You are viewing a plain text version of this content. The canonical link for it is here.
Posted to user@ctakes.apache.org by "Schenk, Gundolf" <Gu...@ucsf.edu> on 2018/03/02 22:41:09 UTC
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 <Br...@hsl.harvard.edu>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org" <us...@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I found the YTEX DBConsumer module but I am not able to install YTEX properly as the links the the zip files seem to be outdated/broken at: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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
Re: YTEX installation
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
Hi Sean,
This is great. I will look through it. Many thanks for sharing!
Cheers,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>
Date: Thursday, March 15, 2018 at 13:40
To: "Schenk, Gundolf" <Gu...@ucsf.edu>, "user@ctakes.apache.org" <us...@ctakes.apache.org>
Subject: RE: YTEX installation
Gundolf,
See attached. Hope this helps. I cut it off when it started to load documents because of PHI concerns in the metadata. If you get your run to that point you will most likely be ok.
Sean
From: Schenk, Gundolf [mailto:Gundolf.Schenk@ucsf.edu]
Sent: Friday, March 09, 2018 5:45 PM
To: Mullane, Sean *HS; user@ctakes.apache.org
Subject: Re: YTEX installation
Hi Sean,
Thanks for pointing to the source installation instructions. I already started to dive into the source code, but we have noticed something in our debug output here. Possibly something goes wrong with the creation of ytexApplicationBean. It may have never been actually created before it gets destroyed right at the end.
[…]
09 Mar 2018 18:38:13 INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@5be51aa<ma...@5be51aa>: defining beans [ytexApplicationContext]; root of factory hierarchy
09 Mar 2018 18:38:13 ERROR PiperFileRunner - Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.DBConsumer" failed. (Descriptor: <unknown>)
Could you share a full debug output of a successful run of yours? We might be able to find something by comparing to my debug output.
Thank you,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>
Date: Thursday, March 8, 2018 at 10:00
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: RE: YTEX installation
I typically run it from a script that calls PiperFileRunner, but for this I used Eclipse to step through the debugger and check the statements at the point where the program was erroring out.
This page has some information about setting up the project in Eclipse: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide
Sean
From: Schenk, Gundolf [mailto:Gundolf.Schenk@ucsf.edu]
Sent: Thursday, March 08, 2018 12:52 PM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: YTEX installation
Hi Sean,
Many thanks for your suggestion. However, it does not change anything apparent in my case. How do you run your pipeline? And, how did you find out about the type conversion error?
Cheers,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Thursday, March 8, 2018 at 09:40
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: RE: YTEX installation
Gundolf,
I found the solution to my error. It was triggered by not specifying the values of parameters that the AE expected, which caused the Java code to error out on a null value in type conversion. Try specifying the parameters in your DBConsumer in a similar way to the text below and see if that fixes the problem for you.
add org.apache.ctakes.ytex.uima.annotators.DBConsumer analysisBatch="yourAnalysisBatchName " 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
Sean
From: Schenk, Gundolf [mailto:Gundolf.Schenk@ucsf.edu]
Sent: Wednesday, March 07, 2018 12:27 PM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>; Mullane, Sean *HS
Subject: Re: YTEX installation
I have found the place where to set the dialect for Hibernate. In ytex.properties obviously. Duh!
Still, my pipeline does not finish without errors, just like before.
From: "Schenk, Gundolf" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Wednesday, March 7, 2018 at 09:23
To: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: Re: YTEX installation
Very interesting, Sean. I don’t think, I would need an explicit reader. The default Clinical Pipeline works fine without one. Or do I?
Since I had to change the mysql dialect from myisam to innodb during creation, I think the following output lines may indicate problems with DB communication:
[…]
06 Mar 2018 17:56:39 INFO PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
06 Mar 2018 17:56:40 INFO Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
06 Mar 2018 17:56:40 INFO Version - HHH000412: Hibernate Core {4.2.6.Final}
06 Mar 2018 17:56:40 INFO Environment - HHH000206: hibernate.properties not found
06 Mar 2018 17:56:40 INFO Environment - HHH000021: Bytecode provider name : javassist
06 Mar 2018 17:56:41 INFO Dialect - HHH000400: Using dialect: org.hibernate.dialect.MySQLMyISAMDialect
06 Mar 2018 17:56:41 WARN RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 WARN RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 INFO TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
06 Mar 2018 17:56:41 INFO ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
06 Mar 2018 17:56:41 INFO UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
06 Mar 2018 17:56:41 INFO StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
06 Mar 2018 17:56:41 INFO TableGenerator - HHH000398: Explicit segment value for id generator [ytex.hibernate_sequences.sequence_name] suggested; using default [default]
06 Mar 2018 17:56:41 WARN AbstractEhcacheRegionFactory - HHH020003: Could not find a specific ehcache configuration for cache named [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults.
