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Posted to user@ctakes.apache.org by Susrutha Gongalla <su...@gmail.com> on 2014/11/19 11:44:25 UTC

cTAKES 3.2.0 CPE error

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

Re: cTAKES 3.2.0 CPE error

Posted by Susrutha Gongalla <su...@gmail.com>.
Thank you Pie for your input. I agree what I have done is just a temporary
way around the blockade.

I am unable to use CPE of cTAKES 3.2.0 with the packed jar files. I have
jre 1.7 along with maven 3.2.3 installed.
For CVD, I am able to use the analysis engine 'AggregatePlaintextProcessor'
but encounter the same URI not hierarchical error if I try to use
'AggregateCdaProcessor' with a CDA file as input.

Is there anything I should check for on my machine? I cannot confirm that
this is a bug in cTAKES unless I am sure that this issue is not due to some
configuration error on my end.

Thanks and Regards,
Susrutha
On Nov 27, 2014 7:55 PM, "Pei Chen" <ch...@apache.org> wrote:

> Susrutha,
> While this will temp work in a single CPE/CVD, it's not recommended once
> you move to a distributed system such as hadoop or similar.  The rationale
> behind this architecture was intentional; and we should definitely fix any
> bugs if exists.
>
> References:
> https://issues.apache.org/jira/browse/CTAKES-183
>
> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201303.mbox/%3C996FC801C05DF64A84246A106FACACD00F3A22%40MSGPEXCHA08A.mfad.mfroot.org%3E
> https://issues.apache.org/jira/browse/CTAKES-320
>
>
> On Thu, Nov 27, 2014 at 7:24 AM, Susrutha Gongalla <
> susrutha.gongalla@gmail.com> wrote:
>
>> Hi Kim,
>>
>> Thank you for your suggestion.
>>
>> I downloaded apache-ctakes-3.2.0-src folder and copied resources from
>> ctakes-*-res into my resources directory
>>
>> apache-ctakes-3.2.0-src/ctakes-*-res/src/main/resources/org/apache/ctakes/*
>> copied into cTAKES_HOME/resources/org/apache/ctakes folder.
>>
>> I am now able to run CPE with plain text, using
>> 'AggregatePlaintextProcessor' analysis engine.
>> I still get the URI not hierarchical error if I try to run CPE with a
>> CDA, using 'AggregateCdaProcessor' analysis engine.
>>
>> I am not clear on how to copy the resources from files other than ctakes-*-res
>> into my resources directory.
>> Is that required to be able to use 'AggregateCdaProcessor' analysis
>> engine?
>>
>> Thanks and Regards,
>> Susrutha
>>
>>
>> On Wed, Nov 26, 2014 at 12:43 PM, Susrutha Gongalla <
>> susrutha.gongalla@gmail.com> wrote:
>>
>>> The original URI not hierarchical error seems to be coming while
>>> initializing a CAS object from the chunker model file.
>>>
>>> 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.
>>>
>>> I am copying the entire log below for your reference.
>>> I will try installing version 3.2.1. Right now I'm working with 3.2.0
>>>
>>> Meanwhile, I will try the way around suggested by Kim and send an update.
>>> Thank you
>>>
