org.xml.sax.SAXParseException

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  • as it says. see note for debug output. WsDbFetch requests fail with an 'Empty response' client side axis fault. Have not been able to duplicate in spite of similar hardware, JRE, and jalview version. ****** ADDITIONAL INFORMATION ****** Java Web Start 1.6.0_01 Using JRE version 1.6.0_01 Java HotSpot(TM) Client VM User home directory = C:\Documents and Settings\Jon ---------------------------------------------------- c: clear console window f: finalize objects on finalization queue g: garbage collect h: display this help message m: print memory usage o: trigger logging p: reload proxy configuration q: hide console r: reload policy configuration s: dump system and deployment properties t: dump thread list v: dump thread stack 0-5: set trace level to <n> ---------------------------------------------------- Java version: 1.6.0_01 x86 Windows XP 5.1 Jalview Version: 2.X DEBUG - getBundle(org.apache.axis,org.apache.axis.i18n,resource,null,...) DEBUG - loadBundle: Ignoring MissingResourceException: Can't find bundle for base name org.apache.axis.resource, locale en_GB DEBUG - Created org.apache.axis.i18n.resource, linked to parent null DEBUG - getBundle(org.apache.axis,org.apache.axis.utils,resource,null,...) DEBUG - loadBundle: Ignoring MissingResourceException: Can't find bundle for base name org.apache.axis.utils.resource, locale en_GB DEBUG - loadBundle: Ignoring MissingResourceException: Can't find bundle for base name org.apache.axis.resource, locale en_GB DEBUG - Root package not found, cross link to org.apache.axis.i18n.resource DEBUG - Root package not found, cross link to org.apache.axis.i18n.resource DEBUG - org.apache.axis.i18n.resource::handleGetObject(engineConfigLoadFactory) DEBUG - Factory org.apache.axis.configuration.EngineConfigurationFactoryServlet Ignored: unable to load/resolve class. DEBUG - org.apache.axis.i18n.resource::handleGetObject(engineFactory) DEBUG - Got EngineFactory: org.apache.axis.configuration.EngineConfigurationFactoryDefault DEBUG - Enter: AxisEngine::init DEBUG - org.apache.axis.i18n.resource::handleGetObject(attachEnabled) DEBUG - Attachment support is enabled? true DEBUG - Enter/Exit: JAFDataHandlerDeserializerFactory(class java.lang.String, {http://xml.apache.org/xml-soap}PlainText) DEBUG - org.apache.axis.i18n.resource::handleGetObject(oddDigits00) DEBUG - org.apache.axis.i18n.resource::handleGetObject(badChars01) DEBUG - Enter/Exit: JAFDataHandlerDeserializerFactory(class java.awt.Image, {http://xml.apache.org/xml-soap}Image) DEBUG - Enter/Exit: JAFDataHandlerDeserializerFactory(class javax.mail.internet.MimeMultipart, {http://xml.apache.org/xml-soap}Multipart) DEBUG - Enter/Exit: JAFDataHandlerDeserializerFactory(interface javax.xml.transform.Source, {http://xml.apache.org/xml-soap}Source) DEBUG - Enter/Exit: JAFDataHandlerDeserializerFactory(class org.apache.axis.attachments.OctetStream, {http://xml.apache.org/xml-soap}octet-stream) DEBUG - Enter/Exit: JAFDataHandlerDeserializerFactory() DEBUG - Enter/Exit: JAFDataHandlerDeserializerFactory(class java.lang.String, {http://xml.apache.org/xml-soap}PlainText) DEBUG - Enter/Exit: JAFDataHandlerDeserializerFactory(class java.awt.Image, {http://xml.apache.org/xml-soap}Image) DEBUG - Enter/Exit: JAFDataHandlerDeserializerFactory(class javax.mail.internet.MimeMultipart, {http://xml.apache.org/xml-soap}Multipart) DEBUG - Enter/Exit: JAFDataHandlerDeserializerFactory(interface javax.xml.transform.Source, {http://xml.apache.org/xml-soap}Source) DEBUG - Enter/Exit: JAFDataHandlerDeserializerFactory(class org.apache.axis.attachments.OctetStream, {http://xml.apache.org/xml-soap}octet-stream) DEBUG - Enter/Exit: JAFDataHandlerDeserializerFactory() DEBUG - Exit: AxisEngine::init DEBUG - org.apache.axis.i18n.resource::handleGetObject(transport00) DEBUG - Transport is org.apache.axis.transport.http.HTTPTransport@4d2af2 DEBUG - @10dc656 added parameter >name: ids typeEntry: null mode: IN position: 0 isReturn: false typeQName: {http://www.w3.org/2001/XMLSchema}string javaType: class java.lang.String inHeader: false outHeader: false @1584807<total parameters:1 DEBUG - @10dc656 added parameter >name: db typeEntry: null mode: IN position: 1 isReturn: false typeQName: {http://www.w3.org/2001/XMLSchema}string javaType: class java.lang.String inHeader: false outHeader: false @e0e515<total parameters:2 DEBUG - @10dc656 added parameter >name: format typeEntry: null mode: IN position: 2 isReturn: false typeQName: {http://www.w3.org/2001/XMLSchema}string javaType: class java.lang.String inHeader: false outHeader: false @dfcb47<total parameters:3 DEBUG - @10dc656 added parameter >name: style typeEntry: null mode: IN position: 3 isReturn: false typeQName: {http://www.w3.org/2001/XMLSchema}string javaType: class java.lang.String inHeader: false outHeader: false @9abc69<total parameters:4 DEBUG - @10dc656setReturnType({http://schemas.xmlsoap.org/soap/encoding/}Array) DEBUG - Enter: Call::invoke(ns, meth, args) DEBUG - operation=name: null returnQName: null returnType: {http://schemas.xmlsoap.org/soap/encoding/}Array returnClass: class [Ljava.lang.Object; elementQName:null soapAction: null style: rpc use: encoded numInParams: 4 method:null ParameterDesc[0]: name: ids typeEntry: null mode: IN position: 0 isReturn: false typeQName: {http://www.w3.org/2001/XMLSchema}string javaType: class java.lang.String inHeader: false outHeader: false ParameterDesc[1]: name: db typeEntry: null mode: IN position: 1 isReturn: false typeQName: {http://www.w3.org/2001/XMLSchema}string javaType: class java.lang.String inHeader: false outHeader: false ParameterDesc[2]: name: format typeEntry: null mode: IN position: 2 isReturn: false typeQName: {http://www.w3.org/2001/XMLSchema}string javaType: class java.lang.String inHeader: false outHeader: false ParameterDesc[3]: name: style typeEntry: null mode: IN position: 3 isReturn: false typeQName: {http://www.w3.org/2001/XMLSchema}string javaType: class java.lang.String inHeader: false outHeader: false DEBUG - operation.getNumParams()=4 DEBUG - getParamList number of params: 4 DEBUG - Enter: Call::invoke(RPCElement) DEBUG - org.apache.axis.i18n.resource::handleGetObject(attachEnabled) DEBUG - Attachment support is enabled? true DEBUG - Enter: SOAPPart ctor(FORM_SOAPENVELOPE) DEBUG - org.apache.axis.i18n.resource::handleGetObject(setMsgForm) DEBUG - Setting current message form to: FORM_SOAPENVELOPE (currentMessage is now org.apache.axis.message.SOAPEnvelope) DEBUG - Exit: SOAPPart ctor() DEBUG - org.apache.axis.i18n.resource::handleGetObject(addBody00) DEBUG - Adding body element to message... DEBUG - Enter: Call::invoke() DEBUG - Enter: SOAPPart::getAsSOAPEnvelope() DEBUG - org.apache.axis.i18n.resource::handleGetObject(currForm) DEBUG - current form is FORM_SOAPENVELOPE DEBUG - MessageContext: setTargetService(urn:Dbfetch) DEBUG - org.apache.axis.i18n.resource::handleGetObject(noService10) DEBUG - Exception: org.apache.axis.ConfigurationException: No service named urn:Dbfetch is available org.apache.axis.ConfigurationException: No service named urn:Dbfetch is available at org.apache.axis.configuration.FileProvider.getService(FileProvider.java:228) at org.apache.axis.AxisEngine.getService(AxisEngine.java:290) at org.apache.axis.MessageContext.setTargetService(MessageContext.java:755) at org.apache.axis.client.Call.invoke(Call.java:2643) at org.apache.axis.client.Call.invoke(Call.java:2378) at org.apache.axis.client.Call.invoke(Call.java:2301) at org.apache.axis.client.Call.invoke(Call.java:1758) at jalview.io.EBIFetchClient.fetchBatch(EBIFetchClient.java:211) at jalview.io.EBIFetchClient.fetchData(EBIFetchClient.java:183) at jalview.io.EBIFetchClient.fetchDataAsFile(EBIFetchClient.java:124) at jalview.gui.SequenceFetcher.getPDBFile(SequenceFetcher.java:419) at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:258) at java.lang.Thread.run(Unknown Source) at org.apache.axis.configuration.FileProvider.getService(FileProvider.java:228) at org.apache.axis.AxisEngine.getService(AxisEngine.java:290) at org.apache.axis.MessageContext.setTargetService(MessageContext.java:755) at org.apache.axis.client.Call.invoke(Call.java:2643) at org.apache.axis.client.Call.invoke(Call.java:2378) at org.apache.axis.client.Call.invoke(Call.java:2301) at org.apache.axis.client.Call.invoke(Call.java:1758) at jalview.io.EBIFetchClient.fetchBatch(EBIFetchClient.java:211) at jalview.io.EBIFetchClient.fetchData(EBIFetchClient.java:183) at jalview.io.EBIFetchClient.fetchDataAsFile(EBIFetchClient.java:124) at jalview.gui.SequenceFetcher.getPDBFile(SequenceFetcher.java:419) at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:258) at java.lang.Thread.run(Unknown