I’m actually getting the same error you are but with the 
ExtractionPrepAnnotator I’m trying to add to my (otherwise-working) pipeline. 
So a resolution to your issue may help me as well.

One thing I notice in your pipeline is there is no reader. You’ll need this to 
process documents.

The only difference in how I’m adding the DBconsumer vs how you are is that I 
have several parameters set away from default values. That shouldn’t make it 
difference but you could try it:

add org.apache.ctakes.ytex.uima.annotators.DBConsumer 
analysisBatch="Radiology_test_DefaultFastPipeline7" storeDocText=false 
storeCAS=false  
typesToIgnore=org.apache.ctakes.typesystem.type.textspan.Sentence,org.apache.ctakes.typesystem.type.syntax.ContractionToken,org.apache.ctakes.typesystem.type.syntax.NewlineToken,org.apache.ctakes.typesystem.type.syntax.NumToken,org.apache.ctakes.typesystem.type.syntax.PunctuationToken,org.apache.ctakes.typesystem.type.syntax.SymbolToken,org.apache.ctakes.typesystem.type.syntax.NP,org.apache.ctakes.typesystem.type.syntax.VP,org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation,org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation,org.apache.ctakes.typesystem.type.syntax.WordToken,org.apache.ctakes.typesystem.type.syntax.TreebankNode,org.apache.ctakes.typesystem.type.syntax.TopTreebankNode,org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode

The step 6 you mention isn’t necessary, unless you want to use the Sense 
Disambiguator, I think.

Sean

From: Schenk, Gundolf [mailto:gundolf.sch...@ucsf.edu]
Sent: Tuesday, March 06, 2018 12:43 PM
To: Mullane, Sean *HS; user@ctakes.apache.org
Subject: Re: YTEX installation

Hi,

Here is my modified clinical pipeline with DBConsumer added at the end:
apache-ctakes-4.0.0> cat 
resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipelineWithYtex.piper
// Commands and parameters to create a default plaintext document processing 
pipeline with UMLS lookup

// Load a simple token processing pipeline from another pipeline file
load DefaultTokenizerPipeline.piper

// Add non-core annotators
add ContextDependentTokenizerAnnotator
addDescription POSTagger

// Add Chunkers
load ChunkerSubPipe.piper

// Default fast dictionary lookup
add DefaultJCasTermAnnotator

// Add Cleartk Entity Attribute annotators
load AttributeCleartkSubPipe.piper

// Add YTEX UIMA Annotator to store annotations in database
add org.apache.ctakes.ytex.uima.annotators.DBConsumer
apache-ctakes-4.0.0>

This file is called via the script 
$CTAKES_HOME/bin/runClinicalPipelineWithYtex.sh:
[…]
PRG="$0"
while [ -h "$PRG" ]; do
  ls=`ls -ld "$PRG"`
  link=`expr "$ls" : '.*-> \(.*\)$'`
  if expr "$link" : '/.*' > /dev/null; then
    PRG="$link"
  else
    PRG=`dirname "$PRG"`/"$link"
  fi
done
PRGDIR=`dirname "$PRG"`

# Only set CTAKES_HOME if not already set
[ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`

cd $CTAKES_HOME
java -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* 
-Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g 
org.apache.ctakes.core.pipeline.PiperFileRunner -p 
org/apache/ctakes/clinical/pipeline/DefaultFastPipelineWithYtex.piper "$@"

Does this look ok?

BTW, I did not do step 6) of the YTEX installations (it says it’s optional). I 
have installed and enabled UMLS for cTAKES (and it’s working for the default 
clinical pipeline). Do I have to do step 6) for YTEX to work properly perhaps?

Cheers,
Gundolf.



From: "Mullane, Sean *HS" 
<sp...@hscmail.mcc.virginia.edu<mailto:sp...@hscmail.mcc.virginia.edu>>
Date: Monday, March 5, 2018 at 17:04
To: "Schenk, Gundolf" 
<gundolf.sch...@ucsf.edu<mailto:gundolf.sch...@ucsf.edu>>, 
"user@ctakes.apache.org<mailto:user@ctakes.apache.org>" 
<user@ctakes.apache.org<mailto:user@ctakes.apache.org>>
Subject: RE: YTEX installation

Can you share the line in your piper file where you add the DBConsumer?

Sean

From: Schenk, Gundolf [mailto:gundolf.sch...@ucsf.edu]
Sent: Monday, March 05, 2018 7:27 PM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
Subject: Re: YTEX installation

Hi,

I was able to solve the errors about missing classes. Somehow, I must have 
skipped accidentally step 2) in the YTEX installations. Unfortunately, the 
final error is still there:
[…]
06 Mar 2018 00:09:05 DEBUG DefaultListableBeanFactory - Retrieved dependent 
beans for bean 'intrinsicInfoContentEvaluator': [conceptDao]
06 Mar 2018 00:09:05 DEBUG DefaultListableBeanFactory - Retrieved dependent 
beans for bean 'conceptDao': [intrinsicInfoContentEvaluator]
06 Mar 2018 00:09:05 DEBUG DisposableBeanAdapter - Invoking destroy() on bean 
with name 'sessionFactory'
06 Mar 2018 00:09:05 DEBUG SessionFactoryImpl - HHH000031: Closing
06 Mar 2018 00:09:05 DEBUG DisposableBeanAdapter - Invoking destroy method 
'close' on bean with name 'dataSource'
06 Mar 2018 00:09:05  INFO DefaultListableBeanFactory - Destroying singletons 
in 
org.springframework.beans.factory.support.DefaultListableBeanFactory@64c8fcfb<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@64c8fcfb>:
 defining beans [ytexApplicationContext]; root of factory hierarchy
06 Mar 2018 00:09:05 ERROR PiperFileRunner - Initialization of annotator class 
"org.apache.ctakes.ytex.uima.annotators.DBConsumer" failed.  (Descriptor: 
<unknown>)

Unclear to me, what might cause it. Any thoughts welcome!

Cheers,
Gundolf.



From: "Schenk, Gundolf" 
<gundolf.sch...@ucsf.edu<mailto:gundolf.sch...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" 
<user@ctakes.apache.org<mailto:user@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 15:12
To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" 
<user@ctakes.apache.org<mailto:user@ctakes.apache.org>>
Subject: Re: YTEX installation

This increased the logging, indeed. Thank you!

I am not really sure what to look out for. Here are a few snippets, that might 
help to shed some light onto it:
[…]
Loading lexica.
Loading model:
................................
Loading model:
.............................
05 Mar 2018 22:35:59 DEBUG DataBinder - DataBinder requires binding of required 
fields [_loggerName]
05 Mar 2018 22:35:59 DEBUG DataBinder - DataBinder requires binding of required 
fields []
05 Mar 2018 22:35:59 DEBUG StandardEnvironment - Initializing new 
StandardEnvironment
05 Mar 2018 22:35:59 DEBUG StandardEnvironment - Adding [systemProperties] 
PropertySource with lowest search precedence
[…]
05 Mar 2018 22:35:59 DEBUG StandardEnvironment - Initialized 
StandardEnvironment with PropertySources [systemProperties,systemEnvironment]
05 Mar 2018 22:35:59 DEBUG BeanUtils - No property editor 
[org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine$FEATURE_CONFIGEditor]
 found for type 
org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine$FEATURE_CONFIG
 according to 'Editor' suffix convention
05 Mar 2018 22:35:59 DEBUG DataBinder - DataBinder requires binding of required 
fields [classifierJarPath]
05 Mar 2018 22:35:59 DEBUG DataBinder - DataBinder requires binding of required 
fields []
05 Mar 2018 22:35:59 DEBUG StandardEnvironment - Initializing new 
StandardEnvironment
05 Mar 2018 22:35:59 DEBUG StandardEnvironment - Adding [systemProperties] 
PropertySource with lowest search precedence
[…]
05 Mar 2018 22:36:00 DEBUG StandardEnvironment - Initialized 
StandardEnvironment with PropertySources [systemProperties,systemEnvironment]
05 Mar 2018 22:36:00  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 22:36:00 DEBUG DefaultDocumentLoader - Using JAXP provider 
[org.apache.xerces.jaxp.DocumentBuilderFactoryImpl]
05 Mar 2018 22:36:00 DEBUG BeansDtdResolver - Found beans DTD 
[http://www.springframework.org/dtd/spring-beans.dtd] in classpath: 
spring-beans.dtd
05 Mar 2018 22:36:00 DEBUG DefaultBeanDefinitionDocumentReader - Loading bean 
definitions
05 Mar 2018 22:36:00 DEBUG BeanDefinitionParserDelegate - No XML 'id' specified 
- using 'ytexApplicationContext' as bean name and [] as aliases
[…]
05 Mar 2018 22:36:00  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 22:36:00 DEBUG XmlBeanDefinitionReader - Loaded 1 bean definitions 
from location pattern 
[classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml]
05 Mar 2018 22:36:00 DEBUG ClassPathXmlApplicationContext - Bean factory for 
org.springframework.context.support.ClassPathXmlApplicationContext@7e18ced7<mailto:org.springframework.context.support.ClassPathXmlApplicationContext@7e18ced7>:
 
