/7.x/modules/cdm_dataportal/settings.php - EDIT - EDIT Project Management

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cdm-dataportal/7.x/modules/cdm_dataportal/settings.php @ ba706bf0

       <?php
       /**
        * @file
        * CDM Dataportal settings.
        */
       // TODO Genus UUID.
       define('DEFAULT_TAXONTREE_RANKLIMIT', '1b11c34c-48a8-4efa-98d5-84f7f66ef43a');
       define('CDM_TAXONOMICTREE_UUID', 'cdm_taxonomictree_uuid');
       define('CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE', 25);
       define('CDM_DATAPORTAL_NOMREF_IN_TITLE', 1);
       define('CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR', 0);
       define('CDM_DATAPORTAL_ALL_FOOTNOTES', 0);
       define('CDM_DATAPORTAL_ANNOTATIONS_FOOTNOTES', 0);
       define('CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX', 999);
       /* annotationTypeKeys */
       $annotationTypeKeys = array_keys(cdm_Vocabulary_as_option(UUID_ANNOTATION_TYPE));
       if (in_array(UUID_ANNOTATION_TYPE_TECHNICAL, $annotationTypeKeys)) {
         $annotationTypeKeys = array_flip($annotationTypeKeys);
         // Technical annotation are off by default.
         unset($annotationTypeKeys[UUID_ANNOTATION_TYPE_TECHNICAL]);
         $annotationTypeKeys = array_flip($annotationTypeKeys);
         // Additional value for the NULL case.
         $annotationTypeKeys[] = 'NULL_VALUE';
+      }
       define('ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT', serialize($annotationTypeKeys));
       /* taxonRelationshipTypes */
       define('CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT', serialize(array(UUID_MISAPPLIED_NAME_FOR, UUID_INVALID_DESIGNATION_FOR)));
       /* Gallery variables. */
       $gallery_settings = array(
         "cdm_dataportal_show_taxon_thumbnails" => 1,
         "cdm_dataportal_show_synonym_thumbnails" => 0,
         "cdm_dataportal_show_thumbnail_captions" => 1,
         "cdm_dataportal_media_maxextend" => 120,
         "cdm_dataportal_media_cols" => 3,
         "cdm_dataportal_media_maxRows" => 1,
       );
       /* ---- MAP SETTING CONSTANTS ---- */
       /**
        * @var array of URIs eg. http://edit.africamuseum.be"
        *   An options array
        */
       define('EDIT_MAPSERVER_URI', serialize(
           array(
             'http://edit.africamuseum.be'=>'Primary (http://edit.africamuseum.be)',
             'http://edit.br.fgov.be'=>'Secondary (http://edit.br.fgov.be)',
+          )
+        )
       );
       define('EDIT_MAPSERVER_PATH', '/edit_wp5');
       /**
        * @var array of versions eg. "v1.2"
        *   An options array
        */
       define('EDIT_MAPSERVER_VERSION', serialize(
           array(
             'v1' => 'v1' ,
             'v1.1' => 'v1.1',
             'v1.2_dev' => 'v1.2_dev'
+          )
+        )
       );
       define('EDIT_MAPSERVER_URI_DEFAULT', 'http://edit.africamuseum.be');
       define('EDIT_MAPSERVER_VERSION_DEFAULT', 'v1.1');
       // --- Taxon profile settings --- /
       define('LAYOUT_SETTING_PREFIX', 'layout_');
       define('FEATURE_TREE_LAYOUT_DEFAULTS', serialize(
         array(
           'enabled' => FALSE,
           'enclosingTag' => 'ul',
           'entryEnclosingTag' => 'li',
           'glue' => ' ',
         )));
       define('DISTRIBUTION_TEXTDATA_DISPLAY_ON_TOP', 'distribution_textdata_on_top');
       /**
        * @todo document this function
        */
       function get_taxon_tabs_list() {
         return array(
 => 'General',
 => 'Synonymy',
 => 'Images',
 => 'Specimens',
 => 'Keys',
         );
+      }
       $taxon_tab_options = get_taxon_tabs_list();
       $taxon_tab_options[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX] = 'Last visited tab';
       define('CDM_DATAPORTAL_DEFAULT_TAXON_TAB', serialize($taxon_tab_options));
       /**
        * @todo document this function.
        */
       function get_taxon_options_list() {
         $taxon_tab_options = array_flip(get_taxon_tabs_list());
         foreach ($taxon_tab_options as $key => $value) {
           $taxon_tab_options[$key] = t($key);
+        }
         return $taxon_tab_options;
+      }
       define('TAXONPAGE_VISIBILITY_OPTIONS_DEFAULT', serialize(get_taxon_options_list()));
       define('CDM_DATAPORTAL_GALLERY_SETTINGS', serialize($gallery_settings));
       define('CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME', 'specimen_gallery');
       define('CDM_DATAPORTAL_DESCRIPTION_GALLERY_NAME', "description_gallery");
       define('CDM_DATAPORTAL_MEDIA_GALLERY_NAME', "media_gallery");
       define('CDM_DATAPORTAL_TAXON_MEDIA_GALLERY_NAME_TAB', "taxon_tab_media_gallery");
       define('CDM_DATAPORTAL_SEARCH_GALLERY_NAME', "search_gallery");
       define('CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS', 'cdm_dataportal_display_taxon_relationships');
       define('CDM_DATAPORTAL_DISPLAY_NAME_RELATIONSHIPS', 'cdm_dataportal_display_name_relations');
       // define('CDM_DATAPORTAL_DISPLAY_NAME_RELATIONSHIPS_2', array("default" => t('Display all')));
       define('CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT', 1);
       define('CDM_DATAPORTAL_DISPLAY_NAME_RELATIONSHIPS_DEFAULT', 1);
       /**
        * The drupal variable key for the array containing the uuids of the taxon relationship types to display in
        * the snonymy.
+       *
        * @var string
        */
       define('CDM_TAXON_RELATIONSHIP_TYPES', 'cdm_taxon_relationship_types');
       /**
        * The drupal variable for the configuration of the information aggregation along
        * the taxon relation ships. The mapped arrayis associative and holds two elements:
        *    - direct: the uuids of the taxon relationship types to take into account in invers
        *      direction.
        *    - invers: the uuids of the taxon relationship types to take into account in direct
        *      direction.
+       *
        * @var String
        */
       define('CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS', 'cdm_aggregate_by_taxon_relationships');
       define('CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT', serialize(
           array(
               'direct'=>array(),
               'invers'=>array()
+           )
          ));
       define('CDM_PROFILE_FEATURETREE_UUID', 'cdm_dataportal_featuretree_uuid');
       define('CDM_OCCURRENCE_FEATURETREE_UUID', 'cdm_occurrence_featuretree_uuid');
       define('CDM_DATAPORTAL_STRUCTURED_DESCRIPTION_FEATURETREE_UUID', 'cdm_dataportal_structdesc_featuretree_uuid');
       /**
        * @todo document this function.
        */
       function getGallerySettings($gallery_config_form_name) {
         $default_values = unserialize(CDM_DATAPORTAL_GALLERY_SETTINGS);
         return variable_get($gallery_config_form_name, $default_values);
+      }
       /**
        * Returns the string representation of the default tab.
+       *
        * @param bool $returnTabIndex
        *   Defaults to FALSE, if set true this function will return the index number
        *   of the default tab. (used to supply default values to form elements).
        */
       function get_default_taxon_tab($returnTabIndex = FALSE) {
         global $user;
         $values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
         $user_tab_active = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
         $user_tab = 'cdm_dataportal_' . $user->uid . '_default_tab';
         // Get the user value if the used has chosen to overwrite the system settings.
         $user_tab_on = variable_get($user_tab_active, FALSE);
         if ($user_tab_on) {
           $user_value = variable_get($user_tab, 0);
           $index_value = $user_value;
           // Get the system value.
+        }
         else {
           $system_value = variable_get('cdm_dataportal_default_tab', 0);
           $index_value = $system_value;
+        }
         // Return the index value or the string representation.
         if ($returnTabIndex) {
           return $index_value;
+        }
         else {
           return ($values[$index_value]);
+        }
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_dataportal_menu_admin(&$items) {
         // Display section on admin/config page.
