ctakes-user mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Susrutha Gongalla <susrutha.gonga...@gmail.com>
Subject Re: cTAKES 3.2.0 CPE error
Date Thu, 27 Nov 2014 20:02:01 GMT
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" <chenpei@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 <chenpei@apache.org> wrote:
>>>>
>>>>
>>>>> ---------- Forwarded message ----------
>>>>> From: Kim Ebert <kim.ebert@imatsolutions.com>
>>>>> Date: Tue, Nov 25, 2014 at 1:27 PM
>>>>> Subject: Re: cTAKES 3.2.0 CPE error
>>>>> To: Susrutha Gongalla <susrutha.gongalla@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 <greg.hubert@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 <greg.hubert@imatsolutions.com>
>>>>>>   On 11/19/2014 03:44 AM, Susrutha Gongalla wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>>  I have installed cTAKES 3.2.0 along with corresponding resources
as
>>>>>> per the instructions given on Apache website.
>>>>>>
>>>>>>  I get the following error when I run the runctakescpe.bat file
>>>>>>
>>>>>> C:\cTAKES_HOME\apache-ctakes-3.2.0>java -cp
>>>>>> "C:\cTAKES_HOME\apache-ctakes-3.2.0/
>>>>>>
>>>>>> lib/*;C:\cTAKES_HOME\apache-ctakes-3.2.0/desc/;C:\cTAKES_HOME\apache-ctakes-3.2.
>>>>>> 0/resources/" -Dlog4j.configuration=
>>>>>> file:/C:\cTAKES_HOME\apache-ctakes-3.2.0/con
>>>>>> fig/log4j.xml -Xms512M -Xmx3g org.apache.uima.tools.cpm.CpmFrame
>>>>>> Nov 19, 2014 1:38:47 PM java.util.prefs.WindowsPreferences <init>
>>>>>> WARNING: Could not open/create prefs root node
>>>>>> Software\JavaSoft\Prefs at root 0
>>>>>> x80000002. Windows RegCreateKeyEx(...) returned error code 5.
>>>>>>
>>>>>>  If I ignore this error and try to run the pipeline using test1.xml
>>>>>> CPE descriptor (example given in the installation guide),
>>>>>> I get an error caused due to java.lang.IllegalArgumentException
>>>>>>
>>>>>>  Given below is the cmd output:
>>>>>>
>>>>>> log4j: reset attribute= "false".
>>>>>> log4j: Threshold ="null".
>>>>>> log4j: Level value for root is  [INFO].
>>>>>> log4j: root level set to INFO
>>>>>> log4j: Class name: [org.apache.log4j.ConsoleAppender]
>>>>>> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
>>>>>> log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy
>>>>>> HH:mm:ss} %5p %c{
>>>>>> 1} - %m%n].
>>>>>> log4j: Adding appender named [consoleAppender] to category [root].
>>>>>> 19 Nov 2014 13:39:35  INFO ClearNLPDependencyParserAE - using Morphy
>>>>>> analysis? t
>>>>>> rue
>>>>>> Loading configuration.
>>>>>> Loading feature templates.
>>>>>> Loading lexica.
>>>>>> Loading model:
>>>>>>
>>>>>> ................................................................................
>>>>>> ........
>>>>>> 19 Nov 2014 13:39:52  INFO TokenizerAnnotatorPTB - Initializing
>>>>>> org.apache.ctake
>>>>>> s.core.ae.TokenizerAnnotatorPTB
>>>>>> 19 Nov 2014 13:39:52  INFO ContextDependentTokenizerAnnotator -
>>>>>> Finite state mac
>>>>>> hines loaded.
>>>>>> 19 Nov 2014 13:39:52  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
>>>>>> 19 Nov 2014 13:39:52  INFO NegationContextAnalyzer -
>>>>>> initBoundaryData() called f
>>>>>> or ContextInitializer
>>>>>> 19 Nov 2014 13:39:52  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
>>>>>> 19 Nov 2014 13:39:52  INFO StatusContextAnalyzer - initBoundaryData()
>>>>>> called for
>>>>>>  ContextInitializer
>>>>>> 19 Nov 2014 13:39:52  INFO SentenceDetector - Sentence detector model
>>>>>> file: org/
>>>>>> apache/ctakes/core/sentdetect/sd-med-model.zip
>>>>>> 19 Nov 2014 13:39:52  INFO POSTagger - POS tagger model file:
>>>>>> org/apache/ctakes/
>>>>>> postagger/models/mayo-pos.zip
>>>>>> 19 Nov 2014 13:39:52  INFO Chunker - Chunker model file:
>>>>>> org/apache/ctakes/chunk
>>>>>> er/models/chunker-model.zip
>>>>>> org.apache.uima.resource.ResourceInitializationException:
>>>>>> Initialization of CAS
>>>>>> Processor with name "AggregateCdaProcessor" failed.
