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<?php
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/**
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* @file
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* Functions for dealing with CDM entities from the package model.taxon
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*
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* @copyright
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* (C) 2007-2016 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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* @defgroup compose Compose functions
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* @{
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* Functions which are composing Drupal render arrays
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*
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* The cdm_dataportal module needs to compose rather complex render arrays from
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* the data returned by the CDM REST service. The compose functions are
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* responsible for creating the render arrays.
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*
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* All these functions are also implementations of the compose_hook()
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* which is used in the proxy_content() function.
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* @}
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*/
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/**
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* Returns HTML for misapplied names and invalid designations.
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*
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* Both relation types are currently treated the same!
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*
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* @param taxonRelationships
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* @param focusedTaxon
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*
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* @return string
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* the rendered html
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*/
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function cdm_taxonRelationships($taxonRelationships, $focusedTaxon){
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static $NULL_AUTHORTEAM = 'NULL_AUTHORTEAM';
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if (!$taxonRelationships) {
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return null;
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}
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RenderHints::pushToRenderStack('taxon_relationships');
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$footnoteListKey = 'taxon_relationships';
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RenderHints::setFootnoteListKey($footnoteListKey);
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$misapplied = array();
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$joinedAuthorTeams = array();
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$taxon_relationship_types = variable_get(CDM_TAXON_RELATIONSHIP_TYPES, unserialize(CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT));
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// Aggregate misapplied names having the same fullname:
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foreach ($taxonRelationships as $taxonRelation) {
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if (in_array($taxonRelation->type->uuid, $taxon_relationship_types)) {
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if ($taxonRelation->type->uuid == UUID_MISAPPLIED_NAME_FOR || $taxonRelation->type->uuid == UUID_INVALID_DESIGNATION_FOR) {
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RenderHints::pushToRenderStack('misapplied_name_for'); // TODO the render path string should in future come from $taxonRelation->type->...
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$name = $taxonRelation->fromTaxon->name->titleCache;
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$authorteam = $NULL_AUTHORTEAM;
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if(isset($taxonRelation->fromTaxon->sec)) {
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// taxa not always are have a sec reference (e.g. doubtful taxa)
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$authorteam = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $taxonRelation->fromTaxon->sec->uuid);
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$authorteam = $authorteam->titleCache;
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}
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if (!isset($misapplied[$name])) {
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// Render the first name found as representative for all others.
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$misapplied[$name]['out'] = cdm_related_taxon($taxonRelation->fromTaxon, UUID_MISAPPLIED_NAME_FOR);
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}
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else {
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// We need to add the anchors for all of the other misapplied names not
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// being rendered explicitly.
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$misapplied[$name]['out'] = uuid_anchor($taxonRelation->fromTaxon->uuid, $misapplied[$name]['out']);
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}
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// Collect all authors for this fullname.
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if (isset($authorteam) && $authorteam != $NULL_AUTHORTEAM) {
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$misapplied[$name]['authorteam'][$authorteam] = '';
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$joinedAuthorTeams[$authorteam] = 'sensu ' . theme('cdm_reference', array('reference' => $taxonRelation->fromTaxon->sec));
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}
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}
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else {
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RenderHints::pushToRenderStack('other_taxon_relationship');
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// All relationsship types but misapplied_name_for
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// invalid_designation_for.
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$taxon_relationships_lines[] = cdm_taxonRelationship($taxonRelation, TRUE, _is_invers_taxonRelationship($taxonRelation, $focusedTaxon));
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}
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RenderHints::popFromRenderStack();
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}
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}
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// Sort the joinedAuthorTeams and create footnotes and footnotekeys.
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ksort($joinedAuthorTeams);
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$author_team_cnt = 0;
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foreach ($joinedAuthorTeams as $authorteam => $sensuCitation) {
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$footnoteKey = FootnoteManager::addNewFootnote($footnoteListKey, $sensuCitation);
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$sensu = ++$author_team_cnt == 0 ? '' : 'sensu ';
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$joinedAuthorTeams[$authorteam] = sprintf(
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'<span class="sensu">%s%s%s</span>',
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$sensu,
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($authorteam != $NULL_AUTHORTEAM ? $authorteam : ''),
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theme('cdm_footnote_key', array('footnoteKey' => $footnoteKey))
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);
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}
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// ---- Generate output ---- //
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$out = '<div class="taxon-relationships">';
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if (is_array($misapplied) && count($misapplied) > 0) {
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$out .= '<ul class="misapplied">';
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foreach ($misapplied as $misapplied_name) {
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$out .= '<li class="synonym"><span class="misapplied">' . $misapplied_name['out'] . ' </span>';
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if (isset($misapplied_name['authorteam'])) {
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// Fill authors with the renderedFootnoteKey and sorting 'em.
