Return-Path: X-Original-To: apmail-ctakes-user-archive@www.apache.org Delivered-To: apmail-ctakes-user-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 29904109B2 for ; Tue, 23 Jul 2013 00:29:14 +0000 (UTC) Received: (qmail 71383 invoked by uid 500); 23 Jul 2013 00:29:14 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 71360 invoked by uid 500); 23 Jul 2013 00:29:14 -0000 Mailing-List: contact user-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: user@ctakes.apache.org Delivered-To: mailing list user@ctakes.apache.org Received: (qmail 71353 invoked by uid 99); 23 Jul 2013 00:29:14 -0000 Received: from nike.apache.org (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 23 Jul 2013 00:29:14 +0000 X-ASF-Spam-Status: No, hits=2.2 required=5.0 tests=HTML_MESSAGE,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (nike.apache.org: domain of Pei.Chen@childrens.harvard.edu designates 134.174.20.73 as permitted sender) Received: from [134.174.20.73] (HELO mailsmtp3.childrenshospital.org) (134.174.20.73) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 23 Jul 2013 00:29:07 +0000 Received: from pps.filterd (mailsmtp3.childrenshospital.org [127.0.0.1]) by mailsmtp3.childrenshospital.org (8.14.5/8.14.5) with SMTP id r6N0N0U4001425 for ; Mon, 22 Jul 2013 20:28:35 -0400 Received: from smtpndc2.chboston.org (smtpndc2.chboston.org [10.20.50.105]) by mailsmtp3.childrenshospital.org with ESMTP id 1ds8dtbg4h-1 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 22 Jul 2013 20:28:34 -0400 Received: from pps.filterd (smtpndc2.chboston.org [127.0.0.1]) by smtpndc2.chboston.org (8.14.5/8.14.5) with SMTP id r6N0PSQM004069 for ; Mon, 22 Jul 2013 20:28:34 -0400 Received: from chexhubcas3.chboston.org (internal-ndc-nat-v1260.tch.harvard.edu [10.20.50.4]) by smtpndc2.chboston.org with ESMTP id 1dpkgxs2mr-2 (version=TLSv1/SSLv3 cipher=AES128-SHA bits=128 verify=NOT) for ; Mon, 22 Jul 2013 20:28:34 -0400 Received: from CHEXMBX1A.CHBOSTON.ORG ([fe80::3c05:8ca9:55a6:f320]) by CHEXHUBCAS3.CHBOSTON.ORG ([::1]) with mapi id 14.02.0342.003; Mon, 22 Jul 2013 20:28:34 -0400 From: "Chen, Pei" To: "user@ctakes.apache.org" Subject: RE: ctakes with uimafit Thread-Topic: ctakes with uimafit Thread-Index: Ac6G9L4le0Uzg6xaT+2BIqqd2L7BGQAIqGMAAAWNkwAABHFMMAABbHEAAADR9YD//+V7qQ== Date: Tue, 23 Jul 2013 00:28:33 +0000 Message-ID: <924DE05C19409B438EB81DE683A942D91057C7F3@CHEXMBX1A.CHBOSTON.ORG> References: , ,<924DE05C19409B438EB81DE683A942D91057C687@CHEXMBX1A.CHBOSTON.ORG>,, In-Reply-To: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [172.18.21.56] Content-Type: multipart/alternative; boundary="_000_924DE05C19409B438EB81DE683A942D91057C7F3CHEXMBX1ACHBOST_" MIME-Version: 1.0 X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10432:5.10.8794,1.0.431,0.0.0000 definitions=2013-07-22_05:2013-07-22,2013-07-22,1970-01-01 signatures=0 X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10432:5.10.8794,1.0.431,0.0.0000 definitions=2013-07-22_05:2013-07-22,2013-07-22,1970-01-01 signatures=0 X-Virus-Checked: Checked by ClamAV on apache.org --_000_924DE05C19409B438EB81DE683A942D91057C7F3CHEXMBX1ACHBOST_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable ctakes 3.0 should be fine with resources 3.0.1 and lucene 3.0.2. Could we confirm the files inside the below: Mainly resources/org/apache/ctakes/dictionary/lookup/OrangeBook resources/org/apache/ctakes/dictionary/lookup/drug_index resources/org/apache/ctakes/dictionary/lookup/rxnorm_index resources/org/apache/ctakes/dictionary/lookup/umls2011ab In the upcoming cTAKES (3.1), the default models will be included in the co= nvenience binaries so it should be simpler. ________________________________ From: Mukhopadhyay, Aveek [mukhopadhyay.11@buckeyemail.osu.edu] Sent: Monday, July 22, 2013 6:00 PM To: user@ctakes.apache.org Subject: RE: ctakes with uimafit If instead of the 3.x lucene jars I use 4.0.0 jars then it fails with the f= ollowing error Exception in thread "main" java.lang.NoSuchMethodError: org.apache.lucene.s= tore.RAMDirectory.(Lorg/apache/lucene/store/Directory;)V probably because the 4.x lucene.store versions do not have the RAMDirectory= (directory) but it exists in the 3.x versions. I believe I have got some ve= rsion wrong, any ideas? -aveek ________________________________ From: Mukhopadhyay, Aveek [mukhopadhyay.11@buckeyemail.osu.edu] Sent: Monday, July 22, 2013 5:36 PM To: user@ctakes.apache.org Subject: RE: ctakes with uimafit Hello Pei, I am using the 3.0.0-incubating version of c-takes and 3.0.1 version of the= resources file. In the pom.xml file I have the lucene version of 3.0.2. -Aveek ________________________________ From: Chen, Pei [Pei.Chen@childrens.harvard.edu] Sent: Monday, July 22, 2013 4:42 PM To: user@ctakes.apache.org Subject: RE: ctakes with uimafit Aveek, Which version of cTAKES are you using (assuming it=92s not trunk)? And als= o, which version of the resources file? --Pei From: Mukhopadhyay, Aveek [mailto:mukhopadhyay.11@buckeyemail.osu.edu] Sent: Monday, July 22, 2013 2:49 PM To: user@ctakes.apache.org Subject: RE: ctakes with uimafit Hi Murali, Yes, I was missing fsm lib. Thanks for that. I am encountering a different problem now. It seems it is not able to load/= read the lucene indexes and throwing up the java.io.IOException: read past = EOF somewhere. Here is the error that I am getting, any thoughts on this? Exception in thread "main" org.apache.uima.resource.ResourceInitializationE= xception at org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(Lucen= eIndexReaderResourceImpl.java:79) at org.apache.uima.resource.impl.ResourceManager_impl.registerResource(Reso= urceManager_impl.java:603) at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalRes= ources(ResourceManager_impl.java:442) at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.= java:153) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(A= nalysisEngineImplBase.java:157) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initia= lize(PrimitiveAnalysisEngine_impl.java:123) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysis= EngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Compo= siteResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:3= 87) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:25= 4) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initAS= B(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initia= lizeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initia= lize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysis= EngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Compo= siteResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:3= 87) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:25= 4) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initAS= B(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initia= lizeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initia= lize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysis= EngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Compo= siteResourceFactory_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.java:4= 25) at org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngine= Factory.java:424) at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:165) at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:190) at com.bmi.app.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:= 63) Caused by: java.io.IOException: Read past EOF at org.apache.lucene.store.RAMInputStream.switchCurrentBuffer(RAMInputStrea= m.java:92) at org.apache.lucene.store.RAMInputStream.readBytes(RAMInputStream.java:76) at org.apache.lucene.store.ChecksumIndexInput.readBytes(ChecksumIndexInput.= java:45) at org.apache.lucene.store.IndexInput.readString(IndexInput.java:124) at org.apache.lucene.index.SegmentInfo.(SegmentInfo.java:173) at org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:258) at org.apache.lucene.index.DirectoryReader$1.doBody(DirectoryReader.java:73= ) at org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.j= ava:677) at org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:69) at org.apache.lucene.index.IndexReader.open(IndexReader.java:316) at org.apache.lucene.index.IndexReader.open(IndexReader.java:188) at org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(Lucen= eIndexReaderResourceImpl.java:69) ... 30 more ________________________________ From: Murali Nagendranath [mminnah@gmail.com] Sent: Monday, July 22, 2013 12:09 PM To: user@ctakes.apache.org Subject: Re: ctakes with uimafit Hi Aveek, Do you have the fsm lib including in your dependencies? Ex: http://svn.apache.org/repos/asf/ctakes/trunk/pom.xml net.sourceforge.openai openaifsm 0.0.1 -- Murali On Mon, Jul 22, 2013 at 12:01 PM, Mukhopadhyay, Aveek > wrote: Hi all, I am trying to use the ctakes Aggregate Analysis Engine with uimafit, and I= am stuck at a problem now. Any ideas on how to solve this? I am using mave= n dependencies for ctakes and have the ctakes resources project in build pa= th. - loading feature template - loading lexica - loading model Exception in thread "main" java.lang.NoClassDefFoundError: net/openai/util/= fsm/State at org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator= .initialize(ContextDependentTokenizerAnnotator.java:95) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initia= lizeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initia= lize(PrimitiveAnalysisEngine_impl.java:156) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysis= EngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Compo= siteResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:3= 87) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:25= 4) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initAS= B(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initia= lizeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initia= lize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysis= EngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Compo= siteResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:3= 87) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:25= 4) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initAS= B(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initia= lizeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initia= lize(AggregateAnalysisEngine_impl.java:185) at org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngine= Factory.java:505) at org.uimafit.factory.AggregateBuilder.createAggregate(AggregateBuilder.ja= va:200) at com.bmi.app.App.main(App.java:54) Caused by: java.lang.ClassNotFoundException: net.openai.util.fsm.State at java.net.URLClassLoader$1.run(Unknown Source) at java.net.URLClassLoader$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) ... 22 more --_000_924DE05C19409B438EB81DE683A942D91057C7F3CHEXMBX1ACHBOST_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
ctakes 3.0 should be fine with resources 3.0.1 and lucene 3.0.2.
Could we confirm the files inside the below:
Mainly
resources/org/apache/ctakes/dictionary/lookup/OrangeBook
resources/org/apache/ctakes/dictionary/lookup/drug_index
resources/org/apache/ctakes/dictionary/lookup/rxnorm_index
resources/org/apache/ctakes/dictionary/lookup/umls2011ab

In the upcoming cTAKES (3.1), the default models will be included in t= he convenience binaries so it should be simpler.
From: Mukhopadhyay, Aveek [mukhopadhyay.= 11@buckeyemail.osu.edu]
Sent: Monday, July 22, 2013 6:00 PM
To: user@ctakes.apache.org
Subject: RE: ctakes with uimafit

If instead of the 3.x lucene jars I use 4.0.0 jars then it fails with = the following error

Exception in thread "main" java.lang.NoSuchMethodError: org.= apache.lucene.store.RAMDirectory.<init>(Lorg/apache/lucene/store/Dire= ctory;)V

probably because the 4.x lucene.store versions do not have the RA= MDirectory(directory) but it exists in the 3.x versions. I believe I have g= ot some version wrong, any ideas?

-aveek
From: Mukhopadhyay, Aveek [mukhopadhyay.11@= buckeyemail.osu.edu]
Sent: Monday, July 22, 2013 5:36 PM
To: user@ctakes.apache.org
Subject: RE: ctakes with uimafit


Hello Pei,

I am using the 3.0.0-incubating version of c-takes and 3.0.1 version o= f the resources file. In the pom.xml file I have the lucene version of 3.0.= 2. 

-Aveek
From: Chen, Pei [Pei.Chen@childrens.harvard= .edu]
Sent: Monday, July 22, 2013 4:42 PM
To: user@ctakes.apache.org
Subject: RE: ctakes with uimafit

Aveek,

Which version of cTAKES= are you using (assuming it=92s not trunk)?  And also, which version o= f the resources file?

--Pei

 

 

From: Mukhop= adhyay, Aveek [mailto:mukhopadhyay.11@buckeyemail.osu.edu]
Sent: Monday, July 22, 2013 2:49 PM
To: user@ctakes.apache.org
Subject: RE: ctakes with uimafit

 

Hi Murali,

 

Yes, I was missing fsm lib= . Thanks for that.

I am encountering a differ= ent problem now. It seems it is not able to load/read the lucene indexes an= d throwing up the java.io.IOExceptio= n: read past EOF somewhere.

 

Here is the error that I = am getting, any thoughts on this?

 

Exception in thread "= ;main" org.apache.uima.resource.ResourceInitializationException=

at org.apache.ctakes.core= .resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.= java:79)

at org.apache.uima.resour= ce.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603= )

at org.apache.uima.resour= ce.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_im= pl.java:442)

at org.apache.uima.resour= ce.Resource_ImplBase.initialize(Resource_ImplBase.java:153)

at org.apache.uima.analys= is_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.jav= a:157)

at org.apache.uima.analys= is_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEng= ine_impl.java:123)

at org.apache.uima.impl.A= nalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:9= 4)

at org.apache.uima.impl.C= ompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.= java:62)

at org.apache.uima.UIMAFr= amework.produceResource(UIMAFramework.java:269)

at org.apache.uima.UIMAFr= amework.produceAnalysisEngine(UIMAFramework.java:387)

at org.apache.uima.analys= is_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)

at org.apache.uima.analys= is_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine= _impl.java:431)

at org.apache.uima.analys= is_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngi= ne(AggregateAnalysisEngine_impl.java:375)

at org.apache.uima.analys= is_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEng= ine_impl.java:185)

at org.apache.uima.impl.A= nalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:9= 4)

at org.apache.uima.impl.C= ompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.= java:62)

at org.apache.uima.UIMAFr= amework.produceResource(UIMAFramework.java:269)

at org.apache.uima.UIMAFr= amework.produceAnalysisEngine(UIMAFramework.java:387)

at org.apache.uima.analys= is_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)

at org.apache.uima.analys= is_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine= _impl.java:431)

at org.apache.uima.analys= is_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngi= ne(AggregateAnalysisEngine_impl.java:375)

at org.apache.uima.analys= is_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEng= ine_impl.java:185)

at org.apache.uima.impl.A= nalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:9= 4)

at org.apache.uima.impl.C= ompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.= java:62)

at org.apache.uima.UIMAFr= amework.produceResource(UIMAFramework.java:269)

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

at org.apache.uima.UIMAFr= amework.produceAnalysisEngine(UIMAFramework.java:425)

at org.uimafit.factory.An= alysisEngineFactory.createAggregate(AnalysisEngineFactory.java:424)<= /p>

at org.uimafit.pipeline.S= implePipeline.runPipeline(SimplePipeline.java:165)

at org.uimafit.pipeline.S= implePipeline.runPipeline(SimplePipeline.java:190)

at com.bmi.app.ClinicalPi= pelineWithUmls.main(ClinicalPipelineWithUmls.java:63)

Caused by: java.io.IOExce= ption: Read past EOF

at org.apache.lucene.stor= e.RAMInputStream.switchCurrentBuffer(RAMInputStream.java:92)

at org.apache.lucene.stor= e.RAMInputStream.readBytes(RAMInputStream.java:76)

at org.apache.lucene.stor= e.ChecksumIndexInput.readBytes(ChecksumIndexInput.java:45)

at org.apache.lucene.stor= e.IndexInput.readString(IndexInput.java:124)

at org.apache.lucene.inde= x.SegmentInfo.<init>(SegmentInfo.java:173)

at org.apache.lucene.inde= x.SegmentInfos.read(SegmentInfos.java:258)

at org.apache.lucene.inde= x.DirectoryReader$1.doBody(DirectoryReader.java:73)

at org.apache.lucene.inde= x.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:677)

at org.apache.lucene.inde= x.DirectoryReader.open(DirectoryReader.java:69)

at org.apache.lucene.inde= x.IndexReader.open(IndexReader.java:316)

at org.apache.lucene.inde= x.IndexReader.open(IndexReader.java:188)

at org.apache.ctakes.core= .resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.= java:69)

... 30 more

 

From: Murali Nagendranath [mmi= nnah@gmail.com]
Sent: Monday, July 22, 2013 12:09 PM
To: user@ctakes.apache.org
Subject: Re: ctakes with uimafit<= /span>

Hi Avee= k,


Do you have the fsm lib including in your = dependencies?


