Develop Reference

Can't retrieve data back from UMLS

I have been trying to run the ctakes-temporal-demo on github.
Currently I have configured everything in eclipse correctly. I have set the correct password and id for UMLS account. When I try to run it I get the following error:
Exception in thread "main" java.lang.Exception: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: <unknown>)
at com.optum.cda.Main.main(Main.java:103)
Caused by: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: <unknown>)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711)
at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207)
at com.optum.cda.Main.main(Main.java:101)
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Could not construct org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:131)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 12 more
Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Could not construct org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:199)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128)
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129)
... 13 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:196)
... 16 more
Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: -7
at java.lang.String.substring(Unknown Source)
at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:110)
at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:63)
at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91)
at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72)
at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
... 21 more
Can someone familiar with ctakes help me find out the error. I have tried the mailing list, but no replies.

Finally found a solution ! It seems like the path to the XML descriptor of the dictionary-fast is not reachable. Thus after validating an UMLS user the database setup could not be proceeded.
One of the solution I used was to use a static address for the database (which I will have to change always if the project is moved.). This is not very elegant but works.
Love to hear if anyone has another solution.

Have you put the data of ctakesnorx.script into the database?
Also we do need to update the following attribute values :
<property key="jdbcUrl" value="jdbc:hsqldb:file:org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx"/>
<property key="jdbcUser" value="sa"/>
<property key="jdbcPass" value=""/>
<property key="rareWordTable" value="cui_terms"/>

BeanManager method getReference() is not available during application initialization

I am trying to deploy a war file into Wildfly 10.0.0.Final, the deployment fails with the following error :
"{\"WFLYCTL0080: Failed services\" => {\"jboss.deployment.unit.\\\"management-app.war\\\".WeldStartService\" => \"org.jboss.msc.service.StartException in service jboss.deployment.unit.\\\"management-app.war\\\".WeldStartService: Failed to start service
Caused by: org.jboss.weld.exceptions.DefinitionException: Exception List with 1 exceptions:
Exception 0 :
org.jboss.weld.exceptions.IllegalStateException: WELD-001332: BeanManager method getReference() is not available during application initialization
at org.jboss.weld.bean.builtin.BeanManagerProxy.checkContainerState(BeanManagerProxy.java:242)
at org.jboss.weld.bean.builtin.BeanManagerProxy.getReference(BeanManagerProxy.java:84)
at morpho.mcp.adapter.cdi.AdapterExtension.getAdapterDefinition(AdapterExtension.java:159)
at morpho.mcp.adapter.cdi.AdapterExtension.afterBeanDiscovery(AdapterExtension.java:109)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.jboss.weld.injection.StaticMethodInjectionPoint.invoke(StaticMethodInjectionPoint.java:88)
at org.jboss.weld.injection.MethodInvocationStrategy$SpecialParamPlusBeanManagerStrategy.invoke(MethodInvocationStrategy.java:144)
at org.jboss.weld.event.ObserverMethodImpl.sendEvent(ObserverMethodImpl.java:309)
at org.jboss.weld.event.ExtensionObserverMethodImpl.sendEvent(ExtensionObserverMethodImpl.java:124)
at org.jboss.weld.event.ObserverMethodImpl.sendEvent(ObserverMethodImpl.java:287)
at org.jboss.weld.event.ObserverMethodImpl.notify(ObserverMethodImpl.java:265)
at org.jboss.weld.event.ObserverNotifier.notifySyncObservers(ObserverNotifier.java:271)
at org.jboss.weld.event.ObserverNotifier.notify(ObserverNotifier.java:260)
at org.jboss.weld.event.ObserverNotifier.fireEvent(ObserverNotifier.java:154)
at org.jboss.weld.event.ObserverNotifier.fireEvent(ObserverNotifier.java:148)
at org.jboss.weld.bootstrap.events.AbstractContainerEvent.fire(AbstractContainerEvent.java:53)
at org.jboss.weld.bootstrap.events.AbstractDefinitionContainerEvent.fire(AbstractDefinitionContainerEvent.java:42)
at org.jboss.weld.bootstrap.events.AfterBeanDiscoveryImpl.fire(AfterBeanDiscoveryImpl.java:61)
at org.jboss.weld.bootstrap.WeldStartup.deployBeans(WeldStartup.java:423)
at org.jboss.weld.bootstrap.WeldBootstrap.deployBeans(WeldBootstrap.java:83)
at org.jboss.as.weld.WeldStartService.start(WeldStartService.java:95)
at org.jboss.msc.service.ServiceControllerImpl$StartTask.startService(ServiceControllerImpl.java:1948)
at org.jboss.msc.service.ServiceControllerImpl$StartTask.run(ServiceControllerImpl.java:1881)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
\"}}"
Assuming that the war was working fine for JBoss AS7. What could be the possible root cause for such behavior ?
It seems that a WAR which is not a bean archive is missing the org.jboss.as.weld.WeldStartService dependency. But how can this issue be resolved ?

