EDIT

<?php

// $Id$

/*

 * @file

 * cdm_dataportal

 *

 * Copyright (C) 2007 EDIT

 * European Distributed Institute of Taxonomy

 * http://www.e-taxonomy.eu

 * 

 */

require_once('cdm_dataportal.theme.php');

/* ====================== hook implementations ====================== */

/**

 * Implementation of hook_help()

 *

 * Display help and module information

 * @param section which section of the site we're displaying help

 * @return help text for section

 */

function cdm_dataportal_help($section='') {

  $out = '';

  switch ($section) {

    case "admin/modules#description":

      $out = t("The dataportal publishes CDM data hosted in a CommunityStore on the web.");

      break;

  }

  return $out;

}

/**

 * Implementation of hook_perm()

 *

 * Valid permissions for this module

 * @return array An array of valid permissions for the portfolio module

 */

function cdm_dataportal_perm() {

  return array(

    	'administer cdm_dataportal',

        'cdm_dataportal view notes',

  //TODO which else permission are required? -> check the WP6 requirements document

  );

}

/**

 * Implementation of hook_menu()

 */

function cdm_dataportal_menu($may_cache) {

  $items = array();

  if ($may_cache) {

    $items[] = array(

      'path' => 'admin/settings/cdm_dataportal',

      'title' => t('CDM Dataportal'),

      'description' => t('Setting for the CDM Dataportal'),

      'access' => user_access('administer cdm_dataportal'),

      'callback' => 'drupal_get_form',

      'callback arguments' => 'cdm_dataportal_settings',

    );

    /*$items[] = array(

      'path' => 'admin/settings/cdm_dataportal/ws',

      'title' => t('Web Service'),

      'description' => t('Setting for the CDM Dataportal'),

      'access' => user_access('administer cdm_dataportal'),

      'callback' => 'drupal_get_form',

      'callback arguments' => 'cdm_dataportal_settings',

      'weight' => 1,

      'type' => MENU_DEFAULT_LOCAL_TASK,

    );*/

    $items[] = array(

	    'path' => 'cdm_dataportal/names',

	    'callback' => 'cdm_dataportal_view_names',

	    'access' => true,

	    'type' => MENU_CALLBACK, 

    );

    // optional callback arguments: page

    $items[] = array(

	    'path' => 'cdm_dataportal/taxon',

	    'callback' => 'cdm_dataportal_view_taxon',

	    'access' => true,

	    'type' => MENU_CALLBACK, 

    // expected callback arguments: name_uuid

    );

    $items[] = array(

      'path' => 'cdm_dataportal/search/taxon',

      'callback' => 'cdm_dataportal_view_search_taxon',

      'access' => true,

      'type' => MENU_CALLBACK, 

    );

    $items[] = array(

      'path' => 'cdm/xml2json',

      'callback' => 'cdm_view_xml2json',

      'access' => true,

      'type' => MENU_CALLBACK, 

    );

  }

  drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal.css');

  //drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');

  drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_screen.css', 'screen');

  return $items;

}

/**

 * Implementation of hook_block()

 *

 * Provides the following blocks:

 *  0: list of links useful during development

 *

 * @param String $op

 * @param int $delta

 */

function cdm_dataportal_block($op='list', $delta=0) {

  // listing of blocks, such as on the admin/block page

  if ($op == "list") {

    $block[0]["info"] = t("CDM DataPortal DevLinks");

    $block[1]["info"] = t("CDM DataPortal Credits");

    $block[2]["info"] = t("CDM Search Taxa");

    $block[3]["info"] = t("CDM Filters");

    return $block;

  }

  else if ($op == 'view') {

    switch($delta){

      case 0:

        $block['subject'] = t('CDM DataPortal DevLinks');

        $block['content'] = '<ul>

        <li>'.l('A Taxon Page', cdm_dataportal_taxon_path('5000001-stub')).'</li>

        <li>'.l('Name List - page1 of A', 'cdm_dataportal/names/A/1')

