[DAS] Ensembl via SOAP
Brian Gilman
gilmanb@genome.wi.mit.edu
Wed, 5 Jun 2002 08:23:29 -0400 (EDT)
This is great!!
Do you need help with a java implementation?? I'd be willing to
help you out in a week or so...
-B
-----------------------
Brian Gilman <gilmanb@genome.wi.mit.edu>
Group Leader Medical & Population Genetics Dept.
MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617 252 1069 / fax +1 617 252 1902
On Wed, 5 Jun 2002, Tony Cox wrote:
>
> I've been playing over the weekend with SOAP access to Ensembl objects. I have a
> test server running that can handle queries.
>
>
> Nutshell:
> =========
>
>
> use SOAP::Lite +autodispatch =>
> uri => 'Bio::EnsEMBL::Remote::Object',
> proxy => 'http://services.ensembl.org:7070/cgi-bin/ensembl_rpcrouter';
>
> my $trans =
> Bio::EnsEMBL::Remote::Object->new('type'=>'transcript','id'=>'ENST00000225283');
> print $trans->seq(), "\n";
> print $trans->translate(), "\n";
>
>
>
> It is a pretty niave implementation but allows fairly reasonable access to
> Ensembl objects via RPC. A remote "proxy" class takes care of creating and
> manipulating ensembl objects on the server side and allows you to make direct
> calls locally. General id/start/end type calls all work. Since ensembl objects
> are all intimately tied to DB connections which all goes horribly wrong over
> SOAP the proxy object takes care creating these connections as necessary on the
> server. Calls that returns an object have been changed to return an ID - which
> can be used to create a remote object. I've only done the main stuff - features,
> SNPs etc, are missing
>
> The good thing is that you don't need any local databases or even ensembl code,
> just a working copy of SOAP::Lite from CPAN. The bad thing is that it is pretty
> __slow__ at the moment. The server is not running under mod_perl so most of the
> response time is taken up in module compilation and XML transport. I'll try to
> get it running under mod_perl and with transport compression enabled.
>
> I don't see this as an interface of choice for the bioinformatician! - it is too
> slow and anyway they will have the "real" ensembl code to turn to. This is much
> more of a lightweight interface for conveniently fetching sequences, genes etc
> where speed is not a critical issue, and the convenience of a simple programming
> interface is the important factor.
>
> I'd be very interested to see interoperability tested. I did write a very small
> java client to make requests but rapidly got out of my depth when having to
> write a deserializer for the remote object. After looking into the Omnigene code
> I see how these work but I'm rather hoping that somebody on the omnigene team
> might have a go at doing this.
>
> Following is a simple script that provides examples of manipulating remote
> objects. You "get" a remote object on the server be creating a new
> Bio::EnsEMBL::Remote::Object and giving a it a type and ID. At the moment you
> can only fetch virtualcontigs, genes, transcripts, exons, clones, contigs and
> translations (peptides). By the magic of "autodispatch", if you get a "thingy"
> back, you can just treat it as a normal object and make calls on it. Perl's
> autoloader will try and satisfy calls that are not overloaded in the remote
> object (I know this sucks). If they are simple get/property calls they will
> probably work - if the call returns an object/objects, bad things will probably
> happen. Trying to write to the object may work (I havn't tried it) but is likely
> not to be a useful thing to do! Remember this is a transaction-type system where
> all the responses need to be marshalled before transport takes place so it will
> not "stream" data to you as if it were a socket-style connection.
