WsDBFetch client fails on jon Manning's vaio

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)