EDIT

<?php

/**

 * @file

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

 *

 * @copyright

 *   (C) 2007-2016 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>

 */

/**

 * @defgroup compose Compose functions

 * @{

 * Functions which are composing Drupal render arrays

 *

 * The cdm_dataportal module needs to compose rather complex render arrays from

 * the data returned by the CDM REST service. The compose functions are

 * responsible for creating the render arrays.

 *

 * All these functions are also implementations of the compose_hook()

 * which is used in the proxy_content() function.

 * @}

 */

define('TAXON_TYPE_SYNONYM', 'Synonym');

define('TAXON_TYPE_MISAPPLIEDNAME', 'misapplied-name');

/**

 * Returns HTML for misapplied names and invalid designations.

 *

 * Both relation types are currently treated the same!

 *

 * @param object taxonRelationships

 *   A TaxonRelationshipsDTO, see taxon/{uuid}/taxonRelationshipsDTO

 *

 * @param object focusedTaxon

 *  The taxon being in the focus of the application

 *

 * @return string

 *    the rendered html

 */

function cdm_taxonRelationships($taxonRelationshipsDTO, $focusedTaxon){

  if (!$taxonRelationshipsDTO || $taxonRelationshipsDTO->size < 1) {

    return null;

  }

  RenderHints::pushToRenderStack('taxon_relationships');

  $footnote_list_key = 'taxon_relationships';

  RenderHints::setFootnoteListKey($footnote_list_key);

  $misapplied = array();

  $joined_sensu_refs = array();

  $taxon_relationship_types = variable_get(CDM_TAXON_RELATIONSHIP_TYPES, unserialize(CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT));

  // Aggregate misapplied names having the same fullname:

  //  - deduplicate misapplied names, so that the same name it not shown multiple times in case it

  //    the duplicates only have different sensu references/author teams (see #5647)

  //  - show only the author team as short citation for the sec reference

  //  - show the according reference as footnote to this short citation

  //

  // Example:

  // "Xenoxylum foobar" sensu Grumbach¹; sensu Lem²

  //    1. Novel marsian species, Grumbach, 2022

  //    2. Flora solaris, Lem, 2019

  if (isset($taxonRelationshipsDTO->relations[0])) {

    foreach($taxonRelationshipsDTO->relations as $taxon_relation){

      if (in_array($taxon_relation->type->uuid, $taxon_relationship_types)) {

        if ($taxon_relation->type->uuid == UUID_MISAPPLIED_NAME_FOR || $taxon_relation->type->uuid == UUID_INVALID_DESIGNATION_FOR) {

          RenderHints::pushToRenderStack('misapplied_name_for'); // TODO the render path string should in future come from $taxonRelation->type->...

          // using name tags + author as full name key

          $full_name_key = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('name', 'authors')));

          // Render the first name found as representative for all others.

          //###OLD: $misapplied[$name]['out'] = cdm_related_taxon($taxon_relation->fromTaxon, UUID_MISAPPLIED_NAME_FOR);

          $sensu_tagged_text = tagged_text_extract_secref($taxon_relation->taggedText, "secReference", true);

          $relsec_tagged_text = tagged_text_extract_secref($taxon_relation->taggedText, "relSecReference", true);

          if (isset($sensu_tagged_text[1])) {

            array_shift($sensu_tagged_text); // remove first element which contains the "sensu", this will be added later in this code

            $sensu_citation_short_markup = cdm_tagged_text_to_markup($sensu_tagged_text);

            $sensu_citation_short = cdm_tagged_text_to_string($sensu_tagged_text);

            $sensu_uuid = $sensu_tagged_text[0]->entityReference->uuid;

            $misapplied[$full_name_key]['sensu_uuids'][] = $sensu_uuid;

            if (!isset($joined_sensu_refs[$sensu_uuid])) {

              $joined_sensu_refs[$sensu_uuid] = array(

                'short_citation' => $sensu_citation_short,

                'markup' => $sensu_citation_short_markup // to be expanded later as short_citation + footnote key

              );

