EDIT

  //    the duplicates only have different sensu references with detail and appended phrase (see #5647)

          // full name with relation symbol, rel sec as de-duplication key

          $symbol_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('symbol')));

          cdm_taxonRelationships_process_relationship_dto($taxon_relation, $misapplied, $joined_refs, $full_name_key);

          RenderHints::popFromRenderStack();

          RenderHints::popFromRenderStack();

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

          if($relsec_data['uuid']) {

            $relsec_refs_with_fkey[$relsec_data['prefix'] . $joined_refs[$relsec_data['uuid']]['order_by_key']] = $relsec_data['prefix'] . $joined_refs[$relsec_data['uuid']]['markup'];

          }

 * @param $taxon_relation

 * @param $name_dedup_key

 * @param $misapplied

 * @param $joined_refs

 */

function cdm_taxonRelationships_process_relationship_dto($taxon_relation, &$misapplied, &$joined_refs, $name_dedup_key = null) {

  $appended_phrase_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('appendedPhrase')));

  // remove/extract appendedPhrase, secReference, relSecReference and add placeholders if needed

  tagged_text_extract($taxon_relation->taggedText, 'appendedPhrase');

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

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

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

    // for de-duplication everything else needs to be equal except for appendedPhrase + MAN.sec + MAN.secDetail. see #7658#note-21

    $name_dedup_key = str_replace(cdm_tagged_text_to_string($sensu_tagged_text), ' ', $name_dedup_key);

    $appended_phrase_text = $appended_phrase_text . array_shift($sensu_tagged_text)->text; // remove first element which contains the "sensu", this will be added later in this code

    $sensu_citation_detail = trim(join(' ', cdm_tagged_text_values($sensu_tagged_text, array('secMicroReference'))));

    $sensu_citation_short_markup = cdm_tagged_text_to_markup($sensu_tagged_text);

    $sensu_citation_short = cdm_tagged_text_to_string($sensu_tagged_text);

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

    $name_dedup_key = preg_replace('/\s+/', ' ', $name_dedup_key); // sanitize multiple whitespace characters

    $misapplied[$name_dedup_key]['sensu_uuids'][] = array('uuid' => $sensu_uuid, 'prefix' => $appended_phrase_text, 'citation_detail' => $sensu_citation_detail);

    $ref_key = $sensu_uuid . ($sensu_citation_detail ? '#' . $sensu_citation_detail : '');

    if (!isset($joined_refs[$ref_key])) {

      $joined_refs[$ref_key] = array(

        'order_by_key' => $sensu_citation_short,

        'markup' => $sensu_citation_short_markup // the footnote key will be appended later

      );

    }

  } else if ($appended_phrase_text) {

    // appended phrase without reference

    $name_dedup_key = preg_replace('/\s+/', ' ', $name_dedup_key); // sanitize multiple whitespace characters

    $misapplied[$name_dedup_key]['sensu_uuids'][] = array('uuid' => null, 'prefix' => $appended_phrase_text);

  }

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

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

    $relsec_citation_detail = trim(join(' ', cdm_tagged_text_values($relsec_tagged_text, array('secMicroReference'))));

    $relsec_citation_short_markup = cdm_tagged_text_to_markup($relsec_tagged_text);

    $relsec_citation_short = cdm_tagged_text_to_string($relsec_tagged_text);

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

    $misapplied[$name_dedup_key]['relsec_uuids'][] = array('uuid' => $relsec_uuid, 'prefix' => $appended_phrase_text, 'citation_detail' => $relsec_citation_detail);;

    $ref_key = $relsec_uuid . ($relsec_citation_detail ? '#' . $relsec_citation_detail : '');

    if (!isset($joined_refs[$ref_key])) {

      $joined_refs[$ref_key] = array(

        'order_by_key' => $relsec_citation_short,

        'markup' => $relsec_citation_short_markup // the footnote key will be appended later

      );

    }

  }

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

    $misapplied[$name_dedup_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.

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

  }

}

/**

        assertEquals("–\nOssaea maculata sec. Lem2, rel. sec. A&S1", p.getMisappliedName(3).getText());