[TAVERNA-187] Wrong/invalid element name from XML splitters for inner complex types

• Type: Bug
• Status: To Do
• Priority: Major
• Resolution: Unresolved
• Component/s: Taverna Common Activities
• Labels: wsdl
• Assignee: Unassigned
• Reporter: Stian Soiland-Reyes
• Created: 21/Jan/10 15:59
• Updated: 28/Apr/15 11:42

Description

Katy reported on 2010-01-21 to Alan (workflow attached):

I'm having some trouble with a complex type asynchronous web service. I
think there is a problem with the xml splitters because I am getting an
error for simply supplying the individual pieces to pass into a splitter
service.

Would you mind having a quick look for me please? The workflow is attached
and the service is here in biocat:
http://www.biocatalogue.org/services/147-wsnetchop_3_1_910208#overview

I am getting the error in the first splitter service sequences_sequences
and I was using the example sequence from the biocat documentation
(ACDEFGHIKLMNPQRSTVWY)

Alan is able to reproduce this stack trace:

I can confirm that Taverna 2.1 runs the workflow but gets an errorDocument with:

Error Trace
net.sf.taverna.t2.reference.impl.ErrorDocumentImpl@a90033
net.sf.taverna.t2.reference.impl.ErrorDocumentImpl@5bf8a2
net.sf.taverna.t2.reference.impl.ErrorDocumentImpl@ab4e86
net.sf.taverna.t2.reference.impl.ErrorDocumentImpl@57ad50
net.sf.taverna.t2.reference.impl.ErrorDocumentImpl@3fb58e
org.jdom.IllegalNameException: The name ">sequences>entry" is not legal for JDOM/XML elements: XML names cannot begin with the character ">".
org.jdom.Element.setName(Element.java:206)
org.jdom.Element.<init>(Element.java:140)
org.jdom.Element.<init>(Element.java:152)
net.sf.taverna.wsdl.xmlsplitter.XMLInputSplitter.execute(XMLInputSplitter.java:61)
net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity$1.run(XMLInputSplitterActivity.java:88)
java.lang.Thread.run(Thread.java:613)

Inspection shows that the XMLInputSplitter does on line 61:

Element outputElement = (this.typeDescriptor.getName().length() > 0 ? new Element(
				this.typeDescriptor.getName())
				: new Element(this.typeDescriptor.getType()));

So this is to create the <entry> element for the topmost XML splitter sequence_sequence in the workflow.

The webservice is defined at http://www.cbs.dtu.dk/ws/NetChop/NetChop_3_1.wsdl and the imported http://www.cbs.dtu.dk/ws/common/ws_common_1_0.xsd shows this complex type as:

<xsd:complexType name="sequences">
		<xsd:sequence>
			<xsd:element name="entry" maxOccurs="unbounded">
				<xsd:complexType>
					<xsd:sequence>
						<xsd:element name="ident">
							<xsd:simpleType>
								<xsd:restriction base="xsd:string">
									<xsd:pattern value=".*"/>
								</xsd:restriction>
							</xsd:simpleType>
						</xsd:element>
						<xsd:element name="seq">
							<xsd:simpleType>
								<xsd:restriction base="xsd:string">
									<xsd:pattern value="[A-Za-z\n]+"/>
								</xsd:restriction>
							</xsd:simpleType>
						</xsd:element>
					</xsd:sequence>
				</xsd:complexType>
			</xsd:element>
		</xsd:sequence>
	</xsd:complexType>

Taverna seems to loose that name="entry" bit - because instead of the splitter making an element <entry> it is trying to make an element >sequences>entry

Inspection in Debug mode shows that setName() is never called when creating the net.sf.taverna.wsdl.parser.ComplexTypeDescriptor – and so the code snippet will instead use the type - which has been set as the local part of the fully qualified name {{

{http://www.cbs.dtu.dk/ws/ws-common}

>sequences>entry}}

It seems the setName() method has logic for this:

public void setName(String name) {
		int i;
		if ((i = name.lastIndexOf('>')) != -1) {
			this.name = name.substring(i + 1);
		} else {
			this.name = name;
		}
	}

but net.sf.taverna.wsdl.parser.WSDLParser.constructComplexType() does not call this, only:

result.setType(type.getQName().getLocalPart());
			cachedComplexTypes.put(type.getQName().toString(), result);
			List containedElements = type.getContainedElements();
			if (containedElements != null) {
				result.getElements().addAll(
						constructElements(containedElements));
			}
			result.setQname(type.getQName());

Even a crude attempt to add setName() here (using Display tab in Eclipse) and reconstructing the workflow from scratch does not seem to work, as at a later stage when creating the splitters, the splitter definitions is serialised and deserialised as XML, and the name seems to be lost again.