        //.'</li><li>'.l('xml2json', 'cdm/xml2json/namelist;startwith=A.xml')

        .'</li>

        </ul>';

        return $block;

      case 1:

        $block['subject'] = t('Credits');

        $block['content'] = theme('cdm_credits');

        return $block;

      case 2:

        $block['subject'] = t('Search Taxa');

        $block['content'] = drupal_get_form('cdm_dataportal_search_taxon_form');

        return $block;

    }

  }

}

/**

 * Implementation of hook_validate()

 *

 * @param $element

 */

function cdm_dataportal_settings_validate($form_id, $form_values){

  if (!str_endsWith($form_values['cdm_webservice_url'], '/')) {

    form_set_error('cdm_webservice_url', t("The URL to the CDM Web Service must end with a slash: '/'."));

  }

  $cdm_webservice_url_changed = variable_get('cdm_webservice_url', '') != $form_values['cdm_webservice_url'];

  if ($cdm_webservice_url_changed) {

    $form_values['cdm_secUuid_default'] = '';

    //TODO does the currentSecUuid need to be stored?

    //   Yes - if switching to another concept is permanent until an other concept switch is used.

    //   NO  - if a user only 'visits' other concepts until this context is left by visiting a non taxon page

    //         , or explicitly when a concept switch is used.

    //         other concept could be activated permanently by personal preference settings

    //

    //  >> NO seems to be the desired solution <<

    //

    _cdm_dataportal_set_currentSecUuid(false);

    // reset all cdm related data stored in the session

    // cdm_dataportal_session_clear($form_values['cdm_webservice_url']); // cdm_webservice_url is not further stored here

    // clear the cdm webservice cache

    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();

  }

  if($form_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();

  }

}

/* 

function cdm_dataportal_session_clear($cdm_ws_uri_update = false){

  $_SESSION['cdm'] = null;

  if(is_string($cdm_ws_uri_update)){

    $_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);

  }

}

function cdm_dataportal_session_validate(){

  if(!isset($_SESSION['cdm']['ws_uri'])){

    $_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', false));

  } else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', false)){

    cdm_dataportal_session_clear(variable_get('cdm_webservice_url', false));

  }

}

*/

function cdm_dataportal_search_taxon_form(){

  $url = 'cdm_dataportal/search/taxon';

  $form['#method'] = 'get';

  $form['#process'] = array('cdm_dataportal_search_process' => array());

  $form['#action'] = url($url, NULL, NULL, true);

  $form['queryString'] = array(

    '#type' => 'textfield',

    '#size' => 20,

    '#attributes' => array('title' => t('Enter the name or part of a name you wish to search for.')),

    '#default_value' => (isset($_SESSION['cdm']['search']['queryString']) ? $_SESSION['cdm']['search']['queryString'] : ''),

  );

  $form['mode'] =  array(

    '#type' => 'select',

    '#title' => t('Search Mode'),

    '#options' => array(

        'EXACT' => t('Exact'),

        'BEGINNING' => t('Beginning'),

        'ANYWHERE' => t('Anywhere')

        ),

    '#description'   => t('* can always be used as wildcard'),

    '#default_value' => (isset($_SESSION['cdm']['search']['mode']) ? $_SESSION['cdm']['search']['mode'] : 'start'),

  );

  /*$form['onlyAccepted'] = array(

    '#type' => 'checkbox',

    '#title' => t('Only Accepted'),

    '#attributes' => array('title' => t('Search only for taxa which are accepted by the current treatment.')),

    '#default_value' => isset($_SESSION['cdm']['search']['onlyAccepted']) && $_SESSION['cdm']['search']['onlyAccepted'],

  );

  */

  /*

  $form['vernacular'] = array(

    '#type' => 'checkbox',

    '#title' => t('Vernacular Names'),

    '#attributes' => array('title' => t('Search for vernacular names.')),

    '#default_value' => isset($_SESSION['cdm']['search']['vernacular']) && $_SESSION['cdm']['search']['vernacular'],

  );