Source) DEBUG - MessageContext: setServiceHandler(null) DEBUG - org.apache.axis.i18n.resource::handleGetObject(targetService) DEBUG - Target service: urn:Dbfetch DEBUG - MessageContext: setTargetService(null) DEBUG - MessageContext: setServiceHandler(null) DEBUG - Enter: SOAPPart::getAsSOAPEnvelope() DEBUG - org.apache.axis.i18n.resource::handleGetObject(currForm) DEBUG - current form is FORM_SOAPENVELOPE DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00) DEBUG - register 'soapenv' - 'http://schemas.xmlsoap.org/soap/envelope/' DEBUG - NSPush (32) DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00) DEBUG - register 'soapenv' - 'http://schemas.xmlsoap.org/soap/envelope/' DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00) DEBUG - register 'xsd' - 'http://www.w3.org/2001/XMLSchema' DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00) DEBUG - register 'xsi' - 'http://www.w3.org/2001/XMLSchema-instance' DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(startElem00) DEBUG - Start element [http://schemas.xmlsoap.org/soap/envelope/]:Envelope DEBUG - org.apache.axis.i18n.resource::handleGetObject(startElem00) DEBUG - Start element [http://schemas.xmlsoap.org/soap/envelope/]:Body DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(startElem00) DEBUG - Start element [urn:Dbfetch]:fetchBatch DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00) DEBUG - register 'ns1' - 'urn:Dbfetch' DEBUG - NSPush (32) DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(startElem00) DEBUG - Start element []:ids DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(endElem00) DEBUG - End element ids DEBUG - NSPop (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(startElem00) DEBUG - Start element []:db DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(endElem00) DEBUG - End element db DEBUG - NSPop (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(startElem00) DEBUG - Start element []:format DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(endElem00) DEBUG - End element format DEBUG - NSPop (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(startElem00) DEBUG - Start element []:style DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(endElem00) DEBUG - End element style DEBUG - NSPop (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(endElem00) DEBUG - End element ns1:fetchBatch DEBUG - NSPop (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(endElem00) DEBUG - End element soapenv:Body DEBUG - NSPop (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(endElem00) DEBUG - End element soapenv:Envelope DEBUG - org.apache.axis.i18n.resource::handleGetObject(empty00) DEBUG - NSPop (empty) DEBUG - <soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><soapenv:Body><ns1:fetchBatch soapenv:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/" xmlns:ns1="urn:Dbfetch"><ids xsi:type="xsd:string">1u04</ids><db xsi:type="xsd:string">pdb</db><format xsi:type="xsd:string">pdb</format><style xsi:type="xsd:string">raw</style></ns1:fetchBatch></soapenv:Body></soapenv:Envelope> DEBUG - Enter: AxisClient::invoke DEBUG - EngineHandler: null DEBUG - Enter: SimpleChain::invoke DEBUG - org.apache.axis.i18n.resource::handleGetObject(enter00) DEBUG - Enter: HTTPSender::invoke DEBUG - Enter: SOAPPart::saveChanges DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00) DEBUG - register 'soapenv' - 'http://schemas.xmlsoap.org/soap/envelope/' DEBUG - NSPush (32) DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00) DEBUG - register 'soapenv' - 'http://schemas.xmlsoap.org/soap/envelope/' DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00) DEBUG - register 'xsd' - 'http://www.w3.org/2001/XMLSchema' DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00) DEBUG - register 'xsi' - 'http://www.w3.org/2001/XMLSchema-instance' DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(startElem00) DEBUG - Start element [http://schemas.xmlsoap.org/soap/envelope/]:Envelope DEBUG - org.apache.axis.i18n.resource::handleGetObject(startElem00) DEBUG - Start element [http://schemas.xmlsoap.org/soap/envelope/]:Body DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(startElem00) DEBUG - Start element [urn:Dbfetch]:fetchBatch DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00) DEBUG - register 'ns1' - 'urn:Dbfetch' DEBUG - NSPush (32) DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(startElem00) DEBUG - Start element []:ids DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(endElem00) DEBUG - End element ids DEBUG - NSPop (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(startElem00) DEBUG - Start element []:db DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(endElem00) DEBUG - End element db DEBUG - NSPop (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(startElem00) DEBUG - Start element []:format DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(endElem00) DEBUG - End element format DEBUG - NSPop (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(startElem00) DEBUG - Start element []:style DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(endElem00) DEBUG - End element style DEBUG - NSPop (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(endElem00) DEBUG - End element ns1:fetchBatch DEBUG - NSPop (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(endElem00) DEBUG - End element soapenv:Body DEBUG - NSPop (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(endElem00) DEBUG - End element soapenv:Envelope DEBUG - org.apache.axis.i18n.resource::handleGetObject(empty00) DEBUG - NSPop (empty) DEBUG - org.apache.axis.i18n.resource::handleGetObject(setMsgForm) DEBUG - Setting current message form to: FORM_OPTIMIZED (currentMessage is now org.apache.axis.utils.ByteArray) DEBUG - Exit: SOAPPart::saveChanges(): org.apache.axis.utils.ByteArray@57e787 DEBUG - org.apache.axis.i18n.resource::handleGetObject(axisUserAgent) DEBUG - Enter: SOAPPart::saveChanges DEBUG - Enter: SOAPPart::saveChanges DEBUG - org.apache.axis.i18n.resource::handleGetObject(createdHTTP00) DEBUG - Created an insecure HTTP connection DEBUG - org.apache.axis.i18n.resource::handleGetObject(xmlSent00) DEBUG - XML sent: DEBUG - --------------------------------------------------- DEBUG - Enter: SOAPPart::saveChanges DEBUG - POST /ws/services/Dbfetch HTTP/1.0 Content-Type: text/xml; charset=utf-8 Accept: application/soap+xml, application/dime, multipart/related, text/* User-Agent: Axis/1.2RC2 Host: www.ebi.ac.uk Cache-Control: no-cache Pragma: no-cache SOAPAction: "" Content-Length: 499 <soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><soapenv:Body><ns1:fetchBatch soapenv:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/" xmlns:ns1="urn:Dbfetch"><ids xsi:type="xsd:string">1u04</ids><db xsi:type="xsd:string">pdb</db><format xsi:type="xsd:string">pdb</format><style xsi:type="xsd:string">raw</style></ns1:fetchBatch></soapenv:Body></soapenv:Envelope> DEBUG - HTTP/1.1 200 OK DEBUG - Server Apache-Coyote/1.1 DEBUG - Date Wed, 11 Apr 2007 15:25:04 GMT DEBUG - Connection close DEBUG - Enter: SOAPPart ctor(FORM_INPUTSTREAM) DEBUG - org.apache.axis.i18n.resource::handleGetObject(setMsgForm) DEBUG - Setting current message form to: FORM_INPUTSTREAM (currentMessage is now org.apache.axis.transport.http.SocketInputStream) DEBUG - Exit: SOAPPart ctor() DEBUG - org.apache.axis.i18n.resource::handleGetObject(no00) DEBUG - no Content-Length DEBUG - org.apache.axis.i18n.resource::handleGetObject(xmlRecd00) DEBUG - XML received: DEBUG - ----------------------------------------------- DEBUG - Enter: SOAPPart::getAsSOAPEnvelope() DEBUG - org.apache.axis.i18n.resource::handleGetObject(currForm) DEBUG - current form is FORM_INPUTSTREAM DEBUG - org.apache.axis.i18n.resource::handleGetObject(pushHandler00) DEBUG - Pushing handler org.apache.axis.message.EnvelopeHandler@5aebd9 DEBUG - org.xml.sax.SAXParseException: Premature end of file. DEBUG - Enter: SOAPPart ctor(FORM_FAULT) DEBUG - org.apache.axis.i18n.resource::handleGetObject(setMsgForm) DEBUG - Setting current message form to: FORM_FAULT (currentMessage is now org.apache.axis.AxisFault) DEBUG - Exit: SOAPPart ctor() DEBUG - org.apache.axis.i18n.resource::handleGetObject(exception00) DEBUG - Exception: DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(empty00) DEBUG - NSPop (empty) DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(empty00) DEBUG - NSPop (empty) AxisFault faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException faultSubcode: faultString: org.xml.sax.SAXParseException: Premature end of file. faultActor: faultNode: faultDetail: {http://xml.apache.org/axis/}stackTrace:org.xml.sax.SAXParseException: Premature end of file. at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown 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.XMLVersionDetector.determineDocVersion(Unknown 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 javax.xml.parsers.SAXParser.parse(Unknown Source) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:226) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:645) at org.apache.axis.Message.getSOAPEnvelope(Message.java:424) at org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:721) at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:94) at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32) at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:147) at org.apache.axis.client.Call.invokeEngine(Call.java:2719) at org.apache.axis.client.Call.invoke(Call.java:2702) at org.apache.axis.client.Call.invoke(Call.java:2378) at org.apache.axis.client.Call.invoke(Call.java:2301) at org.apache.axis.client.Call.invoke(Call.java:1758) at jalview.io.EBIFetchClient.fetchBatch(EBIFetchClient.java:211) at jalview.io.EBIFetchClient.fetchData(EBIFetchClient.java:183) at jalview.io.EBIFetchClient.fetchDataAsFile(EBIFetchClient.java:124) at jalview.gui.SequenceFetcher.getPDBFile(SequenceFetcher.java:419) at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:258) at java.lang.Thread.run(Unknown Source) {http://xml.apache.org/axis/}hostname:tick2 org.xml.sax.SAXParseException: Premature end of file. at org.apache.axis.AxisFault.makeFault(AxisFault.java:101) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:650) at org.apache.axis.Message.getSOAPEnvelope(Message.java:424) at org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:721) at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:94) at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32) at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:147) at org.apache.axis.client.Call.invokeEngine(Call.java:2719) at org.apache.axis.client.Call.invoke(Call.java:2702) at org.apache.axis.client.Call.invoke(Call.java:2378) at org.apache.axis.client.Call.invoke(Call.java:2301) at org.apache.axis.client.Call.invoke(Call.java:1758) at jalview.io.EBIFetchClient.fetchBatch(EBIFetchClient.java:211) at jalview.io.EBIFetchClient.fetchData(EBIFetchClient.java:183) at jalview.io.EBIFetchClient.fetchDataAsFile(EBIFetchClient.java:124) at jalview.gui.SequenceFetcher.getPDBFile(SequenceFetcher.java:419) at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:258) at java.lang.Thread.run(Unknown Source) Caused by: org.xml.sax.SAXParseException: Premature end of file. at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown 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.XMLVersionDetector.determineDocVersion(Unknown 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 javax.xml.parsers.SAXParser.parse(Unknown Source) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:226) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:645) ... 18 more DEBUG - org.apache.axis.i18n.resource::handleGetObject(toAxisFault00) DEBUG - Mapping Exception to AxisFault DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(empty00) DEBUG - NSPop (empty) DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(empty00) DEBUG - NSPop (empty) AxisFault faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException faultSubcode: faultString: org.xml.sax.SAXParseException: Premature end of file. faultActor: faultNode: faultDetail: {http://xml.apache.org/axis/}stackTrace:org.xml.sax.SAXParseException: Premature end of file. at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown 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.XMLVersionDetector.determineDocVersion(Unknown 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 javax.xml.parsers.SAXParser.parse(Unknown Source) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:226) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:645) at org.apache.axis.Message.getSOAPEnvelope(Message.java:424) at org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:721) at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:94) at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32) at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:147) at org.apache.axis.client.Call.invokeEngine(Call.java:2719) at org.apache.axis.client.Call.invoke(Call.java:2702) at org.apache.axis.client.Call.invoke(Call.java:2378) at org.apache.axis.client.Call.invoke(Call.java:2301) at org.apache.axis.client.Call.invoke(Call.java:1758) at