EDIT

<?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',

      'v1.2' => 'v1.2',

      'v1.3_dev' => 'v1.3_dev'

    )

  )

);

define('EDIT_MAPSERVER_URI_DEFAULT', 'http://edit.africamuseum.be');

define('EDIT_MAPSERVER_VERSION_DEFAULT', 'v1.2');

// --- 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');

define('CDM_TAXON_PROFILE_IMAGE', 'cdm_taxon_profile_image');

define('CDM_TAXON_PROFILE_IMAGE_DEFAULT', serialize(

    array(

        'show' => 0,

        'maxextend' => 184,

        'media_uri_query' => '',

        'custom_placeholder_image_on' => 0,

        'custom_placeholder_image_fid' => ''

    )

  )

);

/**

 * @todo document this function

 */

function get_taxon_tabs_list() {

  return array(

    0 => 'General',

    1 => 'Synonymy',

    2 => 'Images',

    3 => 'Specimens',

    4 => '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('CDM_PART_DEFINITIONS', 'cdm-part-definitions');

define('CDM_PART_DEFINITIONS_DEFAULT', serialize(

  array(

      'ZoologicalName' => array(

        'namePart' => array('name' => TRUE),

        'nameAuthorPart' => array('name' => TRUE),

        'referencePart' => array('authors' => TRUE),

        'microreferencePart' => array('microreference' => TRUE),

        'statusPart' => array('status' => TRUE),

        'descriptionPart' => array('description' => TRUE),

      ),

      'BotanicalName'=> array(

        'namePart' => array('name' => TRUE),

        'nameAuthorPart' => array('name' => TRUE, 'authors' => TRUE),

        'referencePart' => array('reference' => TRUE, 'microreference' => TRUE),

        'statusPart' => array('status' => TRUE),

        'descriptionPart' => array('description' => TRUE),

      ),

     '#DEFAULT' => array(

        'namePart' => array(

            'name' => TRUE

        ),

        'nameAuthorPart' => array(

            'name' => TRUE,

            'authors' => TRUE

        ),

        'referencePart' => array(

            'reference' => TRUE

        ),

        'microreferencePart' => array(

            'microreference' => TRUE,

        ),

        'statusPart' => array(

            'status' => TRUE,

        ),

        'descriptionPart' => array(

            'description' => TRUE,

        ),

      )

    )

  )

);

define('CDM_NAME_RENDER_TEMPLATES', 'cdm-name-render-templates');

define('CDM_NAME_RENDER_TEMPLATES_DEFAULT', serialize(

   array (

     'taxon_page_title,polytomousKey'=> array(

          'namePart' => array('#uri' => TRUE),

        ),

      'taxon_page_synonymy,related_taxon'=> array(

          'nameAuthorPart' => array('#uri' => TRUE),

          'referencePart' => TRUE,

          'statusPart' => TRUE,

          'descriptionPart' => TRUE,

        ),

      'acceptedFor,typedesignations,list_of_taxa' => array(

          'nameAuthorPart' => array('#uri' => TRUE),

          'referencePart' => TRUE,

        ),

      '#DEFAULT' => array(

          'nameAuthorPart' => array('#uri' => TRUE),

          'referencePart' => TRUE,

       )

    )

));

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');

define('CDM_TAXON_MEDIA_FILTER', 'cdm_taxon_media_filter');

define('CDM_TAXON_MEDIA_FILTER_DEFAULT', serialize(

    array(

        'includeTaxonDescriptions' => 'includeTaxonDescriptions',

        'includeOccurrences' => 0,

        'includeTaxonNameDescriptions' => 0

     )

  ));

define('CDM_MAP_DISTRIBUTION', 'cdm_map_distribution');

define('CDM_MAP_DISTRIBUTION_DEFAULT', serialize(array(

  // needs to be merged with user setting by drupal_array_merge_deep()

