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.

 */

function theme_cdm_feature_nodesTOC($featureNodes){

  $out .= '<ul>';

  foreach($featureNodes as $node){

    if(hasFeatureNodeDescriptionElements($node)){

      $featureRepresentation = isset($node->feature->representation_L10n) ? $node->feature->representation_L10n : 'Feature';

      // HACK to implement images for taxa, should be removed

      if($node->feature->uuid != UUID_IMAGE){

        $out .= '<li>'.l(t(theme('cdm_feature_name', $featureRepresentation)), $_GET['q'], array("class"=>"toc"), NULL, generalizeString($featureRepresentation)).'</li>';

      }

    }

  }

  $out .= '</ul>';

  return $out;

}

function theme_cdm_feature_name($feature_name){

  //TODO replace by using translations ?

  switch($feature_name){

    default: return t(ucfirst($feature_name));

  }

}

/**

 * Renders the taxon profile. The taxon profile consists of description elements

 * which are ordered by the structure defined by specific FeatureTree. The chosen

 * FeatureTree is merged with the list of desctiprion elements prior to using this

 * method (see function cdm_ws_descriptions_by_featuretree() ).

 *

 * @param unknown_type $mergedTrees

 * @param unknown_type $taxon The taxon whose sprofile to show

 */

function theme_cdm_featureTrees($mergedTrees, $taxon){

  if(!$mergedTrees){

    return;

  }

  foreach($mergedTrees as &$mTree){

    //TODO display title and reference in case of multiple $mergedTrees -> theme

    $out .= theme('cdm_feature_nodes', $mTree->root->children, $taxon);

  }

  return $out;

}

function theme_cdm_featureTreeTOCs($mergedTrees){

  if(!$mergedTrees){

    return;

  }

  //FIXME

  $out = '<div id="featureTOC">';

  $out .= '<h2>' . t('Content') .'</h2>';

  //TODO diplay title and reference in case of multiple $mergedTrees -> theme

  foreach($mergedTrees as &$mTree){

    $out .= theme('cdm_feature_nodesTOC', $mTree->root->children);

  }

  $out .= '</div>';

  return $out;

}

/**

 * Renders the $mergedFeatureNodes for the given $taxon.

 * The merged nodes can be obtained by making use of the

 * function cdm_ws_descriptions_by_featuretree()

 *

 * @param unknown_type $featureNodes

 * @param unknown_type $taxon

 */

function theme_cdm_feature_nodes($mergedFeatureNodes, $taxon){

  RenderHints::pushToRenderStack('feature_nodes');

  $gallery_settings = getGallerySettings(CDM_DATAPORTAL_DESCRIPTION_GALLERY_NAME);

  foreach($mergedFeatureNodes as $node){

    if(hasFeatureNodeDescriptionElements($node)) {

      $featureRepresentation = isset($node->feature->representation_L10n) ? $node->feature->representation_L10n : 'Feature';

      $block->module = 'cdm_dataportal';

      $media_list = array();

      if($node->feature->uuid != UUID_IMAGE) {

        $block->delta = generalizeString($featureRepresentation);

        $block->subject = '<span class="'. html_class_atttibute_ref($node->feature) . '">' . theme('cdm_feature_name', $featureRepresentation) . '</span>';

        $block->module = "cdm_dataportal-feature";

        $block->content = '';

        /*

         * Content/DISTRIBUTION

         */

        if($node->feature->uuid == UUID_DISTRIBUTION){

          if(variable_get(DISTRIBUTION_TEXTDATA_DISPLAY_ON_TOP, 0)){

            $distributionTextDataList = array();

            $distributionElementsList = array();

            foreach($node->descriptionElements as $descriptionElement){

              if($descriptionElement->class == "TextData"){

                $distributionTextDataList[] = $descriptionElement;

              } else {

                $distributionElementsList[] = $descriptionElement;

              }

            }

            if(count($distributionTextDataList) > 0){

              $node->descriptionElements = $distributionElementsList;

              $block->content .= theme('cdm_descriptionElements', $distributionTextDataList, $node->feature->uuid, $taxon->uuid);

            }

          }

          // Display cdm distribution map TODO this is a HACK to a proper generic implementation?

          $block->content .= theme('cdm_distribution_map', $taxon);

          $block->content .= theme('cdm_descriptionElements', $node->descriptionElements, $node->feature->uuid, $taxon->uuid);

        }

        /*

         * Content/COMMON_NAME

         */

        else if ($node->feature->uuid == UUID_COMMON_NAME){

          //TODO why is theme_cdm_descriptionElement_CommonTaxonName not beeing used???

          $block->content .= theme('cdm_common_names', $node->descriptionElements);

        /*

        }else if($node->feature->uuid == UUID_IMAGE_SOURCES) {

          $block->content .= theme('cdm_image_sources', $node->descriptionElements);

        */

        }

        /*

         * Content/ALL OTHER FEATURES

         */

        else {

          $block->content .= theme('cdm_descriptionElements', $node->descriptionElements, $node->feature->uuid, $taxon->uuid);

          /*

           *  Content/ALL OTHER FEATURES/Subordinate Features

           *

           *  subordinate features are printed inline in one floating text,

           *  it is expected that supordinate features only "contain" TextData elements

           */

          // TODO move into own theme

          if(count($node->children) > 0){

            //TODO support more than one level of childen http://dev.e-taxonomy.eu/trac/ticket/2393

            $text = '';

            foreach ($node->children as $child){

             if (is_array($child->descriptionElements)){

               foreach ($child->descriptionElements as $element) {

                 if(is_array($element->media)){

                   // append media of supordinate emelents to list of main feature

                   $media_list = array_merge($media_list, $element->media);

