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cdm-dataportal / modules / cdm_dataportal / theme / cdm_dataportal.name.theme @ ff5d6ecb

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<?php
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/**
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 * @file
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 * Name theming functions.
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 *
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 * @copyright
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 *   (C) 2007-2012 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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/**
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 * Return HTML for the lectotype citation with the correct layout.
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 *
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 * This function prints the lectotype citation with the correct layout.
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 * Lectotypes are renderized in the synonymy tab of a taxon if they exist.
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 *
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 * @param mixed $typeDesignation
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 *   Object containing the lectotype citation to print.
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 *
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 * @return string
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 *   Valid html string.
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 */
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function type_designation_citation_layout($typeDesignation, $footnote_separator = ',') {
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  $res = '';
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  $citation = $typeDesignation->citation;
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  $pages = $typeDesignation->citationMicroReference;
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  if(isset($typeDesignation->typeStatus->uuid) && isset($typeDesignation->typeStatus->representation_L10n)) {
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    if ( $typeDesignation->typeStatus->uuid == UUID_NTD_ORIGINAL_DESIGNATION || $typeDesignation->typeStatus->uuid == UUID_NTD_MONOTYPY) {
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      $res = ' (' . $typeDesignation->typeStatus->representation_L10n . ')';
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      return $res;
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    }
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  }
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  if ($citation) {
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    // $type = $typeDesignation_citation->type;
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    $year = isset($citation->datePublished->start) ? substr($citation->datePublished->start, 0, 4) : '';
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    $author = isset($citation->authorship->titleCache) ? $citation->authorship->titleCache : '';
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    $res .= ' (designated by ';
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    $res .= $author;
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    $res .= ($year ? ' ' . $year : '');
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    $res .= ($pages ? ': ' . $pages : '');
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    // $res .= ')';
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    // footnotes should be rendered in the parent element so we
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    // are relying on the FootnoteListKey set there
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    $fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $typeDesignation->citation->titleCache);
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    $res .= theme('cdm_footnote_key', array(
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      'footnoteKey' => $fkey_typeDesignation,
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      'separator' => $footnote_separator,
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      'highlightable' => TRUE,
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      'separator_off' => TRUE,
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    )) . ')';
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  }
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  return $res;
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}
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/**
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 * Renders and array of CDM TypeDesignations
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 *
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 * @param array $variables
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 *   - typeDesignations: an array of cdm TypeDesignation entities to render
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 */
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function theme_cdm_typedesignations($variables) {
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  $type_designations = $variables['typeDesignations'];
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  // need to add element to render path since type designations
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  // need other name render template
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  RenderHints::pushToRenderStack('typedesignations');
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  $out = '<ul class="typeDesignations">';
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  $typeDesignation_footnotes = FALSE;
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  $is_lectotype = FALSE;
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  $specimen_type_designations = array();
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  $separator = ',';
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  foreach ($type_designations as $type_designation) {
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    if ($type_designation->class == 'SpecimenTypeDesignation') {
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      // SpecimenTypeDesignations should be ordered. Collect theme here only.
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      $specimen_type_designations[] = $type_designation;
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    }
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    // It is a lectotype?
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    else {
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      if (isset($type_designation->typeStatus->uuid) && $type_designation->typeStatus->uuid == UUID_NTD_LECTOTYPE) {
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        $is_lectotype = TRUE;
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      }
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      // It's a NameTypeDesignation.
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      if ($type_designation->notDesignated) {
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        $out .= '<li class="' . html_class_attribute_ref($type_designation) . '"><span class="status">' . ($is_lectotype ? 'Lectotype' : 'Type') . '</span>: ' . t('not designated') . '</li>';
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      }
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      elseif ($type_designation->typeName) {
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        $link_to_name_page = url(path_to_name($type_designation->typeName->uuid));
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        $out .= '<li class="' . html_class_attribute_ref($type_designation) . '"><span class="status">' . ($is_lectotype ? 'Lectotype' : 'Type') . '</span>';
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        if ($type_designation->citation) {
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          $out .= type_designation_citation_layout($type_designation, $separator);
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        }
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        $referenceUri = '';
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        if (isset($type_designation->typeName->nomenclaturalReference)) {
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          $referenceUri = url(path_to_reference($type_designation->typeName->nomenclaturalReference->uuid));
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        }
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        $out .= ': ' . render_taxon_or_name($type_designation->typeName, $link_to_name_page, $referenceUri, TRUE, TRUE);
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      }
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    }
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  }
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  if (!empty($specimen_type_designations)) {
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    // Sorting might be different for dataportals so this has to be
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    // parameterized.
