[MOBY-guts] biomoby commit
Eddie Kawas
kawas at pub.open-bio.org
Tue Dec 14 18:58:20 UTC 2004
kawas
Tue Dec 14 13:58:19 EST 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv9852
Modified Files:
Central.pm CommonSubs.pm CrossReference.pm OntologyServer.pm
Log Message:
hopefully fixed the cdata bug - eddie
moby-live/Perl/MOBY Central.pm,1.142,1.143 CommonSubs.pm,1.54,1.55 CrossReference.pm,1.3,1.4 OntologyServer.pm,1.46,1.47
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.142
retrieving revision 1.143
diff -u -r1.142 -r1.143
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/11/18 17:41:14 1.142
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/12/14 18:58:19 1.143
@@ -392,7 +392,7 @@
my $obj = $Object->nodeName;
return undef unless ( $obj eq 'registerObjectClass' );
my $term = &_nodeTextContent( $Object, "objectType" );
- my $desc = &_nodeTextContent( $Object, "Description" );
+ my $desc = &_nodeCDATAContent( $Object, "Description" );
my $authURI = &_nodeTextContent( $Object, "authURI" );
my $email = &_nodeTextContent( $Object, "contactEmail" );
my $clobber = &_nodeTextContent( $Object, "Clobber" );
@@ -696,7 +696,7 @@
my $type = &_nodeTextContent( $Object, "serviceType" );
my $email = &_nodeTextContent( $Object, "contactEmail" );
my $auth = &_nodeTextContent( $Object, "authURI" );
- my $desc = &_nodeTextContent( $Object, "Description" );
+ my $desc = &_nodeCDATAContent( $Object, "Description" );
my %relationships;
my $x = $doc->getElementsByTagName( "Relationship" );
my $no_relationships = $x->size();
@@ -881,7 +881,7 @@
return undef unless ( $obj eq 'registerNamespace' );
my $type = &_nodeTextContent( $Object, "namespaceType" );
my $authURI = &_nodeTextContent( $Object, "authURI" );
- my $desc = &_nodeTextContent( $Object, "Description" );
+ my $desc = &_nodeCDATAContent( $Object, "Description" );
my $contact = &_nodeTextContent( $Object, "contactEmail" );
return ( $type, $authURI, $desc, $contact );
}
@@ -1593,7 +1593,7 @@
&_nodeTextContent( $Object, "authoritativeService" );
my $URL = &_nodeTextContent( $Object, "URL" );
my $signatureURL = &_nodeTextContent( $Object, "signatureURL" );
- my $desc = &_nodeTextContent( $Object, "Description" );
+ my $desc = &_nodeCDATAContent( $Object, "Description" );
my $INPUTS = &_nodeRawContent( $Object, "Input" ); # returns array ref
my $OUTPUTS = &_nodeRawContent( $Object, "Output" ); # returns array ref
my $SECONDARIES =
@@ -2388,6 +2388,9 @@
my $wsdl =
&_getServiceWSDL( $SI, $InputXML, $OutputXML, $SecondaryXML );
if ( $wsdl ) {
+ if ($wsdl =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/) {
+ $wsdl = $1;
+ }
$wsdls .= "<Service><![CDATA[$wsdl]]></Service>\n";
}
@@ -2519,6 +2522,9 @@
my %types = %{ $OS->retrieveAllServiceTypes() };
my $types = "<serviceTypes>\n";
while ( my ( $serv, $desc ) = each %types ) {
+ if ($desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/) {
+ $desc = $1;
+ }
$types .=
"<serviceType name='$serv'>\n<Description><![CDATA[$desc]]></Description>\n</serviceType>\n";
}
@@ -2558,6 +2564,9 @@
while ( my ( $name, $authdesc ) = each %types ) {
my $auth = $authdesc->[0];
my $desc = $authdesc->[1];
+ if ($desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/) {
+ $desc = $1;
+ }
$types .=
"<relationshipType relationship='$name' authority='$auth'>\n<Description><![CDATA[$desc]]></Description>\n</relationshipType>\n";
}
@@ -2589,6 +2598,9 @@
my %types = %{ $OS->retrieveAllObjectTypes() };
my $obj = "<objectNames>\n";
