EDIT

/**

 * Returns the chosen FeatureTree for SpecimenDescriptions.

 *

 * The FeatureTree returned is the one that has been set in the

 * dataportal settings (layout->taxon:specimen).

 * When the chosen FeatureTree is not found in the database,

 * the standard feature tree (UUID_DEFAULT_FEATURETREE) will be returned.

 *

 * @return mixed

 *   A cdm FeatureTree object.

 */

function cdm_get_occurrence_featureTree() {

  return $occurrence_featureTree;

/**

 * Returns the FeatureTree for structured descriptions

 *

 * The FeatureTree returned is the one that has been set in the

 * dataportal settings (layout->taxon:profile).

 * When the chosen FeatureTree is not found in the database,

 * the standard feature tree (UUID_DEFAULT_FEATURETREE) will be returned.

 *

 * @return mixed

 *   A cdm FeatureTree object.

 */

function get_structured_description_featureTree() {

  static $structured_description_featureTree;

    $structured_description_featureTree = cdm_ws_get(

        CDM_WS_FEATURETREE,

        variable_get(CDM_DATAPORTAL_STRUCTURED_DESCRIPTION_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)

    );

    if (!$structured_description_featureTree) {

      $structured_description_featureTree = cdm_ws_get(

          CDM_WS_FEATURETREE,

          UUID_DEFAULT_FEATURETREE

      );

  }

  return $structured_description_featureTree;

  if ($add_none_option) {

    $taxonomic_tree_options['NONE'] = t('-- None --');

 * The function is null save.

  return isset($object->class) && is_string($object->class) && strlen($object->class) > 2 && is_string($object->uuid) && is_uuid($object->uuid);

module_load_include('inc', 'cdm_dataportal', 'includes/maps');

module_load_include('inc', 'cdm_dataportal', 'includes/occurrences');

 * Implements hook_permission().

 *

 * Implements hook_menu().

 */

    // --- GET Images --- //

    $mediaQueryParameters = array(

        "type" => "ImageFile",

    );

    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));

    $mediaQueryParameters['relationships'] = implode(',', get_selection($relationship_choice['direct']));

    $ws_endpoint = NULL;

    $media[$taxon->uuid] = cdm_ws_get($ws_endpoint,

        array(

            $taxon->uuid,

        ),

  if(!isset($occurences)) {

    $occurences = array();

  }

    $relationship_choice['invers'] = get_selection($relationship_choice['invers']);

    $by_associatedtaxon_query = http_build_query(array(

        'relationshipsInvers' => implode(',', $relationship_choice['invers']),

        'relationships' => implode(',', $relationship_choice['direct']),

        'pageSize' => null // all hits in one page

    )

    );

    $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,

        null,

        $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid

    );

    if(isset($pager->records[0])){

      $occurences[$taxon->uuid] =  $pager->records;

    }

  }

  return array(

    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');

    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');

  $showThumbnails = do_showThumbnails();

  $setSessionUri = url('cdm_api/setvalue/session', array(

      'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),

  ));

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

      // init

      if(' . $showThumbnails . ' == 1){

      jQuery(\'.media_gallery\').show(20);

  } else {

      jQuery(\'.media_gallery\').hide(20);

  }

      // add change hander

      jQuery(\'#showThumbnails\').change(

      function(event){

      var state = 0;

      if(jQuery(this).is(\':checked\')){

      jQuery(\'.media_gallery\').show(20);

      state = 1;

  } else {

      jQuery(\'.media_gallery\').hide(20);

  }

      // store state in session variable

      var uri = \'' . $setSessionUri . '\' + state;

      jQuery.get(uri);

  });

  array('type' => "inline", 'scope' => JS_DEFAULT));

    $showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];

    if (!is_numeric($showThumbnails)) {

      $showThumbnails = 1;

    }

function html_class_attribute_ref($cdmEntity) {

    'artist' => '',// Media_metadata and media.

    'rights',// Media_metadata and media.

    'location',// Media_metadata.

function has_feature_node_description_elements($featureNode) {

      if (has_feature_node_description_elements($child)) {

   * @return FootnoteKey

/**

 * @file

 * Functions for dealing with CDM entities from the package model.common

 *

 * @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

 *

 * @author

 *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>

      '#attributes' => array('class' => html_class_attribute_ref($marker)),

  if (isset($iModifieable->modifiers)) {

    foreach ($iModifieable->modifiers as $modifier) {

      $modifiers_strings[] = cdm_term_representation($modifier);

    }

    if (isset($node->descriptionElements['#type']) || has_feature_node_description_elements($node)) {

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

      $class_attributes = 'feature-toc-item-' . $node->feature->uuid;

        $items[] = toc_list_item(

          theme(

            'cdm_feature_name',

            array('feature_name' => $feature_name))

          ,

          array('class' => $class_attributes)

/**

 * Prepares an empty Drupal block for displaying description elements of a specific CDM Feature.