                 }

                 $description = str_replace("\n", "<br/>", $element->multilanguageText_L10n->text);

                //TODO use localized version of feature name, the locale must match the locale of the multilanguage text (http://dev.e-taxonomy.eu/trac/ticket/2394)

                 $description = str_replace($element->feature->titleCache, '<em>' . $element->feature->titleCache . '</em>', $description);

               }

               $text .= " " . $description;

               $description = '';

             }

            }

            $block->content .= $text;

          }

        }

        /*

         * Media/ALL FEATURES

         */

        $media_list = array_merge($media_list, cdm_dataportal_media_from_descriptionElements($node->descriptionElements));

        $captionElements = array('title', 'rights');

        $gallery = theme('cdm_media_gallerie', $media_list, CDM_DATAPORTAL_DESCRIPTION_GALLERY_NAME.'_'.$node->feature->uuid,

              $gallery_settings['cdm_dataportal_media_maxextend'],

              $gallery_settings['cdm_dataportal_media_cols'],

              $gallery_settings['cdm_dataportal_media_maxRows'],

              $captionElements

        );

        $block->content .= $gallery;

        $block->content .= theme('cdm_footnotes', $node->feature->uuid);

        $block->content .= theme('cdm_annotation_footnotes', $node->feature->uuid);

        // add anchor to subject

        $block->subject = '<a name="'.$block->delta.'"></a>'.  $block->subject;

        $out .= theme('block', $block);

      }

    }

  }

  RenderHints::popFromRenderStack();

  return $out;

}

function theme_FeatureTree_hierarchy($FeatureTreeUuid){

  if(!is_uuid($FeatureTreeUuid)){

    return;

  }

  $out = '';

  $featureTree = cdm_ws_get(CDM_WS_FEATURETREE, array($FeatureTreeUuid));

  if($featureTree && $featureTree->root){

    $out = '<ul class="'.$featureTree->class.'">';

    $out .= theme('FeatureTree_hierarchy_children', $featureTree->root);

    $out .= '</ul>';

  }

  return $out;

}

function theme_FeatureTree_hierarchy_children($node){

  $out = '';

  if($node->children){

    foreach($node->children as $childNode){

      $out .= '<li>'.check_plain($childNode->feature->representation_L10n);

      if($childNode->children && count($childNode->children) > 0){

        $out .= '<ul>'.theme('FeatureTree_hierarchy_children', $childNode).'</ul>';

      }

      $out .= '</li>';

    }

  }

  return $out;

}

/**

 *

 * Join the texts in $elementArray and enclose with a HTML tag

 * @param unknown_type $elementArray

 * @param unknown_type $feature the feature to which the elements given in $elementArray are belonging to

 * @param unknown_type $glue defaults to empty string

 * @param unknown_type $sortArray whether to sort the $elementArray alphabetically

 * @param unknown_type $enclosingHtml

 */

function theme_cdm_descriptionElementArray($elementArray, $feature, $glue = '', $sortArray = false, $enclosingHtml = 'ul'){

  $out = '<'.$enclosingHtml.' class="description" id="'.$feature->representation_L10n.'">';

  if($sortArray) sort($elementArray);

  $out .= join($elementArray, $glue);

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

  return $out;

}

function theme_cdm_descriptionElement_CommonTaxonName($element){

  $out = '<span class="' .  html_class_atttibute_ref($element). '">' . $element->language->representation_L10n . ' (' . $element->area->titleCache . '): ' . $element->name .'</span>';

  return $out;

}

/**

 * TODO: assign a new name to the function? because it is used for the citations

 *       textdata elements and not for all text data description elements

 * @param $element The description element which contains the text information

 * @param $asListElement A boolean which determines whether the citations should

 *                       be renderer as a list or not

 * @return unknown_type Html to be renderized in drupal

 */

function theme_cdm_descriptionElementTextData($element, $asListElement, $feature_uuid = null){

  $description = str_replace("\n", "<br/>", $element->multilanguageText_L10n->text);

  $sourceRefs = '';

  $result = array();

  $out;

  $res_author;

  $res_date;

  if(is_array($element->sources)){

    foreach($element->sources as $source){

      $referenceCitation = theme('cdm_DescriptionElementSource', $source);

      if($description && strlen($description) > 0 && $referenceCitation ){

        $sourceRefs .= ' ('.$referenceCitation.')' ;

      }else if ($referenceCitation){

        $sourceRefs = $referenceCitation;

      }

      if(strlen($sourceRefs) > 0){

        $sourceRefs = '<span class="sources">' . $sourceRefs . '</span>';

      }

      if ($source->nameUsedInSource->uuid){ //do a link to name page

        $name_used_in_source_link_to_show = l($source->nameUsedInSource->titleCache,

	        path_to_name($source->nameUsedInSource->uuid),

	        array(), NULL, NULL, FALSE ,TRUE);

      }else if (strlen($source->nameUsedInSource->originalNameString) > 0){ //show a text without link

        $name_used_in_source_link_to_show = $source->nameUsedInSource->originalNameString;

      }

      if ($asListElement){

        $out = '<li class="descriptionText DescriptionElement">' . $name_used_in_source_link_to_show;

        //adding ":" if necesary

        if ($name_used_in_source_link_to_show && ($description || $sourceRefs)){

          $out .= ': ';

        }

        $out .= $description . $sourceRefs . theme('cdm_annotations_as_footnotekeys', $element, $feature_uuid) . '</li>';

