EDIT

<?php

/**

 * @file

 * Common 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

 */

define('FOOTNOTE_ANNOTATIONS', 'annotations');

/**

 * Get the true path to the root of the Drupal site.

 *

 * Better than using DOCUMENT_ROOT and base_path().

 */

function absolute_path_to_drupal() {

  static $absolute_path_to_drupal = NULL;

  if ($absolute_path_to_drupal === NULL) {

    // Get the absolute path to this file:

    $dir = rtrim(str_replace('\\', '/', dirname(__FILE__)), '/');

    $parts = explode('/', $dir);

    // Iterate up the directory hierarchy until we find the website root:

    $done = FALSE;

    do {

      // Check a couple of obvious things:

      $done = is_dir("$dir/sites") && is_dir("$dir/includes") && is_file("$dir/index.php");

      if (!$done) {

        // If there's no more path to examine, we didn't find the site root:

        if (empty($parts)) {

          $absolute_path_to_drupal = FALSE;

          break;

        }

        // Go up one level and look again:

        array_pop($parts);

        $dir = implode('/', $parts);

      }

    } while (!$done);

    $absolute_path_to_drupal = $dir;

  }

  return $absolute_path_to_drupal;

}

/**

 *

 * @param $taxon_uuid

 * @return bool

  $taxon_in_current_tree = FALSE;

  if (is_array($taxon_nodes)) {

    foreach ($taxon_nodes as $node) {

        break;

      }

    }

  }

  return $taxon_in_current_tree;

}

/**

 * TODO if getting fragment from request is possible remove

 * $_REQUEST['highlite'] HACK

 * NOT WORKING since fragments are not available to the server

 *    if(!$fragment){

 *       $fragment = substr($_SERVER['REQUEST_URI'], strrpos($_SERVER['REQUEST_URI'], '#'));

 *    }

 *   return $fragment;

 */

function uuid_anchor($uuid, $innerHTML) {

  $highlite = FALSE;

  $params = drupal_get_query_parameters();

  if (isset($params['highlite']) && $params['highlite'] == $uuid) {

    $highlite = TRUE;

  }

  return '<a name="' . $uuid . '" ></a><span class="' . ($highlite ? 'highlite' : '') . '">' . $innerHTML . '</span>';

}

/**

 * @todo Enter description here...

 * @deprecated looks like this is not used anymore

 */

/*

function tagNameParts($name, $numOfNameTokens) {

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

  $token = strtok($name, " \n\t");

  $i = 0;

  $noSpace = TRUE;

  while ($token != FALSE) {

    if ($i == $numOfNameTokens) {

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

      $noSpace = TRUE;

    }

    $out .= ($noSpace ? '' : ' ') . $token;

    $noSpace = FALSE;

    $token = strtok(" \n\t");

    $i++;

  }

  return $out . '</span>';

}

*/

/* ============================ annotations ============================= */

/**

 * Returns HTML for annotations to cdm objects.

 *

 * Almost any cdmObject may be annotated. Therefore we provide a generic way to

 * display as well as create or update annotations. The following cdm classes

 * are annotatable:

 *

 * - DescriptionElementBase

 * - EventBase

 * - HomotypicalGroup

 * - IdentifiableEntity

 * - DescriptionBase

 * - IdentifiableMediaEntity

 * - Media

 * - Sequence

 * - TaxonBase

 * - TermBase

 * - LanguageStringBase

 * - ReferencedEntityBase

 * - NomenclaturalStatus

 * - OriginalSourceBase

 * - RelationshipBase

 * - TypeDesignationBase

 * - TaxonNode

 * - WorkingSet

 *

 * @param array $variables

 *   An associative array containing:

 *  - cdmBase_list: An array of CdmBase instances or a single instance.

 *  - footnote_list_key

 *

 * @ingroup themeable

 */

    return '';

  }

  $out = '';

    // array of entities

    // single entity

    $footNoteKeys = cdm_entity_annotations_as_footnotekeys($cdm_entities, $footnote_list_key);

  }

    // $out .= theme('cdm_footnote_key', $a, $a->footnoteListKey, (isset($out)?

    // ',' : ''));

    $out .= theme('cdm_footnote_key', array('footnoteKey' => $a, 'separator' => ($out ? ',' : '')));

  }

  return $out;

}

/**

 * @todo Please document this function.

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

 */

    return '';

  }

  return theme('cdm_footnotes', array('footnoteListKey' => $footnoteListKey . '-annotations', 'enclosingTag' => $enclosingTag));

}

/**

 * @todo Please document this function.

