'; // } // // TODO - the below currently slows down the front page load a lot, find a better way to do this // $count = ''; // $gene_count = return_taxon_gene_count($taxon); // if($gene_count){ // $count = ' - '.$gene_count.' genes'; // } // $return.= '
• '.$taxon->title.$count.''; // foreach($remaining_taxons as $index2 => $taxon2){ // // echo '

  '; var_dump($taxon2);exit;
  // 				if(count($taxon2->field_taxon_parent)){
  // 					if($taxon2->field_taxon_parent[$taxon->language][0]['target_id'] == $taxon->nid){
  // 						//var_dump($taxon2);exit;
  // 						$return.= '
  '.build_tree($taxon2->field_taxon_ncbi_id[$taxon->language][0]['value'],$remaining_taxons).'
  ';
  // 					}
  // 				}
  // 			}
  // 			$return .= "

"; // if($target_id == 1){ // $return.='

';var_dump($results['node']);
// 			$results2 = array_map("map_1", $results['node']);
// 			// echo '

Results 2
';var_dump($results2);
// 			//$taxon no longer seems needed - verify this
// 			$taxon_tree = return_taxon_gene_count();
// 			// $tree = taxon_build_tree($taxon_tree);
// 			cache_set('taxon_tree_cgrb',$taxon_tree,'cache',CACHE_TEMPORARY);
// 			print($taxon_tree);
// 		}
// 	}
	
// }

// function taxon_build_tree($taxon_tree){
// 	foreach($taxon_tree as $value){
// 		if(empty($value['parent'])){
// 			$output = "
";
// 		}

// 		$count = ' - '.$value['gene_count'].' genes';
// 		$output .= '
'.$value['title'].$count.'';
// 		if(!empty($value['parent'])){
// 			$output .= '
'.taxon_build_tree($value['childnodes']).'
';
// 		}

// 		if(empty($value['parent'])){
// 			$output .= "
";
// 		}
// 	}

// 	return $output;
// }

// function print_ten_most_recent_genes(){

// 	$query = db_select('node', 'n');
// 	$query->join('field_data_field_gene', 'g', 'n.nid = g.entity_id');
// 	$query->join('field_data_field_date', 'd', 'n.nid = d.entity_id');
// 	$query->join('node', 'sn', 'sn.nid = g.field_gene_target_id');
// 	//$query->AddExpression('distinct sn.nid', 'nid');
// 	$result = $query
// 	  ->fields('sn', array('nid', 'title'))
// 	  ->distinct()
// 	  ->condition('n.type', 'annotation')
// 	  ->condition('n.status', '1')
// 	  ->orderBy('d.field_date_value', 'DESC')
// 	  ->range(0,10)
// 	  ->execute();

// 	$results = $result->fetchAll();
	
// 	$html = '
10 most recently annotated genes:
';
// 	foreach ($results as $value){
// 		$html.= '
'.$value->title.'
';
// 	}
// 	$html.= '
';
// 	print($html);
// }

// function print_taxon_parent_and_child($node){
// 	$query = new EntityFieldQuery();
// 	$query->entityCondition('entity_type', 'node')
// 		->entityCondition('bundle','taxon')
// 		->propertyCondition('type',array('taxon'))
// 		->fieldCondition('field_taxon_parent', 'target_id', $node->nid);
// 	$results = $query->execute();
// 	// $parent = node_load($node->field_taxon_parent[$node->language][0]['target_id']);
// 	// $tmp = '
None
';
// 	// $out = '
Parent:
';
// 	// if($parent != NULL){
// 	// 	$tmp ='
'.$parent->title.'
';
// 	// }
// 	// $out.= $tmp;
// 	$out = '
Children:
';
// 	$tmp = '
None
';
// 	if($results['node']){
// 		$tmp = '';
// 		$out.= '
';
// 		foreach ($results['node'] as $child){
// 			$child_node = node_load($child->nid);
// 			$out.= '
'.$child_node->title.'
';
// 		}
// 		$out.= $tmp.'
';
// 	}

// 	print $out;
	


// 	//echo '
'; var_dump($parent);exit;
// }

// function return_taxon_gene_count(){
// 	//$query = new EntityFieldQuery();
// 	// $query->entityCondition('entity_type', 'node')
// 	// 	->entityCondition('bundle','gene')
// 	// 	->propertyCondition('type',array('gene'))
// 	// 	->fieldCondition('field_ref_species', 'target_id', $node->nid);
// 	// // $results = $query->execute();
// 	// $results = $query->count()->execute();
// 	$query = db_select('node','n');
// 	$query->leftjoin("field_data_field_gene_count","gc","gc.entity_id = n.nid");
// 	$query->leftjoin("field_data_field_taxon_parent","tp","tp.entity_id = n.nid");
// 	$query->leftjoin("field_data_field_taxon_rank","tr","tr.entity_id = n.nid");
// 	$all_taxons= $query->fields('n',array('nid','title'))
// 					->fields('gc',array('field_gene_count_value'))
// 					->fields('tp',array('field_taxon_parent_target_id'))
// 					->fields('tr',array('field_taxon_rank_tid'))
//                    ->condition('n.type',"taxon",'=')
//                    ->condition('n.status',1,'=')
//                    ->execute()
//                    ->fetchAll(); 
    
//     $taxon_list = array();
//     foreach($all_taxons as $value){
//     	/*if($value->nid != '363'){
//     		echo'
';var_dump(node_load($value->nid));exit;
//     	}*/
//     	$taxon_list[$value->nid]['nid'] = $value->nid;
//     	$taxon_list[$value->nid]['title'] = $value->title;
//     	$taxon_list[$value->nid]['gene_count'] = $value->field_gene_count_value;
//     	$taxon_list[$value->nid]['parent'] = $value->field_taxon_parent_target_id;
//     	$taxon_list[$value->nid]['rank'] = $value->field_taxon_rank_tid;
//     }

//     $taxon_tree = array();

//     foreach ($taxon_list as $key => $value) {
//     	if(!empty($value['parent'])){
//     		if(isset($taxon_tree[$value['parent']])){
//     			$taxon_tree[$value['parent']]['children'][] = $value;
//     			unset($taxon_list[$key]);
//     		}
//     	}else{