while ( my ( $name, $desc ) = each %types ) {
+ if ($desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/) {
+ $desc = $1;
+ }
$obj .=
"<Object name='$name'>\n<Description><![CDATA[$desc]]></Description>\n</Object>\n";
}
@@ -2639,6 +2651,9 @@
; # will return undef if this term does not exist, and does not look like an LSID
return "<retrieveObjectDefinition/>" unless $def;
my %def = %{ $OS->retrieveObject( node => $term ) };
+ if ($def{description} =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/) {
+ $def{description}= $1;
+ }
my $response;
$response = "<retrieveObjectDefinition>
<objectType>$def{objectType}</objectType>
@@ -2685,6 +2700,9 @@
my %types = %{ $OS->retrieveAllNamespaceTypes() };
my $ns = "<Namespaces>\n";
while ( my ( $namespace, $desc ) = each %types ) {
+ if ($desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/) {
+ $desc = $1;
+ }
$ns .=
"<Namespace name='$namespace'>\n<Description><![CDATA[$desc]]></Description>\n</Namespace>\n";
}
@@ -3002,6 +3020,9 @@
$response .= "<Category>$cat</Category>\n";
$response .= "<serviceType>$type</serviceType>\n";
$response .= "<outputObject>$objectOUT</outputObject>\n";
+ if ($desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/) {
+ $desc = $1;
+ }
$response .= "<Description><![CDATA[$desc]]></Description>\n";
$response .= "</Service>\n";
if ( $max_return ) { --$max_return; last unless $max_return }
@@ -3035,6 +3056,9 @@
my $serviceName = $SI->servicename;
my $AuthURI = $SI->authority_uri;
my $desc = $SI->description;
+ if ($desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/) {
+ $desc = $1;
+ }
my $URL = $SI->url;
my $IN = "NOT_YET_DEFINED_INPUTS";
my $OUT = "NOT_YET_DEFINED_OUTPUTS";
@@ -3075,6 +3099,9 @@
my $sth = $dbh->prepare( $sth{get_server_parameters} );
$sth->execute( $id );
my ( $Object, $sprintf, $in ) = $sth->fetchrow_array();
+ if ($sprintf=~ /<!\[CDATA\[((?>[^\]]+))\]\]>/) {
+ $sprintf = $1;
+ }
return "<GETstring><![CDATA[$sprintf]]></GETstring>";
}
@@ -3197,7 +3224,30 @@
}
return $content;
}
+sub _nodeCDATAContent{
+ # will get text of **all** child $node from the given $DOM
+ # regardless of their depth!!
+ my ( $DOM, $node ) = @_;
+ $debug && &_LOG( "_nodeTextContent received DOM: ",
+ $DOM->toString, "\nsearching for node $node\n" );
+ my $x = $DOM->getElementsByTagName( $node );
+ return undef unless $x->get_node( 1 );
+ my @child = $x->get_node( 1 )->childNodes;
+ my $content;
+ foreach ( @child ) {
+ $debug
+ && &_LOG( $_->nodeType, "\t", $_->toString, "\n" );
+
+ #next unless $_->nodeType == TEXT_NODE;
+ if ($_->toString =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/) {
+ $content .= $1;
+ } else {
+ $content .= $_->toString;
+ }
+ }
+ return $content;
+}
#Eddie - converted
sub _nodeRawContent {
@@ -3341,6 +3391,9 @@
$authoritative, $email, $signatureURL
)
= $sth->fetchrow_array;
+ if ($desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/) {
+ $desc = $1;
+ }
#print "\n\nAFTER EXECUTE $category, $servicename, $service_type_uri, $authority_id, $desc, $authoritative\n\n";
$signatureURL ||= "";
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.54
retrieving revision 1.55
diff -u -r1.54 -r1.55
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/11/18 17:41:14 1.54
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/12/14 18:58:19 1.55
@@ -31,7 +31,7 @@
# [SIMPLE, $queryID, $simple]
# the first element is an exported constant SIMPLE, COLLECTION, SECONDARY
# the second element is the queryID (required for enumerating the responses)
- # the third element is the XML::DOM for the Simple, Collection, or Parameter block