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

 */

function theme_cdm_annotation_content($variables) {

  $AnnotationTO = $variables['AnnotationTO'];

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_annotations.js');

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.form.js');

  $annotationUrl = cdm_compose_url(CDM_WS_ANNOTATIONS, array(

    $AnnotationTO->uuid,

  ));

  $annotationProxyUrl = url('cdm_api/proxy/' . urlencode($annotationUrl) . '/cdm_annotation_post');

  // TODO users have to be authenticated to the dataportal to be able to write

  // annotations.

  $out .= '

        <div class="annotation_create">

          <form action="' . $annotationProxyUrl . '" method="POST">

            <textarea name="annotation"></textarea>

            <input type="hidden" name="commentator" value="">

            <input type="submit" value="' . t('Save annotation') . '" />

          </form>

       </div>

  ';

  return $out;

}

/**

 * @todo Please document this function.

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

 */

function theme_cdm_list_of_annotations($variables) {

  $annotationElements = $variables['annotationElements'];

  $out = '<ul class="annotation_list">';

  foreach ($annotationElements as $key => $row) {

    $created[$key] = $row;

  }

  array_multisort($created, SORT_ASC, $annotationElements);

  foreach ($annotationElements as $annotation) {

    $out .= '<li>' . $annotation->text . '</li>';

  }

  $out .= '</ul>';

  return $out;

}

/* ============================ footnotes ============================= */

/**

 * @todo Please document this function.

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

 */

function theme_cdm_footnote_key($variables) {

  $footnoteKey = $variables['footnoteKey'];

  $separator = $variables['separator'];

  $highlightable = $variables['highlightable'];

  $separator_off = $variables['separator_off'];

  if (!is_object($footnoteKey) or !isset($footnoteKey->footnoteListKey)) {

    return '';

  }

  if (variable_get('cdm_dataportal_all_footnotes', CDM_DATAPORTAL_ALL_FOOTNOTES)) {

    return '';

  }

  if ($separator_off) {

    $separator = '';

  }

  $out = '<span class="footnote-key footnote-key-' . $footnoteKey->keyStr . ' member-of-footnotes-' . $footnoteKey->footnoteListKey . '">' . $separator . '<a href="#footnote-' . $footnoteKey->keyStr . '">' . $footnoteKey->keyStr . '</a>' . '</span>';

  return $out;

}

/**

 * @todo Please document this function.

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

 */

function theme_cdm_footnote($variables) {

  $footnoteKey = $variables['footnoteKey'];

  $footnoteText = $variables['footnoteText'];

    . '<span class="footnote-anchor">' . $footnoteKey . '.</span>&nbsp;' . $footnoteText

}

/**

 * @todo Please document this function.

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

 */

function theme_cdm_footnotes($variables) {

  $footnoteListKey = $variables['footnoteListKey'];

  $enclosingTag = $variables['enclosingTag'];

  if (variable_get('cdm_dataportal_all_footnotes', CDM_DATAPORTAL_ALL_FOOTNOTES)) {

    return '';

  }

  $out = '<' . $enclosingTag . ' class="footnotes footnotes-' . $footnoteListKey . ' ">'

    . FootnoteManager::renderFootnoteList($footnoteListKey)

    . '</' . $enclosingTag . '>';

  return $out;

}

 * Renders the footnotes for annotations and sources, etc.

 *

 * @param string $footnote_list_key

 *    RenderHints::getFootnoteListKey() will be used if this parameter is undefined.

 * @param string $enclosingTag

 *    Default tag is 'span'

 *

 * @return string

 *    The markup string

 *

 */

  if (variable_get('cdm_dataportal_all_footnotes', CDM_DATAPORTAL_ALL_FOOTNOTES)) {

    return '';

  }

  if(!$footnote_list_key){

    $footnote_list_key = RenderHints::getFootnoteListKey();

  }

  $out = '<' . $enclosingTag . ' class="footnotes footnotes-' . $footnote_list_key . ' ">'

    . FootnoteManager::renderFootnoteList($footnote_list_key . '-annotations') . ' ' . FootnoteManager::renderFootnoteList($footnote_list_key)

    . '</' . $enclosingTag . '>';

  FootnoteManager::removeFootnoteList($footnote_list_key . '-annotations');

  FootnoteManager::removeFootnoteList($footnote_list_key);

  return $out;

}

 * @todo Please document this function.