         $items['admin/config/cdm_dataportal'] = array(
           'title' => 'CDM Dataportal',
           'description' => 'Settings for the CDM DataPortal.',
           'position' => 'right',
           'weight' => 10,
           'page callback' => 'system_admin_menu_block_page',
           'access arguments' => array('cdm_settings_general'),
           'file' => 'system.admin.inc',
           'file path' => drupal_get_path('module', 'system'),
         );
         $items['admin/config/cdm_dataportal/settings'] = array(
           'title' => 'Settings',
           'description' => 'Settings for the CDM DataPortal.',
           'weight' => 0,
           'page callback' => 'drupal_get_form',
           'page arguments' => array('cdm_settings_general'),
           'access arguments' => array('administer cdm_dataportal'),
           'type' => MENU_NORMAL_ITEM,
         );
         $items['admin/config/cdm_dataportal/settings/general'] = array(
           'title' => 'General',
           'description' => 'General',
           'weight' => 0,
           'page callback' => 'drupal_get_form',
           'page arguments' => array('cdm_settings_general'),
           'access arguments' => array('administer cdm_dataportal'),
           'type' => MENU_DEFAULT_LOCAL_TASK,
         );
         $items['admin/config/cdm_dataportal/settings/cachesite'] = array(
           'title' => 'Cache',
           'description' => 'Cache',
           'access arguments' => array('administer cdm_dataportal'),
           'page callback' => 'drupal_get_form',
           'page arguments' => array('cdm_settings_cache'),
           'weight' => 10,
           'type' => MENU_LOCAL_TASK,
         );
         $items['admin/config/cdm_dataportal/settings/geo'] = array(
           'title' => 'Geo & Map',
           'description' => 'Geo & Map',
           'access arguments' => array('administer cdm_dataportal'),
           'page callback' => 'drupal_get_form',
           'page arguments' => array('cdm_settings_geo'),
           'weight' => 1,
           'type' => MENU_LOCAL_TASK,
         );
         $items['admin/config/cdm_dataportal/settings/layout'] = array(
           'title' => 'Layout',
           'description' => 'Configure and adjust the layout of your DataPortal ',
           'access arguments' => array('administer cdm_dataportal'),
           'page callback' => 'drupal_get_form',
           'page arguments' => array('cdm_settings_layout'),
           'weight' => 2,
           'type' => MENU_LOCAL_TASK,
         );
         $items['admin/config/cdm_dataportal/settings/layout/taxon'] = array(
           'title' => 'Taxon',
           'description' => 'Configure and adjust the layout of your DataPortal ',
           'access arguments' => array('administer cdm_dataportal'),
           'page callback' => 'drupal_get_form',
           'page arguments' => array('cdm_settings_layout_taxon'),
           'weight' => 1,
           'type' => MENU_LOCAL_TASK,
         );
         /*
         $items[] = array(
         'path' => 'admin/config/cdm_dataportal/layout/synonymy',
         'title' => t('Synonymy'),
         'description' => t('Configure and adjust the layout of your DataPortal '),
         'access' => user_access('administer cdm_dataportal'),
         'callback' => 'drupal_get_form',
         'callback arguments' => array('cdm_settings_layout_synonymy'),
         'weight' => 1,
         'type' => MENU_LOCAL_TASK,
         );
         $items[] = array(
         'path' => 'admin/config/cdm_dataportal/layout/specimens',
         'title' => t('Specimens'),
         'description' => t('Configure and adjust the layout of your DataPortal '),
         'access' => user_access('administer cdm_dataportal'),
         'callback' => 'drupal_get_form',
         'callback arguments' => array('cdm_settings_layout_specimens'),
         'weight' => 1,
         'type' => MENU_LOCAL_TASK,
         );
         */
         $items['admin/config/cdm_dataportal/settings/layout/search'] = array(
           'title' => 'Search',
           'description' => 'Configure and adjust the layout of your DataPortal ',
           'access arguments' => array('administer cdm_dataportal'),
           'page callback' => 'drupal_get_form',
           'page arguments' => array('cdm_settings_layout_search'),
           'weight' => 2,
           'type' => MENU_LOCAL_TASK,
         );
         $items['admin/config/cdm_dataportal/settings/layout/media'] = array(
           'title' => 'Media',
           'description' => 'Configure and adjust the layout of your DataPortal ',
           'access arguments' => array('administer cdm_dataportal'),
           'page callback' => 'drupal_get_form',
           'page arguments' => array('cdm_settings_layout_media'),
           'weight' => 3,
           'type' => MENU_LOCAL_TASK,
         );
         /*
         // Path to banners configuration (DEFAULT THEME).
         $items[] = array(
         'path' => 'admin/config/cdm_dataportal/layout/theme',
         'title' => t('Theme'),
         'description' => t('Configure the drupal theme of your DataPortal '),
         'access' => user_access('administer cdm_dataportal'),
         'callback' => 'drupal_get_form',
         'callback arguments' => array('cdm_dataportal_theming_form'),
         'weight' => 4,
         'type' => MENU_LOCAL_TASK,
         );
         */
+      }
       /**
        * @todo document this function.
        */
       function cdm_help_general_cache() {
         $form = array();
         $form['cache_help'] = array(
           '#type' => 'fieldset',
           '#title' => t('Help'),
           '#collapsible' => TRUE,
           '#collapsed' => TRUE,
         );
         $form['cache_help']['test'] = array('#value' => t('probando'));
         return drupal_render($form);
         $res = array();
         $res['default'] = drupal_render($help);
         return $res;
+      }
       /**
        * Configures the settings form for the CDM-API module.
+       *
        * @return array
        *   Drupal settings form.
        */
       function cdm_settings_general() {
         $form['cdm_webservice'] = array(
           '#type' => 'fieldset',
           '#title' => t('CDM Server'),
           '#collapsible' => FALSE,
           '#collapsed' => FALSE,
           '#description' => t('<em>CDM Server</em> makes the dialogue possible with
             <em>CDM Data Portal</em> thanks to its web services.'),
         );
         $form['cdm_webservice']['cdm_webservice_url'] = array(
           '#type' => 'textfield',
           '#title' => t('CDM web service URL') . ':',
           '#description' => t('This is the URL to the CDM-Server exposing your data
             e.g. <em>"http://localhost:8080/cichorieae/"</em> The URL <strong>must end
             with a slash</strong> character!'),
           '#default_value' => variable_get('cdm_webservice_url', NULL),
         );
         $form['cdm_webservice']['cdm_webservice_debug'] = array(
           '#type' => 'checkbox',
           '#title' => t('<b>Debug CDM Web Service</b>'),
           '#default_value' => variable_get('cdm_webservice_debug', 1),
           '#description' => t('The black web service debug box will appear at the top
             of each page. When clicked it toggles open and provides a list of all HTTP
             requests which have been made while building of this page.<br />
             <strong>Note:</strong> this is a feature dedicated to developers. It will
             only be visible when logged in and if the user has suffucicient rights to
             see this debug box.'),
         );
         $form['cdm_webservice']['freetext_index'] = array(
           '#type' => 'fieldset',
           '#title' => t('Freetext index'),
           '#collapsible' => FALSE,
           '#collapsed' => FALSE,
         );
         // Check the cdmserver port number and display a waring if it is not port 80
         preg_match("#http[s]?://[0-9\p{L}\.]*:([0-9]*)/.*#u", variable_get('cdm_webservice_url', ''), $portNumberMatch, PREG_OFFSET_CAPTURE);
         if (isset($portNumberMatch[1]) && $portNumberMatch[1] != '80') {
           $form['cdm_webservice']['freetext_index']['message'] = array(
             '#markup' => "<div class=\"description\">"
             . t("The CDM web service URL contains a portnumber other than standart HTTP port 80: '!port'."
             . " Due to this the reindex and purge fuctions may not be working if there is a firewall in between you and the CDM Server."
             . " You may want to contact the maintainer of the according CDM Server in order to solve this problem.", array('!port' => $portNumberMatch[1][0]))
             . "</div>",
           );
         };
         $frontentURL = urlencode(variable_get('cdm_webservice_url', ''));
         $trigger_link_options = array(
           'attributes' => array(
             'class' => 'index-trigger',
           ),
         );
         $form['cdm_webservice']['freetext_index']['operations'] = array(
           '#markup' => "<div>" . t('Operations: !url1 !url2', array(
               '!url1' => l(t("Purge"), cdm_compose_url(CDM_WS_MANAGE_PURGE, NULL, 'frontendBaseUrl=' . $frontentURL), $trigger_link_options),
               '!url2' => l(t("Reindex"), cdm_compose_url(CDM_WS_MANAGE_REINDEX, NULL, 'frontendBaseUrl=' . $frontentURL), $trigger_link_options),
             ))
           . '<div id="index-progress"></div></div>',
         );
         _add_js_cdm_ws_progressbar(".index-trigger", "#index-progress");
         $form['cdm_webservice']['proxy'] = array(
           '#type' => 'fieldset',
           '#title' => t('Proxy'),
           '#collapsible' => TRUE,
           '#collapsed' => TRUE,
         );
         $form['cdm_webservice']['proxy']['cdm_webservice_proxy_url'] = array(
           '#type' => 'textfield',
           '#title' => t('Proxy URL') . ':',
           '#description' => t('If this proxy url is set the cdm api tries
           to connect the web service over the given proxy server.
           Otherwise proxy usage is deactivated.'),
           '#default_value' => variable_get('cdm_webservice_proxy_url', FALSE),
         );
         $form['cdm_webservice']['proxy']['cdm_webservice_proxy_port'] = array(
           '#type' => 'textfield',
           '#title' => t('Proxy port') . ':',
           '#default_value' => variable_get('cdm_webservice_proxy_port', '80'),
         );
         $form['cdm_webservice']['proxy']['cdm_webservice_proxy_usr'] = array(
           '#type' => 'textfield',
           '#title' => t('Login') . ':',
           '#default_value' => variable_get('cdm_webservice_proxy_usr', FALSE),
         );
         $form['cdm_webservice']['proxy']['cdm_webservice_proxy_pwd'] = array(
           '#type' => 'textfield',
           '#title' => t('Password') . ':',
           '#default_value' => variable_get('cdm_webservice_proxy_pwd', FALSE),
         );
         // TODO: settings are still incomplete, compare with
         // trunk/dataportal/inc/config_default.php.inc.
         $form['cdm_dataportal'] = array(
           '#type' => 'fieldset',
           '#title' => t('Taxon Tree'),
           '#collapsible' => FALSE,
           '#collapsed' => TRUE,
           '#description' => t('<p>When you explore your collection, you can navigate
             it through a tree structure also called <em>Taxon Tree</em>.</p><p>To be
             able to navigate through your collection the
             <a href="http://drupal.org/handbook/blocks">drupal block</a>
             <em>CDM Taxon Tree</em> should be visible for users. Enable the block at
             <a href="./?q=admin/build/block">Administer&#45&#62Site building&#45&#62Blocks
             </a></p>'),
         );
         $form['cdm_dataportal'][CDM_TAXONOMICTREE_UUID] = array(
           '#type' => 'select',
           '#title' => t('Available classifications') . ':',
           '#default_value' => variable_get(CDM_TAXONOMICTREE_UUID, FALSE),
           '#options' => cdm_get_taxontrees_as_options(),
           '#description' => t('Select the default taxa classification for your
             <em>taxon tree</em>, the other classifications will be also available but
             with a manual user change.'),
         );
         $form['cdm_dataportal']['taxontree_ranklimit'] = array(
           '#type' => 'select',
           '#title' => t('Rank of highest displayed taxon') . ':',
            // Before DEFAULT_TAXONTREE_RANKLIMIT_UUID.
           '#default_value' => variable_get('taxontree_ranklimit', DEFAULT_TAXONTREE_RANKLIMIT),
           '#options' => cdm_rankVocabulary_as_option(),
           '#description' => t('This is the rank of the highest displayed taxon in the
             <em>taxon tree</em>. You can select here which rank should be at the top
             level of the tree structure.'),
         );
         $form['cdm_dataportal'][CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS] = array(
             '#type' => 'fieldset',
             '#attributes' => array('class'=>array('clearfix')),
             '#title' => t('Information aggregation via taxon relationsships'),
             '#collapsible' => TRUE,
             '#collapsed' => TRUE,
             '#tree' => TRUE,
             '#description' => t('Information on taxa will be aggregated along the below chosen
                 taxon relation ships. This will affect images and occurrences (specimens).