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    usort($specimen_type_designations, "compare_specimenTypeDesignationStatus");
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    foreach ($specimen_type_designations as $type_designation) {
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      $typeReference = '';
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      if (!empty($type_designation->citation)) {
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        $citation_footnote_str = theme('cdm_reference', array('reference' => $type_designation->citation));
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        $author_team = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $type_designation->citation->uuid);
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        if (isset($author_team->titleCache)) {
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          $year = timePeriodToString($type_designation->citation->datePublished, true, 'YYYY');
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          $authorteam_str = $author_team->titleCache . ($year ? ' ' : '') . $year;
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          if ($authorteam_str == $type_designation->citation->titleCache) {
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            $citation_footnote_str = '';
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          }
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        } else {
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          $authorteam_str = $citation_footnote_str;
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          // no need for a footnote in case in case it is used as replacement for missing author teams
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          $citation_footnote_str = '';
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        }
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        // to be registered a typedesignation MUS HAVE a citation, so it is save to handle the
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        // Registration ouput in if condition checking if the citation is present
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        $registration_markup = render_registrations($type_designation->registrations);
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        $citation_footnote_str .= ($citation_footnote_str ? ' ' : '') . $registration_markup;
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        $footnote_key_markup = '';
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        if ($citation_footnote_str) {
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          // footnotes should be rendered in the parent element so we
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          // are relying on the FootnoteListKey set there
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          $_fkey2 = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $citation_footnote_str);
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          $footnote_key_markup = theme('cdm_footnote_key', array(
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            'footnoteKey' => $_fkey2,
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            'separator' => $separator,
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            'highlightable' => TRUE,
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            'separator_off' => TRUE,
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          ));
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        }
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        $typeReference .= '&nbsp;(' . t('designated by') . '&nbsp;<span class="typeReference">' . $authorteam_str . '</span>';
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        if (!empty($type_designation->citationMicroReference)) {
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          $typeReference .= ': ' . trim($type_designation->citationMicroReference);
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        }
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        $typeReference .= $footnote_key_markup . ')';
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      }
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      $derivedUnitFacadeInstance = null;
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      $out .= '<li class="' . html_class_attribute_ref($type_designation) . '">';
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      $out .= '<span class="status">'
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        . ((isset($type_designation->typeStatus->representation_L10n)) ? $type_designation->typeStatus->representation_L10n : t('Type'))
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        . $typeReference
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        . '</span>';
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      if (isset($type_designation->typeSpecimen)) {
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        $derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, $type_designation->typeSpecimen->uuid);
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      }
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      if (isset($derivedUnitFacadeInstance)) {
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        $out .= ': ' . $derivedUnitFacadeInstance->titleCache; // . ': ' . theme('cdm_specimen', array('specimenTypeDesignation' => $derivedUnitFacadeInstance));
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      }
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      // Footnotes for collection acronyms.
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      // footnotes should be rendered in the parent element so we
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      // are relying on the FootnoteListKey set there
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      $_fkey = FootnoteManager::addNewFootnote(
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        RenderHints::getFootnoteListKey(),
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        (isset($derivedUnitFacadeInstance->collection->titleCache) ? $derivedUnitFacadeInstance->collection->titleCache : FALSE)
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      );
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      $out .= theme('cdm_footnote_key', array('footnoteKey' => $_fkey, 'separator' => $separator));
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      $out .= '</li>';
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    }
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  }
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  $out .= '</ul>';
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  RenderHints::popFromRenderStack();
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  return $out;
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}
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/**
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 * FIXME this definitively has to be in another spot.
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 * just didn't know where to put it right now.
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 * Compares the status of two SpecimenTypeDesignations
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 *
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 * @param string $a
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 *   A SpecimenTypeDesignations.
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 * @param string $b
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 *   SpecimenTypeDesignations.
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 */
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function compare_specimenTypeDesignationStatus($a, $b) {
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  /*
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  This is the desired sort order as of now: Holotype Isotype Lectotype
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  Isolectotype Syntype.
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  TODO Basically, what we are trying to do is, we define
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  an ordered array of TypeDesignation-states and use the index of this array
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  for comparison. This array has to be filled with the cdm- TypeDesignation
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  states and the order should be parameterisable inside the dataportal.
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  */
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  // Make that static for now.
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  $typeOrder = array(
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    'Holotype',
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    'Isotype',
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    'Lectotype',
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    'Isolectotype',
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    'Syntype',
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  );
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  $aQuantifier = FALSE;
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  $bQuantifier = FALSE;
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  if (isset($a->typeStatus->label) && isset($b->typeStatus->label)) {
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    $aQuantifier = array_search($a->typeStatus->label, $typeOrder);
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    $bQuantifier = array_search($b->typeStatus->label, $typeOrder);
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  }
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  if ($aQuantifier == $bQuantifier) {
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    // Sort alphabetically.
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    return (isset($a->typeStatus->label) && isset($b->typeStatus->label) && $a->typeStatus->label < $b->typeStatus->label) ? -1 : 1;
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  }
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  return ($aQuantifier < $bQuantifier) ? -1 : 1;
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}
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/**
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 * @todo Please document this function.
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 * @see http://drupal.org/node/1354
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 */
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function theme_cdm_homotypicSynonymLine($variables) {
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  $taxon = $variables['taxon'];
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  $out = '';
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  $out .= '<li class="synonym">' . cdm_related_taxon($taxon, UUID_HOMOTYPIC_SYNONYM_OF) . '</li>';
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  return $out;
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}
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/**
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 * @todo Please document this function.
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 * @see http://drupal.org/node/1354
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 */
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function theme_cdm_heterotypicSynonymyGroup($variables) {
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  $homotypicalGroup = $variables['homotypicalGroup'];
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  RenderHints::pushToRenderStack('heterotypicSynonymyGroup');
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  $out = '';
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  $out = '<div class="heterotypic-synonymy-group"><ul class="heterotypicSynonymyGroup">';
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  $footnoteListKey = (isset($homotypicalGroup[0]) ? $homotypicalGroup[0]->uuid : 'NULL');
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  RenderHints::setFootnoteListKey($footnoteListKey);
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  $is_first_entry = TRUE;
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  $type_designations = NULL;
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  foreach ($homotypicalGroup as $synonym) {
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    if ($is_first_entry) {
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      $is_first_entry = FALSE;
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      $type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonym->name->uuid);
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      // Is first list entry.
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      $out .= '<li class="firstentry synonym">' . cdm_related_taxon($synonym, UUID_HETEROTYPIC_SYNONYM_OF) . '</li>';
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    }
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    else {
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      $out .= '<li class="synonym">' . cdm_related_taxon($synonym, UUID_HOMOTYPIC_SYNONYM_OF) . '</li>';
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    }
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  }
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  if ($type_designations) {
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    $out .= theme('cdm_typedesignations', array('typeDesignations' => $type_designations));
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  }
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  $out .= '</ul>';
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  // ------- footnotes ------- //
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  $out .= '<ul class="footnotes">';
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  $out .= theme('cdm_annotation_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'li'));
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  $out .= theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'li'));
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  $out .= '</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 the homotypic synonymy group for the accepted taxon in the synonymy.
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 *
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 * Foonotes of the accepted taxon will also be rendered here in the
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 * homotypic synonymy group even if the synonymList or prependedSynonyms are
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 * empty. Therefore  the homotypic group and accepted taxon share the  same
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 * footnote key.
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 *
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 * @param $variables
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 *   an associative array:
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 *   - synonymList: the list of cdm Synonym entities
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 *   - accepted_taxon_uuid: the uuid of the accepted taxon
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 *   - prependedSynonyms: further synonyms which should be prepended
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 *      before the actual list of synonyms
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 */
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function theme_cdm_homotypicSynonymyGroup($variables) {
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  $synonymList = $variables['synonymList'];
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  $accepted_taxon_name_uuid = $variables['accepted_taxon_name_uuid'];
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  $prependedSynonyms = $variables['prependedSynonyms'];
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  RenderHints::pushToRenderStack('homotypicSynonymyGroup');
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  $homonym_typeDesignations = NULL;
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  // TODO improve typeDesignations retrieval: wouldn't it be sufficient to retrieve all typeDesignations
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  // only from the accepted taxon?
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  $accepted_typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $accepted_taxon_name_uuid);
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  $out = '<div class="homotypic-synonymy-group">';
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  if (isset ($accepted_typeDesignations) || is_array($prependedSynonyms) || is_array($synonymList)) {
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    $out .= '<ul class="homotypicSynonyms">';
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  if (!empty($prependedSynonyms)) {
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    foreach ($prependedSynonyms as $taxon) {
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      $out .= '<li class="synonym">' . cdm_related_taxon($taxon, UUID_HOMOTYPIC_SYNONYM_OF) . '</li>';
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    }
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  }
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  $homonym_typeDesignations = NULL;
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  if (isset($synonymList[0])) {
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    foreach ($synonymList as $synonym) {
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      $out .= '<li class="synonym">' . cdm_related_taxon($synonym, UUID_HOMOTYPIC_SYNONYM_OF) . '</li>';
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    }
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    $homonym_typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonymList[0]->name->uuid);
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  }
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  // type designations
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  if ($accepted_typeDesignations) {
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    $type_designations = filter_cdm_entity_list($homonym_typeDesignations, $accepted_typeDesignations);
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  }
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  else {
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    $type_designations = $homonym_typeDesignations;
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  }
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350
  if ($type_designations) {
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    $out .= theme('cdm_typedesignations', array('typeDesignations' => $type_designations));
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  }
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  }
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  $out .= '</ul>';
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  // ------- footnotes ------- //
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  // all foonotes of the homotypic group and also of the accepted taxon are
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  // rendered here, both should have the same footnote key
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  $out .= '<ul class="footnotes">';
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  $out .= theme('cdm_annotation_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'li'));
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  $out .= theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'li'));
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  $out .= '</ul>';
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  $out .= '</div>';
368

    
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  RenderHints::popFromRenderStack();
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  return $out;
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}
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