EDIT

<?php

/**

 * @file

 * Taxon Theming functions.

 *

 * @copyright

 *   (C) 2007-2012 EDIT

 *   European Distributed Institute of Taxonomy

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

 *

 *   The contents of this module are subject to the Mozilla

 *   Public License Version 1.1.

 * @see http://www.mozilla.org/MPL/MPL-1.1.html

 */

/**

 * Returns HTML for misapplied names and invalid designations.

 *

 * Both relation types are currently treated the same!

 *

 * @param array $variables

 *   An associative array containing:

 *   - taxonRelationships

 *   - focusedTaxon

 *

 * @ingroup themeable

 */

function theme_cdm_taxonRelationships($variables) {

  $taxonRelationships = $variables['taxonRelationships'];

  $focusedTaxon = $variables['focusedTaxon'];

  if (!$taxonRelationships) {

    return;

  }

  RenderHints::pushToRenderStack('taxonRelationships');

  $footnoteListKey = 'taxonRelationships';

  RenderHints::setFootnoteListKey($footnoteListKey);

  $misapplied = array();

  $joinedAuthorTeams = array();

  $taxon_relationship_types = variable_get(CDM_TAXON_RELATIONSHIP_TYPES, unserialize(CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT));

  // Aggregate misapplied names having the same fullname:

  foreach ($taxonRelationships as $taxonRelation) {

    if (in_array($taxonRelation->type->uuid, $taxon_relationship_types)) {

      if ($taxonRelation->type->uuid == UUID_MISAPPLIED_NAME_FOR || $taxonRelation->type->uuid == UUID_INVALID_DESIGNATION_FOR) {

        $name = $taxonRelation->fromTaxon->name->titleCache;

        $authorteam = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $taxonRelation->fromTaxon->sec->uuid);

        $authorteam = $authorteam->titleCache;

        if (!isset($misapplied[$name])) {

          // Render the first name found as representative for all others.

          $misapplied[$name]['out'] = cdm_related_taxon($taxonRelation->fromTaxon, UUID_MISAPPLIED_NAME_FOR);

        }

        else {

          // We need to add the anchors for all of the other mispplied names not

          // being rendered explicitly.

          $misapplied[$name]['out'] = uuid_anchor($taxonRelation->fromTaxon->uuid, $misapplied[$name]['out']);

        }

        // Collect all authors for this fullname.

        if (isset($authorteam)) {

          $misapplied[$name]['authorteam'][$authorteam] = '';

          $joinedAuthorTeams[$authorteam] = 'sensu ' . theme('cdm_reference', array('reference' => $taxonRelation->fromTaxon->sec));

        }

      }

      else {

        // All relationsship types but misapplied_name_for

        // invalid_designation_for.

    }

  }

  // Sort the joinedAuthorTeams and create footnotes and footnotekeys.

  ksort($joinedAuthorTeams);

  foreach ($joinedAuthorTeams as $authorteam => $sensuCitation) {

    $footnoteKey = FootnoteManager::addNewFootnote($footnoteListKey, $sensuCitation);

    $joinedAuthorTeams[$authorteam] = '<span class="sensu">sensu ' . $authorteam . theme('cdm_footnote_key', array('footnoteKey' => $footnoteKey)) . '</span>';

  }

  $out = '<div class="taxon-relationships">';

    $out .= '<ul class="misapplied">';

    foreach ($misapplied as $misapplied_name) {

      $out .= '<li class="synonym"><span class="misapplied">' . $misapplied_name['out'] . ' </span>';

      if (isset($misapplied_name['authorteam'])) {

        // Fill authors with the renderedFootnoteKey and sorting 'em.

        foreach ($misapplied_name['authorteam'] as $authorteam => &$renderedFootnoteKey) {

          $renderedFootnoteKey = $joinedAuthorTeams[$authorteam];

        }

        ksort($misapplied_name['authorteam']);

        $out .= join('; ', $misapplied_name['authorteam']);

      }

      $out .= '</li>';

    }

    $out .= '</ul>';

  }

      $out .= '<li class="synonym">' . $taxon_relationship_line . '</li>';

    $out .= '</ul>';

  }

  $footnotes .= theme('cdm_annotation_footnotes', array('footnoteListKey' => $footnoteListKey, 'enclosingTag' => 'li'));

// AK: why splitting footnotes at the sennsu string ??? this is weired and hacky

//     TODO remove below dead code

//   $tr_footnotes_exploded = explode('sensu', $tr_footnotes);

//   $tr_footnotes_aux = '';

//   foreach ($tr_footnotes_exploded as $element) {

//     $tr_footnotes_aux .= $element;

//   }

  $out .= '<ul class="footnotes">' . $footnotes . '</ul>';

  $out .= '</div>';

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * @todo Please document this function.

 * @see http://drupal.org/node/1354

 */

  $accepted_for_uuid = $variables['acceptedFor'];

    return '';

  }

  $out = '';

  if ($synonym) {

    $out .= '<span class="acceptedFor">';

    $out .= t('is accepted for ');

    if (isset($synonym->name->nomenclaturalReference)) {

      $referenceUri = url(path_to_reference($synonym->name->nomenclaturalReference->uuid));

      'taxonName' => $synonym->name,

      'nameLink' => NULL,

      'refenceLink' => $referenceUri,

      ));

    $out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $synonym));

    $out .= '</span>';

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * @todo document this function.

 */

function theme_cdm_list_of_taxa($variables) {

  $freetextSearchResults = $variables['freetextSearchResults'];

  $form_name = 'search_gallery';

  // $default_values = unserialize(CDM_DATAPORTAL_GALLERY_SETTINGS);

  // $gallery_settings = variable_get($form_name, $default_values);

  $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SEARCH_GALLERY_NAME);

  $showMedia_taxa = $gallery_settings['cdm_dataportal_show_taxon_thumbnails'];

  $showMedia_synonyms = $gallery_settings['cdm_dataportal_show_synonym_thumbnails'];

  // $showMedia_taxa =

  // variable_get('cdm_dataportal_findtaxa_show_taxon_thumbnails', 1);

  // $showMedia_synonyms =

  // variable_get('cdm_dataportal_findtaxa_show_synonym_thumbnails', 0);

  $classification_uuid = get_taxonomictree_uuid_selected();

  // .. Well, for sure not as performant as before, but better than nothing.

  $synonym_uuids = array();

  $misappied_uuids = array();

  foreach ($records as $taxon) {

    if ($taxon->class == "Synonym") {

      if (!array_key_exists($taxon->uuid, $synonym_uuids)) {

        $synonym_uuids[$taxon->uuid] = $taxon->uuid;

      }

    }

    elseif (!_cdm_dataportal_acceptedByCurrentView($taxon)) {

      // Assuming that it is a misappied name, will be further examined below.

      $misappied_uuids[$taxon->uuid] = $taxon->uuid;

    }

  }

  // Batch service not jet implemented:

  // thus ...

  $table_of_accepted = array();

  foreach ($synonym_uuids as $relatedUuid) {

      $classification_uuid,

    ));

  }

  foreach ($misappied_uuids as $relatedUuid) {

    $taxonRelations = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS, array(

      $relatedUuid,

    ));

    foreach ($taxonRelations as $relation) {

      if ($relation->type->uuid == UUID_MISAPPLIED_NAME_FOR && _cdm_dataportal_acceptedByCurrentView($relation->toTaxon)) {

        $table_of_accepted[$relatedUuid][] = $relation->toTaxon;

      }

    }

  }

  $out = '<ul class="cdm_names" style="background-image: none;">';

  $itemCnt = -1;

  foreach ($records as $taxon) {

    $itemCnt++;

    if (isset($table_of_accepted[$taxon->uuid])) {

      // Its a synonym or misapplied name.

