EDIT

 *   the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.

 * @return array

 *   the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.

 *    the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.

/**

 * Returns the localized abbreviated label of the relationship term.

 *

 * In case the abbreviated label is not set the normal representation is returned.

 *

 * @param $term

 * @param bool $is_inverse_relation

 * @return string

 *   The abbreviated label

 */

function cdm_relationship_type_term_abbreviated_label($term, $is_inverse_relation = false){

  if($is_inverse_relation) {

    if (isset($term->inverseRepresentation_L10n_abbreviatedLabel) && $term->inverseRepresentation_L10n_abbreviatedLabel) {

      $abbr_label = $term->inverseResentation_L10n_abbreviatedLabel;

    } else {

      $abbr_label = $term->inverseRepresentation_L10n;

    }

  } else {

    if (isset($term->representation_L10n_abbreviatedLabel) && $term->representation_L10n_abbreviatedLabel) {

      $abbr_label = $term->representation_L10n_abbreviatedLabel;

    } else {

      $abbr_label = $term->representation_L10n;

    }

  }

  return $abbr_label;

}

/**

 * Returns the symbol of the relationship term.

 *

 * In case the symbol is not set the function falls back to use the abbreviated label or

 * the normal representation..

 *

 * @param $term

 * @param bool $is_inverse_relation

 * @return string

 *   The abbreviated label

 */

function cdm_relationship_type_term_symbol($term, $is_inverse_relation = false){

  if($is_inverse_relation) {

    if (isset($term->inverseSymbol) && $term->inverseSymbol) {

      $symbol = $term->inverseSymbol;

    } else if (isset($term->inverseRepresentation_L10n_abbreviatedLabel) && $term->inverseRepresentation_L10n_abbreviatedLabel) {

      $symbol = $term->inverseResentation_L10n_abbreviatedLabel;

    } else {

      $symbol = $term->inverseRepresentation_L10n;

    }

  } else {

    if (isset($term->symbol) && $term->symbol) {

      $symbol = $term->symbol;

    } else if (isset($term->representation_L10n_abbreviatedLabel) && $term->representation_L10n_abbreviatedLabel) {

      $symbol = $term->representation_L10n_abbreviatedLabel;

    } else {

      $symbol = $term->representation_L10n;

    }

  }

  return $symbol;

}

/* the relationships_list can replace the unordered list styles */

.relationships_list {

    margin-top: 1em;

    margin-bottom: 1em;

}

.relationships_list .item {

    padding-left: 26px ;

    text-indent: -26px ;

}

    $render_array['name_relations'] = compose_name_relationships_list($name_relations, $registration_dto->nameRef->uuid, null, false);

 * @param $name_rel

 * @param $current_name_uuid

 * @param $current_taxon_uuid

 * @param $suppress_if_current_name_is_source // FIXME UNUSED !!!!

 * @param $show_name_cache_only

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

 * @return null|string

 */

function name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source, $show_name_cache_only = false){

  $relationship_markup = null;

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

  if($current_name_is_toName){

    $name = $name_rel->fromName;

  } else {

    $name = $name_rel->toName;

  }

  $highlited_synonym_uuid = isset ($name->taxonBases[0]->uuid) ? $name->taxonBases[0]->uuid : '';

  if(!$show_name_cache_only){

    $relationship_markup = render_taxon_or_name($name,

      url(path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid))

    );

  } else {

    $relationship_markup = l(

      '<span class="' . html_class_attribute_ref($name) . '"">' . $name->nameCache . '</span>',

      path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid),

      array('html' => true)

    );

  }

  return $relationship_markup;

}

/**

 * Renders an inline representation of selected name relationships

 * Only the following types are displayed: LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR, ORTHOGRAPHIC_VARIANT

 *

 * LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR are displayed as

 * non {titleCache} nec {titleCache} nec {titleCache} whereas the related names

 * are ordered alphabetically.

 *

 * ORTHOGRAPHIC_VARIANT is displayed as 'ort. var. {nameCache}'

 *   - https://dev.e-taxonomy.eu/redmine/issues/2001 "[Cichorieae Portal] Name Relationship -> blocking name are not shown"

  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_INLINE_TYPES, unserialize(CDM_NAME_RELATIONSHIP_INLINE_TYPES_DEFAULT));

      $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source);

/**

 * Composes an list representation of the name relationships.

 *

 * The output of this function will be usually appended to taxon name representations.