                 Taxon relation ships are directed and point form one taxon to another. The taxon
                 relationships to be taken into accunt can therefore configured for the direct direction
                 and for the inverse.'),
         );
         $taxonRelationshipTypeOptions = cdm_Vocabulary_as_option(UUID_TAXON_RELATIONSHIP_TYPE, '_cdm_relationship_type_term_label_callback');
         $aggregate_by_taxon_relationships = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
         $form['cdm_dataportal'][CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS]['direct'] = array(
             '#type' => 'checkboxes',
             '#title' => t('Direct'),
             '#options' => $taxonRelationshipTypeOptions,
             '#default_value' => $aggregate_by_taxon_relationships['direct'],
         );
         $form['cdm_dataportal'][CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS]['invers'] = array(
             '#type' => 'checkboxes',
             '#title' => t('Invers'),
             '#options' => $taxonRelationshipTypeOptions,
             '#default_value' => $aggregate_by_taxon_relationships['invers'],
         );
         // Comment @WA: D7 form api does not support reset buttons,
         // so to mimic the D5 reset button we add one like this.
         $form['actions']['reset'] = array(
           '#markup' => '<input id="reset" type="reset" class="form-submit" value="' . t('Reset to defaults') . '" />',
           '#weight' => 1000,
         );
         return system_settings_form($form);
+      }
       /**
        * LAYOUT settings
        * @return unknown_type
        *   todo
        */
       function cdm_settings_layout() {
         // drupal_goto('admin/config/cdm_dataportal/layout/taxon');
         $form = array();
         /*
          // -- tabbed pages -- //
          $form['cdm_dataportal_taxonpage_tabs'] = array(
          '#type' => 'checkbox',
          '#title' => t('Tabbed taxon page'),
          '#default_value' => variable_get('cdm_dataportal_taxonpage_tabs', 1),
          '#description' => t('If selected split the taxon page into individual tabs for description, images, synonymy. If not the taxon data is rendered as a long single page without tabs.')
          );
          */
         $form['gen_layout'] = array(
           '#type' => 'fieldset',
           '#title' => t('Portal Layout'),
           '#collapsible' => FALSE,
           '#collapsed' => FALSE,
           '#description' => t('This settings contains the general configurations
             layout. If you want to configure the specific sites layout visit the
             respective configuration site for taxon, search or media.'),
         );
         // ---- footnotes --- //
         $form['gen_layout']['footnotes'] = array(
           '#type' => 'fieldset',
           '#title' => t('Footnotes'),
           '#collapsible' => FALSE,
           '#collapsed' => FALSE,
           '#description' => t('Taxa data such authors, synonyms names, descriptions,
             media or distribution areas may have annotations or footnotes. When the
             footnotes are enabled they will be visible (if they exist).'),
         );
         $form['gen_layout']['footnotes']['cdm_dataportal_all_footnotes'] = array(
           '#type' => 'checkbox',
           '#title' => t('Do not show footnotes'),
           '#default_value' => variable_get('cdm_dataportal_all_footnotes', CDM_DATAPORTAL_ALL_FOOTNOTES),
           '#description' => t('Check this if you do not want to show any footnotes'),
         );
         $form['gen_layout']['footnotes']['cdm_dataportal_annotations_footnotes'] = array(
           '#type' => 'checkbox',
           '#title' => t('Do not show annotations footnotes'),
           '#default_value' => variable_get('cdm_dataportal_annotations_footnotes', CDM_DATAPORTAL_ANNOTATIONS_FOOTNOTES),
           '#description' => t('Check this if you do not want to show annotation footnotes'),
         );
         $annotationTypeOptions = cdm_Vocabulary_as_option(UUID_ANNOTATION_TYPE);
         // Additional option for the NULL case.
         $annotationTypeOptions['NULL_VALUE'] = t('untyped');
         $form['gen_layout']['footnotes']['annotations_types_as_footnotes'] = array(
           '#type' => 'checkboxes',
           '#title' => t('Annotation types as footnotes'),
           '#description' => t("Only annotations of the selected type will be displayed
              as footnotes. You may want to turn 'technical annotations' off."),
           '#options' => $annotationTypeOptions,
         );
         $annotationsTypesAsFootnotes = variable_get('annotations_types_as_footnotes', unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT));
         if (!empty($annotationsTypesAsFootnotes)) {
           $form['gen_layout']['footnotes']['annotations_types_as_footnotes']['#default_value'] = $annotationsTypesAsFootnotes;
+        }
         // --- Advanced Search --- //
         $form['gen_layout']['asearch'] = array(
           '#type' => 'fieldset',
           '#title' => t('Advanced search'),
           '#collapsible' => FALSE,
           '#collapsed' => FALSE,
         );
         $form['gen_layout']['asearch']['cdm_dataportal_show_advanced_search'] = array(
           '#type' => 'checkbox',
           '#title' => t('Show advanced search link'),
           '#default_value' => variable_get('cdm_dataportal_show_advanced_search', 1),
           '#description' => t('Check this box if the link to advanced search should be show below the search box.'),
         );
         // @WA: D7 form api does not support reset buttons,
         // so to mimic the D5 reset button we add one like this.
         $form['actions']['reset'] = array(
           '#markup' => '<input id="reset" type="reset" class="form-submit" value="' . t('Reset to defaults') . '" />',
           '#weight' => 1000,
         );
         return system_settings_form($form);
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_dataportal_theming_form() {
         // --- Theme --- //
         /*
          $form['cdm_dataportal_theming'] = array(
          '#type' => 'fieldset',
          '#title' => t('Theme Images'),
          '#collapsible' => FALSE,
          '#collapsed' => FALSE,
          );
          */
         $form = array('#attributes' => array('enctype' => 'multipart/form-data'));
         $form['cdm_dataportal_theming_right_image'] = array(
           '#type' => 'file',
           '#title' => t('Select top right image'),
           '#description' => t('Maximum dimensions are %dimensions and the maximum size is %size kB.',
                                   array('%dimensions' => '250x250', '%size' => '30')),
         );
         $form['cdm_dataportal_theming_middle_image'] = array(
           '#type' => 'file',
           '#title' => t('Select top middle image'),
         );
         $form['test'] = array(
           '#type' => 'textfield',
           '#title' => t('test'),
         );
         // $form['gen_layout']['theme']['#submit'][] = 'settings_validate_theme_pictures';
         $form['cdm_dataportal_theming']['submit'] = array(
           '#type' => 'submit',
           '#value' => t('Submit'),
         );
         return $form;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_dataportal_theming_form_submit($form, &$form_state) {
         $validators = array();
         // Destination path where the files/banners will be saved.
         $dest = absolute_path_to_drupal() . '/' . path_to_theme() . '/images/banners';
         $dest = str_replace('/', DIRECTORY_SEPARATOR, $dest);
         // drupal_set_message($dest);
         // Check if directory exists.
         if (!file_exists($dest)) {
           // TODO: add rights, which rights should I add?
           if (!mkdir($dest, 0777, TRUE)) {
             drupal_set_message(t('Failed uploading the files; the directory !dest
               could not be created.', array('!dest' => $dest)), 'warning');
+          }
+        }
         // Check if files already exist.
         /*
         if (file_exists($dest)) {
+        }
         */
         // Save the files.
         // TODO Modify the validators array to suit your needs.
         // This array is used in the revised file_save_upload.
         $validators = array(
           'file_validate_is_image' => array(),
           'file_validate_image_resolution' => array('85x85'),
           'file_validate_size' => array(30 * 1024),
         );
         $file = file_save_upload($dest, $validators);
         if ($file) {
           drupal_set_message($file->filepath);
           file_move($file->filepath, $dest);
+        }
         else {
           drupal_set_message(t('Fail uploading the file, the file is not accepted.'), 'warning');
+        }
         // Use banners in the selected theme.
         /*
         if (!copy($file, $file.'.bak')) {
           print ("failed to copy $file...<br>\n");
+        }
         */
         // Use the banners as default theme.
+      }
       /*
        function cdm_settings_layout_synonymy(){
        / * ====== SYNONYMY ====== * /
        $form['synonymy'] = array(
        '#type' => 'fieldset',
        '#title' => t('Synonymy'),
        '#collapsible' => TRUE,
        '#collapsed' => TRUE,
        '#description' => t('This section covers the settings related to the taxon <b>synonymy</b> tab.'),
        );
        $form['synonymy']['cdm_dataportal_nomref_in_title'] = array(
        '#type' => 'checkbox',
        '#title' => t('Show accepted taxon on top of the synonymy'),
        '#default_value' => variable_get('cdm_dataportal_nomref_in_title', CDM_DATAPORTAL_NOMREF_IN_TITLE),
        '#description' => t('If checked, the first homotypic taxon is a repetition of the accepted taxon most likely
        with the full nomenclatural reference (depending on the currently chosen theme).')
        );
        $form['synonymy']['cdm_dataportal_display_is_accepted_for'] = array(
        '#type' => 'checkbox',
        '#title' => t('Display <em>is accepted for ...</em> on taxon pages when coming from a synonym link.'),
        '#default_value' => variable_get('cdm_dataportal_display_is_accepted_for', CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR),
        '#description' => t('Check this if after doing a search and clicking on a synonym you want to see the "accept of" text for the accepted synonym.')
        );
        $form['synonymy']['name_relationships']['name_relationships_to_show'] = array(
        '#type' => 'checkboxes',
        '#title' => t('Display name relationships'),
        '#default_value' => variable_get('name_relationships_to_show', 0),
        '#options' => $nameRelationshipTypeOptions,
        '#description' => t('Select the name relationships you want to show for the accepted taxa.'),
        );
        $form['synonymy'][CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS] = array(
        '#type' => 'checkbox',
        '#title' => t('Show taxon relations ships of accepted taxon'),
        '#default_value' => variable_get(CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT),
        '#description' => t('If this option is enabled the synonymy will show the below selected taxon relationships of accepted taxa.')
