EDIT

<?php

/**

 * @file

 * Name 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

 */

/**

 * Return HTML for the lectotype citation with the correct layout.

 *

 * This function prints the lectotype citation with the correct layout.

 * Lectotypes are renderized in the synonymy tab of a taxon if they exist.

 *

 * @param mixed $typeDesignation

 *   Object containing the lectotype citation to print.

 *

 * @return string

 *   Valid html string.

 */

function type_designation_citation_layout($typeDesignation, $footnote_separator = ',') {

  $res = '';

  $citation = $typeDesignation->citation;

  $pages = $typeDesignation->citationMicroReference;

  if(isset($typeDesignation->typeStatus->uuid) && isset($typeDesignation->typeStatus->representation_L10n)) {

    if ( $typeDesignation->typeStatus->uuid == UUID_NTD_ORIGINAL_DESIGNATION || $typeDesignation->typeStatus->uuid == UUID_NTD_MONOTYPY) {

      $res = ' (' . $typeDesignation->typeStatus->representation_L10n . ')';

      return $res;

    }

  }

  if ($citation) {

    // $type = $typeDesignation_citation->type;

    $year = isset($citation->datePublished->start) ? substr($citation->datePublished->start, 0, 4) : '';

    $author = isset($citation->authorTeam->titleCache) ? $citation->authorTeam->titleCache : '';

    $res .= ' (designated by ';

    $res .= $author;

    $res .= ($year ? ' ' . $year : '');

    $res .= ($pages ? ': ' . $pages : '');

    // $res .= ')';

    // footnotes should be rendered in the parent element so we

    // are relying on the FootnoteListKey set there

    $fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $typeDesignation->citation->titleCache);

    $res .= theme('cdm_footnote_key', array(

      'footnoteKey' => $fkey_typeDesignation,

      'separator' => $footnote_separator,

      'highlightable' => TRUE,

      'separator_off' => TRUE,

    )) . ')';

  }

  return $res;

}

/**

 * Searches the $collection for the cdm entitiy given as $element.

 *

 * The elements are compared by their UUID.

 *

 * @param $element

 *  the CDM entitiy to search for

 * @param $collection

 *  the list of CDM entities to search in

 *

 * @return boolean TRUE if the $collection contains the $element, otheriwse FALSE

 *

 * TODO move into module file

 */

function contains_cdm_entitiy($element, $collection) {

  $result = FALSE;

  foreach ($collection as $a) {

    if ($a->uuid == $element->uuid) {

      $result = TRUE;

    }

  }

  return $result;

}

/**

 * Fiters the array $entity_list of CDM entities by the list

 * of $excludes. Any element contained in the $excludes will be removed

 * from included int the retuned list.

 *

 * If the $entity_list is not an array the $excludes will be returned.

 */

function filter_cdm_entity_list($entity_list, $excludes) {

  if (is_array($entity_list)) {

    $result = $entity_list;

    if ($excludes) {

      foreach ($excludes as $exclude) {

        if (!contains_cdm_entitiy($exclude, $entity_list)) {

          $result[] = $exclude;

        }

      }

    }

  }

  else {

    $result = $excludes;

  }

  return $result;

}

/**

 * Renders and array of CDM TypeDesignations

 *

 * @param array $variables

 *   - typeDesignations: an array of cdm TypeDesignation entities to render

 */

function theme_cdm_typedesignations($variables) {

  $typeDesignations = $variables['typeDesignations'];

  // need to add element to render path since type designations

  // need other name render template

  RenderHints::pushToRenderStack('typedesignations');

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

  $typeDesignation_footnotes = FALSE;

  $is_lectotype = FALSE;

  $specimenTypeDesignations = array();

  $separator = ',';

  foreach ($typeDesignations as $typeDesignation) {

    if ($typeDesignation->class == 'SpecimenTypeDesignation') {

      // SpecimenTypeDesignations should be ordered. Collect theme here only.

