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Posted to dev@ctakes.apache.org by "Dunlop, Joyce (HP)" <Jo...@va.gov> on 2017/02/13 16:41:27 UTC

YTEX User Inferace Users?

Is there anyone on this email list that is using the YTEX web interface?

Thanks for the information Sean!

Joyce

-----Original Message-----
From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu] 
Sent: Monday, February 13, 2017 10:26 AM
To: Dunlop, Joyce (HP)
Cc: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: YTEX setup notes

Our main interest in YTEX is the database reader and consumer that it comes with. That is probably a smaller subset of its functionality but it was a good source for those. We are still working on implementation, but we plan to run an annotation pipeline on the new notes we get each day and store the resulting annotations in our database. The notes will be read from a database, parceled out in chunks to several processes, annotated, and consumed by the database consumer.

Sean

-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov] 
Sent: Monday, February 13, 2017 11:17 AM
To: Mullane, Sean *HS
Cc: dev@ctakes.apache.org
Subject: RE: YTEX setup notes

Hi Sean,

I will have to check with the VA Researchers to find out what they planned to for the ytex web. 
So you don't use YTEX web interface but you do use ytex correct?  Could you share the steps in a typical process you run for YTEX?

Thanks,
Joyce

-----Original Message-----
From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu] 
Sent: Monday, February 13, 2017 7:59 AM
To: Dunlop, Joyce (HP)
Cc: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: YTEX setup notes

Hi Joyce,

I wound up solving the error by commenting out the bean definition in ctakes-ytex-res/src/main/resources/org/apache/ctakes/beans-kernel.xml and ctakes-ytex-res/target/classes/org/apache/ctakes/beans-kernel.xml, which resolved that error. I think it was deprecated anyway. 

I did run into another error where I didn't have LookupDesc_SNOMED.xml in the directory path. Added it from the ctakes-src files solved that problem and got it working on Java 8 for us.

I haven't tried using the web interface - we don't have any plans to use it. Can I ask what you want to use it for? I'm not really familiar with what it does.

Thanks,
Sean

-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Friday, February 10, 2017 3:57 PM
To: Mullane, Sean *HS
Subject: RE: YTEX setup notes

Hi Sean,

We had to change the return type from BagOfWordsExporter to WekaBagOfWordsExporter in that file.

From:
	public BagOfWordsExporter getBagOfWordsExporter() {
		return bagOfWordsExporter;
	}

To:
	public WekaBagOfWordsExporter getBagOfWordsExporter() {
		return bagOfWordsExporter;
	}

We have still not be able to get the YTEX web interface to work.  The YTEX application starts up and we are able to access through the URL:  http://localhost:8080/semanticSim.jsf - We see 4 tabs but nothing seems functional.  Is there something we are still missing?  We found references to rest services - are they called separate from the YTEX UI? 

Any clue would be appreciated.

Thanks,
Joyce

PS:  I think there was one other code change to get Java 8 working, so if you get another error just shoot it over and I should have the answer.

-----Original Message-----
From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
Sent: Monday, February 06, 2017 3:33 PM
To: Dunlop, Joyce (HP)
Cc: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: YTEX setup notes

Joyce,

I haven't been able to find further documentation. It seems it is somewhat out of date and some of the Yale sources have been taken down.

In your feedback on my YTEX setup notes, I'm finding that when I try to run YTEX using Java 8 I get an error related to org.apache.ctakes.ytex.weka.GramMatrixExporterImpl. When I run it on Java 7 I get no errors. You mentioned that upgrading to Spring 3.2 solved an issue for you. How did you do that - did you change the Maven build file to pull in the newer version or did you do something else to get the newer Spring version? I'm hoping that will resolve the Java 8 issue here.

Thanks,
Sean

-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Friday, February 03, 2017 4:26 PM
To: Mullane, Sean *HS
Cc: dev@ctakes.apache.org
Subject: RE: YTEX setup notes

Sean/others,

Do you by chance have any of the documentation produced by Yale tucked away locally?

I see quite a few dead links that seem to go back to demo's and documents on cTakes site.

