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Posted to user@ctakes.apache.org by David Kincaid <ki...@gmail.com> on 2014/10/10 22:21:41 UTC
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 might 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
at
org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
... 9 more
Caused by: java.lang.NullPointerException
at
org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
at
org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 24 more
Re: NPE with ytex in ctakes 3.2.0
Posted by Michelle Chen <mw...@mit.edu>.
More specifically,
/usr/local/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-setup.xml:52:
The following error occurred while executing this line:
/usr/local/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/data/build.xml:92:
Java returned: 1
-------
Michelle Chen
Massachusetts Institute of Technology
Electrical Engineering and Computer Science
B.S. '14, M.Eng. '15
On Fri, Oct 24, 2014 at 4:48 PM, Michelle Chen <mw...@mit.edu> wrote:
> Hello,
>
> I'm also trying to get YTex to work and run into the same problem whe
> runnign the build-setup.xml file. I get the DBping error of "[java] Error:
> Could not find or load main class org.apache.ctakes.ytext.tools.DBPing"
>
> I have created a database called YTex, but was unsure if I set it up
> correctly.
>
> @David, Did you find a fix for this?
>
> Thanks.
>
> -------
> Michelle Chen
>
> Massachusetts Institute of Technology
> Electrical Engineering and Computer Science
> B.S. '14, M.Eng. '15
>
>
> On Tue, Oct 14, 2014 at 10:27 AM, David Kincaid <ki...@gmail.com>
> wrote:
>
>> Ok. I just noticed that the typo is in that parameter. Instead of
>> CTAKES_HOME it should be $CTAKES_HOME. I get a little farther with that
>> (although still have to use my installed version of ant), but now get a
>> failure in the dbping: that it can't connect to a database. I don't have a
>> database running, so I assume that is to be expected. I was hoping I could
>> play with it without a database, but maybe that's not possible. I
>> appreciate the help. If you update that ant command line in the wiki page
>> to have $CTAKES_HOME instead of CTAKES_HOME it should work.
>>
>> - Dave
>>
>
>
Re: NPE with ytex in ctakes 3.2.0
Posted by Tim O'Connell <ti...@gmail.com>.
If it helps any, I just did a fresh install of YTex using the new install
instructions and ytex patch (thanks, Vijay!) although I built it from the
3.2.1 version on subversion, not from the 3.2.0 tarball, and it's working
fine.
If you have svn and maven installed, you could try:
-
svn co https://svn.apache.org/repos/asf/ctakes/trunk
-
cd ctakes
-
mvn clean install -DskipTests
to build it. the .zip and .tar.gz files will then be in
<build_root>/ctakes/trunk/ctakes-distribution/target
Cheers,
Tim
On Fri, Oct 24, 2014 at 1:48 PM, Michelle Chen <mw...@mit.edu> wrote:
> Hello,
>
> I'm also trying to get YTex to work and run into the same problem whe
> runnign the build-setup.xml file. I get the DBping error of "[java] Error:
> Could not find or load main class org.apache.ctakes.ytext.tools.DBPing"
>
> I have created a database called YTex, but was unsure if I set it up
> correctly.
>
> @David, Did you find a fix for this?
>
> Thanks.
>
> -------
> Michelle Chen
>
> Massachusetts Institute of Technology
> Electrical Engineering and Computer Science
> B.S. '14, M.Eng. '15
>
>
> On Tue, Oct 14, 2014 at 10:27 AM, David Kincaid <ki...@gmail.com>
> wrote:
>
>> Ok. I just noticed that the typo is in that parameter. Instead of
>> CTAKES_HOME it should be $CTAKES_HOME. I get a little farther with that
>> (although still have to use my installed version of ant), but now get a
>> failure in the dbping: that it can't connect to a database. I don't have a
>> database running, so I assume that is to be expected. I was hoping I could
>> play with it without a database, but maybe that's not possible. I
>> appreciate the help. If you update that ant command line in the wiki page
>> to have $CTAKES_HOME instead of CTAKES_HOME it should work.
>>
>> - Dave
>>
>
>
Re: NPE with ytex in ctakes 3.2.0
Posted by Tim O'Connell <ti...@gmail.com>.