            }

            if (isset($relsec_tagged_text[1])) {

              array_shift($relsec_tagged_text); // remove first element which contains the "err. sec", this will be added later in this code

              $relsec_citation_short_markup = cdm_tagged_text_to_markup($relsec_tagged_text);

              $relsec_citation_short = cdm_tagged_text_to_string($relsec_tagged_text);

              $relsec_uuid = $relsec_tagged_text[0]->entityReference->uuid;

              $misapplied[$full_name_key]['relsec_uuids'][] = $relsec_uuid;

              if (!isset($joined_sensu_refs[$relsec_uuid])) {

                $joined_sensu_refs[$relsec_uuid] = array(

                  'short_citation' => $relsec_citation_short,

                  'markup' => $relsec_citation_short_markup // to be expanded later as short_citation + footnote key

                );

              }

            }

            if (!isset($misapplied[$full_name_key]['out'])) {

              $misapplied[$full_name_key]['out'] = cdm_tagged_text_to_markup($taxon_relation->taggedText);

            } else {

              // We need to add the anchors for all of the other misapplied names not

              // being rendered explicitly.

              $misapplied[$full_name_key]['out'] = uuid_anchor($taxon_relation->taxonUuid, $misapplied[$full_name_key]['out']);

            }

          } else {

            RenderHints::pushToRenderStack('other_taxon_relationship');

            // All relationship types except misapplied_name_for and invalid_designation_for.

            $taxon_relationships_lines[] = cdm_taxonRelationship($taxon_relation, TRUE, _is_invers_taxonRelationship($taxon_relation, $focusedTaxon));

          }

          RenderHints::popFromRenderStack();

        }

      }

    } // END loop over $taxonRelationshipsDTO->relations

  }

  // Sort the $joined_sensu_refs and create footnotes and footnote keys.

  uasort($joined_sensu_refs, function($a, $b) {

    if ($a['short_citation'] == $b['short_citation']) {

      return 0;

    }

    return ($a['short_citation'] < $b['short_citation']) ? -1 : 1;

  });

  foreach ($joined_sensu_refs as $sensu_uuid => $sensu_strings) {

    $footnote_key = '';

    if(!empty($sensu_strings)) {

      $sensu_reference = cdm_ws_get(CDM_WS_REFERENCE, $sensu_uuid);

      if(!$sensu_reference){

        drupal_set_message("Problem fetching sensu reference with uuid " . $sensu_uuid, 'error');

      }

      $footnote_key = FootnoteManager::addNewFootnote($footnote_list_key, $sensu_reference->titleCache);

      $footnote_key = theme('cdm_footnote_key', array('footnoteKey' => $footnote_key));

    }

    $joined_sensu_refs[$sensu_uuid]['markup'] = '<span class="sensu">' . $sensu_strings['markup'] . $footnote_key . '</span>';

  }

  // ---- Generate output ---- //

  $out = '<div class="taxon-relationships">';

  if (is_array($misapplied) && count($misapplied) > 0) {

    ksort($misapplied); // order the misapplied by scientific name

    $out .= '<ul class="misapplied">';

    foreach ($misapplied as $misapplied_name) {

      $misapplied_name_markup = $misapplied_name['out'];

      if (isset($misapplied_name['sensu_uuids'])) {

        $sensu_refs_with_fkey = array();

        foreach ($misapplied_name['sensu_uuids'] as $sensu_uuid) {

          $sensu_refs_with_fkey[$joined_sensu_refs[$sensu_uuid]['short_citation']] = $joined_sensu_refs[$sensu_uuid]['markup'];

        }

        ksort($sensu_refs_with_fkey);

        $sensu_refs_with_fkey_markup = join('; ', $sensu_refs_with_fkey);

        $misapplied_name_markup = str_replace('{PLACEHOLDER_secReference}', ' sensu ' . $sensu_refs_with_fkey_markup, $misapplied_name_markup);