>>>>>>         at
>>>>>> org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initi
>>>>>> alize(CollectionProcessingEngine_impl.java:83)
>>>>>>         at
>>>>>> org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessingE
>>>>>> ngine(UIMAFramework_impl.java:420)
>>>>>>         at
>>>>>> org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIMAF
>>>>>> ramework.java:864)
>>>>>>         at
>>>>>> org.apache.uima.tools.cpm.CpmPanel.startProcessing(CpmPanel.java:573)
>>>>>>
>>>>>>         at
>>>>>> org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel.java:105)
>>>>>>         at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713)
>>>>>> Caused by: org.apache.uima.resource.ResourceConfigurationException:
>>>>>> Initializati
>>>>>> on of CAS Processor with name "AggregateCdaProcessor" failed.
>>>>>>         at
>>>>>> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceInteg
>>>>>> ratedCasProcessor(CPEFactory.java:1104)
>>>>>>         at
>>>>>> org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProces
>>>>>> sors(CPEFactory.java:550)
>>>>>>         at
>>>>>> org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.java
>>>>>> :253)
>>>>>>         at
>>>>>> org.apache.uima.collection.impl.cpm.BaseCPMImpl.<init>(BaseCPMImpl.ja
>>>>>> va:127)
>>>>>>         at
>>>>>> org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initi
>>>>>> alize(CollectionProcessingEngine_impl.java:75)
>>>>>>         ... 5 more
>>>>>> Caused by: java.lang.IllegalArgumentException: URI is not hierarchical
>>>>>>         at java.io.File.<init>(Unknown Source)
>>>>>>         at
>>>>>> org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImp
>>>>>> l.java:44)
>>>>>>         at
>>>>>> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(R
>>>>>> esourceManager_impl.java:603)
>>>>>>         at
>>>>>> org.apache.uima.resource.impl.ResourceManager_impl.initializeExternal
>>>>>> Resources(ResourceManager_impl.java:442)
>>>>>>         at
>>>>>> org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBa
>>>>>> se.java:153)
>>>>>>         at
>>>>>> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initializ
>>>>>> e(AnalysisEngineImplBase.java:157)
>>>>>>         at
>>>>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
>>>>>> tialize(PrimitiveAnalysisEngine_impl.java:123)
>>>>>>         at
>>>>>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy
>>>>>> sisEngineFactory_impl.java:94)
>>>>>>         at
>>>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co
>>>>>> mpositeResourceFactory_impl.java:62)
>>>>>>         at
>>>>>> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>>>>>
>>>>>>         at
>>>>>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav
>>>>>> a:387)
>>>>>>         at
>>>>>> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java
>>>>>> :254)
>>>>>>         at
>>>>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
>>>>>> tASB(AggregateAnalysisEngine_impl.java:431)
>>>>>>         at
>>>>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
>>>>>> tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>>>>>         at
>>>>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
>>>>>> tialize(AggregateAnalysisEngine_impl.java:185)
>>>>>>         at
>>>>>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy
>>>>>> sisEngineFactory_impl.java:94)
>>>>>>         at
>>>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co
>>>>>> mpositeResourceFactory_impl.java:62)
>>>>>>         at
>>>>>> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>>>>>
>>>>>>         at
>>>>>> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
>>>>>>
>>>>>>         at
>>>>>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav
>>>>>> a:425)
>>>>>>         at
>>>>>> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceInteg
>>>>>> ratedCasProcessor(CPEFactory.java:1088)
>>>>>>         ... 9 more
>>>>>>
>>>>>>
>>>>>>  I have followed everything as per the user installation guide.
>>>>>> Can somebody please throw some light on what might be causing this
>>>>>> error?
>>>>>> I would greatly appreciate any help in this regard!
>>>>>>
>>>>>>  Thanks and Regards,
>>>>>> Susrutha Gongalla
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>

Mime
View raw message