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<?php
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/**
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* @file
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* Functions for dealing with CDM entities of type SpeciemenOrOccurrences
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*
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* @copyright
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* (C) 2007-2012 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this module are subject to the Mozilla
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* Public License Version 1.1.
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* @see http://www.mozilla.org/MPL/MPL-1.1.html
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*
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* @author
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* - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
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*/
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/**
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* Compose an render array from a CDM DerivedUnitFacade object.
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*
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* compose_hook() implementation
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*
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* @param object $specimenOrObservation
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* the CDM instance of type SpecimenOrObservation to compose
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* the render array for
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* @param array $derivatives
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* the render array which contains the compositions of the derivatives
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* of the supplied $specimenOrObservation
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*
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* @return array
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* the supplied render array $derivatives to which the composition of the supplied
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* $specimenOrObservation has been added to
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*
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* @ingroup compose
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*/
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function compose_cdm_specimenOrObservation($specimenOrObservation, &$derivatives = null) {
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$exclude_occurrence_fields = &drupal_static(__FUNCTION__);
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if (!isset($exclude_occurrence_fields)) {
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$exclude_occurrence_fields = array(
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'derivationEvents',
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'extensions', // TODO ignored for now, how to handle extensions?
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'titleCache',
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'protectedTitleCache',
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'derivedUnitMedia',
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'created',
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'publish',
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'updated',
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'class',
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'uuid',
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''
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);
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}
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// only show uuid it the user is logged in
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if(user_is_logged_in() && ($a_idx = array_search('uuid', $exclude_occurrence_fields)) !== FALSE ) {
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unset($exclude_occurrence_fields[$a_idx]);
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}
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if (!isset($derivatives)) {
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$derivatives = array();
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}
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$descriptions = null;
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$derivedFrom = null;
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if (is_object($specimenOrObservation)) {
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// request again for deeper initialization
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$specimenOrObservation = cdm_ws_get("portal/" . CDM_WS_OCCURRENCE, $specimenOrObservation->uuid);
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$type_label = $specimenOrObservation->class;
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RenderHints::setFootnoteListKey($type_label . '-' . $specimenOrObservation->uuid);
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// collect typeStatus as label
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if (isset($specimenOrObservation->specimenTypeDesignations)) {
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$type_status = array();
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foreach ($specimenOrObservation->specimenTypeDesignations as $typeDesignation) {
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if (isset($typeDesignation->typeStatus->representation_L10n)){
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$type_status[] = $typeDesignation->typeStatus->representation_L10n;
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}
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}
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if (count($type_status) > 0){
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$type_label = implode(', ', $type_status);
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}
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}
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$title = $type_label . ': '. $specimenOrObservation->titleCache;
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$groups = array();
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// --- add initialized fields
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foreach (get_object_vars($specimenOrObservation) as $field => $value) {
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if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
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switch ($field) {
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/* ---- java.lang.Object --- */
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case 'class':
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if($value != '' /* FieldUnit' */){
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
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}
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break;
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case 'markers':
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$dd_elements = array();
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foreach ($value as $marker) {
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$dd_elements[] = compose_cdm_marker($marker);
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}
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
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break;
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case 'annotations':
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$dd_elements = array();
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foreach ($value as $annotation) {
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// TODO respect annotation type filter settings
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$dd_elements[] = $annotation->text;
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}
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@_description_list_group_add($groups, t('Notes'), $dd_elements);
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break;
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/* ---- SpecimenOrObservationBase --- */
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case 'sex':
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case 'lifeStage':
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case 'kindOfUnit':
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->representation_L10n);
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break;
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case 'definition':
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// TODO
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break;
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case 'specimenTypeDesignations':
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@_description_list_group_add(
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$groups,
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cdm_occurrence_field_name_label($field),
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array(
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'#markup'=>theme('cdm_typedesignations', array('typeDesignations' => $value)),
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)
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);
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break;
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case 'determinations':
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$dd_elements = array();
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$glue = ', ';
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foreach ($value as $determinationEvent){
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$timeperiod_string = NULL;
