Index: trunk/ippScripts/scripts/rawcheck_mddb.pl
===================================================================
--- trunk/ippScripts/scripts/rawcheck_mddb.pl	(revision 40166)
+++ trunk/ippScripts/scripts/rawcheck_mddb.pl	(revision 40178)
@@ -208,6 +208,13 @@
 	my $class_id   = $imfile->{class_id};
 
+	unless(defined($key))        { die "No database uri: $exp_id"; }
+	unless(defined($data_state)) { $data_state = 'no_data_state'; }
+	unless(defined($md5sum))     { die "No database md5sum: $exp_id"; }
+	unless(defined($hostname))   { $hostname = 'ipp004'; }
+	unless(defined($class_id))   { die "No database class_id: $class_id"; }
+
 	# This hash contains all the information about the instances, indexed by the full filename of the instance.
 	my %unified_list = ();
+	my %orphans      = ();
 
 	$timer = time();
@@ -223,4 +230,5 @@
 	for (my $i = 0; $i <= $#files; $i++) {
 	    my $f = $files[$i];
+	    $f =~ s%//%/%g;
 	    my ($instance_exists,$instance_host,$instance_volume,$instance_site);
 	    ($instance_host,$instance_volume) = parse_volume($files[$i]);   
@@ -239,5 +247,4 @@
 
 	# Get md database results for this exp_id/class_id
-
 	my $md_query = "select file_id,ins_id,mvol_name,site_name,file,disk_sum,(STRCMP(md5sum,disk_sum) = 0) AS is_valid FROM obj JOIN ins USING(file_id) JOIN vol USING(mvol_id) WHERE exp_id = $exp_id AND class_id = '${class_id}'";
 	my $md_instances = $mddb->selectall_arrayref( $md_query );
@@ -248,5 +255,5 @@
 	foreach my $r (@{ $md_instances }) {
 	    my ($file_id,$ins_id,$vol_name,$site_name,$f,$disk_sum,$is_valid) = @{ $r };
-
+	    $f =~ s%//%/%g;
 	    unless (exists($unified_list{$f})) {
 		if (-e $f) {
@@ -304,5 +311,5 @@
 	# Check that evrything is consistent.
 	my $good_copies = 0;
-	my $all_copies = length(keys(%unified_list));
+	my $all_copies = scalar(keys(%unified_list));
 	my $a_good_copy = '';
 
@@ -315,27 +322,41 @@
 	    $unified_list{$f}{good_instance} = 0;
 	    print "$f  ";
-
+	    
+	    # Identify orphans, and push their handling until later.
 	    unless (exists($unified_list{$f}{neb_host})) {
-		die "No neb entry for $unified_list{$f}{md_ins_id} $exp_id $class_id $f \n";
-#		mddb_delete_instance($mddb,$unified_list{$f}{md_ins_id});
+		# Handle this.
+		$orphans{$f} = $unified_list{$f};
+		delete($unified_list{$f});
+		warn "No neb entry for $orphans{$f}{md_ins_id} $exp_id $class_id $f \n";
+		next;
 	    }
 	    print "$unified_list{$f}{neb_host} $unified_list{$f}{neb_vol} $unified_list{$f}{neb_site} $unified_list{$f}{exists}  ";
+
+
+	    # Create an entry in the mddb database if that doesn't already exist.
 	    unless (exists($unified_list{$f}{md_vol})) {
 		# Insert a new row in the mddb ins table for this instance.  
+		if ($unified_list{$f}{exists} != 1) {
+		    # Ensure that the file exists, so an md5sum can be performed.
+		    system("touch $f");
+		}
 		my $tmpmd5 = local_md5sum($f);
 		my ($ins_id, $site_name) = mddb_insert_instance($mddb,$md_file_id,$f, $unified_list{$f}{neb_vol}, $tmpmd5);
+
+		$unified_list{$f}{md_vol}     = $unified_list{$f}{neb_vol};
+		$unified_list{$f}{md_site}    = $site_name;
+		$unified_list{$f}{disk_sum}   = $tmpmd5;
+		$unified_list{$f}{md_file_id} = $md_file_id;
+		$unified_list{$f}{md_ins_id}  = $ins_id;
 
