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" <[email protected]> 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 < > [email protected]> 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 < >> [email protected]> 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 <[email protected] >>> > 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 >>>> [email protected] >>>> >>>> On Tue, Nov 25, 2014 at 3:18 PM, Pei Chen <[email protected]> wrote: >>>> >>>> >>>>> ---------- Forwarded message ---------- >>>>> From: Kim Ebert <[email protected]> >>>>> Date: Tue, Nov 25, 2014 at 1:27 PM >>>>> Subject: Re: cTAKES 3.2.0 CPE error >>>>> To: Susrutha Gongalla <[email protected]>, >>>>> [email protected] >>>>> >>>>> >>>>> 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 >>>>> [email protected] <[email protected]> >>>>> 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 < >>>>> [email protected]> 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 >>>>>> [email protected] <[email protected]> >>>>>> 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 >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> >>> >> >