org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03>:
 defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 22:36:00 DEBUG ClassPathXmlApplicationContext - Unable to locate 
MessageSource with name 'messageSource': using default 
[org.springframework.context.support.DelegatingMessageSource@57e4b86c]
05 Mar 2018 22:36:00 DEBUG ClassPathXmlApplicationContext - Unable to locate 
ApplicationEventMulticaster with name 'applicationEventMulticaster': using 
default 
[org.springframework.context.event.SimpleApplicationEventMulticaster@589dfa6f]
05 Mar 2018 22:36:00  INFO DefaultListableBeanFactory - Pre-instantiating 
singletons in 
org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03>:
 defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 22:36:00 DEBUG DefaultListableBeanFactory - Creating shared 
instance of singleton bean 'ytexApplicationContext'
05 Mar 2018 22:36:00 DEBUG DefaultListableBeanFactory - Creating instance of 
bean 'ytexApplicationContext'
05 Mar 2018 22:36:00 DEBUG StandardEnvironment - Initializing new 
StandardEnvironment
[…]
05 Mar 2018 22:36:00 DEBUG StandardEnvironment - Initialized 
StandardEnvironment with PropertySources [systemProperties,systemEnvironment]
05 Mar 2018 22:36:00 DEBUG BeanUtils - No property editor 
[org.springframework.context.ApplicationContextEditor] found for type 
org.springframework.context.ApplicationContext according to 'Editor' suffix 
convention
05 Mar 2018 22:36:00 DEBUG StandardEnvironment - Initializing new 
StandardEnvironment
[…]
05 Mar 2018 22:36:00 DEBUG PluggableSchemaResolver - Found XML schema 
[http://www.springframework.org/schema/beans/spring-beans-2.5.xsd] in 
classpath: org/springframework/beans/factory/xml/spring-beans-2.5.xsd
05 Mar 2018 22:36:00 DEBUG DefaultBeanDefinitionDocumentReader - Loading bean 
definitions
05 Mar 2018 22:36:00 DEBUG BeanDefinitionParserDelegate - Neither XML 'id' nor 
'name' specified - using generated bean name 
[org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0]
05 Mar 2018 22:36:00 DEBUG XmlBeanDefinitionReader - Loaded 8 bean definitions 
from location pattern [org/apache/ctakes/ytex/beans-datasource.xml]
05 Mar 2018 22:36:00  INFO XmlBeanDefinitionReader - Loading XML bean 
definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
05 Mar 2018 22:36:00 DEBUG DefaultDocumentLoader - Using JAXP provider 
[org.apache.xerces.jaxp.DocumentBuilderFactoryImpl]
[…]
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Ignoring bean class 
loading failure for bean 'infogainAttributeEval'
org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find 
class [weka.attributeSelection.InfoGainAttributeEval] for bean with name 
'infogainAttributeEval' defined in class path resource 
[org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is 
java.lang.ClassNotFoundException: weka.attributeSelection.InfoGainAttributeEval
                at 
org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1262)
[…]
                at 
org.apache.ctakes.core.pipeline.PiperFileRunner.main(PiperFileRunner.java:81)
Caused by: java.lang.ClassNotFoundException: 
weka.attributeSelection.InfoGainAttributeEval
                at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
[…]
                ... 57 more
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Ignoring bean class 
loading failure for bean 'rankerSearch'
org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find 
class [weka.attributeSelection.Ranker] for bean with name 'rankerSearch' 
defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; 
nested exception is java.lang.ClassNotFoundException: 
weka.attributeSelection.Ranker
                at 
org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1262)
[…]
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Finished creating 
instance of bean 'hibernateProperties'
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Creating shared 
instance of singleton bean 'dataSource'
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Creating instance of 
bean 'dataSource'
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Returning cached 
instance of singleton bean 
'org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0'
[…]
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Returning cached 
instance of singleton bean 
'org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9'
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Eagerly caching bean 
'dataSource' to allow for resolving potential circular references
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Returning cached 
instance of singleton bean 
'org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0'
[…]
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Returning cached 
instance of singleton bean 
'org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9'
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Finished creating 
instance of bean 'dataSource'
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Creating shared 
instance of singleton bean 'txAdvice'
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Creating instance of 
bean 'txAdvice'
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Eagerly caching bean 
'txAdvice' to allow for resolving potential circular references
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Creating shared 
instance of singleton bean 'transactionManager'
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Creating instance of 
bean 'transactionManager'
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Returning cached 
instance of singleton bean 
'org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0'
[…]
05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Returning cached 
instance of singleton bean 
'org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9'
05 Mar 2018 22:36:01  INFO DefaultListableBeanFactory - Destroying singletons 
in 
org.springframework.beans.factory.support.DefaultListableBeanFactory@26a45089<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@26a45089>:
 defining beans 
[org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,[…],org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8601Converter,documentMapperService];
 root of factory hierarchy
05 Mar 2018 22:36:01 DEBUG DisposableBeanAdapter - Invoking destroy method 
'close' on bean with name 'dataSource'
05 Mar 2018 22:36:01  INFO DefaultListableBeanFactory - Destroying singletons 
in 
org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03>:
 defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 22:36:01 ERROR PiperFileRunner - Initialization of annotator class 
"org.apache.ctakes.ytex.uima.annotators.DBConsumer" failed.  (Descriptor: 
<unknown>)

