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Created June 14, 2014 08:52
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Execution engine fail
ID: 218
Address: http://api.biodtlab.com/execution-engine-ws/rest/workflow/start
Encoding: ISO-8859-1
Http-Method: POST
Content-Type: application/xml
Headers: {Accept=[*/*; q=0.5, application/xml], accept-encoding=[gzip, deflate], connection=[close], Content-Length=[455], content-type=[application/xml], host=[api.biodtlab.com], user-agent=[Ruby], x-biodt-authtoken=[c7c20a0c-f281-45f9-9812-5e6889c379d7], x-forwarded-for=[192.168.0.169], x-forwarded-proto=[https], x-real-ip=[192.168.0.169]}
Payload: <?xml version="1.0"?>
<LaunchWorkflowRequest>
<user>doina</user>
<inputs>
<param name="ref" value="/org/Demo/human_20_dataset/human_b37_20.fasta"/>
</inputs>
<outputs>
<param name="fai" value="/user/doina/test.fai"/>
<param name="index" value="/user/doina/test/index_bwa"/>
<param name="dict" value="/user/doina/test.dict"/>
</outputs>
<workflow-exchange workflow-id="yayat" workflow-version="0.0.1"/>
</LaunchWorkflowRequest>
--------------------------------------
67794299 [http-8080-68] INFO com.biodatomics.executionengine.rest.WorkflowEndpoint.quickLaunch - ##### <LaunchWorkflowRequest>
<user>doina</user>
<inputs>
<param name="ref" value="/org/Demo/human_20_dataset/human_b37_20.fasta"/>
</inputs>
<outputs>
<param name="fai" value="/user/doina/test.fai"/>
<param name="index" value="/user/doina/test/index_bwa"/>
<param name="dict" value="/user/doina/test.dict"/>
</outputs>
<workflow-exchange workflow-id="yayat" workflow-version="0.0.1">
<outputs/>
</workflow-exchange>
</LaunchWorkflowRequest>
67794329 [http-8080-68] INFO com.biodatomics.executionengine.service.WorkflowService.findRemoteWorkflow - Search: yayat + 0.0.1
67794340 [http-8080-68] INFO com.biodatomics.executionengine.service.WorkflowService.findRemoteWorkflow - Found workflow version: com.biodatomics.metastore.api.WorkflowVersion@391cbb47
67794346 [http-8080-68] INFO org.apache.cxf.interceptor.LoggingOutInterceptor.log - Outbound Message
---------------------------
ID: 218
Response-Code: 200
Content-Type: application/json
Headers: {Date=[Sat, 14 Jun 2014 08:48:08 GMT]}
Payload: {"id":0,"status":null,"alias":null,"exceptionClassName":"com.thoughtworks.xstream.converters.ConversionException","exceptionMessage":"Zero length string : Zero length string\n---- Debugging information ----\nmessage : Zero length string\ncause-exception : java.lang.NumberFormatException\ncause-message : Zero length string\nclass : java.lang.Integer\nrequired-type : java.lang.Integer\nconverter-type : com.thoughtworks.xstream.converters.SingleValueConverterWrapper\nwrapped-converter : com.thoughtworks.xstream.converters.basic.IntConverter\npath : /workflow-exchange/workflow/nodes/tool/containers-number\nline number : 15\nclass[1] : com.biodatomics.executionengine.model.external.processing.GalaxyProcessingNode\nconverter-type[1] : com.thoughtworks.xstream.converters.reflection.ReflectionConverter\nclass[2] : java.util.ArrayList\nconverter-type[2] : com.thoughtworks.xstream.converters.collections.CollectionConverter\nclass[3] : com.biodatomics.executionengine.model.external.Workflow\nclass[4] : com.biodatomics.executionengine.model.external.WorkflowExchange\nversion : null\n-------------------------------","exceptionStackTrace":["com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:79)","com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)","com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)","com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshallField(AbstractReflectionConverter.java:355)","com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.doUnmarshal(AbstractReflectionConverter.java:306)","com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:234)","com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)","com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)","com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)","com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:50)","com.thoughtworks.xstream.converters.collections.AbstractCollectionConverter.readItem(AbstractCollectionConverter.java:71)","com.thoughtworks.xstream.converters.collections.CollectionConverter.addCurrentElementToCollection(CollectionConverter.java:79)","com.thoughtworks.xstream.converters.collections.CollectionConverter.populateCollection(CollectionConverter.java:72)","com.thoughtworks.xstream.converters.collections.CollectionConverter.populateCollection(CollectionConverter.java:66)","com.thoughtworks.xstream.converters.collections.CollectionConverter.unmarshal(CollectionConverter.java:61)","com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)","com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)","com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)","com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshallField(AbstractReflectionConverter.java:355)","com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.doUnmarshal(AbstractReflectionConverter.java:306)","com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:234)","com