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foreach ($misapplied_name['authorteam'] as $authorteam => &$renderedFootnoteKey) {
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$renderedFootnoteKey = $joinedAuthorTeams[$authorteam];
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}
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ksort($misapplied_name['authorteam']);
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$out .= join('; ', $misapplied_name['authorteam']);
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}
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$out .= '</li>';
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}
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$out .= '</ul>';
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}
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if (isset($taxon_relationships_lines) && is_array($taxon_relationships_lines) && count($taxon_relationships_lines) > 0) {
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$out .= '<ul class="taxonRelationships">';
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foreach ($taxon_relationships_lines as $taxon_relationship_line) {
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$out .= '<li class="synonym">' . $taxon_relationship_line . '</li>';
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}
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$out .= '</ul>';
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}
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$footnotes = theme('cdm_footnotes', array('footnoteListKey' => $footnoteListKey, 'enclosingTag' => 'li'));
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$footnotes .= theme('cdm_annotation_footnotes', array('footnoteListKey' => $footnoteListKey, 'enclosingTag' => 'li'));
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// AK: why splitting footnotes at the sensu string ??? this is weired and hacky
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// TODO remove below dead code
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// $tr_footnotes_exploded = explode('sensu', $tr_footnotes);
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// $tr_footnotes_aux = '';
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// foreach ($tr_footnotes_exploded as $element) {
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// $tr_footnotes_aux .= $element;
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// }
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$out .= '<ul class="footnotes">' . $footnotes . '</ul>';
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$out .= '</div>';
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RenderHints::popFromRenderStack();
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return $out;
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}
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/**
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* Renders a representation of the given taxon relationship.
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*
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* According name relationships are also being rendered.
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*
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* @param unknown_type $taxonRelationship
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* @param boolean $doLinkTaxon
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* whether to create a link to the related taxon
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* @param boolean $inverse
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* whether the $taxonRelationship should be treaded as invers relation
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*
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* @return void|string
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*/
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function cdm_taxonRelationship($taxonRelationship, $doLinkTaxon = FALSE, $inverse = FALSE) {
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// Validate object.
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if (!(isset($taxonRelationship->toTaxon) && isset($taxonRelationship->fromTaxon) && isset($taxonRelationship->type))) {
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return null;
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}
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$taxonRelationType = $taxonRelationship->type;
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if ($inverse) {
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$toTaxon = $taxonRelationship->fromTaxon;
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$relsign = $taxonRelationType->inverseRepresentation_L10n_abbreviatedLabel;
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$reltype_representation = $taxonRelationType->inverseRepresentation_L10n;
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}
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else {
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$toTaxon = $taxonRelationship->toTaxon;
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$relsign = $taxonRelationType->representation_L10n_abbreviatedLabel;
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$reltype_representation = $taxonRelationType->representation_L10n;
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}
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return cdm_related_taxon($toTaxon, NULL, $relsign, $reltype_representation, $taxonRelationship->doubtful, $doLinkTaxon);
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}
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/**
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* Renders a representation of the given taxon relationship.
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*
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* According name relationships are also being rendered.
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*
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* @param $taxon
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* The CDM TaxonBase entity
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* @param $reltype_uuid
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* The UUID of the TaxonRelationshipType
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* @param $relsign
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* Optional. Can be used to override the internal decision strategy on finding a suitable icon for the relationship
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* @param $reltype_representation
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* Optional: Defines the value for the title attribute of the html element enclosing the relsign
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* @param $doubtful
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* TODO
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* @param $doLinkTaxon
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* The taxon will be rendered as clickable link when true.
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*
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* @return string
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* Markup for the taxon relationship.