//     	}
//     }

//     $taxon_tree = convertToTree($taxon_list,'nid','parent','childnodes');
//     $return_tree = return_html_array_tree_titles($taxon_tree, 0, 1, 1);
//     // echo "
"; var_dump($return_tree);exit;
//     return $return_tree['out_str'];
//     echo "
"; print_r($taxon_list); exit;
// 	$q = new EntityFieldQuery();
// 	$q->entityCondition('entity_type', 'node')
// 		->entityCondition('bundle','taxon')
// 		->propertyCondition('type',array('taxon'))
// 		->fieldCondition('field_taxon_parent', 'target_id', $node->nid);
// 	$r = $q->execute();
// 	//echo '
';var_dump($r);exit;
// 	// if(!array_key_exists('node', $r)){
// 	// 	echo '
';var_dump($r);
// 	// }
// 	if(count($r) && $r['node']){
// 		$ret_count = 0;
// 		foreach($r['node'] as $child_taxon){
// 			$ret_count+= return_taxon_gene_count($child_taxon);
// 		}
// 		// return count($results['node'])+$ret_count;
// 		return $results+$ret_count;
// 	} else {
// 		// return count($results['node']);
// 		return $results;
// 	}
// }

// function return_html_array_tree_titles($array, $count, $rank_index_init, $rank_index_full){
//     // echo "
"; var_dump($array);exit;
//     $out_str = '
';
//     $parent_count = 0;
//     $rank_to_hide = array(11,9,7,6,13,15,14,20,17,16); //can add 5 to remove "no rank" taxons, but this cuts off the entire arabidopsis branch. Needs another look.
//     foreach($array as $k => $v) {
//     	// echo "
"; var_dump($v['title']);var_dump($rank_index_init);
//     	// if($v['rank'] == 4 && $v['title'] == 'Eukaryota'){
//     	// 	exit;
//     	// }
//         if(is_array($v['childnodes']) && count($v['childnodes'])) {
//         	// if($v['title'] == 'Streptophyta'){
//         	// 	echo'
';var_dump($rank_index_init);exit;
//         	// }
//         	if(!in_array($v['rank'], $rank_to_hide)){
//         		$tmp = return_html_array_tree_titles($v['childnodes'], 0, $rank_index_init+1, $rank_index_full+1);
//         	} else {
//         		// exit($v['title']);
//         		$tmp = return_html_array_tree_titles($v['childnodes'], 0, $rank_index_init, $rank_index_full+1);
//         	}
//         	// if($v['title'] == 'Viridiplantae'){
//         	// 	echo'
';var_dump($rank_index_init);exit;
//         	// }
        	
//         	$cnt = $tmp['count']+(int)$v['gene_count'];
//         	$parent_count+= $cnt;
//         	if(in_array($v['rank'], $rank_to_hide)){
//         		$class = '';
//         		// $class = 'class="hide-rank"';
//         		// $rank_index_init = 0;
//         		$out_str.= '
'.$v['title'].' - '.$cnt.'
'.$tmp['out_str'].'
';
//         	}else{
//         		$class = '';
//         		$out_str.= '
'.$v['title'].' - '.$cnt.'
'.$tmp['out_str'].'
';
//         	}
//             // $out_str.= '
'.$v['title'].' - '.$cnt.'
'.$tmp['out_str'].'
';
//             // if($v['title'] == 'Oryza sativa'){
// 		    	// echo "
";var_dump($cnt);var_dump($out_str);exit;
// 		    // }
//             // printArrayList($v);
//             // continue;
//         } else {
//         	if(in_array($v['rank'], $rank_to_hide)){
//         		$class = '';
//         		// $class = 'class="hide-rank"';
//         		// $rank_index_init = 0;
//         	}else{
//         		$class = '';
//         		$rank_index_init = $rank_index_init+1;
//         	}
//         	$out_str.= '
'.$v['title'].' - '.$v['gene_count'].'
';
//         	$cnt = (int)$v['gene_count'];
//         	$parent_count+= $cnt;
//          	// echo "
";var_dump($out_str);exit;
//         }
//         // echo "
" . $v . "
";
//     }
//     $out_str.= '
';
//     return ['out_str' => $out_str, 'count' => $parent_count];
// }

/*function return_html_array_tree_titles($array, $count, $rank_index_init, $rank_index_full){
    // echo "
"; var_dump($array);exit;
    $out_str = '
';
    $parent_count = 0;
    $rank_to_hide = array(11,9,7,6,13,15,14,20,17,16);
    foreach($array as $k => $v) {
    	 //echo "
"; print_r($v); exit;
        if(is_array($v['childnodes']) && count($v['childnodes'])) {
        	if(!in_array($v['rank'], $rank_to_hide)){
        		$rank_index_init = $rank_index_init+1;
        	} else {
        		// exit($v['title']);
        	}
        	$tmp = return_html_array_tree_titles($v['childnodes'], 0, $rank_index_init, $rank_index_full+1);
        	$cnt = $tmp['count']+(int)$v['gene_count'];
        	$parent_count+= $cnt;
        	if(in_array($v['rank'], $rank_to_hide)){
        		$class = '';
        		// $class = 'class="hide-rank"';
        		$rank_index_init = 0;
        	}else{
        		$class = '';
        	}
            $out_str.= '
'.$v['title'].' - '.$cnt.'
'.$tmp['out_str'].'
';
            // if($v['title'] == 'Oryza sativa'){
		    	// echo "
";var_dump($cnt);var_dump($out_str);exit;
		    // }
            // printArrayList($v);
            // continue;
        } else {
        	if(in_array($v['rank'], $rank_to_hide)){
        		$class = '';
        		// $class = 'class="hide-rank"';
        		// $rank_index_init = 0;
        	}else{
        		$class = '';
        		$rank_index_init = $rank_index_init+1;
        	}
        	$out_str.= '
'.$v['title'].' - '.$v['gene_count'].'
';
        	$cnt = (int)$v['gene_count'];
        	$parent_count+= $cnt;
         	// echo "
";var_dump($out_str);exit;
        }
        // echo "
" . $v . "
";
    }
    $out_str.= '
';
    return ['out_str' => $out_str, 'count' => $parent_count];
}*/

// function convertToTree(array $flat, $idField = 'id',
//                         $parentIdField = 'parentId',
//                         $childNodesField = 'childNodes') {
//     $indexed = array();
//     // first pass - get the array indexed by the primary id  
//     foreach ($flat as $row) {
//         $indexed[$row[$idField]] = $row;
//         $indexed[$row[$idField]][$childNodesField] = array();
//     }