 *

 * The block can also be used for pseudo Features like a bibliography. Pseudo features are

 * derived from other data on the fly and so not exist as such in the cdm data. In case

 * of pseudo features the $feature is left empty

 *

 * @param $feature_name

 *    A label describing the feature, usually the localized feature representation.

 * @param $feature

 *    The CDM Feature for which the block is created. (optional)

 * @return object

 *    A Drupal block object

 */

function feature_block($feature_name, $feature = null) {

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

  $block->module = 'cdm_dataportal';

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

  $block->region = null;

  $block->subject = '<a name="' . $block->delta . '"></a><span class="' . html_class_attribute_ref($feature) . '">'

    . theme('cdm_feature_name', array('feature_name' => $feature_name))

    . '</span>';

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

  $block->content = '';

  return $block;

}

/**

 * Creates a list item for a table of content, suitable as data element for a themed list

 *

 * @see theme_list()

 *

 * @param $label

 * @param $http_request_params

 * @param $attributes

 * @return array

 */

function toc_list_item($label, $attributes = array()) {

  // we better cache here since drupal_get_query_parameters has no internal static cache variable

  $http_request_params = drupal_static('http_request_params', drupal_get_query_parameters());

  $item =  array(

    'data' => l(

      $label,

      $_GET['q'],

      array(

        'attributes' => array('class' => array('toc')),

        'fragment' => generalizeString($label),

        'query' => $http_request_params

      )

    )

  );

  $item['attributes'] = $attributes;

  return $item;

}

      $fn_key = FootnoteManager::addNewFootnote(original_source_footnote_list_key(), theme('cdm_OriginalSource', array(

/**

 *

 * @return string the footnote_list_key

 */

function original_source_footnote_list_key($key_suggestion = null) {

  if(!$key_suggestion){

    $key_suggestion = RenderHints::getFootnoteListKey();

  }

  $footnote_list_key = variable_get(BIBLIOGRAPHY_FOR_ORIGINAL_SOURCE,  1) == 1 ? 'BIBLIOGRAPHY' : $key_suggestion;

  return $footnote_list_key;

}

/**

 * @file

 * Functions for dealing with CDM entities of type SpeciemenOrOccurrences

 *

 * @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

 *

 * @author

 *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>

/**

 * Compose an render array from a CDM DerivedUnitFacade object.

 *

 * compose_hook() implementation

 */

        'extensions', // TODO ignored for now, how to handle extensions?

        'protectedTitleCache',

       ''

    $title = $type_label . ': '. $specimenOrObservation->titleCache;

    foreach (get_object_vars($specimenOrObservation) as $field => $value) {

      if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {

            $dd_elements = array();

              $taxon_name = cdm_ws_get(CDM_WS_TAXON . '/$0/name', $determinationEvent->taxon->uuid);

              $taxon_html = theme('cdm_taxonName',

                  array(

                      'taxonName' => $taxon_name,

                      'nameLink' => path_to_taxon($determinationEvent->taxon->uuid),

              }

              if (isset($determinationEvent->description)) {

              }

            @_description_list_group_add($groups, cdm_occurrence_field_name_label('determinations'), $dd_elements);

          case 'descriptions':

              $rendered_description = theme(

                 'cdm_feature_nodes',

            @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);

            break;

            @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);

            );

            @_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description);

              @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);

              @_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),

                  array(

                      array('#markup' => $value->exactLocation->sexagesimalString),

                      array(

                          '#theme' => 'description_list',

                          '#groups' => $sub_dl_groups

                      ),

            }

            break;

              drupal_set_message("Unhandled type in compose_cdm_specimenOrObservation() for field " . $field, "warning");

        }

      }

        '#title' => $title,

        '#theme' => 'description_list',

        '#attributes' => array('class' => html_class_attribute_ref($specimenOrObservation)),

/**

 * @file

 * Page 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.

 *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>

 */

/**

 * Creates a render array representing the ocurrences associetad with the $taxon.

 *

 * The resulting render array contains two elements:

 *  - 'map': A map showing all point locations of the occurences is availabale

 *  - 'specimen_list': the list of occurences prepated as table for theme_table()

 *

 * @param object $taxon

 *   A cdm Taxon object

 * @return

 *   A render array suitable for drupal_render()

 *

function cdm_dataportal_taxon_page_specimens($taxon) {

  $render_array = array();

  RenderHints::pushToRenderStack('taxon_page_specimens');

  $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));

  $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,

      null,

      $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid

  );

  $specimensOrObservations = array();

  if(isset($pager->records[0])){

    $specimensOrObservations =  $pager->records;

  $specimensOrObservations = array_merge($type_specimens, $other_occurrences);

  // Collect media (fieldObjectMedia, derivedUnitMedia) and add as a custom field

  // $occurrence->_fieldObjectMedia

  foreach ($specimensOrObservations as &$occurrence) {

    $occurrence->_fieldObjectMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(

        $occurrence->uuid,

        'fieldObjectMedia',

    ));

    $occurrence->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(

        $occurrence->uuid,

        'derivedUnitMedia',

    ));

