WARN  2010-02-15 14:05:11,475 (net.sf.taverna.raven.repository.impl.ArtifactImpl
:85) - Unable to find a version for the dependency log4j:log4j - skipping
WARN  2010-02-15 14:05:11,486 (net.sf.taverna.raven.repository.impl.ArtifactImpl
:85) - Unable to find a version for the dependency junit:junit - skipping
WARN  2010-02-15 14:05:12,013 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.ui-activities:ws
dl-activity-ui:1.0 instead using from profile net.sf.taverna.t2.ui-activities:ws
dl-activity-ui:1.0.1
Central class is  org.biomoby.client.CentralDigestCachedImpl
WARN  2010-02-15 14:05:18,290 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:dataf
low-activity:1.0 instead using from profile net.sf.taverna.t2.activities:dataflo
w-activity:1.0.1
WARN  2010-02-15 14:05:18,313 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:dataf
low-activity:1.0 instead using from profile net.sf.taverna.t2.activities:dataflo
w-activity:1.0.1
WARN  2010-02-15 14:05:18,347 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:20,660 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:dataf
low-activity:1.0 instead using from profile net.sf.taverna.t2.activities:dataflo
w-activity:1.0.1
WARN  2010-02-15 14:05:20,709 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:21,222 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:21,236 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:21,251 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:21,276 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:21,289 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:21,305 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:21,374 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:21,417 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:dataf
low-activity:1.0 instead using from profile net.sf.taverna.t2.activities:dataflo
w-activity:1.0.1
WARN  2010-02-15 14:05:21,432 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:23,211 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:23,244 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:23,260 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:23,277 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:23,350 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:23,384 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:dataf
low-activity:1.0 instead using from profile net.sf.taverna.t2.activities:dataflo
w-activity:1.0.1
WARN  2010-02-15 14:05:23,399 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:dataf
low-activity:1.0 instead using from profile net.sf.taverna.t2.activities:dataflo
w-activity:1.0.1
WARN  2010-02-15 14:05:23,431 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,070 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,101 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,117 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,133 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,146 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,158 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,226 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,268 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:dataf
low-activity:1.0 instead using from profile net.sf.taverna.t2.activities:dataflo
w-activity:1.0.1
WARN  2010-02-15 14:05:25,284 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,330 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,361 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,376 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,391 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,411 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,423 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,522 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:wsdl-
activity:1.0 instead using from profile net.sf.taverna.t2.activities:wsdl-activi
ty:1.0.1
WARN  2010-02-15 14:05:25,576 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:dataf
low-activity:1.0 instead using from profile net.sf.taverna.t2.activities:dataflo
w-activity:1.0.1
WARN  2010-02-15 14:05:44,487 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:dataf
low-activity:1.0 instead using from profile net.sf.taverna.t2.activities:dataflo
w-activity:1.0.1
WARN  2010-02-15 14:06:15,432 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:dataf
low-activity:1.0 instead using from profile net.sf.taverna.t2.activities:dataflo
w-activity:1.0.1
ERROR 2010-02-15 14:06:24,866 (org.biomoby.shared.MobyException:86) - ; nested e
xception is:
        org.xml.sax.SAXParseException: XML document structures must start and en
d within the same entity.
ERROR 2010-02-15 14:06:24,869 (org.biomoby.shared.MobyException:86) - ===ERROR==
=
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: org.xml.sax.SAXParseException: XML document structures must start
and end within the same entity.
Fault code:   {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor:  null
When calling:
        http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========

ERROR 2010-02-15 14:06:24,879 (net.sf.taverna.t2.activities.biomoby.BiomobyCache
:59) - Error whilst caching for Biomoby registry
org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: org.xml.sax.SAXParseException: XML document structures must start
and end within the same entity.
Fault code:   {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor:  null
When calling:
        http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========

        at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(Central
DigestCachedImpl.java:257)
        at org.biomoby.client.CentralDigestCachedSimpleImpl.updateCache(CentralD
igestCachedSimpleImpl.java:190)
        at net.sf.taverna.t2.activities.biomoby.BiomobyCache.cacheForRegistry(Bi
omobyCache.java:49)
        at net.sf.taverna.t2.activities.biomoby.BiomobyCache.cacheForRegistryEnd
point(BiomobyCache.java:75)
        at net.sf.taverna.t2.activities.biomoby.GetOntologyThread.run(GetOntolog
yThread.java:57)
Caused by: org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: org.xml.sax.SAXParseException: XML document structures must start
and end within the same entity.
Fault code:   {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor:  null
When calling:
        http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========

        at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251)
        at org.biomoby.client.CentralImpl.getDataTypeNamesAsXML(CentralImpl.java
:1009)
        at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(Central
DigestCachedImpl.java:158)
        ... 4 more
Caused by: org.xml.sax.SAXParseException: XML document structures must start and
 end within the same entity.
        at org.apache.axis.AxisFault.makeFault(AxisFault.java:101)
        at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:701)
        at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
        at org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnders
tandChecker.java:62)
        at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
        at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
        at org.apache.axis.client.Call.invoke(Call.java:2767)
        at org.apache.axis.client.Call.invoke(Call.java:2443)
        at org.apache.axis.client.Call.invoke(Call.java:2366)
        at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:247)
        ... 6 more
Caused by: org.xml.sax.SAXParseException: XML document structures must start and
 end within the same entity.
        at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Un
known Source)
        at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)

        at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
        at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
        at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.endEntity(Unkno
wn Source)
        at org.apache.xerces.impl.XMLDocumentScannerImpl.endEntity(Unknown Sourc
e)
        at org.apache.xerces.impl.XMLEntityManager.endEntity(Unknown Source)
        at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
        at org.apache.xerces.impl.XMLEntityScanner.scanContent(Unknown Source)
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanContent(Unk
nown Source)
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContent
Dispatcher.dispatch(Unknown Source)
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Un
known Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Sour
ce)
        at javax.xml.parsers.SAXParser.parse(Unknown Source)
        at org.apache.axis.encoding.DeserializationContext.parse(Deserialization
Context.java:227)
        at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
        ... 14 more
WARN  2010-02-15 14:06:32,242 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:dataf
low-activity:1.0 instead using from profile net.sf.taverna.t2.activities:dataflo
w-activity:1.0.1
Central class is  org.biomoby.client.CentralDigestCachedImpl
WARN  2010-02-15 14:06:59,088 (net.sf.taverna.t2.workflowmodel.serialization.xml
.AbstractXMLDeserializer:155) - XML specified net.sf.taverna.t2.activities:dataf
low-activity:1.0 instead using from profile net.sf.taverna.t2.activities:dataflo
w-activity:1.0.1