      $is_synonym = isset($synonym_uuids[$taxon->uuid]);

      $acceptedTaxa = $table_of_accepted[$taxon->uuid];

      if (count($acceptedTaxa) == 1) {

        $acceptedTaxon = $acceptedTaxa[0];

        $taxonUri = uri_to_synonym($taxon->uuid, $acceptedTaxon->uuid, 'synonymy');

        $referenceUri = '';

        if (isset($acceptedTaxon->name->nomenclaturalReference)) {

          $referenceUri = url(path_to_reference($acceptedTaxon->name->nomenclaturalReference->uuid));

        }

          'nameLink' => $taxonUri,

          'refenceLink' => $referenceUri,

          ));

        if (!$is_synonym) {

          $out .= '<span class="sensu"> sensu ' . theme('cdm_reference', array('reference' => $taxon->sec)) . '</span>';

        }

          $classification_titles = array();

            if (isset($classification->titleCache)) {

              $classification_titles[] = $classification->titleCache;

            }

            $classification_titles[] = $unclassified_snippet;

          }

        }

        if ($showMedia_synonyms) {

          $out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $acceptedTaxon));

        }

      }

      else {

        // TODO avoid using Ajax in the cdm_dynabox .... why?

        // TODO add media.

              'taxonName' => $taxon->name,

              'nameLink' => NULL,

              'refenceLink' => NULL,

              'show_annotations' => FALSE,

            )),

                    $taxon->uuid,

                    $classification_uuid

                )

            ),

            // theme to use for rendering:

            'cdm_list_of_taxa',

            // label to toggle open:

            array('li', 'ul'),

            array('class' => array($taxon_type))

    }

    else {

      // Its a Taxon.

      $taxonUri = url(path_to_taxon($taxon->uuid));

      $referenceUri = '';

      if (isset($taxon->name->nomenclaturalReference)) {

        $referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));

      }

      $out .= '<li class="Taxon">' . theme('cdm_taxonName', array(

        'taxonName' => $taxon->name,

        'nameLink' => $taxonUri,

        'refenceLink' => $referenceUri,

        ));

        $classifications = get_classifications_for_taxon($taxon);

        $classification_titles = array();

        foreach ($classifications as $classification) {

          if (isset($classification->titleCache)) {

            $classification_titles[] = $classification->titleCache;

          }

        if(count($classification_titles) == 0){

          $classification_titles[] = $unclassified_snippet;

        $out .= ' : <span class="classifications">' . implode(', ', $classification_titles) . '</span>';

      if ($showMedia_taxa) {

        $out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $taxon));

      }

    }

    /*

     * the score field will be empty in case of MultiTermQueries like

     * WildcardQueries, since these are  constant score by default

     * since Lucene 2.9

     */

    if(isset($freetextSearchResults[$itemCnt]) && $freetextSearchResults[$itemCnt]->score && $freetextSearchResults[$itemCnt]->maxScore){

      $percentage =  ( $freetextSearchResults[$itemCnt]->score / $freetextSearchResults[$itemCnt]->maxScore ) * 100;

      $out .= '<div class="score-bar"><div class="score-bar-indicator" style="width:' . $percentage .'% "></div></div>';

      $out .= '<div class="score-bar-value">' . number_format($percentage, 2) .'%</div>';

    }

    // Render highlighted fragments, these are made available by free text

    // searches.

    if (isset($freetextSearchResults[$itemCnt]->fieldHighlightMap)) {

      $field_fragments = (array) $freetextSearchResults[$itemCnt]->fieldHighlightMap;

      if (count($field_fragments) > 0) {

        $fragments_out = '';

        foreach ($field_fragments as $fieldName => $fragments) {

          $fragments_out .= '... <span class="' . $fieldName. '">' . filter_xss(join(" ... ", $fragments), array('b') ) . '</span>';

        }

        $out .= '<div class="fragment_highlight">' . $fragments_out . ' ...</div>';

      }

    }

    $out .= '</li>';

  }

  $out .= '</ul>';

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * Renders a representation of the given taxon relationship.