 *

 * Related issues:

 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"

 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"

 *   - https://dev.e-taxonomy.eu/redmine/issues/5857

 *

 * @param $name_relations

 *    The list of CDM NameRelationsips

 * @param $current_name_uuid

 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when

 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.

 * @param $suppress_if_current_name_is_source

 *    The display of the relation will be

 *    suppressed is the current name is on the source of the relation edge.

 *    That is if it is on the from side of the relation. Except for 'blocking name for' which is

 *    an inverse relation. For this relation type the toName is taken in to account.

 * @param $current_taxon_uuid

 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()

 * @return array

 *    A drupal render array

 *

 * @ingroup Compose

 */

function compose_name_relationships_list($name_relations, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source = true) {

  $non_nec_name_reltype_uuids = array(UUID_NAMERELATIONSHIPTYPE_LATER_HOMONYM,

    UUID_NAMERELATIONSHIPTYPE_TREATED_AS_LATER_HOMONYM,

    UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR);

  // $ordered_name_relation_type_uuids = array_keys(cdm_terms_by_type_as_option('NameRelationshipType', CDM_ORDER_BY_ORDER_INDEX_ASC));

  RenderHints::pushToRenderStack('name_relationships');

  RenderHints::setFootnoteListKey('name_relationships');

  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT

  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_LIST_TYPES, unserialize(CDM_NAME_RELATIONSHIP_LIST_TYPES_DEFAULT));

  $render_array = array(

    'list' => array(

      '#prefix' => '<div class="relationships_list name_relationships">',

      '#suffix' => '</div>',

      'items' => array()

    ),

    'footnotes' => array()

  );

  if($name_relations) {

    // remove all relations which are not selected in the settings and

    // sepearate all LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR relations and ORTHOGRAPHIC_VARIANTs

    // for special handling

    $filtered_name_rels = array();

    $non_nec_name_rels = array();

    $orthographic_variants = array();

    foreach($name_relations as $name_rel) {

      if (isset($selected_name_rel_uuids[$name_rel->type->uuid]) && $selected_name_rel_uuids[$name_rel->type->uuid]) {

        if(array_search($name_rel->type->uuid, $non_nec_name_reltype_uuids) !== false){

          $non_nec_name_rels[] = $name_rel;

        } else if(UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT == $name_rel->type->uuid) {

          $orthographic_variants[] = $name_rel;

        } else {

          $filtered_name_rels[] = $name_rel;

        }

      }

    }

    $name_relations = $filtered_name_rels;

    usort($name_relations, 'compare_name_relations_by_term_order_index');

    foreach($name_relations as $name_rel) {

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

      $footnote_key_markup = name_relationship_footnote_markup($name_rel);

      $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source);

      $is_inverse_relation = $current_name_is_toName;

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

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

      $relationship_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span> ' . $relationship_markup . $footnote_key_markup;

      if($relationship_markup){

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

          null,

          '<div class="item">',

          '</div>');

      }

    }

    // 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){

        $footnote_key_markup = name_relationship_footnote_markup($name_rel);

        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source);

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

        $non_nec_markup .= '<span class="symbol" title="' . $label . '">' . $symbol . '</span> ' . $relationship_markup . $footnote_key_markup;

      }

       if($non_nec_markup){

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

           null,

           '<div class="item">',

           '</div>');

       }

    }

    // orthographic variants

    if(count($orthographic_variants) > 0){

      foreach($orthographic_variants as $name_rel){

        $footnote_key_markup = name_relationship_footnote_markup($name_rel);

        $footnote_key_markup .= ($footnote_key_markup ? ', ' : '') . nomenclatural_reference_footnote_markup($name_rel->toName);

        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source, TRUE);

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

        $relationship_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span> ' . $relationship_markup . $footnote_key_markup;

      }

      if($relationship_markup){

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

          null,

          '<div class="item">',

          '</div>');

      }

    }

  }

  RenderHints::popFromRenderStack();

  $render_array['footnotes'] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey())));

  RenderHints::clearFootnoteListKey();

  return $render_array;

}

/**

 * @param $name_rel

 * @return string

 */

function name_relationship_footnote_markup($name_rel)

{

  $footnote_markup = '';

  $footnote_key_markup = '';

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

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

  }

  if (isset($name_rel->citation)) {

    $footnote_markup .= '<span class="reference">' . $name_rel->citation->abbrevTitleCache . '</span>';