David, Michelle,
If it helps any - I create install logs of what I do while I'm doing a
complex install. Here's my log of instructions. It's for linux (I run
Ubuntu server, but that shouldn't matter for this), so you may have to
translate to Windows if that's your OS. Before doing any of the below, I
already had UMLS set up in MySQL, with a db name of 'umls'. Let me know if
anything seems unclear.
Tim
-
install java, svn, maven
-
sudo add-apt-repository ppa:webupd8team/java
-
sudo apt-get update
-
sudo apt-get install oracle-java7-installer
-
sudo apt-get install maven
- sudo apt-get install subversion
-
set up the ytex database, executing the following in MySQL:
-
CREATE DATABASE ytex CHARACTER SET utf8;
-
CREATE USER 'ytex'@'localhost' IDENTIFIED BY 'ytex';
-
GRANT ALL PRIVILEGES ON ytex.* TO 'ytex'@'localhost';
-
GRANT SELECT on umls.* to 'ytex'@'localhost';
-
download and build latest ctakes using subversion
-
cd ~
-
svn co https://svn.apache.org/repos/asf/ctakes/trunk
-
cd ctakes
-
mvn clean install -DskipTests
-
unpack cTakes build:
-
cd ~/ctakes/trunk/ctakes-distribution/target
-
tar -xvf ./apache-ctakes-3.2.1-SNAPSHOT-bin.tar.gz -C ~
-
Download ctakes-ytex-lib-3.1.2-SNAPSHOT.zip to ~
-
cp ~/ctakes-ytex-lib-3.1.2-SNAPSHOT.zip /tmp
-
cd /tmp
-
unzip ctakes-ytex-lib-3.1.2-SNAPSHOT.zip
-
cp -R /tmp/lib/* ~/apache-ctakes-3.2.1-SNAPSHOT/lib/
-
rm -rf /tmp/lib
-
Download ctakes-ytex-resources-3.1.2-SNAPSHOT.zip to ~
-
cd ~/ctakes-ytex-resources-3.1.2-SNAPSHOT.zip /tmp
-
cd /tmp
-
unzip ./ctakes-ytex-resources-3.1.2-SNAPSHOT.zip
-
cp -R /tmp/resources/* ~/apache-ctakes-3.2.1-SNAPSHOT/resources/
-
sudo rm -rf /tmp/resources
-
Download ctakes-resources-3.2.0.zip
-
ct /tmp
-
wget
http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.2.0.zip
-
unzip ./ctakes-resources-3.2.0.zip
-
cp -R /tmp/resources/* ~/apache-ctakes-3.2.1-SNAPSHOT/resources/
-
Download the new ytex Patch from:
https://cwiki.apache.org/confluence/download/attachments/40504828/ytex-patch-3.2.0.zip?version=2&modificationDate=1413291939000&api=v2
(link is from the ctakes-ytex installation page on confluence) and put it
in ~
-
cp ~/ytex-patch.zip /tmp
-
cd /tmp
-
unzip ./ytex-patch.zip
-
cd ytex-patch
-
cp -R * ~/apache-ctakes-3.2.1-SNAPSHOT/
-
cd /tmp
-
rm -rf ./ytex-patch
-
Edit:
-
CTAKES_HOME/bin/runctakesCVD.sh to use 64-bit java, increase the heap
size
-
CTAKES_HOME/bin/runctakesCPE.sh to use 64-bit java, increase the heap
size
-
CTAKES_HOME/config/log4j.xml to use the file appender
-
Create CTAKES_HOME/resources/org/apache/ctakes/ytex/ytex.properties
-
While the current instructions say this can be extracted from
CTAKES_HOME/lib/ctakes-ytex-res-3.2.0.jar, I couldn’t get my jar unpacker
to work, so I just copied the MySQL version of this file over from a
previous installation. The only change I had to make was to uncomment the
umls.schema line.
-
Move the ctakes.profile file to my home directory:
-
cp ~/apache-ctakes-3.2.1-SNAPSHOT/bin/ctakes.profile ~/ctakes.profile
-
edit the CTAKES_HOME environment variable
-
chmod u+x ~/ctakes.profile
-
Execute the ytex setup script:
-
cd ~
-
./ctakes.profile
-
cd ./apache-ctakes-3.2.1-SNAPSHOT/bin
-
chmod u+x ant
-
chmod u+x *.sh
-
cd ctakes-ytex/scripts
-
nohup ../../ant -f build-setup.xml all > setup.out 2>&1 &
-
tail -f setup.out
That's it. After this, I can run the CVD and CPE via X11.