>
> In the event of an error, you usually end up with undef (the code is pretty raw
> at the moment). If you really want you can track down errors, use the following
> block:
>
> if(SOAP::Lite->self->call->fault) {
> print "Fault code: ", SOAP::Lite->self->call->faultcode, "\n";
> print "Fault string: ", SOAP::Lite->self->call->faultstring, "\n";
> print "Fault detail: ", SOAP::Lite->self->call->faultdetail, "\n";
> print "Fault actor: ", SOAP::Lite->self->call->faultactor, "\n";
> exit;
> }
>
>
> comments and suggestions welcome,
>
> cheers
>
> Tony
>
>
>
>
>
>
> To try the server out enable one or more of the following blocks:
>
>
> #!/usr/local/bin/perl
>
> package MySoapClient;
>
> use strict;
> use SOAP::Lite +autodispatch =>
> uri => 'Bio::EnsEMBL::Remote::Object',
> proxy => 'http://services.ensembl.org:7070/cgi-bin/ensembl_rpcrouter';
>
> if(1){
> my @g = (qw(ENSG00000131591 BRCA1));
> foreach my $g (@g){
> print "Getting gene: $g...\n";
> $g = Bio::EnsEMBL::Remote::Object->new('type'=>'gene','id'=>$g);
> print "\tGene ID: ", $g->id(), "\n";
> foreach my $t ($g->transcripts()){
> my $t =
> Bio::EnsEMBL::Remote::Object->new('type'=>'transcript','id'=>$t);
> print "\t\tTranscript ID: ", $t->id(), "\n";
> print "\t\tTranscript length: ", $t->length(), "\n";
> #print "\t\tTranscript seq: ", $t->seq(), "\n";
> print "\t\tTranscript protein: ", $t->translate(), "\n";
> }
> }
> }
>
> if(0){
> print "Getting remote clone AP000869...\n";
> my $cl =
> Bio::EnsEMBL::Remote::Object->new('type'=>'clone','id'=>'AP000869');
> print "Clone: ", $cl->embl_id(), "\n";
> print "Version: ", $cl->version(), "\n";
>
> foreach my $c ($cl->contigs()){
> my $c = Bio::EnsEMBL::Remote::Object->new('type'=>'contig','id'=>$c);
> my $id = $c->id();
> if($c->is_static_golden()){
> print "\tContig ID: $id (golden)\n";
> print "\tContig length: ", $c->length(), "\n";
> print "\tContig is golden?: yes\n";
> print "\t\tContig global start: ", $c->static_golden_start(), "\n";
> print "\t\tContig global end: ", $c->static_golden_end(), "\n";
> print "\t\tContig global ori: ", $c->static_golden_ori(), "\n";
> #print "\tContig seq: ", $c->seq(), "\n";
> } else {
> print "\tContig ID: $id (non-golden)\n";
> }
> }
> }
>
>
> if(0){
> my $chr = 1;
> my $start = 100000;
> my $end = 200000;
> print "Getting remote virtualcontig for $chr, $start-$end...\n";
> my $v =
> Bio::EnsEMBL::Remote::Object->new('type'=>'virtualcontig','chr'=>$chr,
> 'start'=>$start, 'end'=>$end);
> print "Virtual contig ID: ", $v->id(), "\n";
> print "Virtual contig length: ", $v->length(), "\n";
> print "Virtual contig chromosome: ", $v->_chr_name(), "\n";
> print "Virtual contig chromosome length: ", $v->fetch_chromosome_length(),
> "\n";
>
> foreach my $g ($v->genes()){
> $g = Bio::EnsEMBL::Remote::Object->new('type'=>'gene','id'=>$g);
> print "\tGene ID: ", $g->id(), "\n";
> foreach my $t ($g->transcripts()){
> my $t =
> Bio::EnsEMBL::Remote::Object->new('type'=>'transcript','id'=>$t);
> print "\t\tTranscript ID: ", $t->id(), "\n";
> print "\t\tTranscript length: ", $t->length(), "\n";
> #print "\t\tTranscript seq: ", $t->seq(), "\n";
> #print "\t\tTranscript protein: ", $t->translate(), "\n";
> foreach my $e ($t->exons()){
> my $e =
> Bio::EnsEMBL::Remote::Object->new('type'=>'exon','id'=>$e);
> print "\t\t\tExon ID: ", $e->id(), "\n";
> print "\t\t\tExon start: ", $e->ori_start(), "\n";
> print "\t\t\tExon end: ", $e->ori_end(), "\n";
> print "\t\t\tExon strand: ", $e->strand(), "\n";
> print "\t\t\tExon seq: ", $e->seq(), "\n";
> }
> }
>
> }
> }
>
> if(0){
> my $p = "ENSP00000223439";
> print "Getting remote peptide $p...\n";
> my $p = Bio::EnsEMBL::Remote::Object->new('type'=>'translation','id'=>$p);
> print $p->seq();
> }
>
>
>
>
> ******************************************************
> Tony Cox Email:avc@sanger.ac.uk
> Sanger Institute WWW:www.sanger.ac.uk
> Wellcome Trust Genome Campus Webmaster
> Hinxton Tel: +44 1223 834244
> Cambs. CB10 1SA Fax: +44 1223 494919
> ******************************************************
>
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