//     //second pass  
//     $root = null;
//     foreach ($indexed as $id => $row) {
//         $indexed[$row[$parentIdField]][$childNodesField][$id] =& $indexed[$id];
//         if (!$row[$parentIdField]) {
//             $root = $id;
//         }
//     }

//     return array($root => $indexed[$root]);
// }

// function return_ontology_summary($node){
// 	$query = new EntityFieldQuery();
// 	$query->entityCondition('entity_type', 'node')
// 		->entityCondition('bundle','annotation')
// 		->fieldCondition('field_gene','target_id',$node->nid,'=');
// 	$results = $query->execute();
// 	$aspects = array();
// 	$out = '';
// 	if(count($results['node'])){
// 		foreach($results['node'] as $ann){
// 			$annotation = node_load($ann->nid);
// 			$aspect = taxonomy_term_load($annotation->field_aspect[$annotation->language][0]['tid']);
// 			$aspects[$aspect->name][] = get_ontology_term_from_id($annotation->field_ontology_id[$annotation->language][0]['value']);
// 			/*if(array_key_exists($aspect->name, $aspects)){
// 				$aspects[$aspect->name][] = get_ontology_term_from_id($annotation->field_ontology_id[$annotation->language][0]['value']);
// 			} else {

// 			}*/
// 		}
// 		if(count($aspects)){
// 			$out.= '

// 					
// 						
// 							
// 								
// 								
// 							
// 						
// 						';
// 			foreach ($aspects as $aspect_name => $terms) {
// 				$out.= '';
// 			}
// 			$out.= '
ASPECT
ONTOLOGY TERMS
'.$aspect_name.'
';
// 				for($x=0;$x'.$terms[$x].'('.get_ontology_id_from_term($terms[$x]).')';
// 					if($x+1 < count($terms)){
// 						$out.= ', ';
// 					}
// 				}
// 				$out.= '
';
// 		} else {
// 			$out.= '
No Onotology Summary to show
';
// 		}
// 	} else {
// 		$out.= '
No Onotology Summary to show
';
// 	}
// 	return $out;
// }


// function return_gene_annotations($node){
// 	$query = new EntityFieldQuery();
// 	$query->entityCondition('entity_type', 'node')
// 		->entityCondition('bundle','annotation')
// 		->fieldCondition('field_gene','target_id',$node->nid,'=');
// 	$results = $query->execute();
// 	$out = '';/*'
Annotations Table:
';*/
// 	if(count($results['node'])){
// 		$out.= '
// 					
// 						
// 							
// 							
// 							
// 							
// 							
// 							
// 							
// 							
// 							
// 						
// 					
// 					';
// 		/*for($x=0;$xnid);
// 			$aspect = taxonomy_term_load($annotation->field_aspect[$annotation->language][0]['tid']);
// 			$data_source_fc_id = $annotation->field_data_source[$annotation->language][0]['value'];
// 			$data_source = entity_load('field_collection_item', array($data_source_fc_id));
// 			$source_term = taxonomy_term_load($data_source[$data_source_fc_id]->field_source_name[$annotation->language][0]['tid']);
// 			$db = $source_term->field_machine_name['und'][0]['value'];
// 			$db_object_id = $data_source[$data_source_fc_id]->field_object_id[$annotation->language][0]['value'];
// 			$gpfid = $annotation->field_gene_product_form_id[$annotation->language][0]['value'];
// 			$qual = $annotation->field_qualifier[$annotation->language][0]['value'];
// 			$extension = $annotation->field_extension[$annotation->language][0]['value'];
// 			$evidence = taxonomy_term_load($annotation->field_evidence_code[$annotation->language][0]['tid']);
// 			$evid = $evidence->field_machine_name[$annotation->language][0]['value'];
// 			$by = $annotation->field_assigned_by[$annotation->language][0]['value'];
// 			$date = date('Y/m/d', $annotation->field_date[$annotation->language][0]['value']);
// 			$out.= '
// 						
// 						
// 						
// 						
// 						
// 						
// 						
// 						
// 						
// 					';
// 		}
// 		$out.= '
ANNOTATION ACCESSION
GENE PRODUCT FORM ID
ASPECT
ONTOLOGY TERMS
QUALIFIER
EXTENSION
EVIDENCE CODE
ASSIGNED BY
DATE
'.$annotation->title.'
'.$gpfid.'
'.$aspect->name.'
'.$annotation->field_ontology_id[$annotation->language][0]['value'].' - '.get_ontology_term_from_id($annotation->field_ontology_id[$annotation->language][0]['value']).'
'.$qual.'
'.$extension.'
'.$evid.'
'.$by.'
'.$date.'
';
// 		return $out;
// 	} else {
// 		return '
No annotations currently
';
// 	}
// 	//echo'
';var_dump($results);exit;
// }
// function print_annotation_sources($node){
// 	$out = '
// 				
// 					
// 					
// 				';
// 	// echo '
';var_dump($node->field_db_reference);
// 	if(count($node->field_db_reference) && count($node->field_db_reference[$node->language])){
// 		//echo 'good count';
// 		for($x=0;$xfield_db_reference[$node->language]);$x++){
// 			$db_reference_fc_id = $node->field_db_reference[$node->language][$x]['value'];
// 			$db_reference = entity_load('field_collection_item', array($db_reference_fc_id));
// 			$reference_term = taxonomy_term_load($db_reference[$db_reference_fc_id]->field_source_name[$node->language][0]['tid']);
// 			// if($x==1){
// 			// 	echo '
';var_dump($reference_term);
// 			// }
// 			if($reference_term->field_machine_name['und'][0]['value'] != '' && $reference_term->field_machine_name['und'][0]['value'] != 'PMID'){
// 				//echo 'good annotation';
// 				$out.= '
';
// 				if($db_reference[$db_reference_fc_id]->field_object_id[$node->language][0]['value'] != ''){
// 					$out.= '';
// 				} else {
// 					$out.= '';
// 				}
// 			}
// 		}
// 	}
// 	// echo '
';var_dump($node->field_with_or_from);exit;
// 	if(count($node->field_with_or_from) && count($node->field_with_or_from[$node->language])){
// 		//echo 'good count';
// 		for($x=0;$xfield_with_or_from[$node->language]);$x++){
// 			$with_from_fc_id = $node->field_with_or_from[$node->language][$x]['value'];
// 			$with_from = entity_load('field_collection_item', array($with_from_fc_id));
// 			$reference_term = taxonomy_term_load($with_from[$with_from_fc_id]->field_source_name[$node->language][0]['tid']);
// 			//echo '
';var_dump($annotation->field_db_reference);
// 			if($reference_term->field_machine_name['und'][0]['value'] != '' && $reference_term->field_machine_name['und'][0]['value'] != 'PMID'){
// 				//echo 'good annotation';
// 				$out.= '
';
// 				if($with_from[$with_from_fc_id]->field_object_id[$node->language][0]['value'] != ''){
// 					$out.= '';
// 				} else {
// 					$out.= '';
// 				}
// 			}
// 		}
// 	}
// 	$out.= '
Source Name
Source ID
'.$reference_term->field_machine_name['und'][0]['value'].'
'.$db_reference[$db_reference_fc_id]->field_object_id[$node->language][0]['value'].'
'.$reference_term->field_machine_name['und'][0]['value'].'
'.$with_from[$with_from_fc_id]->field_object_id[$node->language][0]['value'].'
';
// 	print $out;
// }

