EDIT

<?php

/**

 * @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

 *

 * @param object $specimenOrObservation

 *   the CDM instance of type SpecimenOrObservation to compose

 *   the render array for

 * @param array $derivatives

 *   the render array which contains the compositions of the derivatives

 *   of the supplied $specimenOrObservation

 *

 * @return array

 *   the supplied render array $derivatives to which the composition of the supplied

 *   $specimenOrObservation has been added to

 *

 * @ingroup compose

 */

function compose_cdm_specimenOrObservation($specimenOrObservation, &$derivatives = null) {

  $exclude_occurrence_fields = &drupal_static(__FUNCTION__);

  if (!isset($exclude_occurrence_fields)) {

     $exclude_occurrence_fields = array(

        'derivationEvents',

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

        'titleCache',

        'protectedTitleCache',

        'derivedUnitMedia',

        'created',

        'updated',

        'class',

        'uuid'

    );

  }

  // only show uuid it the user is logged in

  if(user_is_logged_in() && ($a_idx = array_search('uuid', $exclude_occurrence_fields)) !== FALSE ) {

    unset($exclude_occurrence_fields[$a_idx]);

  }

  if (!isset($derivatives)) {

    $derivatives = array();

  }

  $descriptions = null;

  $derivedFrom = null;

  if (is_object($specimenOrObservation)) {

    // request again for deeper initialization

    $specimenOrObservation = cdm_ws_get("portal/" . CDM_WS_OCCURRENCE, $specimenOrObservation->uuid);

    $type_label = $specimenOrObservation->class;

    RenderHints::setFootnoteListKey($type_label . '-' . $specimenOrObservation->uuid);

    // collect typeStatus as label

    if (isset($specimenOrObservation->specimenTypeDesignations)) {

      $type_status = array();

      foreach ($specimenOrObservation->specimenTypeDesignations as $typeDesignation) {

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

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

        }

      }

      if (count($type_status) > 0){

        $type_label = implode(', ', $type_status);

      }

    }

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

    $groups = array();

    // --- add initialized fields

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

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

        switch ($field) {

          /* ---- java.lang.Object --- */

          case 'class':

            if($value != '' /* FieldObservation' */){

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

            }

          break;

          case 'markers':

            $dd_elements = array();

            foreach ($value as $marker) {

              $dd_elements[] = compose_cdm_marker($marker);

            }

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

            break;

          case 'annotations':

            $dd_elements = array();

            foreach ($value as $annotation) {

              // TODO respect annotation type filter settings

              $dd_elements[] = $annotation->text;

            }

            @_description_list_group_add($groups, t('Notes'), $dd_elements);

            break;

          /* ---- SpecimenOrObservationBase --- */

          case 'sex':

          case 'lifeStage':

            @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->representation_L10n);

            break;

          case 'definition':

            // TODO

            break;

          case 'specimenTypeDesignations':

            @_description_list_group_add(

              $groups,

              cdm_occurrence_field_name_label($field),

              array(

                '#markup'=>theme('cdm_typedesignations', array('typeDesignations' => $value)),

              )

            );

            break;

          case 'determinations':

            $dd_elements = array();

            $glue = ', ';

            foreach  ($value as $determinationEvent){

              $timeperiod_string = NULL;

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

                $timeperiod_string = timePeriodToString($determinationEvent->timeperiod);

              }

              $weight = isset($determinationEvent->preferred) && $determinationEvent->preferred == 1 ? '0' : ($timeperiod_string ? $timeperiod_string : '1');

              // check key exists

              while (array_key_exists($weight, $dd_elements)) {

                $weight .= '0';

              }

              $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),

                  )

              );

              $dd_elements[$weight] = $taxon_html;

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

                $dd_elements[$weight] .= cdm_term_representation($determinationEvent->modifier);

              }

              if ($timeperiod_string) {

                $dd_elements[$weight] .= $glue . $timeperiod_string;

              }

              if (isset($determinationEvent->actor->titleCache)) {

                $dd_elements[$weight] .= $glue . $determinationEvent->actor->titleCache;

              }

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

                $dd_elements[$weight] .= $glue . $determinationEvent->description;

              }

            }

            ksort($dd_elements);

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

            break;

          case 'descriptions':

            $descriptions = $value;

            $occurrence_featureTree = cdm_get_occurrence_featureTree();