 		if ($tmpmd5 ne $md5sum) { 
 		    # Insert even if we fail so we can try fixing next time.
 		    # This may cause a problem if the first instance we checked has a bad md5sum.
-		    die "Post-replication md5sum does not match! $tmpmd5 != $md5sum";
-		}
-
-		$unified_list{$f}{md_vol}     = $unified_list{$f}{neb_vol};
-		$unified_list{$f}{md_site}    = $site_name;
-		$unified_list{$f}{disk_sum}   = $tmpmd5;
-		$unified_list{$f}{is_valid}   = 1;
-		$unified_list{$f}{md_file_id} = $md_file_id;
-		$unified_list{$f}{md_ins_id}  = $ins_id;
+		    warn "Post-replication md5sum does not match! $tmpmd5 != $md5sum";
+		    $unified_list{$f}{is_valid}   = 0;
+		}
+		else {
+		    $unified_list{$f}{is_valid}   = 1;
+		}
 	    }
 
@@ -349,16 +370,18 @@
 		}
 		if ($tmpmd5 ne $md5sum) {
-		    die "Revalidated md5sum does not match!";
+		    warn "Revalidated md5sum does not match!";
 		}
 	    }
 
 	    print "$unified_list{$f}{md_file_id} $unified_list{$f}{md_ins_id} $unified_list{$f}{md_vol} $unified_list{$f}{md_site} $unified_list{$f}{disk_sum} $unified_list{$f}{is_valid}  ";
-	    if ($unified_list{$f}{neb_vol} ne $unified_list{$f}{md_vol}) {
-		die "Inconsistent volumes for $exp_id $class_id $f $unified_list{$f}{neb_vol} $unified_list{$f}{md_vol}\n";
-	    }
+
+
 	    if ($unified_list{$f}{exists} != 1) {
 		warn "Instance does not exist $exp_id $class_id $f\n";
 		next;
 	    }
+	    if ($unified_list{$f}{neb_vol} ne $unified_list{$f}{md_vol}) {
+		die "Inconsistent volumes for $exp_id $class_id $f $unified_list{$f}{neb_vol} $unified_list{$f}{md_vol}\n";
+	    }
 	    if ($unified_list{$f}{is_valid} != 1) {
 		warn "Instance is not valid $exp_id $class_id $f\n";
@@ -369,5 +392,4 @@
 		die "Inconsistent md5sum values $exp_id $class_id $f $md5sum $unified_list{$f}{disk_sum}\n";
 	    }
-
 	    
 	    # If none of that stopped us, then this instance is probably fine.
@@ -383,5 +405,17 @@
 
 	if ($good_copies == 0) {
-	    die "No good copies available for $exp_id $class_id\n";
+	    my $orphan_copy = '';
+	    foreach my $orph (keys (%orphans)) {
+		if ($orphans{$orph}{is_valid} == 1) {
+		    $orphan_copy = $orph;
+		}
+	    }
+
+	    if ($orphan_copy eq '') {
+		die "No good copies available for $exp_id $class_id\n";
+	    }
+	    else {
+		die "No good copies available for $exp_id $class_id (but $orphan_copy may exist)\n";
+	    }
 	}
 
@@ -390,4 +424,5 @@
 
 	# Attempt to repair any bad instance.
+	print "COUNT CHECK $good_copies $all_copies\n";
 	if ($good_copies != $all_copies) {
 	    foreach my $f (keys(%unified_list)) {
@@ -497,4 +532,12 @@
 		}
 	    }
+
+	    # If we're here, then we've sucessfully sorted out this instance.
+	    foreach my $f (keys %orphans) {
+		print "ORPHAN $f $orphans{$f}{md_ins_id}\n";
+		mddb_delete_instance($mddb,$orphans{$f}{md_ins_id});
+#		unlink($f) or warn "Could not unlink $f: $!";
+	    }
+	    
 	} # End culling