  }

  // --- get map service HTTP query paramaters

  if (count($specimensOrObservations) > 0) {

    $occurrence_query = cdm_ws_get(CDM_WS_GEOSERVICE_OCCURRENCEMAP, $taxon->uuid,  $by_associatedtaxon_query);

    if( isset($occurrence_query->String) ) {

      $occurrence_query = $occurrence_query->String;

      $distribution_query = NULL;

      $render_array['map'] = compose_map($occurrence_query, $distribution_query, $legend_format_query);

    }

  }

  // --- generate the specimen list as table

  $specimen_table = array(

      '#theme' => 'table',

      '#weight' => 2,

      // prefix attributes and rows with '#' to let it pass to the theme function,

      // otherwise it is handled as child render array

      '#attributes' => array('class' => 'specimens'),

      '#rows' => array(),

  );

  if ($specimensOrObservations) {

    foreach ($specimensOrObservations as $specimenOrObservation) {

      $mediaList = array();

      if (is_array($specimenOrObservation->_fieldObjectMedia)) {

        $mediaList = array_merge($mediaList, $specimenOrObservation->_fieldObjectMedia);

      }

      if (is_array($specimenOrObservation->_derivedUnitMedia)) {

        $mediaList = array_merge($mediaList, $specimenOrObservation->_derivedUnitMedia);

            $type_status[] = $typeDesignation->typeStatus->representation_L10n;

          }

        }

        }

      }

      $gallery_name = $specimenOrObservation->uuid;

      $label_html = cdm_dynabox(

          $specimenOrObservation->uuid,

          $type_label . $specimenOrObservation->titleCache,

          $derived_unit_ws_request,

          'cdm_specimenOrObservation', // the theme or compose function to use

          array('div','div'),

          'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').hide(); }', // open_callback

          'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').show(); }' // close_callback

      );

      // --- Render associated media.

      $gallery_html = '';

      if (count($mediaList) > 0) {

        $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);

        $captionElements = array(

            '#uri' => t('open media'),

        );

        $gallery_html = 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' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,

            'captionElements' => $captionElements,

            'mediaLinkType' => 'LIGHTBOX',

            'alternativeMediaUri' => NULL,

            'galleryLinkUri' => NULL,

        ));

      }

      $specimen_table['#rows'][] = array(

          // An array of table rows. Every row is an array of cells, or an associative array

          'data' => array(

              // Each cell can be either a string or an associative array

              $label_html . $gallery_html

          ),

          'class' =>  array(

              'descriptionElement',

              'descriptionElement_IndividualsAssociation'

          ),

      );

    }

  }

  );

  RenderHints::popFromRenderStack();

  return $render_array;

      // 5. put all distribution data into the distribution feature node

  $toc = array(

    '#theme' => 'item_list',

    '#items' => cdm_feature_node_toc_items($merged_tree->root->childNodes),

    '#title' => t('Content'),

    '#weight' => -100,                  // move to the top

    '#suffix' => '</div>',

    '#prefix'=> '<div id="page-toc">'

  );

  $render_array['taxon_description_feature_toc'] = $toc; //markup_to_render_array($toc_html);

  if(variable_get(BIBLIOGRAPHY_FOR_ORIGINAL_SOURCE, 1) == 1){

    $bibliography_block = feature_block(t('Bibliography'));

    $bibliography_block->content = FootnoteManager::renderFootnoteList('BIBLIOGRAPHY');

    $render_array['taxon_description_bibliography'] =  markup_to_render_array(

      theme('block',

        array(

          'elements' => array(

            '#block' => $bibliography_block,

            '#children' => $bibliography_block->content,

          )

        )

      ),

      100 // weight

    );

    $render_array['taxon_description_feature_toc']['#items'][] = toc_list_item('Bibliography', array('class' => 'bibliography'));

  }

  }

}

define('BIBLIOGRAPHY_FOR_ORIGINAL_SOURCE', 'bibliography_for_original_source');

/**

 * @var array of URIs eg. http://edit.africamuseum.be"

 *   An options array

define('EDIT_MAPSERVER_VERSION', serialize(

    )

  array(

      'ZoologicalName' => array(

        'nameAuthorPart' => array('name' => TRUE),

        'referencePart' => array('authors' => TRUE),

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

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

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

      ),

      ),

     '#DEFAULT' => array(

        'namePart' => array(

            'name' => TRUE

        ),

        'referencePart' => array(

            'reference' => TRUE

        ),

        'microreferencePart' => array(

            'microreference' => TRUE,

        ),

        'statusPart' => array(

            'status' => TRUE,

        ),

        'descriptionPart' => array(

            'description' => TRUE,

        ),

      )

define('CDM_NAME_RENDER_TEMPLATES', 'cdm-name-render-templates');

   array (

       )

  $form['aggregation'] = array(

      '#type' => 'fieldset',

      '#title' => t('Aggregation of data'),

      '#collapsible' => FALSE,

          </p>',