pager, $path, $parameters = array(), $attributes) {

  $out = '';

  $parameters['search']['pageNumber'] = $linkIndex;

  if ($linkIndex == $pager->currentIndex) {

    $out = '<strong>'.$text.'</strong>';

  } else {

    $queryString = drupal_query_string_encode($parameters);

    $out = l($text, $path, $attributes, $queryString);

  }

  return $out;

}

/* ============================ special buttons ============================= */

function theme_cdm_back_to_search_result_button(){

  $out = '';

  $show_button = variable_get('cdm_dataportal_show_back_to_search_results', 1);

  if($_SESSION['cdm']['search'] && $show_button){

    /*['cdm']['last_search']*/

    //$out .= '<div id="backButton">'.l(t('Back to search result'), $_SESSION ).'</div>';

    $out .= '<div id="backButton">'.l(t('Back to search result'), "http://" . $_SERVER['SERVER_NAME'] . $_SESSION['cdm']['last_search'] ).'</div>';

  }

  return $out;

}

function theme_cdm_back_to_image_gallery_button(){

  $out = '<div id="backToGalleryButton">'.l(t('Back to Images'), $_SESSION['cdm']['last_gallery'] ).'</div>';

  return $out;

}

function theme_cdm_print_button(){

  drupal_add_js ('$(document).ready(function() {

         $(\'#print_button\').click(function () {

         window.print();

     });

  });', 'inline');

  $output = '<div id="print_button"><img src="'

  .drupal_get_path('module', 'cdm_dataportal').'/images/print_icon.gif'

  . ' "alt="' . t('Print this page') . ' "title="'.t('Print this page').'" />'; //.t(' Print this page');

  //$output .= l(' Print this page', '');

  $output .= '<span>Print this page</span>';

  $output .= '</div>';

  return $output;

}

/* ============================ java script functions ============================= */

function _add_js_thickbox(){

  // ---- jQuery thickbox:

  /*

   * bug: compat-1.0.js && thickbox.js line 237 .trigger("unload")

   * -> event is not triggered because of problems with compat-1.0.js'

   * see INSTALL.txt

   *

   */

  //drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/jquery.imagetool.min.js');

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/thickbox/thickbox.js');

  drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/js/thickbox/cdm_thickbox.css');

}

function _add_js_lightbox($galleryID){

  /*

   * Important Notice:

   * The jquery.lightbox-0.5.js has been modified in order to allow using the "alt" attribute

   * for captions instead of the "title" attribute

   */

  $lightBoxBasePath = drupal_get_path('module', 'cdm_dataportal') .'/js/jquery-lightbox-0.5';

  drupal_add_js($lightBoxBasePath.'/js/jquery.lightbox-0.5.js');

  drupal_add_css($lightBoxBasePath.'/css/jquery.lightbox-0.5.css');

  drupal_add_js ('$(document).ready(function() {

      $(\'#'.$galleryID.' a.lightbox\').lightBox({

        fixedNavigation:  true,

        imageLoading:     \''.$lightBoxBasePath.'/images/lightbox-ico-loading.gif\',

        imageBtnPrev:     \''.$lightBoxBasePath.'/images/lightbox-btn-prev.gif\',

        imageBtnNext:     \''.$lightBoxBasePath.'/images/lightbox-btn-next.gif\',

        imageBtnClose:    \''.$lightBoxBasePath.'/images/lightbox-btn-close.gif\',

        imageBlank:       \''.$lightBoxBasePath.'/images/lightbox-blank.gif\'

      });

    });

    ', 'inline');

}

function _add_js_footnotes(){

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/footnotes.js');

}

function _add_js_cluetip(){

  //TODO replace by http://www.socialembedded.com/labs/jQuery-Tooltip-Plugin/jQuery-Tooltip-Plugin.html

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/cluetip/jquery.cluetip.js');

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/jquery.dimensions.js');

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/cluetip/jquery.hoverIntent.js');

  drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/js/cluetip/jquery.cluetip.css');

  drupal_add_js ("$(document).ready(function(){

      $('.cluetip').css({color: '#0062C2'}).cluetip({

        splitTitle: '|',

        showTitle: true,

        activation: 'hover',

        sicky: true,

        arrows: true,

        dropShadow: false,

        cluetipClass: 'rounded'

      });

    });", 'inline');

}

function _add_js_ahah(){

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/ahah-content.js');

}