EDIT

<?php

/**

 * @file

 * Functions for dealing with CDM entities of type SpecimenOrOccurrences

 *

 * @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>

 */

/**

 * Provides the HTML markup for a specimen page

 *

 * @param $specimen

 *

 * @return string

 *  The markup for a specimen page

 */

function render_cdm_specimen_page($specimen, $is_specimen_page = false)

{

    $detail_html = "";

    //link to specimen page

    $pathToSpecimen = path_to_specimen($specimen->uuid);

    if (!$is_specimen_page) {

        $specimenPageLink = l($specimen->accessionNumber, $pathToSpecimen, array('attributes' => array('target' => '_blank')));

        $detail_html .= "<strong>$specimenPageLink</strong><br>";

    }

    if ($is_specimen_page) {

        if ($specimen->citation) {

            $detail_html .= "<br>" . create_label("Citation") . $specimen->citation . "<br>";

        }

    }

    if ($specimen->preferredStableUri) {

        $stableIdentifierLink = l($specimen->preferredStableUri, $specimen->preferredStableUri, array('attributes' => array('target' => '_blank')));

        $detail_html .= create_label("Preferred stable URI") . $stableIdentifierLink . "<br>";

    }

    if ($is_specimen_page) {

        // associated taxa

        if ($specimen->associatedTaxa) {

            $detail_html .= "<br>";

            $detail_html .= create_label("Associated with");

            if (sizeof($specimen->associatedTaxa) > 1) {

                $detail_html .= "<br>";

            }

            foreach ($specimen->associatedTaxa as $associatedTaxon) {

                $detail_html .= l($associatedTaxon->second, path_to_taxon($associatedTaxon->first, "specimens"));//$associatedTaxon->second."<br>";

            }

            $detail_html .= "<br>";

        }

    }

    // - type information

    $types = "";

    if (isset($specimen->types)) {

        //typed taxa

        foreach ($specimen->types as $typeStatus => $typedTaxa) {

            if ($is_specimen_page) {

                if ($specimen->types) {

                    $detail_html .= "<i>" . $typeStatus . "</i>: ";

                    foreach ($typedTaxa as $typedTaxon) {

                        $detail_html .= $typedTaxon . " ";

                    }

                    $detail_html .= "<br>";

                }

            } else {

                $types .= $typeStatus . " ";

            }

        }

    }

    $derivateDataDTO = $specimen->derivateDataDTO;

    // - specimen scans

    $specimenScans = create_html_links($derivateDataDTO->specimenScans, true);

    // - molecular data

    $molecularData = "";

    if ($derivateDataDTO->molecularDataList) {

        foreach ($derivateDataDTO->molecularDataList as $molecular) {

            //provider link

            if (isset($molecular->providerLink)) {

                $molecularData .= create_html_link($molecular->providerLink, true);

            } else {

                $molecularData .= "[no provider]";

            }

            //contig link

            if (isset($molecular->contigFiles)) {

                $molecularData .= "[";

                if (sizeof($molecular->contigFiles) > 0) {

                    foreach ($molecular->contigFiles as $contigFile) {

                        if (isset($contigFile->contigLink)) {

                            if (isset($contigFile->contigLink->uri) and $contigFile->contigLink->uri != null) {

                                $molecularData .= create_html_link($contigFile->contigLink, true) . " ";

                            }

                        } else {

                            $molecularData .= "no contig ";

                        }

                        //primer links

                        if (isset($contigFile->primerLinks)) {

                            $molecularData .= create_html_links($contigFile->primerLinks, true);

                        }

                    }

                }

                $molecularData = rtrim($molecularData, " ");

                $molecularData .= "]";

            }

            //FIXME separate with comma (remove trailing comma)

        }

    }

    // - detail images

    $detailImages = create_html_links($derivateDataDTO->detailImages, true);

    if ($types) {

        $detail_html .= $is_specimen_page ? "<br>" : "";

        $detail_html .= create_label("Type(s)") . $types . "<br>";

    }

    if ($specimenScans and !$is_specimen_page) {

        $detail_html .= create_label("Specimen Scans") . $specimenScans . "<br>";

