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  1. Jalview
  2. JAL-293

WsDBFetch client fails on jon Manning's vaio

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Minor
    • Resolution: Won't Fix
    • Affects Version/s: 2.2.1
    • Fix Version/s: None
    • Component/s: web service bug
    • Labels:
      None
    • Mantis ID:
      21218

      Description

      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/&#39;
      DEBUG - NSPush (32)
      DEBUG - NSPush (32)
      DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00)
      DEBUG - register 'soapenv' - 'http://schemas.xmlsoap.org/soap/envelope/&#39;
      DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00)
      DEBUG - register 'xsd' - 'http://www.w3.org/2001/XMLSchema&#39;
      DEBUG - NSPush (32)
      DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00)
      DEBUG - register 'xsi' - 'http://www.w3.org/2001/XMLSchema-instance&#39;
      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/&#39;
      DEBUG - NSPush (32)
      DEBUG - NSPush (32)
      DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00)
      DEBUG - register 'soapenv' - 'http://schemas.xmlsoap.org/soap/envelope/&#39;
      DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00)
      DEBUG - register 'xsd' - 'http://www.w3.org/2001/XMLSchema&#39;
      DEBUG - NSPush (32)
      DEBUG - org.apache.axis.i18n.resource::handleGetObject(register00)
      DEBUG - register 'xsi' - 'http://www.w3.org/2001/XMLSchema-instance&#39;
      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)


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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Created:
              Updated:
              Resolved: