EDIT

<?php

/**

 * @file

 * Reference theming functions.

 *

 * @copyright

 *   (C) 2007-2012 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

 */

/**

 * Creates a pager widget for the given CDM Pager containing CDM Reference entities.

 *

 * @param $referencePager object

 *    A CDM Pager  containing CDM Reference entities

 * @param $path

 *    The base path to be used when generating the pager item links

 * @$parameters

 *

 * @return string

 *   Markup

 */

function cdm_reference_pager($referencePager, $path, $parameters) {

  drupal_set_title(t('Bibliographic index'), PASS_THROUGH);

  $out = '';

  if (count($referencePager->records) > 0) {

    $out .= '<ul>';

    foreach ($referencePager->records as $reference) {

      // FIXME remove hack.

      $reference->fullCitation = $reference->titleCache;

      // For matching cdm entity to STO.

      $out .= '<li>' . theme('cdm_reference', array(

        'reference' => $reference,

        'microReference' => NULL,

        'doLink' => TRUE,

        )) . '</li>';

    }

    $out .= '</ul>';

    $out .= theme('cdm_pager', array(

      'pager' => $referencePager,

      'path' => $path,

      'parameters' => $parameters,

    ));

  }

  else {

    $out = '<h4 class="error">Sorry, this page contains not entries.</h4>';

  }

  return $out;

}

/**

 * Creates a HTML representations for a CDM Reference instance..

 *

 * Used by:

 * - theme_cdm_typedesignations

 * - cdm_reference_pager

 * - cdm_taxonRelationships

 *

 * @param array $variables

 *   An associative array containing:

 *   - reference

 *   - microReference

 *   - doLink:

 *      Whether to create a link to the reference page, links to the reference URI or DOI are always

 *      created when this data is available

 *   - referenceStyle: the value "zoology" will cause a specific rendeting of the

 *      reference suitable for zoological publications.

 *

 * @return string

 *    the markup for the reference

 *

 * @ingroup themeable

 */

function theme_cdm_reference($variables) {

  $reference = $variables['reference'];

  $microReference = $variables['microReference'];

  $doLink = $variables['doLink'];

  $referenceStyle = $variables['referenceStyle'];

  if (!isset($reference->authorship)) {

    $author_team = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $reference->uuid);

  }

  else {

    $author_team = $reference->authorship;

  }

  if ($referenceStyle == "zoology") {

    $year = '';

    if (isset($reference->datePublished->start)) {

      $year = partialToYear($reference->datePublished->start);

    }

    $citation = $author_team->titleCache . (!empty($year) ? '. ' . $year : '');

  }

  else {

    $citation = $reference->titleCache;

  }

  if (isset($doLink) && $doLink === TRUE) {

    $out = '<span class="reference">';

    $out .= l($citation, path_to_reference($reference->uuid), array(

      'attributes' => array(

        "class" => "reference",

      ),

      'absolute' => TRUE,

      'html' => TRUE,

    ));

    $out .= '</span>';

  }

  else {

    $out = '<span class="reference">' . $citation . '</span>';

  }

  if (!empty($microReference)) {

    $out .= ": " . $microReference;

  }

  if (isset($reference->doi) && !empty($reference->doi)) {

    $doi_resolve_uri = 'http://doi.org/' . $reference->doi->prefix;

    if(isset($reference->doi->suffix)){

      $doi_resolve_uri .= '/' . $reference->doi->suffix;

    }

    $out .= l(font_awesome_icon_markup('fa-external-link-square', array('class' => array('superscript'))), $doi_resolve_uri, array('html' => TRUE));

  }

  if (isset($reference->uri) && !empty($reference->uri)) {

    $out .= l(font_awesome_icon_markup('fa-external-link', array('class' => array('superscript'))), $reference->uri, array('html' => TRUE));

  }

  return $out;

}

/**

 * @todo Please document this function.

 * @see http://drupal.org/node/1354

 */

function theme_cdm_OriginalSource($variables) {

  $out = '';

  $source = $variables['source'];

  $do_link_to_reference = $variables['doLink'];

  $do_link_to_name_used_in_source = $variables['do_link_to_name_used_in_source'];

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

    $out = theme('cdm_reference', array(

        'reference' => $source->citation,

        'microReference' => $source->citationMicroReference,

        'doLink' => $do_link_to_reference,

    ));

    $name_in_source_render_array = compose_name_in_source($source, $do_link_to_name_used_in_source);

    if(!empty($name_in_source_render_array)) {

      $out .=  ' <span class="nameUsedInSource">(' . t('as') . ' ' . $name_in_source_render_array['#markup'] . ')</span>';

    }

    $id_with_namespace = '';

    if( isset($source->idNamespace) && $source->idNamespace ) {

      $id_with_namespace = $source->idNamespace . '/';

    }

    if( isset($source->idInSource) && $source->idInSource ) {

      $id_with_namespace .= $source->idInSource;

    } else {

      $id_with_namespace = NULL;

    }

    if($id_with_namespace){

      $out .=  ' <span class="idInSource">[' . $id_with_namespace . ']</span>';

    }

  }

  return $out;

}