06 Mar 2018 17:56:41 WARN EhcacheAccessStrategyFactoryImpl - HHH020007: read-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.model.UimaType]
06 Mar 2018 17:56:44 INFO HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1554eaa4] of Hibernate SessionFactory for HibernateTransactionManager
[…]
How can I teach Hibernate to use innodb, i.e. where do I set the properties? Should I create a configuration file hibernate.cfg.xml and save it directly in $CTAKES_HOME/resources?
Cheers,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>
Date: Tuesday, March 6, 2018 at 11:33
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: RE: YTEX installation
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.Schenk@ucsf.edu]
Sent: Tuesday, March 06, 2018 12:43 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 17:04
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 7:27 PM
To: user@ctakes.apache.org<ma...@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<ma...@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" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 15:12
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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<ma...@7e18ced7>: org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<ma...@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<ma...@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<ma...@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<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 14:32
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: YTEX installation
Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.
Gundolf,
See attached. Hope this helps. I cut it off when it started to load documents because of PHI concerns in the metadata. If you get your run to that point you will most likely be ok.
Sean
From: Schenk, Gundolf [mailto:Gundolf.Schenk@ucsf.edu]
Sent: Friday, March 09, 2018 5:45 PM
To: Mullane, Sean *HS; user@ctakes.apache.org
Subject: Re: YTEX installation
Hi Sean,
Thanks for pointing to the source installation instructions. I already started to dive into the source code, but we have noticed something in our debug output here. Possibly something goes wrong with the creation of ytexApplicationBean. It may have never been actually created before it gets destroyed right at the end.
[…]
09 Mar 2018 18:38:13 INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@5be51aa<ma...@5be51aa>: defining beans [ytexApplicationContext]; root of factory hierarchy
09 Mar 2018 18:38:13 ERROR PiperFileRunner - Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.DBConsumer" failed. (Descriptor: <unknown>)
Could you share a full debug output of a successful run of yours? We might be able to find something by comparing to my debug output.
Thank you,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>
Date: Thursday, March 8, 2018 at 10:00
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: RE: YTEX installation
I typically run it from a script that calls PiperFileRunner, but for this I used Eclipse to step through the debugger and check the statements at the point where the program was erroring out.
This page has some information about setting up the project in Eclipse: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide
Sean
From: Schenk, Gundolf [mailto:Gundolf.Schenk@ucsf.edu]
Sent: Thursday, March 08, 2018 12:52 PM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: YTEX installation
Hi Sean,
Many thanks for your suggestion. However, it does not change anything apparent in my case. How do you run your pipeline? And, how did you find out about the type conversion error?
Cheers,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Thursday, March 8, 2018 at 09:40
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: RE: YTEX installation
Gundolf,
I found the solution to my error. It was triggered by not specifying the values of parameters that the AE expected, which caused the Java code to error out on a null value in type conversion. Try specifying the parameters in your DBConsumer in a similar way to the text below and see if that fixes the problem for you.
add org.apache.ctakes.ytex.uima.annotators.DBConsumer analysisBatch="yourAnalysisBatchName " 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
Sean
From: Schenk, Gundolf [mailto:Gundolf.Schenk@ucsf.edu]
Sent: Wednesday, March 07, 2018 12:27 PM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>; Mullane, Sean *HS
Subject: Re: YTEX installation
I have found the place where to set the dialect for Hibernate. In ytex.properties obviously. Duh!
Still, my pipeline does not finish without errors, just like before.
From: "Schenk, Gundolf" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Wednesday, March 7, 2018 at 09:23
To: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: Re: YTEX installation
Very interesting, Sean. I don’t think, I would need an explicit reader. The default Clinical Pipeline works fine without one. Or do I?
