'planteome_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' => 'planteome_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 $items; } function planteome_form_alter_form_node_form_alter(&$form, $form_state) { // echo'
';var_dump($form['options']);exit;
}

/*
 * Implementation of hook_form_alter()
 */
function planteome_form_alter_form_alter(&$form, &$form_state, $form_id){
	// drupal_set_message($form_id);
	global $user;
	if(isset($form_state['#node'])){
		$node = $form_state['#node'];
	}
	else{
		$node = '';	
	}
	// if($form_id == 'edit_options'){
	// 	exit();
	// }
	// echo'
';var_dump($node);exit;


	if ($form_id == 'gene_node_form' || $form_id == 'annotation_node_form'){
		drupal_add_js(base_path().drupal_get_path('module','planteome_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;
    		$form['field_publication'][LANGUAGE_NONE][$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','btn-success btn');
	        	$form['field_publication'][LANGUAGE_NONE][$key]['biblio_link'] = array(
	        		'#type' => 'item',
	        		'#markup' => $output,
	        		'#weight' => 21,
	        		'#prefix' => '
',
	        	);
	        } else {
	        	if(isset($form['#node']->field_publication[LANGUAGE_NONE][$key]['target_id']) && isset($form_state['build_info']['args'][0]->field_publication[LANGUAGE_NONE][$key]['target_id'])){
	        		 //echo "
"; print_r($form_state['build_info']['args'][0]->field_publication[LANGUAGE_NONE][$key]['target_id']); exit();
	        		$form['field_publication'][LANGUAGE_NONE][$key]['operation_type']['#options'] = array(t('Add new publication'), t('Edit publication'));
	        		$entity_nid = $form['#node']->field_publication[LANGUAGE_NONE][$key]['target_id'];
	        		$node_bilio = node_load($entity_nid);
	        		$node_view = node_view($node_bilio,'teaser');
					$rendered_node = "
".drupal_render($node_view)."
";

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

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

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

	    if( isset($node->nid) && in_array('Contributors', $user->roles) ){
	    	
	    	$form['field_ref_species']['und']['0']['value']['#attributes']['disabled'] = TRUE;
	    	$form['field_data_source']['und']['0']['value']['#attributes']['disabled'] = TRUE;

		    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']);
		        }
		    }
	    }

	    $form['options']['help'] = [
	    	'#markup' => '
Moderation Notes:
  • Add a brief description of the changes made.
Moderation State:
  • Draft - save the content without submitting it for review, used to save work (privately) to be finished later.
  • Needs Review - save the content and submit it for review, shares work with Curators who will go through the moderation process.
  • Published - save the content as ready to be displayed on the site (Contributors must go through the moderation workflow, this option is only shown to Curators and above)
',
	    	/*'#type' => 'textarea',
	    	'#title' => 'text',
	    	'#description' => 'test desc',*/
	    ];

	    // echo'
';var_dump($form['options']);exit;
	}

	if($form_id == 'annotation_node_form'){
		
		// annotation form setup
		
		$form['field_ontology_id'][LANGUAGE_NONE][0]['value']['#autocomplete_path'] = 'autocomplete/ontology_term_extended';
		$form['#validate'][] = 'ontology_qa_validate';
		
		$form['field_date']['#access'] = FALSE;

		$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');

		$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',
	    );
	    $form['field_assigned_by']['#disabled'] = TRUE;
	    $accession_int = format_annotation_accession_alt_1();
		$form['title']['#default_value'] = 'A'.$accession_int;
		$form['title']['#access'] = FALSE;
		$form['field_data_source']['und'][0]['field_object_id']['und'][0]['value']['#default_value'] = 'A'.$accession_int;
		$form['field_data_source']['#disabled'] = TRUE;
		$form['actions']['submit']['#submit'][] = 'format_annotation_accession_alt_2';
	    // echo'
';var_dump($form);exit;

	    // annotation form change for contributors
	    if(in_array('Contributors', array_values($user->roles))){
			$form['field_db_reference']['#access'] = FALSE;
		}

