[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Thu Jul 17 11:50:14 EDT 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv15177/scripts/Services

Modified Files:
	LocalServices.pm 
Log Message:
added a new service that takes Snapdragon allele names and returns a collection of base64-encoded images of that mutant.  Also changed CommonSubs so that it does not take liberties with whitespace when constructing its XML, as this buggers up base64 encoded data

moby-live/Perl/scripts/Services LocalServices.pm,1.24,1.25
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.24
retrieving revision 1.25
diff -u -r1.24 -r1.25
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2003/07/17 02:30:15	1.24
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2003/07/17 15:50:14	1.25
@@ -427,6 +427,85 @@
     return $SOAPResponse;	
 }
 
+#################################################
+#################################################
+####   DragonDB Subroutines #####################
+#################################################
+#################################################
+
+sub getDragonMutantImages {
+	my $SOM = pop;  
+    my ($self, $data) = @_;
+	use Ace;
+	use LWP::UserAgent;
+	use MIME::Base64;
+
+# prepare myself
+	my $OS = MOBY::Client::OntologyServer->new;
+	my ($s, $m, $nsAllele) = $OS->namespaceExists(term => "DragonDB_Allele");
+
+	unless ($nsAllele){  # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
+		print STDERR "the namespace DragonDB_Allele does not exist in the MOBY namespace ontology\n";
+		return SOAP::Data->type('base64' => responseHeader() . responseFooter());  # base 64 encode it (optional)
+	}
+# make the database connection once
+	my $db = Ace->connect(-host => 'bioinfo.usask.ca',
+								  -port => 23100);
+###################################
+	
+# now start retrieving the input data
+	my @input_nodes = getInputArticles($data); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
+	my @inputs;
+	foreach (@input_nodes){
+		push @inputs, $_->[0];  # we only allow one input object per query
+	}
+
+# Start iterating through the queries
+	my $response; 
+	foreach my $node(@inputs){
+ 
+		my $namespace_LSID = getSimpleArticleNamespaceURI($node);  # get the LSID of the namespace for this input object
+		unless ($namespace_LSID eq $nsAllele){ # validate the namespace
+			$response .= collectionResponse([]);  # because we have to send one response per input, send a blank if bad namespace
+			next;
+		}
+			
+		my ($Allele)= getSimpleArticleIDs($namespace_LSID, [$node]);  # get the ID within this namespace
+		unless (defined $Allele){  # send a blank if we failed to get an id, 
+			$response .= collectionResponse([]);  # because we have to send one response per input
+			next;
+		}
+# Prepare query on DragonDB with that allele name
+		my $query = qq(select Gif from Gif in object("Allele","$Allele") -> Phenotype_picture -> Pick_me_to_call[2]);
+		print STDERR "QUERY TO DRAGONDB WAS $query\n";
+		my @jpgnames= $db->aql($query);
+		# I really need to learn AQL better so that I can also retrieve the
+		# Locus as a Cross-reference, and the Sequence as a cross-reference!
+		my @simples;
+		foreach my $jpg (@jpgnames){
+			$jpg = $jpg->[0];
+			$jpg =~ s/([^\w\-\.\@])/$1 eq " "?"+":sprintf("%%%2.2x",ord($1))/eg; # URL Encode the image filename
+			$jpg = "http://antirrhinum.net/ace/images/DragonDB/external/".$jpg; # make the URL
+			my $ua = LWP::UserAgent->new; 
+			my $req = HTTP::Request->new(GET => $jpg);  # get the image
+			my $res = $ua->request($req);
+
+			# Check the outcome of the response
+			if ($res->is_success) {  # if successful, then base64 encide the data
+				my $image_data = encode_base64($res->content);  # and create the simple image object
+				push @simples, "<moby:b64_encoded_jpeg namespace='$namespace_LSID' id='$Allele'>$image_data</moby:b64_encoded_jpeg>";  # push it onto the collection list
+			}
+		}
+		$response .= collectionResponse(\@simples); # after all images have been collected, create the collection
+	}
+    $response =  responseHeader() . $response . responseFooter();  # now wrap the collection(s) with the appropriate headers etc
+    my $SOAPResponse = SOAP::Data->type('base64' => $response);
+    return $SOAPResponse	# and return them.	
+}
+
+
+###############################################################
+######################  for My Machine Only ###################
 sub _dbAccess {
     my ($dbname) = @_;
     return undef unless $dbname;