      }

      if (isset($misapplied_name['relsec_uuids'])) {

        $relsec_refs_with_fkey = array();

        foreach ($misapplied_name['relsec_uuids'] as $relsec_uuid) {

          $relsec_refs_with_fkey[$joined_sensu_refs[$relsec_uuid]['short_citation']] = $joined_sensu_refs[$relsec_uuid]['markup'];

        }

        ksort($relsec_refs_with_fkey);

        $relsec_refs_with_fkey_markup = join('; ', $relsec_refs_with_fkey);

        $misapplied_name_markup = str_replace('{PLACEHOLDER_relSecReference}', ', err. sec. ' . $relsec_refs_with_fkey_markup, $misapplied_name_markup);

      }

      $out .= '<li class="synonym"><span class="misapplied">' . $misapplied_name_markup . ' </span>';

      $out .= '</li>';

    }

    $out .= '</ul>';

  }

  if (isset($taxon_relationships_lines) && is_array($taxon_relationships_lines) && count($taxon_relationships_lines) > 0) {

    $out .= '<ul class="taxonRelationships">';

    foreach ($taxon_relationships_lines as $taxon_relationship_line) {

      $out .= '<li class="synonym">' . $taxon_relationship_line . '</li>';

    }

    $out .= '</ul>';

  }

  $footnotes = theme('cdm_footnotes', array('footnoteListKey' => $footnote_list_key, 'enclosingTag' => 'li'));

  $footnotes .= theme('cdm_annotation_footnotes', array('footnoteListKey' => $footnote_list_key, 'enclosingTag' => 'li'));

  $out .= '<ul class="footnotes">' . $footnotes . '</ul>';

  $out .= '</div>';

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * Renders a representation of the given taxon relationship.

 *

 * According name relationships are also being rendered.

 *

 * @param $taxonRelationship

 * @param boolean $doLinkTaxon

 *     whether to create a link to the related taxon

 * @param boolean $inverse

 *     whether the $taxonRelationship should be treaded as invers relation

 *

 * @return string

 *

 */

function cdm_taxonRelationship($taxonRelationship, $doLinkTaxon = FALSE, $inverse = FALSE) {

  // Validate object.

  if (!(isset($taxonRelationship->toTaxon) && isset($taxonRelationship->fromTaxon) && isset($taxonRelationship->type))) {

    return null;

  }

  $taxonRelationType = $taxonRelationship->type;

  if ($inverse) {

    $toTaxon = $taxonRelationship->fromTaxon;

    $relsign = $taxonRelationType->inverseSymbol;

    $reltype_representation = $taxonRelationType->inverseRepresentation_L10n;

  }

  else {

    $toTaxon = $taxonRelationship->toTaxon;

    $relsign = $taxonRelationType->symbol;

    $reltype_representation = $taxonRelationType->representation_L10n;

  }

  return cdm_related_taxon($toTaxon, NULL, $relsign, $reltype_representation, $taxonRelationship->doubtful, $doLinkTaxon);

}

/**

 * Renders a representation of the given taxon relationship.

 *

 * According name relationships are also being rendered.

 *

 * @param $taxon

 *  The CDM TaxonBase entity

 * @param $reltype_uuid

 *  The UUID of the TaxonRelationshipType

 * @param $relsign

 *  Optional. Can be  used to override the internal decision strategy on finding a suitable icon for the relationship

 * @param $reltype_representation

 *   Optional: Defines the value for the title attribute of the html element enclosing the relsign

 * @param $doubtful

 *   TODO

 * @param $doLinkTaxon

 *   The taxon will be rendered as clickable link when true.

 *

 * @return string

 *   Markup for the taxon relationship.