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*/
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function cdm_related_taxon($taxon, $reltype_uuid = NULL, $relsign = NULL, $reltype_representation = NULL, $doubtful=false, $doLinkTaxon = FALSE) {
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static $relsign_homo = '≡';
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static $relsign_hetero = '=';
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static $relsign_invalid = '–';
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static $nom_status_invalid_type_uuids = array(
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UUID_NOMENCLATURALSTATUS_TYPE_INVALID,
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UUID_NOMENCLATURALSTATUS_TYPE_NUDUM,
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UUID_NOMENCLATURALSTATUS_TYPE_COMBINATIONINVALID,
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UUID_NOMENCLATURALSTATUS_TYPE_PROVISIONAL
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);
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// 'taxonRelationships';
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$footnoteListKey = NULL;
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$skip_tags = array();
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$is_invalid = false;
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if (!$relsign) {
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switch ($reltype_uuid) {
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case UUID_HETEROTYPIC_SYNONYM_OF:
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case UUID_SYNONYM_OF:
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$relsign = $relsign_hetero;
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break;
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case UUID_HOMOTYPIC_SYNONYM_OF:
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$relsign = $relsign_homo;
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break;
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case UUID_MISAPPLIED_NAME_FOR:
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case UUID_INVALID_DESIGNATION_FOR:
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$skip_tags[] = 'authors';
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$is_invalid = true;
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$relsign = $relsign_invalid;
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break;
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default:
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$relsign = $relsign_invalid;
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}
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}
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if($doubtful) {
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$relsign = '?' . $relsign;
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}
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/*
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Names with status invalid or nudum are to be displayed with the
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$relsign_invalid, these names appear at the end of all names in their
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homotypic group (ordered correctly by the java cdm_lib).
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*/
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if (isset($taxon->name->status) && is_array($taxon->name->status)) {
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foreach ($taxon->name->status as $status) {
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if (in_array($status->type->uuid , $nom_status_invalid_type_uuids)) {
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$relsign = $relsign_invalid;
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break;
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}
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}
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}
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// Now rendering starts ..
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RenderHints::pushToRenderStack('related_taxon');
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if (isset($taxon->name->nomenclaturalReference)) {
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$referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));
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}
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$taxonUri = '';
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if ($doLinkTaxon) {
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$taxonUri = url(path_to_taxon($taxon->uuid, "synonymy"));
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}
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// Printing the taxonName and the handling the special case of annotations.
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if (!isset($referenceUri)) {
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$referenceUri = FALSE;
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}
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$out_taxon_part = render_taxon_or_name($taxon, $taxonUri, $referenceUri, TRUE, FALSE, $skip_tags, $is_invalid);
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$taxon_footnotes = theme('cdm_annotations_as_footnotekeys',
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array('cdmBase_list' => array(
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$taxon->name,
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$taxon,
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),
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'footnote_list_key' => $footnoteListKey)
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);
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$homonyms = cdm_name_relationships_of($taxon);
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$out = '<span class="relation_sign" title="' . $reltype_representation . '">' . $relsign . '</span>'
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. $out_taxon_part . $taxon_footnotes . ' ' . $homonyms;
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$out = uuid_anchor($taxon->uuid, $out);
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RenderHints::popFromRenderStack();
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return $out;
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}
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/**
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* Creates markup for a taxon which is the accepted of another one
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*
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* @param $accepted_for_uuid
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* The uuid of the accepted taxon
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*/
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function cdm_accepted_for($accepted_for_uuid) {
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338
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if(!is_uuid($accepted_for_uuid)){
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return '';
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}
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RenderHints::pushToRenderStack('acceptedFor');
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$out = '';
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$synonym = cdm_ws_get(CDM_WS_PORTAL_TAXON, $accepted_for_uuid);
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if ($synonym) {
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$out .= '<span class="acceptedFor">';
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$out .= t('is accepted for ');
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if (isset($synonym->name->nomenclaturalReference)) {
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$referenceUri = url(path_to_reference($synonym->name->nomenclaturalReference->uuid));
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}
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$out .= render_taxon_or_name($synonym->name, NULL, $referenceUri);
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$out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $synonym));
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$out .= '</span>';
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}
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RenderHints::popFromRenderStack();
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return $out;
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}
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360
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361
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/**
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362
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* Compose function for a list of taxa.
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363
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*
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* This function is for example used to display search results or the taxa for a taxon name in the name page.
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365
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*
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366
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* @param $taxon_list array
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* The list of CDM Taxon entities. e.g. The records array as contained in a pager object.
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* @param $freetext_search_results array
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* @param $show_classification boolean
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*
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* @ingroup compose
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*
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*/
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374
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function compose_list_of_taxa($taxon_list, $freetext_search_results = array(), $show_classification = false) {
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375
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$unclassified_snippet = '<span class="unclassified">' . t('unclassified') . '</span>';
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RenderHints::pushToRenderStack('list_of_taxa');
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$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SEARCH_GALLERY_NAME);
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$showMedia_taxa = $gallery_settings['cdm_dataportal_show_taxon_thumbnails'];
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$showMedia_synonyms = $gallery_settings['cdm_dataportal_show_synonym_thumbnails'];
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$searched_in_classification = cdm_dataportal_searched_in_classification();
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$searched_in_classification_uuid = null;
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if(isset($searched_in_classification->uuid)){
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$searched_in_classification_uuid = $searched_in_classification->uuid;
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}
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389
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// .. Well, for sure not as performant as before, but better than nothing.