Seems to me that some classes were not found?
Is my $CLASSPATH correct?
> echo $CLASSPATH
/mnt/apache-ctakes-4.0.0/desc/:/mnt/apache-ctakes-4.0.0/resources/:/mnt/apache-ctakes-4.0.0/lib/*

Cheers,
Gundolf.




From: "Mullane, Sean *HS" 
<sp...@hscmail.mcc.virginia.edu<mailto:sp...@hscmail.mcc.virginia.edu>>
Reply-To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" 
<user@ctakes.apache.org<mailto:user@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 14:32
To: "Schenk, Gundolf" 
<gundolf.sch...@ucsf.edu<mailto:gundolf.sch...@ucsf.edu>>, 
"user@ctakes.apache.org<mailto:user@ctakes.apache.org>" 
<user@ctakes.apache.org<mailto:user@ctakes.apache.org>>
Subject: RE: YTEX installation

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:gundolf.sch...@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<mailto:user@ctakes.apache.org>
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" 
<sp...@hscmail.mcc.virginia.edu<mailto:sp...@hscmail.mcc.virginia.edu>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" 
<gundolf.sch...@ucsf.edu<mailto:gundolf.sch...@ucsf.edu>>, 
"user@ctakes.apache.org<mailto:user@ctakes.apache.org>" 
<user@ctakes.apache.org<mailto:user@ctakes.apache.org>>
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:gundolf.sch...@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
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" 
<sp...@hscmail.mcc.virginia.edu<mailto:sp...@hscmail.mcc.virginia.edu>>
Reply-To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" 
<user@ctakes.apache.org<mailto:user@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" 
<gundolf.sch...@ucsf.edu<mailto:gundolf.sch...@ucsf.edu>>, 
"user@ctakes.apache.org<mailto:user@ctakes.apache.org>" 
<user@ctakes.apache.org<mailto:user@ctakes.apache.org>>
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:gundolf.sch...@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<mailto:user@ctakes.apache.org>
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" 
<sp...@hscmail.mcc.virginia.edu<mailto:sp...@hscmail.mcc.virginia.edu>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" 
<gundolf.sch...@ucsf.edu<mailto:gundolf.sch...@ucsf.edu>>, 
"user@ctakes.apache.org<mailto:user@ctakes.apache.org>" 
<user@ctakes.apache.org<mailto:user@ctakes.apache.org>>
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:gundolf.sch...@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
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 
<gandhi.natara...@arisglobal.com<mailto:gandhi.natara...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" 
<user@ctakes.apache.org<mailto:user@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" 
<user@ctakes.apache.org<mailto:user@ctakes.apache.org>>
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:gundolf.sch...@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
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 
<brianwil...@hsl.harvard.edu<mailto:brianwil...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" 
<user@ctakes.apache.org<mailto:user@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" 
<user@ctakes.apache.org<mailto:user@ctakes.apache.org>>
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: brianwil...@hsl.harvard.edu<mailto:brianwil...@hsl.harvard.edu>

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