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

 */

/**

 * Used by:

 * - theme_cdm_typedesignations

 * @param array $variables

 *   An associative array containing:

 *   - reference

 *   - microReference

 *      Show the citation string as link to the reference page. This option does not affect links to the reference URI or DOI.

 *      These links are always created when this data is available

 *   - doIconLink:

 *      Append an icon to the citation string which links to the reference page, links to the reference URI or DOI are always

 *      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'];

  $doIconLink = $variables['doIconLink'];

  else {

    $year = '';

      $year = timePeriodToString($reference->datePublished, true, 'YYYY');

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

  }

  else {

    $citation = $reference->titleCache;

  }

    $iconlink = l(custom_icon_font_markup('icon-interal-link-alt-solid', array('class' => array('superscript'))), path_to_reference($reference->uuid), array('html' => true));

  }

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

      'attributes' => array(

        "class" => "reference",

      ),

      'absolute' => TRUE,

      'html' => TRUE,

    ));

  else {

  if (!empty($microReference)) {

    $out .= ": " . $microReference;

  }

    $out .= cdm_doi($reference->doi);

  }

  if (isset($reference->uri)){

      // the cdm cache strategy adds the uri to the titleCache which is unwanted in this case,

      // so is is removed from there

      $out = str_replace('- ' . $reference->uri, '',  $out);

    }

  }

  return $out;

}

 * The resulting link will have no 'target' attribute, so the link will open in the same tab by default.

 * So the users can decide.

 *

 * @param $uri

 *    The uri to link to

 * @param $iconified

 *    The link will be rendered as icon of this is true.

function cdm_external_uri($uri, $iconified = true)

{

    'external' => true,

    'html' => false,

    );

    if($iconified){

      return l(font_awesome_icon_markup('fa-external-link', array('class' => array('superscript'))), $uri, $options);

/**

 * Creates markup for a CDM Doi entity.

 *

 * @param $doi

 *  The CDM DOI

 *

 * @return string

 *  Markup

 */

function cdm_doi($doi, $iconified = true) {

  if (!empty($doi)) {

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

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

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

    }

    if($iconified){

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

    } else {

      return l($doi_resolve_uri, $doi_resolve_uri);

    }

 *

 * @param $source

 *  The cdm OriginalSourceBase entity

 * @param $do_link_to_reference

 * @param $do_link_to_name_used_in_source

 * @return string

        'reference' => $source->citation,

        'microReference' => $source->citationMicroReference,

    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 ) {

    } else {

      $id_with_namespace = NULL;

    }

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

  }

  return $out;