EDIT

files[] = classes/ItemComposeHandler.php

files[] = classes/RegistrationDtoComposeHandler.php

files[] = classes/AgentComposeHandler.php

configure = admin/config/cdm_dataportal/settings

  RenderHints::setAnnotationsAndSourceConfig(handle_annotations_and_sources_config($feature_block_settings));

  $annotations_and_sources = handle_annotations_and_sources(

  );

  $timescope_markup = '';

  // handle the special case were the TextData is used as container for original source with name

  // used in source information without any text stored in it.

  $names_used_in_source_markup = '';

    // remove all <span class="nameUsedInSource">...</span> from all source_references

    // these are expected to be at the end of the strings

    $pattern = '/ <span class="nameUsedInSource">.*$/';

      $source_reference = preg_replace($pattern , '', $source_reference);

    }

  }

  $source_references_markup = '';

  }

  $feature_label = '';

  }

    $render_array['#value'] = $feature_label . $content_markup;

  return $render_array;

}

  foreach ($description_elements as $description_element) {

    RenderHints::setAnnotationsAndSourceConfig(handle_annotations_and_sources_config($feature_block_settings));

    $annotations_and_sources = handle_annotations_and_sources(

    );

    $status = distribution_status_label_and_markup([$description_element->status]);

      . ' " title="' . $status['label']. '">'

      . $description_element->area->representation_L10n

      . $status['markup'];

    }

    $markup_array[] = $out;

  }

      if($distribution_aggregate) {

        RenderHints::setAnnotationsAndSourceConfig(handle_annotations_and_sources_config($feature_block_settings));

        $annotations_and_sources = handle_annotations_and_sources(

        );

        $status = distribution_status_label_and_markup($distribution_aggregate->status, $level_style['status_glue']);

      }

      ;

      if(isset($annotations_and_sources)){

        }

        }

      }

 *

 * @param $cdm_entity

 *   A CDM entity

 * @param $footnote_list_key string

 *    Optional parameter. If this parameter is left empty (null, 0, "") the footnote key will be determined by the nested

 *    method calls by calling RenderHints::getFootnoteListKey().

 *    For original sources the $footnote_list_key will be overwritten

 *    by bibliography_footnote_list_key() when

 *    $is_bibliography_aware is set TRUE.

 *

 * NOTE: Only used in @see handle_annotations_and_sources()

 */

  $cdm_entity,

  $footnote_list_key = NULL,

  $do_link_to_reference = FALSE,

  $do_link_to_name_used_in_source = FALSE,

  }

  // Sort and render footnote keys.

  asort($footnote_keys);

}

/**

 *

 * @param $name_rel

 *   The cdm name relationship

 */

function handle_name_relationship_as_footnote($name_rel)

{

  $footnote_markup = '';

  if (isset($name_rel->ruleConsidered) && $name_rel->ruleConsidered) {

    $footnote_markup = '<span class="rule_considered">' . $name_rel->ruleConsidered . '</span> ';

  }

  }

  if ($footnote_markup) {

    $fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);

  }

}

/**

 * key is returned as markup.

 *

 * @param $nom_status

 */

function handle_nomenclatural_status_as_footnote($nom_status)

{

 *

 * @param $name

 * The name whose nomenclatural reference is to be shown as footnote

 */

function handle_nomenclatural_reference_as_footnote($name)

{

  if (isset($name->nomenclaturalSource->citationMicroReference)) {

    $footnote_markup .= ($footnote_key_markup ? ':' : '') . '<span class="reference_detail">' . $name->nomenclaturalSource->citationMicroReference . '</span>';

  }

  if ($footnote_markup) {

    $fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);

  }

}

/* ============ annotations_and_sources handling =================== */

 *   Optional parameter. If this parameter is left empty (null, 0, "") the

 *   footnote key will be determined by the nested method calls by calling

 *   RenderHints::getFootnoteListKey().

