Merge pull request #383 from micheldumontier/release3

updates

Author: micheldumontier

common/php/oboparser.php

@@ -0,0 +1,54 @@
+<?php
+
+function OBOParser($in)
+{
+	if($in === NULL) return NULL;
+	
+	while($l = fgets($in)) {
+		if(strlen(trim($l)) == 0) continue;
+		
+		if(strstr($l,"[Term]")) {
+			if(isset($term)) {
+				$terms[$term['id'][0]] = $term;			
+			}
+			$term = '';
+		} else if(strstr($l,"[Typedef]")) {
+			if(isset($term)) {
+				$terms[$term['id'][0]] = $term;			
+				unset($term);
+			}
+			$typedef = '';
+		} else {
+			if(isset($term)) {
+				$a = explode(": ",trim($l));
+				$a[1] = str_replace('"','',$a[1]); // remove brackets
+				
+				preg_match("/(.*) \! (.*)/",$a[1],$m); // parse out the label that may come with an id
+				if(count($m)) {
+					$a[1] = $m[1];
+				}
+				$term[$a[0]][] = $a[1];		
+			
+			} else if(isset($typedef))  {
+				
+			} else {
+				// in the header
+				//format-version: 1.0
+				$a = explode(": ",trim($l));
+				$terms['ontology'][$a[0]][] = $a[1];
+			} 
+		}
+	}
+	if(isset($term)) $terms[$term['id'][0]] = $term;
+
+	return $terms;
+}
+
+function BuildNamespaceSearchList($terms, &$out)
+{
+	foreach($terms AS $term) {
+		if(isset($term['namespace'][0]) && isset( $term['id'][0] ) && isset( $term['name'][0])) 
+			$out[$term['namespace'][0]][$term['id'][0]] = $term['name'][0];
+	}
+}
+?>

goa/goa.php

@@ -66,7 +66,8 @@ function run(){
 			$rfile = $rdir.strtoupper($file)."/gene_association.goa_".$file.".gz";
 			if($download == true) {
 				echo "downloading $file ... ";
-				file_put_contents($lfile,file_get_contents($rfile));
+				//file_put_contents($lfile,file_get_contents($rfile));
+				utils::DownloadSingle($rfile,$lfile);
 			}
 
 			$gz = (strstr(parent::getParameterValue('output_format'),".gz") === FALSE)?false:true;