>>> Command Prompt log:
>>>
>>> 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.
>>>
>>> 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
>>>
>>> --
>>> Best Wishes,
>>> Susrutha
>>>
>>> On Wed, Nov 26, 2014 at 1:58 AM, Pei Chen <pei.chen@wiredinformatics.com
>>> > wrote:
>>>
>>>> The premise behind the *res.jar's was that you should be able to read
>>>> the models/resources from within a jar which could be deployed to maven
>>>> central.  The dependency parser should be able to read the models from the
>>>> -res.jar via InputStream.  I believe the only ones that currently require
>>>> physical java.io.File is LVG and Dictionary Lookup.  Could you confirm
>>>> which component the original URI is not hierarchical is coming from?
>>>> We can see if we can get that fixed in the next patch...
>>>>
>>>> I'm working on a release candidate 2 for 3.2.1 and should be ready in a
>>>> day or so.  If you're willing to give that a shot (I vaguely recall there
>>>> were some fixes to similar issues)
>>>>
>>>>     Pei Chen
>>>> Wired Informatics <http://www.wiredinformatics.com>
>>>> 265 Franklin St Ste 1702
>>>> Boston, MA 02110
>>>> tel: (617) 433-7544
>>>> Pei.Chen@wiredinformatics.com
>>>>
>>>> On Tue, Nov 25, 2014 at 3:18 PM, Pei Chen <ch...@apache.org> wrote:
>>>>
>>>>
>>>>> ---------- Forwarded message ----------
>>>>> From: Kim Ebert <ki...@imatsolutions.com>
>>>>> Date: Tue, Nov 25, 2014 at 1:27 PM
>>>>> Subject: Re: cTAKES 3.2.0 CPE error
>>>>> To: Susrutha Gongalla <su...@gmail.com>,
>>>>> user@ctakes.apache.org
>>>>>
>>>>>
>>>>>  Hi Susrutha,
>>>>>
>>>>> Sorry for the difficulty on getting things to run here.
>>>>>
>>>>> I have a custom system that packages things for me a bit differently.
>>>>> It appears the default bin release doesn't include all the resources in the
>>>>> the directory. You could download the src folder, and then copy each of the
>>>>> resource directories from the subdirectory of the project into your
>>>>> resource directory.
>>>>>
>>>>> This should get you around any of the errors you were receiving
>>>>> originally, and allow you to have all the resources be accessible.
>>>>>
>>>>> apache-ctakes-3.2.0-src/ctakes-relation-extractor-res/src/main/resources/*
>>>>> -> your resources directory
>>>>> apache-ctakes-3.2.0-src/ctakes-smoking-status/src/main/resources/* ->
>>>>> your resources directory
>>>>> apache-ctakes-3.2.0-src/*/resources/* -> your resources directory
>>>>>
>>>>> Let me know if that works for you.
>>>>>
>>>>>
>>>>>  [image: IMAT Solutions] <http://imatsolutions.com>
>>>>>  Kim Ebert
>>>>> Software Engineer
>>>>> [image: Office:] 801.669.7342
>>>>> kim.ebert@imatsolutions.com <gr...@imatsolutions.com>
>>>>>  On 11/25/2014 04:43 AM, Susrutha Gongalla wrote:
>>>>>
>>>>> 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 <gr...@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
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>