 *

 * @throws Exception

 */

function cdm_related_taxon($taxon, $reltype_uuid = NULL, $relsign = NULL, $reltype_representation = NULL, $doubtful=false, $doLinkTaxon = FALSE) {

  static $relsign_homo = '≡';

  static $relsign_hetero = '=';

  static $relsign_invalid = '–';

  static $nom_status_invalid_type_uuids =  array(

    UUID_NOMENCLATURALSTATUS_TYPE_INVALID,

    UUID_NOMENCLATURALSTATUS_TYPE_NUDUM,

    UUID_NOMENCLATURALSTATUS_TYPE_COMBINATIONINVALID,

    UUID_NOMENCLATURALSTATUS_TYPE_PROVISIONAL

  );

  // 'taxonRelationships';

  $footnoteListKey = NULL;

  $skip_tags = array();

  $is_invalid = false;

  if (!$relsign) {

    switch ($reltype_uuid) {

      case UUID_HETEROTYPIC_SYNONYM_OF:

      case UUID_SYNONYM_OF:

        $relsign = $relsign_hetero;

        break;

      case UUID_HOMOTYPIC_SYNONYM_OF:

        $relsign = $relsign_homo;

        break;

      case UUID_MISAPPLIED_NAME_FOR:

      case UUID_INVALID_DESIGNATION_FOR:

        $skip_tags[] = 'authors';

        $is_invalid = true;

        $relsign = $relsign_invalid;

        break;

      default:

        $relsign = $relsign_invalid;

    }

  }

  if($doubtful) {

    $relsign = '?' . $relsign;

  }

  /*

  Names with status invalid or nudum are to be displayed with the

  $relsign_invalid, these names appear at the end of all names in their

  homotypic group (ordered correctly by the java cdm_lib).

  */

  if (isset($taxon->name->status) && is_array($taxon->name->status)) {

    foreach ($taxon->name->status as $status) {

      if (in_array($status->type->uuid , $nom_status_invalid_type_uuids)) {

        $relsign = $relsign_invalid;

        break;

      }

    }

  }

  // Now rendering starts ..

  RenderHints::pushToRenderStack('related_taxon');

  if (isset($taxon->name->nomenclaturalReference)) {

    $referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));

  }

  $taxonUri = '';

  if ($doLinkTaxon) {

    $taxonUri = url(path_to_taxon($taxon->uuid, "synonymy"));

  }

  // Printing the taxonName and the handling the special case of annotations.

  if (!isset($referenceUri)) {

    $referenceUri = FALSE;

  }

  $out_taxon_part = render_taxon_or_name($taxon, $taxonUri, $referenceUri, TRUE, FALSE, $skip_tags, $is_invalid);

  $taxon_footnotes = theme('cdm_annotations_as_footnotekeys',

    array('cdmBase_list' => array(

      $taxon->name,

      $taxon,

    ),

      'footnote_list_key' => $footnoteListKey)

  );

  $homonyms = cdm_name_relationships_of($taxon);

  $out = '<span class="relation_sign" title="' . $reltype_representation . '">' . $relsign . '</span>'

    . $out_taxon_part . $taxon_footnotes . ' '  . $homonyms;

  $out = uuid_anchor($taxon->uuid, $out);

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * Creates markup for a taxon which is the accepted of another one

 *

 * @param $accepted_for_uuid

 *   The uuid of the accepted taxon

 */

function cdm_accepted_for($accepted_for_uuid) {

  if(!is_uuid($accepted_for_uuid)){

    return '';

  }

  RenderHints::pushToRenderStack('acceptedFor');

  $out = '';

  $synonym = cdm_ws_get(CDM_WS_PORTAL_TAXON, $accepted_for_uuid);

  if ($synonym) {

    $out .= '<span class="acceptedFor">';

    $out .= t('is accepted for ');

    if (isset($synonym->name->nomenclaturalReference)) {

      $referenceUri = url(path_to_reference($synonym->name->nomenclaturalReference->uuid));

    }

    $out .= render_taxon_or_name($synonym->name, NULL, $referenceUri);

    $out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $synonym));

    $out .= '</span>';

  }

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * Compose function for a list of taxa.

 *

 * This function is for used to:

 *

 * 1. Display search results

 * 2. List the taxa for a taxon name in the name page.

 *

 * @param $taxon_list array

 *   The list of CDM Taxon entities. e.g. The records array as contained in a pager object.