// function print_gene_annotation_sources($node){
// 	$query = new EntityFieldQuery();
// 	$query->entityCondition('entity_type', 'node')
// 		->entityCondition('bundle','annotation')
// 		->fieldCondition('field_gene','target_id',$node->nid,'=');
// 	$results = $query->execute();
// 	$out = '
Citations:
';
// 	if(count($results['node'])){
// 		$out.= '
';
// 		foreach($results['node'] as $ann){
// 			$annotation = node_load($ann->nid);
// 			//var_dump($annotation);
// 			//echo '
';var_dump($annotation->field_with_or_from);

// 			if(count($annotation->field_db_reference) > 0){
// 				//echo 'good count';
// 				for($x=0;$xfield_db_reference[$annotation->language]);$x++){
// 					$db_reference_fc_id = $annotation->field_db_reference[$annotation->language][$x]['value'];
// 					$db_reference = entity_load('field_collection_item', array($db_reference_fc_id));
// 					$reference_term = taxonomy_term_load($db_reference[$db_reference_fc_id]->field_source_name[$annotation->language][0]['tid']);
// 					// if($x==1){
// 					// 	echo '
';var_dump($reference_term);
// 					// }
// 					if($reference_term->field_machine_name['und'][0]['value'] == 'PMID'){
// 						$pminfoarray = pubmed_id_to_article_info($db_reference[$db_reference_fc_id]->field_object_id[$annotation->language][0]['value']);
// 						$out.= '
'.$pminfoarray['authors'].', '.$pminfoarray['title'].', '.$pminfoarray['journal'].', '.$pminfoarray['volume'].', '.$pminfoarray['issue'].', '.$pminfoarray['epubdate'].'
';
// 					} else if($reference_term->field_machine_name['und'][0]['value'] != '' && $reference_term->field_machine_name['und'][0]['value'] != 'PMID'){
// 						//echo 'good annotation';
// 						$out.= '
'.$reference_term->field_machine_name['und'][0]['value'].', '.$db_reference[$db_reference_fc_id]->field_object_id[$annotation->language][0]['value'].'
';
// 					}
// 				}
// 			}
// 			if(count($annotation->field_with_or_from) > 0){
// 				//echo 'good count';
// 				for($x=0;$xfield_with_or_from[$annotation->language]);$x++){
// 					$with_from_fc_id = $annotation->field_with_or_from[$annotation->language][$x]['value'];
// 					$with_from = entity_load('field_collection_item', array($with_from_fc_id));
// 					$reference_term = taxonomy_term_load($with_from[$with_from_fc_id]->field_source_name[$annotation->language][0]['tid']);
// 					//echo '
';var_dump($annotation->field_db_reference);
// 					if($reference_term->field_machine_name['und'][0]['value'] == 'PMID'){
// 						$pminfoarray = pubmed_id_to_article_info($with_from[$with_from_fc_id]->field_object_id[$annotation->language][0]['value']);
// 						$out.= '
'.$pminfoarray['authors'].', '.$pminfoarray['title'].', '.$pminfoarray['journal'].', '.$pminfoarray['volume'].', '.$pminfoarray['issue'].', '.$pminfoarray['epubdate'].'
';
// 					} else if($reference_term->field_machine_name['und'][0]['value'] != '' && $reference_term->field_machine_name['und'][0]['value'] != 'PMID'){
// 						//echo 'good annotation';
// 						$out.= '
'.$reference_term->field_machine_name['und'][0]['value'].', '.$with_from[$with_from_fc_id]->field_object_id[$annotation->language][0]['value'].'
';
// 					}
// 				}
// 			}
// 		}
// 		$out.= '
';
// 		print $out;
// 	} else {
// 		print '
No source information to show
';
// 	}
// }

// function print_annotation_pubmed_citations($node){
// 	$out = '
PubMED Citations:
';
// 	if(count($node->field_db_reference) > 0){
// 		//echo 'good count';
// 		for($x=0;$xfield_db_reference[$node->language]);$x++){
// 			$db_reference_fc_id = $node->field_db_reference[$node->language][$x]['value'];
// 			$db_reference = entity_load('field_collection_item', array($db_reference_fc_id));
// 			$reference_term = taxonomy_term_load($db_reference[$db_reference_fc_id]->field_source_name[$node->language][$x]['tid']);
// 			//echo '
';var_dump($annotation->field_db_reference);
// 			if($reference_term->field_machine_name['und'][0]['value'] != '' && $db_reference[$db_reference_fc_id]->field_object_id[$node->language][0]['value'] != '' && $reference_term->field_machine_name['und'][0]['value'] == 'PMID'){
// 				//echo 'good annotation';
// 				$pminfoarray = pubmed_id_to_article_info($db_reference[$db_reference_fc_id]->field_object_id[$node->language][0]['value']);
// 				$out.= '
'.$pminfoarray['authors'].', '.$pminfoarray['title'].', '.$pminfoarray['journal'].', '.$pminfoarray['volume'].', '.$pminfoarray['issue'].', '.$pminfoarray['epubdate'].'
';
// 			}
// 		}
// 	}
// 	$out.= '
';
// 	print $out;
// }

