';var_dump($form);exit;
			}
			// echo'
';var_dump('nope');exit;
			//if there is gene query parameter, prefill
			$accession_int = format_annotation_accession_alt_1();
			$form['title']['#default_value'] = 'A'.$accession_int;
			$form['actions']['submit']['#submit'][]='format_annotation_accession_alt_2';
		}
      $form['field_with_or_from'][LANGUAGE_NONE]['add_more']['#value'] = t('add another data source');
      $form['field_db_reference'][LANGUAGE_NONE]['add_more']['#value'] = t('add another DB reference');
		//here goes the ajaxification of the sources dropdown
		//$tmp = entity_load('field_collection_item', $form['field_db_reference']['und'][0]['value']);
		// echo'
';var_dump($form['field_db_reference']['und'][0]);exit;
    //echo "
"; print_r($form); exit();
    // $form['field_gene'][LANGUAGE_NONE][0]['target_id']['#ajax'] = array(
    //       'callback' => 'gene_link_to_species',
    //       'event' => 'autocompleteFill',
    //       'wrapper' => 'annotation_gene_form',
    //     ); 
    // $form['#prefix'] = '
';
    // $form['#suffix'] = '
';

    $form['field_ontology_id'][LANGUAGE_NONE][0]['#suffix'] = "
";
    $form['field_ontology_id'][LANGUAGE_NONE][0]['value']['#ajax'] = array(
      'callback' => 'ontology_field_get_info',
      'wrapper' => 'ontology-descr',
      'method' => 'replace',
      'effect' => 'fade',
    );
    

	}
	if ($form_id == 'user_profile_form' && !in_array('administrator', $user->roles)) {
		$form['field_curation_species']['#access'] = false;
	}

	if($form_id == 'views_exposed_form' && $form_state['view']->name == 'workbench_moderation'){
		if(isset($form['type']['#options'])){
			$form['type']['#options'] = array('All' => '- Any -',
											'annotation' => 'Annotation',
										 	'gene' => 'Gene');
		}

    $form['#suffix'] = "
Filter content you've created/edited with the dropdowns above, search by title, and sort results by clicking on the column header.
";

    global $user;

    $query = db_select('users', 'u');
    $query->Leftjoin('field_data_field_firstname', 'fn', 'u.uid = fn.entity_id');
    $query->Leftjoin('field_data_field_lastname', 'ln', 'u.uid = ln.entity_id');
    $query
      ->fields('u', array('name'))
      ->fields('fn',array('field_firstname_value'))
      ->fields('ln',array('field_lastname_value'))
      ->condition('u.uid', $user->uid);
    $result = $query->execute()->fetchAll();

    $user_name = $result[0]->name;
    /*$comment->created ->$format_date;*/
    if(isset($result[0]->field_firstname_value) && !empty($result[0]->field_firstname_value) && isset($result[0]->field_lastname_value)){
      $user_name = $result[0]->field_firstname_value." ".$result[0]->field_lastname_value;
    }

    $form['#prefix'] = "
".$user_name."'s workbench: 
";

	}
  


  if($form_id == 'gene_node_form' || $form_id == 'annotation_node_form'){
    //echo "
"; print_r($form); exit(); 
      drupal_add_js(base_path().drupal_get_path('module','cgrb_form_alter').'/js/form_alter.js','file');
      ctools_include('ajax');
      ctools_include('modal');
      ctools_modal_add_js();

      foreach ($form['field_publication'][LANGUAGE_NONE] as $key => $value) {
        if(!is_numeric($key)) continue;

        if(!isset($form_state['values']['field_publication'][LANGUAGE_NONE][$key]['target_id']) || empty($form_state['values']['field_publication'][LANGUAGE_NONE][$key]['target_id'])){
          $form['field_publication'][LANGUAGE_NONE][$key]['operation_type']= array(
            '#type' => 'radios',
            '#weight' => -1,
            '#title' => t(''),
            '#options' => array(t('Select Publication from Database'), t('Add New Publication to Database')),
            '#default_value' => 0,
            '#prefix' => "
",
            '#suffix' => '
',
          );
        }
        

        $biblio_ciation = '';
        if(isset($form_state['values']['field_publication'][LANGUAGE_NONE][$key]['target_id']) && !empty($form_state['values']['field_publication'][LANGUAGE_NONE][$key]['target_id'])){
          $node_bilio = node_load($form_state['values']['field_publication'][LANGUAGE_NONE][$key]['target_id']);
          $node_view = node_view($node_bilio,'teaser');
          $biblio_ciation = drupal_render($node_view);
        }