Since I had to change the mysql dialect from myisam to innodb during creation, I think the following output lines may indicate problems with DB communication:
[…]
06 Mar 2018 17:56:39 INFO PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
06 Mar 2018 17:56:40 INFO Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
06 Mar 2018 17:56:40 INFO Version - HHH000412: Hibernate Core {4.2.6.Final}
06 Mar 2018 17:56:40 INFO Environment - HHH000206: hibernate.properties not found
06 Mar 2018 17:56:40 INFO Environment - HHH000021: Bytecode provider name : javassist
06 Mar 2018 17:56:41 INFO Dialect - HHH000400: Using dialect: org.hibernate.dialect.MySQLMyISAMDialect
06 Mar 2018 17:56:41 WARN RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 WARN RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 INFO TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
06 Mar 2018 17:56:41 INFO ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
06 Mar 2018 17:56:41 INFO UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
06 Mar 2018 17:56:41 INFO StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
06 Mar 2018 17:56:41 INFO TableGenerator - HHH000398: Explicit segment value for id generator [ytex.hibernate_sequences.sequence_name] suggested; using default [default]
06 Mar 2018 17:56:41 WARN AbstractEhcacheRegionFactory - HHH020003: Could not find a specific ehcache configuration for cache named [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults.
06 Mar 2018 17:56:41 WARN EhcacheAccessStrategyFactoryImpl - HHH020007: read-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.model.UimaType]
06 Mar 2018 17:56:44 INFO HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1554eaa4] of Hibernate SessionFactory for HibernateTransactionManager
[…]
How can I teach Hibernate to use innodb, i.e. where do I set the properties? Should I create a configuration file hibernate.cfg.xml and save it directly in $CTAKES_HOME/resources?
Cheers,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>
Date: Tuesday, March 6, 2018 at 11:33
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: RE: YTEX installation
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.Schenk@ucsf.edu]
Sent: Tuesday, March 06, 2018 12:43 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 17:04
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 7:27 PM
To: user@ctakes.apache.org<ma...@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<ma...@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" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 15:12
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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<ma...@7e18ced7>: org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<ma...@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<ma...@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<ma...@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<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 14:32
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: YTEX installation
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
Hi Sean,
Thanks for pointing to the source installation instructions. I already started to dive into the source code, but we have noticed something in our debug output here. Possibly something goes wrong with the creation of ytexApplicationBean. It may have never been actually created before it gets destroyed right at the end.
[…]
09 Mar 2018 18:38:13 INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@5be51aa: defining beans [ytexApplicationContext]; root of factory hierarchy
09 Mar 2018 18:38:13 ERROR PiperFileRunner - Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.DBConsumer" failed. (Descriptor: <unknown>)
Could you share a full debug output of a successful run of yours? We might be able to find something by comparing to my debug output.
Thank you,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>
Date: Thursday, March 8, 2018 at 10:00
To: "Schenk, Gundolf" <Gu...@ucsf.edu>, "user@ctakes.apache.org" <us...@ctakes.apache.org>
Subject: RE: YTEX installation
I typically run it from a script that calls PiperFileRunner, but for this I used Eclipse to step through the debugger and check the statements at the point where the program was erroring out.
This page has some information about setting up the project in Eclipse: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide
Sean
From: Schenk, Gundolf [mailto:Gundolf.Schenk@ucsf.edu]
Sent: Thursday, March 08, 2018 12:52 PM
To: user@ctakes.apache.org
Subject: Re: YTEX installation
Hi Sean,
Many thanks for your suggestion. However, it does not change anything apparent in my case. How do you run your pipeline? And, how did you find out about the type conversion error?
Cheers,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Thursday, March 8, 2018 at 09:40
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: RE: YTEX installation
Gundolf,
I found the solution to my error. It was triggered by not specifying the values of parameters that the AE expected, which caused the Java code to error out on a null value in type conversion. Try specifying the parameters in your DBConsumer in a similar way to the text below and see if that fixes the problem for you.
add org.apache.ctakes.ytex.uima.annotators.DBConsumer analysisBatch="yourAnalysisBatchName " 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
Sean
From: Schenk, Gundolf [mailto:Gundolf.Schenk@ucsf.edu]
Sent: Wednesday, March 07, 2018 12:27 PM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>; Mullane, Sean *HS
Subject: Re: YTEX installation
I have found the place where to set the dialect for Hibernate. In ytex.properties obviously. Duh!
Still, my pipeline does not finish without errors, just like before.
From: "Schenk, Gundolf" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Wednesday, March 7, 2018 at 09:23
To: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: Re: YTEX installation
Very interesting, Sean. I don’t think, I would need an explicit reader. The default Clinical Pipeline works fine without one. Or do I?