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if (isset($determinationEvent->timeperiod)) {
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$timeperiod_string = timePeriodToString($determinationEvent->timeperiod);
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}
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$weight = isset($determinationEvent->preferred) && $determinationEvent->preferred == 1 ? '0' : ($timeperiod_string ? $timeperiod_string : '1');
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// check key exists
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while (array_key_exists($weight, $dd_elements)) {
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$weight .= '0';
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}
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$taxon_name = cdm_ws_get(CDM_WS_TAXON . '/$0/name', $determinationEvent->taxon->uuid);
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$taxon_html = theme('cdm_taxonName',
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array(
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'taxonName' => $taxon_name,
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'nameLink' => path_to_taxon($determinationEvent->taxon->uuid),
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)
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);
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$dd_elements[$weight] = $taxon_html;
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if (isset($determinationEvent->modifier)) {
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$dd_elements[$weight] .= cdm_term_representation($determinationEvent->modifier);
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}
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if ($timeperiod_string) {
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$dd_elements[$weight] .= $glue . $timeperiod_string;
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}
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if (isset($determinationEvent->actor->titleCache)) {
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$dd_elements[$weight] .= $glue . $determinationEvent->actor->titleCache;
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}
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if (isset($determinationEvent->description)) {
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$dd_elements[$weight] .= $glue . $determinationEvent->description;
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}
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}
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ksort($dd_elements);
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@_description_list_group_add($groups, cdm_occurrence_field_name_label('determinations'), $dd_elements);
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break;
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case 'descriptions':
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$descriptions = $value;
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$occurrence_featureTree = cdm_get_occurrence_featureTree();
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$dd_elements = array();
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foreach ($value as $description) {
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$description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $description->uuid);
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// if($description->imageGallery == TRUE) {
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// continue;
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// }
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$elements_by_feature = _mergeFeatureTreeDescriptions($occurrence_featureTree->root->childNodes, $description->elements);
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$rendered_description = theme(
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'cdm_feature_nodes',
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array('mergedFeatureNodes' => $elements_by_feature)
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);
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$description_render_elements = array();
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// $description_render_elements[] = array('#markup' => '<h4>'. $description->titleCache . '</h4>');
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$description_render_elements[] = array('#markup' => $rendered_description);
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$dd_elements[] = $description_render_elements;
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}
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
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break;
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case 'sources':
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$dd_elements = array();
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foreach ($value as $identifiable_source) {
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$dd_elements[] = theme('cdm_OriginalSource', array('source' => $identifiable_source));
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}
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
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break;
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/* ---- DerivedUnitBase --- */
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case 'derivedFrom':
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$derivedFrom = $value;
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break;
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case 'collection':
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$sub_dl_groups = array();
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@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
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@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'), $value->codeStandard, NULL, 2);
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@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
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@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
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// TODO "superCollection"
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// TODO may have media
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
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array(
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array('#markup' => $value->titleCache),
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array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
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)
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);
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break;
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case 'storedUnder':
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@_description_list_group_add($groups, cdm_occurrence_field_name_label('storedUnder'), theme('cdm_taxonName', $value));
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break;
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243
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/* ---- Specimen --- */
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245
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case 'sequences':
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$dd_elements = array();
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247
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foreach ($value as $sequence) {
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$dd_elements[] = compose_cdm_sequence($sequence);
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}
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
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break;
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252
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253
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// TODO preservation
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254
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// TODO exsiccatum
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255
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256
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257
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/* ---- FieldObservation --- */
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258
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case 'gatheringEvent':
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@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->actor->titleCache);
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@_description_list_group_add($groups, t('Gathering time'), timePeriodToString($value->timeperiod));
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@_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description);
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262
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@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality->text);
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@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country->representation_L10n);
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264
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@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod);
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265
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@_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $value->absoluteElevation, ' m');
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@_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevationError'), $value->absoluteElevationError, ' m');
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267
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@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $value->distanceToGround, ' m');