        $form['field_publication'][LANGUAGE_NONE][$key]['target_id']['#weight'] = 1;
        $form['field_publication'][LANGUAGE_NONE][$key]['target_id']['#prefix'] = "
";
       $form['field_publication'][LANGUAGE_NONE][$key]['target_id']['#suffix'] = "
".$biblio_ciation."
 ";
        
        if(!isset($form['#node']->nid) || isset($form['#node']->is_new)){
          $output = ctools_modal_text_button(t('Add Biblio'), 'biblio/nojs/add/'.$key, 'Add Biblio');
          $form['field_publication'][LANGUAGE_NONE][$key]['biblio_link'] = array(
            '#type' => 'item',
            '#markup' => $output,
            '#weight' => 21,
            '#prefix' => '
',
            '#suffix' => '
',
          );
        }else{
          if(isset($form['#node']->field_publication[LANGUAGE_NONE][$key]['target_id'])){
            $form['field_publication'][LANGUAGE_NONE][$key]['operation_type']['#options'] = array(t('Add new publication'), t('Edit publication'));


            $entity_nid = $form['#node']->field_publication[LANGUAGE_NONE][$key]['target_id'];
            $output = ctools_modal_text_button(t('Edit Biblio content'), 'modal/node/'.$entity_nid.'/edit/nojs/'.$key, 'Edit Biblio content');
            $form['field_publication'][LANGUAGE_NONE][$key]['biblio_link'] = array(
              '#type' => 'item',
              '#markup' => $output,
              '#weight' => 21,
              '#prefix' => '
',
              '#suffix' => '
',
            );
          }else{
            $output = ctools_modal_text_button(t('Add Biblio'), 'biblio/nojs/add/'.$key, 'Add Biblio');
            $form['field_publication'][LANGUAGE_NONE][$key]['biblio_link'] = array(
              '#type' => 'item',
              '#markup' => $output,
              '#weight' => 21,
              '#prefix' => '
',
              '#suffix' => '
',
            );
          }
        }

        $form['field_publication'][LANGUAGE_NONE][$key]['target_id']['#ajax'] = array(
          'callback' => 'publications_put_full_citation',
          'wrapper' => 'biblio-full_citation-'.$key,
          'method' => 'replace',
          'effect' => 'fade',
        );
        
      }
  }




  if($form_id == 'gene_node_form' || $form_id == 'annotation_node_form'){

    global $user;
     //echo "
"; print_r($form); exit();
    $form['field_publication'][LANGUAGE_NONE]['add_more']['#value'] = t('Add another Publication');


    //  $form['immutable'] = array(
    //   '#type' => 'textarea', //you can find a list of available types in the form api
    //   '#title' => 'Description',
    //   '#size' => 60,
    //   '#weight' => -1,
    //   '#access' => 0,
    //   '#value' => $form['node']->body,

    // );
     //echo "
"; print_r($form['node']->body); exit();
    $node = $form_state['node'];
    // echo'
';var_dump( $node->is_new );exit;
//echo'
';print_r($form['field_synonyms']['und'][0]['value']['#attributes']['disabled']);exit;

    if( isset($node->nid) && in_array('Contributors', $user->roles) ){
      $form['body'][LANGUAGE_NONE][0]['summary']['#access'] = FALSE;
      $form['field_gene_symbol']['und']['0']['value']['#attributes']['disabled'] = TRUE; 
      $form['field_gene_name']['und']['0']['value']['#attributes']['disabled'] = TRUE;
      
      
      $form['field_synonyms']['und']['0']['value']['#attributes']['disabled'] = TRUE;
      $form['field_gene_id']['und']['0']['value']['#attributes']['disabled'] = TRUE; 
      $form['field_ref_species']['und']['0']['value']['#attributes']['disabled'] = TRUE; 
      $form['field_gene_type']['und']['0']['value']['#attributes']['disabled'] = TRUE; 
      $form['field_data_source']['und']['0']['value']['#attributes']['disabled'] = TRUE;
      
      foreach($form['field_synonyms']['und'] as $key => $v){
        if(!is_numeric($key)){
          continue;
        }
        
        if(isset($form['field_synonyms']['und'][$key]['value']['#default_value']) && !empty($form['field_synonyms']['und'][$key]['value']['#default_value'])){
          $form['field_synonyms']['und'][$key]['value']['#attributes']['disabled']=TRUE;
          unset($form['field_synonyms']['und'][$key]['remove_button']);
        }
      }

      foreach($form['field_publication']['und'] as $key => $v){
        if(!is_numeric($key)){
          continue;
        }
        
        if(isset($form['field_publication']['und'][$key]['target_id']['#default_value']) && !empty($form['field_publication']['und'][$key]['target_id']['#default_value'])){
          $form['field_publication']['und'][$key]['target_id']['#attributes']['disabled']=TRUE;
          unset($form['field_publication']['und'][$key]['remove_button']);
        }
      }