On Fri, Oct 24, 2014 at 8:27 PM, David Kincaid <ki...@gmail.com>
wrote:
> Sadly, no. I have not been able to get it working.
>
> - Dave
>
> On Fri, Oct 24, 2014 at 3:48 PM, Michelle Chen <mw...@mit.edu> wrote:
>
>> Hello,
>>
>> I'm also trying to get YTex to work and run into the same problem whe
>> runnign the build-setup.xml file. I get the DBping error of "[java] Error:
>> Could not find or load main class org.apache.ctakes.ytext.tools.DBPing"
>>
>> I have created a database called YTex, but was unsure if I set it up
>> correctly.
>>
>> @David, Did you find a fix for this?
>>
>> Thanks.
>>
>> -------
>> Michelle Chen
>>
>> Massachusetts Institute of Technology
>> Electrical Engineering and Computer Science
>> B.S. '14, M.Eng. '15
>>
>>
>> On Tue, Oct 14, 2014 at 10:27 AM, David Kincaid <ki...@gmail.com>
>> wrote:
>>
>>> Ok. I just noticed that the typo is in that parameter. Instead of
>>> CTAKES_HOME it should be $CTAKES_HOME. I get a little farther with that
>>> (although still have to use my installed version of ant), but now get a
>>> failure in the dbping: that it can't connect to a database. I don't have a
>>> database running, so I assume that is to be expected. I was hoping I could
>>> play with it without a database, but maybe that's not possible. I
>>> appreciate the help. If you update that ant command line in the wiki page
>>> to have $CTAKES_HOME instead of CTAKES_HOME it should work.
>>>
>>> - Dave
>>>
>>
>>
>
Re: NPE with ytex in ctakes 3.2.0
Posted by David Kincaid <ki...@gmail.com>.
Sadly, no. I have not been able to get it working.
- Dave
On Fri, Oct 24, 2014 at 3:48 PM, Michelle Chen <mw...@mit.edu> wrote:
> Hello,
>
> I'm also trying to get YTex to work and run into the same problem whe
> runnign the build-setup.xml file. I get the DBping error of "[java] Error:
> Could not find or load main class org.apache.ctakes.ytext.tools.DBPing"
>
> I have created a database called YTex, but was unsure if I set it up
> correctly.
>
> @David, Did you find a fix for this?
>
> Thanks.
>
> -------
> Michelle Chen
>
> Massachusetts Institute of Technology
> Electrical Engineering and Computer Science
> B.S. '14, M.Eng. '15
>
>
> On Tue, Oct 14, 2014 at 10:27 AM, David Kincaid <ki...@gmail.com>
> wrote:
>
>> Ok. I just noticed that the typo is in that parameter. Instead of
>> CTAKES_HOME it should be $CTAKES_HOME. I get a little farther with that
>> (although still have to use my installed version of ant), but now get a
>> failure in the dbping: that it can't connect to a database. I don't have a
>> database running, so I assume that is to be expected. I was hoping I could
>> play with it without a database, but maybe that's not possible. I
>> appreciate the help. If you update that ant command line in the wiki page
>> to have $CTAKES_HOME instead of CTAKES_HOME it should work.
>>
>> - Dave
>>
>
>
Re: NPE with ytex in ctakes 3.2.0
Posted by Michelle Chen <mw...@mit.edu>.
Hello,
I'm also trying to get YTex to work and run into the same problem whe
runnign the build-setup.xml file. I get the DBping error of "[java] Error:
Could not find or load main class org.apache.ctakes.ytext.tools.DBPing"
I have created a database called YTex, but was unsure if I set it up
correctly.
@David, Did you find a fix for this?
Thanks.
-------
Michelle Chen
Massachusetts Institute of Technology
Electrical Engineering and Computer Science
B.S. '14, M.Eng. '15
On Tue, Oct 14, 2014 at 10:27 AM, David Kincaid <ki...@gmail.com>
wrote:
> Ok. I just noticed that the typo is in that parameter. Instead of
> CTAKES_HOME it should be $CTAKES_HOME. I get a little farther with that
> (although still have to use my installed version of ant), but now get a
> failure in the dbping: that it can't connect to a database. I don't have a
> database running, so I assume that is to be expected. I was hoping I could
> play with it without a database, but maybe that's not possible. I
> appreciate the help. If you update that ant command line in the wiki page
> to have $CTAKES_HOME instead of CTAKES_HOME it should work.