  }

  if (isset($name_rel->citationMicroReference)) {

    $footnote_markup .= (isset($name_rel->citation) ? ':' : '') . '<span class="reference_detail">' . $name_rel->citationMicroReference . '</span>';

  }

  if ($footnote_markup) {

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

    $footnote_key_markup = theme('cdm_footnote_key', array(

      'footnoteKey' => $fnkey,

      'separator' => ',',

      'highlightable' => TRUE,

      'separator_off' => TRUE,

    ));

  }

  return $footnote_key_markup;

}

/**

 * @param $name

 * @return string

 */

function nomenclatural_reference_footnote_markup($name)

{

  $footnote_markup = '';

  $footnote_key_markup = '';

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

    $footnote_markup .= '<span class="reference">' . $name->nomenclaturalReference->titleCache . '</span>';

  }

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

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

  }

  if ($footnote_markup) {

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

    $footnote_key_markup = theme('cdm_footnote_key', array(

      'footnoteKey' => $fnkey,

      'separator' => ',',

      'highlightable' => TRUE,

      'separator_off' => TRUE,

    ));

  }

  return $footnote_key_markup;

}

function compare_name_relations_by_term_order_index($name_rel1, $name_rel2){

  return compare_terms_by_order_index($name_rel1->type, $name_rel2->type);

}

define('CDM_NAME_RELATIONSHIP_INLINE_TYPES', 'cdm_name_relationship_types');

define('CDM_NAME_RELATIONSHIP_INLINE_TYPES_DEFAULT', serialize(

define('CDM_NAME_RELATIONSHIP_LIST_TYPES', 'cdm_name_relationship_list_types');

define('CDM_NAME_RELATIONSHIP_LIST_TYPES_DEFAULT', serialize(

    array(

      UUID_NAMERELATIONSHIPTYPE_LATER_HOMONYM => UUID_NAMERELATIONSHIPTYPE_LATER_HOMONYM,

      UUID_NAMERELATIONSHIPTYPE_TREATED_AS_LATER_HOMONYM => UUID_NAMERELATIONSHIPTYPE_TREATED_AS_LATER_HOMONYM,

      UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR => UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR,

      UUID_NAMERELATIONSHIPTYPE_BASIONYM => UUID_NAMERELATIONSHIPTYPE_BASIONYM,

      UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT => UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT,

      UUID_NAMERELATIONSHIPTYPE_VALIDATED_BY_NAME => UUID_NAMERELATIONSHIPTYPE_VALIDATED_BY_NAME,

      UUID_NAMERELATIONSHIPTYPE_LATER_VALIDATED_BY_NAME => UUID_NAMERELATIONSHIPTYPE_LATER_VALIDATED_BY_NAME,

      UUID_NAMERELATIONSHIPTYPE_REPLACED_SYNONYM => UUID_NAMERELATIONSHIPTYPE_REPLACED_SYNONYM

    )

  )

);

  $form['taxon_synonymy']['name_relations'][CDM_NAME_RELATIONSHIP_INLINE_TYPES] = array(

    '#default_value' => variable_get(CDM_NAME_RELATIONSHIP_INLINE_TYPES, unserialize(CDM_NAME_RELATIONSHIP_INLINE_TYPES_DEFAULT)),

    $form['blast_search_settings'][CDM_SEARCH_BLAST_ENABLED] = array(

        '#default_value' => variable_get(CDM_SEARCH_BLAST_ENABLED, 0), // '05b0dd06-30f8-477d-bf4c-30d9def56320' =>  Caucasia (Ab + Ar + Gg + Rf(CS)) (Cc)

    $form['blast_search_settings'][CDM_SEARCH_BLAST_SERVICE_URI] = array(

        '#default_value' => variable_get(CDM_SEARCH_BLAST_SERVICE_URI, 'http://127.0.0.1:9001/api/sequence'), // '05b0dd06-30f8-477d-bf4c-30d9def56320' =>  Caucasia (Ab + Ar + Gg + Rf(CS)) (Cc)

    protected List<BaseElement> nameRelationsipsElements;

    protected List<BaseElement> nameRelationsipFootnotes;

                    // typifiedNameElement must exist when nameElement is not present, so we throw the  Exception in this case:

            try{

                List<WebElement> std = containerElement.findElements(By.cssSelector(".name_relationships .item"));

                nameRelationsipsElements = new ArrayList<BaseElement>(std.size());

                for(WebElement we : std){

                    nameRelationsipsElements.add(new BaseElement(we));

                }

            } catch (Exception e) { /* IGNORE */}

            try{

                List<WebElement> std = containerElement.findElements(By.cssSelector(".footnotes-name_relationships .footnote"));

                nameRelationsipFootnotes = new ArrayList<BaseElement>(std.size());

                for(WebElement we : std){

                    nameRelationsipFootnotes.add(new BaseElement(we));

                }

            } catch (Exception e) { /* IGNORE */}

    public List<BaseElement> getNameRelationsipsElements() {

        return nameRelationsipsElements;

    }

    public List<BaseElement> getNameRelationsipFootnotes() {

        return nameRelationsipFootnotes;

    }

/**

* Copyright (C) 2019 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.dataportal.selenium.tests.reference;

import java.io.UnsupportedEncodingException;

import java.net.MalformedURLException;

import java.util.List;

import org.junit.Before;

import org.junit.Test;

import eu.etaxonomy.dataportal.DataPortalSite;

import eu.etaxonomy.dataportal.elements.BaseElement;

import eu.etaxonomy.dataportal.elements.RegistrationItemFull;

import eu.etaxonomy.dataportal.junit.CdmDataPortalTestBase;

import eu.etaxonomy.dataportal.junit.DataPortalContextSuite.DataPortalContexts;

import eu.etaxonomy.dataportal.pages.RegistrationPage;

/**

 * @author a.kohlbecker

 * @since Feb 5, 2019

 *

 */

@DataPortalContexts( { DataPortalSite.reference })

public class NameRelationshipsTest extends CdmDataPortalTestBase {

    private static final String reg_nodosilinea_sensensia_id = "http://testbank.org/100009";

    String titleSuffix = " | Integration test reference";

    @Before

    public void setUp() throws Exception {

        driver.get(getContext().getBaseUri().toString());

    }

    @Test

    public void testNodosilinea_sensensia_RegPage() throws MalformedURLException, UnsupportedEncodingException{

        RegistrationPage p = new RegistrationPage(driver, getContext(), reg_nodosilinea_sensensia_id);

        assertEquals("Registration Id: http://testbank.org/100009" + titleSuffix, driver.getTitle());

        RegistrationItemFull regItem = p.getRegistrationItem();

        assertNotNull(regItem);

        assertEquals(

                "Nodosilinea sensensia (Blanco) Heidari & Hauer ex Lem, Nonsens species of the developers Vol1",

                regItem.getNameElement().getText());

        assertEquals(

                "Lem, Nonsens species of the developers Vol1",

                regItem.getCitation().getText());

        List<BaseElement> nameRelationshipElements = regItem.getNameRelationsipsElements();

        assertEquals(5,  nameRelationshipElements.size());

        assertEquals("is new combination for Nepenthes alata Blanco, Fl. Filip., ed. 1: 805. 1837", nameRelationshipElements.get(0).getText());

        assertEquals("is new name for Nepenthes blancoi Blume in Mus. Bot. Lugd.-Bat. 2: 10. 1852", nameRelationshipElements.get(1).getText());

        assertEquals("is validating Nodosilinea radiophila Heidari & Hauer in Fottea 18(2): 142. fig. 5C, D. 1.11.20181", nameRelationshipElements.get(2).getText());

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

        assertEquals("has orthographic variant Nodosilinea sensensi2, 3", nameRelationshipElements.get(4).getText());

        List<BaseElement> nameRelationshipFootnotes = regItem.getNameRelationsipFootnotes();

        assertEquals(3, nameRelationshipFootnotes.size());

        assertEquals("1. Art.99.9 Turland, Wiersema, Barrie, Greuter, D.Hawksw., Herend., S.Knapp, Kusber, D.Z.Li, Marhold, T.W.May, McNeill, A.M.Monro, J.Prado, M.J.Price & Gideon F.Sm., International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017:22", nameRelationshipFootnotes .get(0).getText());

        assertEquals("2. Art. 88.9 Turland, Wiersema, Barrie, Greuter, D.Hawksw., Herend., S.Knapp, Kusber, D.Z.Li, Marhold, T.W.May, McNeill, A.M.Monro, J.Prado, M.J.Price & Gideon F.Sm., International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017:33", nameRelationshipFootnotes .get(1).getText());

        assertEquals("3. Lem, Nonsens species of the developers Vol1", nameRelationshipFootnotes .get(2).getText());

    }

}