    }  

    if(in_array('Contributors', $user->roles)){
      //Making revision message mandatory for contributors
      // echo'
';var_dump($form['workbench_moderation']);exit;
      $form['revision_information']['log']['#required'] = true;
      $form['revision_information']['log']['#title'] = t('Provide us a comment about your edits');

      $form['revision_information']['text'] = [
        '#type' => 'textarea',
        '#default_value' => 'To submit your revision for review, change the dropdown to "Needs Review". To save your current state and continue work later, leave the dropdown as "Draft"',
        '#disabled' => TRUE,
      ];
      //echo "
"; print_r($form); exit;      
    }
  } 
  if($form_id == 'gene_node_form'){
    //echo "
"; print_r($form['#node']);exit;
    if(isset($form['#node']->nid)){
      $form['immutable'] = array(
        '#type' => 'textarea', //you can find a list of available types in the form api
        '#title' => 'Current Description',
        '#size' => 60,
        '#weight' => -1,
        '#attributes' => array('disabled' => 'disabled'),
        '#default_value' => $form['#node']->body[LANGUAGE_NONE][0]['value'],
      );
    }
       $form['field_synonyms'][LANGUAGE_NONE]['add_more']['#value'] = t('Add another Synonym');  
        //echo "
"; print_r($form); exit();
  }    

  if($form_id == 'biblio_node_form'){
    $form['#prefix'] = "
If your source does not have a PMID or DOI, and is not in BibTex format, please select a source type from the dropdown below and fill out the resulting form. If you select a type and the form does not automatically redirect you, click next.
";
  }

}



//helper functions
/*function format_annotation_accession_alt_1(){
	$results = db_select('annotation_accession', 'ann_acc')
			->fields('ann_acc')
			->execute()
			->fetchAssoc();
	$accession_int = $results['accession'];
	$accession_number = (string)$accession_int;
	$acc_len = strlen($accession_number);
	for($acc_len;$acc_len < 12; $acc_len++){
		$accession_number = '0'.$accession_number;
	}
	return $accession_number;
}

function format_annotation_accession_alt_2(){
	$results = db_select('annotation_accession', 'ann_acc')
			->fields('ann_acc')
			->execute()
			->fetchAssoc();
	$accession_int = $results['accession'];
	$accession_number = (string)$accession_int;
	$acc_len = strlen($accession_number);
	for($acc_len;$acc_len < 12; $acc_len++){
		$accession_number = '0'.$accession_number;
	}
	$accession_int++;
	$query = db_update('annotation_accession')
		->fields(array(
			'accession' => $accession_int))
		->execute();
	$results = db_select('annotation_accession', 'ann_acc')
			->fields('ann_acc')
			->execute()
			->fetchAssoc();
}*/

function cgrb_form_alter_menu() {
  $items['biblio/%ctools_js/add/%'] = array(
    'page callback' => 'cgrb_form_alter_node_add_modal_callback',
    'page arguments' => array(1,3),
    'access arguments' => array('access content'),
    'theme callback' => 'ajax_base_page_theme',
  );

  $items['modal/node/%/edit/%ctools_js/%'] = array(
    'page callback' => 'cgrb_form_alter_page_edit',
     'page arguments' => array(2, 4,5),
    'access callback' => 'node_access',
    'access arguments' => array('update', 2),
    'theme callback' => 'ajax_base_page_theme',
  );

  return $items;
}

function ontology_field_get_info($form,$form_state){
  $ontoloty_term = $form_state['values']['field_ontology_id'][LANGUAGE_NONE][0]['value'];
  $ontology_term_info = get_ontology_term_info_api($ontoloty_term);

  $output = '';

  if($ontology_term_info != $ontoloty_term){
    $output .= "
";
    $output .= "
Annotation Class Label:  ".$ontology_term_info->annotation_class_label."
";
    $output .= "
Description:  ".$ontology_term_info->description."
";
    $output .= "
";
  }

  $commands = array();
  $commands[] = ajax_command_replace('#ontology-descr',$output);

  return array('#type' => 'ajax','#commands' => $commands);