		//annotation form for cloned annotation handled in node_clone module

		//annotation form change for new annotation from gene page
		$q_params = drupal_get_query_parameters();
		// echo'
';var_dump(current_path());exit;
		if(count($q_params) && isset($q_params['gene'])) {
			$gene = node_load($q_params['gene']);
			$form['field_gene']['und'][0]['target_id']['#default_value'] = $gene->title.' ('.$gene->nid.')';
			$form['field_gene']['#attributes'] = array('readonly' =>'readonly');
			$form['field_gene']['#disabled'] = TRUE;
			$species = node_load($gene->field_ref_species['und'][0]['target_id']);
			$form['field_ref_species']['und'][0]['target_id']['#default_value'] = $species->title.' ('.$species->nid.')';
			$form['field_ref_species']['#disabled'] = TRUE;
			$form['field_ref_species']['#attributes'] = array('readonly' =>'readonly');
		}

		if(isset($node->nid)) {
			$form['field_gene']['#attributes'] = array('readonly' =>'readonly');
			$form['field_ref_species']['#attributes'] = array('readonly' =>'readonly');
		}

		$form['optional_divider'] = [
			'#markup' => '
'.variable_get('optional_divider_text').'
',
			'#weight' => 9,
		];
	}

	if($form_id == 'gene_node_form'){
		if(!isset($form['nid']['#value'])) {
			$accession_int = format_gene_accession_alt_1();
			// echo'
';var_dump($form['field_data_source']);exit;
			$form['field_accession']['und'][0]['value']['#default_value'] = 'P'.$accession_int;//.$accession_int;
			$form['field_data_source']['und'][0]['field_object_id']['und'][0]['value']['#default_value'] = 'P'.$accession_int;
			$form['actions']['submit']['#submit'][] = 'format_gene_accession_alt_2';
			$form['field_data_source']['#disabled'] = TRUE;
		}
		if(isset($form['nid']['#value'])){
			$n = node_load($form['nid']['#value']);
			$form['text'] = [
				// '#markup' => '
You are currently editing a gene. To view the original content, follow this link: '.drupal_get_path_alias('node/'.$node->nid).'
',
				'#markup' => '
'.t('Note: ').''.t('You are currently editing a gene. To view the original content, follow this link: ').l(t($n->title), 'node/'.$n->nid).'
',
			];
			// drupal_set_message('You are currently editing a gene. To view the original content, follow this link: '.drupal_get_path_alias('node/'.$node->nid));
		}
		// echo'
';var_dump($form['body']['und'][0]['#rows']);exit;
		$form['body']['und'][0]['#rows'] = 10;
		$form['field_gene_ontology_terms']['#disabled'] = TRUE;
		$form['field_accession']['und']['0']['value']['#attributes']['disabled'] = TRUE; 
		if (isset($form['nid']['#value']) && in_array('Contributors', $user->roles)){
			$node = node_load($form['nid']['#value']);
			if($node->uid != $user->uid){
				$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_gene_id']['und'][0]['value']['#attributes']['disabled'] = TRUE; 
		    	$form['field_chromosome_no']['und'][0]['value']['#attributes']['disabled'] = TRUE; 
		    	$form['field_chromosome_start']['und'][0]['value']['#attributes']['disabled'] = TRUE; 
		    	$form['field_chromosome_stop']['und'][0]['value']['#attributes']['disabled'] = TRUE;
		    	$form['field_ref_species']['und'][0]['target_id']['#attributes']['disabled'] = TRUE;
		    	$form['field_gene_type']['#disabled'] = TRUE;
		    	$form['field_data_source']['#disabled'] = TRUE;
		    	// $form['field_gene_type']['und']['0']['value']['#attributes']['disabled'] = TRUE; 
		    	foreach($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']);
			        }
			    }
			}
		}

		if (isset($node->nid) && !in_array('administrator', array_values($user->roles))) {
			$node = node_load($form['nid']['#value']);
			if($node->uid != $user->uid){
				// echo'
';var_dump($form);exit;
				//shoud hide title, accession, gene ontology terms
				$form['title']['#type'] = 'value';
				// $form['field_gene_ontology_terms']['#access'] = FALSE;
				// $form['field_gene_ontology_terms']['#type'] = 'value';
				$form['field_gene_ontology_terms']['#access'] = FALSE;
				$form['field_accession']['#access'] = FALSE;
				$form['field_ref_species']['#disabled'] = TRUE;
				$form['field_gene_type']['#disabled'] = TRUE;
				$form['field_chromosome_no']['#disabled'] = TRUE;
				$form['field_chromosome_start']['#disabled'] = TRUE;
				$form['field_chromosome_stop']['#disabled'] = TRUE;
				$form['field_data_source']['#disabled'] = TRUE;
				// $form['field_accession']['#access'] = FALSE;
				// echo'
';var_dump($form['field_gene_ontology_terms']);exit;
			}
		}

