[spam] [MOBY-l] Changes to registry? Signatures lost?

[Mark Wilkinson]

Try again now... should be fixed.

It was a miscommunication between Nina and I last week that led to a
small and easily repaired change to the database.  All should be back to
normal now.

M


On Mon, 2004-11-15 at 14:58, Frank Gibbons wrote:
> Hi MOBYers,
> 
> I've been away from the MOBY world for a while (apart from bumping into 
> Martin and Gary at the Semantic Web for Life Sciences Workshop in 
> Cambridge), so perhaps I've missed out on some changes.
> 
> Today I noticed that while my older services are still around, they seem to 
> have lost their namespace information - whereas before they reported 
> consuming information in specific namespaces, now they report that they do 
> not support any particular namespace.
> 
> I have a number of newly registered services (as of this morning), which 
> correctly report namespaces. So, I'm wondering if perhaps the namespace 
> information was accidentally dropped recently (was there a DB migration?) 
> Or is it something more planned, where namespace info is no longer being 
> reliably supplied, and I shouldn't rely on it (if this is the case, I'm in 
> trouble!).
> 
> Appended below is the code I use to determine this (originally provided by 
> Mark, I suspect) - might help someone determine what's going on, or whether 
> it's my problem. The services Ito/Uetz/Tong are the new ones, others are 
> older. Strangely, YAService has been up for a month or two, yet still 
> reports supporting namespace SGD.
> 
> All services were registered by the old method, with no RDF generated. I 
> believe I generated RDF for the older (non-namespace-supporting) ones, 
> after having registered them, using Mark's script. Is this related to that?
> 
> Sorry I can't make it out to Santa Fe, look forward to reading about the 
> latest MOBY developments here.
> 
> Thanks for help,
> 
> -Frank
> 
> ------------------------------- appended Perl script to see 
> function/namespaces -----------------------------
> #!/usr/bin/perl
> 
> use lib qw(/share/local/share/perl/5.6.1
>             /share/lib/perl5/site_perl/5.8.3); # Use latest MOBY
> use MOBY::Client::Central;
> use MOBY::Client::Service;
> $m = MOBY::Client::Central->new();
> my ($auth, $name) = ('llama.med.harvard.edu', 'YAService');
> ($ss, $r) = $m->findService(authURI => $auth); #, serviceName => $name);
> my $i = 0;
> my %Count = (authority => (), type => (), input => ());
> foreach my $service (sort { lc $a->name cmp lc $b->name } @{$ss} ) {
>    $i++;
>    $Count{authority}{$service->authority}++;
>    $Count{type}{$service->type}++;
>    $Count{input}{$service->input}++;
>    print "$i: Service ", $service->name, " from ",
>      $service->authority, " is of type ", $service->type, "\n";
>    print "It consumes: \n";
>    $inputs = $service->input;
>    foreach $in ( @{$inputs} ) {
>        eval {print "\t", $in->objectType, "\n"; };
>        print "\t\tin namespace(s)\n";
>        eval {
>            my $namespaces = $in->namespaces;
>            foreach $ns ( @{$namespaces} ) {
>                print "\t\t\t\t$ns\n";
>            }
>        };
>    }
> 
>    print "It generates ";
>    $outputs = $service->output;
>    foreach $out ( @{$outputs} ) {
>      # Check for isCollection, each element of the collection should have 
> an objectType
>      if ($out->isCollection) {
>        print "a collection of outputs:\n";
>        foreach my $simple (@{$out->Simples}) {
>          print "\t", $simple->objectType, "\n";
>          print "\t\tin namespace(s)\n";
>          foreach $ns ( @{$simple->namespaces} ) { print "\t\t\t\t$ns\n"; }
>        }
>      }
>      else {
>        print "a single output:\n";
>        print "\t", $out->objectType, "\n";
>        print "\t\tin namespace(s)\n";
>        foreach $ns ( @{$out->namespaces} ) { print "\t\t\t\t$ns\n"; }
>      }
>    }
> print "\n", '-'x80, "\n";
> }
> 
> print "Services by authority:\n";
> #while (my ($k, $v) = each $Count{authority}) {
> for my $s (sort {lc $a cmp lc $b} keys %{$Count{authority}}) {
>      print "$Count{authority}{$s} $s\n";
> }
> 
> 
> PhD, Computational Biologist,
> Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
> Tel: 617-432-3555       Fax: 
> 617-432-3557       http://llama.med.harvard.edu/~fgibbons
> 
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-- 
Mark Wilkinson
Assistant Professor (Bioinformatics)
Dept. Medical Genetics, UBC, Canada