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$synonym_uuids = array();
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$misappied_uuids = array();
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foreach ($taxon_list as $taxon) {
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if ($taxon->class == "Synonym") {
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if (!array_key_exists($taxon->uuid, $synonym_uuids)) {
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$synonym_uuids[$taxon->uuid] = $taxon->uuid;
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}
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}
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elseif (!_cdm_dataportal_acceptedByCurrentView($taxon)) {
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// Assuming that it is a misappied name, will be further examined below.
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$misappied_uuids[$taxon->uuid] = $taxon->uuid;
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}
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403
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}
|
404
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405
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// Batch service not jet implemented:
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// $table_of_accepted = cdm_ws_property(CDM_WS_PORTAL_TAXON_ACCEPTED,
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407
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// join(',', $synonym_uuids));
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408
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// thus ...
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$table_of_accepted = array();
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410
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411
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foreach ($synonym_uuids as $relatedUuid) {
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412
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$table_of_accepted[$relatedUuid] = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array(
|
413
|
$relatedUuid,
|
414
|
$searched_in_classification_uuid,
|
415
|
));
|
416
|
}
|
417
|
|
418
|
foreach ($misappied_uuids as $relatedUuid) {
|
419
|
$taxonRelations = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS, array(
|
420
|
$relatedUuid,
|
421
|
));
|
422
|
foreach ($taxonRelations as $relation) {
|
423
|
if ($relation->type->uuid == UUID_MISAPPLIED_NAME_FOR && _cdm_dataportal_acceptedByCurrentView($relation->toTaxon)) {
|
424
|
$table_of_accepted[$relatedUuid][] = $relation->toTaxon;
|
425
|
}
|
426
|
}
|
427
|
}
|
428
|
|
429
|
$out = '<ul class="cdm_names" style="background-image: none;">';
|
430
|
$itemCnt = -1;
|
431
|
foreach ($taxon_list as $taxon) {
|
432
|
$itemCnt++;
|
433
|
if (isset($table_of_accepted[$taxon->uuid])) {
|
434
|
// Its a synonym or misapplied name.
|
435
|
$is_synonym = isset($synonym_uuids[$taxon->uuid]); //TODO better use the $taxon->class attribute?
|
436
|
$taxon_type = $is_synonym ? "Synonym" : "misapplied-name";
|
437
|
|
438
|
$acceptedTaxa = $table_of_accepted[$taxon->uuid];
|
439
|
|
440
|
if (count($acceptedTaxa) == 1) {
|
441
|
|
442
|
$acceptedTaxon = $acceptedTaxa[0];
|
443
|
$taxonUri = uri_to_synonym($taxon->uuid, $acceptedTaxon->uuid);
|
444
|
$referenceUri = '';
|
445
|
if (isset($acceptedTaxon->name->nomenclaturalReference)) {
|
446
|
$referenceUri = url(path_to_reference($acceptedTaxon->name->nomenclaturalReference->uuid));
|
447
|
}
|
448
|
$taxon_or_name = $is_synonym ? $taxon->name : $taxon;
|
449
|
// $taxon_or_name this is a trick to suppress the sec reference for sysnonyms
|
450
|
// supplying the name will cause render_taxon_or_name() to not show the sec reference
|
451
|
$out .= '<li class="' . $taxon_type . '">' . render_taxon_or_name($taxon_or_name, $taxonUri, $referenceUri);
|
452
|
if ($show_classification) {
|
453
|
$classifications = get_classifications_for_taxon($taxon);
|
454
|
$classification_titles = array();
|
455
|
foreach ($classifications as $classification) {
|
456
|
if (isset($classification->titleCache)) {
|
457
|
$classification_titles[] = $classification->titleCache;
|
458
|
}
|
459
|
}
|
460
|
if(count($classification_titles) == 0){
|
461
|
$classification_titles[] = $unclassified_snippet;
|
462
|
}
|
463
|
$out .= ' : <span class="classifications">' . implode(', ', $classification_titles) . '</span>';
|
464
|
}
|
465
|
$out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $taxon));
|
466
|
if ($showMedia_synonyms) {
|
467
|
$out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $acceptedTaxon));
|
468
|
}
|
469
|
}
|
470
|
else {
|
471
|
|
472
|
// TODO avoid using Ajax in the cdm_dynabox .... why?
|
473
|
// TODO add media.