 *

 * According name relationships are also being rendered.

 * @param unknown_type $taxonRelationship

 * @param boolean $doLinkTaxon

 *     whether to create a link to the related taxon

 * @param boolean $inverse

 *     whether the $taxonRelationship should be treaded as invers relation

 * @param unknown_type $showSecReference

 *     whether the secundum reference for the related taxon should be shown

 *

 * @return void|string

  // Validate object.

  if (!(isset($taxonRelationship->toTaxon) && isset($taxonRelationship->fromTaxon) && isset($taxonRelationship->type))) {

    return;

  }

  $reltype_uuid = $taxonRelationship->type->uuid;

  $taxonRelationType = $taxonRelationship->type;

  $reltype_representation = '';

  if ($inverse) {

    $toTaxon = $taxonRelationship->fromTaxon;

    $fromTaxon = $taxonRelationship->toTaxon;

    $relsign = $taxonRelationType->inverseRepresentation_L10n_abbreviatedLabel;

    $reltype_representation = $taxonRelationType->inverseRepresentation_L10n;

  }

  else {

    $toTaxon = $taxonRelationship->toTaxon;

    $fromTaxon = $taxonRelationship->fromTaxon;

    $relsign = $taxonRelationType->representation_L10n_abbreviatedLabel;

    $reltype_representation = $taxonRelationType->representation_L10n;

  }

  return cdm_related_taxon($toTaxon, NULL, $relsign, $reltype_representation, $doLinkTaxon, $showSecReference);

}

/**

 * Renders a representation of the given taxon relationship.

 *

function cdm_related_taxon($taxon, $reltype_uuid = NULL, $relsign = NULL, $reltype_representation = NULL, $doLinkTaxon = FALSE, $showSecReference = FALSE) {

  static $relsign_homo = '≡';

  static $relsign_hetero = '=';

  static $relsign_invalid = '–';

  // 'taxonRelationships';

  $footnoteListKey = NULL;

  $name_prefix = '';

  $name_postfix = '';

  $skiptags = array();

  if (!$relsign) {

    $relsign = '';

    switch ($reltype_uuid) {

      case UUID_HETEROTYPIC_SYNONYM_OF:

      case UUID_SYNONYM_OF:

        $relsign = $relsign_hetero;

        break;

      case UUID_HOMOTYPIC_SYNONYM_OF:

        $relsign = $relsign_homo;

        break;

      case UUID_MISAPPLIED_NAME_FOR:

      case UUID_INVALID_DESIGNATION_FOR:

        $skiptags[] = 'authors';

        $relsign = $relsign_invalid;

        $name_prefix = '"';

        $name_postfix = '"';

        break;

      default:

        $relsign = $relsign_invalid;

    }

  }

  /*

  Names with status invalid or nudum are to be displayed with the

  $relsign_invalid, these names appear at the end of all names in their

  homotypic group (ordered correctly by the java cdm_lib).

  */

  if (isset($taxon->name->status) && is_array($taxon->name->status)) {

    foreach ($taxon->name->status as $status) {

      if ($status->type->uuid == UUID_NOMENCLATURALSTATUS_TYPE_INVALID || $status->type->uuid == UUID_NOMENCLATURALSTATUS_TYPE_NUDUM) {

        $relsign = $relsign_invalid;

      }

    }

  }

  // Now rendering starts ..