Examples:
The demo similarity web app is available under http://informatics.med.yale.edu/ytex.web;

http://ytex.googlecode.com/svn/trunk/projects/nlm.wsd/doc/YTEX%20Semantic%20Similarity%20Measures.pdf

Thanks,
Joyce

-----Original Message-----
From: Dunlop, Joyce (HP)
Sent: Monday, January 30, 2017 8:27 PM
To: 'Mullane, Sean *HS'; dev@ctakes.apache.org
Subject: RE: YTEX setup notes

Sean M,
This is perfect!  

Thanks,
Joyce

-----Original Message-----
From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
Sent: Monday, January 30, 2017 3:06 PM
To: Dunlop, Joyce (HP); dev@ctakes.apache.org
Subject: [EXTERNAL] RE: YTEX setup notes

Joyce,

Thanks for the notes. I'm glad to see you had success using Java 8 - I'll have to try that.

To answer your question about table contents, see below for the rowcounts in the YTEX tables after in my installation. Apologies in advance for the formatting:

tablename	tot_cnt
anno_base		0
anno_base_sequence	1
anno_contain		0
anno_date		0
anno_link		0
anno_markable	0
anno_med_event	0
anno_mm_acronym	0
anno_mm_candidate	0
anno_mm_cuiconcept	0
anno_mm_negation	0
anno_mm_utterance	0
anno_named_entity	0
anno_ontology_concept	0
anno_segment		0
anno_sentence	0
anno_token		0
anno_treebank_node	0
classifier_eval		0
classifier_eval_ir	0
classifier_eval_semil	0
classifier_eval_svm	0
classifier_instance_eval	0
classifier_instance_eval_prob	0
corpus_doc		0
corpus_label		0
cv_best_svm		0
cv_fold			0
cv_fold_instance	0
document		0
feature_eval		0
feature_parchd	0
feature_rank		0
fracture_demo		31
hibernate_sequences	1
hotspot		0
hotspot_instance	0
hotspot_sentence	0
kernel_eval		0
kernel_eval_instance	0
ref_named_entity_regex	0
ref_segment_regex	0
ref_stopword		360
ref_uima_type		38
tfidf_doclength	0
umls_aui_fword	6902003
v_snomed_fword_lookup	1374810

Sean

-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Friday, January 27, 2017 10:12 AM
To: dev@ctakes.apache.org
Subject: YTEX setup notes

Hi Sean M, 

Notes from :
Step
-The Needed to add sqljdbc4.jar to CTAKES_HOME/lib probably need to happen after -3. Install cTAKES "as usual"

-Java 7 is throwing errors because Spring needs to be upgraded to at least 3.2.
--It looks like Spring was previously upgraded from 2.5 to 3.1, but spring context files -  xsi:schemaLocation were not previous upgraded and remained 2.5.

-We have been able to successful run the script with JAVA 8 after upgrading Spring to 3.2.18-Release from the 3.1/2.5 version.   We also upgraded the version of Jetty.

-Step 7 which I think you list as 8 below to execute the setup script. It looks like it has mostly been successful but I do have a few errors at the bottom related to the database password we chose which had an & (AMP) character is being parsed on the & character.

3 tables that are showing errors related to the amp characters:
-ref_uima_type.xml
-fracture_demo.xml
-stopword.xml

2 tables are the only table will significant record counts:
-umls_aui_fword
-v_snomed_fword_lookup  

2 other table seem to have one row inserted.

The question I have is when this step completes how many of the tables should have data? 

Thanks again.
Joyce

-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 12:33 PM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: New to CTAKES 

Sean M,

I will try to work through the process this tomorrow.

Thanks!

Joyce

-----Original Message-----
From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
Sent: Tuesday, January 17, 2017 11:10 AM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: New to CTAKES 

Joyce,

This may help, here are some notes I put together when installing YTEX in our Windows/SQL Server test environment. I didn't build from source here, this is just installation (including UMLS). I'm working on writing up these instructions more thoroughly so if you use this please let me know if you find any points of improvement.