  $form['language'] =  array(

    '#type' => 'select',

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

    '#options' => array(

        '*' => t('ALL')

        ),

    '#description'   => t('The language of the vernacular name'),

    '#default_value' => (isset($_SESSION['cdm']['search']['language']) ? $_SESSION['cdm']['search']['language'] : ''),

  );

  */

  $form['page'] = array(

  '#type' => 'hidden',

  '#value' => '1',

  );

  $form['submit'] = array(

  '#type' => 'submit',

  '#name' => '', 

  '#value' => t('Search'),

  );

  // clean URL get forms breaks if we don't give it a 'q'.

  if (!(bool)variable_get('clean_url', '0')) {

    $form['q'] = array(

      '#type' => 'hidden',

      '#value' => $url,

      '#name' => 'q',

    );

  }

  return $form;

}

//TODO is this function REACHABLE and thus in use??

function cdm_dataportal_search_process($form) {

  unset($form['form_id']);

  unset($form['form_token']);

  return $form;

}

/**

 * Filters $_REQUEST by a list of valid request  parameters and also sets defaults if required.

 * returns the processed request parameters submitted by the search form.

 */

function cdm_dataportal_search_form_request(){

  // keys map $REQUEST Keys values are optional default parameters if not null

  static $search_form_params = array('queryString'=>null, 'onlyAccepted' =>'0', 'page'=>null,  'pagesize'=>15, 'mode'=>null);

  $form_params = array();

  foreach($search_form_params as $key=>$default ){

    $form_params[$key] = ( isset($_REQUEST[$key]) && $_REQUEST[$key] != '' ? $_REQUEST[$key] : $default);

  }

  $_SESSION['cdm']['search'] = $form_params;

  return $form_params;

}

/* UNREACHABLE since action of form directly links to view

function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {

  $_SESSION['cdm']['search'] = $form_values;

  //return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];      

  return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');  

  //$paramstr = compose_url_prameterstr($form_values);

  //return url('/cdm_dataportal/search/taxon/', $paramstr);

}

*/

/* ====================== menu callback functions ====================== */

/**

 * Generate main administration form.

 *

 * @return

 *   An array containing form items to place on the module settings page.

 */

function cdm_dataportal_settings(){

  $form = cdm_api_settings_form();

  //TODO: settings are still incomplete, compare with trunk/dataportal/inc/config_default.php.inc

  $form['cdm_dataportal'] = array(

      '#type' => 'fieldset',

      '#title' => t('CDM DataPortal'),

      '#collapsible' => FALSE,

      '#collapsed' => TRUE,

  );

  $form['cdm_dataportal']['secuuid_widget'] = array(

    '#type' => 'select_secuuid',

    '#title' => t('Default Concept Reference'),

    '#description'   => t('The default \'sensu\' reference to start the cdm_dataportal with. Per user choices are possible and may override this value.'),

    '#varname' => 'cdm_secUuid_default',

    '#multiple' => false

  );

  return system_settings_form($form);

}

/**

 * Implementation of hook_elements().

 */

function cdm_dataportal_elements() {

  $type['select_secuuid'] = array(

    '#input' => TRUE, 

    '#process' => array('cdm_dataportal_select_secuuid_expand' => array()),

    //'#validate' => array('cdm_dataportal_select_secuuid_validate' => array()),

    //'#default_value' => array(),

  );

  return $type;

}

/*

 * 

 */

function cdm_dataportal_select_secuuid_expand($element){

  $element['#tree'] = FALSE;

  // any value submitted?

  if(isset($element['#post'][$element['#varname']])){

    $selected_values = $element['#post'][$element['#varname']];

  } else {

    // use those store in drupal

    $selected_values = variable_get( $element['#varname'], array());

  }

  if(!is_array($selected_values)){

    $selected_values = array($selected_values);

  }

  $options = array();

  foreach($selected_values as $secUuid){

    $options[$secUuid] = cdm_taxontree_secRefTitle_for($secUuid);