+ # the third element is the XML::LibXML for the Simple, Collection, or Parameter block
my (@inputs)= genericServiceInputParser($data);
# or fail properly with an empty response
return SOAP::Data->type('base64' => responseHeader("my.authURI.com") . responseFooter()) unless (scalar(@inputs));
@@ -258,9 +258,9 @@
1. COLLECTION|SIMPLE (i.e. constants 1, 2)
2. queryID
3. $data - the data takes several forms
- a. $article XML::DOM node for Simples
+ a. $article XML::LibXML node for Simples
<mobyData...>...</mobyData>
- b. \@article XML:DOM nodes for Collections
+ b. \@article XML:LibXML nodes for Collections
for example, the input message:
@@ -303,7 +303,7 @@
my ( $message ) = @_; # get the incoming MOBY query XML
my @inputs; # set empty response
my @queries =
- getInputs( $message ); # returns XML::DOM nodes <mobyData>...</mobyData>
+ getInputs( $message ); # returns XML::LibXML nodes <mobyData>...</mobyData>
foreach my $query ( @queries ) {
my $queryID =
getInputID( $query ); # get the queryID attribute of the mobyData
@@ -331,7 +331,7 @@
name : DO NOT USE!!
function : to take a MOBY message and break the objects out of it. This is identical
to the genericServiceInputParser method above, except that it returns the data as
- Objects rather than XML::DOM nodes. This is an improvement!
+ Objects rather than XML::LibXML nodes. This is an improvement!
usage : my @inputs = serviceInputParser($MOBY_mssage));
args : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message
returns : @inputs - the structure of @inputs is a list of listrefs.
@@ -346,7 +346,7 @@
my ( $message ) = @_; # get the incoming MOBY query XML
my @inputs; # set empty response
my @queries =
- getInputs( $message ); # returns XML::DOM nodes <mobyData>...</mobyData>
+ getInputs( $message ); # returns XML::LibXML nodes <mobyData>...</mobyData>
# mark, this doesn't work for complex services. We need to allow more than one input per invocation
foreach my $query ( @queries ) {
@@ -402,7 +402,7 @@
[SECONDARY, $DOM_cutoff] # $DOM_cutoff= <Parameter> block
]
- Please see the XML::DOM pod documentation for information about how
+ Please see the XML::LibXML pod documentation for information about how
to parse XML DOM objects.
@@ -431,7 +431,7 @@
[SECONDARY, $DOM_cutoff] # $DOM_cutoff = <Parameter> Block
]
- Please see the XML::DOM pod documentation for information about how
+ Please see the XML::LibXML pod documentation for information about how
to parse XML DOM objects.
@@ -441,7 +441,7 @@
my ( $message ) = @_; # get the incoming MOBY query XML
my @inputs; # set empty response
my @queries =
- getInputs( $message ); # returns XML::DOM nodes <mobyData>...</mobyData>
+ getInputs( $message ); # returns XML::LibXML nodes <mobyData>...</mobyData>
my %input_parameters; # $input_parameters{$queryID} = [
foreach my $query ( @queries ) {
my $queryID =
@@ -470,7 +470,7 @@
name : getArticles
function : get the Simple/Collection/Parameter articles for a single mobyData
usage : @articles = getArticles($XML)
- args : raw XML or XML::DOM of a queryInput, mobyData, or queryResponse block (e.g. from getInputs)
+ args : raw XML or XML::LibXML of a queryInput, mobyData, or queryResponse block (e.g. from getInputs)
returns : a list of listrefs; each listref is one component of the queryInput or mobyData block
a single block may consist of one or more named or unnamed
simple, collection, or parameter articles.