Re: cTAKES 3.2.0 CPE error

Posted by Pei Chen <ch...@apache.org>.
Susrutha,
While this will temp work in a single CPE/CVD, it's not recommended once
you move to a distributed system such as hadoop or similar.  The rationale
behind this architecture was intentional; and we should definitely fix any
bugs if exists.

References:
https://issues.apache.org/jira/browse/CTAKES-183
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201303.mbox/%3C996FC801C05DF64A84246A106FACACD00F3A22%40MSGPEXCHA08A.mfad.mfroot.org%3E
https://issues.apache.org/jira/browse/CTAKES-320


On Thu, Nov 27, 2014 at 7:24 AM, Susrutha Gongalla <
susrutha.gongalla@gmail.com> wrote:

> Hi Kim,
>
> Thank you for your suggestion.
>
> I downloaded apache-ctakes-3.2.0-src folder and copied resources from
> ctakes-*-res into my resources directory
>
> apache-ctakes-3.2.0-src/ctakes-*-res/src/main/resources/org/apache/ctakes/*
> copied into cTAKES_HOME/resources/org/apache/ctakes folder.
>
> I am now able to run CPE with plain text, using
> 'AggregatePlaintextProcessor' analysis engine.
> I still get the URI not hierarchical error if I try to run CPE with a CDA,
> using 'AggregateCdaProcessor' analysis engine.
>
> I am not clear on how to copy the resources from files other than ctakes-*-res
> into my resources directory.
> Is that required to be able to use 'AggregateCdaProcessor' analysis
> engine?
>
> Thanks and Regards,
> Susrutha
>
>
> On Wed, Nov 26, 2014 at 12:43 PM, Susrutha Gongalla <
> susrutha.gongalla@gmail.com> wrote:
>
>> The original URI not hierarchical error seems to be coming while
>> initializing a CAS object from the chunker model file.
>>
>> 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.
>>
>> I am copying the entire log below for your reference.
>> I will try installing version 3.2.1. Right now I'm working with 3.2.0
>>
>> Meanwhile, I will try the way around suggested by Kim and send an update.
>> Thank you
>>
>> Command Prompt log:
>>
>> 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.
>>
>> 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
>>
>> --
>> Best Wishes,
>> Susrutha
>>
>> On Wed, Nov 26, 2014 at 1:58 AM, Pei Chen <pe...@wiredinformatics.com>
>> wrote:
>>
>>> The premise behind the *res.jar's was that you should be able to read
>>> the models/resources from within a jar which could be deployed to maven
>>> central.  The dependency parser should be able to read the models from the
>>> -res.jar via InputStream.  I believe the only ones that currently require
>>> physical java.io.File is LVG and Dictionary Lookup.  Could you confirm
>>> which component the original URI is not hierarchical is coming from?
>>> We can see if we can get that fixed in the next patch...
>>>
>>> I'm working on a release candidate 2 for 3.2.1 and should be ready in a
>>> day or so.  If you're willing to give that a shot (I vaguely recall there
>>> were some fixes to similar issues)
>>>
>>>     Pei Chen
>>> Wired Informatics <http://www.wiredinformatics.com>
>>> 265 Franklin St Ste 1702
>>> Boston, MA 02110
>>> tel: (617) 433-7544
>>> Pei.Chen@wiredinformatics.com
>>>
>>> On Tue, Nov 25, 2014 at 3:18 PM, Pei Chen <ch...@apache.org> wrote:
>>>
>>>
>>>> ---------- Forwarded message ----------
>>>> From: Kim Ebert <ki...@imatsolutions.com>
>>>> Date: Tue, Nov 25, 2014 at 1:27 PM
>>>> Subject: Re: cTAKES 3.2.0 CPE error
>>>> To: Susrutha Gongalla <su...@gmail.com>,
>>>> user@ctakes.apache.org
>>>>
>>>>
>>>>  Hi Susrutha,
>>>>
>>>> Sorry for the difficulty on getting things to run here.
>>>>
>>>> I have a custom system that packages things for me a bit differently.
>>>> It appears the default bin release doesn't include all the resources in the
>>>> the directory. You could download the src folder, and then copy each of the
>>>> resource directories from the subdirectory of the project into your
>>>> resource directory.
>>>>
>>>> This should get you around any of the errors you were receiving
>>>> originally, and allow you to have all the resources be accessible.
>>>>
>>>> apache-ctakes-3.2.0-src/ctakes-relation-extractor-res/src/main/resources/*
>>>> -> your resources directory
>>>> apache-ctakes-3.2.0-src/ctakes-smoking-status/src/main/resources/* ->
>>>> your resources directory
>>>> apache-ctakes-3.2.0-src/*/resources/* -> your resources directory
>>>>
>>>> Let me know if that works for you.
>>>>
>>>>
>>>>  [image: IMAT Solutions] <http://imatsolutions.com>
>>>>  Kim Ebert
>>>> Software Engineer
>>>> [image: Office:] 801.669.7342
>>>> kim.ebert@imatsolutions.com <gr...@imatsolutions.com>
>>>>  On 11/25/2014 04:43 AM, Susrutha Gongalla wrote:
>>>>
>>>> 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 <gr...@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
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>
>

Re: cTAKES 3.2.0 CPE error

Posted by Susrutha Gongalla <su...@gmail.com>.
Hi Kim,

Thank you for your suggestion.

I downloaded apache-ctakes-3.2.0-src folder and copied resources from
ctakes-*-res into my resources directory

apache-ctakes-3.2.0-src/ctakes-*-res/src/main/resources/org/apache/ctakes/*
copied into cTAKES_HOME/resources/org/apache/ctakes folder.

I am now able to run CPE with plain text, using
'AggregatePlaintextProcessor' analysis engine.
I still get the URI not hierarchical error if I try to run CPE with a CDA,
using 'AggregateCdaProcessor' analysis engine.

I am not clear on how to copy the resources from files other than ctakes-*-res
into my resources directory.
Is that required to be able to use 'AggregateCdaProcessor' analysis engine?

Thanks and Regards,
Susrutha


On Wed, Nov 26, 2014 at 12:43 PM, Susrutha Gongalla <
susrutha.gongalla@gmail.com> wrote:

> The original URI not hierarchical error seems to be coming while
> initializing a CAS object from the chunker model file.
>
> 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.
>
> I am copying the entire log below for your reference.
> I will try installing version 3.2.1. Right now I'm working with 3.2.0
>
> Meanwhile, I will try the way around suggested by Kim and send an update.
> Thank you
>
> Command Prompt log:
>
> 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.
>
> 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
>
> --
> Best Wishes,
> Susrutha
>
> On Wed, Nov 26, 2014 at 1:58 AM, Pei Chen <pe...@wiredinformatics.com>
> wrote:
>
>> The premise behind the *res.jar's was that you should be able to read the
>> models/resources from within a jar which could be deployed to maven
>> central.  The dependency parser should be able to read the models from the
>> -res.jar via InputStream.  I believe the only ones that currently require
>> physical java.io.File is LVG and Dictionary Lookup.  Could you confirm
>> which component the original URI is not hierarchical is coming from?  We
>> can see if we can get that fixed in the next patch...
>>
>> I'm working on a release candidate 2 for 3.2.1 and should be ready in a
>> day or so.  If you're willing to give that a shot (I vaguely recall there
>> were some fixes to similar issues)
>>
>>     Pei Chen
>> Wired Informatics <http://www.wiredinformatics.com>
>> 265 Franklin St Ste 1702
>> Boston, MA 02110
>> tel: (617) 433-7544
>> Pei.Chen@wiredinformatics.com
>>
>> On Tue, Nov 25, 2014 at 3:18 PM, Pei Chen <ch...@apache.org> wrote:
>>
>>
>>> ---------- Forwarded message ----------
>>> From: Kim Ebert <ki...@imatsolutions.com>
>>> Date: Tue, Nov 25, 2014 at 1:27 PM
>>> Subject: Re: cTAKES 3.2.0 CPE error
>>> To: Susrutha Gongalla <su...@gmail.com>,
>>> user@ctakes.apache.org
>>>
>>>
>>>  Hi Susrutha,
>>>
>>> Sorry for the difficulty on getting things to run here.
>>>
>>> I have a custom system that packages things for me a bit differently. It
>>> appears the default bin release doesn't include all the resources in the
>>> the directory. You could download the src folder, and then copy each of the
>>> resource directories from the subdirectory of the project into your
>>> resource directory.
>>>
>>> This should get you around any of the errors you were receiving
>>> originally, and allow you to have all the resources be accessible.
>>>
>>> apache-ctakes-3.2.0-src/ctakes-relation-extractor-res/src/main/resources/*
>>> -> your resources directory
>>> apache-ctakes-3.2.0-src/ctakes-smoking-status/src/main/resources/* ->
>>> your resources directory
>>> apache-ctakes-3.2.0-src/*/resources/* -> your resources directory
>>>
>>> Let me know if that works for you.
>>>
>>>
>>>  [image: IMAT Solutions] <http://imatsolutions.com>
>>>  Kim Ebert
>>> Software Engineer
>>> [image: Office:] 801.669.7342
>>> kim.ebert@imatsolutions.com <gr...@imatsolutions.com>
>>>  On 11/25/2014 04:43 AM, Susrutha Gongalla wrote:
>>>
>>> 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 <gr...@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
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
>

Re: cTAKES 3.2.0 CPE error

Posted by Susrutha Gongalla <su...@gmail.com>.
The original URI not hierarchical error seems to be coming while
initializing a CAS object from the chunker model file.

