[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Mon Jul 14 17:17:13 EDT 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv2031/scripts/Services

Modified Files:
	LocalServices.pm 
Log Message:
added new subroutine to start dealing with Collection outputs.  Added a service (untested so far) that outputs a collection of GO terms that are related to a keyword input

moby-live/Perl/scripts/Services LocalServices.pm,1.17,1.18
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2003/07/14 20:05:27	1.17
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2003/07/14 21:17:13	1.18
@@ -4,6 +4,7 @@
 use lib "/var/www/cgi-bin";
 use lib "/usr/local/apache/cgi-bin/bioperl/core";
 use lib "/usr/local/apache/cgi-bin/MOBY05/";
+use lib "/export/root/BIOPERL/go/perl-api";
 
 use strict;
 use SOAP::Lite;
@@ -78,6 +79,73 @@
     
 }
 
+
+sub RetrieveGOFromKeywords {
+	my $SOM = pop; 	
+	my ($self, $query) = @_;
+	use GO::AppHandle;
+
+	my $ua = new LWP::UserAgent;
+	my $req = new HTTP::Request GET => 'http://www.godatabase.org/dev/database/server.cfg';
+	my $res = $ua->request($req);
+	my $host;
+	if ($res->is_success) {
+		my $resp =  $res->content;
+		$host = ($resp =~ /\w+\s+(.*)/ && $1);
+		&_LOG("found go database server at $host\n");
+	} else {
+		&_LOG("can't connect to godatabase nameserver\n");
+		return SOAP::Data->type('base64' => responseHeader() . responseFooter());  # base 64 encode it (optional)
+	}
+	my %connect_hash;
+	$connect_hash{-dbname}="go";
+	$connect_hash{-dbhost}=$host;
+	
+	my $GO_API = GO::AppHandle->connect(%connect_hash);
+	&_LOG("made connection $GO_API\n");
+	unless ($GO_API){
+		&_LOG("unable to connect to the GO database at $host\n");
+		return SOAP::Data->type('base64' => responseHeader() . responseFooter());  # base 64 encode it (optional)
+	}
+	
+	# first, get the valid URI for the namespace that we accept
+	my $OS = MOBY::Client::OntologyServer->new;
+	my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'Global_Keyword');
+	unless ($VALID_NAMESPACE){  # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
+		print STDERR "the namespace Global_Keyword does not exist in the MOBY namespace ontology\n";
+		return SOAP::Data->type('base64' => responseHeader() . responseFooter());  # base 64 encode it (optional)
+	}
+
+	# now start analyzing the input data
+	my @input_nodes = getInputArticles($query); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
+	my $response;
+	foreach (@input_nodes){
+		my $input =  $_->[0];  # we only allow one input object per query
+		my ($kw) = getSimpleArticleIDs($VALID_NAMESPACE, [$input]);
+		($kw) = (($kw =~ /^\s*(.*)\s*$/) && ($1));
+		_LOG("searching for ||$kw||\n");
+		my @terms = @{$GO_API->get_terms({search=>"$kw"})};
+		_LOG("found term $terms[0]");
+		next unless($terms[0]);
+		_LOG("found term $terms[0]");
+		my @simples;
+		foreach my $term(@terms){
+			my $acc = $term->public_acc;
+			my $def = $term->definition;
+			my $name = $term->name;
+            push @simples, "<moby:GO_Term namespace='GO' id='$acc'>
+                    <moby:String namespace='' id='' articleName='Term'>$term</moby:String>
+                    <moby:String namespace='' id='' articleName='Definition'>$def</moby:String>
+                </moby:GO_Term>";
+		}
+		$response .= collectionResponse(\@simples);
+	}
+    $response =  responseHeader() . $response . responseFooter();
+    my $SOAPResponse = SOAP::Data->type('base64' => $response);
+    return $SOAPResponse	
+}
+
+
 #  ===============================================
 #  =    Genbank Retrieval Scripts                =
 #  =                                             =
@@ -378,6 +446,11 @@
 }
     
     
-    
+sub _LOG {
+	open OUT, ">/tmp/LocalServices.log";
+	print OUT @_;
+	close OUT;
+}
+
     
 1;