[MOBY-guts] biomoby commit
Eddie Kawas
kawas at dev.open-bio.org
Thu Feb 21 17:15:41 UTC 2008
kawas
Thu Feb 21 12:15:40 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv26411/Perl/MOBY-Server/lib/MOBY/Client
Modified Files:
SimpleInput.pm Central.pm SecondaryArticle.pm SimpleArticle.pm
Service.pm CollectionArticle.pm
Log Message:
update of pod - found warnings when i ran podchecker so i am correcting them
moby-live/Perl/MOBY-Server/lib/MOBY/Client SimpleInput.pm,1.1,1.2 Central.pm,1.1,1.2 SecondaryArticle.pm,1.1,1.2 SimpleArticle.pm,1.1,1.2 Service.pm,1.1,1.2 CollectionArticle.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleInput.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleInput.pm 2008/02/21 00:21:27 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleInput.pm 2008/02/21 17:15:40 1.2
@@ -15,6 +15,8 @@
=head1 AUTHORS
+Mark Wilkinson (markw at illuminae dot com)
+
=cut
=head1 METHODS
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm 2008/02/21 00:21:27 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm 2008/02/21 17:15:40 1.2
@@ -40,7 +40,7 @@
foreach my $SERVICE(@{$Services}){
print "Service Name: ", $SERVICE->name, "\n";
print "Service Provider: ", $SERVICE->authority,"\n";
-
+
}
=cut
@@ -77,7 +77,7 @@
Function : connect to one or more MOBY-Central
registries for searching
Returns : MOBY::Client::Central object
-
+
ENV & PROXY : you can set environment variables to change the defaults.
By default, a call to 'new' will initialize MOBY::Client::Central
to connect to the MOBY Central registry at:
@@ -89,7 +89,7 @@
MOBY_SERVER (default http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl)
MOBY_URI (default http://mobycentral.cbr.nrc.ca/MOBY/Central)
MOBY_PROXY (no default)
-
+
Args : user_agent - optional. The name of your software application
Registries - optional.
- takes the form
@@ -571,7 +571,7 @@
authURI => your.authority.URI (required)
description => "human readable description of namespace" (required)
contactEmail => "your at address.here" (required)
-
+
=cut
@@ -633,7 +633,7 @@
Function : register a new MOBY Service instance
Returns : MOBY::Registration object
Common Required Args :
-
+
serviceName => $serviceName,
serviceType => $serviceType,
authURI => $authURI,
@@ -649,7 +649,7 @@
[articleName3,[[objType3 => \@namespaces],
[objType4 => \@namespaces]]] # collection of multiple object types
]
-
+
output: listref; (articleName may be undef)
output =>[
@@ -658,7 +658,7 @@
[articleName3,[[objType3 => \@namespaces],
[objType4 => \@namespaces]]] # collection of multiple object types
]
-
+
secondary: hashref
secondary => {parametername1 => {
datatype => TYPE,
@@ -675,7 +675,7 @@
min => MIN,
enum => [one, two]}
}
-
+
=cut
@@ -1699,7 +1699,7 @@
Args : registry => $reg - name of MOBY Central you want to use (must pass undef otherwise)
objectType => $name - object name (from ontology) or undef to get all objects
as_lsid => $boolean - return $name as its corresponding LSID (default off)
-
+
=cut
sub retrieveObject {
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SecondaryArticle.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SecondaryArticle.pm 2008/02/21 00:21:27 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SecondaryArticle.pm 2008/02/21 17:15:40 1.2
@@ -24,7 +24,7 @@
$prameter_value = $input->value; # get the value of the secondary parameter
# do your business here and fill $invocation_output
}
-
+
$MOBY_RESPONSE .= simpleResponse( # create an empty response for this queryID
$invocation_output # response for this query
, "myOutput" # the article name of that output object
@@ -34,7 +34,7 @@
or to construct a representation of a Secondary article from a findService call
to MOBY::Central
-
+
=cut
@@ -45,6 +45,8 @@
Mark Wilkinson (markw at illuminae dot com)
+=cut
+
=head1 METHODS
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleArticle.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleArticle.pm 2008/02/21 00:21:27 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleArticle.pm 2008/02/21 17:15:40 1.2
@@ -23,10 +23,10 @@
$DOM = $input->XML_DOM; # get the XML as a LibXML DOM object
$namespace = $input->namespace; # get the namespace of the object
$id = $input->id; # get the id of the object (the id of the outermost MOBY object XML block)
-
+
# do your business here and fill $invocation_output
}
-
+
$MOBY_RESPONSE .= simpleResponse( # create an empty response for this queryID
$invocation_output # response for this query
, "myOutput" # the article name of that output object
@@ -37,7 +37,7 @@
or to construct a representation of a simple article from a findService call
to MOBY::Central
-
+
=cut
@@ -84,7 +84,7 @@
Returns : MOBY::Client::SimpleArticle object
Args : either of the following two methods may be used to auto-generate the
object by passing the appropriate XML node as a string, or XML::DOM node object
-
+
XML => $XML
XML_DOM => $XML::LibXML::Node
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Service.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Service.pm 2008/02/21 00:21:27 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Service.pm 2008/02/21 17:15:40 1.2
@@ -7,7 +7,7 @@
=head1 SYNOPSIS
use MOBY::Client::Service;
-
+
my $Service = MOBY::Client::Service->new(service => $WSDL);
my $result = $Service->execute(@args);
@@ -379,15 +379,15 @@
Args : Input => %data
Comment : %data is a hash of single invocation inputs
the structure of %data is:
-
+
$data{$queryID} = {articleName => $inputXML1, # for simples and parameters
articleNmae => [$inputXML2, $inputXML3], # for collections
}
$inputXML is the actual XML of the Input object
for example <Object namespace="NCBI_gi" id="163483"/>
-
+
a full example might be:
-
+
$data{invocation1} = {id_to_match => "<Object namespace="GO" id="0003875"/>",
id_list => ["<Object namespace="GO" id="0003875"/>,
"<Object namespace="GO" id="0009984"/>,...
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/CollectionArticle.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/CollectionArticle.pm 2008/02/21 00:21:27 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/CollectionArticle.pm 2008/02/21 17:15:40 1.2
@@ -22,7 +22,7 @@
Parsing a MOBY Service Invocation
use MOBY::CommonSubs qw(:all);
-
+
sub myService {
my ($caller, $data) = @_;
@@ -41,7 +41,7 @@
# @simples contains a list of MOBY::Client::SimpleArticles
# do your business here and fill $invocation_output
}
-
+
$MOBY_RESPONSE .= simpleResponse( # create an empty response for this queryID
$invocation_output # response for this query
, "myOutput" # the article name of that output object
@@ -53,7 +53,7 @@
or to construct a representation of a collection article from a findService call
to MOBY::Central
-
+
=head1 DESCRIPTION
This describes the Collection articles from either the findService Response of MOBY Central
@@ -107,7 +107,7 @@
Returns : MOBY::Client::SimpleArticle object
Args : either of the following two methods may be used to auto-generate the
object by passing the appropriate XML node as a string, or XML::DOM node object
-
+
XML => $XML
XML_DOM => $XML::DOM::NODE
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