>
> - Dave
>
Re: NPE with ytex in ctakes 3.2.0
Posted by David Kincaid <ki...@gmail.com>.
Ok. I just noticed that the typo is in that parameter. Instead of
CTAKES_HOME it should be $CTAKES_HOME. I get a little farther with that
(although still have to use my installed version of ant), but now get a
failure in the dbping: that it can't connect to a database. I don't have a
database running, so I assume that is to be expected. I was hoping I could
play with it without a database, but maybe that's not possible. I
appreciate the help. If you update that ant command line in the wiki page
to have $CTAKES_HOME instead of CTAKES_HOME it should work.
- Dave
Re: NPE with ytex in ctakes 3.2.0
Posted by vijay garla <vn...@gmail.com>.
can you drop the -Dlog4j.conf=xxx param?
On Tue, Oct 14, 2014 at 3:59 PM, David Kincaid <ki...@gmail.com>
wrote:
> Yes. I did do that. I just redid that step again to be sure and am still
> getting the same error.
>
> On Tue, Oct 14, 2014 at 8:50 AM, vijay garla <vn...@gmail.com> wrote:
>
>> Hi Dave,
>>
>> I uploaded scripts to the wiki page (step 1.5) - that issue should be
>> ironed out with the updated scripts - did you unpack them?
>>
>> -vj
>>
>> On Tue, Oct 14, 2014 at 3:43 PM, David Kincaid <ki...@gmail.com>
>> wrote:
>>
>>> 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=CTAKES_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=CTAKES_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.xml
>>>
>>> BUILD FAILED
>>> /home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-setup.xml:44:
>>> The following error occurred while executing this line:
>>> /home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-classpath.xml:109:
>>> A source file is missing:
>>> /home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/CTAKES_HOME/config/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 <vn...@gmail.com> 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 <vn...@gmail.com> 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 <kincaid.dave@gmail.com
>>>>> > 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 <vn...@gmail.com>
>>>>>> 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 <
>>>>>>> kincaid.dave@gmail.com> 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’s in ctakes-ytex-res.jar (is that in your classpath)?
>>>>>>>> > This is just a guess… vj may have a better idea if it still
>>>>>>>> doesn’t 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
>>>>>>>> > <ma...@childrens.harvard.edu>> wrote:
>>>>>>>> > I’m 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
>>>>>>>> those exists?
>>>>>>>> >
>>>>>>>> > From: David Kincaid [mailto:kincaid.dave@gmail.com<mailto:
>>>>>>>> > kincaid.dave@gmail.com>]
>>>>>>>> > Sent: Friday, October 10, 2014 4:23 PM
>>>>>>>> > To: user@ctakes.apache.org<ma...@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
>>>>>>>> might 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>>>>>>>> > at
>>>>>>>> >
>>>>>>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
>>>>>>>> > at
>>>>>>>> >
>>>>>>>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>>>>>>>> > at
>>>>>>>> >
>>>>>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>>>>>>>> > at
>>>>>>>> >
>>>>>>>> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>>>>>>> > at
>>>>>>>> >
>>>>>>>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
>>>>>>>> > at
>>>>>>>> >
>>>>>>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>>>>>>> > at
>>>>>>>> >
>>>>>>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>>>>>>>> > at
>>>>>>>> >
>>>>>>>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>>>>>>>> > at
>>>>>>>> >
>>>>>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
>>>>>>>> > at
>>>>>>>> >
>>>>>>>> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
>>>>>>>> > ... 9 more
>>>>>>>> > Caused by: java.lang.NullPointerException
>>>>>>>> > at
>>>>>>>> >
>>>>>>>> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
>>>>>>>> > at
>>>>>>>> >
>>>>>>>> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
>>>>>>>> > at
>>>>>>>> >
>>>>>>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>>>>>>>> > ... 24 more
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
Re: NPE with ytex in ctakes 3.2.0
Posted by David Kincaid <ki...@gmail.com>.
Yes. I did do that. I just redid that step again to be sure and am still
getting the same error.
