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 757D6175FE for ; Tue, 14 Oct 2014 13:44:19 +0000 (UTC) Received: (qmail 2392 invoked by uid 500); 14 Oct 2014 13:44:19 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 2353 invoked by uid 500); 14 Oct 2014 13:44:19 -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 2340 invoked by uid 99); 14 Oct 2014 13:44:18 -0000 Received: from athena.apache.org (HELO athena.apache.org) (140.211.11.136) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 14 Oct 2014 13:44:18 +0000 X-ASF-Spam-Status: No, hits=1.5 required=5.0 tests=HTML_MESSAGE,RCVD_IN_DNSWL_LOW,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (athena.apache.org: domain of kincaid.dave@gmail.com designates 209.85.218.41 as permitted sender) Received: from [209.85.218.41] (HELO mail-oi0-f41.google.com) (209.85.218.41) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 14 Oct 2014 13:44:14 +0000 Received: by mail-oi0-f41.google.com with SMTP id u20so16466891oif.28 for ; Tue, 14 Oct 2014 06:43:53 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:from:date:message-id:subject:to :content-type; bh=YQn9dEoEF2sMEsMol+84Bg2hqLFaRS5UTMBZt2ed7sg=; b=vH8aYIiuZwN6bGFVMxSxwvp6YwC/GPNg3OlCMG8mDtravMRCgZzdUZGhzb6RwCaszm vzsVz/jrFLfPm7m5kJuOvOe2lSSvYf53Y8WnzmB6LuQvaN7sr8nL5I67rgLh7bhduuh9 LwA2yBFme+HxsCrJAoQFyd9IawWJcUTppYXKkWKQnodKHo7U1M2H/CNpqGnKiWkYrB0g 7Zi5M2mAvV/VZU470YPWvY22z6yLZcf4e+Q/lMWHt0YCS9JzcbaXHky860mSHg1z7VkT PPIXtu4Ltq3SeiHG+o0pqsrAokT2102+K/ayszHuZVdnd4iRf0Y5jUqtVYGCzG7hhoyK 6CFA== X-Received: by 10.60.52.115 with SMTP id s19mr1171359oeo.63.1413294233617; Tue, 14 Oct 2014 06:43:53 -0700 (PDT) MIME-Version: 1.0 Received: by 10.76.151.1 with HTTP; Tue, 14 Oct 2014 06:43:13 -0700 (PDT) In-Reply-To: References: <924DE05C19409B438EB81DE683A942D9109D1CC3@CHEXMBX1A.CHBOSTON.ORG> <924DE05C19409B438EB81DE683A942D9109D1CE0@CHEXMBX1A.CHBOSTON.ORG> From: David Kincaid Date: Tue, 14 Oct 2014 08:43:13 -0500 Message-ID: Subject: Re: NPE with ytex in ctakes 3.2.0 To: "user@ctakes.apache.org" Content-Type: multipart/alternative; boundary=001a11331132c20aae0505623461 X-Virus-Checked: Checked by ClamAV on apache.org --001a11331132c20aae0505623461 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thanks. I'm getting an error on step 7 (Execute the setup script). When I try to run it using the command line given I get the following: [~/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts]> nohup ../../ant -f build-setup.xml -Dlog4j.conf=3DCTAKES_HOME/config/log4j.xml all > setup.out 2>&1 & [1] 8129 [~/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts]> tail -f setup.out nohup: ignoring input Error: Could not find or load main class org.apache.tools.ant.Main So, I tried to run it using my already installed version of ant and get this different error: [~/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts]> nohup ant -f build-setup.xml -Dlog4j.conf=3DCTAKES_HOME/config/log4j.xml all > setup.out 2>&1 & [1] 8178 [~/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts]> tail -f setup.out nohup: ignoring input Buildfile: /home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-setup.xm= l BUILD FAILED /home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-setup.xm= l:44: The following error occurred while executing this line: /home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-classpat= h.xml:109: A source file is missing: /home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/CTAKES_HOME/co= nfig/log4j.xml that second one looks like a typo in the build.xml, but since I'm not too familiar with ant scripts I can't spot where it is. On Tue, Oct 14, 2014 at 8:07 AM, vijay garla wrote: > OK, updated the ytex install page: > https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation > > > On Tue, Oct 14, 2014 at 2:54 PM, vijay garla wrote: > >> Hi Dave, >> >> Let me update the instructions first - I'll tell you when I'm done. >> >> -vj >> >> On Tue, Oct 14, 2014 at 2:46 PM, David Kincaid >> wrote: >> >>> Thanks, Vijay. I'm running from the ctakes distro. I'll run through the >>> steps in the link you included. >>> >>> - Dave >>> >>> On Tue, Oct 14, 2014 at 3:25 AM, vijay garla wrote: >>> >>>> The error is caused by not finding the required properties files/xml >>>> config files. >>>> There are some issues with the ytex setup scripts for the 3.2 release; >>>> I have fixed that in trunk. I am updating the 3.2 installation guide = with >>>> the patched setup scripts. >>>> >>>> It's not clear to me if you're running from a dev environment/eclipse, >>>> or running from the ctakes distro. >>>> If running from a development environment, see >>>> https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-ytex/README >>>> If running from the ctakes distro, make sure you follow the ytex setup= : >>>> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation >>>> >>>> For the dev environment, the xml config file is in the ctakes-ytex-res= ( >>>> https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-ytex-res/src/main= /resources/org/apache/ctakes/ytex/uima/beanRefContext.xml >>>> ) >>>> For the binary distro, the xml config files are in >>>> lib\ctakes-ytex-res-3.2.0.jar >>>> >>>> >>>> -vj >>>> >>>> >>>> On Fri, Oct 10, 2014 at 10:56 PM, David Kincaid >>> > wrote: >>>> >>>>> I don't have that file anywhere either. Where do I get it from? >>>>> >>>>> On Fri, Oct 10, 2014 at 3:53 PM, Chen, Pei < >>>>> Pei.Chen@childrens.harvard.edu> >>>>> wrote: >>>>> >>>>> > I think it=E2=80=99s in ctakes-ytex-res.jar (is that in your classp= ath)? >>>>> > This is just a guess=E2=80=A6 vj may have a better idea if it still= doesn=E2=80=99t >>>>> work >>>>> > for you. >>>>> > >>>>> > From: David Kincaid [mailto:kincaid.dave@gmail.com] >>>>> > Sent: Friday, October 10, 2014 4:51 PM >>>>> > To: user@ctakes.apache.org >>>>> > Subject: Re: NPE with ytex in ctakes 3.2.0 >>>>> > >>>>> > No. I have no file named beanRefContext.xml anywhere on my hard >>>>> drive. >>>>> > >>>>> > >>>>> > >>>>> > On Fri, Oct 10, 2014 at 3:45 PM, Chen, Pei < >>>>> Pei.Chen@childrens.harvard.edu >>>>> > > wrote: >>>>> > I=E2=80=99m not too familiar with the ytex component, >>>>> > but my guess is that the ytexApplicationContext bean is null? >>>>> > It seems that it would be expected to be in the >>>>> > classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml? Do thos= e >>>>> exists? >>>>> > >>>>> > From: David Kincaid [mailto:kincaid.dave@gmail.com>>>> > kincaid.dave@gmail.com>] >>>>> > Sent: Friday, October 10, 2014 4:23 PM >>>>> > To: user@ctakes.apache.org >>>>> > Subject: NPE with ytex in ctakes 3.2.0 >>>>> > >>>>> > I'm trying to experiment the ytex in 3.2.0. Trying to run >>>>> > AggregatePlaintextUMLSProcessor with the >>>>> FilesInDirectoryCollectionReader >>>>> > and FileWriterCASConsumer. When I try to run it against some text >>>>> files it >>>>> > blows up with a null pointer exception during initialization. Here'= s >>>>> the >>>>> > relevant part of the stack trace. Anyone have any ideas what I migh= t >>>>> have >>>>> > wrong?: >>>>> > >>>>> > Caused by: org.apache.uima.resource.ResourceInitializationException= : >>>>> > Initialization of annotator class >>>>> > "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" >>>>> failed. >>>>> > (Descriptor: >>>>> > >>>>> file:/home/davek/apps/apache-ctakes-3.2.0/desc/ctakes-ytex-uima/desc/= analysis_engine/SegmentRegexAnnotator.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:26= 9) >>>>> > 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:26= 9) >>>>> > at >>>>> > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:31= 4) >>>>> > 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: java.lang.NullPointerException >>>>> > at >>>>> > >>>>> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationCo= ntext(ApplicationContextHolder.java:79) >>>>> > at >>>>> > >>>>> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initiali= ze(SegmentRegexAnnotator.java:64) >>>>> > at >>>>> > >>>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini= tializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) >>>>> > ... 24 more >>>>> > >>>>> > >>>>> > >>>>> >>>> >>>> >>> >> > --001a11331132c20aae0505623461 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Thanks. I'm getting an error on step 7 (Execute the se= tup script). When I try to run it using the command line given I get the fo= llowing:

[~/a= pps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts]> nohup ../../ant -f bui= ld-setup.xml -Dlog4j.conf=3DCTAKES_HOME/config/log4j.xml all > setup.out= 2>&1 &
[= 1] 8129
[~/apps/apac= he-ctakes-3.2.0/bin/ctakes-ytex/scripts]> tail -f setup.out=C2=A0=
nohup: ignoring input
Error: Could not find or= load main class org.apache.tools.ant.Main

So, I tried to run it using my already installed version of ant and g= et this different error:

[~/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts]> = nohup ant -f build-setup.xml -Dlog4j.conf=3DCTAKES_HOME/config/log4j.xml al= l > setup.out 2>&1 &
[1] 8178
[~/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts]> tail -f setup.= out=C2=A0
nohup: ign= oring input
Buildfil= e: /home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-setup= .xml

BUILD FAILED
= /home/davek/apps/apache-ctakes-3.2.0/= bin/ctakes-ytex/scripts/build-setup.xml:44: The following error occurred wh= ile executing this line:
/home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-cla= sspath.xml:109: A source file is missing: /home/davek/apps/apache-ctakes-3.= 2.0/bin/ctakes-ytex/scripts/CTAKES_HOME/config/log4j.xml
<= br>
that second one looks like a typo in the build.xml, but= since I'm not too familiar with ant scripts I can't spot where it = is.

