[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Mon Sep 22 12:25:20 EDT 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv20398/Perl/MOBY

Modified Files:
	CommonSubs.pm 
Log Message:
moving some common subs around so that they are not module-specific

moby-live/Perl/MOBY CommonSubs.pm,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2003/09/14 18:28:47	1.14
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2003/09/22 16:25:20	1.15
@@ -76,6 +76,7 @@
     validateNamespaces
     isSimpleArticle
     isCollectionArticle
+    extractResponseArticles
     );
 %EXPORT_TAGS =(all => [qw(
     getSimpleArticleIDs
@@ -89,6 +90,7 @@
     validateNamespaces
     isSimpleArticle
     isCollectionArticle
+    extractResponseArticles
     )]);
 
 
@@ -554,4 +556,67 @@
         push @lsids, $s?$LSID:undef;
     }
     return @lsids;
+}
+
+
+=head2 extractResponseArticles
+
+ name     : extractResponseArticles
+ function : get the DOM nodes corresponding to individual
+            Simple or Collection outputs from a MOBY Response
+ usage    : ($collections, $simples) = extractResponseArticles($node)
+ args     : $node - either raw XML or an XML::DOM::Document to be searched            
+ returns  : an array-ref of Collection article XML::DOM::Node's
+            an array-ref of Simple article XML::DOM::Node's
+
+=cut
+
+
+sub extractResponseArticles {
+    my ($result) = @_;
+    return ([], []) unless $result;
+    my $moby;
+    unless (ref($result) =~ /XML\:\:DOM/){
+        my $parser = new XML::DOM::Parser;
+        my $doc = $parser->parse($result);
+        $moby = $doc->getDocumentElement();
+    } else {
+        $moby = $result->getDocumentElement();
+    }
+    my @objects;
+    my @collections;
+    my @Xrefs;
+    my $success = 0;
+    my $responses = $moby->getElementsByTagName('moby:queryResponse');
+    $responses ||= $moby->getElementsByTagName('queryResponse');
+    foreach my $n(0..($responses->getLength - 1)){
+        my $resp = $responses->item($n);
+        foreach my $response_component($resp->getChildNodes){ 
+            next unless $response_component->getNodeType == ELEMENT_NODE;
+            if (($response_component->getTagName eq "Simple") || ($response_component->getTagName eq "moby:Simple")){
+
+                my $simples = $resp->getElementsByTagName('Simple');
+                $simples ||=$resp->getElementsByTagName('moby:Simple');
+                next unless $simples->item(0);
+                foreach my $Object($simples->item(0)->getChildNodes) {
+                    next unless $Object->getNodeType == ELEMENT_NODE;
+                    $success = 1;
+                    push @objects,$Object;
+                }
+            } elsif (($response_component->getTagName eq "Collection") || ($response_component->getTagName eq "moby:Collection")){
+                my @objects;
+                foreach my $simple($response_component->getChildNodes){
+                    next unless $simple->getNodeType == ELEMENT_NODE;
+                    next unless (($simple->getTagName eq "Simple") || ($simple->getTagName eq "moby:Simple"));
+                    foreach my $Object($simple->getChildNodes) {
+                        next unless $Object->getNodeType == ELEMENT_NODE;
+                        $success = 1;
+                        push @objects,$Object;
+                    }
+                }
+                push @collections, \@objects;    #I'm not using collections yet, so we just use Simples.
+            }
+        }
+    }
+    return (\@collections, \@objects);
 }
\ No newline at end of file