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)","com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)","com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)","com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:50)","com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.doUnmarshal(AbstractReflectionConverter.java:322)","com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:234)","com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)","com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)","com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)","com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:50)","com.thoughtworks.xstream.core.TreeUnmarshaller.start(TreeUnmarshaller.java:134)","com.thoughtworks.xstream.core.AbstractTreeMarshallingStrategy.unmarshal(AbstractTreeMarshallingStrategy.java:32)","com.thoughtworks.xstream.XStream.unmarshal(XStream.java:1058)","com.thoughtworks.xstream.XStream.unmarshal(XStream.java:1042)","com.thoughtworks.xstream.XStream.fromXML(XStream.java:913)","com.biodatomics.executionengine.service.imprt.impl.ImportServiceImpl.processWorkflowImport(ImportServiceImpl.java:265)","com.biodatomics.executionengine.service.WorkflowService.findRemoteWorkflow(WorkflowService.java:446)","com.biodatomics.executionengine.rest.WorkflowEndpoint.quickLaunch(WorkflowEndpoint.java:105)","sun.reflect.GeneratedMethodAccessor662.invoke(Unknown Source)","sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)","java.lang.reflect.Method.invoke(Method.java:622)","org.apache.cxf.service.invoker.AbstractInvoker.performInvocation(AbstractInvoker.java:180)","org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:96)","org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:165)","org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:89)","org.apache.cxf.interceptor.ServiceInvokerInterceptor$1.run(ServiceInvokerInterceptor.java:57)","org.apache.cxf.interceptor.ServiceInvokerInterceptor.handleMessage(ServiceInvokerInterceptor.java:93)","org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:263)","org.apache.cxf.transport.ChainInitiationObserver.onMessage(ChainInitiationObserver.java:121)","org.apache.cxf.transport.http.AbstractHTTPDestination.invoke(AbstractHTTPDestination.java:237)","org.apache.cxf.transport.servlet.ServletController.invokeDestination(ServletController.java:239)","org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:213)","org.apache.cxf.transport.servlet.CXFNonSpringServlet.invoke(CXFNonSpringServlet.java:131)","org.apache.cxf.transport.servlet.AbstractHTTPServlet.handleRequest(AbstractHTTPServlet.java:266)","org.apache.cxf.transport.servlet.AbstractHTTPServlet.doPost(AbstractHTTPServlet.java:186)","javax.servlet.http.HttpServlet.service(HttpServlet.java:637)","org.apache.cxf.transport.servlet.AbstractHTTPServlet.service(AbstractHTTPServlet.java:242)","org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)","org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)","org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)","org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)","org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)","org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)","org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)","org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)","org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)","org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)","org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)","org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)","com.biodatomics.security.BiodtRequestAuthenticationFilter.doFilter(BiodtRequestAuthenticationFilter.java:67)","org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)","org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)","org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)","org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)","org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)","org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:346)","org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:259)","org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)","org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)","org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:99)","org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)","org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)","org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)","org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)","org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)","org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)","org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)","org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)","org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)","org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:857)","org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)","org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)","java.lang.Thread.run(Thread.java:701)"]}
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