On Tue, Oct 14, 2014 at 8:50 AM, vijay garla <vn...@gmail.com> wrote:
> Hi Dave,
>
> I uploaded scripts to the wiki page (step 1.5) - that issue should be
> ironed out with the updated scripts - did you unpack them?
>
> -vj
>
> On Tue, Oct 14, 2014 at 3:43 PM, David Kincaid <ki...@gmail.com>
> wrote:
>
>> 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=CTAKES_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=CTAKES_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.xml
>>
>> BUILD FAILED
>> /home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-setup.xml:44:
>> The following error occurred while executing this line:
>> /home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-classpath.xml:109:
>> A source file is missing:
>> /home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/CTAKES_HOME/config/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 <vn...@gmail.com> 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 <vn...@gmail.com> 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 <ki...@gmail.com>
>>>> 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 <vn...@gmail.com>
>>>>> 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 <
>>>>>> kincaid.dave@gmail.com> 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’s in ctakes-ytex-res.jar (is that in your classpath)?
>>>>>>> > This is just a guess… vj may have a better idea if it still
>>>>>>> doesn’t 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
>>>>>>> > <ma...@childrens.harvard.edu>> wrote:
>>>>>>> > I’m 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
>>>>>>> those exists?
>>>>>>> >
>>>>>>> > From: David Kincaid [mailto:kincaid.dave@gmail.com<mailto:
>>>>>>> > kincaid.dave@gmail.com>]
>>>>>>> > Sent: Friday, October 10, 2014 4:23 PM
>>>>>>> > To: user@ctakes.apache.org<ma...@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
>>>>>>> might 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>>>>>>> > at
>>>>>>> >
>>>>>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
>>>>>>> > at
>>>>>>> >
>>>>>>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>>>>>>> > at
>>>>>>> >
>>>>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>>>>>>> > at
>>>>>>> >
>>>>>>> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>>>>>> > at
>>>>>>> >
>>>>>>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
>>>>>>> > at
>>>>>>> >
>>>>>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>>>>>> > at
>>>>>>> >
>>>>>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>>>>>>> > at
>>>>>>> >
>>>>>>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>>>>>>> > at
>>>>>>> >
>>>>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
>>>>>>> > at
>>>>>>> >
>>>>>>> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
>>>>>>> > ... 9 more
>>>>>>> > Caused by: java.lang.NullPointerException
>>>>>>> > at
>>>>>>> >
>>>>>>> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
>>>>>>> > at
>>>>>>> >
>>>>>>> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
>>>>>>> > at
>>>>>>> >
>>>>>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>>>>>>> > ... 24 more
>>>>>>> >
>>>>>>> >
>>>>>>> >
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
Re: NPE with ytex in ctakes 3.2.0
Posted by vijay garla <vn...@gmail.com>.
Hi Dave,
I uploaded scripts to the wiki page (step 1.5) - that issue should be
ironed out with the updated scripts - did you unpack them?
-vj
On Tue, Oct 14, 2014 at 3:43 PM, David Kincaid <ki...@gmail.com>
wrote:
> 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=CTAKES_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=CTAKES_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.xml
>
> BUILD FAILED
> /home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-setup.xml:44:
> The following error occurred while executing this line:
> /home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-classpath.xml:109:
> A source file is missing:
> /home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/CTAKES_HOME/config/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 <vn...@gmail.com> 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 <vn...@gmail.com> 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 <ki...@gmail.com>
>>> 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 <vn...@gmail.com> 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 <
>>>>> kincaid.dave@gmail.com> 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’s in ctakes-ytex-res.jar (is that in your classpath)?
>>>>>> > This is just a guess… vj may have a better idea if it still doesn’t
>>>>>> 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
>>>>>> > <ma...@childrens.harvard.edu>> wrote:
>>>>>> > I’m 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
>>>>>> those exists?
