Samir, you're a genius!!! I executed the AggregatePlaintextUMLSProcessor and watched the command window since the log files didn't provide any additional details....sure enough there was an 'out of memory' error that appeared. I did what you said about updating the memory min and max to 500m and 1500m (respectively) and reran AggregatePlaintextUMLSProcessor and it loaded!!! Thanks so much for your help, I really appreciate it man. Also, thanks to Stamatis, Murali and Pei for their responses. Now I can focus on learning how this tool works now that it's working. :-) Regards, Paula Fromsamir chabou <[email protected]>SubjectRe: Resource Initialization Exception with cTakes 3.1.0DateThu, 03 Oct 2013 16:33:31 GMTif it hangs may be you have a heap size problem. Does the console show any error ? When you double click on UIMA_CVD--clinical_documents_pipeline.launch can you check if -Xms and -Xmx set to these values -Xms500M -Xmx1500M" as shown bellow (the latest line). Also try the analysis engine in the ctakes-core project the AggregateAE.xml (more simple and does not cause problem of heap) <?xml version="1.0" encoding="UTF-8" standalone="no"?> <launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication"> <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS"> <listEntry value="/ctakes-clinical-pipeline"/> </listAttribute> <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES"> <listEntry value="4"/> </listAttribute> <booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/> <mapAttribute key="org.eclipse.debug.core.preferred_launchers"> <mapEntry key="[debug]" value="com.Instantiations.profiler.localJavaApplicationDelegate"/> </mapAttribute> <stringAttribute key="org.eclipse.debug.ui.target_debug_perspective" value="perspective_default"/> <stringAttribute key="org.eclipse.debug.ui.target_run_perspective" value="perspective_default"/> <stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/> <stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.annot_view.Gladis"/> <stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-clinical-pipeline"/> <stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/> <stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value=""-Djava.util.logging.config.file=${env_var:UIMA_HOME}/Logger.properties" -XX:+UseConcMarkSweepGC -Xms500M -Xmx1500M"/> </launchConfiguration>
------------- From: [email protected] To: [email protected] Subject: RE: Resource Initialization Exception with cTakes 3.1.0 Date: Wed, 2 Oct 2013 15:48:58 -0400 Hi Samir, Thanks for the prompt reply. Okay, I reinstalled cTakes 3.1.0 and did not do the full resource zip file copy, I just copied over the two directories: rxnorm_index and umls2011ab. I ran the AggregatePlaintextUMLSProcessor and it didn't load so I checked the log and nothing appeared so I changed the log setting to show all information and tried again. I got the following information in the log which states no errors unlike what got before (see original email below). However, I'm still back we I started with not being able to see this thing in action. In addition I also tried to use the simplified AggregatePlaintextProcessor and the application just hangs. I'm at a complete loss here. I really would love to work with cTakes and I'm hoping someone could help me out. ---below is information taken from log when running AggregatePlaintextUMLSProcessor.------ 10/2/13 3:37:11 PM - 14: org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [AggregateCdaUMLSProcessor] initialization begin 10/2/13 3:37:12 PM - 14: org.apache.uima.analysis_engine.asb.impl.ASB_impl.initialize: CONFIG: ASB initialization begin 10/2/13 3:37:12 PM - 14: org.apache.uima.analysis_engine.asb.impl.ASB_impl.initialize: CONFIG: ASB initialization successful 10/2/13 3:37:12 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [ClearNLPDependencyParserAE] initialization begin 10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [TokenizerAnnotatorPTB] initialization begin 10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [ContextDependentTokenizerAnnotator] initialization begin 10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [NegationAnnotator] initialization begin 10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [StatusAnnotator] initialization begin 10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [Sentence Detector annotator] initialization begin 10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [Adjust NP in NP NP to span both] initialization begin 10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [Adjust NP in NP PP NP to span all three] initialization begin 10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [POSTagger] initialization begin 10/2/13 3:37:22 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG: trying Resource class org.apache.uima.resource.impl.DataResource_impl 10/2/13 3:37:22 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [Chunker] initialization begin 10/2/13 3:37:23 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG: trying Resource class org.apache.uima.resource.impl.DataResource_impl 10/2/13 3:37:23 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG: trying Resource class org.apache.uima.resource.impl.ConfigurableDataResource_impl 10/2/13 3:37:23 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG: trying Resource class org.apache.uima.resource.impl.ConfigurableDataResource_impl 10/2/13 3:37:23 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG: trying Resource class org.apache.uima.resource.impl.ConfigurableDataResource_impl 10/2/13 3:37:23 