Ex: http://svn.ap= ache.org/repos/asf/ctakes/trunk/pom.xml

<dep= endency>


       =             &nb= sp;           <groupId= >net.sourceforge.openai</groupId>


       =             &nb= sp;           <artifac= tId>openaifsm</artifactId>

 

<ver= sion>0.0.1</version>


            &nb= sp;          </dependency&g= t;  

 

-- Murali

On Mon, Jul 22, 2013 at = 12:01 PM, Mukhopadhyay, Aveek <mukhopadhyay.11@buckeyemail.osu.edu>= wrote:

Hi all,

 

I am trying to use the cta= kes Aggregate Analysis Engine with uimafit, and I am stuck at a problem now= . Any ideas on how to solve this? I am using maven dependencies for ctakes and have the ctakes resources project in build path.

 

- loading feature template=

- loading lexica

- loading model

Exception in thread "= main" java.lang.NoClassDefFoundError: net/openai/util/fsm/State=

at org.apache.ctakes.conte= xttokenizer.ae.ContextDependentTokenizerAnnotator.initialize(ContextDepende= ntTokenizerAnnotator.java:95)

at org.apache.uima.analysi= s_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(Prim= itiveAnalysisEngine_impl.java:250)

at org.apache.uima.analysi= s_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngi= ne_impl.java:156)

at org.apache.uima.impl.An= alysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94= )

at org.apache.uima.impl.Co= mpositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.j= ava:62)

at org.apache.uima.UIMAFra= mework.produceResource(UIMAFramework.java:269)

at org.apache.uima.UIMAFra= mework.produceAnalysisEngine(UIMAFramework.java:387)

at org.apache.uima.analysi= s_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)

at org.apache.uima.analysi= s_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_= impl.java:431)

at org.apache.uima.analysi= s_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngin= e(AggregateAnalysisEngine_impl.java:375)

at org.apache.uima.analysi= s_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngi= ne_impl.java:185)

at org.apache.uima.impl.An= alysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94= )

at org.apache.uima.impl.Co= mpositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.j= ava:62)

at org.apache.uima.UIMAFra= mework.produceResource(UIMAFramework.java:269)

at org.apache.uima.UIMAFra= mework.produceAnalysisEngine(UIMAFramework.java:387)

at org.apache.uima.analysi= s_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)

at org.apache.uima.analysi= s_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_= impl.java:431)

at org.apache.uima.analysi= s_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngin= e(AggregateAnalysisEngine_impl.java:375)

at org.apache.uima.analysi= s_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngi= ne_impl.java:185)

at org.uimafit.factory.Ana= lysisEngineFactory.createAggregate(AnalysisEngineFactory.java:505)

at org.uimafit.factory.Agg= regateBuilder.createAggregate(AggregateBuilder.java:200)

at com.bmi.app.App.main(Ap= p.java:54)

Caused by: java.lang.Class= NotFoundException: net.openai.util.fsm.State

at java.net.URLClassLoader= $1.run(Unknown Source)

at java.net.URLClassLoader= $1.run(Unknown Source)

at java.security.AccessCon= troller.doPrivileged(Native Method)

at java.net.URLClassLoader= .findClass(Unknown Source)

at java.lang.ClassLoader.l= oadClass(Unknown Source)

at sun.misc.Launcher$AppCl= assLoader.loadClass(Unknown Source)

at java.lang.ClassLoader.l= oadClass(Unknown Source)

... 22 more

 

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