>>>>>> >
>>>>>> > From: David Kincaid [mailto:kincaid.dave@gmail.com<mailto:
>>>>>> > kincaid.dave@gmail.com>]
>>>>>> > Sent: Friday, October 10, 2014 4:23 PM
>>>>>> > To: user@ctakes.apache.org<ma...@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
>>>>>> might 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>>>>>> > at
>>>>>> >
>>>>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
>>>>>> > at
>>>>>> >
>>>>>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>>>>>> > at
>>>>>> >
>>>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>>>>>> > at
>>>>>> >
>>>>>> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>>>>> > at
>>>>>> >
>>>>>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
>>>>>> > at
>>>>>> >
>>>>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>>>>> > at
>>>>>> >
>>>>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>>>>>> > at
>>>>>> >
>>>>>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>>>>>> > at
>>>>>> >
>>>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
>>>>>> > at
>>>>>> >
>>>>>> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
>>>>>> > ... 9 more
>>>>>> > Caused by: java.lang.NullPointerException
>>>>>> > at
>>>>>> >
>>>>>> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
>>>>>> > at
>>>>>> >
>>>>>> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
>>>>>> > at
>>>>>> >
>>>>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>>>>>> > ... 24 more
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
Re: NPE with ytex in ctakes 3.2.0
Posted by David Kincaid <ki...@gmail.com>.
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=CTAKES_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=CTAKES_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.xml
BUILD FAILED
/home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-setup.xml:44:
The following error occurred while executing this line:
/home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-classpath.xml:109:
A source file is missing:
/home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/CTAKES_HOME/config/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 <vn...@gmail.com> 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 <vn...@gmail.com> 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 <ki...@gmail.com>
>> 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 <vn...@gmail.com> 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 <kincaid.dave@gmail.com
>>>> > 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’s in ctakes-ytex-res.jar (is that in your classpath)?
>>>>> > This is just a guess… vj may have a better idea if it still doesn’t
>>>>> 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
>>>>> > <ma...@childrens.harvard.edu>> wrote:
>>>>> > I’m 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 those
>>>>> exists?
>>>>> >
>>>>> > From: David Kincaid [mailto:kincaid.dave@gmail.com<mailto:
>>>>> > kincaid.dave@gmail.com>]
>>>>> > Sent: Friday, October 10, 2014 4:23 PM
>>>>> > To: user@ctakes.apache.org<ma...@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 might
>>>>> 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>>>>> > at
>>>>> >
>>>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
>>>>> > at
>>>>> >
>>>>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>>>>> > at
>>>>> >
>>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>>>>> > at
>>>>> > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>>>> > at
>>>>> >
>>>>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
>>>>> > at
>>>>> >
>>>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>>>> > at
>>>>> >
>>>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>>>>> > at
>>>>> >
>>>>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>>>>> > at
>>>>> >
>>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
>>>>> > at
>>>>> >
>>>>> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
>>>>> > ... 9 more
>>>>> > Caused by: java.lang.NullPointerException
>>>>> > at
>>>>> >
>>>>> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
>>>>> > at
>>>>> >
>>>>> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
>>>>> > at
>>>>> >
>>>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>>>>> > ... 24 more
>>>>> >
>>>>> >
>>>>> >
>>>>>
>>>>
>>>>
>>>
>>
>
Re: NPE with ytex in ctakes 3.2.0
Posted by vijay garla <vn...@gmail.com>.
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 <vn...@gmail.com> 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 <ki...@gmail.com>
> 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 <vn...@gmail.com> 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 <ki...@gmail.com>
>>> 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’s in ctakes-ytex-res.jar (is that in your classpath)?
>>>> > This is just a guess… vj may have a better idea if it still doesn’t
>>>> 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
>>>> > <ma...@childrens.harvard.edu>> wrote:
>>>> > I’m 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 those
>>>> exists?
>>>> >
>>>> > From: David Kincaid [mailto:kincaid.dave@gmail.com<mailto:
>>>> > kincaid.dave@gmail.com>]
>>>> > Sent: Friday, October 10, 2014 4:23 PM
>>>> > To: user@ctakes.apache.org<ma...@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 might
>>>> 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>>>> > at
>>>> >
>>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
>>>> > at
>>>> >
>>>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>>>> > at
>>>> >
>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>>>> > at
>>>> > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>>> > at
>>>> >
>>>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
>>>> > at
>>>> >
>>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>>> > at
>>>> >
>>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>>>> > at
>>>> >
>>>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>>>> > at
>>>> >
>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
>>>> > at
>>>> >
>>>> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
>>>> > ... 9 more
>>>> > Caused by: java.lang.NullPointerException
>>>> > at
>>>> >
>>>> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
>>>> > at
>>>> >
>>>> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
>>>> > at
>>>> >
>>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>>>> > ... 24 more
>>>> >
>>>> >
>>>> >
>>>>
>>>
>>>
>>
>
Re: NPE with ytex in ctakes 3.2.0
Posted by vijay garla <vn...@gmail.com>.