jalview.io.EBIFetchClient.fetchBatch(EBIFetchClient.java:211) at jalview.io.EBIFetchClient.fetchData(EBIFetchClient.java:183) at jalview.io.EBIFetchClient.fetchDataAsFile(EBIFetchClient.java:124) at jalview.gui.SequenceFetcher.getPDBFile(SequenceFetcher.java:419) at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:258) at java.lang.Thread.run(Unknown Source) {http://xml.apache.org/axis/}hostname:tick2 org.xml.sax.SAXParseException: Premature end of file. at org.apache.axis.AxisFault.makeFault(AxisFault.java:101) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:650) at org.apache.axis.Message.getSOAPEnvelope(Message.java:424) at org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:721) at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:94) at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32) at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:147) at org.apache.axis.client.Call.invokeEngine(Call.java:2719) at org.apache.axis.client.Call.invoke(Call.java:2702) at org.apache.axis.client.Call.invoke(Call.java:2378) at org.apache.axis.client.Call.invoke(Call.java:2301) at org.apache.axis.client.Call.invoke(Call.java:1758) at jalview.io.EBIFetchClient.fetchBatch(EBIFetchClient.java:211) at jalview.io.EBIFetchClient.fetchData(EBIFetchClient.java:183) at jalview.io.EBIFetchClient.fetchDataAsFile(EBIFetchClient.java:124) at jalview.gui.SequenceFetcher.getPDBFile(SequenceFetcher.java:419) at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:258) at java.lang.Thread.run(Unknown Source) Caused by: org.xml.sax.SAXParseException: Premature end of file. at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown 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.XMLVersionDetector.determineDocVersion(Unknown 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 javax.xml.parsers.SAXParser.parse(Unknown Source) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:226) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:645) ... 18 more Unexpected exception when retrieving from pdb Query was : '1U04' DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(empty00) DEBUG - NSPop (empty) DEBUG - NSPush (32) DEBUG - org.apache.axis.i18n.resource::handleGetObject(empty00) DEBUG - NSPop (empty) AxisFault faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException faultSubcode: faultString: org.xml.sax.SAXParseException: Premature end of file. faultActor: faultNode: faultDetail: {http://xml.apache.org/axis/}stackTrace:org.xml.sax.SAXParseException: Premature end of file. at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown 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.XMLVersionDetector.determineDocVersion(Unknown 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 javax.xml.parsers.SAXParser.parse(Unknown Source) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:226) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:645) at org.apache.axis.Message.getSOAPEnvelope(Message.java:424) at org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:721) at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:94) at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32) at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:147) at org.apache.axis.client.Call.invokeEngine(Call.java:2719) at org.apache.axis.client.Call.invoke(Call.java:2702) at org.apache.axis.client.Call.invoke(Call.java:2378) at org.apache.axis.client.Call.invoke(Call.java:2301) at org.apache.axis.client.Call.invoke(Call.java:1758) at jalview.io.EBIFetchClient.fetchBatch(EBIFetchClient.java:211) at jalview.io.EBIFetchClient.fetchData(EBIFetchClient.java:183) at jalview.io.EBIFetchClient.fetchDataAsFile(EBIFetchClient.java:124) at jalview.gui.SequenceFetcher.getPDBFile(SequenceFetcher.java:419) at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:258) at java.lang.Thread.run(Unknown Source) {http://xml.apache.org/axis/}hostname:tick2 org.xml.sax.SAXParseException: Premature end of file. at org.apache.axis.AxisFault.makeFault(AxisFault.java:101) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:650) at org.apache.axis.Message.getSOAPEnvelope(Message.java:424) at org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:721) at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:94) at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32) at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:147) at