      }else{

        if ($name_used_in_source_link_to_show){

          $name_used_in_source_link_to_show = ' (name in source: '. $name_used_in_source_link_to_show . ')';

        }

        $out = '<span class="DescriptionElement DescriptionElement-' . $element->class .'">' . $description . $sourceRefs . $name_used_in_source_link_to_show . '</span>';

      }

    }

  }

  //if no sources, print the description

  if(!isset($out)) {

    $out = $description;

  }

  return $out;

}

function theme_cdm_common_names($elements){

  $text_data_out = '';

  $common_name_out = '';

  $separator = ',';

  $textData_commonNames = array();

  if (is_array($elements)){

    foreach ($elements as $element){

      if ($element->class == 'CommonTaxonName'){

        //$key = '<b>' . $element->language->representation_L10n . '</b> (' . $element->area->titleCache . ')';

        if ($element->language->representation_L10n){

          $key = '<b>' . $element->language->representation_L10n . '</b>';

          $key .= (strlen($element->area->titleCache)>0) ? ' (' . $element->area->titleCache . ')' : '';

        }

        $common_names[$key][] = $element;

      }else if ($element->class == 'TextData'){

     //else if ($element->class == 'TextData' && $element->feature->uuid == UUID_COMMON_NAME){

        $textData_commonNames[] = $element;

      }

    }

  }

  //handling common names

  if (count($common_names) > 0){

    //sorting the a-array based on the area (key)

    ksort($common_names);

    //creating the output to be render by drupal

    foreach ($common_names as $key => $elements){

      $rendered_element_list = '';

      foreach($elements as $element){

        $sourcesFootnoteKeyList = '';

        // adding footnotes sources

        foreach($element->sources as $source){

          if(_is_original_source_type($source)){

            $_fkey = FootnoteManager::addNewFootnote(UUID_COMMON_NAME, theme('cdm_DescriptionElementSource', $source, false));

            $sourcesFootnoteKeyList .= theme('cdm_footnote_key', $_fkey, ($sourcesFootnoteKeyList ? $separator : ''));

          }

        }

        if($element->name){

          $rendered_element_list .= '<span class="' .  html_class_atttibute_ref($element). '">' . (strlen($rendered_element_list) > 0 ? ', ': '') . $element->name . $sourcesFootnoteKeyList . '</span>';

        }

      }

      if ($key){

       $common_name_out .= (strlen($common_name_out) > 0 ? '; ': '') . $key . ': ' . $rendered_element_list;

      }else{

        $common_name_out .= (strlen($common_name_out) > 0 ? '; ': '') . $rendered_element_list;

      }

    }

  }

  //handling commons names as text data

  foreach($textData_commonNames as $text_data_element){

    $text_data_out .= theme('cdm_descriptionElementTextData', $text_data_element, true, $text_data_element->feature->uuid);

  }

  $common_name_out = "<div class=common_names_as_common_names> $common_name_out </div>";

    $out_array[] = $text_data_out;

  $common_name_out_text_data = '<div class=common_names_as_text_data>' . theme('cdm_descriptionElementArray', $out_array, $element->feature) . '</div>';

  return $common_name_out . $common_name_out_text_data;

  //return $common_name_out . theme('cdm_descriptionElementArray', $out_array, $element->feature);

  //return "<div class=common_names> $common_name_out $common_name_out_text_data";

}

/**

 * Theme a list of description elements, usually of a specific feature type

 * @param $descriptionElements

 * @return unknown_type

 */

function theme_cdm_descriptionElements($descriptionElements, $featureUuid, $taxon_uuid){

  $outArray = array();

/*

  $userDefined = mixed_variable_get(LAYOUT_SETTING_PREFIX . $featureUuid, FEATURE_TREE_LAYOUT_DEFAULTS);

  if(variable_get('distribution_sort', 'NO_SORT')  != 'NO_SORT'){

    $glue = '';

    $enclosingTag = 'dl';

    $entryEnclosingTag = null;

  } else if($userDefined && $userDefined['enabled']){

      $glue = $userDefined['glue'];

      $enclosingTag = $userDefined['enclosingTag'];

      $entryEnclosingTag = $userDefined['entryEnclosingTag'];

  } else {

    // TODO remove once LAYOUT_SETTING_PREFIX-{uuid} seeting are confired to work for all portals (selenium test still missing!!!)

    $glue = '';

    $enclosingTag = 'ul';

    $entryEnclosingTag = null ;

  }

*/

	if(variable_get('distribution_sort', 'NO_SORT')  != 'NO_SORT'){

		$glue = '';

		$enclosingTag = 'dl';

	} else {

		$glue = '';

		$enclosingTag = 'ul';

	}

  $sortOutArray = false;

  $distributionElements = array();

  RenderHints::pushToRenderStack('cdm_descriptionElements');

  if(is_array($descriptionElements)){//avoiding warning box in drupal for flora malesiana

    foreach($descriptionElements as $descriptionElement) {

      // --- DISTRIBUTION ---- //

      if($descriptionElement->feature->uuid == UUID_DISTRIBUTION){

        if($descriptionElement->class == 'Distribution'){

          $sortKey = $descriptionElement->area->representation_L10n;

          $distributionElements[$sortKey]= $descriptionElement;

        } else if($descriptionElement->class == 'TextData'){

          $asListElement = false;

          $repr = theme ('cdm_descriptionElementTextData', $descriptionElement, $asListElement, $descriptionElement->feature->uuid);

          if( !array_search($repr, $outArray)){

          	$outArray[] = $repr;

            //TODO HINT: sorting in theme_cdm_descriptionElementArray will not work since this array contains html attributes with uuids !!!!