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@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $value->distanceToWaterSurface, ' m');
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269
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if (isset($value->collectingAreas)) {
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270
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$area_representations = array();
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271
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foreach($value->collectingAreas as $area) {
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272
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$area_representations[] = $area->representation_L10n;
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}
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274
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@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'), implode(', ', $area_representations));
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275
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}
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276
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if (isset($value->exactLocation)) {
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277
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$sub_dl_groups = array();
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@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
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279
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@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
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280
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@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
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281
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if (isset($value->exactLocation->referenceSystem)) {
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282
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@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
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283
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}
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284
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285
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@_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
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286
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array(
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287
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array('#markup' => $value->exactLocation->sexagesimalString),
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288
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array(
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289
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'#theme' => 'description_list',
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290
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'#groups' => $sub_dl_groups
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291
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),
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292
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)
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293
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);
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294
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}
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295
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break;
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296
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|
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297
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default:
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298
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if(is_object($value) || is_array($value)){
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299
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drupal_set_message("Unhandled type in compose_cdm_specimenOrObservation() for field " . $field, "warning");
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300
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} else {
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301
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_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
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302
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}
|
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303
|
|
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304
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}
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305
|
|
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306
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}
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307
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} // END of loop over $derivedUnitFacade fields
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|
308
|
|
|
309
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|
|
310
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// template_preprocess_description_list() is not worting by weight so we do it right here
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311
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uasort($groups, 'element_sort');
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|
312
|
|
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313
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$occurrence_elements = array(
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|
314
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'#title' => $title,
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315
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'#theme' => 'description_list',
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316
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'#groups' => $groups,
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317
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'#attributes' => array('class' => html_class_attribute_ref($specimenOrObservation)),
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318
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);
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319
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$derivatives[] = $occurrence_elements;
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320
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// all footnotes which has been assembled so far (e.g. from typeDesignations) to here
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321
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$foonote_li_elements = theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'span'));
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322
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if (!empty($foonote_li_elements)) {
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323
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$derivatives[] = array(
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324
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'#markup' => '<div class="footnotes">' . $foonote_li_elements . '</div>',
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325
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);
|
|
326
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}
|
|
327
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|
|
328
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// --- recurse into originals
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|
329
|
if (!isset($derivedFrom)) {
|
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330
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$derivedFrom = cdm_ws_get(
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331
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CDM_WS_OCCURRENCE,
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332
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array($specimenOrObservation->uuid, 'derivedFrom')
|
|
333
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);
|
|
334
|
}
|
|
335
|
|
|
336
|
if (isset($derivedFrom)) {
|
|
337
|
if (isset($derivedFrom->originals)) {
|
|
338
|
$derived_from_label = t('derived');
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|
339
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$preposition = t('from');
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|
340
|
if(isset($derivedFrom->type)){
|
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341
|
$derived_from_label = $derivedFrom->type->representation_L10n;
|
|
342
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if($derivedFrom->type->uuid == UUID_DERIVATIONEVENTTYPE_ACCESSIONING){
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343
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$preposition = t('of');
|
|
344
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}
|
|
345
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}
|
|
346
|
if (count($groups) > 0) {
|
|
347
|
// TODO annotations
|
|
348
|
|
|
349
|
// only display the derived from information when the derivative has any element which will be diplayed
|
|
350
|
$derivatives[] = array(
|
|
351
|
'#markup' => '<div class="derived_from">' . $derived_from_label . ' ' . $preposition . ': </div>',
|
|
352
|
);
|
|
353
|
}
|
|
354
|
foreach ($derivedFrom->originals as $original) {
|
|
355
|
compose_cdm_specimenOrObservation($original, $derivatives);
|
|
356
|
}
|
|
357
|
}
|
|
358
|
}
|
|
359
|
|
|
360
|
} // END of $specimenOrObservation exists
|
|
361
|
|
|
362
|
return $derivatives;
|
|
363
|
}
|
|
364
|
|
|
365
|
/**
|
|
366
|
* Compose an render array from a CDM Sequence object.