        );
        $taxonRelationshipTypeOptions = cdm_Vocabulary_as_option(UUID_TAXON_RELATIONSHIP_TYPE);
        $form['synonymy'][CDM_TAXON_RELATIONSHIP_TYPES] = array(
        '#type' => 'checkboxes',
        '#title' => t('Taxon relationship types'),
        '#description' => t('Only taxon relationships of the selected type will be displayed'),
        '#options' => $taxonRelationshipTypeOptions,
        '#default_value' => variable_get('CDM_TAXON_RELATIONSHIP_TYPES', unserialize(CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT)),
        '#disabled' => !variable_get(CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT)
        );
        return system_settings_form($form);
+       }
        */
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_dataportal_create_gallery_settings_form($form_name, $form_title, $collapsed, $form_description = '') {
         $form[$form_name] = array(
           '#type' => 'fieldset',
           '#title' => t($form_title),
           '#collapsible' => TRUE,
           '#collapsed' => $collapsed,
           '#tree' => TRUE,
           '#description' => t($form_description),
         );
         $default_values = unserialize(CDM_DATAPORTAL_GALLERY_SETTINGS);
         $gallery_settings = variable_get($form_name, $default_values);
         // $test = variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE);
         if ($form_name == CDM_DATAPORTAL_SEARCH_GALLERY_NAME) {
           /*
           TODO: why cdm_dataportal_search_items_on_page does not save the value on $test???
           $form[$form_name]['cdm_dataportal_search_items_on_page'] = array(
           '#type' => 'textfield',
           '#title' => t('Search Page Size'),
           '#default_value' => $test,
           '#description' => t('Number of Names to display per page in search results.')
           );
           */
           $form[$form_name]['cdm_dataportal_show_taxon_thumbnails'] = array(
             '#type' => 'checkbox',
             '#title' => t('Show media thumbnails for accepted taxa'),
             '#default_value' => $gallery_settings['cdm_dataportal_show_taxon_thumbnails'],
           );
           $form[$form_name]['cdm_dataportal_show_synonym_thumbnails'] = array(
             '#type' => 'checkbox',
             '#title' => t('Show media thumbnails for synonyms'),
             '#default_value' => $gallery_settings['cdm_dataportal_show_synonym_thumbnails'],
             '#description' => '',
           );
+        }
         // $showCaption = variable_get('cdm_dataportal_findtaxa_show_thumbnail_captions', 0);
         $form[$form_name]['cdm_dataportal_show_thumbnail_captions'] = array(
           '#type' => 'checkbox',
           '#title' => t('Show captions under thumbnails'),
           '#default_value' => $gallery_settings['cdm_dataportal_show_thumbnail_captions'],
           '#description' => '',
         );
         $form[$form_name]['cdm_dataportal_media_maxextend'] = array(
           '#type' => 'textfield',
           '#title' => t('Thumbnail size') . ':',
           '#default_value' => $gallery_settings['cdm_dataportal_media_maxextend'],
           '#description' => t('Select the size of each individual thumbnail.'),
         );
         if ($form_name != CDM_DATAPORTAL_MEDIA_GALLERY_NAME) {
           $form[$form_name]['cdm_dataportal_media_cols'] = array(
             '#type' => 'textfield',
             '#title' => t('Number of columns') . ':',
             '#default_value' => $gallery_settings['cdm_dataportal_media_cols'],
             '#description' => t('Group the thumbnails in columns: select how many
               columns the gallery should display.'),
           );
+        }
         if ($form_name == CDM_DATAPORTAL_SEARCH_GALLERY_NAME) {
           $form[$form_name]['cdm_dataportal_media_maxRows'] = array(
             '#type' => 'textfield',
             '#title' => t('Maximum number of rows') . ':',
             '#default_value' => $gallery_settings['cdm_dataportal_media_maxRows'],
             '#description' => t('You can group the thumbnails in rows, select in how
               many rows should be the thumbnails grouped.<br/><strong>Note:</strong>
               If you want an unlimited number of rows please set to 0.'),
           );
+        }
         return $form;
+      }
       /**
        * @todo document this function.
        */
       function cdm_settings_layout_taxon() {
         $collapsed = FALSE;
         $form = array();
         // --------- TABBED TAXON ------- //
         $form['taxon_tabs'] = array(
           '#type' => 'fieldset',
           '#title' => t('Taxon tabs'),
           '#collapsible' => TRUE,
           '#collapsed' => FALSE,
           '#description' => t('If tabbed taxon page is enabled the taxon profile will
             be splitted in four diferent tabs; General, Synonymy, Images and
             Specimens. If the taxon has no information for any of the tabs/sections
             such tab will be not displayed.'),
         );
         $form['taxon_tabs']['cdm_dataportal_taxonpage_tabs'] = array(
           '#type' => 'checkbox',
           '#title' => t('Tabbed taxon page'),
           '#default_value' => variable_get('cdm_dataportal_taxonpage_tabs', 1),
           '#description' => t('<p>If selected split the taxon page into individual
             tabs for description, images, synonymy and specimens. If not the taxon
             data is rendered as a long single page without tabs.</p>'),
         );
         $form['taxon_tabs']['cdm_taxonpage_tabs_visibility'] = array(
           '#type' => 'checkboxes',
           '#title' => t('Tabs visibility options') . ':',
           '#default_value' => variable_get('cdm_taxonpage_tabs_visibility', get_taxon_options_list()),
           '#options' => get_taxon_options_list(),
           '#description' => t('Enable or disable Tabs in the Tabbed page display'),
         );
         $form['taxon_tabs']['cdm_dataportal_default_tab'] = array(
           '#type' => 'select',
           '#title' => t('Default tab to display') . ':',
           '#default_value' => variable_get('cdm_dataportal_default_tab', 0),
           '#options' => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),
           '#description' => t('<p>Select the default tab to display when visiting a
             taxon page. Only available if Tabbed Taxon Page is enable.</p>
             <strong>Note:</strong> After performing a search and clicking in any
             synonym, the taxon tab to be rendered will be the synonymy of the accepted
             taxon and not the above selected tab.'),
         );
         $form['cdm_dataportal_show_back_to_search_results'] = array(
           '#type' => 'checkbox',
           '#title' => t('Show <em>Back to search results</em> link at the taxon site.'),
           '#default_value' => variable_get('cdm_dataportal_show_back_to_search_results', 1),
           '#description' => t('<p>If checked the link to search results is rendered at
              the top of the taxon site. Clicking on the link the last search performed
              is rendered again.</p>'),
         );
         /* ======  TAXON_PROFILE ====== */
         $form['taxon_profile'] = array(
           '#type' => 'fieldset',
           '#title' => t('Taxon profile (tab)'),
           '#description' => t('<p>This section covers the setting related to the taxon
             profile tab, also known as the <strong>"General"</strong> tab.</p>'),
           '#collapsible' => TRUE,
           '#collapsed' => TRUE,
         );
         // ---- PROFILE PICTURE ----//
         $form['taxon_profile']['picture'] = array(
           '#type' => 'fieldset',
           '#title' => t('Profile Picture'),
           '#collapsible' => TRUE,
           '#collapsed' => FALSE,
           '#description' => t('Select a profile picture for taxa. Like a facebook of plants.'),
         );
         $form['taxon_profile']['picture']['cdm_dataportal_show_default_image'] = array(
           '#type' => 'checkbox',
           '#title' => t('Enable profil picture'),
           '#default_value' => variable_get('cdm_dataportal_show_default_image', FALSE),
           '#description' => t('Show the profil picture.'),
         );
         $options = cdm_rankVocabulary_as_option();
         array_unshift($options, '-- DISABLED --');
         $form['taxon_profile']['picture']['image_hide_rank'] = array(
           '#type' => 'select',
           '#title' => t('Hide picture for taxa above') . ':',
           '#default_value' => variable_get('image_hide_rank', '0'),
           '#options' => $options,
           '#description' => t('Select which rank of pictures should not have
             a profile picture.'),
         );
         // Show picture.
         $selectShowMedia = array(
 => "Show only taxon pictures",
 => "Show taxon and child taxa pictures",
         );
         $form['taxon_profile']['picture']['cdm_dataportal_show_media'] = array(
           '#type' => 'select',
           '#title' => t('Available picture files') . ':',
           '#default_value' => variable_get('cdm_dataportal_show_media', FALSE),
           '#options' => $selectShowMedia,
           '#description' => t("Show the profile pictures current taxon's children."),
         );
         // -- MEDIA THUMBNAILS -- //
         $form_name = CDM_DATAPORTAL_DESCRIPTION_GALLERY_NAME;
         $form_title = 'Taxon Profile Images';
         $form_description = '<p>The different section in the taxon  profile can have images associated with them. These images are displayed in a gallery of thumbnails wich can be configuered here:</p>';
         $form['taxon_profile'][] = cdm_dataportal_create_gallery_settings_form($form_name, $form_title, $collapsed, $form_description);
         // ---- FEATURE TREE ---- //
         $form['taxon_profile']['taxon_profile'] = array(
           '#type' => 'fieldset',
           '#title' => t('Features'),
           '#collapsible' => TRUE,
           '#collapsed' => FALSE,
           '#description' => t("This section covers settings related to the taxon's
             <em>Feature Tree</em>. The <em>feature tree</em> are the taxon's
             features such as description, distribution, common names, etc. that Drupal
             will render at the taxon profile page."),
         );
         $featureTrees = cdm_get_featureTrees_as_options(TRUE);
         $form['taxon_profile']['feature_trees'][CDM_PROFILE_FEATURETREE_UUID] = array(
           '#type' => 'radios',
           '#title' => t('Taxon profile sections') . ':',
           '#default_value' => variable_get(CDM_PROFILE_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE),
           '#options' =>  $featureTrees['options'],
           // Comment @WA: because #options are sanitized in D7, it would
           // strip html like <fieldset>, so we put the fieldset in a suffix.
           '#field_suffix' => $featureTrees['treeRepresentations'],
           '#description' => t('Select the Feature Tree to be displayed at the taxon
             profile. Click "Show Details" to see the Feature Tree elements.'