Since I had to change the mysql dialect from myisam to innodb during creation, I think the following output lines may indicate problems with DB communication:
[…]
06 Mar 2018 17:56:39 INFO PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
06 Mar 2018 17:56:40 INFO Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
06 Mar 2018 17:56:40 INFO Version - HHH000412: Hibernate Core {4.2.6.Final}
06 Mar 2018 17:56:40 INFO Environment - HHH000206: hibernate.properties not found
06 Mar 2018 17:56:40 INFO Environment - HHH000021: Bytecode provider name : javassist
06 Mar 2018 17:56:41 INFO Dialect - HHH000400: Using dialect: org.hibernate.dialect.MySQLMyISAMDialect
06 Mar 2018 17:56:41 WARN RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 WARN RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 INFO TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
06 Mar 2018 17:56:41 INFO ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
06 Mar 2018 17:56:41 INFO UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
06 Mar 2018 17:56:41 INFO StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
06 Mar 2018 17:56:41 INFO TableGenerator - HHH000398: Explicit segment value for id generator [ytex.hibernate_sequences.sequence_name] suggested; using default [default]
06 Mar 2018 17:56:41 WARN AbstractEhcacheRegionFactory - HHH020003: Could not find a specific ehcache configuration for cache named [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults.
06 Mar 2018 17:56:41 WARN EhcacheAccessStrategyFactoryImpl - HHH020007: read-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.model.UimaType]
06 Mar 2018 17:56:44 INFO HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1554eaa4] of Hibernate SessionFactory for HibernateTransactionManager
[…]
How can I teach Hibernate to use innodb, i.e. where do I set the properties? Should I create a configuration file hibernate.cfg.xml and save it directly in $CTAKES_HOME/resources?
Cheers,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>
Date: Tuesday, March 6, 2018 at 11:33
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: RE: YTEX installation
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.Schenk@ucsf.edu]
Sent: Tuesday, March 06, 2018 12:43 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 17:04
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 7:27 PM
To: user@ctakes.apache.org<ma...@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<ma...@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" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 15:12
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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<ma...@7e18ced7>: org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<ma...@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<ma...@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<ma...@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<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 14:32
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: YTEX installation
Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.
I typically run it from a script that calls PiperFileRunner, but for this I used Eclipse to step through the debugger and check the statements at the point where the program was erroring out.
This page has some information about setting up the project in Eclipse: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide
Sean
From: Schenk, Gundolf [mailto:Gundolf.Schenk@ucsf.edu]
Sent: Thursday, March 08, 2018 12:52 PM
To: user@ctakes.apache.org
Subject: Re: YTEX installation
Hi Sean,
Many thanks for your suggestion. However, it does not change anything apparent in my case. How do you run your pipeline? And, how did you find out about the type conversion error?
Cheers,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Thursday, March 8, 2018 at 09:40
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: RE: YTEX installation
Gundolf,
I found the solution to my error. It was triggered by not specifying the values of parameters that the AE expected, which caused the Java code to error out on a null value in type conversion. Try specifying the parameters in your DBConsumer in a similar way to the text below and see if that fixes the problem for you.
add org.apache.ctakes.ytex.uima.annotators.DBConsumer analysisBatch="yourAnalysisBatchName " 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
Sean
From: Schenk, Gundolf [mailto:Gundolf.Schenk@ucsf.edu]
Sent: Wednesday, March 07, 2018 12:27 PM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>; Mullane, Sean *HS
Subject: Re: YTEX installation
I have found the place where to set the dialect for Hibernate. In ytex.properties obviously. Duh!
Still, my pipeline does not finish without errors, just like before.
From: "Schenk, Gundolf" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Wednesday, March 7, 2018 at 09:23
To: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: Re: YTEX installation
Very interesting, Sean. I don’t think, I would need an explicit reader. The default Clinical Pipeline works fine without one. Or do I?