    }

    //specimen scan image gallery

    if ($is_specimen_page and isset($derivateDataDTO->specimenScanUuids) and !empty($derivateDataDTO->specimenScanUuids)) {

        $detail_html .= addImageGallery("Specimen scans", $derivateDataDTO->specimenScanUuids);

    }

    if ($molecularData) {

        $detail_html .= $is_specimen_page ? "<br>" : "";

        $detail_html .= create_label("Molecular Data") . $molecularData . "<br>";

    }

    if ($detailImages and !$is_specimen_page) {

        $detail_html .= create_label("Detail Images") . $detailImages . "<br>";

    }

    //detail image gallery

    if ($is_specimen_page and isset($derivateDataDTO->detailImageUuids) and !empty($derivateDataDTO->detailImageUuids)) {

        $detail_html .= addImageGallery("Detail Images", $derivateDataDTO->detailImageUuids);

    }

    //character data

    if ($specimen->characterData) {

        $detail_html .= $is_specimen_page ? "<br>" : "";

        $detail_html .= create_label("Character Data");

        if ($is_specimen_page) {

            $detail_html .= "<br>";

            foreach ($specimen->characterData as $characterStatePair) {

                $detail_html .= "<i>" . $characterStatePair->first . "</i>:" . $characterStatePair->second;

                $detail_html .= "<br>";

            }

        } else {

            $detail_html .= l("detail page", $pathToSpecimen, array('attributes' => array('target' => '_blank')));

            $detail_html .= "<br>";

        }

    }

    return $detail_html;

}

function addImageGallery($galleryName, $imageUuids)

{

    $images = array();

    foreach ($imageUuids as $uuid) {

        $images[] = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $uuid);

    }

    $gallery_html = '';

    if (count($imageUuids) > 0) {

        $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);

        $captionElements = array(

            'title',

            'rights',

        );

        $alternativeMediaUris = array();

        foreach ($images as $image) {

            $mediaUri = getMediaUri($image);

            if ($mediaUri) {

                $alternativeMediaUris[] = $mediaUri;

            } else {

                $alternativeMediaUris[] = path_to_media($image->uuid);

            }

        }

        $gallery_html = compose_cdm_media_gallerie(array(

            'mediaList' => $images,

            'galleryName' => $galleryName,

            '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' => $alternativeMediaUris,

            'galleryLinkUri' => NULL,

        ));

    }

    return "<br>" . create_label($galleryName) . "<br>" . $gallery_html;

}

function getMediaUri($media)

{

    if (isset($media->representations) && sizeof($media->representations) == 1

        && isset($media->representations[0]->parts) &&

        sizeof($media->representations[0]->parts) == 1) {

        return $media->representations[0]->parts[0]->uri;

    }

    return null;

}

/**

 * Formats the given string to a label for displaying key-object pairs in HTML

 * @return string

 */

function create_label($label)

{

    return "<span class='specimen_table_label'>" . $label . ": </span>";

}

/**

 * 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_specimen_or_observation($specimenOrObservation, &$derivatives = null)

{

    $exclude_occurrence_fields = &drupal_static(__FUNCTION__);

    if (!isset($exclude_occurrence_fields)) {

        $exclude_occurrence_fields = array(

            'derivationEvents',

            'titleCache',

            'protectedTitleCache',

            'derivedUnitMedia',

            'created',

            'publish',

            '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 != '' /* FieldUnit' */) {

                            @_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':

                    case 'kindOfUnit':

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

                        break;

                    case 'definition':

                        // TODO

                        break;

                    case 'preferredStableUri':

                        @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), array(array('#markup' => cdm_external_uri($value, false))));

                        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 = '';

                            $name_link = '';

                            if ($determinationEvent->taxonName) {

                                $taxon_name = $determinationEvent->taxonName;

                            } else if ($determinationEvent->taxon) {

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

                                $name_link = path_to_taxon($determinationEvent->taxon->uuid);

                            }

                            if ($taxon_name) {

                                $taxon_html = render_taxon_or_name($taxon_name, $name_link);