  }

  $element[$element['#varname']] =  array(

    '#type' => 'select',

    '#options' => $options,

    '#default_value' => array_values($options),

    '#size' => $element['#multiple'] ? 12 : 2,

    '#multiple' => $element['#multiple'],

  );

  return $element;

}

/**

 * Displays a list of the known taxonomic names. Long lists are split up into multiple pages

 *

 * TODO: parameters are still preliminar

 * @param String $page page number to diplay defaults to page 1

 * @param boolean $hide_unaccepted whether to hide nams which are not accepted by the current view

 */

function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = false ){

  $request_params  = array(

    'q' => $beginsWith, 

         //'sec' = '',

         //'higherTaxa' => getFiters(),

          // 'matchAnywhere' => false, // default is false

    'page' => $page, 

    'onlyAccepted' => $onlyAccepted, 

    'pagesize' => 20  /*$_SESSION['cdm']['namelist_pagesize'] */);

  $taxonSTOs = cdm_ws_get(CDM_WS_FIND_TAXA, $request_params);

  /*

   * FIXME the filter for accepted names will be a form element, thus this widget

   * should be generated via form api preferably as block

   */

  //$out  = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);

  //$out .= theme('cdm_dataportal_widget_names_list', $names, $page);

  $out .= theme('cdm_listof_taxa', $taxonSTOs);

  return $out;

}

/**

 * The taxon page gives detailed information on a taxon, it shows:

 *  - Taxon name

 *  - Full list of synonyms homotypic synonyms on top, followed by the

 *    heterotypic and finally followed by misapplied names.

 *    The list is ordered historically.

 *  - All facts associated with the very taxon concept and taxon name.

 *

 * @param String $uuid the UUID of the taxon

 */

function cdm_dataportal_view_taxon($uuid, $arg2 = null){

  if(isset($arg2) && !is_numeric($arg2)){

    switch ($args[0]){

      case 'alternatives':

        $alternatives = cdm_ws_get(CDM_WS_TAXON_ALTERNATIVES, $uuid);

        return theme('cdm_alternative_taxa', $alternatives);

    }

  } else {

    // display the page for the taxon defined by $uuid

    $taxonTO = cdm_ws_get(CDM_WS_TAXON ,$uuid);

    if(!$taxonTO){

      drupal_set_title(t('Taxon does not exist'));

      return false;   

    }

    _cdm_dataportal_set_currentSecUuid($taxonTO->sec->uuid);

    drupal_set_title(theme('cdm_taxon', $taxonTO, true));

    //TODO retrieve complete synonymy and other data

    $out = theme('cdm_taxon_page', $taxonTO);

    return $out;

  }

}

/**

 * Expected URL request parameters:

 *  - text

 *  - language

 *  - vernacular

 * 

 * future extensions to meet palmweb mockup requirements:

 *  - habitat

 *  - uses

 *  - conservation status

 *  - locality / tdwg region

 */

function cdm_dataportal_view_search_taxon(){

  $request_params = cdm_dataportal_search_form_request();

  $sw_params = array_replace_key($request_params, array('queryString'=> 10 ));

  $resultPageSTO = cdm_ws_get(CDM_WS_FIND_TAXA, $sw_params);

  $resultPageSTO->pageNumber = $request_params['page'];

  return theme('cdm_search_results', $resultPageSTO, 'cdm_dataportal/search/taxon', $request_params);

}

function cdm_view_xml2json(){

  $file = arg(2);

  $datastr = get_content(variable_get('cdm_webservice_url', '').$file);

  return  xml2json::transformXmlStringToJson($datastr);

}

/**

 * Get a term for the current locale from the $localised_terms array.

 * Uses global variable $locale from drupal (see drupal functions locale_initialize() for details)

 * Function name is adapted from the drupal function t().

 *

 */

function cdm_dataportal_t($localised_terms){

  global $locale;  // drupal variable containing the current locale

  return cdm_get_localised_term($localised_terms, $locale);

}

/* ====================== other functions ====================== */

/**

 * Enter description here...