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.

I am copying the entire log below for your reference.
I will try installing version 3.2.1. Right now I'm working with 3.2.0

Meanwhile, I will try the way around suggested by Kim and send an update.
Thank you

Command Prompt log:

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.

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

--
Best Wishes,
Susrutha

On Wed, Nov 26, 2014 at 1:58 AM, Pei Chen <pe...@wiredinformatics.com>
wrote:

> The premise behind the *res.jar's was that you should be able to read the
> models/resources from within a jar which could be deployed to maven
> central.  The dependency parser should be able to read the models from the
> -res.jar via InputStream.  I believe the only ones that currently require
> physical java.io.File is LVG and Dictionary Lookup.  Could you confirm
> which component the original URI is not hierarchical is coming from?  We
> can see if we can get that fixed in the next patch...
>
> I'm working on a release candidate 2 for 3.2.1 and should be ready in a
> day or so.  If you're willing to give that a shot (I vaguely recall there
> were some fixes to similar issues)
>
>     Pei Chen
> Wired Informatics <http://www.wiredinformatics.com>
> 265 Franklin St Ste 1702
> Boston, MA 02110
> tel: (617) 433-7544
> Pei.Chen@wiredinformatics.com
>
> On Tue, Nov 25, 2014 at 3:18 PM, Pei Chen <ch...@apache.org> wrote:
>
>
>> ---------- Forwarded message ----------
>> From: Kim Ebert <ki...@imatsolutions.com>
>> Date: Tue, Nov 25, 2014 at 1:27 PM
>> Subject: Re: cTAKES 3.2.0 CPE error
>> To: Susrutha Gongalla <su...@gmail.com>,
>> user@ctakes.apache.org
>>
>>
>>  Hi Susrutha,
>>
>> Sorry for the difficulty on getting things to run here.
>>
>> I have a custom system that packages things for me a bit differently. It
>> appears the default bin release doesn't include all the resources in the
>> the directory. You could download the src folder, and then copy each of the
>> resource directories from the subdirectory of the project into your
>> resource directory.
>>
>> This should get you around any of the errors you were receiving
>> originally, and allow you to have all the resources be accessible.
>>
>> apache-ctakes-3.2.0-src/ctakes-relation-extractor-res/src/main/resources/*
>> -> your resources directory
>> apache-ctakes-3.2.0-src/ctakes-smoking-status/src/main/resources/* ->
>> your resources directory
>> apache-ctakes-3.2.0-src/*/resources/* -> your resources directory
>>
>> Let me know if that works for you.
>>
>>
>>  [image: IMAT Solutions] <http://imatsolutions.com>
>>  Kim Ebert
>> Software Engineer
>> [image: Office:] 801.669.7342
>> kim.ebert@imatsolutions.com <gr...@imatsolutions.com>
>>  On 11/25/2014 04:43 AM, Susrutha Gongalla wrote:
>>
>> 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 <gr...@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
>>>
>>>
>>>
>>
>>
>>
>

Re: cTAKES 3.2.0 CPE error

Posted by Pei Chen <pe...@wiredinformatics.com>.
The premise behind the *res.jar's was that you should be able to read the
models/resources from within a jar which could be deployed to maven
central.  The dependency parser should be able to read the models from the
-res.jar via InputStream.  I believe the only ones that currently require
physical java.io.File is LVG and Dictionary Lookup.  Could you confirm
which component the original URI is not hierarchical is coming from?  We
can see if we can get that fixed in the next patch...