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [UmlsDictionaryLookupAnnotator] initialization begin 10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [ExtractionPrepAnnotator] initialization begin 10/2/13 3:37:24 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG: trying Resource class org.apache.uima.resource.impl.DataResource_impl 10/2/13 3:37:24 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG: trying Resource class org.apache.uima.resource.impl.DataResource_impl 10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [CdaCasInitializer] initialization begin 10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [LookupWindowAnnotator] initialization begin 10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.asb.impl.ASB_impl.initialize: CONFIG: ASB initialization begin 10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.asb.impl.ASB_impl.initialize: CONFIG: ASB initialization successful 10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [NP to LookupWindow] initialization begin 10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [Maximize Lookup Windows] initialization begin 10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [LookupWindowAnnotator] initialization successful 10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [assertionMiniPipelineAnalysisEngine] initialization begin 10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.asb.impl.ASB_impl.initialize: CONFIG: ASB initialization begin 10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.asb.impl.ASB_impl.initialize: CONFIG: ASB initialization successful 10/2/13 3:37:24 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG: trying Resource class org.apache.uima.resource.impl.DataResource_impl 10/2/13 3:37:24 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG: trying Resource class org.apache.uima.resource.impl.DataResource_impl 10/2/13 3:37:24 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG: trying Resource class org.apache.uima.resource.impl.DataResource_impl 10/2/13 3:37:24 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG: trying Resource class org.apache.uima.resource.impl.DataResource_impl 10/2/13 3:37:24 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG: trying Resource class org.apache.uima.resource.impl.DataResource_impl 10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize: CONFIG: AnalysisEngine [assertionAnalysisEngine] initialization begin Paula ----------------------------------------------------------------------------------- hi Pei and Paula, this a description of a problem that i had with the resource zipped file it may probably help ... I got some set up problem first time with the zipped resource file. this is how i proceed : I'm using using eclipse to install cTAKES 3.1. First you have to register in UMLS to get your password and userId in order to use umls2011ab (Pei, is password and userId also need it for user-installation as in developer installation ?) 1) I created a new workspace 1) I followed the installation guide BUT I skipped the step 5 "Unzip the cTAKES resources file into a temporary location and copied". I got some problem of this unziped resource file (i think not sure that the zipped resource file is out of sync) 2) once the installation is finished search for resource rxnorm_index and umls2011ab in the folder of the installation (i found them in .../.m2/repository/...) and I copied them in proper resource path (...ctakes-dictionary-lookup-res/.../dictionary/lookup/) Thanks Samir ---------------- From: [email protected] To: [email protected] Subject: Resource Initialization Exception with cTakes 3.0.1 Date: Mon, 30 Sep 2013 00:03:22 -0400 Hi, I found a similar email posted on the mailing list archives but the specific errors I got are different. I had installed the user version of cTakes 3.0.1 as well as the resources files stated on the user guide. In addition I have a UMLS license. I get the following error when I try to run the AggregatePlaintextUMLSProcessor. I also tried running just the AggregatePlaintextProcessor but it just states not loaded and nothing shows in the log file. I got the below error from running the UMLS aggregate processor. Please advise on how to resolve. Thanks. Regards, Paula ------------------------- 9/29/13 11:52:46 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Exception occurred org.apache.uima.resource.ResourceInitializationException at org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:130) at org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603) at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442) at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123) 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.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:354) at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484) at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477) at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.AbstractButton.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$200(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Caused by: java.sql.SQLException: File input/output error: java.io.IOException: Stream closed at org.hsqldb.jdbc.Util.sqlException(Unknown Source) at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source) at org.hsqldb.jdbcDriver.getConnection(Unknown Source) at org.hsqldb.jdbcDriver.connect(Unknown Source) at java.sql.DriverManager.getConnection(Unknown Source) at java.sql.DriverManager.getConnection(Unknown Source) at org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:109) ... 58 more