 *   - foot_note_keys: all footnote keys as markup

 *   - source_references: an array of the source references citations

 *   - names used in source: an associative array of the names in source,

 *        the name in source strings are de-duplicated

 *        !!!NOTE!!!!: this field will most probably be removed soon (TODO)

 */

  // some entity types only have single sources:

  $sources = cdm_entity_sources_sorted($entity);

        if ($reference_citation) {

          if (empty($inline_text_prefix)) {

          } else {

          }

        }

        );

        if (!empty($name_in_source_render_array)) {

        }

      }

    } // END of loop over sources

    // annotations footnotes separate from sources

  } // END of references inline

  // footnotes for sources and annotations or put into into bibliography if requested ...

  if ($config['add_footnote_keys']) {

      $footnote_list_key_suggestion,

      $config['link_to_reference'],

      $config['link_to_name_used_in_source'],

      (!empty($config['bibliography_aware']) ? $config['bibliography_aware'] : FALSE)

  }

}

/**

 * @param $name_link

 *    URI to the taxon, @param $reference_link

 *    URI to the reference,

 * @param bool $is_type_designation

 *    To indicate that the supplied taxon name is a name type designation.

 *    (default: false)

 * @see path_to_reference(), must be processed by url() before passing to this method

 */

function render_taxon_or_name($taxon_name_or_taxon_base, $name_link = NULL, $reference_link = NULL,

  $is_doubtful = false;

  $taxon_base = null;

  if($taxon_name_or_taxon_base->class == 'Taxon' || $taxon_name_or_taxon_base->class == 'Synonym'){

    $taxon_base = $taxon_name_or_taxon_base;

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

    // default separator

    $separator = '';

    // Komma nach dem Autornamen ist überall dort falsch, wo ein "in" folgt."

    if (isset($renderTemplate['referencePart']['reference'])) {

      $microreference = NULL;

         if($tt->type == 'nomStatus'&& isset($tt->entityReference)) {

           $nom_status = cdm_ws_get(CDM_WS_NOMENCLATURALSTATUS, array($tt->entityReference->uuid));

           $nom_status_fkey = handle_nomenclatural_status_as_footnote($nom_status);

           $tt_to_markup_options['html'] = true;

         }

        }

      $partHtml .= '<span class="' . $part . '">' . $html . '</span>';

    }

    if ($uri) {

      $out .= $separator . '<a href="' . $uri . '" class="' . $partName . '">' . $partHtml . '</a>';

    }

    }

  }

  $out .= '</span>';

    if($taxon_base){

    }

  }

  return $out;

}

      }

      RenderHints::setAnnotationsAndSourceConfig(annotations_and_sources_config_typedesignations());

      $annotations_and_sources = handle_annotations_and_sources($name_type_designation);

    }

  } // END NameTypeDesignation

        if(!empty($derivedUnitFacadeInstance->preferredStableUri)){

          $out .= ' ' . l($derivedUnitFacadeInstance->preferredStableUri, $derivedUnitFacadeInstance->preferredStableUri, array('absolute' => true));

        }

      }

      $out .= '</'. $element_tag .'>';

    }

      $annotations_and_sources = handle_annotations_and_sources($textual_type_designation);

      $encasement =  $textual_type_designation->verbatim ? '"' : '';

      $out .= '<' . $element_tag . ' class="' . html_class_attribute_ref($textual_type_designation) . '">' . type_designation_status_label_markup(null)

//      }

//      $out .= $citation_markup;

    }

      RenderHints::setAnnotationsAndSourceConfig(annotations_and_sources_config_typedesignations());

      $annotations_and_sources = handle_annotations_and_sources($name_type_entity_ref);

        . $name_type_entity_ref->label

        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')

        . '</div>');

      }

  }

      // annotations and sources for the $derived_unit_facade_dto

      RenderHints::setAnnotationsAndSourceConfig(annotations_and_sources_config_typedesignations());

      $annotations_and_sources = handle_annotations_and_sources($derived_unit_facade_dto);

      // preferredStableUri

      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){

        // citation and detail for the media specimen

        RenderHints::setAnnotationsAndSourceConfig(annotations_and_sources_config_typedesignations());

        $annotations_and_sources = handle_annotations_and_sources($mediaSpecimen);

        }

        }

      }

}

/**

 *

 * @param $current_taxon_uuid

 * @param $show_name_cache_only

 *    The nameCache will be shown instead of the titleCache if this parameter is true.