 *

 * @param String $uuid the UUID of the taxon

 * @return the URL

 */

function cdm_dataportal_taxon_path($uuid){

  return 'cdm_dataportal/taxon/'.$uuid;

}

/**

 * Creates a short taxonname by using the taggename field of NameSTO or NameTO instances.

 * If the taggename if empty the fullname will be returned.

 *

 * @param unknown_type $NameSTO a NameSTO, TreeNode or NameTO instance

 * @return string

 */

function cdm_dataportal_shortname_of($NameSTO){

  $name = '';

  // get all tagged text tokens of the scientific name

  foreach($NameSTO->taggedName as $tagtxt){

      if($tagtxt->type == 'name' || $tagtxt->type == 'rank'){

        $name .= ($name ? ' ' : '').$tagtxt->text;

      }

  }

  $name = trim($name);

  if($name){

    if(strpos($name, 'Incertae sedis') === false && $pos = stripos($name, ' ')){

      return substr($name, 0, 1).'. '.substr($name, $pos);

    } else {

      return $name;

    }

  } else {

    return $NameSTO->fullname;

  }

}

/**

 * @param UUID $secUuid

 */

function _cdm_dataportal_set_currentSecUuid($secUuid){

  if(is_array($secUuid)){

    $secUuid = $secUuid[0];

  }

  if( !isset($_SESSION['cdm']['currentSecRef']['uuid']) ||  $_SESSION['cdm']['currentSecRef']['uuid'] != $secUuid){

    if(!$secUuid){

      $_SESSION['cdm']['currentSecRef'] = null;

    } else {

      $secRef = cdm_ws_get(CDM_WS_SIMPLE_REFERENCE ,$secUuid);

      if(isset($secRef[0])){

        $_SESSION['cdm']['currentSecRef'] = (array)($secRef[0]);

      }

    }

  }

}

/**

 * returns the current secRef array from the users session. 

 * If the according session variable is not jet set the default

 * as configured in the setting is used otherwise null.

 * 

 * currentSecRef['uuid']

 * currentSecRef[....

 *

 * @return array

 */

function _cdm_dataportal_currentSecRef_array(){

  if( !isset($_SESSION['cdm']['currentSecRef']['uuid'])){

     $secUuid = variable_get('cdm_secUuid_default', null);

     _cdm_dataportal_set_currentSecUuid($secUuid);

  }

  return  $_SESSION['cdm']['currentSecRef'];

}

function _cdm_dataportal_acceptetByCurrentView($taxonTO){

  $current_secref = _cdm_dataportal_currentSecRef_array();

  return $current_secref->uuid == $taxonTO->secuuid && $taxonTO->accepted;

}

/**

 * @param $str the string to truncate

 * @param $len the maximun length

 * @param $appendix an optional appendix.

 *

 * @return the string truncated to the specified length or the original string as given as parameter.

 * if an appendix has been defined the resulting string

 * will have the specified length inculding the the appendix.

 */

function str_trunk(&$str, $len, $appendix=''){

  if(strlen($str) >= $len )

  return  substr($str, 0, $len - strlen($appendix)).$appendix;

  else

  return $str;

}

/**

 * @param string $str

 * @param string $sub

 * @return boolean

 */

function str_beginsWith( $str, $sub ) {

  return ( substr( $str, 0, strlen( $sub ) ) === $sub );

}

/**

 *

 * @param string $str

 * @param string $sub

 * @return boolean

 */

function str_endsWith( $str, $sub ) {

  return ( substr( $str, strlen( $str ) - strlen( $sub ) ) === $sub );

}

function array_replace_key($array, $replace_map){

  foreach($replace_map as $key=>$newkey){

    if(isset($array[$key])){

      $array[$newkey] = $array[$key];

      unset($array[$key]);

    }

  }

  return $array;

}

function compose_url_prameterstr($parameters = array()){

  $pstr = '';

  foreach($parameters as $key=>$value){

     $pstr .= ($pstr ? '&' :'').$key.'='.urlencode($value);

  }

  return $pstr;

}