Requirements and steps to set up YTEX
These notes refer to the installation instructions at https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
1. They suggest installing UMLS in our database
	Follow instructions here to install UMLS: https://cwiki.apache.org/confluence/display/CTAKES/UMLS+MS+SQL+Server+Installation
	-http://groups.csail.mit.edu/medg/projects/text/Load_UMLS_mysql.html is useful when installing from .zip file. The mmsys.zip file needs to be unzipped to access the run64.bat file but also needs to be present as a .zip file for the run64.bat file to read from.
2. Create a database user and schema for use with YTEX 3. Load UMLS into database
	-Needed to create ytex.properties file from examples files in the developer/source version of cTAKES
	-Needed to change path in ctakes.profile to match version name of CTAKES_HOME directory
	-Needed to add sqljdbc4.jar to CTAKES_HOME/lib and sqljdbc_auth.dll to C:\Program Files\Java\jre_Version\bin
	-Needed to open port 1433 for TCP/IP traffic and clear dynamic ports
	-Need to change table definitions as follows to install UMLS-2016AB:
		MRCONSO.CODE varchar(75) -- was varchar(50)
		MRDEF.DEF varchar(max) -- was varchar(4000)
		MRSAB.VSAB varchar(24) -- was varchar(20)
		MRSAT.ATN varchar(64) -- was varchar(50)
		MRSAT.ATV varchar(max) -- was varchar(4000) 3. Install cTAKES "as usual"
4. Download and unzip ctakes-ytex-lib-3.1.2-SNAPSHOT.zip 'over' your installation.
	-I believe this step is deprecated - skip to step 6 5. Unzip YTEX Resources (Optional - UTS login required)
	-I believe this step is deprecated - skip to step 6
	-may be needed for concept graphs and dictionary lookup table for NER 6. Fix the path references in shell script to match your environment 7. Create CTAKES_HOME\resources\org\apache\ctakes\ytex\ytex.properties and specify database connection parameters.
8. Execute the setup script
	-Need to use Java 7 - Java 8 errors out
	-If SQL errors encountered, appenders can be added to log4j.xml to collect SQL queries

Sean

-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 11:57 AM
To: dev@ctakes.apache.org
Subject: RE: New to CTAKES 

Hi Joyce,

If you are building from source then you should not need to manually download the resources.  Maven should be doing it for you.  Well, that is the behavior of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...

Otherwise, I think that if the latest was the 3.2.1.1 then that is probably the most appropriate for the 3.2.2 release if you want all of the resources.

As for building and deploying ytex, I don't have any advice.  Perhaps some ytex power-user out there can help.

Sean

-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 11:25 AM
To: dev@ctakes.apache.org
Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
Subject: New to CTAKES 

Good Morning,

I am trying to set up a development environment using the source release of 3.2.2.

Reading though the documentation on

https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .

Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e=  into your ctakes-dictionary-lookup-res project.

ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is available for download.  Is there a 3.2.2 version of the resources?

After reading some of the posts from the email box, and reading the documentation on the site above.  It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.

Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?

Thanks,
Joyce

RE: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by "Dunlop, Joyce (HP)" <Jo...@va.gov>.

Sorry I read the error to quickly, you are not missing ehcache but springs support for ehcache.

Do you have in your YTEX pom?

<dependency>
   <groupId>org.springframework</groupId>
   <artifactId>spring-context-support</artifactId>
   <version>${spring.version}</version>
</dependency>

-----Original Message-----
From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
Sent: Friday, March 03, 2017 9:15 AM
To: dev@ctakes.apache.org
Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?

Yes it is - I've got ehcache-core-2.4.6.jar in the lib folder. Any ideas why ctakes can't find it?


