if 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: digital girl <[email protected]>
To: "[email protected]" <[email protected]>
Sent: Wednesday, October 2, 2013 3:48:58 PM
Subject: RE: Resource Initialization Exception with cTakes 3.1.0
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