            $sortOutArray = true;

            $glue = '<br/> ';

            $enclosingTag = 'p';

          }

        }

      }

       // --- IMAGE_SOURCES --- //

      else if($descriptionElement->feature->uuid == UUID_IMAGE_SOURCES){

        $image_sources[] = $descriptionElement;

      }

      // ---- class == TextData ---- //

      else if($descriptionElement->class == 'TextData'){

        $asListElement = true;

        $outArray[] = theme('cdm_descriptionElementTextData', $descriptionElement, $asListElement, $descriptionElement->feature->uuid);

      }else if ($descriptionElement->class == 'CommonTaxonName') {

        $outArray[] = theme('cdm_descriptionElement_CommonTaxonName', $descriptionElement);

      }else {

        $outArray[] = '<li>No method for rendering unknown description class: '.$descriptionElement->classType.'</li>';

      }

    }

  }

  //if feature = NAME USAGE sort the list of sources

  //this is ONLY for FLORA MALESIANA and FLORE d'AFRIQUE CENTRALE

  if($descriptionElement->feature->uuid == UUID_NAME_USAGE){

    sort($outArray);

  }

  if($image_sources){

      $outArray[] = theme('cdm_description_element_image_source', $image_sources, true);

  }

  if(variable_get('distribution_sort', 'NO_SORT') != 'NO_SORT'){

    $outArray[] = theme('cdm_description_ordered_distributions', $taxon_uuid, $distributionElements);

  }else{

    ksort($distributionElements);

    $outArray[] = theme('cdm_descriptionElementDistribution', $distributionElements); // TODO , $entryEnclosingTag);

  }

  // take the feature of the last $descriptionElement

  $feature = $descriptionElement->feature;

  $out = theme('cdm_descriptionElementArray', $outArray, $feature, $glue, $sortOutArray, $enclosingTag);

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 *

 * Enter description here ...

 * @param unknown_type $a

 * @param unknown_type $b

 */

function compare_image_sources($a, $b){

    if($a->multilanguageText_L10n->text == $b->multilanguageText_L10n->text){

      return 0;

    }

    return ($a->multilanguageText_L10n->text < $b->multilanguageText_L10n->text) ? -1 : 1;

}

/**

 *

 */

function theme_cdm_description_element_image_source($image_sources, $asListElement) {

    $out = '';

    $separator = ',';

    RenderHints::pushToRenderStack('descriptionElementImageSource');

    RenderHints::setFootnoteListKey(UUID_IMAGE_SOURCES);

    //sorting the image sources

    usort($image_sources, "compare_image_sources");

    //generate the footnotes

    foreach($image_sources as $image_source){

        $footNoteKeys = cdm_annotations_as_footnotekeys($image_source);

        foreach($image_source->sources as $source){

            if(_is_original_source_type($source)){

                $fn_key = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), theme('cdm_DescriptionElementSource', $source, false));

                cdm_add_footnote_to_array($footNoteKeys, $fn_key);// ensure uniqueness of the footnote keys

            }

        }

        //sort and render footnote keys

        $footnoteKeyListStr = '';

        asort($footNoteKeys);

        foreach($footNoteKeys as $footNoteKey){

            $footnoteKeyListStr .= theme('cdm_footnote_key', $footNoteKey, ($footnoteKeyListStr ? $separator : ''));

        }

        //return value!

        $out .= '<span class="descriptionElement descriptionElement-'.$image_source->uuid.'">'.$image_source->multilanguageText_L10n->text . $footnoteKeyListStr . '; </span>';

    }

    RenderHints::popFromRenderStack();

    return $out;

}

/**

 *

 * @param unknown_type $descriptionElements

 * @param String $enclosingTag

 */

function theme_cdm_descriptionElementDistribution($descriptionElements, $enclosingTag = "span"){

	if(!$enclosingTag){

		$enclosingTag = "span";

	}

  $out = '';

  $separator = ',';

  RenderHints::pushToRenderStack('descriptionElementDistribution');

  RenderHints::setFootnoteListKey(UUID_DISTRIBUTION);

  foreach($descriptionElements as $descriptionElement){

    // annotations as footnotes

    $footNoteKeys = cdm_annotations_as_footnotekeys($descriptionElement);

    // source references as footnotes

    foreach($descriptionElement->sources as $source){

      if(_is_original_source_type($source)){

        $fn_key = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), theme('cdm_DescriptionElementSource', $source, false));

        cdm_add_footnote_to_array($footNoteKeys, $fn_key);// ensure uniqueness of the footnote keys

      }

    }

    // sort and render footnote keys

    $footnoteKeyListStr = '';

    asort($footNoteKeys);

    foreach($footNoteKeys as $footNoteKey){

      $footnoteKeyListStr .= theme('cdm_footnote_key', $footNoteKey, ($footnoteKeyListStr ? $separator : ''));

    }

    $out .= '<'. $enclosingTag .' class="descriptionElement descriptionElement-'.$descriptionElement->uuid.'">'

      . $descriptionElement->area->representation_L10n . $footnoteKeyListStr . ' </'. $enclosingTag .'>';

  }

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * Function target is to compare two different foootnotes objects.

 * The comparation is based on the footnote key. The one which is

 * displayed as footnote number.