      $specimenTypeDesignations[] = $typeDesignation;

    }

    // It is a lectotype?

    else {

      if (isset($typeDesignation->typeStatus->uuid) && $typeDesignation->typeStatus->uuid == UUID_NTD_LECTOTYPE) {

        $is_lectotype = TRUE;

      }

      // It's a NameTypeDesignation.

      if ($typeDesignation->notDesignated) {

        $out .= '<li class="nameTypeDesignation"><span class="status">' . ($is_lectotype ? 'Lectotype' : 'Type') . '</span>: ' . t('not designated') . '</li>';

      }

      elseif ($typeDesignation->typeName) {

        $link_to_name_page = '?q=' . path_to_name($typeDesignation->typeName->uuid);

        $out .= '<li class="nameTypeDesignation"><span class="status">' . ($is_lectotype ? 'Lectotype' : 'Type') . '</span>';

        if ($typeDesignation->citation) {

          $out .= type_designation_citation_layout($typeDesignation, $separator);

        }

        $referenceUri = '';

        if (isset($typeDesignation->typeName->nomenclaturalReference)) {

          $referenceUri = url(path_to_reference($typeDesignation->typeName->nomenclaturalReference->uuid));

        }

        $out .= ': ' . theme('cdm_taxonName', array(

          'taxonName' => $typeDesignation->typeName,

          'nameLink' => $link_to_name_page,

          'refenceLink' => $referenceUri,

          'show_annotations' => TRUE,

          'is_type_designation' => TRUE,

          ));

      }

    }

  }

  if (!empty($specimenTypeDesignations)) {

    // Sorting might be different for dataportals so this has to be

    // parameterized.

    usort($specimenTypeDesignations, "compare_specimenTypeDesignationStatus");

    foreach ($specimenTypeDesignations as $std) {

      $typeReference = '';

      if (!empty($std->citation)) {

        $author_team = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $std->citation->uuid);

        $shortCitation = $author_team->titleCache;

        $shortCitation .= (strlen($shortCitation) > 0 ? ' ' : '') . partialToYear($std->citation->datePublished->start);

        $missingShortCitation = FALSE;

        if (strlen($shortCitation) == 0) {

          $shortCitation = theme('cdm_reference', array('reference' => $std->citation));

          $missingShortCitation = TRUE;

        }

        $typeReference .= ' (' . t('designated by');

        $typeReference .= '&nbsp;<span class="typeReference ' . ($missingShortCitation ? '' : 'cluetip') . ' no-print" title="' . htmlspecialchars('|' . theme('cdm_reference', array('reference' => $std->citation)) . '|') . '">';

        $typeReference .= $shortCitation . '</span>';

        if (!empty($std->citationMicroReference)) {

          $typeReference .= ':' . $std->citationMicroReference;

        }

        $typeReference .= ')';

        // footnotes should be rendered in the parent element so we

        // are relying on the FootnoteListKey set there

        $_fkey2 = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $std->citation->titleCache);

        $typeReference .= theme('cdm_footnote_key', array(

          'footnoteKey' => $_fkey2,

          'separator' => $separator,

          'highlightable' => TRUE,

          'separator_off' => TRUE,

         ));

      }

      $derivedUnitFacadeInstance = null;

      $out .= '<li class="specimenTypeDesignation">';

      $out .= '<span class="status">'

        . ((isset($std->typeStatus->representation_L10n)) ? $std->typeStatus->representation_L10n : t('Type'))

        . $typeReference

        . '</span>: ';

      if (isset($std->typeSpecimen)) {

        $derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, $std->typeSpecimen->uuid);

      }

      if ( isset($derivedUnitFacadeInstance ) ){

        $out .= $derivedUnitFacadeInstance->titleCache; // . ': ' . theme('cdm_specimen', array('specimenTypeDesignation' => $derivedUnitFacadeInstance));

      }

      // Footnotes for collection acronyms.