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 <ki...@gmail.com>
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 <vn...@gmail.com> 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 <ki...@gmail.com>
>> 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’s in ctakes-ytex-res.jar (is that in your classpath)?
>>> > This is just a guess… vj may have a better idea if it still doesn’t
>>> 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
>>> > <ma...@childrens.harvard.edu>> wrote:
>>> > I’m 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 those
>>> exists?
>>> >
>>> > From: David Kincaid [mailto:kincaid.dave@gmail.com<mailto:
>>> > kincaid.dave@gmail.com>]
>>> > Sent: Friday, October 10, 2014 4:23 PM
>>> > To: user@ctakes.apache.org<ma...@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 might
>>> 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>>> > at
>>> >
>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
>>> > at
>>> >
>>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>>> > at
>>> >
>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>>> > at
>>> > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>> > at
>>> >
>>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
>>> > at
>>> >
>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>> > at
>>> >
>>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>>> > at
>>> >
>>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>>> > at
>>> >
>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
>>> > at
>>> >
>>> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
>>> > ... 9 more
>>> > Caused by: java.lang.NullPointerException
>>> > at
>>> >
>>> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
>>> > at
>>> >
>>> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
>>> > at
>>> >
>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>>> > ... 24 more
>>> >
>>> >
>>> >
>>>
>>
>>
>
Re: NPE with ytex in ctakes 3.2.0
Posted by David Kincaid <ki...@gmail.com>.
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 <vn...@gmail.com> 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 <ki...@gmail.com>
> 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’s in ctakes-ytex-res.jar (is that in your classpath)?
>> > This is just a guess… vj may have a better idea if it still doesn’t 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
>> > <ma...@childrens.harvard.edu>> wrote:
>> > I’m 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 those
>> exists?
>> >
>> > From: David Kincaid [mailto:kincaid.dave@gmail.com<mailto:
>> > kincaid.dave@gmail.com>]
>> > Sent: Friday, October 10, 2014 4:23 PM
>> > To: user@ctakes.apache.org<ma...@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 might
>> 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>> > at
>> >
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
>> > at
>> >
>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>> > at
>> >
>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>> > at
>> > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>> > at
>> >
>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
>> > at
>> >
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>> > at
>> >
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>> > at
>> >
>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>> > at
>> >
>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
>> > at
>> >
>> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
>> > ... 9 more
>> > Caused by: java.lang.NullPointerException
>> > at
>> >
>> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
>> > at
>> >
>> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
>> > at
>> >
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>> > ... 24 more
>> >
>> >
>> >
>>
>
>
Re: NPE with ytex in ctakes 3.2.0
Posted by vijay garla <vn...@gmail.com>.
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 <ki...@gmail.com>
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’s in ctakes-ytex-res.jar (is that in your classpath)?
> > This is just a guess… vj may have a better idea if it still doesn’t 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
> > <ma...@childrens.harvard.edu>> wrote:
> > I’m 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 those
> exists?
> >
> > From: David Kincaid [mailto:kincaid.dave@gmail.com<mailto:
> > kincaid.dave@gmail.com>]
> > Sent: Friday, October 10, 2014 4:23 PM
> > To: user@ctakes.apache.org<ma...@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 might 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> > at
> >
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
> > at
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> > at
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> > at
> > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> > at
> >
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
> > at
> >
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> > at
> >
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> > at
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> > at
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
> > at
> >
> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
> > ... 9 more
> > Caused by: java.lang.NullPointerException
> > at
> >
> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
> > at
> >
> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
> > at
> >
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> > ... 24 more
> >
> >
> >
>
Re: NPE with ytex in ctakes 3.2.0
Posted by vijay garla <vn...@gmail.com>.
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 <ki...@gmail.com>
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’s in ctakes-ytex-res.jar (is that in your classpath)?
> > This is just a guess… vj may have a better idea if it still doesn’t 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
> > <ma...@childrens.harvard.edu>> wrote:
> > I’m 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 those
> exists?