}

/**
 * modal node edit modal callback
 */
function cgrb_form_alter_page_edit($nid, $js, $key) {
  //echo "
"; print_r($node); exit();
  if (!$js) {
     return drupal_goto('node/' . $nid . '/edit/');

    // return drupal_goto('node/4/edit');
  }

   // Include your ctools crap here
  ctools_include('node.pages', 'node', '');
  ctools_include('modal');
  ctools_include('ajax');
  $node = node_load($nid);
  $form_state = array(
    'title' => t('Add my conten type'),
    'ajax' => TRUE,
  );
  $form_state['build_info']['args'] = array($node);

  // change this to your type node form
  $output = ctools_modal_form_wrapper('biblio_node_form', $form_state);

  if (!empty($form_state['executed'])) {
    $output = array();
    // Close the modal
    $output[] = ctools_modal_command_dismiss();

    $messages = drupal_get_messages('status', TRUE);
      
    $msg_opt = "
\n";
    //if (count($messages['status']) > 1) {
      $msg_opt .= " 
\n";
      foreach ($messages['status'] as $message) {
        $msg_opt .= '  
' . $message . "
\n";
      }
      $msg_opt .= " 
\n";
    //}
    $msg_opt .= "
\n";
    $output[] = ajax_command_replace('#biblio-message-'.$key, $msg_opt);
    // I use this method a lot on pages that have views, so what I do is get the latest view content
    // with the latest node and replace the current view. magic!
    /*
    $html = views_embed_view('my_view', 'my_display';
    $output[] = ajax_command_html('.view-display-id-my_display', $html);
    */

    if(isset($form_state['values']['nid'])){
      $nid = $form_state['values']['nid'];
      
      $node_bilio = node_load($nid);
      $node_view = node_view($node_bilio,'teaser');    

      $rendered_node = "
".drupal_render($node_view)."
";    

      $output[] = ajax_command_replace('#biblio-full_citation-'.$key,$rendered_node);
    }
  }
  
  print ajax_render($output);  
  exit;
}
/**
 * modal node add modal callback
 */
function cgrb_form_alter_node_add_modal_callback($js = FALSE,$key) {
  global $user;
  //$error_message = $_SESSION['messages']['error'];
  // If people aren't using javascript, then I just boot em. sorry. its 2011.
  if (!$js) return "Javascript required";
  
  // Include your ctools crap here
  ctools_include('node.pages', 'node', '');
  ctools_include('modal');
  ctools_include('ajax');
  // Create a blank node object here. You can also set values for your custom fields here as well.
  $node = (object) array(
    'uid' => $user->uid, 
    'name' => (isset($user->name) ? $user->name : ''), 
    'type' => 'biblio', 
    'language' => LANGUAGE_NONE,
    );
  $form_state = array(
    'title' => t('Add my publication'),
    'ajax' => TRUE,
  );
  $form_state['build_info']['args'] = array($node);
  // change this to your type node form
  $output = ctools_modal_form_wrapper('biblio_node_form', $form_state);
  // This means the form has been exectued
  if (!empty($form_state['executed'])) {
  	
  	if(isset($form_state['values']['nid']) && !empty($form_state['values']['nid'])){
  		// Close the modal
    	// $output[] = ctools_modal_command_dismiss();
    	$output = array(ctools_modal_command_dismiss());

    	$nid = $form_state['values']['nid'];
      $title = $form_state['values']['title'];

      $inputValue = $title." (".$nid.")";

      $node_bilio = node_load($nid);
      $node_view = node_view($node_bilio,'teaser');    

      $rendered_node = "
".drupal_render($node_view)."
";    

      $output[] = ajax_command_replace('#biblio-full_citation-'.$key,$rendered_node);  

    	$link = ctools_modal_text_button(t('Edit Content'), 'modal/node/'.$nid.'/edit/nojs/'.$key, 'test_biblio');
    	$output[] = ajax_command_replace('#biblio-link-'.$key.' a.ctools-use-modal', $link);

      $messages = drupal_get_messages('status', TRUE);
      
      $msg_opt = "
\n";
      //if (count($messages['status']) > 1) {
        $msg_opt .= " 
\n";
        foreach ($messages['status'] as $message) {
          $msg_opt .= '  
' . $message . "
\n";
        }
        $msg_opt .= " 
\n";
      //}
      $msg_opt .= "
\n";
      $output[] = ajax_command_replace('#biblio-message-'.$key, $msg_opt);

      $output[] = ajax_command_invoke('#operation-target-'.$key.' input.form-text', 'val', array($inputValue));

      $output[] = ajax_command_invoke('#operation-type-'.$key, 'hide');