|
474
|
$out .= cdm_dynabox(
|
475
|
$taxon->uuid,
|
476
|
render_taxon_or_name($taxon->name, NULL, NULL, FALSE),
|
477
|
cdm_compose_url(CDM_WS_PORTAL_TAXON_ACCEPTED,
|
478
|
array(
|
479
|
$taxon->uuid,
|
480
|
$searched_in_classification_uuid
|
481
|
)
|
482
|
),
|
483
|
'cdm_list_of_taxa',
|
484
|
'show accepted taxa of this ' . $taxon_type,
|
485
|
array('li', 'ul'),
|
486
|
array('class' => array($taxon_type))
|
487
|
);
|
488
|
}
|
489
|
}
|
490
|
else {
|
491
|
// Its a Taxon.
|
492
|
$taxonUri = url(path_to_taxon($taxon->uuid));
|
493
|
$referenceUri = '';
|
494
|
if (isset($taxon->name->nomenclaturalReference)) {
|
495
|
$referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));
|
496
|
}
|
497
|
$out .= '<li class="Taxon">' . render_taxon_or_name($taxon, $taxonUri, $referenceUri);
|
498
|
if ($show_classification) {
|
499
|
$classifications = get_classifications_for_taxon($taxon);
|
500
|
$classification_titles = array();
|
501
|
foreach ($classifications as $classification) {
|
502
|
if (isset($classification->titleCache)) {
|
503
|
$classification_titles[] = $classification->titleCache;
|
504
|
}
|
505
|
}
|
506
|
if(count($classification_titles) == 0){
|
507
|
$classification_titles[] = $unclassified_snippet;
|
508
|
}
|
509
|
$out .= ' : <span class="classifications">' . implode(', ', $classification_titles) . '</span>';
|
510
|
}
|
511
|
$out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $taxon));
|
512
|
|
513
|
if ($showMedia_taxa) {
|
514
|
$out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $taxon));
|
515
|
}
|
516
|
}
|
517
|
|
518
|
/*
|
519
|
* the score field will be empty in case of MultiTermQueries like
|
520
|
* WildcardQueries, since these are constant score by default
|
521
|
* since Lucene 2.9
|
522
|
*/
|
523
|
if(isset($freetext_search_results[$itemCnt]) && $freetext_search_results[$itemCnt]->score && $freetext_search_results[$itemCnt]->maxScore){
|
524
|
$percentage = ( $freetext_search_results[$itemCnt]->score / $freetext_search_results[$itemCnt]->maxScore ) * 100;
|
525
|
$out .= '<div class="score-bar"><div class="score-bar-indicator" style="width:' . $percentage .'% "></div></div>';
|
526
|
$out .= '<div class="score-bar-value">' . number_format($percentage, 2) .'%</div>';
|
527
|
}
|
528
|
|
529
|
// Render highlighted fragments, these are made available by free text
|
530
|
// searches.
|
531
|
if (isset($freetext_search_results[$itemCnt]->fieldHighlightMap)) {
|
532
|
$field_fragments = (array) $freetext_search_results[$itemCnt]->fieldHighlightMap;
|
533
|
if (count($field_fragments) > 0) {
|
534
|
$fragments_out = '';
|
535
|
foreach ($field_fragments as $fieldName => $fragments) {
|
536
|
$fragments_out .= '... <span class="' . $fieldName. '">' . filter_xss(join(" ... ", $fragments), array('b') ) . '</span>';
|
537
|
}
|
538
|
$out .= '<div class="fragment_highlight">' . $fragments_out . ' ...</div>';
|
539
|
}
|
540
|
}
|
541
|
|
542
|
$out .= '</li>';
|
543
|
}
|
544
|
|
545
|
$out .= '</ul>';
|
546
|
RenderHints::popFromRenderStack();
|
547
|
|
548
|
return markup_to_render_array($out); // TODO create render array of all list items in function
|
549
|
}
|
550
|
|
551
|
|
552
|
function compose_taxonomic_children($taxon_uuid){
|
553
|
|
554
|
$render_array = array();
|
555
|
|
556
|
if($taxon_uuid) {
|
557
|
$children = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_OF_TAXON, array(
|
558
|
get_current_classification_uuid(),
|
559
|
$taxon_uuid
|
560
|
));
|
561
|
if($children){
|
562
|
$taxonomic_children = theme('cdm_taxontree', array('tree' => $children));
|
563
|
$render_array = markup_to_render_array($taxonomic_children);
|
564
|
}
|
565
|
}
|
566
|
return $render_array;
|
567
|
}
|
568
|
|