            $dd_elements = array();

            foreach ($value as $description) {

              $description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $description->uuid);

//               if($description->imageGallery == TRUE) {

//                 continue;

//               }

              $elements_by_feature = _mergeFeatureTreeDescriptions($occurrence_featureTree->root->children, $description->elements);

              $rendered_description = theme(

                 'cdm_feature_nodes',

                 array('mergedFeatureNodes' => $elements_by_feature)

              );

              $description_render_elements = array();

//               $description_render_elements[] = array('#markup' => '<h4>'. $description->titleCache . '</h4>');

              $description_render_elements[] = array('#markup' => $rendered_description);

              $dd_elements[] = $description_render_elements;

            }

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

            break;

          case 'sources':

              $dd_elements = array();

              foreach ($value as $identifiable_source) {

                $dd_elements[] = theme('cdm_OriginalSource', array('source' => $identifiable_source));

              }

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

              break;

          /* ---- DerivedUnitBase --- */

          case 'derivedFrom':

            $derivedFrom = $value;

            break;

          case 'collection':

            $sub_dl_groups = array();

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

            @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'),  $value->codeStandard, NULL, 2);

            @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);

            @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);

            // TODO "superCollection"

            // TODO may have media

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

                array(

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

                    array('#theme' => 'description_list', '#groups' => $sub_dl_groups)

                )

            );

            break;

            case 'storedUnder':

              @_description_list_group_add($groups, cdm_occurrence_field_name_label('storedUnder'), theme('cdm_taxonName', $value));

              break;

            /* ---- Specimen --- */

            case 'sequences':

              $dd_elements = array();

              foreach ($value as $sequence) {

                $dd_elements[] = compose_cdm_sequence($sequence);

              }

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

            break;

            // TODO preservation

            // TODO exsiccatum

          /* ---- FieldObservation --- */

          case 'gatheringEvent':

            @_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->actor->titleCache);

            @_description_list_group_add($groups, t('Gathering time'), timePeriodToString($value->timeperiod));

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

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

            @_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country->representation_L10n);

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

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

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

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

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

            if (isset($value->collectingAreas)) {

              $area_representations = array();

              foreach($value->collectingAreas as $area) {

                $area_representations[] = $area->representation_L10n;

              }

              @_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'), implode(', ', $area_representations));

            }

            if (isset($value->exactLocation)) {

              $sub_dl_groups = array();

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

              @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);

              @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);

              if (isset($value->exactLocation->referenceSystem)) {

                @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);

              }

              @_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;

          default:

            if(is_object($value) || is_array($value)){

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

            } else {

              _description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);

            }

        }

      }

    } // END of loop over $derivedUnitFacade fields

    // template_preprocess_description_list() is not worting by weight so we do it right here

    uasort($groups, 'element_sort');

    $occurrence_elements = array(

        '#title' => $title,

        '#theme' => 'description_list',

        '#groups' => $groups,

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

    );

    $derivatives[] = $occurrence_elements;

    // all footnotes which has been assembled so far (e.g. from typeDesignations) to here

    $foonote_li_elements = theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'span'));

    if (!empty($foonote_li_elements)) {

      $derivatives[] =  array(

          '#markup' =>  '<div class="footnotes">' . $foonote_li_elements . '</div>',

      );

    }

    // --- recurse into originals

    if (!isset($derivedFrom)) {

      $derivedFrom = cdm_ws_get(

          CDM_WS_OCCURRENCE,

          array($specimenOrObservation->uuid, 'derivedFrom')

        );

    }

    if (isset($derivedFrom)) {

      if (isset($derivedFrom->originals)) {

        $derived_from_label = t('derived');

        $preposition = t('from');

        if(isset($derivedFrom->type)){

          $derived_from_label = $derivedFrom->type->representation_L10n;

          if($derivedFrom->type->uuid == UUID_DERIVATIONEVENTTYPE_ACCESSIONING){

            $preposition = t('of');

          }

        }

        if (count($groups) > 0) {

          // TODO  annotations

          // only display the derived from information when the derivative has any element which will be diplayed

          $derivatives[] = array(

              '#markup' => '<div class="derived_from">' . $derived_from_label . ' ' . $preposition . ': </div>',

          );

        }

        foreach ($derivedFrom->originals as $original) {

          compose_cdm_specimenOrObservation($original, $derivatives);

        }

      }

    }

  } // END of $specimenOrObservation exists

  return $derivatives;

}

/**

 * Compose an render array from a CDM Sequence object.