@@ -508,7 +508,7 @@
sub getArticles {
my ( $moby ) = @_;
- unless ( ref( $moby ) =~ /XML\:\:DOM/ ) {
+ unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) {
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string( $moby );
$moby = $doc->getDocumentElement();
@@ -548,8 +548,8 @@
usage : my @ids = getSimpleArticleIDs("NCBI_gi", \@SimpleArticles);
my @ids = getSimpleArticleIDs(\@SimpleArticles);
args : $Namespace - (optional) a namespace stringfrom the MOBY namespace ontology, or undef if you don't care
- \@Simples - (required) a listref of Simple XML::DOM nodes
- i.e. the XML::DOM representing an XML structure like this:
+ \@Simples - (required) a listref of Simple XML::LibXML nodes
+ i.e. the XML::LibXML representing an XML structure like this:
<Simple>
<Object namespace="NCBI_gi" id="163483"/>
</Simple>
@@ -643,8 +643,8 @@
name : getSimpleArticleNamespaceURI
function : to get the namespace of a simple article
usage : my $ns = getSimpleArticleNamespaceURI($SimpleArticle);
- args : $Simple - (required) a single XML::DOM node representing a Simple Article
- i.e. the XML::DOM representing an XML structure like this:
+ args : $Simple - (required) a single XML::LibXML node representing a Simple Article
+ i.e. the XML::LibXML representing an XML structure like this:
<Simple>
<Object namespace="NCBI_gi" id="163483"/>
</Simple>
@@ -700,7 +700,7 @@
my ( $data, $articleName, $qID ) = @_; # articleName optional
$qID = &_getQueryID( $qID )
if ref( $qID ) =~
- /XML::DOM/; # in case they send the DOM instead of the ID
+ /XML::LibXML/; # in case they send the DOM instead of the ID
$data ||= ''; # initialize to avoid uninit value errors
$qID ||= "";
$articleName ||= "";
@@ -726,7 +726,7 @@
#Eddie - converted
sub _getQueryID {
my ( $query ) = @_;
- unless ( ref( $query ) =~ /XML\:\:DOM/ ) {
+ unless ( ref( $query ) =~ /XML\:\:LibXML/ ) {
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string( $query );
$query = $doc->getDocumentElement();
@@ -849,10 +849,10 @@
=head2 getInputs
name : getInputs
- function : get the mobyData block(s) as XML::DOM nodes
+ function : get the mobyData block(s) as XML::LibXML nodes
usage : @queryInputs = getInputArticles($XML)
- args : the raw XML of a <MOBY> query, or an XML::DOM document
- returns : a list of XML::DOM::Node's, each is a queryInput or mobyData block.
+ args : the raw XML of a <MOBY> query, or an XML::LibXML document
+ returns : a list of XML::LibXML::Node's, each is a queryInput or mobyData block.
Note : Remember that these blocks are enumerated! This is what you
pass as the third argument to the simpleResponse or collectionResponse
subroutine to associate the numbered input to the numbered response
@@ -863,7 +863,7 @@
sub getInputs {
my ( $XML ) = @_;
my $moby;
- unless ( ref( $XML ) =~ /XML\:\:DOM/ ) {
+ unless ( ref( $XML ) =~ /XML\:\:LibXML/ ) {
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string( $XML );
$moby = $doc->getDocumentElement();
@@ -887,7 +887,7 @@
name : getInputID
function : get the value of the queryID element
usage : @queryInputs = getInputID($XML)
- args : the raw XML or XML::DOM of a queryInput or mobyData block (e.g. from getInputs)
+ args : the raw XML or XML::LibXML of a queryInput or mobyData block (e.g. from getInputs)
returns : integer, or ''
Note : Inputs and Responses are coordinately enumerated!