  'width' => 512, // optimum size for OSM layers is 512

  'height' => 512 / 2, // optimum size for OSM layers 256

  'bbox' => '', // empty to allow automatic zooming to extend

  'show_labels' => FALSE,

  'caption' => '',

  'distribution_opacity' => '0.5',

  'map_type' => 1, //  1 = 'openlayers', 0 = 'image'

  'image_map' => array(

    'base_layer' => '', // none, formerly this was cyprusdivs

    'bg_color' => '1874CD',

    'layer_style' => 'ffffff,606060,,',

  ),

  'openlayers' => array(

    'base_layers' =>  array(

      // A layer MUST NOT BE SET in the defaults,

      // otherwise it can not be overidden by the user settings:

      // 'osgeo_vmap0' => 'osgeo_vmap0',

      // it is sufficient to define the preferred layer,

      // since it will automatically be enabled:

      'PREFERRED' => 'osgeo_vmap0'),

     'custom_wms_base_layer' => array(

            'name' => NULL,

            'url' => NULL,

            'params' =>  NULL,

            'projection' => NULL,

            'max_extent' => NULL,

            'units' => NULL

     ),

    'show_layer_switcher' => TRUE,

    'display_outside_max_extent' => FALSE

  ),

  'legend' => array(

    'show' => TRUE,

    'opacity' => '0.5',

    'font_size' => 10,

    'font_style' => FALSE,

    'icon_width' => 35,

    'icon_height' => 15

  )

)));

/**

 * Merges the named array variable with the array of defaults.

 *

 * @param string $variable_name

 *     The variable name

 * @param string | array $default

 *     The array containing the default values either as array or serialized as string.

 *     Unserialization is cared for if nessecary

 * @return array

 *     The merged array as returnd by drupal_array_merge_deep()

 */

function get_array_variable_merged($variable_name, $default){

    // unserialize if nessecary

    if(!is_array($default)){

      $default = unserialize($default);

    }

    $variable = variable_get($variable_name, array());

    return drupal_array_merge_deep($default, $variable);

}

/**

 * @todo document this function.

 */

function getGallerySettings($gallery_config_form_name) {

  return get_array_variable_merged($gallery_config_form_name, CDM_DATAPORTAL_GALLERY_SETTINGS);

}

/**

 * 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('administer cdm_dataportal'),

    '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,

  );

}

/**

 * @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('The <em>CDM Server</em> exposes data stored in a

        CDM data base to the web via RESTful web services and thus is the source of the data

        to be displayed by a CDM DataPotal.'),

  );

  $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://myserver.net/cdmserver/myproject"</em>'),

    '#default_value' => variable_get('cdm_webservice_url', NULL),

  );

  $form['cdm_webservice']['cdm_webservice_debug'] = array(

    '#type' => 'markup',

    '#markup' => '<b>Debug CDM Web Service:</b> The web service debug box has completely been replaced '

      . 'by  the ' . l('CDM web service debug block', 'admin/structure/block/manage/cdm_api/cdm_ws_debug/configure')

      . '. It is usually only visible for administrative roles like <i>administrator</i> and <i>CDM admin</i>'

  );

  $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['taxon_tree'] = 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['taxon_tree'][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['taxon_tree']['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['aggregation'] = array(

      '#type' => 'fieldset',

      '#title' => t('Aggregation of data'),

      '#collapsible' => FALSE,

      '#description' => t("This section covers the different aspects of aggregating information.