Since I had to change the mysql dialect from myisam to innodb during creation, I think the following output lines may indicate problems with DB communication:
[…]
06 Mar 2018 17:56:39 INFO PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
06 Mar 2018 17:56:40 INFO Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
06 Mar 2018 17:56:40 INFO Version - HHH000412: Hibernate Core {4.2.6.Final}
06 Mar 2018 17:56:40 INFO Environment - HHH000206: hibernate.properties not found
06 Mar 2018 17:56:40 INFO Environment - HHH000021: Bytecode provider name : javassist
06 Mar 2018 17:56:41 INFO Dialect - HHH000400: Using dialect: org.hibernate.dialect.MySQLMyISAMDialect
06 Mar 2018 17:56:41 WARN RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 WARN RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 INFO TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
06 Mar 2018 17:56:41 INFO ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
06 Mar 2018 17:56:41 INFO UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
06 Mar 2018 17:56:41 INFO StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
06 Mar 2018 17:56:41 INFO TableGenerator - HHH000398: Explicit segment value for id generator [ytex.hibernate_sequences.sequence_name] suggested; using default [default]
06 Mar 2018 17:56:41 WARN AbstractEhcacheRegionFactory - HHH020003: Could not find a specific ehcache configuration for cache named [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults.
06 Mar 2018 17:56:41 WARN EhcacheAccessStrategyFactoryImpl - HHH020007: read-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.model.UimaType]
06 Mar 2018 17:56:44 INFO HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1554eaa4] of Hibernate SessionFactory for HibernateTransactionManager
[…]
How can I teach Hibernate to use innodb, i.e. where do I set the properties? Should I create a configuration file hibernate.cfg.xml and save it directly in $CTAKES_HOME/resources?
Cheers,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>
Date: Tuesday, March 6, 2018 at 11:33
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: RE: YTEX installation
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.Schenk@ucsf.edu]
Sent: Tuesday, March 06, 2018 12:43 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 17:04
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 7:27 PM
To: user@ctakes.apache.org<ma...@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<ma...@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" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 15:12
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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<ma...@7e18ced7>: org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<ma...@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<ma...@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<ma...@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<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 14:32
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: YTEX installation
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
Hi Sean,
Many thanks for your suggestion. However, it does not change anything apparent in my case. How do you run your pipeline? And, how did you find out about the type conversion error?
Cheers,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Thursday, March 8, 2018 at 09:40
To: "Schenk, Gundolf" <Gu...@ucsf.edu>, "user@ctakes.apache.org" <us...@ctakes.apache.org>
Subject: RE: YTEX installation
Gundolf,
I found the solution to my error. It was triggered by not specifying the values of parameters that the AE expected, which caused the Java code to error out on a null value in type conversion. Try specifying the parameters in your DBConsumer in a similar way to the text below and see if that fixes the problem for you.
add org.apache.ctakes.ytex.uima.annotators.DBConsumer analysisBatch="yourAnalysisBatchName " 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
Sean
From: Schenk, Gundolf [mailto:Gundolf.Schenk@ucsf.edu]
Sent: Wednesday, March 07, 2018 12:27 PM
To: user@ctakes.apache.org; Mullane, Sean *HS
Subject: Re: YTEX installation
I have found the place where to set the dialect for Hibernate. In ytex.properties obviously. Duh!
Still, my pipeline does not finish without errors, just like before.
From: "Schenk, Gundolf" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Wednesday, March 7, 2018 at 09:23
To: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: Re: YTEX installation
Very interesting, Sean. I don’t think, I would need an explicit reader. The default Clinical Pipeline works fine without one. Or do I?
Since I had to change the mysql dialect from myisam to innodb during creation, I think the following output lines may indicate problems with DB communication:
[…]
06 Mar 2018 17:56:39 INFO PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
06 Mar 2018 17:56:40 INFO Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
06 Mar 2018 17:56:40 INFO Version - HHH000412: Hibernate Core {4.2.6.Final}
06 Mar 2018 17:56:40 INFO Environment - HHH000206: hibernate.properties not found
06 Mar 2018 17:56:40 INFO Environment - HHH000021: Bytecode provider name : javassist
06 Mar 2018 17:56:41 INFO Dialect - HHH000400: Using dialect: org.hibernate.dialect.MySQLMyISAMDialect
06 Mar 2018 17:56:41 WARN RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 WARN RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 INFO TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
06 Mar 2018 17:56:41 INFO ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
06 Mar 2018 17:56:41 INFO UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
06 Mar 2018 17:56:41 INFO StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
06 Mar 2018 17:56:41 INFO TableGenerator - HHH000398: Explicit segment value for id generator [ytex.hibernate_sequences.sequence_name] suggested; using default [default]
06 Mar 2018 17:56:41 WARN AbstractEhcacheRegionFactory - HHH020003: Could not find a specific ehcache configuration for cache named [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults.