The integer you get here is what you
@@ -898,7 +898,7 @@
sub getInputID {
my ( $XML ) = @_;
- unless ( ref( $XML ) =~ /XML\:\:DOM/ ) {
+ unless ( ref( $XML ) =~ /XML\:\:LibXML/ ) {
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string( $XML );
$XML = $doc->getDocumentElement();
@@ -918,7 +918,7 @@
or queryResponse node, rethrning them as SimpleArticle,
SecondaryArticle, or ServiceInstance objects
usage : @articles = getArticles($XML)
- args : raw XML or XML::DOM of a moby:mobyData block
+ args : raw XML or XML::LibXML of a moby:mobyData block
returns :
=cut
@@ -926,7 +926,7 @@
#Eddie - converted
sub getArticlesAsObjects {
my ( $moby ) = @_;
- unless ( ref( $moby ) =~ /XML\:\:DOM/ ) {
+ unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) {
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string( $moby );
$moby = $doc->getDocumentElement();
@@ -964,14 +964,14 @@
name : getCollectedSimples
function : get the Simple articles collected in a moby:Collection block
usage : @Simples = getCollectedSimples($XML)
- args : raw XML or XML::DOM of a moby:Collection block
- returns : a list of XML::DOM nodes, each of which is a moby:Simple block
+ args : raw XML or XML::LibXML of a moby:Collection block
+ returns : a list of XML::LibXML nodes, each of which is a moby:Simple block
=cut
sub getCollectedSimples {
my ( $moby ) = @_;
- unless ( ref( $moby ) =~ /XML\:\:DOM/ ) {
+ unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) {
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string( $moby );
$moby = $doc->getDocumentElement();
@@ -997,7 +997,7 @@
args : the raw XML of a moby:MOBY query
returns : a list of listrefs, each listref is the input to a single query.
Remember that the input to a single query may be one or more Simple
- and/or Collection articles. These are provided as XML::DOM nodes.
+ and/or Collection articles. These are provided as XML::LibXML nodes.
i.e.: @queries = ([$SIMPLE_DOM_NODE], [$SIMPLE_DOM_NODE2])
or : @queries = ([$COLLECTION_DOM_NODE], [$COLLECTION_DOM_NODE2])
@@ -1024,7 +1024,7 @@
#Eddie - converted
sub getInputArticles {
my ( $moby ) = @_;
- unless ( ref( $moby ) =~ /XML\:\:DOM/ ) {
+ unless ( ref( $moby ) =~ /XML\:\:LibXML/ ) {
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string( $moby );
$moby = $doc->getDocumentElement();
@@ -1054,7 +1054,7 @@
name : isSimpleArticle
function : tests XML (text) or an XML DOM node to see if it represents a Simple article
usage : if (isSimpleArticle($node)){do something to it}
- input : an XML::DOM node, an XML::DOM::Document or straight XML
+ input : an XML::LibXML node, an XML::LibXML::Document or straight XML
returns : boolean
=cut
@@ -1062,7 +1062,7 @@
#Eddie - converted
sub isSimpleArticle {
my ( $DOM ) = @_;
- unless ( ref( $DOM ) =~ /XML\:\:DOM/ ) {
+ unless ( ref( $DOM ) =~ /XML\:\:LibXML/ ) {
my $parser = XML::LibXML->new();
my $doc;
eval { $doc = $parser->parse_string( $DOM ); };
@@ -1079,7 +1079,7 @@
name : isCollectionArticle
function : tests XML (text) or an XML DOM node to see if it represents a Collection article
usage : if (isCollectionArticle($node)){do something to it}
- input : an XML::DOM node, an XML::DOM::Document or straight XML
+ input : an XML::LibXML node, an XML::LibXML::Document or straight XML
returns : boolean
=cut
@@ -1087,7 +1087,7 @@
#Eddie - converted
sub isCollectionArticle {
my ( $DOM ) = @_;
- unless ( ref( $DOM ) =~ /XML\:\:DOM/ ) {
+ unless ( ref( $DOM ) =~ /XML\:\:LibXML/ ) {
my $parser = XML::LibXML->new();
my $doc;
eval { $doc = $parser->parse_string( $DOM ); };
@@ -1104,7 +1104,7 @@
name : isSecondaryArticle
function : tests XML (text) or an XML DOM node to see if it represents a Secondary article
usage : if (isSecondaryArticle($node)){do something to it}
- input : an XML::DOM node, an XML::DOM::Document or straight XML
+ input : an XML::LibXML node, an XML::LibXML::Document or straight XML
returns : boolean
=cut
@@ -1112,7 +1112,7 @@
#Eddie - converted
sub isSecondaryArticle {
my ( $DOM ) = @_;
- unless ( ref( $DOM ) =~ /XML\:\:DOM/ ) {
+ unless ( ref( $DOM ) =~ /XML\:\:LibXML/ ) {
my $parser = XML::LibXML->new();
my $doc;
eval { $doc = $parser->parse( _string $DOM); };
@@ -1138,7 +1138,7 @@
sub extractRawContent {
my ( $article ) = @_;
return "" unless $article;
- return "" unless ref( $article ) =~ /XML::DOM/;
+ return "" unless ref( $article ) =~ /XML::LibXML/;
my $response;
foreach ( $article->childNodes ) {
$response .= $_->toString;
@@ -1154,7 +1154,7 @@
or get the value of a Parameter element.