 *

 * compose_hook() implementation

 *

 * @param object $sequence

 *   CDM instance of type Sequence

 * @return array

 *   A render array containing the fields of the supplied $sequence

 *

 * @ingroup compose

 */

function compose_cdm_sequence($sequence) {

  $exclude_sequence_fields = &drupal_static(__FUNCTION__);

  if (!isset($exclude_sequence_fields)) {

    $exclude_sequence_fields = array(

      'titleCache',

      'protectedTitleCache',

      'microReference',

      'created',

      'updated',

      'class',

    );

  }

  $groups = array();

  // -- retrieve additional data if neesscary

  // TODO bellow call disabled since sequences are not yet supported,

  //      see  #3347 (services and REST service controller for molecular classes implemented)

  //

  // cdm_load_annotations($sequence);

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

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

      switch ($field) {

        case 'genBankAccession';

          $dd_elements = array();

          foreach ($value as $accession) {

            if (isset($accession->uri) ){

              $dd_elements[] = l($accession->accessionNumber, $accession->uri);

            } else {

              $dd_elements[] = $accession->accessionNumber;

            }

          }

          @_description_list_group_add($groups, cdm_occurrence_field_name_label($field),  $dd_elements, NULL, 1);

          break;

        case 'length':

          @_description_list_group_add($groups, t('Sequence length'),  $value , ' ' . t('Nucleotites'), 2);

          break;

        case 'locus':

          if (isset($value->name)) {

            @_description_list_group_add($groups, cdm_occurrence_field_name_label($field),  $value->name, NULL, 3);

          }

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

            @_description_list_group_add($groups, cdm_occurrence_field_name_label($field) . ' ' . t('description') , $value->description, NULL, 4);

          }

          break;

        case 'sequence':

          // format in genbank style, force linebreaks after each 70 nucleotites

          // see also http://stackoverflow.com/questions/499137/css-how-can-i-force-a-long-string-without-any-blank-to-be-wrapped-in-xul-and

          @_description_list_group_add(

            $groups,

            cdm_occurrence_field_name_label($field),

            array(

              array(

                '#markup' => '<div>' . wordwrap($value, 70, '</br>', TRUE) . '</div>',

                '#wrapper_attributes' => array('class'=>'dna-sequence')

                )

              ),

            5);

          break;

        case 'dateSequenced':

          @_description_list_group_add($groups, t('Sequencing date'),  timePeriodToString($value), NULL, 6);

          break;

        case 'barcode': // boolean

          @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value ? 'Yes': 'No', NULL, 7);

          break;

        case 'citation':

          @_description_list_group_add($groups,

            cdm_occurrence_field_name_label($field),

            theme('cdm_reference', array('reference' =>$value, 'microReference' => $sequence->microReference)),

            NULL,

            8

          );

          break;

        case 'publishedIn':

          @_description_list_group_add($groups,

            cdm_occurrence_field_name_label($field),

            theme('cdm_reference', array('reference'=>$value)),

            NULL,

            7

          );

        case 'rights':

          array_merge($groups, cdm_rights_as_dl_groups($value));

        break;

        case 'annotations':

          $dd_elements = array();

          foreach ($value as $annotation) {

            // TODO respect annotation type filter settings

            $dd_elements[] = $annotation->text;

          }

          @_description_list_group_add($groups, t('Notes'), $dd_elements, NULL, 9);

          break;

        case 'markers':

          $dd_elements = array();

          foreach ($value as $marker) {

            $dd_elements[] = compose_cdm_marker($marker);

          }

          @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 10);

          break;

        case 'chromatograms':

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

              array(

                  '#markup'=>theme('cdm_media_gallerie', array('medialist'=>$value)),

              ),

              NULL,

              11);

          break;

        default:

          if(is_object($value) || is_array($value)){

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

          } else {

            _description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 20);

          }

      }

    }

  }

  // template_preprocess_description_list() is not worting by weight so we do it right here

  uasort($groups, 'element_sort');

  $sequence_elements = array(

      '#theme' => 'description_list',

      '#groups' => $groups

  );

  return $sequence_elements;

}