           ),
         );
         $featureTrees = cdm_get_featureTrees_as_options();
         $form['taxon_profile']['feature_trees'][CDM_DATAPORTAL_STRUCTURED_DESCRIPTION_FEATURETREE_UUID] = array(
           '#type' => 'radios',
           '#title' => t('Natural language representation of structured descriptions') . ':',
           '#default_value' => variable_get(CDM_DATAPORTAL_STRUCTURED_DESCRIPTION_FEATURETREE_UUID, NULL),
           '#options' => $featureTrees['options'],
             // Comment @WA: because #options are sanitized in D7, it would
             // strip html like <fieldset>, so we put the fieldset in a suffix.
           '#field_suffix' => $featureTrees['treeRepresentations'],
           '#description' => t('Taxon descriptions can be stored in a highly structured
             form. The feature tree selected here will be used to generate textual
             representation in natural language.'
             // If there is no applicable FeatureTree you can create a new one using the <a href="">FeatureTreeManager</a>'
           ),
         );
         // ---- LAYOUT PER FEATURE ---- //
         $feature_tree = get_profile_featureTree();
         if (isset($feature_tree->root->children)) {
           $form_feature_list_layout = array(
             '#title' => t('Taxon profile layout'),
             '#collapsible' => TRUE,
             '#collapsed' => FALSE,
             '#type' => 'fieldset',
             '#description' => t('Will be available in a future release.'),
           );
           $feature_list_layout_settings_disabled = TRUE;
           foreach ($feature_tree->root->children as $featureNode) {
             if (!$feature_list_layout_settings_disabled && isset($featureNode->feature)) {
               // Must not exceed 45 characters !!!
               $subform_id = LAYOUT_SETTING_PREFIX . $featureNode->feature->uuid;
               $settings = mixed_variable_get($subform_id, FEATURE_TREE_LAYOUT_DEFAULTS);
               $systemDefaults = unserialize(FEATURE_TREE_LAYOUT_DEFAULTS);
               $form_feature_list_layout[$subform_id] = array(
                 '#tree' => TRUE,
                 '#title' => 'test' . $featureNode->feature->representation_L10n,
                 '#collapsible' => FALSE,
                 '#collapsed' => FALSE,
                 '#type' => 'fieldset',
                 '#description' => t(''),
               );
               $form_feature_list_layout[$subform_id]['enabled'] = array(
                 '#type' => 'checkbox',
                 '#title' => t('Enable'),
                 '#default_value' => $settings['enabled'],
                 '#description' => t('Enable user defined layout for this feature'),
               );
               $form_feature_list_layout[$subform_id]['enclosingTag'] = array(
                 '#type' => 'textfield',
                 '#title' => t('Enclosing tag'),
                 '#disabled' => !$settings['enabled'],
                 '#default_value' => $settings['enclosingTag'],
                 '#description' => t('Default is: ') . "'<code>" . $systemDefaults['enclosingTag'] . "</code>'",
               );
               $form_feature_list_layout[$subform_id]['entryEnclosingTag'] = array(
                 '#type' => 'textfield',
                 '#title' => t('Entry enclosing tag'),
                 '#disabled' => !$settings['enabled'],
                 '#default_value' => $settings['entryEnclosingTag'],
                 '#description' => t('Default is: ') . "'<code>" . $systemDefaults['entryEnclosingTag'] . "</code>'",
               );
               $form_feature_list_layout[$subform_id]['glue'] = array(
                 '#type' => 'textfield',
                 '#title' => t('Glue'),
                 '#disabled' => !$settings['enabled'],
                 '#default_value' => $settings['glue'],
                 '#description' => t('Default is: ') . "'<code>" . $systemDefaults['glue'] . "</code>'",
               );
+            }
             $form['taxon_profile']['feature_list_layout'] = $form_feature_list_layout;
+          }
+        }
         // ---- DISTRIBUTION LAYOUT ---- //
         $form['taxon_profile']['distribution_layout'] = array(
           '#title' => t('Distribution'),
           '#collapsible' => TRUE,
           '#collapsed' => FALSE,
           '#type' => 'fieldset',
           '#description' => t('Select if you want to sort or not the distribution text
             located below the distribution map.'),
         );
         $form['taxon_profile']['distribution_layout']['distribution_sort'] = array(
           '#type' => 'radios',
           '#title' => t('Sort') . ':',
           '#default_value' => variable_get('distribution_sort', 'NO_SORT'),
           '#options' => array(
             'NO_SORT' => t('Standard (No sort)'),
             'HIDE_TDWG2' => t('Sorted without TDWG Level 2'),
           ),
         );
         $form['taxon_profile']['distribution_layout'][DISTRIBUTION_TEXTDATA_DISPLAY_ON_TOP] = array(
           '#type' => 'checkbox',
           '#title' => t('Show TextData elements on top of the map'),
           '#default_value' => variable_get(DISTRIBUTION_TEXTDATA_DISPLAY_ON_TOP, 0),
           '#description' => t('Check this if you want to appear all <code>TextData</code>
             elements on top of the map. Otherwise all <code>TextData</code>
             distribution elements will be listed below the other area elements.
             This option is useful if you need to have descriptive texts for each
             distribution map.'),
         );
         /* ====== SYNONYMY ====== */
         $form['taxon_synonymy'] = array(
           '#type' => 'fieldset',
           '#title' => t('Taxon synonymy (tab)'),
           '#collapsible' => TRUE,
           '#collapsed' => TRUE,
           '#description' => t('This section covers the settings related to the taxon
             <strong>synonymy</strong> tab.####'),
         );
         $form['taxon_synonymy']['cdm_dataportal_nomref_in_title'] = array(
           '#type' => 'checkbox',
           '#title' => t('Show accepted taxon on top of the synonymy'),
           '#default_value' => variable_get('cdm_dataportal_nomref_in_title', CDM_DATAPORTAL_NOMREF_IN_TITLE),
           '#description' => t('If checked, the first homotypic taxon is a repetition
             of the accepted taxon most likely with the full nomenclatural reference
             (depending on the currently chosen theme).'),
         );
         $form['taxon_synonymy']['cdm_dataportal_display_is_accepted_for'] = array(
           '#type' => 'checkbox',
           '#title' => t('Display <em>is accepted for ...</em> on taxon pages when
             coming from a synonym link.'),
           '#default_value' => variable_get('cdm_dataportal_display_is_accepted_for', CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR),
           '#description' => t('Check this if after doing a search and clicking on a
             synonym you want to see the "accept of" text for the accepted synonym.'),
         );
         $nameRelationshipTypeOptions = cdm_Vocabulary_as_option(UUID_NAME_RELATIONSHIP_TYPE);
         $form['taxon_synonymy']['name_relationships']['name_relationships_to_show'] = array(
           '#type' => 'checkboxes',
           '#title' => t('Display name relationships') . ':',
           '#default_value' => variable_get('name_relationships_to_show', 0),
           '#options' => $nameRelationshipTypeOptions,
           '#description' => t('Select the name relationships you want to show for the
             accepted taxa.'),
         );
         $form['taxon_synonymy'][CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS] = array(
           '#type' => 'checkbox',
           '#title' => t('Show taxon relations ships of accepted taxon'),
           '#default_value' => variable_get(CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT),
           '#description' => t('If this option is enabled the synonymy will show the
             below selected taxon relationships of accepted taxa.'),
         );
         $taxonRelationshipTypeOptions = cdm_Vocabulary_as_option(UUID_TAXON_RELATIONSHIP_TYPE, '_cdm_relationship_type_term_label_callback');
         $form['taxon_synonymy'][CDM_TAXON_RELATIONSHIP_TYPES] = array(
           '#type' => 'checkboxes',
           '#title' => t('Taxon relationship types') . ':',
           '#description' => t('Only taxon relationships of the selected type will be
             displayed'),
           '#options' => $taxonRelationshipTypeOptions,
           '#default_value' => variable_get(CDM_TAXON_RELATIONSHIP_TYPES, unserialize(CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT)),
           '#disabled' => !variable_get(CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT),
         );
         // ====== SPECIMENS ====== //
         $form['taxon_specimens'] = array(
           '#type' => 'fieldset',
           '#title' => t('Taxon specimens (tab)'),
           '#collapsible' => TRUE,
           '#collapsed' => TRUE,
           '#description' => t('This section covers the settings related to the taxon
             <strong>specimens</strong> tab.'),
         );
         $featureTrees = cdm_get_featureTrees_as_options(TRUE);
         $form['taxon_specimens']['feature_trees'][CDM_OCCURRENCE_FEATURETREE_UUID] = array(
             '#type' => 'radios',
             '#title' => t('Specimen description feature tree') . ':',
             '#default_value' => variable_get(CDM_OCCURRENCE_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE),
             '#options' =>  $featureTrees['options'],
             // Comment @WA: because #options are sanitized in D7, it would
             // strip html like <fieldset>, so we put the fieldset in a suffix.
             '#field_suffix' => $featureTrees['treeRepresentations'],
             '#description' => t('Select the feature tree to be used for displaying specimen descriptions. Click "Show Details" to see the Feature Tree elements.'
             ),
         );
         $form_name = CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME;
         $form_title = t('Specimen media');
         $form_description = t('Specimens may have media which is displayed at the
            Specimen tab/section as a gallery. It is possible to configure the
            thumbnails gallery here, however for configuring how a single media should
            be displayed please go to !url.</p>',
            array(
              '!url' => l(t('Layout -> Media'), 'admin/config/cdm_dataportal/settings/layout/media'),
            ));
         $form['taxon_specimens'][] = cdm_dataportal_create_gallery_settings_form($form_name, $form_title, FALSE, $form_description);
         // --- MEDIA GALLERY ---- //
         $form_name = CDM_DATAPORTAL_TAXON_MEDIA_GALLERY_NAME_TAB;
         $form_title = 'Media gallery (tab)';
         $form_description = '<p>This section covers the settings related to the taxon <strong>media</strong> tab.