 * @param $freetext_search_results array

 * @param $show_classification boolean

 *

 * @ingroup compose

 *

 */

function compose_list_of_taxa($taxon_list, $freetext_search_results = array(), $show_classification = false) {

  $unclassified_snippet = '<span class="unclassified">' . t('unclassified') . '</span>';

  RenderHints::pushToRenderStack('list_of_taxa');

  $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SEARCH_GALLERY_NAME);

  $showMedia_taxa = $gallery_settings['cdm_dataportal_show_taxon_thumbnails'];

  $showMedia_synonyms = $gallery_settings['cdm_dataportal_show_synonym_thumbnails'];

  $searched_in_classification = cdm_dataportal_searched_in_classification();

  $searched_in_classification_uuid = null;

  if(isset($searched_in_classification->uuid)){

    $searched_in_classification_uuid = $searched_in_classification->uuid;

  }

  // .. Well, for sure not as performant as before, but better than nothing.

  $synonym_uuids = array();

  $misappied_uuids = array();

  foreach ($taxon_list as $taxon) {

    if ($taxon->class == "Synonym") {

      if (!array_key_exists($taxon->uuid, $synonym_uuids)) {

        $synonym_uuids[$taxon->uuid] = $taxon->uuid;

      }

    }

    elseif (!_cdm_dataportal_acceptedByCurrentView($taxon)) {

      // Assuming that it is a misappied name, will be further examined below.

      $misappied_uuids[$taxon->uuid] = $taxon->uuid;

    }

  }

  // Batch service not jet implemented:

  // $table_of_accepted = cdm_ws_property(CDM_WS_PORTAL_TAXON_ACCEPTED,

  // join(',', $synonym_uuids));

  // thus ...

  $table_of_accepted = array();

  foreach ($synonym_uuids as $relatedUuid) {

    $classification_filter = '';

    if($searched_in_classification_uuid){

      $classification_filter = 'classificationFilter=' . $searched_in_classification_uuid;

    }

    $table_of_accepted[$relatedUuid] = cdm_ws_get(

      CDM_WS_PORTAL_TAXON_ACCEPTED,

      array($relatedUuid),

      $classification_filter

    );

  }

  foreach ($misappied_uuids as $relatedUuid) {

    $taxonRelations = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS, array(

      $relatedUuid,

    ));

    foreach ($taxonRelations as $relation) {

      if ($relation->type->uuid == UUID_MISAPPLIED_NAME_FOR && _cdm_dataportal_acceptedByCurrentView($relation->toTaxon)) {

        $table_of_accepted[$relatedUuid][] = $relation->toTaxon;

      }

    }

  }

  $out = '<div class="cdm-item-list" style="background-image: none;">';

  $itemCnt = -1;

  foreach ($taxon_list as $taxon) {

    $itemCnt++;

    if (isset($table_of_accepted[$taxon->uuid])) {

      // Its a synonym or misapplied name.

      $is_synonym = isset($synonym_uuids[$taxon->uuid]); //TODO better use the $taxon->class attribute?

      $taxon_type = $is_synonym ? TAXON_TYPE_SYNONYM :TAXON_TYPE_MISAPPLIEDNAME;

      $acceptedTaxa = $table_of_accepted[$taxon->uuid];

      if (!is_array($acceptedTaxa)) {

        $acceptedTaxa = array($acceptedTaxa);

      }

      foreach ($acceptedTaxa as $acceptedTaxon) {

        if (is_object($acceptedTaxon)) {

          $taxonUri = uri_to_synonym($taxon->uuid, $acceptedTaxon->uuid);

          $referenceUri = '';

          if (isset($acceptedTaxon->name->nomenclaturalReference)) {

            $referenceUri = url(path_to_reference($acceptedTaxon->name->nomenclaturalReference->uuid));

          }

          $taxon_or_name = $is_synonym ? $taxon->name : $taxon;

          // $taxon_or_name this is a trick to suppress the sec reference for synonyms

          // supplying the name will cause render_taxon_or_name() to not show the sec reference

          $out .= "<div class=\"item " . $taxon_type . "\">" . render_taxon_or_name($taxon_or_name, $taxonUri, $referenceUri);

          if($taxon_type == TAXON_TYPE_MISAPPLIEDNAME && is_object($taxon->sec)){

            if(isset($taxon->sec->authorship)){

              $authorship = $taxon->sec->authorship->titleCache;