|
|
367
|
*
|
|
368
|
* compose_hook() implementation
|
|
369
|
*
|
|
370
|
* @param object $sequence
|
|
371
|
* CDM instance of type Sequence
|
|
372
|
* @return array
|
|
373
|
* A render array containing the fields of the supplied $sequence
|
|
374
|
*
|
|
375
|
* @ingroup compose
|
|
376
|
*/
|
|
377
|
function compose_cdm_sequence($sequence) {
|
|
378
|
|
|
379
|
$exclude_sequence_fields = &drupal_static(__FUNCTION__);
|
|
380
|
if (!isset($exclude_sequence_fields)) {
|
|
381
|
$exclude_sequence_fields = array(
|
|
382
|
'titleCache',
|
|
383
|
'protectedTitleCache',
|
|
384
|
'microReference',
|
|
385
|
'created',
|
|
386
|
'updated',
|
|
387
|
'class',
|
|
388
|
);
|
|
389
|
}
|
|
390
|
|
|
391
|
$groups = array();
|
|
392
|
|
|
393
|
// -- retrieve additional data if neesscary
|
|
394
|
// TODO below call disabled since sequences are not yet supported,
|
|
395
|
// see #3347 (services and REST service controller for molecular classes implemented)
|
|
396
|
//
|
|
397
|
// cdm_load_annotations($sequence);
|
|
398
|
|
|
399
|
foreach (get_object_vars($sequence) as $field => $value) {
|
|
400
|
|
|
401
|
|
|
402
|
if (!in_array($field, $exclude_sequence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
|
403
|
switch ($field) {
|
|
404
|
|
|
405
|
case 'geneticAccessionNumber';
|
|
406
|
$dd_elements = array();
|
|
407
|
foreach ($value as $accession) {
|
|
408
|
if (isset($accession->uri) ){
|
|
409
|
$dd_elements[] = l($accession->accessionNumber, $accession->uri);
|
|
410
|
} else {
|
|
411
|
$dd_elements[] = $accession->accessionNumber;
|
|
412
|
}
|
|
413
|
}
|
|
414
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 1);
|
|
415
|
break;
|
|
416
|
|
|
417
|
|
|
418
|
case 'locus': // FIXME 3.3 now dnaMarker (DefinedTerm) if multiple amplifications where used to build this consensus sequence it may be the super set of the markers used in amplification.