          Taxa may have media (usually images) and they are as thumbnails displayed. It is possible to configure
          the thumbnails gallery here, however for configuring how a single media should be displayed please go to
          <a href="./?q=admin/settings/cdm_dataportal/layout/media">Layout -&gt; Media</a></p>
          <p><strong>Note:</strong> These settings are only taken into account when the standard
          gallery viewer is selected at <a href="./?q=admin/settings/cdm_dataportal/layout/media">Layout -&gt; Media</a>.</p>';
         $form['taxon_media'][] = cdm_dataportal_create_gallery_settings_form($form_name, $form_title, TRUE, $form_description);
         // Comment @WA: D7 form api does not support reset buttons,
         // so to mimic the D5 reset button we add one like this.
         $form['actions']['reset'] = array(
           '#markup' => '<input id="reset" type="reset" class="form-submit" value="' . t('Reset to defaults') . '" />',
           '#weight' => 1000,
         );
         return system_settings_form($form);
+      }
       /**
        * @todo document this function.
        */
       function cdm_settings_layout_search() {
         $form = array();
         $form['search_settings'] = array(
           '#type' => 'fieldset',
           '#title' => t('Taxa Search'),
           '#collapsible' => TRUE,
           '#collapsed' => TRUE,
           '#description' => t('<p>The data portal allows the users to perform searchs.</p><p>To perform searchs
                the block <em>CDM Taxon Search</em> should be enabled and visible for users
                where they can write the text to be searched. You can find Drupal block configuration
                site at <a href="./?q=admin/build/block">Administer&#45&#62Site building&#45&#62Blocks</a></p> '),
         );
         $form['search_settings']['cdm_dataportal_search_items_on_page'] = array(
           '#type' => 'textfield',
           '#title' => t('Results per page') . ':',
           '#default_value' => variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE),
           '#description' => t('Number of results to display per page.'),
         );
         $form['search_settings']['cdm_search_taxa'] = array(
           '#type' => 'checkbox',
           '#title' => t('Sets the default value of <em>Search for accepted taxa</em> in the advanced search form.'),
           '#default_value' => variable_get('cdm_search_taxa', 1),
           '#description' => t('<p>If checked the <em>Search for accepted taxa </em> option will be enabled in the advanced form.</p>'),
         );
         $form['search_settings']['cdm_search_synonyms'] = array(
           '#type' => 'checkbox',
           '#title' => t('Sets the default value of <em>Search for synonyms</em> in the advanced search form.'),
           '#default_value' => variable_get('cdm_search_synonyms', 1),
           '#description' => t('<p>If checked the <em>Search for synonyms</em> option will be enabled in the advanced form.</p>'),
         );
         $form['search_settings']['cdm_search_common_names'] = array(
           '#type' => 'checkbox',
           '#title' => t('Sets the default value of <em>Search for common names</em> in the advanced search form.'),
           '#default_value' => variable_get('cdm_search_common_names', 0),
           '#description' => t('<p>If checked the <em>Search for common names</em> option will be enabled in the advanced form.</p>'),
         );
         $form['search_settings']['cdm_search_use_default_values'] = array(
           '#type' => 'checkbox',
           '#title' => t('Sets use of default values in the advanced search form.'),
           '#default_value' => variable_get('cdm_search_use_default_values', 1),
           '#description' => t('<p>If checked the defqult values set abovewill be used for the search.</p>'),
         );
         // --- SEARCH TAXA GALLERY ---- //
         $items = variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE);
         $collapsed = FALSE;
         $form_name = CDM_DATAPORTAL_SEARCH_GALLERY_NAME;
         $form_title = 'Taxa Search thumbnails';
         $form_description = 'Search results may show thumbnails. ';
         $form[] = cdm_dataportal_create_gallery_settings_form($form_name, $form_title, $collapsed, $form_description);
         // Comment @WA: D7 form api does not support reset buttons,
         // so to mimic the D5 reset button we add one like this.
         $form['actions']['reset'] = array(
           '#markup' => '<input id="reset" type="reset" class="form-submit" value="' . t('Reset to defaults') . '" />',
           '#weight' => 1000,
         );
         return system_settings_form($form);
+      }
       /**
        * @todo document this function.
        */
       function cdm_settings_layout_media() {
         $form = array();
         $form['media_settings'] = array(
           '#type' => 'fieldset',
           '#title' => t('Media display settings'),
           '#collapsible' => TRUE,
           '#collapsed' => FALSE,
           '#description' => t('This section covers the settings related to the taxa media, that is how each single media should be displayed.'),
         );
         $form['media_settings']['image_gallery_viewer'] = array(
           '#type' => 'select',
           '#title' => t('Image viewer') . ':',
           '#default_value' => variable_get('image_gallery_viewer', 'default'),
           '#options' => array(
             'default' => t('Standard image viewer'),
             'fsi' => t('FSI viewer (requires FSI server!)'),
           ),
         );
         // --- MEDIA GALLERY ---- //
         $form_name = CDM_DATAPORTAL_MEDIA_GALLERY_NAME;
         $form_title = 'Standard viewer';
         $form_description = '<p>Configure the standard image viewer.</p><p><strong>Note:</strong> the image viewer should selected otherwise settings are not taking into account.</p>';
         // $form[] = cdm_dataportal_create_gallery_settings_form($form_name, $form_title, $collapsed);
         // Comment @WA: $collapsed is not defined.
         // $form['media_settings'][] = cdm_dataportal_create_gallery_settings_form($form_name, $form_title, $collapsed, $form_description);
         $form['media_settings'][] = cdm_dataportal_create_gallery_settings_form($form_name, $form_title, FALSE, $form_description);
         // @WA: D7 form api does not support reset buttons,
         // so to mimic the D5 reset button we add one like this.
         $form['actions']['reset'] = array(
           '#markup' => '<input id="reset" type="reset" class="form-submit" value="' . t('Reset to defaults') . '" />',
           '#weight' => 1000,
         );
         return system_settings_form($form);
+      }
       /**
        * GEOSERVICE and Map settings.
        */
       function cdm_settings_geo($form, &$form_state) {
         $form = array();
         /*
         GEO SERVER
         */
         $form['edit_map_server'] = array(
           '#type' => 'fieldset',
           '#tree' => true,
           '#title' => t('EDIT map service'),
           '#collapsible' => TRUE,
           '#collapsed' => TRUE,
           '#description' => t('Configuration and selection of your geo server.
             The Geo Server is responsible for generating the maps.'),
         );
         $current_geoserver_settings = get_edit_map_service_settings();
         $form['edit_map_server']['base_uri'] = array(
           '#type' => 'select',
           '#title' => t('EDIT map service') . ':',
           '#default_value' => $current_geoserver_settings['base_uri'],
           '#options' => unserialize(EDIT_MAPSERVER_URI),
           '#description' => t('Select the EDIT map server you want to use within your data portal.'),
         );
         $form['edit_map_server']['version'] = array(
             '#type' => 'select',
             '#title' => t('Version') . ':',
             '#default_value' => $current_geoserver_settings['version'],
             '#options' => unserialize(EDIT_MAPSERVER_VERSION),
             '#description' => t('The version of the EDIT map services'),
         );
         /*
         MAP SETTINGS
         */
         $form['map_settings'] = array(
           '#type' => 'fieldset',
           '#title' => t('Maps settings'),
           '#collapsible' => TRUE,
           '#collapsed' => TRUE,
           '#description' => t('General configuration for all map types.'),
         );
         $form['map_settings']['cdm_dataportal_geoservice_display_width'] = array(
           '#type' => 'textfield',
           '#title' => t('Maps width') . ':',
           '#default_value' => variable_get('cdm_dataportal_geoservice_display_width', 390),
           '#description' => t('Choose the width of your maps, the height will always
             be the half of the width. A value of 500 means the size will be 500 pixels
             width and 250 pixels height.'),
         );
         $form['map_settings']['cdm_dataportal_geoservice_bounding_box'] = array(
           '#type' => 'textfield',
           '#title' => t('Fixed bounding box') . ':',
           '#default_value' => variable_get('cdm_dataportal_geoservice_bounding_box', '-180,-90,180,90'),
           '#description' => t('Define surrounding of area to be displayed in maps.
             Use "-180,-90,180,90" for the whole world. Leave <strong>empty</strong>
             to let the map <strong>automatically zoom</strong> to the distribution
             area.'),
         );
         $form['map_settings']['cdm_dataportal_geoservice_labels_on'] = array(
           '#type' => 'checkbox',
           '#title' => '<b>' . t('Display area labels') . '</b>',
           '#default_value' => variable_get('cdm_dataportal_geoservice_labels_on', FALSE),
           '#description' => t('Check this if you like area names to be displayed in the maps. DOES IT WORK???? '),
         );
         $form['map_settings']['cdm_dataportal_geoservice_map_caption'] = array(
           '#type' => 'textfield',
           '#title' => t('Map caption') . ':',
           '#default_value' => variable_get('cdm_dataportal_geoservice_map_caption', ''),
           '#description' => t('Define a caption for the map.'),
         );
         $form['map_settings']['cdm_dataportal_geoservice_distributionOpacity'] = array(
           '#type' => 'textfield',
           '#title' => t('Distribution layer opacity') . ':',
           '#default_value' => variable_get('cdm_dataportal_geoservice_distributionOpacity', '0.5'),
           '#description' => t('Valid values range from 0.0 to 1.0. Value 1.0 means the distributions (the countries or regions) will
                                  fully visible, while a value near to 0.0 will be not much visible.'),
         );
         $form['map_settings']['cdm_dataportal_map_openlayers'] = array(
           '#type' => 'radios',
           '#title' => t('Map Viewer') . ':',
           '#options' => array(
 => "OpenLayers dynamic mapviewer",
 => "Plain image",
           ),
           '#default_value' => variable_get('cdm_dataportal_map_openlayers', 1),
           '#description' => t('You can choose from two different map viewers:
             <ul><li><em>OpenLayers</em> displays the maps in an interactive viewer
             which allows zooming and panning. If not enabled the maps will consist
             on a static image. If enabled you can configure the default layer
             (background of your maps) below. Only one of them will be rendered.</li>
             <li><em>Plain image</em> displays the map as a plain non interactive
             image.</li></ul>'),
         );
         $openLayersEnabled = variable_get('cdm_dataportal_map_openlayers', 1) == 1;
         // --- Plain Image Settings --- //
         $form['map_image'] = array(
           '#type' => 'fieldset',
           '#title' => t('Plain image map settings'),
           '#collapsible' => TRUE,
           '#collapsed' => $openLayersEnabled,
           '#description' => t('The settings in this section are still expertimental
             and can only be used with the EDIT map service version 1.1 or above.'),
         );
         $edit_mapserver_version = get_edit_map_service_version_number();
         if ($edit_mapserver_version < 1.1) {
           $form['map_image']['#description'] = '<div class="messages warning">' . t("The selected EDIT map service version has to small version number: $edit_mapserver_version") . '</div>'
             . $form['map_image']['#description'];
+        }
         $form['map_image']['map_base_layer'] = array(
           '#type' => 'textfield',
           '#title' => t('Background layer') . ':',
           '#default_value' => variable_get('map_base_layer', 'cyprusdivs'),
           '#description' => t('Background layer. For available layers inspect !url1 or !url2.', array(
             '!url1' => l(t('deegree-csw'), 'http://edit.africamuseum.be:8080/deegree-csw/md_search.jsp'),
             '!url2' => l(t('geoserver layers'), 'http://edit.africamuseum.be/geoserver/web/'), // http://edit.africamuseum.be/geoserver/rest/layers
           )),
         );
         $form['map_image']['map_bg_color'] = array(
           '#type' => 'textfield',
           '#title' => t('Background color') . ':',
           '#default_value' => variable_get('map_bg_color', '1874CD'),
         );
         $form['map_image']['map_base_layer_style'] = array(
           '#type' => 'textfield',
           '#title' => t('Background layer area style') . ':',
            // Only line color by now.
