[MOBY-l] help with MobyXMLObject...

[Ken Steube]

I included a working example for your XML, but a little explanation is
required:

A MOBY object is

  <myCLASS namespace='myNS' id='myID' articleName='myNAME'>myVALUE</myCLASS>

so a MobyXmlObject $mobj returns five values
  $mobj->class()		myCLASS
  $mobj->namespace()		myNS
  $mobj->id()			myID
  $mobj->articleName()		myNAME
  $mobj->value()		myVALUE

If myVALUE includes XML, then these are separate MOBY objects.  You
need to use MobyXmlObject to access these additional MOBY objects using
the $mobj->getIncludedObjects() call, which returns a list of new
MobyXmlObject objects corresponding to the included objects.

This is demonstrated in the included example.

Ken

On Tue, 30 Dec 2003, Michael Jensen wrote:

> I am trying to put a few services together into one script, so taking
> the output of one to another. I can get a few working together, but the
> getGOTerm service output has me stuck. Here is the output from the
> simple script just running this service and trying to get some of
> return values by themselves:
>
> <?xml version='1.0' encoding='UTF-8'?>
>        <moby:MOBY xmlns:moby='http://www.biomoby.org/moby'
> xmlns='http://www.biomoby.org/moby'>
>          <moby:Response moby:authority='illuminae.com'>
>
>          <moby:queryResponse moby:queryID=''>
>              <moby:Simple articleName='GO_Term_From_ID'>
>                                          <moby:GO_Term namespace='GO'
> id='GO:0004623'>
>                                                  <moby:String
> namespace='' id='' articleName='Term'>phospholipase A2
> activity</moby:String>
>                                                  <moby:String
> namespace='' id='' articleName='Definition'>Catalysis of the reaction:
> phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a
> carboxylate.</moby:String>
>                                          </moby:GO_Term></moby:Simple>
>          </moby:queryResponse>
>
>      </moby:Response>
>        </moby:MOBY>
>
>
> Found an input Simple object:
>    Class     'moby:GO_Term'
>    xml_tag   'GO_Term'
>    Namespace 'GO'
>    ID        'GO:0004623'
>    Name      ''
>    Value     ''
>
>
> So I can get the articleName and even the GO:00004623 out of the
> various elements, but I can't figure out how to get the values of the
> Term and Definition from within the tags (phospholipase A2 activity).
> My code is as follows:
>
> #!/usr/bin/perl
> ##### put in 0004623 from the command line for it to run on
> something#######
>
> use MOBY::Client::Central;
> use MOBY::Client::Service;
> use MobyXmlObject;
>
> ################## getGOTerm ##################
>
> my $Central = MOBY::Client::Central->new();
>
> my ($Services, $REG) = $Central->findService(
>    authURI => 'www.illuminae.com',
>    serviceName => 'getGoTerm',
> );
> unless ($Services) { print "Discovery failed: ", $REG->message;
> exit(1); }
>
> my $svc = $Services->[0];
> print "Executing service ", $svc->name, "\n", $svc->description, "\n\n";
> my $wsdl = $Central->retrieveService($svc);
> my $S = MOBY::Client::Service->new(service => $wsdl);
>
> my $result;
> foreach my $goterm(@ARGV) {
>      $result = $S->execute(
>        XMLinputlist => [ ['', qq{<Object namespace="go" id="$goterm"/>}]
> ]
>      ) || 'No result';
>      print $result, "\n";
> }
>
> my @simples = MobyXmlObject->getMobySimples($result);
> my @go_list;
>
> foreach my $s (@simples) {
>    my $class     = $s->class();
>    my $namespace = $s->namespace();
>    my $id        = $s->id();
>    my $name      = $s->articleName();
>    my $value     = $s->valueTrimmed();
>    my $xml_tag   = $s->xml_tag();
>    print qq{
> Found an input Simple object:
>    Class     '$class'
>    xml_tag   '$xml_tag'
>    Namespace '$namespace'
>    ID        '$id'
>    Name      '$name'
>    Value     '$value'
> };
> }
>
> Note to run it you should pass in 0004623 or another go id.
>
> Any help would be greatly appreciated!
>
> THANKS!
>
> -Michael Jensen
> mdjgf8 at mizzou.edu
>
>
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>

-- 
-------------------------------------
Ken Steube            steube at sdsc.edu
San Diego Supercomputer Center @ UCSD
San Diego, California             USA
-------------- next part --------------
use MobyXmlObject;

my $query = qq{<?xml version='1.0' encoding='UTF-8'?>
<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' xmlns='http://www.biomoby.org/moby'>
<moby:Response moby:authority='illuminae.com'>
<moby:queryResponse moby:queryID=''>
<moby:Simple articleName='GO_Term_From_ID'>
<moby:GO_Term namespace='GO' id='GO:0004623'>
  <moby:String namespace='' id='' articleName='Term'>phospholipase A2 activity</moby:String>
  <moby:String namespace='' id='' articleName='Definition'>Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.</moby:String>
</moby:GO_Term>
</moby:Simple>
</moby:queryResponse>
</moby:Response>
</moby:MOBY>
};

my @simples = MobyXmlObject->getMobySimples($query);
foreach my $s (@simples) {
  my ($class, $ns, $id) = ($s->class(), $s->namespace(), $s->id());
  print "class=$class,ns=$ns,id=$id\n";
  print "  Included MOBY objects:\n";
  foreach my $inc ($s->getIncludedObjects()) {
    my $class = $inc->class();
    my $name  = $inc->articleName();
    my $value = $inc->valueTrimmed();
    print "  class=$class,name=$name,value=$value\n"; next;
  }
}