            } else {

              $authorship = $taxon->sec->titleCache;

            }

            $out .=  ' sensu ' . $authorship;

          }

          if ($show_classification) {

            $classifications = get_classifications_for_taxon($taxon);

            $classification_titles = array();

            foreach ($classifications as $classification) {

              if (isset($classification->titleCache)) {

                $classification_titles[] = $classification->titleCache;

              }

            }

            if (count($classification_titles) == 0) {

              $classification_titles[] = $unclassified_snippet;

            }

            $out .= '<span class="classifications"><span class="separator"> : </span>' . implode(', ', $classification_titles) . '</span>';

          }

          $out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $taxon));

          if ($showMedia_synonyms) {

            $out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $acceptedTaxon));

          }

        }

      }

    }

    else {

      // Its a Taxon.

      $taxonUri = url(path_to_taxon($taxon->uuid));

      $referenceUri = '';

      if (isset($taxon->name->nomenclaturalReference)) {

        $referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));

      }

      $out .= '<div class="item Taxon">' . render_taxon_or_name($taxon, $taxonUri, $referenceUri);

      if ($show_classification) {

        $classifications = get_classifications_for_taxon($taxon);

        $classification_titles = array();

        foreach ($classifications as $classification) {

          if (isset($classification->titleCache)) {

            $classification_titles[] = $classification->titleCache;

          }

        }

        if(count($classification_titles) == 0){

          $classification_titles[] = $unclassified_snippet;

        }

        $out .= '<span class="classifications"><span class="separator"> : </span>' . implode(', ', $classification_titles) . '</span>';

      }

      $out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $taxon));

      if ($showMedia_taxa) {

        $out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $taxon));

      }

    }

    /*

     * the score field will be empty in case of MultiTermQueries like

     * WildcardQueries, since these are  constant score by default

     * since Lucene 2.9

     */

    if(isset($freetext_search_results[$itemCnt]) && $freetext_search_results[$itemCnt]->score && $freetext_search_results[$itemCnt]->maxScore){

      $percentage =  ( $freetext_search_results[$itemCnt]->score / $freetext_search_results[$itemCnt]->maxScore ) * 100;

      $out .= '<div class="score-bar"><div class="score-bar-indicator" style="width:' . $percentage .'% "></div></div>';

      $out .= '<div class="score-bar-value">' . number_format($percentage, 2) .'%</div>';

    }

    // Render highlighted fragments, these are made available by free text

    // searches.

    if (isset($freetext_search_results[$itemCnt]->fieldHighlightMap)) {

      $field_fragments = (array) $freetext_search_results[$itemCnt]->fieldHighlightMap;

      if (count($field_fragments) > 0) {

        $fragments_out = '';

        foreach ($field_fragments as $fieldName => $fragments) {

          $fragments_out .= '... <span class="' . $fieldName. '">' . filter_xss(join(" ... ", $fragments), array('b') ) . '</span>';

        }

        $out .= '<div class="fragment_highlight">' . $fragments_out . ' ...</div>';

      }

    }

    $out .= '</div>';

  }

  $out .= '</div>';

  RenderHints::popFromRenderStack();

  return markup_to_render_array($out); // TODO create render array of all list items in function

}

/**

 * Compose function for the taxonomic children

 *

 * @param $taxon_uuid

 *    The uuuid of the taxon to compose the list of taxonomic children for

 * @return

 *   A drupal render array.

 *

 * @ingroup compose

 */

function compose_taxonomic_children($taxon_uuid){

  $render_array = array();

  if($taxon_uuid) {

    $children = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_OF_TAXON, array(

      get_current_classification_uuid(),

      $taxon_uuid

      ));

    if($children){

      $taxonomic_children = theme('cdm_taxontree', array('tree' => $children));

      $render_array = markup_to_render_array($taxonomic_children);

    }

  }

  return $render_array;

}