usage : @strings = getNodeContentWithArticle($node, $tagname, $articleName)
args : (in order)
- $node - an XML::DOM node, or straight XML. It may even
+ $node - an XML::LibXML node, or straight XML. It may even
be the entire mobyData block.
$tagname - the tagname (effectively from the Object type ontology),
or "Parameter" if you are trying to get secondaries
@@ -1243,7 +1243,7 @@
# carriage returns, as these might be meaningful!
my ( $node, $element, $articleName ) = @_;
my @contents;
- return () unless ref( $node ) =~ /XML::DOM/;
+ return () unless ref( $node ) =~ /XML::LibXML/;
return () unless $element;
return () unless $articleName;
my $nodes = $node->getElementsByTagName( $element );
@@ -1355,9 +1355,9 @@
function : get the DOM nodes corresponding to individual
Simple or Collection outputs from a MOBY Response
usage : ($collections, $simples) = getResponseArticles($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
+ args : $node - either raw XML or an XML::LibXML::Document to be searched
+ returns : an array-ref of Collection article XML::LibXML::Node's
+ an array-ref of Simple article XML::LibXML::Node's
=cut
@@ -1369,7 +1369,7 @@
my ( $result ) = @_;
return ( [], [] ) unless $result;
my $moby;
- unless ( ref( $result ) =~ /XML\:\:DOM/ ) {
+ unless ( ref( $result ) =~ /XML\:\:LibXML/ ) {
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string( $result );
$moby = $doc->getDocumentElement();
@@ -1426,7 +1426,7 @@
name : getServiceNotes
function : to get the content of the Service Notes block of the MOBY message
usage : getServiceNotes($message)
- args : $message is either the XML::DOM of the MOBY message, or plain XML
+ args : $message is either the XML::LibXML of the MOBY message, or plain XML
returns : String content of the ServiceNotes block of the MOBY Message
=cut
@@ -1436,7 +1436,7 @@
my ( $result ) = @_;
return ( "" ) unless $result;
my $moby;
- unless ( ref( $result ) =~ /XML\:\:DOM/ ) {
+ unless ( ref( $result ) =~ /XML\:\:LibXML/ ) {
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string( $result );
$moby = $doc->getDocumentElement();
@@ -1470,7 +1470,7 @@
usage : @xrefs = getCrossReferences($XML)
args : $XML is either a SIMPLE article (<Simple>...</Simple>)
or an object (the payload of a Simple article), and
- may be either raw XML or an XML::DOM node.
+ may be either raw XML or an XML::LibXML node.
returns : an array of MOBY::CrossReference objects
example :
@@ -1492,7 +1492,7 @@
#Eddie - converted
sub getCrossReferences {
my ( $XML ) = @_;
- unless ( ref( $XML ) =~ /XML::DOM/ ) {
+ unless ( ref( $XML ) =~ /XML::LibXML/ ) {
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string( $XML );
$XML = $doc->getDocumentElement();
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CrossReference.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.46
retrieving revision 1.47
diff -u -r1.46 -r1.47
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