  RenderHints::pushToRenderStack('related_taxon');

  if (isset($taxon->name->nomenclaturalReference)) {

    $referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));

  }

  $taxonUri = '';

  if ($doLinkTaxon) {

    $taxonUri = url(path_to_taxon($taxon->uuid, "synonymy"));

  }

  // Printing the taxonName and the handling the special case of annotations.

  if (!isset($referenceUri)) {

    $referenceUri = FALSE;

  }

  $out_taxon_part = theme('cdm_taxonName', array(

    'taxonName' => $taxon->name,

    'nameLink' => $taxonUri,

    'refenceLink' => $referenceUri,

    'show_annotations' => TRUE,

    'is_type_designation' => FALSE,

    'skiptags' => $skiptags,

    ));

       array('cdmBase_list' => array(

         $taxon->name,

         $taxon,

       ),

       'footnote_list_key' => $footnoteListKey)

  );

  if ($showSecReference) {

    $out_taxon_part .= ' sec. ' . theme('cdm_reference', array('reference' => $taxon->sec));

  }

  // =========== START OF HOMONYMS ========== //

  RenderHints::pushToRenderStack('homonym');

  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT

  $to_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS, $taxon->uuid);

  $homonyms_array = array();

    foreach ( $name_relations as $element ) {

              $elementTaxonBasesUuid = isset ($element->toName->taxonBases [0]->uuid) ? $element->toName->taxonBases [0]->uuid : '';

                  $taxon_html = theme('cdm_taxonName', array(

                      'taxonName' => $element->toName,

                      'nameLink' => path_to_name($element->toName->uuid, $taxon->uuid, $elementTaxonBasesUuid)

                  ));

              }

              break;

          case UUID_TREATED_AS_LATER_HOMONYM :

              $elementTaxonBasesUuid = isset ($element->toName->taxonBases [0]->uuid) ? $element->toName->taxonBases [0]->uuid : '';

                  $taxon_html = theme('cdm_taxonName', array(

                      'taxonName' => $element->toName,

                      'nameLink' => path_to_name($element->toName->uuid)

                  ));

              }

              break;

          case UUID_BLOCKING_NAME_FOR :

              $elementTaxonBasesUuid = isset ($element->fromName->taxonBases [0]->uuid) ? $element->fromName->taxonBases [0]->uuid : '';

                  $taxon_html = theme('cdm_taxonName', array(

                      'taxonName' => $element->fromName,

                      'nameLink' => path_to_name($element->fromName->uuid, $taxon->uuid, $elementTaxonBasesUuid)

                  ));

              }

              break;

          default:

              $taxon_html = null;

          $homonyms_array [] = 'nec ' . $taxon_html;

        } else {

          $homonyms_array [] = 'non ' . $taxon_html;

      }

    }

  }

  RenderHints::popFromRenderStack();

  // =========== END OF HOMONYMS ========== //

  $out = '<span class="relation_sign" title="' . $reltype_representation . '">' . $relsign . '</span>'

      . $name_prefix . $out_taxon_part . $name_postfix . ' '

      . (count($homonyms_array) ?'[' . trim(join(" ", $homonyms_array)) . ']' : '');

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * @todo document this function.

 */

function theme_cdm_taxon_list_thumbnails($variables) {

  $taxon = $variables['taxon'];

  $out = '';

  $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SEARCH_GALLERY_NAME);

  $showCaption = $gallery_settings['cdm_dataportal_show_thumbnail_captions'];

  if ($showCaption) {

    $captionElements = array(

      'title',

      'rights',

    );

    $captionElements = array();

  $gallery_name = $taxon->uuid;

  $out .= theme('cdm_media_gallerie', array(

    'mediaList' => $mediaList,

    'galleryName' => $gallery_name,

    'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],

    'cols' => $gallery_settings['cdm_dataportal_media_cols'],

    'maxRows' => $gallery_settings['cdm_dataportal_media_maxRows'],

    'captionElements' => $captionElements,

    'mediaLinkType' => 'LIGHTBOX',

    'alternativeMediaUri' => NULL,

    'galleryLinkUri' => $galleryLinkUri,

     ));

  return $out;

}