      // footnotes should be rendered in the parent element so we

      // are relying on the FootnoteListKey set there

      $_fkey = FootnoteManager::addNewFootnote(

          RenderHints::getFootnoteListKey(),

          (isset($derivedUnitFacadeInstance->collection->titleCache) ? $derivedUnitFacadeInstance->collection->titleCache : FALSE)

        );

      $out .= theme('cdm_footnote_key', array('footnoteKey' => $_fkey, 'separator' => $separator));

      $out .= '</li>';

    }

  }

  $out .= '</ul>';

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * FIXME this definitively has to be in another spot.

 * just didn't know where to put it right now.

 * Compares the status of two SpecimenTypeDesignations

 *

 * @param string $a

 *   A SpecimenTypeDesignations.

 * @param string $b

 *   SpecimenTypeDesignations.

 */

function compare_specimenTypeDesignationStatus($a, $b) {

  /*

  This is the desired sort order as of now: Holotype Isotype Lectotype

  Isolectotype Syntype.

  TODO Basically, what we are trying to do is, we define

  an ordered array of TypeDesignation-states and use the index of this array

  for comparison. This array has to be filled with the cdm- TypeDesignation

  states and the order should be parameterisable inside the dataportal.

  */

  // Make that static for now.

  $typeOrder = array(

    'Holotype',

    'Isotype',

    'Lectotype',

    'Isolectotype',

    'Syntype',

  );

  $aQuantifier = FALSE;

  $bQuantifier = FALSE;

  if (isset($a->typeStatus->label) && isset($b->typeStatus->label)) {

    $aQuantifier = array_search($a->typeStatus->label, $typeOrder);

    $bQuantifier = array_search($b->typeStatus->label, $typeOrder);

  }

  if ($aQuantifier == $bQuantifier) {

    // Sort alphabetically.

    return (isset($a->typeStatus->label) && isset($b->typeStatus->label) && $a->typeStatus->label < $b->typeStatus->label) ? -1 : 1;

  }

  return ($aQuantifier < $bQuantifier) ? -1 : 1;

}

/**

 * @todo Please document this function.

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

 */

function theme_cdm_nameRelationships($variables) {

  $nameRelationships = $variables['nameRelationships'];

  $skipTypes = $variables['skipTypes'];

  if (!$nameRelationships) {

    return;

  }

  RenderHints::pushToRenderStack('nameRelationships');

  $footnoteListKey = 'nameRelationships';

  RenderHints::setFootnoteListKey($footnoteListKey);

  // Group by relationship type.

  $relationshipGroups = array();

  foreach ($nameRelationships as $nameRelationship) {

    if (!array_key_exists($nameRelationship->type->uuid, $relationshipGroups)) {

      $relationshipGroups[$nameRelationship->type->uuid] = array();

    }

    $relationshipGroups[$nameRelationship->type->uuid][] = $nameRelationship;

  }

  // Generate output.

  $out = '';

  $block = new stdclass(); // Empty object.

  foreach ($relationshipGroups as $group) {

    $type = $group[0]->type;

    if (is_array($skipTypes) && in_array($type->uuid, $skipTypes)) {

      continue;

    }

    $block->module = 'cdm_dataportal';

    $block->subject = t(ucfirst($type->inverseRepresentation_L10n));

    $block->delta = generalizeString(strtolower($type->inverseRepresentation_L10n));

    foreach ($group as $relationship) {

      $relatedNames[] = cdm_taggedtext2html($relationship->fromName->taggedName);

    }

    $block->content .= implode('; ', $relatedNames);

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

  }

  $out .= theme('cdm_footnotes', array('footnoteListKey' => $footnoteListKey, 'enclosingTag' => 'li'));

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * @todo Please document this function.

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

 */

function theme_cdm_homotypicSynonymLine($variables) {

  $taxon = $variables['taxon'];

  $out = '';

  $out .= '<li class="synonym">' . cdm_related_taxon($taxon, UUID_HOMOTYPIC_SYNONYM_OF) . '</li>';

  return $out;

}

/**

 * @todo Please document this function.