 *

 * @param footnote object $a

 * @param footnote object $b

 */

function footnotes_key_compare($a, $b){

  $res = 0;

  if ($a->keyStr < $b->keyStr){

    $res = -1;

  }elseif ($a->keyStr > $b->keyStr){

    $res = 1;

  }

  return $res;

}

function theme_cdm_description_ordered_distributions($taxon_uuid, $descriptionElements){

  //returning null if no description elements

  if ($descriptionElements == null){

    return '';

  }

  //initialization some variables

  $out = '';

  $separator = ',';

  RenderHints::pushToRenderStack('descriptionElementDistribution');

  RenderHints::setFootnoteListKey(UUID_DISTRIBUTION);

  //getting all the taxon description for a given taxon

  $taxonDescriptions = cdm_ws_get(CDM_WS_PORTAL_TAXON_DESCRIPTIONS, $taxon_uuid);

  foreach ($taxonDescriptions as $description){

    $descriptions_uuids[] = $description->uuid;

  }

  //getting the sortered distributions (omiting level ??)

  $request_params = array();

  $request_params['omitLevels'] = UUID_NAMEDAREALEVEL_TDWGLEVEL_2;

  $ordered_areas = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION_DISTRIBUTION_TREE, join(',',$descriptions_uuids), queryString($request_params));

  $ordered_areas = $ordered_areas->rootElement->children;

  //printing the distributions

  foreach ($ordered_areas as $element_level1){

    //level1

    if ($element_level1->data){

      $out .= '<dt>' . $element_level1->data->area->representation_L10n . ':</dt> ';

    }

    $out .= '<dd>';

    //level3

    foreach ($element_level1->children as $element_level3){

      if ($element_level3->data){

        $text_l3 = $element_level3->data->area->representation_L10n;

      }

      $fnKeysLevel3Str = '';

      $fnKeysLevel3 = cdm_annotations_as_footnotekeys($element_level3->data);

      foreach($element_level3->data->sources as $source){

        if(_is_original_source_type($source)){

          $fn_key3 = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), theme('cdm_DescriptionElementSource', $source, false));

          cdm_add_footnote_to_array($fnKeysLevel3, $fn_key3);

        }

      }

      //level4

      $l4_regions = array();

      foreach ($element_level3->children as $element_level4){

        if ($element_level4->data){

          $text_l4 = $element_level4->data->area->representation_L10n;

          $l4_regions[$element_level3->data->area->representation_L10n] = '';

          $fnKeysLevel4Str = '';

          $fnKeysLevel4 = cdm_annotations_as_footnotekeys($element_level4->data);

          foreach($element_level4->data->sources as $source){

            if(_is_original_source_type($source)){

              $fn_key4 = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), theme('cdm_DescriptionElementSource', $source, false));

              cdm_add_footnote_to_array($fnKeysLevel4, $fn_key4);

            }

          }

          usort($fnKeysLevel4, "footnotes_key_compare");

          $l4_regions[$text_l4] = $fnKeysLevel4;

        }

      }//level4

      //managing level3 and level4 for generating the right output

      usort($fnKeysLevel3, "footnotes_key_compare");

      foreach ($fnKeysLevel3 as $key3){

        foreach ($l4_regions as $key4 => $value4){

          cdm_add_footnote_to_array($l4_regions[$key4], $key3);

        }

      }

      if ($element_level3->numberOfChildren == 1 &&

       $text_l3 == $element_level3->children[0]->data->area->representation_L10n){

        //var_dump($element_level3->children[0]->data->area->representation_L10n);

        $fnStr = '';

        $region = array_pop($l4_regions);

        foreach($region as $key){

          $fnStr .= theme('cdm_footnote_key', $key, ($fnStr ? $separator : ''));

        }

        $out .= "$text_l3 $fnStr; ";

              //removing whitespaces when &fnStr is empty

        if(substr($out, -3) == ' ; '){

          $out = substr($out, 0, -3) . '; ';

        }

      }else{

        $fnKeysLevel3Str = '';

        foreach($fnKeysLevel3 as $key){

          $fnKeysLevel3Str .= theme('cdm_footnote_key', $key, ($fnKeysLevel3Str ? $separator : ''));

        }

        $text_l4_aux = '';

        foreach ($l4_regions as $key => $value){

          $fnKeysLevel4Str = '';

          if (is_array($l4_regions[$key])) {

            foreach ($l4_regions[$key] as $fnkey){//warning why?

              $fnKeysLevel4Str .= theme('cdm_footnote_key', $fnkey, ($fnKeysLevel4Str ? $separator : ''));

            }

          }

          //if ($key != $text_l3 || sizeof($l4_regions > 1)){

          if ($key != $text_l3){

            $text_l4_aux .= "$key $fnKeysLevel4Str, ";

          }

        }

        $text_l4_aux = substr($text_l4_aux, 0, -2);

        if (strlen($text_l4_aux) > 0){

          $out .= "$text_l3 $fnKeysLevel3Str ($text_l4_aux); ";

        }else{

          $out .= "$text_l3 $fnKeysLevel3Str; ";

        }

      }

    }//level3

    $out = substr($out, 0, -2);

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

  }//level1

  RenderHints::popFromRenderStack();

  return $out;

}

function theme_cdm_DescriptionElementSource($descriptionElementSource, $doLink = TRUE){

  if(isset($descriptionElementSource->citation)){

    $out = theme('cdm_reference', $descriptionElementSource->citation, $descriptionElementSource->citationMicroReference, $doLink);

  }

  return $out;

}

function theme_cdm_IdentifieableSource($source, $doLink = TRUE){

  if(isset($source->citation)){

    $out = theme('cdm_reference', $source->citation, $source->citationMicroReference, $doLink);

  }

  return $out;