But how can this issue be resolved ?
Do not use BeanManager.getReference before AfterDeploymentValidation. Refactor your code accordingly. The reason is - getReference might give you incomplete results. At that point, the bootstrap is not yet done and getReference method might fail to retrieve a reference as there might not be one at a given time (although it would be there later on).
As for how to workaround this:
Use Weld non-portable mode although that might have more undesirable effects. You should firstly try to refactor the code before falling back to this configuration.

WebSphere onMessage error : Exception data: java.lang.reflect.InvocationTargetException

Here's my problem :
We have a banking Websphere application (version 7.0.0.27 ) on an AIX multi-instance server. On this application, we have received 51 MQ messages in 1 min to process but for 5 of them, we have the following errors :
[9/23/15 9:18:36:301 CEST] 00000065 LocalExceptio E CNTR0020E: EJB threw an unexpected (non-declared) exception during invocation of method "onMessage" on bean "BeanId(TrefleIntermediationEAR#TrefleEJB-3.4.3.4.jar#OPFRestitutionReception, null)". Exception data: java.lang.reflect.InvocationTargetException
at sun.reflect.GeneratedMethodAccessor521.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
at java.lang.reflect.Method.invoke(Method.java:611)
at com.ibm.ejs.jms.listener.ServerSessionDispatcher.dispatch(ServerSessionDispatcher.java:47)
at com.ibm.ejs.container.MDBWrapper.onMessage(MDBWrapper.java:98)
at com.ibm.ejs.container.MDBWrapper.onMessage(MDBWrapper.java:136)
at com.ibm.ejs.jms.listener.ServerSession.run(ServerSession.java:574)
at com.ibm.ws.util.ThreadPool$Worker.run(ThreadPool.java:1646)
Caused by: java.lang.RuntimeException: JMSCC0109: A message driven bean threw a runtime exception 'java.lang.ExceptionInInitializerError'.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:56)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:39)
at java.lang.reflect.Constructor.newInstance(Constructor.java:527)
at com.ibm.msg.client.commonservices.j2se.NLSServices.createException(NLSServices.java:313)
at com.ibm.msg.client.commonservices.nls.NLSServices.createException(NLSServices.java:388)
at com.ibm.msg.client.jms.internal.JmsErrorUtils.createException(JmsErrorUtils.java:104)
at com.ibm.msg.client.jms.internal.JmsSessionImpl.run(JmsSessionImpl.java:3018)
at com.ibm.msg.client.jms.internal.JmsXAQueueSessionImpl$1.run(JmsXAQueueSessionImpl.java:395)
at com.ibm.mq.jms.MQSession.run(MQSession.java:862)
at com.ibm.ejs.jms.JMSSessionHandle.run(JMSSessionHandle.java:1055)
at com.ibm.ejs.jms.listener.ServerSession.connectionConsumerOnMessage(ServerSession.java:1082)
at com.ibm.ejs.jms.listener.ServerSession.onMessage(ServerSession.java:752)
at com.ibm.ejs.jms.listener.ServerSession.dispatch(ServerSession.java:718)
... 8 more
Caused by: java.lang.ExceptionInInitializerError
at java.lang.J9VMInternals.initialize(J9VMInternals.java:222)
at fr.bdf.trefle.trf.launcher.AbstractLauncher.retrieveOverridingStandaloneConnectionData(AbstractLauncher.java:117)
at fr.bdf.trefle.trf.launcher.AbstractLauncher.createFactory(AbstractLauncher.java:83)
at fr.bdf.trefle.trf.launcher.AbstractLauncher.<clinit>(AbstractLauncher.java:71)
at java.lang.J9VMInternals.initializeImpl(Native Method)
at java.lang.J9VMInternals.initialize(J9VMInternals.java:200)
at fr.bdf.trefle.trf.dao.FlowMonitorServiceImpl.insertFlowMonitor(FlowMonitorServiceImpl.java:465)
at fr.bdf.trefle.trf.dao.FlowMonitorServiceImpl.createFlowMonitor(FlowMonitorServiceImpl.java:176)
at fr.bdf.trefle.trf.mdb.OPFRestitutionReception.onMessage(OPFRestitutionReception.java:213)
at com.ibm.ejs.jms.listener.MDBWrapper$PriviledgedOnMessage.run(MDBWrapper.java:302)
at com.ibm.ws.security.util.AccessController.doPrivileged(AccessController.java:63)
at com.ibm.ejs.jms.listener.MDBWrapper.callOnMessage(MDBWrapper.java:271)
at com.ibm.ejs.jms.listener.MDBWrapper.onMessage(MDBWrapper.java:240)
at com.ibm.mq.jms.MQSession$FacadeMessageListener.onMessage(MQSession.java:147)
at com.ibm.msg.client.jms.internal.JmsSessionImpl.run(JmsSessionImpl.java:2846)
... 14 more
Caused by: java.util.MissingResourceException: Can't find resource for bundle configTechStandalone, key en_US
at java.util.ResourceBundle.getBundleImpl(ResourceBundle.java:379)
at java.util.ResourceBundle.getBundle(ResourceBundle.java:108)
at fr.bdf.trefle.common.util.StandaloneTechConfigurable.<clinit>(StandaloneTechConfigurable.java:31)
at java.lang.J9VMInternals.initializeImpl(Native Method)
at java.lang.J9VMInternals.initialize(J9VMInternals.java:200)
... 28 more
From my analysis, here's what I can conclude :
In the stack trace, the root error, mainly java.util.MissingResourceException, doesn't seem like the real cause because the resource the process is trying to get exists and for the other process, this works fine.
I tried to see if the method used to get the resource, getBundle(), has some performance issue but I didn't find anything.
I also tried to see if this was an already existing IBM bug but if it is the case, I can't find it.