> On 3 Mar 2017, at 16:04, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
> 
> You are right id does not need to be the parent pom if it was already included in the YTEX pom.
> 
> Did you verify the ehcache-core jar is in the lib folder after you compile and package?
> 
> 
> 
> -----Original Message-----
> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
> Sent: Friday, March 03, 2017 8:59 AM
> To: dev@ctakes.apache.org
> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
> 
> Joyce,
> 
> I've added 
> 
> 		<dependency>
> 			<groupId>net.sf.ehcache</groupId>
> 			<artifactId>ehcache-core</artifactId>
> 			<version>2.4.6</version>
> 		</dependency>
> 
> to my pom file at the root dir. It is already included in the pom.xml of ./ctakes-ytex. It felt wrong, but I gave it a shot resulting in the same error. Where do I have to add the ehcache-core dependency?
> 
> Leander
> 
> 
>> On 3 Mar 2017, at 15:16, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>> 
>> Leander,
>> You are still making progress.  
>> 
>> Your next issue is...
>> 
>> nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>> 
>> It cannot find ehcache
>> 
>> My pom has ehcache-core version 2.4.6
>> 
>> Joyce
>> 
>> -----Original Message-----
>> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
>> Sent: Thursday, March 02, 2017 4:41 PM
>> To: dev@ctakes.apache.org
>> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
>> 
>> I've modified the bin.xml accordingly and hibernate, weka and the mysql connector are now available in the classpath! Thank you for your help. I really appreciate that!
>> 
>> But still, I'm getting the same output like before, complaining about BeanCreationException: Error creating bean with name 'kernelApplicationContext', BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext] and so on.
>> 
>> Any ideas what I'm doing wrong?
>> 
>> [java] 02 Mar 2017 23:34:42  WARN ClassPathXmlApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 02 Mar 2017 23:34:42  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7ed7259e: defining beans [kernelApplicationContext]; root of factory hierarchy
>>    [java] Exception in thread "main" java.lang.ExceptionInInitializerError
>>    [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
>>    [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
>>    [java] Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
>>    [java] 	at org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:29)
>>    [java] 	... 2 more
>>    [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1077)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:981)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
>>    [java] 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
>>    [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
>>    [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>>    [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>>    [java] 	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
>>    [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
>>    [java] 	... 3 more
>>    [java] Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
>>    [java] 	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:121)
>>    [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:277)
>>    [java] 	... 16 more
>>    [java] Caused by: org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1278)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.predictBeanType(AbstractAutowireCapableBeanFactory.java:573)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:1347)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:913)
>>    [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:619)
>>    [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>>    [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>>    [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
>>    [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
>>    [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>>    [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>>    [java] 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>>    [java] 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>>    [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:148)
>>    [java] 	... 18 more
>>    [java] Caused by: java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>    [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>    [java] 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>    [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>    [java] 	at org.springframework.util.ClassUtils.forName(ClassUtils.java:268)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanDefinition.resolveBeanClass(AbstractBeanDefinition.java:419)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doResolveBeanClass(AbstractBeanFactory.java:1299)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1270)
>>    [java] 	... 31 more
>> 
>> BUILD FAILED
>> 
>> Leander
>>> On 2 Mar 2017, at 22:45, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>>> 
>>> hibernate
>> 
>> 
> 
>

Re: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by Leander Melms <Me...@students.uni-marburg.de>.

Thanks you for your help, Sean! When commenting out the grammatrixexporterimpl bean, I'm getting the error below.

Did you face this error too?


[java] 03 Mar 2017 19:03:37  INFO DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-res-3.2.3-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.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:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]
     [java] 03 Mar 2017 19:03:37  INFO DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@3427b02d: defining beans [kernelApplicationContext]; root of factory hierarchy
     [java] 03 Mar 2017 19:03:37  INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@4d5d943d: startup date [Fri Mar 03 19:03:37 CET 2017]; root of context hierarchy
     [java] 03 Mar 2017 19:03:37  INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
     [java] 03 Mar 2017 19:03:38  INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
     [java] Exception in thread "main" java.lang.ExceptionInInitializerError
     [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
     [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
     [java] Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.xml.XmlBeanDefinitionStoreException: Line 80 in XML document from class path resource [org/apache/ctakes/ytex/beans-kernel.xml] is invalid; nested exception is org.xml.sax.SAXParseException; lineNumber: 80; columnNumber: 4; The element type "beans" must be terminated by the matching end-tag "</beans>".
     [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
     [java] 	at org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:29)
     [java] 	... 2 more
     [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.xml.XmlBeanDefinitionStoreException: Line 80 in XML document from class path resource [org/apache/ctakes/ytex/beans-kernel.xml] is invalid; nested exception is org.xml.sax.SAXParseException; lineNumber: 80; columnNumber: 4; The element type "beans" must be terminated by the matching end-tag "</beans>".
     [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1077)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:981)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
     [java] 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
     [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
     [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
     [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
     [java] 	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
     [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
     [java] 	... 3 more
     [java] Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.xml.XmlBeanDefinitionStoreException: Line 80 in XML document from class path resource [org/apache/ctakes/ytex/beans-kernel.xml] is invalid; nested exception is org.xml.sax.SAXParseException; lineNumber: 80; columnNumber: 4; The element type "beans" must be terminated by the matching end-tag "</beans>".