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

 */

function theme_cdm_heterotypicSynonymyGroup($variables) {

  $homotypicalGroup = $variables['homotypicalGroup'];

  RenderHints::pushToRenderStack('heterotypicSynonymyGroup');

  $out = '';

  $out = '<div class="heterotypic-synonymy-group"><ul class="heterotypicSynonymyGroup">';

  $footnoteListKey = (isset($homotypicalGroup[0]) ? $homotypicalGroup[0]->uuid : 'NULL');

  RenderHints::setFootnoteListKey($footnoteListKey);

  $is_first_entry = TRUE;

  $typeDesignations = NULL;

  foreach ($homotypicalGroup as $synonym) {

    if ($is_first_entry) {

      $is_first_entry = FALSE;

      $typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonym->name->uuid);

      // Is first list entry.

      $out .= '<li class="firstentry synonym">' . cdm_related_taxon($synonym, UUID_HETEROTYPIC_SYNONYM_OF) . '</li>';

    }

    else {

      $out .= '<li class="synonym">' . cdm_related_taxon($synonym, UUID_HOMOTYPIC_SYNONYM_OF) . '</li>';

    }

  }

  if ($typeDesignations) {

    $out .= theme('cdm_typedesignations', array('typeDesignations' => $typeDesignations));

  }

  $out .= '</ul>';

  // ------- footnotes ------- //

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

  $out .= theme('cdm_annotation_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'li'));

  $out .= theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'li'));

  $out .= '</ul>';

  $out .= '</div>';

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * Renders the homotypic synonymy group for the accepted taxon in the synonymy.

 *

 * Foonotes of the accepted taxon will also be rendered here in the

 * homotypic synonymy group even if the synonymList or prependedSynonyms are

 * empty. Therefore  the homotypic group and accepted taxon share the  same

 * footnote key.

 *

 * @param $variables

 *   an associative array:

 *   - synonymList: the list of cdm Synonym entities

 *   - accepted_taxon_uuid: the uuid of the accepted taxon

 *   - prependedSynonyms: further synonyms which should be prepended

 *      before the actual list of synonyms

 */

function theme_cdm_homotypicSynonymyGroup($variables) {

  $synonymList = $variables['synonymList'];

  $accepted_taxon_uuid = $variables['accepted_taxon_uuid'];

  $prependedSynonyms = $variables['prependedSynonyms'];

  RenderHints::pushToRenderStack('homotypicSynonymyGroup');

  $homonym_typeDesignations = NULL;

// no new $footnoteListKey since homotypic group and accepted taxon should share the same key!

//   $footnoteListKey = isset($prependedSynonyms[0]) ? $prependedSynonyms[0]->uuid : (isset($synonymList[0]) ? $synonymList[0]->uuid : 'NULL');

//   // store the FootnoteListKey from the parent element which is the accepted taxon

//   $accepted_taxon_footnoteListKey = RenderHints::getFootnoteListKey();

//   // new FootnoteListKey for this homotypicSynonymyGroup

//   RenderHints::setFootnoteListKey($footnoteListKey);

  // TODO improve typeDesignations retrieval: wouldn't it be suffcient to retrieve all typeDesignations

  // only from the accepted taxon?

  $accepted_typeDesignations = cdm_ws_get(CDM_WS_PORTAL_TAXON_NAMETYPEDESIGNATIONS, $accepted_taxon_uuid);

  $out = '<div class="homotypic-synonymy-group">';

  if (isset ($accepted_typeDesignations) || is_array($prependedSynonyms) || is_array($synonymList)) {

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

	if (!empty($prependedSynonyms)) {

	  foreach ($prependedSynonyms as $taxon) {

	    $out .= '<li class="synonym">' . cdm_related_taxon($taxon, UUID_HOMOTYPIC_SYNONYM_OF) . '</li>';

	  }

	}

	$homonym_typeDesignations = NULL;

	if (isset($synonymList[0])) {

		foreach ($synonymList as $synonym) {

			$out .= '<li class="synonym">' . cdm_related_taxon($synonym, UUID_HOMOTYPIC_SYNONYM_OF) . '</li>';