06 Mar 2018 17:56:41 WARN EhcacheAccessStrategyFactoryImpl - HHH020007: read-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.model.UimaType]
06 Mar 2018 17:56:44 INFO HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1554eaa4] of Hibernate SessionFactory for HibernateTransactionManager
[…]
How can I teach Hibernate to use innodb, i.e. where do I set the properties? Should I create a configuration file hibernate.cfg.xml and save it directly in $CTAKES_HOME/resources?
Cheers,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>
Date: Tuesday, March 6, 2018 at 11:33
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: RE: YTEX installation
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.Schenk@ucsf.edu]
Sent: Tuesday, March 06, 2018 12:43 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 17:04
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 7:27 PM
To: user@ctakes.apache.org<ma...@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<ma...@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" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 15:12
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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<ma...@7e18ced7>: org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<ma...@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<ma...@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<ma...@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<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 14:32
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: YTEX installation
Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.
Gundolf,
I found the solution to my error. It was triggered by not specifying the values of parameters that the AE expected, which caused the Java code to error out on a null value in type conversion. Try specifying the parameters in your DBConsumer in a similar way to the text below and see if that fixes the problem for you.
add org.apache.ctakes.ytex.uima.annotators.DBConsumer analysisBatch="yourAnalysisBatchName " 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
Sean
From: Schenk, Gundolf [mailto:Gundolf.Schenk@ucsf.edu]
Sent: Wednesday, March 07, 2018 12:27 PM
To: user@ctakes.apache.org; Mullane, Sean *HS
Subject: Re: YTEX installation
I have found the place where to set the dialect for Hibernate. In ytex.properties obviously. Duh!
Still, my pipeline does not finish without errors, just like before.
From: "Schenk, Gundolf" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Wednesday, March 7, 2018 at 09:23
To: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: Re: YTEX installation
Very interesting, Sean. I don’t think, I would need an explicit reader. The default Clinical Pipeline works fine without one. Or do I?
Since I had to change the mysql dialect from myisam to innodb during creation, I think the following output lines may indicate problems with DB communication:
[…]
06 Mar 2018 17:56:39 INFO PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
06 Mar 2018 17:56:40 INFO Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
06 Mar 2018 17:56:40 INFO Version - HHH000412: Hibernate Core {4.2.6.Final}
06 Mar 2018 17:56:40 INFO Environment - HHH000206: hibernate.properties not found
06 Mar 2018 17:56:40 INFO Environment - HHH000021: Bytecode provider name : javassist
06 Mar 2018 17:56:41 INFO Dialect - HHH000400: Using dialect: org.hibernate.dialect.MySQLMyISAMDialect
06 Mar 2018 17:56:41 WARN RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 WARN RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 INFO TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
06 Mar 2018 17:56:41 INFO ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
06 Mar 2018 17:56:41 INFO UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
06 Mar 2018 17:56:41 INFO StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
06 Mar 2018 17:56:41 INFO TableGenerator - HHH000398: Explicit segment value for id generator [ytex.hibernate_sequences.sequence_name] suggested; using default [default]
06 Mar 2018 17:56:41 WARN AbstractEhcacheRegionFactory - HHH020003: Could not find a specific ehcache configuration for cache named [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults.
06 Mar 2018 17:56:41 WARN EhcacheAccessStrategyFactoryImpl - HHH020007: read-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.model.UimaType]
06 Mar 2018 17:56:44 INFO HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1554eaa4] of Hibernate SessionFactory for HibernateTransactionManager
[…]
How can I teach Hibernate to use innodb, i.e. where do I set the properties? Should I create a configuration file hibernate.cfg.xml and save it directly in $CTAKES_HOME/resources?
Cheers,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>>
Date: Tuesday, March 6, 2018 at 11:33
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: RE: YTEX installation
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.Schenk@ucsf.edu]
Sent: Tuesday, March 06, 2018 12:43 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 17:04
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 7:27 PM
To: user@ctakes.apache.org<ma...@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<ma...@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" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 15:12
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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<ma...@7e18ced7>: org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<ma...@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<ma...@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<ma...@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<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 14:32
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: YTEX installation
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
I have found the place where to set the dialect for Hibernate. In ytex.properties obviously. Duh!
Still, my pipeline does not finish without errors, just like before.