I'm working on a release candidate 2 for 3.2.1 and should be ready in a day
or so.  If you're willing to give that a shot (I vaguely recall there were
some fixes to similar issues)

    Pei Chen
Wired Informatics <http://www.wiredinformatics.com>
265 Franklin St Ste 1702
Boston, MA 02110
tel: (617) 433-7544
Pei.Chen@wiredinformatics.com

On Tue, Nov 25, 2014 at 3:18 PM, Pei Chen <ch...@apache.org> wrote:

>
> ---------- Forwarded message ----------
> From: Kim Ebert <ki...@imatsolutions.com>
> Date: Tue, Nov 25, 2014 at 1:27 PM
> Subject: Re: cTAKES 3.2.0 CPE error
> To: Susrutha Gongalla <su...@gmail.com>,
> user@ctakes.apache.org
>
>
>  Hi Susrutha,
>
> Sorry for the difficulty on getting things to run here.
>
> I have a custom system that packages things for me a bit differently. It
> appears the default bin release doesn't include all the resources in the
> the directory. You could download the src folder, and then copy each of the
> resource directories from the subdirectory of the project into your
> resource directory.
>
> This should get you around any of the errors you were receiving
> originally, and allow you to have all the resources be accessible.
>
> apache-ctakes-3.2.0-src/ctakes-relation-extractor-res/src/main/resources/*
> -> your resources directory
> apache-ctakes-3.2.0-src/ctakes-smoking-status/src/main/resources/* -> your
> resources directory
> apache-ctakes-3.2.0-src/*/resources/* -> your resources directory
>
> Let me know if that works for you.
>
>
>  [image: IMAT Solutions] <http://imatsolutions.com>
>  Kim Ebert
> Software Engineer
> [image: Office:] 801.669.7342
> kim.ebert@imatsolutions.com <gr...@imatsolutions.com>
>  On 11/25/2014 04:43 AM, Susrutha Gongalla wrote:
>
> 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 <gr...@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
>>
>>
>>
>
>
>

Re: cTAKES 3.2.0 CPE error

Posted by Kim Ebert <ki...@imatsolutions.com>.
Hi Susrutha,

Sorry for the difficulty on getting things to run here.

I have a custom system that packages things for me a bit differently. It
appears the default bin release doesn't include all the resources in the
the directory. You could download the src folder, and then copy each of
the resource directories from the subdirectory of the project into your
resource directory.

This should get you around any of the errors you were receiving
originally, and allow you to have all the resources be accessible.

apache-ctakes-3.2.0-src/ctakes-relation-extractor-res/src/main/resources/* 
-> your resources directory
apache-ctakes-3.2.0-src/ctakes-smoking-status/src/main/resources/* ->
your resources directory
apache-ctakes-3.2.0-src/*/resources/* -> your resources directory

Let me know if that works for you.


IMAT Solutions <http://imatsolutions.com>
Kim Ebert
Software Engineer
Office: 801.669.7342
kim.ebert@imatsolutions.com <ma...@imatsolutions.com>
On 11/25/2014 04:43 AM, Susrutha Gongalla wrote:
> 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
> <ma...@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,
>
>     IMAT Solutions <http://imatsolutions.com>
>     Kim Ebert
>     Software Engineer
>     Office: 801.669.7342
>     kim.ebert@imatsolutions.com <ma...@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
>
>

Re: cTAKES 3.2.0 CPE error

Posted by Susrutha Gongalla <su...@gmail.com>.
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 <ki...@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 <gr...@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
>
>
>

Re: cTAKES 3.2.0 CPE error

Posted by Kim Ebert <ki...@perfectsearchcorp.com>.
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,

IMAT Solutions <http://imatsolutions.com>
Kim Ebert
Software Engineer
Office: 801.669.7342
kim.ebert@imatsolutions.com <ma...@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