           '#default_value' => variable_get('map_base_layer_style', 'ffffff,606060,,'),
           '#description' => t('Syntax: {Area fill color},{Area stroke color},{Area stroke width},{Area stroke dash style}'),
         );
         // --- OpenLayers Settings --- //
         $form['openlayers'] = array(
           '#type' => 'fieldset',
           '#title' => t('OpenLayers settings'),
           '#collapsible' => TRUE,
           '#collapsed' => !$openLayersEnabled,
           '#description' => '',
         );
         if (!$openLayersEnabled) {
           $form['openlayers']['#description'] = '<div class="messages warning">' . t('The Openlayers viewer is currently not enabled! (see section Maps settings above )') . '</div>'
             . $form['openlayers']['#description'];
+        }
         $baselayer_options = array(
           /*
          NOTICE: must correspond to the layers defined in
          js/openlayers_,ap.js#getLayersByName()
          */
           'osgeo_vmap0' => "Metacarta Vmap0 (OSGeo server)", // EPSG:4326: EPSG:900913
           'metacarta_vmap0' => "Metacarta Vmap0 (MetaCarta Labs server)", // EPSG:4326, EPSG:900913
           // all others EPSG:900913
           // 'edit-vmap0_world_basic' => 'EDIT Vmap0',
           'edit-etopo1' => "ETOPO1 Global Relief Model",
           'mapnik' => 'OpenStreetMap',
           'osmarender' => 'OpenStreetMap (Tiles@home)',
           'gmap' => 'Google Streets',
           'gsat' => 'Google Satellite',
           'ghyb' => 'Google Hybrid',
           'veroad' => 'Virtual Earth Roads',
           'veaer' => 'Virtual Earth Aerial',
           'vehyb' => 'Virtual Earth Hybrid',
           // 'yahoo' => 'Yahoo Street',
           // 'yahoosat' => 'Yahoo Satellite',
           // 'yahoohyb' => 'Yahoo Hybrid',
         );
         $form['openlayers']['baselayers'] = array(
           '#type' => 'checkboxes_preferred',
           '#title' => t('Base Layers') . ':',
           '#options' => $baselayer_options,
           '#default_value' => variable_get('baselayers', array('metacarta_vmap0' => "metacarta_vmap0", 'PREFERRED' => 'metacarta_vmap0')),
           '#description' => t('Choose the baselayer layer you prefer to use as map background in the OpenLayers dynamic mapviewer.'),
         );
         // cdm_dataportal_geoservice_showLayerSwitcher
         $form['openlayers']['cdm_dataportal_geoservice_showLayerSwitcher'] = array(
           '#type' => 'checkbox',
           '#title' => '<b>' . t('Show Layer Switcher') . '</b>',
           '#default_value' => variable_get('cdm_dataportal_geoservice_showLayerSwitcher', TRUE),
           '#description' => t('
             The Layer Switcher control displays a table of contents
             for the map.  This allows the user interface to switch between
             BaseLayers and to show or hide Overlays.  By default the switcher is
             shown minimized on the right edge of the map, the user may expand it
             by clicking on the handle.'
           ),
         );
         $localhostkey = 'ABQIAAAAFho6eHAcUOTHLmH9IYHAeBRi_j0U6kJrkFvY4-OX2XYmEAa76BTsyMmEq-tn6nFNtD2UdEGvfhvoCQ';
         $gmap_api_key = variable_get('gmap_api_key', 'ABQIAAAAFho6eHAcUOTHLmH9IYHAeBRi_j0U6kJrkFvY4-OX2XYmEAa76BTsyMmEq-tn6nFNtD2UdEGvfhvoCQ');
         $form['openlayers']['gmap_api_key'] = array(
           '#type' => 'textfield',
           '#title' => t('Google maps API key') . ':',
           '#default_value' => variable_get('gmap_api_key', $gmap_api_key),
           '#description' => t('If you want to use the Google Maps Layer, a key is
             needed. If you need a key, visit
             <a href="http://code.google.com/intl/en/apis/maps/signup.html">google maps api key</a>.
             <br/><strong>Note:</strong> The following key: <code>!localhostkey</code>
             is the default key for the localhost (127.0.0.1). The key in use is the
             one above this text.', array('!localhostkey' => $localhostkey)),
         );
         $form['cdm_dataportal_geoservice_map_legend'] = array(
           '#type' => 'fieldset',
           '#title' => t('Map legend'),
           '#collapsible' => TRUE,
           '#collapsed' => TRUE,
           '#description' => t('Configure the maps legend.'),
         );
         $form['cdm_dataportal_geoservice_map_legend']['cdm_dataportal_geoservice_legend_on'] = array(
           '#type' => 'checkbox',
           '#title' => '<b>' . t('Display a map legend') . '</b>',
           '#default_value' => variable_get('cdm_dataportal_geoservice_legend_on', TRUE),
           '#description' => t('Check this if you like a legend to be displayed with the maps.'),
         );
         $form['cdm_dataportal_geoservice_map_legend']['cdm_dataportal_geoservice_legendOpacity'] = array(
           '#type' => 'textfield',
           '#title' => t('Legend opacity'),
           '#default_value' => variable_get('cdm_dataportal_geoservice_legendOpacity', '0.5'),
           '#description' => t('Valid values range from 0.0 to 1.0. Value 1.0 means the legend will be fully visible, while a value near
                                to 0.0 will be not much visible.'),
         );
         $form['cdm_dataportal_geoservice_map_legend']['cdm_dataportal_geoservice_legend_font_size'] = array(
           '#type' => 'textfield',
           '#title' => t('Font size'),
           '#default_value' => variable_get('cdm_dataportal_geoservice_legend_font_size', 10),
           '#description' => t('Font size in pixels.'),
         );
         $fontStyles = array(
 => "plane",
 => "italic",
         );
         $form['cdm_dataportal_geoservice_map_legend']['cdm_dataportal_geoservice_legend_font_style'] = array(
           '#type' => 'select',
           '#title' => t('Available font styles'),
           '#default_value' => variable_get('cdm_dataportal_geoservice_legend_font_style', FALSE),
           '#options' => $fontStyles,
           '#description' => t('Select a font style for the map legend.'),
         );
         $form['cdm_dataportal_geoservice_map_legend']['cdm_dataportal_geoservice_legend_icon_width'] = array(
           '#type' => 'textfield',
           '#title' => t('Legend icon width'),
           '#default_value' => variable_get('cdm_dataportal_geoservice_legend_icon_width', 35),
           '#description' => t('Legend icon width in pixels.'),
         );
         $form['cdm_dataportal_geoservice_map_legend']['cdm_dataportal_geoservice_legend_icon_height'] = array(
           '#type' => 'textfield',
           '#title' => t('Legend icon height'),
           '#default_value' => variable_get('cdm_dataportal_geoservice_legend_icon_height', 15),
           '#description' => t('Legend icon height in pixels.'),
         );
         // @WA: D7 form api does not support reset buttons,
         // so to mimic the D5 reset button we add one like this.
         $form['actions']['reset'] = array(
           '#markup' => '<input id="reset" type="reset" class="form-submit" value="' . t('Reset to defaults') . '" />',
           '#weight' => 1000,
         );
         return system_settings_form($form);
+      }
       /**
        * @todo document this function.
        */
       function cdm_settings_cache() {
         $form = array();
         $form['cache_settings'] = array(
           '#type' => 'fieldset',
           '#title' => t('Cache Settings'),
           '#collapsible' => FALSE,
           '#collapsed' => FALSE,
           '#description' => t('<p>When caching is enabled all single taxon sites are
             stored in an internal drupal cache doing the portal response of taxa pages
             faster. This is possible because the sites are loaded from the cache and
             are not created from scratch.</p>'),
         );
         $form['cache_settings']['cdm_webservice_cache'] = array(
           '#type' => 'checkbox',
           '#title' => t('<strong>Enable caching</strong>'),
           '#options' => cdm_help_general_cache(),
           '#default_value' => variable_get('cdm_webservice_cache', 1),
           '#description' => t('<p>Enable drupal to load taxa pages from the cache.</p>
              <p><strong>Note:</strong> If taxa are modified by the editor or any other
              application the changes will be not visible till the cache is erased.
              Therefore developers should deactived this feature when they are working
              on the CDM Dataportal Module.</p>'),
         );
         $form['cache_settings']['cdm_run_cache'] = array(
           '#markup' => cdm_view_cache_site(),
         );
         // @WA: D7 form api does not support reset buttons,
         // so to mimic the D5 reset button we add one like this.
         $form['actions']['reset'] = array(
           '#markup' => '<input id="reset" type="reset" class="form-submit" value="' . t('Reset to defaults') . '" />',
           '#weight' => 1000,
         );
         return system_settings_form($form);
+      }
       /**
        * Walk and cache all taxon pages.