          <p>

          </p>"),

  );

  $form['aggregation'][CDM_TAXON_MEDIA_FILTER] = array(

      '#type' => 'checkboxes',

      '#title' => 'Taxon media filter',

      '#default_value' => variable_get(CDM_TAXON_MEDIA_FILTER, unserialize(CDM_TAXON_MEDIA_FILTER_DEFAULT)),

      '#options' => array(

          'includeTaxonDescriptions' => 'Media in taxon descriptions',

          'includeTaxonNameDescriptions' => 'Media in name descriptions',

          'includeOccurrences' => 'Media related to specimens and occurrences',

      ),

      '#description' => 'This filter configures which images should be taken into account.',

  );

  $form['aggregation']['notice'] = array(

      '#markup' => '<strong>NOTICE:</strong> The below aggregation settings can slow down the data portal, so you may want to sensibly apply these setting and you may also

          want to make use of the caching capabilities of the dataportal.',

  );

  $form['aggregation']['media_aggregation'] = array(

      '#type' => 'fieldset',

      '#title' => t('Media aggregation'),

      '#collapsible' => FALSE,

      '#collapsed' => TRUE,

      '#description' => t("The media aggregation is also affected by the settigs in \"<strong>Aggregation via taxon relationsships</strong>\" below."),

  );

  $form['aggregation']['media_aggregation']['cdm_images_include_children'] = array(

      '#type' => 'select',

      '#title' => t('Aggregation of taxon pictures') . ':',

      '#default_value' => variable_get('cdm_images_include_children', FALSE),

      '#options' => array(

          0 => "Show only pictures of the current taxon",

          1 => "Include pictures of taxonomic children",

      ),

      '#description' => t("Choose whether to include the images of the taxonomic children. This will affect the <em>Images</em> tab and image tumbnails like in the search results."),

  );

  $form['aggregation']['aggregate_by_taxon_relationships'][CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS] = array(

      '#type' => 'fieldset',

      '#attributes' => array('class'=>array('clearfix')),

      '#title' => t('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['aggregation']['aggregate_by_taxon_relationships'][CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS]['direct'] = array(

      '#type' => 'checkboxes',

      '#title' => t('Direct'),

      '#options' => $taxonRelationshipTypeOptions,

      '#default_value' => $aggregate_by_taxon_relationships['direct'],

  );

  $form['aggregation']['aggregate_by_taxon_relationships'][CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS]['invers'] = array(

      '#type' => 'checkboxes',

      '#title' => t('Invers'),

      '#options' => $taxonRelationshipTypeOptions,

      '#default_value' => $aggregate_by_taxon_relationships['invers'],

  );

  // ----------------------

  $form['cdm_js_devel_mode'] = array(

      '#type' => 'checkbox',

      '#title' => 'Java-script developer mode',

      '#default_value' => variable_get('cdm_js_devel_mode', FALSE),

      '#description' => 'In production envirionments the java script libraries

      the cdm_dataportal is making use of are compressed and optimized. This

      is good for performance but a caveat if you need to debug java-script. When the

      java-script developer mode is enabled the uncompressed and commented developer

      versions of java-script libraries will be used where possible.

      <br/><strong>Do not use this option in production!</strong>'

  );

  // 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() {

  $form = array();

  $form['about'] = array(

    '#markup' => '<h4>' . t('Portal Layout') . '</h4><p>' . 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.') . '</p>',

  );

  // ---- footnotes --- //

  $form['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['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['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['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['footnotes']['annotations_types_as_footnotes']['#default_value'] = $annotationsTypesAsFootnotes;

  }

  // --- Advanced Search --- //

  $form['asearch'] = array(

      '#type' => 'fieldset',

      '#title' => t('Advanced search'),

      '#collapsible' => FALSE,

      '#collapsed' => FALSE,

  );

  $form['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.'),

  );

  // ---- Taxon Name Rendering --- //

  $form['taxon_name'] = array(

      '#type' => 'fieldset',

      '#title' => t('Taxon name display'),

      '#collapsible' => TRUE,

      '#collapsed' => TRUE,

      '#description' => t('The display of taxon names is configured by two parts.'

          . 'The <srong>name render templates</strong> define the parts of the name to be displayed in the different areas of the data portal pages.'