                                $dd_elements[$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':

                        $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->childNodes, $description->elements);

                            $description_render_elements = _block_get_renderable_array(make_feature_block_list($elements_by_feature, null));

                            $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($groups, cdm_occurrence_field_name_label('storedUnder'), render_taxon_or_name($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);

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

                            $min_max_markup = min_max_measure($value, 'absoluteElevation');

                            @_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup);

                        }

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

                            $min_max_markup = min_max_measure($value, 'distanceToGround');

                            @_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup);

                        }

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

                            $min_max_markup = min_max_measure($value, 'distanceToWaterSurface');

                            @_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup);

                        }

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

                            $area_representations = array();

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

                                $area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid));

                            }

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

                                array(

                                    array('#markup' => implode(', ', $area_representations))

                                )

                            );

                        }

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

                            $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_specimen_or_observation() for field " . $field, "warning");

                        } else {

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

                        }

                }

            }

        } // END of loop over $derivedUnitFacade fields

        // Extensions

        $extensions = cdm_ws_fetch_all(CDM_WS_PORTAL_OCCURRENCE . '/'  . $specimenOrObservation->uuid . '/extensions', array($specimenOrObservation->uuid));

        if ($extensions && count($extensions)) {

            $extensions_render_array = compose_extensions($extensions);

            @_description_list_group_add($groups, t('Extensions') . ':',

                $extensions_render_array,

                '', 100);

        }

        // 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_attribute_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_specimen_or_observation($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 below 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 'geneticAccessionNumber';

                    $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, 2);

                    break;

                case 'locus': // FIXME 3.3 now dnaMarker (DefinedTerm)  if multiple amplifications where used to build this consensus sequence it may be the super set of the markers used in amplification.

                    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 'consensusSequence':

                    // 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 class="sequence-length">' . $value->length . ' ' . t('pb') . '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',

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

                            )

                        ),

                        5);

                    break;

                case 'dnaSample': // FIXME 3.3 implement

                    break;

                case 'singleReads': // FIXME 3.3 implement

                    break;

                case 'contigFile': // FIXME 3.3 implement - Media

                    break;

                case 'pherograms': // FIXME 3.3 implement - Media

                    break;

                case 'haplotype': // FIXME 3.3 implement

                    break;

                case 'dateSequenced': // FIXME 3.3 now in SingelRead

                    @_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 'barcodeSequencePart': // FIXME 3.3 implement, compose sequence

                    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

                    );

                    break;

                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' => compose_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;

}

/**

 * Creates an array from a list of FieldUnitDTOs.

 *

 *

 * @param object $specimenOrObservations

 *   list of FieldUnitDTOs

 * @return array

 *   An array containing the hierarchy of the field units corresponding to the taxon

 *

 * @ingroup compose

 */

function create_specimen_array(array $specimenOrObservations){

    $items_specimen = array();

    $items = array();

    //we need one more item to contain the items of one level (fieldunit, derivate data etc.)

    foreach ($specimenOrObservations as &$specimenOrObservation) {

        $items['data'] = $specimenOrObservation->listLabel;

        $specimen = create_cdm_specimen_or_observation($specimenOrObservation);

        $children = array();

        $child = array();

        $child['data'] =$specimen;

       // $children[] = create_specimen_array($specimenOrObservation->derivates);

       if (isset($specimenOrObservation->derivates) && sizeof($specimenOrObservation->derivates) > 0){

           $child['children']= create_specimen_array($specimenOrObservation->derivates);

       }

       $children[]=$child;

       $items['children'] = $children;

       $items_specimen[] = $items;

    }

    return $items_specimen;

}

/**

 * 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 create_cdm_specimen_or_observation($specimenOrObservation)

{

    $exclude_occurrence_fields = &drupal_static(__FUNCTION__);

    if (!isset($exclude_occurrence_fields)) {

        $exclude_occurrence_fields = array(

            'type',

            'derivationEvent',

            'taxonRelatedDerivedUnits',

            'label',

            'titleCache',

            'listLabel',

            'protectedTitleCache',