This sounds like you are reading in a file in a mismatching character set, and therefore it does not compose well with the XML if it is passed in as a binary.
Taverna will generally assume files are UTF-8 - but I believe the Read File worker used in getModel uses the system encoding (typically Latin1/iso8859-1 in western Europe, but I guess it could be koi-8 or similar on your installation. However the URL http://bioputer.mimuw.edu.pl/tav4sb/models/enzyme.xml returns UTF8 - so the file reader does something wrong. (I believe this was a bug in Taverna, if you replace getModel with "Get web page from URL" or "Read text file" it does correctly handle content encoding) Alan points out he's made a non-file-version, which will probably bypass this problem. 2011/7/16 Mikołaj Rybiński <[email protected]>: > Hi, > > under > > Taverna Workbench 2.3 > Windows Vista 64bit > > when running workflow (no inputs required) > > http://bioputer.mimuw.edu.pl/tav4sb/workflows/sim.xml > > I get the following Error Trace: > > Processor 'OdeSolver' - Port 'error' > Processor 'odeSolverResultXml' - Port 'error' > Processor 'odeSolver' - Port 'odeSolverResult': An error occurred > invoking the WSDL service > > and the Stack Trace: > > org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte > 2 of 3-byte UTF-8 sequence. > org.apache.xerces.parsers.DOMParser.parse(unknown file) > org.apache.xerces.jaxp.DocumentBuilderImpl.parse(unknown file) > javax.xml.parsers.DocumentBuilder.parse(unknown file) > net.sf.taverna.wsdl.soap.AbstractBodyBuilder.populateElementWithObjectData(AbstractBodyBuilder.java:241) > net.sf.taverna.wsdl.soap.AbstractBodyBuilder.createBodyElementForData(AbstractBodyBuilder.java:152) > net.sf.taverna.wsdl.soap.AbstractBodyBuilder.build(AbstractBodyBuilder.java:125) > net.sf.taverna.wsdl.soap.LiteralBodyBuilder.build(LiteralBodyBuilder.java:81) > net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.makeSoapBody(WSDLSOAPInvoker.java:194) > net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.makeRequestEnvelope(WSDLSOAPInvoker.java:180) > net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invoke(WSDLSOAPInvoker.java:136) > net.sf.taverna.t2.activities.wsdl.T2WSDLSOAPInvoker.invoke(T2WSDLSOAPInvoker.java:281) > net.sf.taverna.t2.activities.wsdl.WSDLActivity$1.run(WSDLActivity.java:289) > java.lang.Thread.run(unknown file) > > The thing is it's working under Mac OS X 10.6 with Tav. 2.3 and Ubuntu > Linux, although I have to verify it yet with Tav. 2.3. Additional > context: the port 'error' of 'odeSolver' Web service processor should > be empty - element only exists in response if there was an error and > everything looks fine on the server side. Any ideas/suggestion on what > may be wrong? > > Best regards, > Mikołaj > > ------------------------------------------------------------------------------ > AppSumo Presents a FREE Video for the SourceForge Community by Eric > Ries, the creator of the Lean Startup Methodology on "Lean Startup > Secrets Revealed." This video shows you how to validate your ideas, > optimize your ideas and identify your business strategy. > http://p.sf.net/sfu/appsumosfdev2dev > _______________________________________________ > taverna-users mailing list > [email protected] > [email protected] > Web site: http://www.taverna.org.uk > Mailing lists: http://www.taverna.org.uk/about/contact-us/ > -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester ------------------------------------------------------------------------------ AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on "Lean Startup Secrets Revealed." This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev _______________________________________________ taverna-users mailing list [email protected] [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/