> >
> > From: David Kincaid [mailto:kincaid.dave@gmail.com<mailto:
> > kincaid.dave@gmail.com>]
> > Sent: Friday, October 10, 2014 4:23 PM
> > To: user@ctakes.apache.org<ma...@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 might 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> > at
> >
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
> > at
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> > at
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> > at
> > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> > at
> >
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
> > at
> >
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> > at
> >
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> > at
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> > at
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
> > at
> >
> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
> > ... 9 more
> > Caused by: java.lang.NullPointerException
> > at
> >
> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
> > at
> >
> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
> > at
> >
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> > ... 24 more
> >
> >
> >
>
Re: NPE with ytex in ctakes 3.2.0
Posted by David Kincaid <ki...@gmail.com>.
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 <Pe...@childrens.harvard.edu>
wrote:
> I think it’s in ctakes-ytex-res.jar (is that in your classpath)?
> This is just a guess… vj may have a better idea if it still doesn’t 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
> <ma...@childrens.harvard.edu>> wrote:
> I’m 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 those exists?
>
> From: David Kincaid [mailto:kincaid.dave@gmail.com<mailto:
> kincaid.dave@gmail.com>]
> Sent: Friday, October 10, 2014 4:23 PM
> To: user@ctakes.apache.org<ma...@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 might 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
> at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
> ... 9 more
> Caused by: java.lang.NullPointerException
> at
> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
> at
> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> ... 24 more
>
>
>
Re: NPE with ytex in ctakes 3.2.0
Posted by David Kincaid <ki...@gmail.com>.
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 <Pe...@childrens.harvard.edu>
wrote:
> I think it’s in ctakes-ytex-res.jar (is that in your classpath)?
> This is just a guess… vj may have a better idea if it still doesn’t 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
> <ma...@childrens.harvard.edu>> wrote:
> I’m 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 those exists?
>
> From: David Kincaid [mailto:kincaid.dave@gmail.com<mailto:
> kincaid.dave@gmail.com>]
> Sent: Friday, October 10, 2014 4:23 PM
> To: user@ctakes.apache.org<ma...@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 might 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
> at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
> ... 9 more
> Caused by: java.lang.NullPointerException
> at
> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
> at
> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> ... 24 more
>
>
>
RE: NPE with ytex in ctakes 3.2.0
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
I think it’s in ctakes-ytex-res.jar (is that in your classpath)?
This is just a guess… vj may have a better idea if it still doesn’t 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 <Pe...@childrens.harvard.edu>> wrote:
I’m 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 those exists?
From: David Kincaid [mailto:kincaid.dave@gmail.com<ma...@gmail.com>]
Sent: Friday, October 10, 2014 4:23 PM
To: user@ctakes.apache.org<ma...@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 might 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
at org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
... 9 more
Caused by: java.lang.NullPointerException
at org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
at org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 24 more
RE: NPE with ytex in ctakes 3.2.0
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
I think it’s in ctakes-ytex-res.jar (is that in your classpath)?
This is just a guess… vj may have a better idea if it still doesn’t 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 <Pe...@childrens.harvard.edu>> wrote:
I’m 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 those exists?
From: David Kincaid [mailto:kincaid.dave@gmail.com<ma...@gmail.com>]
Sent: Friday, October 10, 2014 4:23 PM
To: user@ctakes.apache.org<ma...@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 might 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
at org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
... 9 more
Caused by: java.lang.NullPointerException
at org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
at org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 24 more
Re: NPE with ytex in ctakes 3.2.0
Posted by David Kincaid <ki...@gmail.com>.
No. I have no file named beanRefContext.xml anywhere on my hard drive.
On Fri, Oct 10, 2014 at 3:45 PM, Chen, Pei <Pe...@childrens.harvard.edu>
wrote:
> I’m 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 those exists?
>
>
>
> *From:* David Kincaid [mailto: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 might 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
>
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>
> at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
>
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
>
> at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
>
> ... 9 more
>
> Caused by: java.lang.NullPointerException
>
> at
> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
>
> at
> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
>
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>
> ... 24 more
>
>
>
RE: NPE with ytex in ctakes 3.2.0
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
I’m 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 those exists?
From: David Kincaid [mailto: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 might 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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java: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.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:425)
at org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
... 9 more
Caused by: java.lang.NullPointerException
at org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
at org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 24 more