		}

		$homonym_typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonymList[0]->name->uuid);

	}

	// type designations

	if ($accepted_typeDesignations) {

	  $type_designations = filter_cdm_entity_list($homonym_typeDesignations, $accepted_typeDesignations);

	}

	else {

	  $type_designations = $homonym_typeDesignations;

	}

	if ($type_designations) {

	  $out .= theme('cdm_typedesignations', array('typeDesignations' => $type_designations));

	}

  }

  $out .= '</ul>';

  // ------- footnotes ------- //

  // all foonotes of the homotypic group and also of the accepted taxon are

  // rendered here, both should have the same footnote key

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

  $out .= theme('cdm_annotation_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'li'));

  $out .= theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'li'));

  $out .= '</ul>';

  $out .= '</div>';

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * Provides the name render template to be used within the page elements identified the the $renderPath.

 *

 * The render templates arrays contains one or more name render template to be used within the page elements identified the the

 * renderPath. The renderPath is the key of the subelements whereas the value is the name render template.

 * The following keys are curretly recogized:

 *

 *   - list_of_taxa:

 *   - acceptedFor:

 *   - taxon_page_synonymy

 *   - typedesignations

 *   - taxon_page_title

 *   - polytomousKey

 *   - na: name + authorship

 *   - nar:name + authorship + reference

 *   - #DEFAULT

 *

 * A single render template can be used for multiple render paths. In this case the according key of the render templates

 * array element should be the list of these render paths concatenated by ONLY a comma character without any whitespace.

 *

 * A render template is an associative array. The keys of this array are referring to the keys as defined in the part

 * definitions array.

 * @see get_partDefinition($taxonNameType) for more information

 *

 * The value of the render template element must be set to TRUE in order to let this part being rendered.

 * The namePart, nameAuthorPart and referencePart can also hold an associative array with a single

 * element: array('#uri' => TRUE). The value of the #uri element will be replaced by the according

 * links if the paramters $nameLink or $refenceLink are set.

 *

 * @param string $renderPath

 *   The render path can consist of multiple dot separated elements

 *   @see RenderHints::getRenderPath()

 * @param string $nameLink

 *   The link path ot URL to be used for name parts if a link is forseen in the template

 *   matching the given $renderPath.

 * @param string $referenceLink

 *   The link path ot URL to be used for nomencaltural reference parts if a link is forseen

 *   in the template matching the given $renderPath.

 * @return array

 *   An assciative array, the render template

 */

function get_nameRenderTemplate($renderPath, $nameLink = NULL, $refenceLink = NULL) {

  $template = NULL;

  static $default_render_templates = NULL;

  if (!isset($default_render_templates)) {

    $default_render_templates = unserialize(CDM_NAME_RENDER_TEMPLATES_DEFAULT);

  }

  // get the base element of the renderPath

  if (($separatorPos = strpos($renderPath, '.')) > 0) {

    $renderPath_base = substr($renderPath, 0, $separatorPos);

  } else {

    $renderPath_base = $renderPath;

  }

  // --- preliminar solution: using themes.

  $render_templates = theme('get_nameRenderTemplate', array());

  if (!isset($render_templates)) {

    // from the variables

    $render_templates = variable_get(CDM_NAME_RENDER_TEMPLATES, $default_render_templates);

  }

  // 1. try to find a template using the render path base element

  if(array_key_exists($renderPath_base, $render_templates)){

    $template = $render_templates[$renderPath_base];

  }

  // 2. Find best matching default RenderTemplate in theme

  // by stripping the dot separated render path element by element

  // is no matching template is found the DEFAULT will be used.

  while (!is_array($template) && strlen($renderPath) > 0) {

    foreach ($render_templates as $k => $t) {

      if (strpos(',' . $k . ',', $renderPath ) !== FALSE) {

        $template = $t;

        break;

      }

    }

    // shorten by one element

    $renderPath = substr($renderPath, 0, strrpos($renderPath, '.'));