}

/*

 function theme_cdm_descriptionElementDistribution($descriptionElements){

 $out = '';

 $separator = ',';

 RenderHints::pushToRenderStack('descriptionElementDistribution');

 RenderHints::setFootnoteListKey(UUID_DISTRIBUTION);

 foreach($descriptionElements as $descriptionElement){

 // annotations as footnotes

 $annotationFootnoteKeys = theme('cdm_annotations_as_footnotekeys', $descriptionElement);

 // source references as footnotes

 $sourcesFootnoteKeyList = '';

 foreach($descriptionElement->sources as $source){

 if(_is_original_source_type($source)){

 $_fkey = FootnoteManager::addNewFootnote(UUID_DISTRIBUTION, theme('cdm_DescriptionElementSource', $source, false));

 $sourcesFootnoteKeyList .= theme('cdm_footnote_key', $_fkey, UUID_DISTRIBUTION, ($sourcesFootnoteKeyList ? $separator : ''));

 }

 }

 if($annotationFootnoteKeys && $sourcesFootnoteKeyList){

 $annotationFootnoteKeys .= $separator;

 }

 $out .= $descriptionElement->area->representation_L10n . $annotationFootnoteKeys . $sourcesFootnoteKeyList . ' ';

 }

 $out = substr($out, 0, strlen($out)-strlen($separator) );

 RenderHints::popFromRenderStack();

 return $out;

 }

 */

/**

 * TODO

 * Quick-and-dirty solution to show distribution service to exemplar groups

 *

 * @param unknown_type $featureTo

 * @return unknown

 */

function theme_cdm_distribution_map($taxon){

  $server = getEDITMapServiceURI();

  if(!$server){

    //warning message

    drupal_set_message('No \'Geoservice Access Point\' has been set so far. '

    . 'Please configure the variable \'Geoservice Access Point\' here '

    . l('CDM Dataportal Settings', 'admin/settings/cdm_dataportal/geo'), 'warning');

    //message to render

    return "<p>No geoservice specified</p>";

  }else{

    $fontStyles = array(0 => "plane", 1 => "italic");

    // query cdm server for map service uri parameters

    $map_data_parameters = cdm_ws_get(CDM_WS_GEOSERVICE_DISTRIBUTIONMAP, $taxon->uuid);

    $out .= "<!-- map_data_parameters:". print_r($map_data_parameters, true) . " -->";

    $query_string = $map_data_parameters->String;

    if(!$query_string){

      // the $query_string is empty if there are no distribution areas defined

      return ;

    }

    // some cleaning of the URI paramters, TODO is this still needed?

    $query_string = str_replace('%3A', ":", $query_string);

    // additional query parameters as set in the data portal admin section

    $display_width = variable_get('cdm_dataportal_geoservice_display_width', false);

    $bounding_box = variable_get('cdm_dataportal_geoservice_bounding_box', false);

    $labels_on = variable_get('cdm_dataportal_geoservice_labels_on', 0);

    $query_string .= ($display_width ? '&ms=' . $display_width: '').

    ($bounding_box ? '&bbox=' .  $bounding_box : '')

    . ($labels_on ? '&label=' .  $labels_on : '');

    /* ------ choose the display mode, either openlayers or static image ------ */

    if(variable_get('cdm_dataportal_map_openlayers', 1)){

      $query_string .= '&img=false';

      /* =========== display distributions using the openlayers map viewer =========== */

      $legend_url_font_size = variable_get('cdm_dataportal_geoservice_legend_font_size', 10);

      $legend_url_font_style = variable_get('cdm_dataportal_geoservice_legend_font_style', 1);

      $legend_url_font_style = $fontStyles[$legend_url_font_style];

      $legend_url_icon_width  = variable_get('cdm_dataportal_geoservice_legend_icon_width', 35);

      $legend_url_icon_height = variable_get('cdm_dataportal_geoservice_legend_icon_height', 15);

      $legendFormatQueryStr  = "format=image".urlencode('/')."png&TRANSPARENT=TRUE";

      $legendFormatQueryStr .= "&WIDTH=".$legend_url_icon_width."&HEIGHT=".$legend_url_icon_height."&";

      //TODO why is the layer=topp:tdwg_level_4 parameter neede at all here??

      $legendFormatQueryStr .="layer=topp".urlencode(':')."tdwg_level_4&LEGEND_OPTIONS=forceLabels".urlencode(':')."on;fontStyle".urlencode(':').$legend_url_font_style.";fontSize".urlencode(':').$legend_url_font_size."&SLD=".urlencode($sldLegend);

      $out .= get_openlayers_map(

        $display_width,

        null,

        $query_string,

        $legendFormatQueryStr,

        variable_get('cdm_dataportal_geoservice_map_caption', '')

      );

    } else {

      // simple image

      $mapStaticCaption = '&mc_s=Georgia,15,blue&mc=' . variable_get('cdm_dataportal_geoservice_map_caption', '');

      $query_string .= '&img=true';

      $query_string .= '&legend=1&mlp=3' . $mapStaticCaption . '&recalculate=false';

      $map_service_script_name = "areas.php";

      // apply Plain Image map settings

      if (getEDITMapServiceVersionNumber() >= 1.1){

        /*

         * example : title=a:Naturalized++non-invasive

         * &ad=cyprusdivs:bdcode:a:5&as=a:ff9900,,0.1,&l=tdwg4

         * &ms=500&bbox=32,34,35,36&img=true&legend=1&mlp=3

         * &mc_s=Georgia,15,blue&mc=&recalculate=false

         *

         * http://edit.br.fgov.be/edit_wp5/v1/rest_gen.php?