Oracle BPEL fault selectionFailure

I have an Oracle SOA Composite that is generating a BPEL fault in Weblogic 11g. In EnterpriseManager I see the fault and the message:
<bpelFault>
<faultType>0</faultType>
<selectionFailure xmlns="http://schemas.xmlsoap.org/ws/2003/03/business-process/"></selectionFailure>
</bpelFault>
When I drill into the instance I see the following message listed on an assignement:
Error in evaluate expression at line "493". The result is empty for the XPath expression :
"/ns27:UsersCollection/ns27:Users/ns27:id"
I see the following error in the WLS-SOA1-diagnostic.log:
com.oracle.bpel.client.BPELFault: faultName: {{http://schemas.xmlsoap.org/ws/2003/03/business-process/}selectionFailure}
messageType: {{http://schemas.oracle.com/bpel/extension}RuntimeFaultMessage}
at com.collaxa.cube.engine.ext.bpel.common.BPELWMPHelper.evalFromValue(BPELWMPHelper.java:344)
at com.collaxa.cube.engine.ext.bpel.v1.wmp.BPEL1AssignWMP.__executeStatements(BPEL1AssignWMP.java:138)
at com.collaxa.cube.engine.ext.bpel.common.wmp.BaseBPELActivityWMP.perform(BaseBPELActivityWMP.java:166)
at com.collaxa.cube.engine.CubeEngine.performActivity(CubeEngine.java:2687)
at com.collaxa.cube.engine.CubeEngine._handleWorkItem(CubeEngine.java:1190)
at com.collaxa.cube.engine.CubeEngine.handleWorkItem(CubeEngine.java:1093)
at com.collaxa.cube.engine.dispatch.message.instance.PerformMessageHandler.handleLocal(PerformMessageHandler.java:78)
at com.collaxa.cube.engine.dispatch.DispatchHelper.handleLocalMessage(DispatchHelper.java:218)
at com.collaxa.cube.engine.dispatch.DispatchHelper.sendMemory(DispatchHelper.java:297)
at com.collaxa.cube.engine.CubeEngine.endRequest(CubeEngine.java:4609)
at com.collaxa.cube.engine.CubeEngine.endRequest(CubeEngine.java:4541)
at com.collaxa.cube.engine.CubeEngine._createAndInvoke(CubeEngine.java:713)
at com.collaxa.cube.engine.CubeEngine.createAndInvoke(CubeEngine.java:560)
at com.collaxa.cube.engine.ejb.impl.CubeEngineBean.createAndInvoke(CubeEngineBean.java:103)
at com.collaxa.cube.engine.ejb.impl.CubeEngineBean.syncCreateAndInvoke(CubeEngineBean.java:145)
at com.collaxa.cube.engine.ejb.impl.bpel.BPELEngineBean.syncCreateAndInvoke(BPELEngineBean.java:112)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
Has anyone run into this issue before? It seems strange as we only occasionally see this fault and error.