          . 'The name parts are defined in the <stong>part definitions</strong>'),

  );

  drupal_add_js(

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

         // pretty print json

         var json_text = jQuery(\'#edit-' . CDM_PART_DEFINITIONS . '\').val();

         var obj = JSON.parse(json_text);

         jQuery(\'#edit-' . CDM_PART_DEFINITIONS . '\').val(JSON.stringify(obj, undefined, 2));

         json_text = jQuery(\'#edit-' . CDM_NAME_RENDER_TEMPLATES . '\').val();

         obj = JSON.parse(json_text);

         jQuery(\'#edit-' . CDM_NAME_RENDER_TEMPLATES . '\').val(JSON.stringify(obj, undefined, 2));

       });'

      ,array(

          'type' => 'inline',

          'scope' => 'footer'

      )

  );

  //TODO remove after all portals are using the settings

  $default_part_definitions = theme('get_partDefinition', array());

  if(!is_array($default_part_definitions)) {

    $default_part_definitions = unserialize(CDM_PART_DEFINITIONS_DEFAULT);

  }

  $form['taxon_name'][CDM_PART_DEFINITIONS] = array(

      '#type' => 'textarea',

      '#title' => t('Part definitions'),

      '#element_validate' => array('form_element_validate_json'),

      '#default_value' =>  json_encode(variable_get(CDM_PART_DEFINITIONS, $default_part_definitions)),

      '#description' => '

          <p>

          (Clearing the text area will reset it to the default)

          </p>

          <p>

           The part definitions define the specific parts of which a rendered taxon name plus additional information will consist.

          </p>

          <p>

           A full taxon name plus additional information can consist of the following elements:

          <ul>

             <li>name: the taxon name inclugin rank nbut without author</li>

             <li>authors:  The authors of a reference, also used in taxon names</li>

             <li>reference: the nomenclatural reference,</li>

             <li>microreference:  Volume, page number etc.</li>

             <li>status:  The nomenclatural status of a name</li>

             <li>description: name descriptions like protologues etc ...</li>

          </ul>

          </p>

          <p>

           These elements are combined in the part definitions array to from the specific parts to be rendered.

           (The taxon name "Lapsana communis L., Sp. Pl.: 811. 1753" shall be an example in the following)

           Usually the following parts are formed:

          <ul>

            <li>namePart: the name and rank (in example: "Lapsana communis")</li>

            <li>authorshipPart: the author (in example: "L.")</li>

            <li>nameAuthorPart: the combination of name and author part (in example: "Lapsana communis L.").</li>

               This is useful for zoological names where the authorshipPart belongs to the name and both should</li>

               be combined when a link to the taxon is rendered.</li>

            <li>referencePart: the nomencaltural reference (in example: "Sp. Pl. 1753")</li>

            <li>microreferencePart: usually the page number (in example ": 811.")</li>

            <li>statusPart: the nomenclatorical status</li>

            <li>descriptionPart: name descriptions like protologues etc ...</li>

          </ul>

          </p>

          <p>

           Each set of parts is dedicated to render a specific TaxonName type, the type names are used as keys for the

           specific parts part definitions:

          <ul>

            <li>BotanicalName</li>

            <li>ZoologicalName</li>

            <li>#DEFAULT: covers ViralNames and other NonViralNames

          </ul>

           An example:

          <pre>

           {

            "ZoologicalName": {

              "namePart": {

                "name": true

              },

              "referencePart": {

                "authors": true

              },

              "microreferencePart": {

                "microreference": true

              },

              "statusPart": {

                "status": true

              },

              "descriptionPart": {

                "description": true

              }

            },

            "BotanicalName": {

              "namePart": {

                "name": true,

                "authors": true

              },

              "referencePart": {

                "reference": true,

                "microreference": true

              },

              "statusPart": {

                "status": true

              },

              "descriptionPart": {

                "description": true

              }

            }

          }

           </pre>',

  );

  //TODO remove after all portals are using the settings

  $default_render_templates = theme('get_nameRenderTemplate', array());

  if(!is_array($default_render_templates)) {