|
|
419
|
if (isset($value->name)) {
|
|
420
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->name, NULL, 3);
|
|
421
|
}
|
|
422
|
if (isset($value->description)) {
|
|
423
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) . ' ' . t('description') , $value->description, NULL, 4);
|
|
424
|
}
|
|
425
|
break;
|
|
426
|
|
|
427
|
case 'consensusSequence':
|
|
428
|
// format in genbank style, force linebreaks after each 70 nucleotites
|
|
429
|
// see also http://stackoverflow.com/questions/499137/css-how-can-i-force-a-long-string-without-any-blank-to-be-wrapped-in-xul-and
|
|
430
|
@_description_list_group_add(
|
|
431
|
$groups,
|
|
432
|
cdm_occurrence_field_name_label($field),
|
|
433
|
array(
|
|
434
|
array(
|
|
435
|
'#markup' => '<div class="sequence-length">' . $value->length . ' ' . t('pb'). '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',
|
|
436
|
'#wrapper_attributes' => array('class'=>'dna-sequence')
|
|
437
|
)
|
|
438
|
),
|
|
439
|
5);
|
|
440
|
break;
|
|
441
|
|
|
442
|
case 'dnaSample': // FIXME 3.3 implement
|
|
443
|
break;
|
|
444
|
case 'singleReads': // FIXME 3.3 implement
|
|
445
|
break;
|
|
446
|
case 'contigFile': // FIXME 3.3 implement - Media
|
|
447
|
break;
|
|
448
|
case 'pherograms': // FIXME 3.3 implement - Media
|
|
449
|
break;
|
|
450
|
case 'haplotype': // FIXME 3.3 implement
|
|
451
|
break;
|
|
452
|
case 'dateSequenced': // FIXME 3.3 now in SingelRead
|
|
453
|
@_description_list_group_add($groups, t('Sequencing date'), timePeriodToString($value), NULL, 6);
|
|
454
|
break;
|
|
455
|
|
|
456
|
case 'barcode': // boolean
|
|
457
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value ? 'Yes': 'No', NULL, 7);
|
|
458
|
break;
|
|
459
|
case 'barcodeSequencePart': // FIXME 3.3 implement, compose sequence
|
|
460
|
break;
|
|
461
|
|
|
462
|
case 'citation':
|
|
463
|
@_description_list_group_add($groups,
|
|
464
|
cdm_occurrence_field_name_label($field),
|
|
465
|
theme('cdm_reference', array('reference' =>$value, 'microReference' => $sequence->microReference)),
|
|
466
|
NULL,
|
|
467
|
8
|
|
468
|
);
|
|
469
|
break;
|
|
470
|
|
|
471
|
case 'publishedIn':
|
|
472
|
@_description_list_group_add($groups,
|
|
473
|
cdm_occurrence_field_name_label($field),
|
|
474
|
theme('cdm_reference', array('reference'=>$value)),
|
|
475
|
NULL,
|
|
476
|
7
|
|
477
|
);
|
|
478
|
|
|
479
|
case 'rights':
|
|
480
|
array_merge($groups, cdm_rights_as_dl_groups($value));
|
|
481
|
break;
|
|
482
|
|
|
483
|
case 'annotations':
|
|
484
|
$dd_elements = array();
|
|
485
|
foreach ($value as $annotation) {
|
|
486
|
// TODO respect annotation type filter settings
|
|
487
|
$dd_elements[] = $annotation->text;
|
|
488
|
}
|
|
489
|
@_description_list_group_add($groups, t('Notes'), $dd_elements, NULL, 9);
|
|
490
|
break;
|
|
491
|
|
|
492
|
case 'markers':
|
|
493
|
$dd_elements = array();
|
|
494
|
foreach ($value as $marker) {
|
|
495
|
$dd_elements[] = compose_cdm_marker($marker);
|
|
496
|
}
|
|
497
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 10);
|
|
498
|
break;
|
|
499
|
|
|
500
|
case 'chromatograms':
|
|
501
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
|
502
|
array(
|
|
503
|
'#markup'=>theme('cdm_media_gallerie', array('medialist'=>$value)),
|
|
504
|
),
|
|
505
|
NULL,
|
|
506
|
11);
|
|
507
|
break;
|
|
508
|
|
|
509
|
default:
|
|
510
|
if(is_object($value) || is_array($value)){
|
|
511
|
drupal_set_message("Unhandled type in compose_cdm_sequence() for field " . $field, "warning");
|
|
512
|
} else {
|
|
513
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 20);
|
|
514
|
}
|
|
515
|
}
|
|
516
|
}
|
|
517
|
}
|
|
518
|
|
|
519
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
|
520
|
uasort($groups, 'element_sort');
|
|
521
|
|
|
522
|
$sequence_elements = array(
|
|
523
|
'#theme' => 'description_list',
|
|
524
|
'#groups' => $groups
|
|
525
|
);
|
|
526
|
|
|
527
|
return $sequence_elements;
|
|
528
|
}
|
|
529
|
|
|
530
|
|