        */
       function cdm_view_cache_site() {
         $out = '';
         drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cache_all_taxa.js');
         $request_params = array();
         $request_params['query'] = '%';
         // Cache only the dafault classification.
         $request_params['tree'] = variable_get('cdm_taxonomictree_uuid', FALSE);
         $request_params['doTaxa'] = 1;
         $request_params['doSynonyms'] = 0;
         $request_params['doTaxaByCommonNames'] = 0;
         $search_url = cdm_compose_url(CDM_WS_PORTAL_TAXON_FIND . ".json", NULL, queryString($request_params));
         $search_url = uri_uriByProxy($search_url);
         $search_url = rtrim($search_url, '/');
         $taxon_page_url = url('cdm_dataportal/taxon/');
         $out .= t('<p><strong>Cache all taxon pages</strong></p>');
         $out .= '<p>When you launch the cache process the cache is filled and ready to be enabled.<br/>
         Remember that when you load the taxa from the cache last changes on taxa will be not visible till you erase
         the cache and fill it again.</p>';
         $out .= '<p>Before  running the cache bot you have to empty the cache manually.</p>';
         $out .= '<div>' . t('This caching process may take long time and could cause heavy load on your server') . '</div>';
         $out .= '<div id="progress"></div>';
         // Comment @WA: A form within a form is not valid html and not needed here.
         // Also, it would be recommended just to include this part of the form in the
         // rest of the form array in cdm_settings_cache().
         // $out .= '<form id="cache_site">';
         $out .= '<input type="hidden" name="searchTaxaUrl" value="' . $search_url . '"/>';
         $out .= '<input type="hidden" name="taxonPageUrl" value="' . $taxon_page_url . '"/>';
         $out .= '<input type="button" name="start" value="' . t('Start') . '"/>';
         $out .= '<input type="button" name="stop" value="' . t('Stop') . '"/>';
         // $out .= '</form>';
         $out .= '</div>';
         /*
         foreach($taxonPager->records as $taxon){
           cdm_dataportal_taxon_view($uuid);
+        }
         */
         return $out;
+      }
       /**
        * Form validation handler for ?
+       *
        * Comment @WA: currently this handler is not used.
        * It seems partly for cdm_settings_general en partly for cdm_settings_cache?
        * Then you can change the name into cdm_settings_general_validate() or
        * cdm_settings_cache_validate().
        * But cdm_api_secref_cache_clear is not doing anything (yet)?
        */
       function cdm_settings_validate($form, &$form_state) {
         if (!str_endsWith($form_state['values']['cdm_webservice_url'], '/')) {
           // form_set_error('cdm_webservice_url', t("The URL to the CDM Web Service must end with a slash: '/'."));
           $form_state['values']['cdm_webservice_url'] .= '/';
+        }
         if ($form_state['values']['cdm_webservice_cache'] != variable_get('cdm_webservice_cache', 1)) {
           cache_clear_all(NULL, 'cache_cdm_ws');
           // Better clear secref_cache since I can not be sure if the cache has not
           // be used during this response.
           cdm_api_secref_cache_clear();
+        }
+      }
       /**
        * Returns an associative array of the currently chosen settings for the EDIT map service or the defaults as
        * specified in EDIT_MAPSERVER_URI_DEFAULT and EDIT_MAPSERVER_VERSION_DEFAULT:
        *  - base_uri: the protocol and host part , e.g.: http://edit.africamuseum.be
        *  - version: the version, e.g.: v1.1
+       *
        * @return array
        *    An associative array of the currently chosen settings for the EDIT map service or the defaults.
        */
       function get_edit_map_service_settings() {
         $settings = variable_get('edit_map_server', array(
             'base_uri' => EDIT_MAPSERVER_URI_DEFAULT,
             'version' => EDIT_MAPSERVER_VERSION_DEFAULT
+            )
         );
         // replace old non tree like settings by default
         // TODO to be removed after release 3.1.5
         if(!is_array($settings)){
           variable_del('edit_map_server');
           return get_edit_map_service_settings();
+        }
         return $settings;
+      }
       /**
        * Returns the full edit map service URI e.g.: http://edit.africamuseum.be/edit_wp5/v1.1
+       *
        * @return string
        *   The full edit map service URI e.g.: http://edit.africamuseum.be/edit_wp5/v1.1
        */
       function get_edit_map_service_full_uri() {
         $settings = get_edit_map_service_settings();
         return $settings['base_uri'] . EDIT_MAPSERVER_PATH .  '/' . $settings['version'];
+      }
       /**
        * Returns the version number of the currently selected edit mapserver as a float
+       *
        * @return float
        *   The version number of the currently selected edit mapserver as a float.
        *   Returns 0 on error.
        */
       function get_edit_map_service_version_number() {
         $pattern = '/v([\d\.]+).*$/';
         $settings = get_edit_map_service_settings();
         preg_match($pattern, $settings['version'], $matches, PREG_OFFSET_CAPTURE);
         if (isset($matches[1])) {
           // Convert string to float.
           $version = 1 + $matches[1][0] - 1;
           return $version;
+        }
         else {
           // Report error.
           drupal_set_message(t(" Invalid EDIT map service version number: '!version'",
               array(
                 '!version' => $settings['version'],
                 'warning')
+              )
             );
           return 0;
+        }
+      }
       /**
        * Returns the array of selected items in a options array
+       *
        * @param array $options
        *   An options array as generated by a form element like checkoxes, select ...,
        */
       function get_selection($options) {
         $selection = array();
         foreach ($options as $key=>$val) {
           if (!empty($val)) {
             $selection[] = $val;
+          }
+        }
         return $selection;
+      }
       /**
        * Implements hook_element_info().
+       *
        * Allows modules to declare their own Form API element types and specify their default values.
+       *
        * @see http://api.drupal.org/api/drupal/modules!system!system.api.php/function/hook_element_info/7
        */
       function cdm_dataportal_element_info() {
         $type['checkboxes_preferred'] = array(
           '#input' => TRUE,
           '#process' => array('checkboxes_preferred_expand'),
           '#after_build' => array('checkboxes_preferred_after_build'),
           '#theme' => array('checkboxes_preferred'),
           // '#theme_wrapper' => array('form_element'),
         );
         return $type;
+      }
       /**
        * #process callback function for the custom form element type 'checkbox_preferred'
+       *
+       *
        */
       function checkboxes_preferred_expand($element, &$form_state, $form) {
         // First of all create checkboxes for each of the elements
         $element = form_process_checkboxes($element);
         $children = element_children($element);
         $element['table_start'] = array(
           '#markup' => '<table class="checkboxes_preferred"><tr><th></th><th>' . t('Enabled') . '</th><th>' . t('Default') . '</th></tr>',
           '#weight' => -1,
         );
         // prepare first part each of the table rows which contains the row label
         $weight = 0;
         foreach ($children as $key) {
           $odd_even = $weight % 4 == 0 ? 'odd' : 'even';
           $element[$key]['#weight'] = $weight;
           $element[$key]['#prefix'] = '<tr class="' . $odd_even . '"><td>' . t($element['#options'][$key]) . '</td><td>';
           $element[$key]['#suffix'] = '</td>';
           unset($element[$key]['#title']);
           $weight += 2;
+        }
         $weight = 0;
         // add a radio button to each of the checkboxes, the
         // check boxes have already been created at the beginning
         // of this function
         if (count($element['#options']) > 0) {
           foreach ($element['#options'] as $key => $choice) {
             if (!isset($element[$key . '_preferred'])) {
               $element[$key . '_preferred'] = array(
                 '#type' => 'radio',
                 '#name' => $element['#parents'][0] . '_preferred',
                 '#return_value' => check_plain($key),
                 '#default_value' => empty($element['#default_value_2']) ? NULL : $element['#default_value_2'],
                 '#attributes' => $element['#attributes'],
                 '#parents' => $element['#parents'],
                 // '#spawned' => TRUE,
                 '#weight' => $weight + 1,
                 '#prefix' => '<td>',        // add a prefix to start a new table cell
                 '#suffix' => '</td></tr>',  // add a prefix to close the tabel row
               );
+            }
             $weight += 2;
+          }
+        }
         // end the table
         $element['table_end'] = array(
           '#markup' => '</table>',
           '#weight' => $weight++,
         );
         return $element;
+      }
       /**
        * Theme function for the custom form field 'checkboxes_preferred'.
        */
       function theme_checkboxes_preferred($variables) {
         $element = $variables['element'];
         $out = '<div id="edit-baselayers-wrapper" class="form-item">';
         $out .= '<label for="edit-baselayers">' . $element['#title'] . '</label>';
         $out .= drupal_render_children($element);
         $out .= '<div class="description">' . $element['#description'] . '</div>';
         $out .= '</div>';
         return $out;
+      }
       /**
        * Callback for checkboxes preferred for widget which will
        * be called after the form or element is built. The call
        * back is configured in the form element by setting it as
        * #after_build parameter.
+       *
        * @see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#after_build
+       *
        * @param $form
        *   Nested array of form elements that comprise the form.
        * @param $form_state
        *   A keyed array containing the current state of the form.
+       *
        * @return the modified form array
        */
       function checkboxes_preferred_after_build($form, &$form_state) {
         $parent_id = $form['#parents'][0];
         if ($_POST && count($_POST) > 0) {
           // First pass of form processing.
           $preferred_layer = $_POST[$parent_id . '_preferred'];
           $form['#value']['PREFERRED'] = $preferred_layer;
           $form_state[$parent_id] = $form['#value'];
           $form_state['values']['baselayers'] = $form['#value'];
+        }
         else {
           // Second pass of form processing.
           $preferred_layer = $form['#value']['PREFERRED'];
+        }
         // Also set the chosen value (not sure if this is good Drupal style ....).
         foreach ($children = element_children($form) as $key) {
           if (!empty($form[$key]['#type']) && $form[$key]['#type'] == 'radio') {
             $form[$key]['#value'] = $preferred_layer;
+          }
+        }
         // The default layer must always be enabled.
         $form[$preferred_layer]['#value'] = $preferred_layer;
         return $form;
+      }

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