On= Tue, Oct 14, 2014 at 8:07 AM, vijay garla <vngarla@gmail.com> wrote:

On Tue, Oct 14, 2014 at 2:54 PM, vijay garla <vngarla@gma= il.com> wrote:
Hi Dave,

Let me update the instructions first - I&#= 39;ll tell you when I'm done.

-vj
<= div>

On Tue, = Oct 14, 2014 at 2:46 PM, David Kincaid <kincaid.dave@gmail.com>= ; wrote:
Thanks, = Vijay. I'm running from the ctakes distro. I'll run through the ste= ps in the link you included.

- Dave

On Tue, Oct 14, = 2014 at 3:25 AM, vijay garla <vngarla@gmail.com> wrote:
<= blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px= #ccc solid;padding-left:1ex">
The error is caused by = not finding the required properties files/xml config files.
There= are some issues with the ytex setup scripts for the 3.2 release; I have fi= xed that in trunk.=C2=A0 I am updating the 3.2 installation guide with the = patched setup scripts.

It's not clear to me if = you're running from a dev environment/eclipse, or running from the ctak= es distro.
If running from a development environment, see=C2=A0https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-ytex/READ= ME
If running from the ctakes distro, make sure you follow th= e ytex setup: https://cwiki.apache.org/confluence/d= isplay/CTAKES/YTEX+Installation

For the binary distro, the xml config files are in lib\ctakes-yte= x-res-3.2.0.jar


-vj


On Fri, Oct 10, 2014 at 10:56 PM, David Kincaid <kincaid.d= ave@gmail.com> wrote:
I don't have th= at file anywhere either. Where do I get it from?

On Fri, Oct 10, 2014 at 3:53 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu&= gt;
wrote:

> I think it=E2=80=99s in ctakes-ytex-res.jar (is that in your classpath= )?
> This is just a guess=E2=80=A6 vj may have a better idea if it still do= esn=E2=80=99t work
> for you.
>
> From: David Kincaid [mailto:kincaid.dave@gmail.com]
> Sent: Friday, October 10, 2014 4:51 PM
> To: user@c= takes.apache.org
> Subject: Re: NPE with ytex in ctakes 3.2.0
>
> No. I have no file named beanRefContext.xml anywhere on my hard drive.=
>
>
>
> On Fri, Oct 10, 2014 at 3:45 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu=
> <mailto:Pei.Chen@childrens.harvard.edu>> wrote:
> I=E2=80=99m not too familiar with the ytex component,
> but my guess is that the ytexApplicationContext bean is null?
> It seems that it would be expected to be in the
> classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml?=C2=A0 Do th= ose exists?
>
> From: David Kincaid [mailto:kincaid.dave@gmail.com<mailto:
> kinc= aid.dave@gmail.com>]
> Sent: Friday, October 10, 2014 4:23 PM
> To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
> Subject: NPE with ytex in ctakes 3.2.0
>
> I'm trying to experiment the ytex in 3.2.0. Trying to run
> AggregatePlaintextUMLSProcessor with the FilesInDirectoryCollectionRea= der
> and FileWriterCASConsumer. When I try to run it against some text file= s it
> blows up with a null pointer exception during initialization. Here'= ;s the
> relevant part of the stack trace. Anyone have any ideas what I might h= ave
> wrong?:
>
> Caused by: org.apache.uima.resource.ResourceInitializationException: > Initialization of annotator class
> "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator&quo= t; failed.
> (Descriptor:
> file:/home/davek/apps/apache-ctakes-3.2.0/desc/ctakes-ytex-uima/desc/a= nalysis_engine/SegmentRegexAnnotator.xml)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init= ializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init= ialize(PrimitiveAnalysisEngine_impl.java:156)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys= isEngineFactory_impl.java:94)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Com= positeResourceFactory_impl.java:62)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)<= br> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java= :387)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:= 254)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init= ASB(AggregateAnalysisEngine_impl.java:431)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init= ializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init= ialize(AggregateAnalysisEngine_impl.java:185)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys= isEngineFactory_impl.java:94)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Com= positeResourceFactory_impl.java:62)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)<= br> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)<= br> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java= :425)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegr= atedCasProcessor(CPEFactory.java:1088)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0... 9 more
> Caused by: java.lang.NullPointerException
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationCon= text(ApplicationContextHolder.java:79)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initializ= e(SegmentRegexAnnotator.java:64)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init= ializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0... 24 more
>
>
>





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