    /*

    if(!is_array($template)){

      echo "<br/>->".$renderPath;

    }

    */

  }

  // 3. Otherwise get default RenderTemplate from theme.

  if (!is_array($template)) {

      $template = $render_templates['#DEFAULT'];

  }

  // --- set the link uris to the according template fields if they exist

  if ($nameLink && isset($template['nameAuthorPart']['#uri'])) {

    $template['nameAuthorPart']['#uri'] = $nameLink;

  }

  else {

    unset($template['nameAuthorPart']['#uri']);

  }

  if ($nameLink && isset($template['namePart']['#uri'])) {

    $template['namePart']['#uri'] = $nameLink;

  }

  else {

    unset($template['namePart']['#uri']);

  }

  if ($refenceLink && isset($template['referencePart']['#uri'])) {

    $template['referencePart']['#uri'] = $refenceLink;

  }

  else {

    unset($template['referencePart']['#uri']);

  }

  return $template;

}

/**

 * The part definitions define the specific parts of which a rendered taxon name plus additional information will consist.

 *

 * A full taxon name plus additional information can consist of the following elements:

 *

 *   - name: the taxon name inclugin rank nbut without author

 *   - authorTeam:  The authors of a reference, also used in taxon names

 *   - authors:  The authors of a reference, also used in taxon names

 *   - reference: the nomenclatural reference,

 *   - microreference:  Volume, page number etc.

 *   - status:  The nomenclatural status of a name

 *   - description: name descriptions like protologues etc ...

 *

 * These elements are combined in the part definitions array to from the specific parts to be rendered.

 * Usually the following parts are formed:

 *

 * The name "Lapsana communis L., Sp. Pl.: 811. 1753" shall be an example here:

 *  - namePart: the name and rank (in example: "Lapsana communis")

 *  - authorshipPart: the author (in example: "L.")

 *  - nameAuthorPart: the combination of name and author part (in example: "Lapsana communis L.").

 *     This is useful for zoological names where the authorshipPart belongs to the name and both should

 *     be combined when a link to the taxon is rendered.

 *  - referencePart: the nomencaltural reference (in example: "Sp. Pl. 1753")

 *  - microreferencePart: usually the page number (in example ": 811.")

 *  - statusPart: the nomenclatorical status

 *  - descriptionPart:

 *

 * Each set of parts is dedicated to render a specific TaxonName type, the type names are used as keys for the

 * specific parts part definitions:

 *

 *  - BotanicalName

 *  - ZoologicalName

 *  - #DEFAULT:  covers ViralNames and general NonViralNames

 *

 * An example:

 * @code

 * array(

 *    'ZoologicalName' => array(

 *        'namePart' => array('name' => TRUE),

 *        'referencePart' => array('authorTeam' => TRUE),

 *        'microreferencePart' => array('microreference' => TRUE),

 *        'statusPart' => array('status' => TRUE),

 *        'descriptionPart' => array('description' => TRUE),

 *    ),

 *    'BotanicalName' => array(

 *        'namePart' => array(

 *            'name' => TRUE,

 *            'authors' => TRUE,

 *        ),

 *        'referencePart' => array(

 *            'reference' => TRUE,

 *            'microreference' => TRUE,

 *        ),

 *        'statusPart' => array('status' => TRUE),

 *        'descriptionPart' => array('description' => TRUE),

 *    ),

 *  );

 * @endcode

 *

 * @todo document this function.

 */

function get_partDefinition($taxonNameType) {

  static $default_part_definitions = null;

  if (!isset($default_part_definitions)) {

    $default_part_definitions= unserialize(CDM_PART_DEFINITIONS_DEFAULT);

  }

  // Preliminar solution: using themes.

