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From Susrutha Gongalla <susrutha.gonga...@gmail.com>
Subject Re: cTAKES 3.2.0 CPE error
Date Tue, 25 Nov 2014 11:43:12 GMT
Hello Kim,

Thank you for your response.

I have removed the resource jar files suggested by you and tried it out.
I am now facing the following error.

java.io.FileNotFoundException: org\apache\ctakes\dependency\parser\mo
dels\lemmatizer\dictionary-1.3.1.jar (The system cannot find the path
specified)

Could you please suggest if there is anything else I can try?

Given below is the complete log of command prompt:

C:\cTAKES_HOME\apache-ctakes-3.2.0>java -cp
"C:\cTAKES_HOME\apache-ctakes-3.2.0/
lib/*;C:\cTAKES_HOME\apache-ctakes-3.2.0/desc/;C:\cTAKES_HOME\apache-ctakes-3.2.
0/resources/"
-Dlog4j.configuration=file:/C:\cTAKES_HOME\apache-ctakes-3.2.0/con
fig/log4j.xml -Xms512M -Xmx3g org.apache.uima.tools.cpm.CpmFrame
Nov 25, 2014 4:04:03 PM java.util.prefs.WindowsPreferences <init>
WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at
root 0
x80000002. Windows RegCreateKeyEx(...) returned error code 5.
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Level value for root is  [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss}
%5p %c{
1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
25 Nov 2014 16:05:42  INFO ClearNLPDependencyParserAE - using Morphy
analysis? t
rue
org.apache.uima.resource.ResourceInitializationException: Initialization of
CAS
Processor with name "AggregateCdaProcessor" failed.
        at
org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initi
alize(CollectionProcessingEngine_impl.java:83)
        at
org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessingE
ngine(UIMAFramework_impl.java:420)
        at
org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIMAF
ramework.java:864)
        at
org.apache.uima.tools.cpm.CpmPanel.startProcessing(CpmPanel.java:573)

        at org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel.java:105)
        at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713)
Caused by: org.apache.uima.resource.ResourceConfigurationException:
Initializati
on of CAS Processor with name "AggregateCdaProcessor" failed.
        at
org.apache.uima.collection.impl.cpm.container.CPEFactory.produceInteg
ratedCasProcessor(CPEFactory.java:1104)
        at
org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProces
sors(CPEFactory.java:550)
        at
org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.java
:253)
        at
org.apache.uima.collection.impl.cpm.BaseCPMImpl.<init>(BaseCPMImpl.ja
va:127)
        at
org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initi
alize(CollectionProcessingEngine_impl.java:75)
        ... 5 more
Caused by: org.apache.uima.resource.ResourceInitializationException:
Initializat
ion of annotator class
"org.apache.ctakes.dependency.parser.ae.ClearNLPDependenc
yParserAE" failed.  (Descriptor:
file:/C:/cTAKES_HOME/apache-ctakes-3.2.0/desc/c
takes-dependency-parser/desc/analysis_engine/ClearNLPDependencyParserAE.xml)
        at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
tializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
        at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
tialize(PrimitiveAnalysisEngine_impl.java:156)
        at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy
sisEngineFactory_impl.java:94)
        at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co
mpositeResourceFactory_impl.java:62)
        at
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)

        at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav
a: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.ini
tASB(AggregateAnalysisEngine_impl.java:431)
        at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
        at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
tialize(AggregateAnalysisEngine_impl.java:185)
        at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy
sisEngineFactory_impl.java:94)
        at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co
mpositeResourceFactory_impl.java:62)
        at
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)

        at
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)

        at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav
a:425)
        at
org.apache.uima.collection.impl.cpm.container.CPEFactory.produceInteg
ratedCasProcessor(CPEFactory.java:1088)
        ... 9 more
Caused by: org.apache.uima.resource.ResourceInitializationException
        at
org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE.ini
tialize(ClearNLPDependencyParserAE.java:138)
        at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
tializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
        ... 24 more
Caused by: java.io.FileNotFoundException:
org\apache\ctakes\dependency\parser\mo
dels\lemmatizer\dictionary-1.3.1.jar (The system cannot find the path
specified)

        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(Unknown Source)
        at
org.apache.ctakes.core.resource.FileLocator.getAsStream(FileLocator.j
ava:50)
        at
org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE.ini
tialize(ClearNLPDependencyParserAE.java:125)
        ... 25 more

Thank you in advance.

Regards,
Susrutha

On Wed, Nov 19, 2014 at 9:04 PM, Kim Ebert <kim.ebert@perfectsearchcorp.com>
wrote:

>  Susrutha,
>
> Caused by: java.lang.IllegalArgumentException: URI is not hierarchical
>
> I believe this is caused in some versions by having the resources in jar
> files. I found it effective to remove the resource jar files and rely upon
> the resources directory. So ctakes*-res-*.jar
>
> Let me know if that helps.
>
> Thanks,
>
>  [image: IMAT Solutions] <http://imatsolutions.com>
>  Kim Ebert
> Software Engineer
> [image: Office:] 801.669.7342
> kim.ebert@imatsolutions.com <greg.hubert@imatsolutions.com>
>  On 11/19/2014 03:44 AM, Susrutha Gongalla wrote:
>
> Hi,
>
>  I have installed cTAKES 3.2.0 along with corresponding resources as per
> the instructions given on Apache website.
>
>  I get the following error when I run the runctakescpe.bat file
>
> C:\cTAKES_HOME\apache-ctakes-3.2.0>java -cp
> "C:\cTAKES_HOME\apache-ctakes-3.2.0/
>
> lib/*;C:\cTAKES_HOME\apache-ctakes-3.2.0/desc/;C:\cTAKES_HOME\apache-ctakes-3.2.
> 0/resources/" -Dlog4j.configuration=
> file:/C:\cTAKES_HOME\apache-ctakes-3.2.0/con
> fig/log4j.xml -Xms512M -Xmx3g org.apache.uima.tools.cpm.CpmFrame
> Nov 19, 2014 1:38:47 PM java.util.prefs.WindowsPreferences <init>
> WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at
> root 0
> x80000002. Windows RegCreateKeyEx(...) returned error code 5.
>
>  If I ignore this error and try to run the pipeline using test1.xml CPE
> descriptor (example given in the installation guide),
> I get an error caused due to java.lang.IllegalArgumentException
>
>  Given below is the cmd output:
>
> log4j: reset attribute= "false".
> log4j: Threshold ="null".
> log4j: Level value for root is  [INFO].
> log4j: root level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss}
> %5p %c{
> 1} - %m%n].
> log4j: Adding appender named [consoleAppender] to category [root].
> 19 Nov 2014 13:39:35  INFO ClearNLPDependencyParserAE - using Morphy
> analysis? t
> rue
> Loading configuration.
> Loading feature templates.
> Loading lexica.
> Loading model:
>
> ................................................................................
> ........
> 19 Nov 2014 13:39:52  INFO TokenizerAnnotatorPTB - Initializing
> org.apache.ctake
> s.core.ae.TokenizerAnnotatorPTB
> 19 Nov 2014 13:39:52  INFO ContextDependentTokenizerAnnotator - Finite
> state mac
> hines loaded.
> 19 Nov 2014 13:39:52  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
> 19 Nov 2014 13:39:52  INFO NegationContextAnalyzer - initBoundaryData()
> called f
> or ContextInitializer
> 19 Nov 2014 13:39:52  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
> 19 Nov 2014 13:39:52  INFO StatusContextAnalyzer - initBoundaryData()
> called for
>  ContextInitializer
> 19 Nov 2014 13:39:52  INFO SentenceDetector - Sentence detector model
> file: org/
> apache/ctakes/core/sentdetect/sd-med-model.zip
> 19 Nov 2014 13:39:52  INFO POSTagger - POS tagger model file:
> org/apache/ctakes/
> postagger/models/mayo-pos.zip
> 19 Nov 2014 13:39:52  INFO Chunker - Chunker model file:
> org/apache/ctakes/chunk
> er/models/chunker-model.zip
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of CAS
> Processor with name "AggregateCdaProcessor" failed.
>         at
> org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initi
> alize(CollectionProcessingEngine_impl.java:83)
>         at
> org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessingE
> ngine(UIMAFramework_impl.java:420)
>         at
> org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIMAF
> ramework.java:864)
>         at
> org.apache.uima.tools.cpm.CpmPanel.startProcessing(CpmPanel.java:573)
>
>         at org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel.java:105)
>         at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713)
> Caused by: org.apache.uima.resource.ResourceConfigurationException:
> Initializati
> on of CAS Processor with name "AggregateCdaProcessor" failed.
>         at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceInteg
> ratedCasProcessor(CPEFactory.java:1104)
>         at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProces
> sors(CPEFactory.java:550)
>         at
> org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.java
> :253)
>         at
> org.apache.uima.collection.impl.cpm.BaseCPMImpl.<init>(BaseCPMImpl.ja
> va:127)
>         at
> org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initi
> alize(CollectionProcessingEngine_impl.java:75)
>         ... 5 more
> Caused by: java.lang.IllegalArgumentException: URI is not hierarchical
>         at java.io.File.<init>(Unknown Source)
>         at
> org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImp
> l.java:44)
>         at
> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(R
> esourceManager_impl.java:603)
>         at
> org.apache.uima.resource.impl.ResourceManager_impl.initializeExternal
> Resources(ResourceManager_impl.java:442)
>         at
> org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBa
> se.java:153)
>         at
> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initializ
> e(AnalysisEngineImplBase.java:157)
>         at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
> tialize(PrimitiveAnalysisEngine_impl.java:123)
>         at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy
> sisEngineFactory_impl.java:94)
>         at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co
> mpositeResourceFactory_impl.java:62)
>         at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>
>         at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav
> a: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.ini
> tASB(AggregateAnalysisEngine_impl.java:431)
>         at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
> tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>         at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
> tialize(AggregateAnalysisEngine_impl.java:185)
>         at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy
> sisEngineFactory_impl.java:94)
>         at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co
> mpositeResourceFactory_impl.java:62)
>         at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>
>         at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
>
>         at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav
> a:425)
>         at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceInteg
> ratedCasProcessor(CPEFactory.java:1088)
>         ... 9 more
>
>
>  I have followed everything as per the user installation guide.
> Can somebody please throw some light on what might be causing this error?
> I would greatly appreciate any help in this regard!
>
>  Thanks and Regards,
> Susrutha Gongalla
>
>
>

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