         * l=background_gis:b,cyprusdivs&ad=cyprusdivs%3Abdcode%3Aa%3A8%2C4

         * &as=a%3A339966%2C%2C0.1%2C|b:0000ff,,

         * &bbox=32%2C34%2C35%2C36&img=true&legend=1&mc=&mc_s=Georgia%2C15%2Cblue

         * &mlp=3&ms=500&recalculate=false&title=a%3Aindigenous

         */

        $map_service_script_name = "rest_gen.php";

        $bgcolor_areaStyleId= "y";

        $baselayer_areaStyleId= "z";

        $bgcolor_layer='';

        $additional_area_styles = array();

        // background color:

        if(variable_get('map_bg_color', '')){

          $bgcolor_layer = "background_gis:".$bgcolor_areaStyleId;

          $additional_area_styles[] = $bgcolor_areaStyleId . ":" . variable_get('map_bg_color', '') . ",,";

        }

        //TODO HACK to replace the default base layer which currently is tdwg4 !!!

        if(strpos($query_string, "?l=") !== FALSE){

          $layer_param_token = "?l=";

        } else {

          $layer_param_token = "&l=";

        }

        if(strpos($query_string, "?as=") !== FALSE){

          $areystyle_param_token = "?as=";

        } else {

          $areystyle_param_token = "&as=";

        }

        if(variable_get('map_base_layer', '')){

          $query_string = str_replace($layer_param_token."tdwg4", "$layer_param_token".variable_get('map_base_layer', ''). ":" . $baselayer_areaStyleId, $query_string);

        } else {

          $query_string = str_replace($layer_param_token."tdwg4", $layer_param_token."tdwg4:".$baselayer_areaStyleId . ",", $query_string);

        }

        if($bgcolor_layer){

          $query_string = str_replace($layer_param_token, $layer_param_token . $bgcolor_layer . ",", $query_string);

        }

        if(variable_get('map_base_layer_style', '')){

          $additional_area_styles[] = $baselayer_areaStyleId . ":" . variable_get('map_base_layer_style', '');

        }

        foreach ($additional_area_styles as $as) {

          $query_string = str_replace($areystyle_param_token, $areystyle_param_token . $as . "|", $query_string);

        }

      }

      $mapUri = url("$server/$map_service_script_name?$query_string");

      $out .= '<img class="distribution_map" src="' . $mapUri . '" alt="Distribution Map" />';

    }

    return $out;

  }

}

/**

 * Returns a list of a specific type of IdentificationKeys, the list can be restricteded by a taxon.

 * @param $type The simple name of the cdm class implementing the interface IIdentificationKey,

 *          valid values are : PolytomousKey, MediaKey, MultiAccessKey

 * @param $taxonUuid if given this parameter restrict the listed keys to

 *          those which have the taxon identified be this uuid in scope.

 */

function _list_IdentificationKeys($type, $taxonUuid = null, $pageSize = null, $pageNumber = null){

  if(!$type){

    drupal_set_message("Type parameter is missing", "error");

    return;

  }

  $cdm_ws_pasepath = null;

  switch($type){

    case "PolytomousKey" : $cdm_ws_pasepath = CDM_WS_POLYTOMOUSKEY; break;

    case "MediaKey" : $cdm_ws_pasepath = CDM_WS_MEDIAKEY; break;

    case "MultiAccessKey" : $cdm_ws_pasepath = CDM_WS_MULTIACCESSKEY; break;

  }

  if(!$cdm_ws_pasepath){

    drupal_set_message("Type parameter is not valid: ".$type, "error");

  }

  $queryParameters  = '';

  if(is_numeric($pageSize)){

    $queryParameters  = "pageSize=".$pageSize;

  } else {

    $queryParameters  = "pageSize=0";

  }

  if(is_numeric($pageNumber)){

    $queryParameters  = "pageNumber=".$pageNumber;

  } else {

    $queryParameters  = "pageNumber=0";

  }

  $queryParameters  = null;

  if($taxonUuid){

    $queryParameters = "findByTaxonomicScope=$taxonUuid";

  }

  $pager = cdm_ws_get($cdm_ws_pasepath, null, $queryParameters);

  if(!$pager || $pager->count == 0){

      return array();

  }

  return $pager->records;

}

function theme_cdm_IdentificationKey($identificationKey, $doLinkToKeyPage = true, $showIdentificationKeyTitle = true){

   $parentRenderPath = RenderHints::getRenderPath();

   RenderHints::pushToRenderStack("IdentificationKey");

   if($showIdentificationKeyTitle){

     if($doLinkToKeyPage) {

       $out = l($identificationKey->titleCache, path_to_key($identificationKey->class, $identificationKey->uuid));

     } else {

       $out = $identificationKey->titleCache;

     }

   }

   if(is_array($identificationKey->sources)){

     // display sources

     $i = 0;

     $out .= '<div>';

     foreach($identificationKey->sources as $source){

      $out .= ($i++ > 0 ? ', ' : '' ) . theme("cdm_IdentifieableSource", $source);

     }

     $out .= '</div>';

   }

     // display annotations

   $out .= theme('cdm_annotations', cdm_ws_getAnnotationsFor($identificationKey), 'div');

   RenderHints::popFromRenderStack();

   return $out;

}

function theme_cdm_polytomousKey(&$polytomousKey){

  $keyStyle = "linkedStyle"; // TODO settings needed

  RenderHints::pushToRenderStack("polytomousKey");