  	}else{
	    // $output = array();
	    $output[] = ajax_command_html('array()');  		
  	}
    
    // I use this method a lot on pages that have views, so what I do is get the latest view content
    // with the latest node and replace the current view. magic!
    /*
    $html = views_embed_view('my_view', 'my_display';
    $output[] = ajax_command_html('.view-display-id-my_display', $html);
    */    
  }
   //$output.= theme('status_messages', array('display' => 'error'));
  print ajax_render($output);  
  exit;
}

function publications_put_full_citation($form,$form_states){
  //echo "
"; print_r($form_states['input']);exit;

  $triggering_ele = $form_states['input']['_triggering_element_name'];
  $key = explode('field_publication[und][', $triggering_ele);
  $key = $key[1];
  $key = explode('][target_id]', $key);
  $key = $key[0];

  $commands = array();

  if(isset($form_states['values']['field_publication'][LANGUAGE_NONE][$key]['target_id']) && !empty($form_states['values']['field_publication'][LANGUAGE_NONE][$key]['target_id']) && is_numeric($key)){
    $node_bilio = node_load($form_states['values']['field_publication'][LANGUAGE_NONE][$key]['target_id']);
    $node_view = node_view($node_bilio,'teaser');
    $rendered_node = "
".drupal_render($node_view)."
";    

    $commands[] = ajax_command_replace('#biblio-full_citation-'.$key,$rendered_node);

    $commands[] = ajax_command_invoke('#operation-type-'.$key, 'hide');
  }

  return array('#type' => 'ajax','#commands' => $commands);
}
// function cgrb_form_alter_js_alter(&$javascript) {
//   // remove the JS that does the show/hide summary
//   unset($javascript['modules/field/modules/text/text.js']);
// }

function cgrb_form_alter_form_comment_form_alter(&$form, &$form_state, $form_id, &$name, $account) {
  global $user;
  //$label = t('New label');
  $account = user_load($user->uid);
  $first_name= $account->field_firstname['und'][0]['value'];
  $last_name= $account->field_lastname['und'][0]['value'];
  //echo "
"; print_r($form); exit();

  if (isset($form['author']['_author'])) {
    $form['author']['_author']['#markup'] = $first_name ." " . $last_name;
  }
   $form['subject']['#access'] = FALSE;
    //$form['body_field']['und'][0]['format']['#attributes']['class'] = 'invisible';
  // else {
  //   $form['author']['name']['#title'] = $label;
  // }
}
// function cgrb_form_alter_username_alter(&$name, $account, $form_id, $form_state) {
//     // With user_load we get all fields with are added not by core and add them to the orginal $account
//    if($form_id == 'comment_form'){
//         echo "
"; print_r($from); exit();
//       $account = user_load($account->uid);
       
//       if (!empty($account->field_firstname) && !empty($account->field_lastname)) {
       
//       $name = $account->field_firstname['und'][0]['value'] . ' ' . $account->field_lastname['und'][0]['value'];

//       }
//    }   
// }
  // if($form_id == 'comment_form'){
  //       echo "
"; print_r($from); exit();
  //  }     
// function gene_link_to_species(&$form, $form_state) {
//   //echo "
"; print_r($form_states['input']);exit;

//   if(isset($form_state['values']['field_gene'])) {
//       $nid = $form_state['values']['field_gene']['und'][0]['nid'];
//       $node = node_load($nid);
//       //echo "
"; print_r($node); exit();

//   }
//     $commands = array();

//   return array('#type' => 'ajax', '#commands' => $commands);

// }


function cgrb_form_alter_translated_menu_link_alter(&$link) {
  global $user;

  // Hide the "User account" link for anonymous users.
  if ($link['href'] == 'admin/workbench') {
    echo "
"; print_r($link);exit;
    $link['href'] = 'admin/workbench/my-published-content';
  }
}

function cgrb_form_alter_module_implements_alter(&$implementations, $hook) {
  if ($hook == 'translated_menu_link_alter') {
    $group = $implementations['cgrb_form_alter'];
    unset($implementations['cgrb_form_alter']);
    $implementations['cgrb_form_alter'] = $group;
  }
}

function get_ontology_term_info_api($id_string){
  $html_json = htmlspecialchars(curl_get_contents("http://browser.planteome.org/api/autocomplete/ontology?q=".url_encode_2($id_string)));
  $tmp = html_entity_decode($html_json);
  $json_obj = json_decode($tmp);
  $output = $id_string;
  if(is_object($json_obj) && count($json_obj->data)){
    $output = $json_obj->data[0];
  }
  return $output;
}