diff VCF_to_VariantDB.pl @ 2:d03a63a57e82 draft

New version, better following configuration guidelines

--- a/VCF_to_VariantDB.pl	Wed May 08 04:34:30 2013 -0400
+++ b/VCF_to_VariantDB.pl	Wed Feb 19 06:45:32 2014 -0500
@@ -22,7 +22,7 @@
 # H = (H)ost of the galaxy web server (http://my.galaxy.server/galaxy/)
 getopts('v:u:n:a:g:o:b:B:V:c:S:R:H:', \%opts);  # option are in %opts
 
-
+$|++;
 #################
 ## CHECK INPUT ##
 #################
@@ -55,6 +55,7 @@
 $url =~ s/\/\/$/\//;
 $url .= "cgi-bin/galaxy_communication.cgi";
 my $conn = LWP::UserAgent->new();
+$conn->timeout(1800);
 my $response = $conn->post( $url, {'HelloWorld' => 1} );
 my $content = $response->decoded_content();
 
@@ -113,20 +114,42 @@
 $gender = $opts{'g'};
 # post form to the variantDB host. 
 if (exists($opts{'b'})) {
-	$response = $conn->post( $url, {'VCFurl1' => "$vcfurl", 'BAMurl1' => "$bamurl", 'BAIurl1' => "$bamidxurl",'storedata' => 1, 'name1' => "$sample", 'gender1' => "$gender", 'User' => $email} );
+	$response = $conn->post( $url, {'VCFurl1' => "$vcfurl", 'BAMurl1' => "$bamurl", 'BAIurl1' => "$bamidxurl",'storedata1' => 1, 'name1' => "$sample", 'gender1' => "$gender", 'User' => $email, 'GalaxyUpload' => 1} );
 }
 else {
-	$response = $conn->post( $url, {'VCFurl1' => "$vcfurl",  'sample1' => "$sample", 'gender1' => "$gender", 'User' => $email} );
+	$response = $conn->post( $url, {'VCFurl1' => "$vcfurl",  'name1' => "$sample", 'gender1' => "$gender", 'User' => $email, 'GalaxyUpload' =>1 } );
 }
 my $content = $response->decoded_content();
 chomp($content);
-if ($content =~ m/OK$/) {
-	print OUT "Processing Datafiles : OK.\n";
-	print OUT "\n$content\n";
-}
-else {
+## check if upload went ok.
+if (substr($content,0,2) ne 'OK') {
 	die("ERROR: $content");
 }
+## extract wd from content.
+print OUT "Uploading datafiles to VariantDB : OK.\n";
+$content =~ m/OK-(.+)$/;
+$rwd = $1;
+if ($rwd eq '') {
+	die("ERROR : No remote working directory provided to check status.");
+}
+## now wait for the import to finish.
+$status = 0;
+while ($status == 0) {
+	my $response = $conn->post( $url, {'CheckStatus' => 1,'rwd' => $rwd}) ;
+	$content = $response->decoded_content();
+	chomp($content);
+	if (substr($content,0,2) ne 'OK') {
+		die("ERROR: $content");
+	}
+	$status = substr($content,3,1);
+	sleep 10;
+}
+
+## Loading OK
+# latest respons : OK-1-Content
+$content = substr($content,5);
+print OUT "Processing Datafiles : OK.\n";
+print OUT "\n$content\n";
 close OUT;
 
 # clean up