From: "Schenk, Gundolf" <Gu...@ucsf.edu>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Wednesday, March 7, 2018 at 09:23
To: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>, "user@ctakes.apache.org" <us...@ctakes.apache.org>
Subject: Re: YTEX installation
Very interesting, Sean. I don’t think, I would need an explicit reader. The default Clinical Pipeline works fine without one. Or do I?
Since I had to change the mysql dialect from myisam to innodb during creation, I think the following output lines may indicate problems with DB communication:
[…]
06 Mar 2018 17:56:39 INFO PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
06 Mar 2018 17:56:40 INFO Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
06 Mar 2018 17:56:40 INFO Version - HHH000412: Hibernate Core {4.2.6.Final}
06 Mar 2018 17:56:40 INFO Environment - HHH000206: hibernate.properties not found
06 Mar 2018 17:56:40 INFO Environment - HHH000021: Bytecode provider name : javassist
06 Mar 2018 17:56:41 INFO Dialect - HHH000400: Using dialect: org.hibernate.dialect.MySQLMyISAMDialect
06 Mar 2018 17:56:41 WARN RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 WARN RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 INFO TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
06 Mar 2018 17:56:41 INFO ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
06 Mar 2018 17:56:41 INFO UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
06 Mar 2018 17:56:41 INFO StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
06 Mar 2018 17:56:41 INFO TableGenerator - HHH000398: Explicit segment value for id generator [ytex.hibernate_sequences.sequence_name] suggested; using default [default]
06 Mar 2018 17:56:41 WARN AbstractEhcacheRegionFactory - HHH020003: Could not find a specific ehcache configuration for cache named [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults.
06 Mar 2018 17:56:41 WARN EhcacheAccessStrategyFactoryImpl - HHH020007: read-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.model.UimaType]
06 Mar 2018 17:56:44 INFO HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1554eaa4] of Hibernate SessionFactory for HibernateTransactionManager
[…]
How can I teach Hibernate to use innodb, i.e. where do I set the properties? Should I create a configuration file hibernate.cfg.xml and save it directly in $CTAKES_HOME/resources?
Cheers,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>
Date: Tuesday, March 6, 2018 at 11:33
To: "Schenk, Gundolf" <Gu...@ucsf.edu>, "user@ctakes.apache.org" <us...@ctakes.apache.org>
Subject: RE: YTEX installation
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.Schenk@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>>
Date: Monday, March 5, 2018 at 17:04
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 7:27 PM
To: user@ctakes.apache.org<ma...@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<ma...@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" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 15:12
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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<ma...@7e18ced7>: org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<ma...@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<ma...@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<ma...@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<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 14:32
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: YTEX installation
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
Very interesting, Sean. I don’t think, I would need an explicit reader. The default Clinical Pipeline works fine without one. Or do I?
Since I had to change the mysql dialect from myisam to innodb during creation, I think the following output lines may indicate problems with DB communication:
[…]
06 Mar 2018 17:56:39 INFO PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
06 Mar 2018 17:56:40 INFO Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
06 Mar 2018 17:56:40 INFO Version - HHH000412: Hibernate Core {4.2.6.Final}
06 Mar 2018 17:56:40 INFO Environment - HHH000206: hibernate.properties not found
06 Mar 2018 17:56:40 INFO Environment - HHH000021: Bytecode provider name : javassist
06 Mar 2018 17:56:41 INFO Dialect - HHH000400: Using dialect: org.hibernate.dialect.MySQLMyISAMDialect
06 Mar 2018 17:56:41 WARN RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 WARN RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
06 Mar 2018 17:56:41 INFO TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
06 Mar 2018 17:56:41 INFO ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
06 Mar 2018 17:56:41 INFO UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
06 Mar 2018 17:56:41 INFO StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
06 Mar 2018 17:56:41 INFO TableGenerator - HHH000398: Explicit segment value for id generator [ytex.hibernate_sequences.sequence_name] suggested; using default [default]
06 Mar 2018 17:56:41 WARN AbstractEhcacheRegionFactory - HHH020003: Could not find a specific ehcache configuration for cache named [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults.
06 Mar 2018 17:56:41 WARN EhcacheAccessStrategyFactoryImpl - HHH020007: read-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.model.UimaType]
06 Mar 2018 17:56:44 INFO HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1554eaa4] of Hibernate SessionFactory for HibernateTransactionManager
[…]
How can I teach Hibernate to use innodb, i.e. where do I set the properties? Should I create a configuration file hibernate.cfg.xml and save it directly in $CTAKES_HOME/resources?