// function return_pubmed_citations($node){
// 	//TODO - find bug related to where the source terms are pointing in annotations
// 	$query = new EntityFieldQuery();
// 	$query->entityCondition('entity_type', 'node')
// 		->entityCondition('bundle','annotation')
// 		->fieldCondition('field_gene','target_id',$node->nid,'=');
// 	$results = $query->execute();
// 	$out = '
Citations
';
// 	if(count($results['node'])){
// 		foreach($results['node'] as $ann){
// 			$annotation = node_load($ann->nid);
// 			//var_dump($annotation);
// 			if(count($annotation->field_db_reference) > 0){
// 				// echo 'good count';
// 				for($x=0;$xfield_db_reference[$annotation->language]);$x++){
// 					$db_reference_fc_id = $annotation->field_db_reference[$annotation->language][$x]['value'];
// 					$db_reference = entity_load('field_collection_item', array($db_reference_fc_id));
// 					$reference_term = taxonomy_term_load($db_reference[$db_reference_fc_id]->field_source_name[$annotation->language][$x]['tid']);
// 					// echo '
';var_dump($reference_term->field_machine_name['und'][0]['value']);exit;
// 					if($reference_term->field_machine_name['und'][0]['value'] != '' && $db_reference[$db_reference_fc_id]->field_object_id[$annotation->language][0]['value'] != '' && $reference_term->field_machine_name['und'][0]['value'] == 'PMID'){
// 						// echo 'good annotation';
// 						$pminfoarray = pubmed_id_to_article_info($db_reference[$db_reference_fc_id]->field_object_id[$annotation->language][0]['value']);
// 						// print_r($pminfoarray);exit;
// 						$out.= '
'.$pminfoarray['authors'].', '.$pminfoarray['title'].', '.$pminfoarray['journal'].', '.$pminfoarray['volume'].', '.$pminfoarray['issue'].', '.$pminfoarray['epubdate'].'
';
// 					} else if($reference_term->field_machine_name['und'][0]['value'] != ''){
// 						$out.= '
'.$reference_term->field_machine_name['und'][0]['value'].':'.$db_reference[$db_reference_fc_id]->field_object_id[$annotation->language][0]['value'].'
';
// 					}
// 				}
// 			}
// 		}
// 		$out.= '
';
// 		return $out;
// 	} else {
// 		return '
No citation information to show
';
// 	}
// }

// // returns an associative array with authors, title, journal, vol, issue, epubdate
// // https://www.ncbi.nlm.nih.gov/pmc/tools/get-metadata/
// function pubmed_id_to_article_info($pmid){
// 	$html = curl_get_contents("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=".$pmid."&retmode=json");
// 	$json = json_decode($html);
// 	$trimmed_pmid = ltrim($pmid, '0');
// 	// $tmp = isset($json->result->$trimmed_pmid->error);
// 	// $tmp2 = $tmp->$pmid;
// 	// echo'
';var_dump($tmp);
// 	// echo'
';var_dump($pmid);exit;
// 	if(isset($json->result->$trimmed_pmid->error)){
// 		$out_array = array(
// 			'authors' 	=> '',
// 			'title'		=> '',
// 			'journal'	=> '',
// 			'volume'	=> '',
// 			'issue'		=> '',
// 			'epubdate'	=> '',
// 		);
// 		//echo '
';var_dump($out_array);
// 		return $out_array;
// 	} else {
// 		$article_metadata = $json->result->$pmid;
// 		if(count($article_metadata->authors)>1){
// 			$authors = $article_metadata->authors[0]->name.', et. all';
// 		} else {
// 			$authors = $article_metadata->authors[0]->name;
// 		}
// 		$out_array = array(
// 			'authors' 	=> $authors,
// 			'title'		=> $article_metadata->title,
// 			'journal'	=> $article_metadata->source,
// 			'volume'	=> $article_metadata->volume,
// 			'issue'		=> $article_metadata->issue,
// 			'epubdate'	=> $article_metadata->epubdate
// 		);
// 		//echo '
';var_dump($out_array);
// 		return $out_array;
// 	}
// }

// function return_gene_synonyms($node){
// 	$out = [];
// 	if(count($node->field_synonyms)){
// 		foreach($node->field_synonyms['und'] as $index){
// 			$out[] = str_replace(' ', ' ', $index['value']);
// 		}
// 		return implode(' | ', $out);
// 	} else {
// 		return 'No synonyms to show.';
// 	}
// }

// function return_gene_location($node){
// 	return 'Chromosome '.$node->field_chromosome_no['und'][0]['value'].': '.$node->field_chromosome_start['und'][0]['value'].' - '.$node->field_chromosome_stop['und'][0]['value'];
// }

// function return_gene_phenotype($node){
// 	if($node->field_has_phenotype['und'][0]['value']){
// 		return $node->field_phenotype_description['und'][0]['value'];
// 	} else {
// 		return '';
// 	}
// }

// function return_data_source_fc($node){
// 	$data_source_fc_id = $node->field_data_source['und'][0]['value'];
// 	$data_source = entity_load('field_collection_item', [$data_source_fc_id]);
// 	$source_term = taxonomy_term_load($data_source[$data_source_fc_id]->field_source_name['und'][0]['tid']);
// 	$source_name = $source_term->name;
// 	$object_id = $data_source[$data_source_fc_id]->field_object_id['und'][0]['value'];
// 	return 'Object ID: '.$object_id.'
Source Name: '.$source_name;
// }

// function return_data_source_source($node){
// 	$data_source_fc_id = $node->field_data_source['und'][0]['value'];
// 	$data_source = entity_load('field_collection_item', [$data_source_fc_id]);
// 	$source_term = taxonomy_term_load($data_source[$data_source_fc_id]->field_source_name['und'][0]['tid']);
// 	return $source_term->name;
// }

// function return_data_source_id($node){
// 	$data_source_fc_id = $node->field_data_source['und'][0]['value'];
// 	$data_source = entity_load('field_collection_item', [$data_source_fc_id]);
// 	$source_term = taxonomy_term_load($data_source[$data_source_fc_id]->field_source_name['und'][0]['tid']);
// 	$object_id = $data_source[$data_source_fc_id]->field_object_id['und'][0]['value'];
// 	if($source_term->name == 'Planteome (planteome)' && $object_id == ''){
// 		$object_id = $node->title;
// 	}
// 	return $object_id;
// }

// function return_translated_ontology_term($node){
// 	$term = $node->field_ontology_id['und'][0]['value'];
// 	$translated = get_ontology_term_from_id($term);
// 	return $term.' - '.$translated;
// }

