I’m assuming you’re using a file called ‘log4j.xml’ in the directory
%CTAKES_HOME%\config – let me know if this is not the case.
In my log4j.xml file, I would make that change by replacing INFO with DEBUG in
these lines:
<root>
<level value="INFO"/>
<appender-ref ref="consoleAppender" />
</root>
If you are using the consoleAppender appender, you should just see logs in the
CLI. You would only see file-based logs if you use a fileAppender appender.
These are also set within the log4j.xml file.
Sean
From: Schenk, Gundolf [mailto:[email protected]]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; [email protected]
Subject: Re: YTEX installation
Hi Sean,
Do you mean that I should set debug=true in config.log4j.xml ? This is what I
already have. I do not see any log-files (only logging I can see is in the
CLI). Is there a place where I might find log-files? Do I have to set a
command-line parameter?
Many thanks for helping,
Gundolf.
From: "Mullane, Sean *HS"
<[email protected]<mailto:[email protected]>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf"
<[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: RE: YTEX installation
You could try setting the log level to DEBUG in log4j.xml if you haven’t
already, then re-run the pipeline. You should get more detailed feedback in the
logs that way.
Sean
From: Schenk, Gundolf [mailto:[email protected]]
Sent: Monday, March 05, 2018 2:03 PM
To: [email protected]<mailto:[email protected]>
Subject: Re: YTEX installation
Yes, step 7) of the YTEX install instructions worked successfully. Which
environment variables need to be set?
I have (manually) sourced ~/ctakes.profile, which sets $CTAKES_HOME and
$CLASSPATH. What else should I check?
Cheers,
Gundolf.
From: "Mullane, Sean *HS"
<[email protected]<mailto:[email protected]>>
Reply-To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf"
<[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: RE: YTEX installation
Have you done step 7 listed here? (
https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation )
If so, maybe check that your environment variables are set correctly.
From: Schenk, Gundolf [mailto:[email protected]]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; [email protected]<mailto:[email protected]>
Subject: Re: YTEX installation
Hi Sean,
Thanks for your reply. I think, I did set the DB access parameters correctly.
This was already done for the DB creation and has worked there. Any other
thoughts?
Cheers,
Gundolf.
From: "Mullane, Sean *HS"
<[email protected]<mailto:[email protected]>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf"
<[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: RE: YTEX installation
Have you set the references to your database in the ytex.properties file? This
is necessary so that ctakes knows how to connect to the database.
Sean
From: Schenk, Gundolf [mailto:[email protected]]
Sent: Monday, March 05, 2018 12:57 PM
To: [email protected]<mailto:[email protected]>
Subject: Re: YTEX installation
Hi Gandhi,
Many thanks for your reply! It looks like cTAKES can find the DBConsumer module
now. However, I am getting an initialization error when I run the pipeline.
Here is the output:
apache-ctakes-4.0.0> bin/runClinicalPipelineWithYtex.sh -i input/ --xmiOut
output/ --user xxx –pass xxx
[…]
Loading model:
.............................
05 Mar 2018 17:13:51 INFO ApplicationContextHolder - loading ytex.properties
from:
file:/mnt/apache-ctakes-4.0.0/resources/org/apache/ctakes/ytex/ytex.properties
05 Mar 2018 17:13:51 INFO ApplicationContextHolder -
beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml
05 Mar 2018 17:13:51 INFO ClassPathXmlApplicationContext - Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@7e18ced7<mailto:org.springframework.context.support.ClassPathXmlApplicationContext@7e18ced7>:
startup date [Mon Mar 05 17:13:51 UTC 2018]; root of context hierarchy
05 Mar 2018 17:13:51 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from URL
[jar:file:/mnt/apache-ctakes-4.0.0/lib/ctakes-ytex-res-4.0.0.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]
05 Mar 2018 17:13:52 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from URL
[jar:file:/mnt/apache-ctakes-4.0.0/lib/ctakes-ytex-web-4.0.0-classes.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]
05 Mar 2018 17:13:52 INFO DefaultListableBeanFactory - Overriding bean
definition for bean 'ytexApplicationContext': replacing [Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[jar:file:/mnt/apache-ctakes-4.0.0/lib/ctakes-ytex-res-4.0.0.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]]
with [Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[jar:file:/mnt/apache-ctakes-4.0.0/lib/ctakes-ytex-web-4.0.0-classes.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]]
05 Mar 2018 17:13:52 INFO DefaultListableBeanFactory - Pre-instantiating
singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@21be14c2<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@21be14c2>:
defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<mailto:org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93>:
startup date [Mon Mar 05 17:13:52 UTC 2018]; root of context hierarchy
05 Mar 2018 17:13:52 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/beans-datasource.xml]
05 Mar 2018 17:13:52 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