Cheers,
Gundolf.
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>
Date: Tuesday, March 6, 2018 at 11:33
To: "Schenk, Gundolf" <Gu...@ucsf.edu>, "user@ctakes.apache.org" <us...@ctakes.apache.org>
Subject: RE: YTEX installation
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.Schenk@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>>
Date: Monday, March 5, 2018 at 17:04
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 7:27 PM
To: user@ctakes.apache.org<ma...@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<ma...@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" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 15:12
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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<ma...@7e18ced7>: org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<ma...@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<ma...@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<ma...@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<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 14:32
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: YTEX installation
Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.
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.Schenk@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>>
Date: Monday, March 5, 2018 at 17:04
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 7:27 PM
To: user@ctakes.apache.org<ma...@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<ma...@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" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 15:12
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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<ma...@7e18ced7>: org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<ma...@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<ma...@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<ma...@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<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 14:32
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: YTEX installation
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
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>
Date: Monday, March 5, 2018 at 17:04
To: "Schenk, Gundolf" <Gu...@ucsf.edu>, "user@ctakes.apache.org" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 7:27 PM
To: 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<ma...@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" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 15:12
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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<ma...@7e18ced7>: org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<ma...@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<ma...@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<ma...@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<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 14:32
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: YTEX installation
Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.
Can you share the line in your piper file where you add the DBConsumer?
Sean
From: Schenk, Gundolf [mailto:Gundolf.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 7:27 PM
To: 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<ma...@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" <Gu...@ucsf.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 15:12
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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<ma...@7e18ced7>: org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<ma...@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<ma...@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<ma...@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<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 14:32
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: YTEX installation
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
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: 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" <Gu...@ucsf.edu>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Monday, March 5, 2018 at 15:12
To: "user@ctakes.apache.org" <us...@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: 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: 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: 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: 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>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Monday, March 5, 2018 at 14:32
To: "Schenk, Gundolf" <Gu...@ucsf.edu>, "user@ctakes.apache.org" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; 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>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: YTEX installation
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
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: 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: 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: 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: 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>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Monday, March 5, 2018 at 14:32
To: "Schenk, Gundolf" <Gu...@ucsf.edu>, "user@ctakes.apache.org" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; 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>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: YTEX installation
Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.
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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 5:25 PM
To: Mullane, Sean *HS; 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>>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: user@ctakes.apache.org<ma...@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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: YTEX installation
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
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>
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" <Gu...@ucsf.edu>, "user@ctakes.apache.org" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: 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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: YTEX installation
Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.
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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 2:03 PM
To: 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>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; user@ctakes.apache.org<ma...@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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: YTEX installation
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
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>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" <Gu...@ucsf.edu>, "user@ctakes.apache.org" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; 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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: YTEX installation
Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.
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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 1:38 PM
To: Mullane, Sean *HS; 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>>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>>, "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: user@ctakes.apache.org<ma...@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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: YTEX installation
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
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>
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, Gundolf" <Gu...@ucsf.edu>, "user@ctakes.apache.org" <us...@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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: 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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: YTEX installation
Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.
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.Schenk@ucsf.edu]
Sent: Monday, March 05, 2018 12:57 PM
To: 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<ma...@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<ma...@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<ma...@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<ma...@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<ma...@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<ma...@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 <Ga...@arisglobal.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: user@ctakes.apache.org<ma...@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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: YTEX installation
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
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: 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: defining beans [ytexApplicationContext]; root of factory hierarchy
05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing 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: 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: 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: 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 <Ga...@arisglobal.com>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org" <us...@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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: 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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: YTEX installation
Posted by Gandhi Rajan Natarajan <Ga...@arisglobal.com>.
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.Schenk@ucsf.edu]
Sent: Saturday, March 03, 2018 4:11 AM
To: 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 <Br...@hsl.harvard.edu>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@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: brianwilson@hsl.harvard.edu<ma...@hsl.harvard.edu>
________________________________
CONFIDENTIAL NOTICE:
This electronic mail transmission contains confidential information
including Protected Health Information (PHI) that is legally privileged.
If you are not the intended recipient, or designee, you are hereby
notified that any disclosure, copying, distribution or use of any and
all attachments to this transmission is STRICTLY PROHIBITED. If you
have received this transmission in error, please notify the sender
immediately to arrange for return or destruction of these documents.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.