// function return_annotation_curators($node){
// 	$result = db_select('workbench_moderation_node_history','wmnh')
// 				->fields('wmnh')
// 				->condition('nid', $node->nid,'=')
// 				->execute()
// 				->fetchAll();
// 	$out = 'No curator data to show';
// 	if(count($result)){
// 		$out = '';
// 		$exclude = [];
// 		$exclude[] = $node->uid;
// 		foreach($result as $tablerowobj){
// 			if(isset($tablerowobj->uid) && !in_array($tablerowobj->uid, $exclude)){
// 				$user = user_load($tablerowobj->uid);
// 				$out.= '
'.$user->name.'
';
// 				$exclude[] = $user->uid;
// 			}
// 		}
// 	}
// 	return $out;
// }

// function return_formatted_author($node){
// 	$user = user_load($node->uid);
// 	return ''.$user->name.'';
// }

// function return_related_synonyms($node){
// 	$out = 'N/A';
// 	if(count($node->field_taxon_related_synonyms)){
// 		$out = '';
// 		foreach($node->field_taxon_related_synonyms['und'] as $synonym_array){
// 			$targ = str_replace(' ', ' ', $synonym_array['value']);
// 			$out.= ($out == '') ? ($targ) : (' | '.$targ);
// 		}
// 	}
// 	return $out;
// }

// function return_exact_synonyms($node){
// 	$out = 'N/A';
// 	if(count($node->field_taxon_exact_synonyms)){
// 		$out = '';
// 		foreach($node->field_taxon_exact_synonyms['und'] as $synonym_array){
// 			$targ = str_replace(' ', ' ', $synonym_array['value']);
// 			$out.= ($out == '') ? ($targ) : (' | '.$targ);
// 		}
// 	}
// 	return $out;
// }

// function return_ncbi_number_link($node){
// 	$ncbi_num = $node->field_taxon_ncbi_id['und'][0]['value'];
// 	return ''.$ncbi_num.'';
// }

// function return_gene_link($node){
// 	return l($node->field_gene['und'][0]['entity']->title, '/node/'.$node->field_gene['und'][0]['target_id']);
// 	// return ''.$node->field_gene['und'][0]['entity']->title.'';
// }

// function return_with_or_from($node){
// 	$out = '
N/A
';
// 	if(count($node->field_with_or_from)){
// 		$out = '';
// 		foreach($node->field_with_or_from['und'] as $index){
// 			$with_from_fc_id = $index['value'];
// 			$with_from = entity_load('field_collection_item', [$with_from_fc_id]);
// 			$source_term = taxonomy_term_load($with_from[$with_from_fc_id]->field_source_name['und'][0]['tid']);
// 			$object_id = $with_from[$with_from_fc_id]->field_object_id['und'][0]['value'];
// 			$out.= '
'.$source_term->name.', '.$object_id.'
';
// 		}
// 	}
// 	return $out;
// }

// function return_db_ref($node){
// 	$out = '
N/A
';
// 	if(count($node->field_db_reference)){
// 		$out = '';
// 		foreach($node->field_db_reference['und'] as $index){
// 			$db_ref_fc_id = $index['value'];
// 			$db_ref = entity_load('field_collection_item', [$db_ref_fc_id]);
// 			$source_term = taxonomy_term_load($db_ref[$db_ref_fc_id]->field_source_name['und'][0]['tid']);
// 			$object_id = $db_ref[$db_ref_fc_id]->field_object_id['und'][0]['value'];
// 			$out.= '
'.$source_term->name.', '.$object_id.'
';
// 		}
// 	}
// 	return $out;
// }

// function return_data_source($node){
// 	$out = '
N/A
';
// 	if(count($node->field_data_source)){
// 		$out = '';
// 		foreach($node->field_data_source['und'] as $index){
// 			$data_source_fc_id = $index['value'];
// 			$data_source = entity_load('field_collection_item', [$data_source_fc_id]);
// 			$source_term = taxonomy_term_load($data_source[$data_source_fc_id]->field_source_name['und'][0]['tid']);
// 			$object_id = $data_source[$data_source_fc_id]->field_object_id['und'][0]['value'];
// 			$out.= $source_term->name.', '.$object_id;
// 		}
// 	}
// 	return $out;
// }

// function return_gene_counts($node){
// 	// $vocab = taxonomy_vocabulary_machine_name_load('gene_type');
// 	// $terms = entity_load('taxonomy_term', FALSE, ['vid'=>$vocab->vid]);
// 	// // echo'
';var_dump($terms);exit;
// 	// foreach($terms as $term){
// 	// 	$q = new EntityFieldQuery();
// 	// }

// 	// $query = db_select('node',"n");
// 	// $query->leftjoin("field_data_field_gene_type","gt","gt.entity_id = n.nid");
// 	// $query->leftjoin("field_data_field_ref_species","rf","rf.entity_id = n.nid");
// 	// $all_taxons= $query->fields('n',array('nid','title'))
// 	// 				->fields('gc',array('field_gene_count_value'))
// 	// 				->fields('tp',array('field_taxon_parent_target_id'))
//  //                   ->condition('n.type',"taxon",'=')
//  //                   ->condition('n.status',1,'=')
//  //                   ->execute()
//  //                   ->fetchAll(); 
//     $taxon_id = arg(1);

//     $query = db_query("SELECT gt.field_gene_type_tid, count(n.nid) as total_gene FROM {node} as n
//     	LEFT JOIN {field_data_field_gene_type} as gt ON gt.entity_id = n.nid
//     	LEFT JOIN {field_data_field_ref_species} as rf ON rf.entity_id = n.nid
//     	WHERE n.type = 'gene' AND n.status = 1 AND rf.field_ref_species_target_id = ".$taxon_id." 
//     	GROUP BY gt.field_gene_type_tid
// 	");
	
// 	$result = $query->fetchAll();

// 	if(is_array($result)){
// 		$total = 0;
// 		foreach ($result as $key => $value) {
// 			$total += $value->total_gene;
// 		}

// 		$output = "
Total - ".$total."
";
// 		foreach ($result as $key => $value) {
// 			$term = taxonomy_term_load($value->field_gene_type_tid);
// 			$output .= "
".$term->field_human_name['und'][0]['value']." - ".$value->total_gene."
";
// 		}

// 		return $output;
// 	}else{
// 		return "";
// 	}
// }

// function return_species_link($node){
// 	return l($node->field_ref_species['und'][0]['entity']->title, '/node/'.$node->field_ref_species['und'][0]['entity']->nid);
// }

// /*
//  * builds two arrays, each 5 elements long, for paralogs/orthologs
//  * $base_gene - base gene, sent to justin's api
//  *		at# -> ok
//  *		os# -> replace first G w/ T
//  *		zm# -> need to translate to GRMZM number
//  * $base_species - base species, sent to justin's api. Transformed first as follows:
//  *		Oryza Sativa Japonica Group -> Oryza_sativa.japonica.IRGSP
//  *		Zea Mays -> Zea_mays
//  *		Arabidopsis Thaliana -> Arabidopsis_thaliana
//  *
//  *		More IDs will need to be added
//  *	$gene_synonyms - used for zea mays only
//  * return: [[$paralogs],[$orthologs]]
//  */
// function return_homolog_array($base_gene_id, $base_species, $gene_synonyms){
// 	//transform gene/species as needed
// 	//send gene/species to API
// 	//transform JSON into array & iterate
// 	//	first 5 paralogs go into paralog array
// 	//	maintain array of species in ortholog array
// 	//	first 5 orthologs go into ortholog array
// 	//	continue iterating over homologs, if encounter a species not in ortholog array already, replace index of array based on species in ortholog array +1
// 	//	when species in ortholog array = 5, break, or let loop run its course.
// 	switch ($base_species) {
// 		case '433':
// 			//Zea Mays
// 			foreach($gene_synonyms['und'] as $synonym){
// 				if(strpos($synonym['value'], 'GRMZM') !== false){
// 					//break out of both
// 					//this might actually need to be break 3 since we're in the if statement?
// 					$base_gene_id = $synonym['value'];
// 					$base_species = 'Zea_mays';
// 					break 2;
// 				}
// 			}
// 			//either synonyms are empty or synonyms don't contain a GRMZM, can't query API
// 			return [[],[]];
// 			break;
// 		case '465':
// 			// Oryza Sativa Japonica Group
// 			if($base_gene_id[4] == 'G'){
// 				$base_gene_id[4] = 'T';
// 				$base_species = 'Oryza_sativa.japonica.IRGSP';
// 			} else {
// 				//incorrect gene ID, can't query API
// 				return [[],[]];
// 			}
// 			break;
// 		case '636':
// 			// Arabidopsis Thaliana
// 			$base_species = 'Arabidopsis_thaliana';
// 			break;
		
// 		default:
// 			return [[],[]];
// 			break;
// 	}
// 	//if we reach here, the data should have been cleaned.
// 	// echo'
';
// 	// var_dump($base_gene_id);
// 	// var_dump($base_species);
// 	// exit;
// 	$availible_species = ['Arabidopsis_thaliana', 'Oryza_sativa.japonica.IRGSP', 'Zea_mays'];
// 	$json = htmlspecialchars(curl_get_contents("http://dev.planteome.org/ortho_service/?q=".$base_gene_id."&species=".$base_species.""));
// 	$json_arr = json_decode(html_entity_decode($json));
// 	$ortholog_species = [];
// 	$paralogs = [];
// 	$orthologs = [];
// 	// $needed_unique_num = 
// 	foreach ($json_arr as $homolog_json_obj) {
// 		if($homolog_json_obj->species == $base_species){
// 			//paralog
// 			if(count($paralogs) < 5){
// 				$paralogs[] = $homolog_json_obj->gene;
// 				if(count($ortholog_species == 5) && count($paralogs) == 5){
// 					//multiple break levels?
// 					break;
// 				}
// 			}

// 		} else {
// 			//ortholog
// 			if(in_array($homolog_json_obj->species, $availible_species)){
// 				if(count($orthologs) < 5){
// 					//add ortholog
// 					$orthologs[] = $homolog_json_obj->gene;
// 					$ortholog_species[] = $homolog_json_obj->species;
// 				} elseif (count(array_unique($ortholog_species)) < min(count($availible_species)-1, 5)){
// 					//need more species in ortholog_species, can find indexes of species and then replace corresponding index in $orthologs?
// 				}
// 			}
// 		}
// 	}

// 	echo'
';var_dump($json_arr);exit;
// }


// /**************theme_hooks*****************/

// function cgrb_preprocess_page(&$variables){
// 	// if($variables[''])
// 	// echo'
';print_r($variables['node']->type);exit;
// 	if($variables['is_front']){
// 		// $tmp = drupal_get_path('theme', 'cgrb');
// 		// echo'
';var_dump($tmp);exit;
// 		drupal_add_css(drupal_get_path('theme', 'cgrb').'/js/themes/default/style.min.css');
// 		drupal_add_js(drupal_get_path('theme', 'cgrb').'/js/jstree.min.js');
// 		// /*echo'
';*/print_r(drupal_get_js());exit;
// 		// $variables['scripts'] = drupal_get_js();
// 		drupal_add_js(drupal_get_path('theme', 'cgrb').'/js/fp_scripts.js');
// 	} elseif(isset($variables['node']->type) && $variables['node']->type == 'taxon'){
// 		drupal_add_css(drupal_get_path('theme', 'cgrb').'/js/themes/default/style.min.css');
// 		drupal_add_js(drupal_get_path('theme', 'cgrb').'/js/jstree.min.js');
// 		// /*echo'
';*/print_r(drupal_get_js());exit;
// 		// $variables['scripts'] = drupal_get_js();
// 		drupal_add_js(drupal_get_path('theme', 'cgrb').'/js/taxon_scripts.js');
// 	}
// 	// echo'
';var_dump($variables['is_front']);exit;
// }

// function cgrb_preprocess_user_login(&$variables) {
// 	$varr = user_login(array(),$form_state);
// 	$variables['form'] = drupal_build_form('user_login', $varr); ## I have to build the user login myself.
// }

// function cgrb_theme(&$existing, $type, $theme, $path) {
//   return array(
//     'user_login' => array(
//       'template' => 'user-login',
//       'variables' => array('form' => NULL), ## you may remove this line in this case
//     ),
//   );

// }

// function cgrb_form_alter(&$form, &$form_state, $form_id){
// 	if ($form_id == 'user_register_form'){
// 		//echo "
"; print_r($form); exit();
// 		$form['#prefix'] = '

// 							

// 								

// 									

// 										

// 											
User Register
';
// 		$form['#suffix']  = '
';
// 	}

// 	if($form_id == 'user_pass'){
// 		$form['#prefix'] = '

// 							

// 								

// 									

// 										

// 											
Forgot password?
';
// 		$form['#suffix']  = '
';
// 	}

// 	if ($form_id == 'views_exposed_form') {
//         $view = $form_state['view'];
//         if ($view->name == 'search_for_gene' && $view->current_display == 'page') {
            