I made a change to the assignment in question here to "ignoreMissingFromData" and deployed it a few weeks ago and it seems to have worked fine ever since.
Thanks,
Tom

com.google.gdata.util.PreconditionFailedException on ListEntry.update() in Google Docs Java API

I have an application which manipulates the rows of a google spreadsheet. Occasionally, when I call ListEntry.update(), I receive the following stack trace:
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: com.google.gdata.util.PreconditionFailedException: Precondition Failed
Mismatch: etags = ["E10QemAgYit7ImA-CEFaShYM"], version = [2ag9hk74om621l]
at com.google.gdata.client.http.HttpGDataRequest.handleErrorResponse(HttpGDataRequest.java:614)
at com.google.gdata.client.http.GoogleGDataRequest.handleErrorResponse(GoogleGDataRequest.java:564)
at com.google.gdata.client.http.HttpGDataRequest.checkResponse(HttpGDataRequest.java:560)
at com.google.gdata.client.http.HttpGDataRequest.execute(HttpGDataRequest.java:538)
at com.google.gdata.client.http.GoogleGDataRequest.execute(GoogleGDataRequest.java:536)
at com.google.gdata.client.Service.update(Service.java:1563)
at com.google.gdata.client.Service.update(Service.java:1530)
at com.google.gdata.client.GoogleService.update(GoogleService.java:597)
at com.google.gdata.data.BaseEntry.update(BaseEntry.java:639)
at feedProcessor.ProcessClientFeed.UpdateRow(ProcessClientFeed.java:466)
at feedProcessor.ProcessClientFeed.updateGoogleSpreadsheet(ProcessClientFeed.java:404)
at feedProcessor.ProcessClientFeed.processFeed(ProcessClientFeed.java:318)
at feedProcessor.ProcessClientFeed.main(ProcessClientFeed.java:61)
... 5 more

Here is the relevant documentation:
https://developers.google.com/gdata/javadoc/com/google/gdata/data/spreadsheet/ListEntry
https://developers.google.com/gdata/javadoc/com/google/gdata/data/BaseEntry#update()
According to these docs, the update() function is not even capable of throwing a PreconditionFailedException, so the docs are essentially useless here. Testing the issue has shown that this exception is thrown when you try to call the update() function on the same row more than once in a session. Exactly what defines a 'session' is still unclear, but if you loop through all your rows more than once, and call update() on each row in each iteration, you will get this error. The only resolution I am aware of is to write your software such that each row (ListEntry) has update() called only once.

The problem is caused by Google Spreadsheet API Resource Versioning mecanism.
To be able to edit the entry no matter what - just use:
entry.setEtag("*")
before update.
And yes, this is not multi-user friendly. Refetch the feed if you need multi-user support.