  // TODO remove this once all themes are using the newly introcuded part_definition settings

  $part_definitions = theme('get_partDefinition', array());

  // try to get get part definitions from variables

  if(!is_array($part_definitions)) {

    $part_definitions = variable_get(CDM_PART_DEFINITIONS, $default_part_definitions);

  }

  if (array_key_exists($taxonNameType, $part_definitions)) {

    return $part_definitions[$taxonNameType];

  } else {

    return $part_definitions['#DEFAULT']; // covers ViralNames and general NonViralNames

  }

}

/**

 * @param $variables

 *    - taxonName : cdm TaxonNameBase instance

 *    - nameLink: URI to the taxon, @see path_to_taxon()

 *    - refenceLink: URI to the reference, @see path_to_reference()

 *    - show_annotations: ...

 *    - is_type_designation: ...

 *    - skiptags: an array of tags to skip ....

 *

 * @todo Please document this function.

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

 */

function theme_cdm_taxonName($variables) {

  $taxonName = $variables['taxonName'];

  $nameLink = $variables['nameLink'];

  $refenceLink = $variables['refenceLink'];

  $show_annotations = $variables['show_annotations'];

  $is_type_designation = $variables['is_type_designation'];

  $skiptags = $variables['skiptags'];

  $renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $nameLink, $refenceLink);

  $partDefinition = get_partDefinition($taxonName->class);

  // Apply definitions to template.

  foreach ($renderTemplate as $part => $uri) {

    if (isset($partDefinition[$part])) {

      $renderTemplate[$part] = $partDefinition[$part];

    }

    if (is_array($uri) && isset($uri['#uri'])) {

      $renderTemplate[$part]['#uri'] = $uri['#uri'];

    }

  }

  normalize_TaggedName($taxonName->taggedName);

  $firstEntryIsValidNamePart = isset($taxonName->taggedName) && is_array($taxonName->taggedName) && isset($taxonName->taggedName[0]->text) && is_string($taxonName->taggedName[0]->text) && $taxonName->taggedName[0]->text != '' && isset($taxonName->taggedName[0]->type) && $taxonName->taggedName[0]->type == 'name';

  // Got to use second entry as first one, see ToDo comment below ...

  if ($firstEntryIsValidNamePart) {

    $taggedName = $taxonName->taggedName;

    $lastAuthorElementString = FALSE;

    $hasNamePart_with_Authors = isset($renderTemplate['namePart']) && isset($renderTemplate['namePart']['authors']);

    $hasNameAuthorPart_with_Authors = isset($renderTemplate['nameAuthorPart']) && isset($renderTemplate['nameAuthorPart']['authors']);

    if (!(($hasNamePart_with_Authors) || ($hasNameAuthorPart_with_Authors))) {

      // Find author and split off from name.

      // TODO expecting to find the author as the last element.

      /*

      if($taggedName[count($taggedName)- 1]->type == 'authors'){

        $authorTeam = $taggedName[count($taggedName)- 1]->text;

        unset($taggedName[count($taggedName)- 1]);

      }

      */

      // Remove all authors.

      $taggedNameNew = array();

      foreach ($taggedName as $element) {

        if ($element->type != 'authors') {

          $taggedNameNew[] = $element;

        }

        else {

          $lastAuthorElementString = $element->text;

        }

      }

      $taggedName = $taggedNameNew;

    }

    $name = '<span class="' . $taxonName->class . '">' . theme('cdm_taggedtext2html', array(

      'taggedtxt' => $taggedName,

      'tag' => 'span',

      'glue' => ' ',

      'skiptags' => $skiptags,

      )) . '</span>';

  }

  else {

    $name = '<span class="' . $taxonName->class . '_titleCache">' . $taxonName->titleCache . '</span>';

  }

  // Fill name into $renderTemplate.

  array_setr('name', $name, $renderTemplate);

  // Fill with authorTeam.