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

 */

function theme_cdm_annotations($variables) {

  $annotations = $variables['annotations'];

  $enclosingTag = $variables['enclosingTag'];

  if (!is_array($annotations)) {

    return;

  }

  $out = '<' . $enclosingTag . ' class="annotations">';

  $i = 0;

  foreach ($annotations as $annotation) {

    $out .= ($i++ > 0 ? ', ' : '') . $annotation->text;

  }

  $out .= '</' . $enclosingTag . '>';

  return $out;

}

/**

 * @todo Please document this function.

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

 */

function cdm_exist_footnote($footnote_list, $footnote) {

  $result = FALSE;

  if (is_array($footnote_list)) {

    foreach ($footnote_list as $element) {

      if ($element == $footnote) {

        $result = TRUE;

      }

    }

  }

  return $result;

}

/**

 * @todo Please document this function.

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

 */

function cdm_add_footnote_to_array(&$footnote_list, $footnote) {

  if (!cdm_exist_footnote($footnote_list, $footnote)) {

    $footnote_list[] = $footnote;

  }

}

 * Theme function for CDM marker instances

 *

 * @see compose_cdm_marker();

 * @param array $variables

 *   - markerType_representation_l10n: the localized representation of the marker.markerType field

 */

function theme_cdm_marker($variables) {

  $class_attribute = null;

  //TODO class attribute hacked?, use generic drupal way?

  if(isset($variables['attributes']['class'])){

    $class_attribute = $variables['attributes']['class'];

  }

  return '<span class="' . $class_attribute . '">' . $variables['label'] . '</span>';

}

 * @todo Please document this function.

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

 */

function theme_cdm_pager($variables) {

  $pager = $variables['pager'];

  $path = $variables['path'];

  $parameters = $variables['parameters'];

  $out = '';

  if ($pager->pagesAvailable > 1) {

    $out .= '<div class="pager">';

    if ($pager->currentIndex > 0) {

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

        'pager' => $pager,

        'path' => $path,

        'parameters' => $parameters,

        'attributes' => array('class' => array('pager-first')),

        ));

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

        'pager' => $pager,

        'path' => $path,

        'parameters' => $parameters,

        'attributes' => array('class' => array('pager-previous')),

        ));

    }

    if ($pager->indices[0] > 0) {

      $out .= '<div class="pager-list-dots-left">...</div>';

    }

    foreach ($pager->indices as $index) {

      $label = $index + 1;

      $out .= theme('cdm_pager_link', array('text' => $label, 'linkIndex' => $index, 'pager' => $pager, 'path' => $path, 'parameters' => $parameters, 'attributes' => array(

  'class' => array('pager-first'),

)));

    }

    if ($pager->indices[count($pager->indices) - 1] < $pager->pagesAvailable - 1) {

      $out .= '<div class="pager-list-dots-right">...</div>';

    }

    if ($pager->nextIndex) {

        'cdm_pager_link',

        array(

          'text' => t('Next') . ' ›',

          'linkIndex' => $pager->nextIndex,

          'pager' => $pager,

          'path' => $path,

          'parameters' => $parameters,

          'attributes' => array(

            'class' => array('pager-next'),

          )

        )

      );

      $out .= theme(

        'cdm_pager_link',

        array(

          'text' => t('Last') . ' »',

          'linkIndex' => $pager->pagesAvailable - 1,

          'pager' => $pager,

          'path' => $path,

          'parameters' => $parameters,

          'attributes' => array(

            'class' => array('pager-last'),

          )

        )

      );

    $out .= '</div>';

    return $out;

  }

}

/**

 * @todo Please document this function.

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

 */

function theme_cdm_pager_link($variables) {

  $text = $variables['text'];

  $linkIndex = $variables['linkIndex'];

  $pager = $variables['pager'];

  $path = $variables['path'];

  $parameters = $variables['parameters'];

  $attributes = $variables['attributes'];

  // but this is already in the path variable

  unset($parameters['q']);

    $out = '<strong>' . $text . '</strong>';

  }

  else {

    // $queryString = drupal_query_string_encode($parameters);

    $queryString = $parameters;

    $out = l($text, $path, array(

      'attributes' => $attributes,

      'query' => $queryString,

    ));

  }

  return $out;

}

/* ============================ special buttons ============================= */

/**

 * @todo Please document this function.

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

 */

function theme_cdm_print_button() {

  drupal_add_js('jQuery(document).ready(function() {

         jQuery(\'#print_button\').click(function () {

         window.print();

     });

  });', array('type' => 'inline'));

  // $output .= l('Print this page', '');

  $output .= '<span>Print this page</span>';

  $output .= '</div>';

  return $output;

}