//             $form['field_aspect_tid']['#attributes']['class'][] = 'selectpicker';
//             $form['field_aspect_tid']['#prefix'] = '
';
//             $form['field_aspect_tid']['#suffix'] = '
';

//             $form['field_gene_type_tid_1']['#attributes']['class'][] = 'selectpicker';
//             $form['field_gene_type_tid_1']['#prefix'] = '
';
//             $form['field_gene_type_tid_1']['#suffix'] = '
';

//             $options = array();
//             $query = db_select('node', 'n');
//             $query->leftjoin("field_data_field_taxon_rank","tr","tr.entity_id = n.nid");
// 			$nodes = $query->fields('n', array('nid','title'))
// 			    ->orderBy('n.title', 'ASC')
// 			    ->condition('n.type', 'taxon')
// 			    ->condition('tr.field_taxon_rank_tid', array(10,18),'IN')
// 			    ->execute()->fetchAll();
// 			 //$query; // returns an indexed array
			 
// 			$options[''] = '- Any -';
// 			foreach ($nodes as $key => $value) {				
// 				$options[$value->nid] = $value->title;
// 			}
//   			//echo "
"; print_r($options); exit();
//             $form['field_ref_species_target_id']['#attributes']['class'][] = 'selectpicker selectpicker-species';
//             $form['field_ref_species_target_id']['#type'] = 'select';
//             $form['field_ref_species_target_id']['#size'] = '';
//             $form['field_ref_species_target_id']['#default_value'] = '';
//             $form['field_ref_species_target_id']['#options'] = $options;

//             $form['submit']['#value'] = html_entity_decode('');
//             $form['field_ref_species_target_id']['#prefix'] = '
';
//             $form['field_ref_species_target_id']['#suffix'] = '
';
//             //echo "
"; print_r($form); exit();
//         // $form['keys']['#prefix'] = '
';
//         //  $form['keys']['#suffix'] = '
';

//         }
//     }
// 	//	echo "
"; print_r($form_id); exit();
// 	// function cgrb_preprocess_node(&$variables){

// 	// }
// }

/**************theme_hooks*****************/

function cgrb_preprocess_page(&$variables){
	// if($variables[''])
	// echo'
';print_r($variables['node']->type);exit;
	if($variables['is_front']){
		// $tmp = drupal_get_path('theme', 'cgrb');
		// echo'
';var_dump($tmp);exit;
		drupal_add_css(drupal_get_path('theme', 'cgrb').'/js/themes/default/style.min.css');
		drupal_add_js(drupal_get_path('theme', 'cgrb').'/js/jstree.min.js');
		// /*echo'
';*/print_r(drupal_get_js());exit;
		// $variables['scripts'] = drupal_get_js();
		drupal_add_js(drupal_get_path('theme', 'cgrb').'/js/fp_scripts.js');
	} elseif(isset($variables['node']->type) && $variables['node']->type == 'taxon'){
		drupal_add_css(drupal_get_path('theme', 'cgrb').'/js/themes/default/style.min.css');
		drupal_add_js(drupal_get_path('theme', 'cgrb').'/js/jstree.min.js');
		// /*echo'
';*/print_r(drupal_get_js());exit;
		// $variables['scripts'] = drupal_get_js();
		drupal_add_js(drupal_get_path('theme', 'cgrb').'/js/taxon_scripts.js');
	}
	// echo'
';var_dump($variables['is_front']);exit;
}

function cgrb_preprocess_user_login(&$variables) {
	$varr = user_login(array(),$form_state);
	$variables['form'] = drupal_build_form('user_login', $varr); ## I have to build the user login myself.
}

function cgrb_theme(&$existing, $type, $theme, $path) {
  return array(
    'user_login' => array(
      'template' => 'user-login',
      'variables' => array('form' => NULL), ## you may remove this line in this case
    ),
  );

}

function cgrb_form_alter(&$form, &$form_state, $form_id){
	if ($form_id == 'user_register_form'){
		//echo "
"; print_r($form); exit();
		$form['#prefix'] = '

							

								

									

										

											
User Register
';
		$form['#suffix']  = '
';
	}

	if($form_id == 'user_pass'){
		$form['#prefix'] = '

							

								

									

										

											
Forgot password?
';
		$form['#suffix']  = '
';
	}

	if ($form_id == 'views_exposed_form') {
        $view = $form_state['view'];
        if ($view->name == 'search_for_gene' && $view->current_display == 'page') {
            
            $form['field_aspect_tid']['#attributes']['class'][] = 'selectpicker';
            $form['field_aspect_tid']['#prefix'] = '
';
            $form['field_aspect_tid']['#suffix'] = '
';

            $form['field_gene_type_tid_1']['#attributes']['class'][] = 'selectpicker';
            $form['field_gene_type_tid_1']['#prefix'] = '
';
            $form['field_gene_type_tid_1']['#suffix'] = '
';

            $options = array();
            $query = db_select('node', 'n');
            $query->leftjoin("field_data_field_taxon_rank","tr","tr.entity_id = n.nid");
			$nodes = $query->fields('n', array('nid','title'))
			    ->orderBy('n.title', 'ASC')
			    ->condition('n.type', 'taxon')
			    ->condition('tr.field_taxon_rank_tid', array(10,18),'IN')
			    ->execute()->fetchAll();
			 //$query; // returns an indexed array
			 
			$options[''] = '- Any -';
			foreach ($nodes as $key => $value) {				
				$options[$value->nid] = $value->title;
			}
  			//echo "
"; print_r($options); exit();
            $form['field_ref_species_target_id']['#attributes']['class'][] = 'selectpicker selectpicker-species';
            $form['field_ref_species_target_id']['#type'] = 'select';
            $form['field_ref_species_target_id']['#size'] = '';
            $form['field_ref_species_target_id']['#default_value'] = '';
            $form['field_ref_species_target_id']['#options'] = $options;

            $form['submit']['#value'] = html_entity_decode('');
            $form['field_ref_species_target_id']['#prefix'] = '
';
            $form['field_ref_species_target_id']['#suffix'] = '
';
            //echo "
"; print_r($form); exit();
        // $form['keys']['#prefix'] = '
';
        //  $form['keys']['#suffix'] = '
';

        }
    }
	//	echo "
"; print_r($form_id); exit();
	// function cgrb_preprocess_node(&$variables){

	// }
}