  /*

  if($authorTeam){

    $authorTeamHtml = ' <span class="authorTeam">'.$authorTeam.'</span>';

    array_setr('authorTeam', $authorTeamHtml, $renderTemplate);

  }

  */

  // Fill with reference.

  if (isset($renderTemplate['referencePart']) && !$is_type_designation) {

    // [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,

    // Komma nach dem Autornamen ist überall dort falsch, wo ein "in" folgt."

    if (isset($renderTemplate['referencePart']['reference']) && isset($taxonName->nomenclaturalReference)) {

      $microreference = NULL;

      if (isset($renderTemplate['referencePart']['microreference'])&& isset($taxonName->nomenclaturalMicroReference)) {

        $microreference = $taxonName->nomenclaturalMicroReference;

      }

      $citation = cdm_ws_getNomenclaturalReference($taxonName->nomenclaturalReference->uuid, $microreference);

      // Find preceding element of the reference.

      $precedingKey = get_preceding_contentElementKey('reference', $renderTemplate);

      if (str_beginsWith($citation, ", in")) {

        $citation = substr($citation, 2);

        $separator = ' ';

      }

      elseif (!str_beginsWith($citation, "in") && $precedingKey == 'authors') {

        $separator = ', ';

      }

      else {

        $separator = ' ';

      }

      $referenceArray['#separator'] = $separator;

      $referenceArray['#html'] = '<span class="reference">' . $citation . '</span>';

      array_setr('reference', $referenceArray, $renderTemplate);

    }

    // If authors have been removed from the name part the last named authorteam

    // should be added to the reference citation, otherwise, keep the separator

    // out of the reference.

    if (isset($renderTemplate['referencePart']['authors']) && $lastAuthorElementString) {

      // If the nomenclaturalReference citation is not included in the

      // reference part but diplay of the microreference

      // is wanted, append the microreference to the authorTeam.

      if (!isset($renderTemplate['referencePart']['reference']) && isset($renderTemplate['referencePart']['microreference'])) {

        $separator = ": ";

        $citation = $taxonName->nomenclaturalMicroReference;

      }

      $referenceArray['#html'] = ' <span class="reference">' . $lastAuthorElementString . $separator . $citation . '</span>';

      array_setr('authors', $referenceArray, $renderTemplate);

    }

  }

  // Fill with status.

  $statusHtml = '';

  if (isset($taxonName->status) && is_array($taxonName->status)) {

    if (array_setr('status', TRUE, $renderTemplate)) {

      if (isset($taxonName->status[0])) {

        foreach ($taxonName->status as $status) {

          $statusHtml .= ', ' . $status->type->representation_L10n_abbreviatedLabel;

        }

      }

      array_setr('status', '<span class="nomenclatural_status">' . $statusHtml . '</span>', $renderTemplate);

    }

  }

  // Fill with protologues etc...

  $descriptionHtml = '';

  if (array_setr('description', TRUE, $renderTemplate)) {

    $descriptions = cdm_ws_get(CDM_WS_PORTAL_NAME_DESCRIPTIONS, $taxonName->uuid);

    foreach ($descriptions as $description) {

      if (!empty($description)) {

        foreach ($description->elements as $description_element) {

          $second_citation = '';

          if (isset($description_element->multilanguageText_L10n) && $description_element->multilanguageText_L10n->text) {

            $second_citation = '[& ' . $description_element->multilanguageText_L10n->text . '].';

          }

          $descriptionHtml .= $second_citation;

          $descriptionHtml .= theme("cdm_media", array(

              'descriptionElement' => $description_element,

              'mimeTypePreference' => array(

                  'application/pdf',

                  'image/png',

                  'image/jpeg',

                  'image/gif',

                  'text/html',

                )

              )

            );

        }

      }

    }

    array_setr('description', $descriptionHtml, $renderTemplate);

  }

  // Render.

  $out = '<span ref="/name/' . $taxonName->uuid . '">';

  foreach ($renderTemplate as $partName => $part) {

    $separator = '';

    $partHtml = '';

    $uri = FALSE;

    if (!is_array($part)) {

      continue;

    }

    if (isset($part['#uri']) && is_string($part['#uri'])) {

      $uri = $part['#uri'];

      unset($part['#uri']);

    }

    foreach ($part as $key => $content) {

      $html = '';

      if (is_array($content)) {

        $html = $content['#html'];