 * @return null|string

 *    The markup or null

 */

  $relationship_markup = null;

    $relationship_markup = l(

      array('html' => true)

    );

  }

  return $relationship_markup;

}

/**

 * Composes an inline representation of selected name relationships

    usort($name_relations, 'compare_name_relations_by_term_order_index');

    // compose

    foreach ($name_relations as $name_rel) {

      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;

      $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);

      $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);

      $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup . ' ';

      $relationship_markup = $symbol_markup . $relationship_markup;

    // name relationships to be displayed as non nec

    if (count($non_nec_name_rels) > 0) {

      $non_nec_markup = '';

      foreach ($non_nec_name_rels as $name_rel) {

        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;

        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);

        $symbol = $non_nec_markup ? ' nec ' : 'non';

        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';

        $non_nec_markup .= $symbol_markup . $relationship_markup;

    // orthographic variants

    if (count($orthographic_variants) > 0) {

      foreach ($orthographic_variants as $name_rel) {

        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;

        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);

        $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);

        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';

      }

      if (isset($relationship_markup) && $relationship_markup) {

        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,

                          'bibliography_aware' => FALSE

                        ]);

                        $annotations_and_sources = handle_annotations_and_sources($specimen_or_observation);

                        }

                        break;

        }

        $classification = cdm_ws_get(CDM_WS_CLASSIFICATION, array($taxon_node->classificationUUID));

        $status_markup_tokens[$state_label . '-' . $taxon_node->uuid]  = [

          'classification' => ' <span class="' . html_class_attribute_ref($classification) .'">[' . $classification->titleCache . ']</span>'

        ];

      }

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

    }

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

    $out .= '</span>';

  }

  RenderHints::popFromRenderStack();

      'bibliography_aware' => FALSE

    ]);

  $annotations_and_sources = handle_annotations_and_sources(

  );

  $out = '';

  // Title.

  if ($doTitle) {

    $title_string = $media_metadata['title']

    $title_string = trim($title_string);

    if (empty($title_string) && !($doDescription && $media_metadata['description'])) {

      // Use filename as fallback option if no description and no source citations are available.

    $groups = array_merge($groups, cdm_rights_as_dl_groups($media_metadata['rights']));

  }

  }

  // TODO add all other metadata elements generically.

        assertEquals("is validating3 Nodosilinea radiophila Heidari & Hauer in Fottea 18(2): 142. fig. 5C, D. 1 Nov 2018, nom. illeg.4", nameRelationshipElements.get(2).getText());

        assertEquals("non Nodosilinea blockensis, New Species in the solar system5 nec Nodosilinea sensensia, Plantas vasculares de Oz6 nec Nodosilinea sensensia, Species solaris7", nameRelationshipElements.get(3).getText());

        BaseElement orthVarElement = nameRelationshipElements.get(4);

        assertEquals("has orthographic variant", orthVarElement.getElement().findElement(By.className("symbol")).getAttribute("title"));

        List<BaseElement> footnotes = regItem.getRegistrationFootnotes();

        assertEquals(

                "1. Art. 99.9 Turland, N.J., Wiersema, J.H., Barrie, F.R. & al., International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017: 11",

                footnotes .get(0).getText());

        assertEquals(

                "9. Editorial annotation on Nodosilinea sensensi",

                footnotes .get(8).getText());

    }

    @Test

        WebElement accName = p.getAcceptedName();

        assertEquals("Nodosilinea sensensia (Blanco) Heidari & Hauer ex Lem, Nonsens species of the developers Vol1. 2001, comb. nov.1,2 [non Nodosilinea sensensia3 "

        List<BaseElement> footnotes = p.getHomotypicalGroupFootNotes();

        assertEquals(

                "1. Art. 99.9 Turland, N.J., Wiersema, J.H., Barrie, F.R. & al., International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017: 11",

                footnotes .get(0).getText());

        assertEquals(

                "7. Editorial annotation on Nodosilinea sensensi",

                footnotes.get(6).getText());

    }