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;

	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

 *

 * TODO it should be configurable which objects can be annotated as this might differ in dataportals

 *

 */

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

  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 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(){

	//$galleryLinkUri = path_to_taxon($taxon->uuid).'/images';

	//$gallery_name = $taxon->uuid;

	//$mediaList = cdm_ws_get(CDM_WS_PORTAL_TAXON_MEDIA, array($taxon->uuid, $prefMimeTypeRegex, $prefMediaQuality));

	$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');

}