05 Mar 2018 17:13:52 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel-sim.xml]
05 Mar 2018 17:13:52 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/uima/beans-uima.hbm.xml]
05 Mar 2018 17:13:52 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/uima/beans-uima-dao.xml]
05 Mar 2018 17:13:52 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/uima/beans-uima-mapper.xml]
05 Mar 2018 17:13:52 INFO DefaultListableBeanFactory - Overriding bean
definition for bean 'mapperOperation': replacing [Root bean: class
[org.springframework.aop.aspectj.AspectJExpressionPointcut]; scope=prototype;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null] with [Root
bean: class [org.springframework.aop.aspectj.AspectJExpressionPointcut];
scope=prototype; abstract=false; lazyInit=false; autowireMode=0;
dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null]
05 Mar 2018 17:13:52 INFO PropertyPlaceholderConfigurer - Loading properties
file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
05 Mar 2018 17:13:52 INFO PropertyPlaceholderConfigurer - Loading properties
file from class path resource [org/apache/ctakes/ytex/ytex.properties]
05 Mar 2018 17:13:52 INFO PropertyPlaceholderConfigurer - Loading properties
file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
05 Mar 2018 17:13:52 INFO DefaultListableBeanFactory - Pre-instantiating
singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@5b665a30<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@5b665a30>:
defining beans
[org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService,conceptSimilarityService,abstractConceptKernel,abstractLinKernel,abstractSemanticSimKernel,mainSuiSemanticTypeKernel,tuiSemanticTypeKernel,wordSenseDisambiguator,sessionFactory,ytexDaoOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#8,documentDao,namedEntityRegexDao,segmentRegexDao,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8601Converter,documentMapperService];
root of factory hierarchy
05 Mar 2018 17:13:52 INFO PropertiesFactoryBean - Loading properties file from
class path resource [org/apache/ctakes/ytex/ytex.properties]
05 Mar 2018 17:13:52 INFO DefaultListableBeanFactory - Destroying singletons
in
org.springframework.beans.factory.support.DefaultListableBeanFactory@5b665a30<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@5b665a30>:
defining beans
[org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService,conceptSimilarityService,abstractConceptKernel,abstractLinKernel,abstractSemanticSimKernel,mainSuiSemanticTypeKernel,tuiSemanticTypeKernel,wordSenseDisambiguator,sessionFactory,ytexDaoOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#8,documentDao,namedEntityRegexDao,segmentRegexDao,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8601Converter,documentMapperService];
root of factory hierarchy
05 Mar 2018 17:13:52 INFO DefaultListableBeanFactory - Destroying singletons
in
org.springframework.beans.factory.support.DefaultListableBeanFactory@21be14c2<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@21be14c2>:
defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 ERROR PiperFileRunner - Initialization of annotator class
"org.apache.ctakes.ytex.uima.annotators.DBConsumer" failed. (Descriptor:
<unknown>)
I am not sure where to look next. Any clues of what it could be?
Cheers,
Gundolf.
From: Gandhi Rajan Natarajan
<[email protected]<mailto:[email protected]>>
Reply-To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Date: Saturday, March 3, 2018 at 02:15
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: RE: YTEX installation
HI Gundolf,
Try using – “add org.apache.ctakes.ytex.uima.annotators.DBConsumer”
Also “documentMapperService” bean should be available in your application
context.
Regards,
Gandhi
From: Schenk, Gundolf [mailto:[email protected]]
Sent: Saturday, March 03, 2018 4:11 AM
To: [email protected]<mailto:[email protected]>
Subject: Re: YTEX installation
Hi Brian,
The link helped indeed. Thanks!
I had to change also the db engine to innodb on mysql. So now that I am through
with the DB creation, I am unsure how to include (add) the DBConsumer
annotator. A simple:
add DBConsumer
at the end of the DefaultClinicalPipeline.piper results in an error:
02 Mar 2018 22:09:01 ERROR PiperFileRunner - MESSAGE LOCALIZATION FAILED: Can't
find resource for bundle java.util.PropertyResourceBundle, key No Analysis
Component found for DBConsumer
How can I tell the system where to look at?
Thanks,
Gundolf.
From: Brian Wilson
<[email protected]<mailto:[email protected]>>
Reply-To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Date: Friday, February 23, 2018 at 15:13
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: YTEX installation
might help...
https://code.google.com/archive/p/ytex/downloads
On 02/23/2018 05:45 PM, Schenk, Gundolf wrote:
Hi,
Does anyone know how to export the resulting XMI files to a sql database
efficiently? I found the YTEX DBConsumer module but I am not able to install
YTEX properly as the links the the zip files seem to be outdated/broken at:
https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
Are there updated instructions anywhere?
Many thanks,
Gundolf.
--
Brian Wilson
Data Warehouse Architect
Hebrew SeniorLife
1200 Centre Street
Boston, MA 02131
Tel: (617) 971-5742
email: [email protected]<mailto:[email protected]>
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