  // key nodes in linked style

  $out = '<table class="polytomousKey polytomousKey_'.$keyStyle.'">';

  $out .= theme('cdm_polytomousKey_'.$keyStyle.'_subgraph', $polytomousKey->root);

  $out .= '</table>';

  RenderHints::popFromRenderStack();

  return $out;

}

function theme_cdm_polytomousKey_linkedStyle_subgraph(&$polytomousKeyNode){

  static $statementCountCharacter = '\'';

  $out = "";

  if(is_array($polytomousKeyNode->children)){

    $childCount = 0;

    // render edges of the current node

    foreach($polytomousKeyNode->children as &$child){

      if(!isset($child->statement)){

        // skip node with empty statements (see below for explanation: "Special case")

        continue;

      }

      $out .= '<tr class="childCount_' . $childCount . '">';

      $out .= '<td class="nodeNumber">'. uuid_anchor($polytomousKeyNode->uuid, $polytomousKeyNode->nodeNumber . str_pad("", $childCount++ , $statementCountCharacter)) . "</td>";

      /*

       * Special case:

       * Child nodes with empty statements but taxa as leaf are to

       * treated as if all those taxa where direct children of the source node.

       */

      $islinkToManyTaxa = !isset($child->children[0]->statement) && isset($child->children[0]->taxon->uuid);

      $islinkToTaxon = isset($child->taxon->uuid);

      $islinkToSubKey = isset($child->subkey->uuid);

      $islinkToOtherNode = isset($child->otherNode);

      $islinkToNode = $child->nodeNumber && !$islinkToManyTaxa && !$islinkToOtherNode; // either null or 0

      $out .= '<td ' . RenderHints::getHtmlElementID($child) . '  class="edge">';

      if(isset($polytomousKeyNode->question->label_l10n)){

        $out .= $polytomousKeyNode->question->label_l10n .  ": ";

      }

      $out .= $child->statement->label_l10n;

      // --- links to nodes taxa and subkeys

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

     // link to a PolytomousKeyNode

      if($islinkToNode){

        $out .= '<div class="nodeLinkToNode">' . l($child->nodeNumber, $_REQUEST["q"], null, null, $child->uuid) . '</div>';

      }

      // link to a PolytomousKeyNode

      if($islinkToOtherNode){

        $out .= '<div class="nodeLinkToOtherNode">' . l($child->otherNode->nodeNumber, $_REQUEST["q"], null, null, $child->otherNode->uuid) . '</div>';

      }

      // link to one or many taxa

      if($islinkToTaxon || $islinkToManyTaxa){

        if($islinkToManyTaxa){

          $taxonChildren = $child->children;

        } else {

          $taxonChildren = array($child);

        }

        foreach($taxonChildren as $taxonChild){

          // TODO many taxa $child->children->taxon

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

          if(is_object($taxonChild->modifyingText)){

            $i = 0;

            foreach(get_object_vars($taxonChild->modifyingText) as $language=>$languageString){

              $out .= ($i++ > 0 ? ', ' : '') . '<span class="modifyingText">'. $languageString->text . '</span> ';

            }

          }

          $out .=  theme("cdm_taxonName", $taxonChild->taxon->name, url(path_to_taxon($taxonChild->taxon->uuid)));

          $out .=  '</div>';

        }

        // link to a subkey

        if($islinkToSubKey){

          $out .= '<div class="nodeLinkToSubkey">' . theme('cdm_IdentificationKey', $child->subkey) . '</div>';

        }

      }

      $out .= '</div>'; // end node link

      $out .= '</td>'; // end edge

      $out .= '</tr>';

    }

    // recurse into child nodes

    foreach($polytomousKeyNode->children as &$child){

      $out .= theme('cdm_polytomousKey_linkedStyle_subgraph', $child);

    }

  }

  return $out;

}

/**

 * Renders a list of a specific type of IdentificationKeys, the list can be restricteded by a taxon.

 * @param $type The simple name of the cdm class implementing the interface IIdentificationKey,

 *          valid values are : PolytomousKey, MediaKey, MultiAccessKey

 * @param $taxonUuid if given this parameter restrict the listed keys to

 *          those which have the taxon identified be this uuid in scope.

 */

function theme_cdm_list_IdentificationKeys($type, $taxonUuid = null, $pageSize, $pageNumber){

  $keyList = _list_IdentificationKeys($type, $taxonUuid);

  if(!$keyList || count ($keyList) == 0){

    return;

  }

  RenderHints::pushToRenderStack('list_IdentificationKeys');

  $out = '<ul>';

  foreach ($keyList as $key){

    $out .= '<li>';

    $out .= theme('cdm_IdentificationKey', $key);

    $out .= '</li>';

  }

  $out .= '</ul>';

  $out .= theme("cdm_annotation_footnotes", RenderHints::getRenderPath());

  RenderHints::popFromRenderStack();

  return $out;

}

function theme_cdm_block_IdentificationKeys($taxonUuid = null, $pageSize = null){

  static $types = array("PolytomousKey"=>"Polytomous", "MediaKey"=>"Media", "MultiAccessKey"=>"Multiaccess");

  RenderHints::pushToRenderStack('block_IdentificationKeys');

  $out = '';

  foreach($types as $type=>$label){

    $keylist = theme('cdm_list_IdentificationKeys', $type, $taxonUuid, $pageSize, $pageNumber);

    if(!$keylist){

      continue;

    }

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

    $out .= '<h3>'.t($label)."</h3>";

    $out .= $keylist;

    $out .= '</div>';

  }

  RenderHints::popFromRenderStack();

  return $out;

}