org.apache.axis.client.Call.invokeEngine(Call.java:2719) at org.apache.axis.client.Call.invoke(Call.java:2702) at org.apache.axis.client.Call.invoke(Call.java:2378) at org.apache.axis.client.Call.invoke(Call.java:2301) at org.apache.axis.client.Call.invoke(Call.java:1758) at jalview.io.EBIFetchClient.fetchBatch(EBIFetchClient.java:211) at jalview.io.EBIFetchClient.fetchData(EBIFetchClient.java:183) at jalview.io.EBIFetchClient.fetchDataAsFile(EBIFetchClient.java:124) at jalview.gui.SequenceFetcher.getPDBFile(SequenceFetcher.java:419) at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:258) at java.lang.Thread.run(Unknown Source) Caused by: org.xml.sax.SAXParseException: Premature end of file. at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown 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.XMLVersionDetector.determineDocVersion(Unknown 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 javax.xml.parsers.SAXParser.parse(Unknown Source) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:226) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:645) ... 18 more WARN - Exception when retrieving 1u04 from PDB java.lang.Exception: WsDBFetch for PDB id resulted in zero result size at jalview.gui.SequenceFetcher.getPDBFile(SequenceFetcher.java:466) at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:258) at java.lang.Thread.run(Unknown Source)
    via by Jim Procter,
    • org.xml.sax.SAXParseException: Premature end of file. at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown 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.XMLVersionDetector.determineDocVersion(Unknown 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 javax.xml.parsers.SAXParser.parse(SAXParser.java:375) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:227) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696) at org.apache.axis.Message.getSOAPEnvelope(Message.java:424) at org.apache.axis.server.AxisServer.initSOAPConstants(AxisServer.java:345) at org.apache.axis.server.AxisServer.invoke(AxisServer.java:279) at org.apache.axis.transport.http.AxisServlet.doPost(AxisServlet.java:699) at coldfusion.xml.rpc.CFCServlet.doAxisPost(CFCServlet.java:270) at coldfusion.filter.AxisFilter.invoke(AxisFilter.java:43) at coldfusion.filter.ApplicationFilter.invoke(ApplicationFilter.java:273) at coldfusion.filter.RequestMonitorFilter.invoke(RequestMonitorFilter.java:48) at coldfusion.filter.MonitoringFilter.invoke(MonitoringFilter.java:40) at coldfusion.filter.PathFilter.invoke(PathFilter.java:86) at coldfusion.filter.LicenseFilter.invoke(LicenseFilter.java:27) at coldfusion.filter.ExceptionFilter.invoke(ExceptionFilter.java:70) at coldfusion.filter.ClientScopePersistenceFilter.invoke(ClientScopePersistenceFilter.java:28) at coldfusion.filter.GlobalsFilter.invoke(GlobalsFilter.java:38) at coldfusion.filter.DatasourceFilter.invoke(DatasourceFilter.java:22) at coldfusion.xml.rpc.CFCServlet.invoke(CFCServlet.java:138) at coldfusion.xml.rpc.CFCServlet.doPost(CFCServlet.java:289) at javax.servlet.http.HttpServlet.service(HttpServlet.java:760) at org.apache.axis.transport.http.AxisServletBase.service(AxisServletBase.java:327) at javax.servlet.http.HttpServlet.service(HttpServlet.java:853) at coldfusion.bootstrap.BootstrapServlet.service(BootstrapServlet.java:89) at jrun.servlet.FilterChain.doFilter(FilterChain.java:86) at coldfusion.monitor.event.MonitoringServletFilter.doFilter(MonitoringServletFilter.java:42) at coldfusion.bootstrap.BootstrapFilter.doFilter(BootstrapFilter.java:46) at jrun.servlet.FilterChain.doFilter(FilterChain.java:94) at jrun.servlet.FilterChain.service(FilterChain.java:101) at jrun.servlet.ServletInvoker.invoke(ServletInvoker.java:106) at jrun.servlet.JRunInvokerChain.invokeNext(JRunInvokerChain.java:42) at jrun.servlet.JRunRequestDispatcher.invoke(JRunRequestDispatcher.java:286) at jrun.servlet.ServletEngineService.dispatch(ServletEngineService.java:543) at jrun.servlet.jrpp.JRunProxyService.invokeRunnable(JRunProxyService.java:203) at jrunx.scheduler.ThreadPool$DownstreamMetrics.invokeRunnable(ThreadPool.java:320) at jrunx.scheduler.ThreadPool$ThreadThrottle.invokeRunnable(ThreadPool.java:428) at jrunx.scheduler.ThreadPool$UpstreamMetrics.invokeRunnable(ThreadPool.java:266) at jrunx.scheduler.WorkerThread.run(WorkerThread.java:66)

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