		if(isset($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');
	}

	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',
			);
		}
	}

	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.
";
	}

	if($form_id == 'planteom_mycontent_filter_form' || $form_id == 'planteom_needs_review_filter_form'){
		$form['form_build_id']['#access'] = FALSE;
  		$form['form_token']['#access'] = FALSE;
  		$form['form_id']['#access'] = FALSE;
	}

  	return $form;
}


function planteome_form_alter_page_edit($nid, $js, $key) {
	if (!$js) {
		return drupal_goto('node/'.$nid.'/edit/');
	}

	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;
}

function planteome_form_alter_node_add_modal_callback($js=FALSE, $key){
	global $user;
	if (!$js) return "Javascript required";
	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));

  	}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 planteome_form_alter_views_query_alter(&$view, &$query){
	if($view->name == 'workbench_moderation' && $view->current_display == 'page_3'){
		global $user;
		// this should possibly be written more correctly?
		//$query->where[2]['conditions'][0]['value'][':node_uid_revision'][0] = $user->uid;
		// echo'
';var_dump($user);exit;
	}
}

function planteome_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 planteome_form_alter_translated_menu_link_alter(&$link) {
  global $user;

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

function planteome_form_alter_module_implements_alter(&$implementations, $hook) {
  if ($hook == 'translated_menu_link_alter') {
    $group = $implementations['planteome_form_alter'];
    unset($implementations['planteome_form_alter']);
    $implementations['planteome_form_alter'] = $group;
  }
  if (($hook == 'form_node_form_alter' || $hook == 'form_alter') && isset($implementations['planteome_form_alter'])) {
  	$group = $implementations['planteome_form_alter'];
    unset($implementations['planteome_form_alter']);
    $implementations['planteome_form_alter'] = $group;
  }
}

//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 format_gene_accession_alt_1(){
	$results = db_select('accession', 'acc')
			->fields('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_gene_accession_alt_2(){
	$results = db_select('accession', 'acc')
			->fields('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('accession')
		->fields(array(
			'accession' => $accession_int))
		->execute();
	$results = db_select('accession', 'acc')
			->fields('acc')
			->execute()
			->fetchAssoc();
}



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);
  }

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

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;
}

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);

  // echo'
';var_dump($ontology_term_info->source);exit;
  $output = '';

  if(!empty($ontoloty_term) && $ontology_term_info != $ontoloty_term){
  	$output .= "
";
  	$output .= "
 ".$ontology_term_info->source."
";
    $output .= "
 ".$ontology_term_info->annotation_class_label."
";
    $output .= "
 ".$ontology_term_info->description."
";
    $output .= "
";
  }else{
  	$output .= "
";
  }

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

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

}

function ontology_qa_validate($form, &$form_state){
	$aspect_tid = $form['field_aspect']['und']['#value'];
	$ontology_term = $form['field_ontology_id']['und'][0]['value']['#value'];

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

		switch ($aspect_tid) {
			case '609':
				if($data_source != 'cellular_component'){
					form_set_error('field_ontology_id', 'Ontology ID does not match Ontology Type');
				}
				break;
			case '2327':
				if($data_source != 'plant_trait_ontology'){
					form_set_error('field_ontology_id', 'Ontology ID does not match Ontology Type');
				}
				break;
			case '603':
				if($data_source != 'biological_process'){
					form_set_error('field_ontology_id', 'Ontology ID does not match Ontology Type');
				}
				break;
			case '605':
				if($data_source != 'molecular_function'){
					form_set_error('field_ontology_id', 'Ontology ID does not match Ontology Type');
				}
				break;
			case '614':
				if($data_source != 'plant_anatomy'){
					form_set_error('field_ontology_id', 'Ontology ID does not match Ontology Type');
				}
				break;
			case '2328':
				if($data_source != 'plant_environment_ontology'){
					form_set_error('field_ontology_id', 'Ontology ID does not match Ontology Type');
				}
				break;
			case '2329':
				if($data_source != 'plant_structure_development_stage'){
					form_set_error('field_ontology_id', 'Ontology ID does not match Ontology Type');
				}
				break;
			
			default:
				form_set_error('field_ontology_id', 'Ontology type does not match existing Ontology types.');
				break;
		}
	}
}