> On 3 Mar 2017, at 18:23, Mullane, Sean *HS <SP...@hscmail.mcc.virginia.edu> wrote:
> 
> I think Joyce solved the GramMatrixExporterImpl issue differently than I did, but the way I got past that was to comment out the bean for grammatrixexporterimpl in these two files before I ran Maven:
> ctakes-ytex-res/src/main/resources/org/apache/ctakes/beans-kernel.xml
> ctakes-ytex-res/target/classes/org/apache/ctakes/beans-kernel.xml
> 
> Sean
> 
> -----Original Message-----
> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
> Sent: Friday, March 03, 2017 11:43 AM
> To: dev@ctakes.apache.org
> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
> 
> I'm running 3.2.3 and tried to get it running. However, it fails with the output below.
> 
> Did you face this as well? Is the line:
> 	Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods the issue here?
> 
> Could you share what your team did to make ytex running? I'm working at the Phillips University in Marburg, Germany, Department for rare and orphan diseases. We're a small team of students, physicians and developers commited to make use of supporting systems for differential diagnosis.
> 
> 
> 
> 03 Mar 2017 17:33:20  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2f162cc0: defining beans [ytexApplicationContext]; root of factory hierarchy Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" failed.  (Descriptor: file:/Users/leandermelms/coding/ctakes-server/desc/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml)
> 	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> 	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
> 	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> 	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> 	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> 	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> 	at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> 	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
> 	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> 	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> 	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> 	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> 	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> 	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
> 	at de.dfki.lt.ctakes.Server$.main(Server.scala:35)
> 	at de.dfki.lt.ctakes.Server.main(Server.scala)
> Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml], factory key [ytexApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ytexApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-server/target/ctakes-server-0.1.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
> 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
> 	at org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
> 	at org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:65)
> 	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> 	... 15 more
> Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ytexApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-server/target/ctakes-server-0.1.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
> 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:288)
> 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1035)
> 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:939)
> 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
> 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
> 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
> 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
> 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
> 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
> 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
> 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
> 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
> 	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
> 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
> 	... 18 more
> Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
> 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:162)
> 	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:110)
> 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:280)
> 	... 31 more
> Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
> 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:527)
> 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
> 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
> 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
> 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
> 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
> 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
> 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
> 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
> 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
> 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
> 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
> 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
> 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
> 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
> 	... 33 more
> Caused by: org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
> 	at org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:262)
> 	at org.springframework.beans.CachedIntrospectionResults.forClass(CachedIntrospectionResults.java:149)
> 	at org.springframework.beans.BeanWrapperImpl.getCachedIntrospectionResults(BeanWrapperImpl.java:324)
> 	at org.springframework.beans.BeanWrapperImpl.getPropertyDescriptors(BeanWrapperImpl.java:331)
> 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.filterPropertyDescriptorsForDependencyCheck(AbstractAutowireCapableBeanFactory.java:1242)
> 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1101)
> 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
> 	... 48 more
> Caused by: java.beans.IntrospectionException: type mismatch between read and write methods
> 	at java.beans.PropertyDescriptor.findPropertyType(PropertyDescriptor.java:661)
> 	at java.beans.PropertyDescriptor.setReadMethod(PropertyDescriptor.java:257)
> 	at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:282)
> 	at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:180)
> 	at org.springframework.beans.ExtendedBeanInfo.<init>(ExtendedBeanInfo.java:100)
> 	at org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:224)
> 	... 54 more
> 
> 
> Leander
>> On 3 Mar 2017, at 17:25, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>> 
>> ed to work with Java 8 so manual intervention is not needed.  It would be nice if the instructions mentioned the bin.xml and the pom to include the database resources you may need.  I am sure, some database(s) jars cannot be included because of licensing concerns.
>> 
>> We are working with 3.2.2 version of cTAKES and the group is working to release 3.2.3, so I don't know what has already been included.
>> 
>> We were able to get YTEX started but it is still not fully functional.
> 
> 
>

RE: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.

I think Joyce solved the GramMatrixExporterImpl issue differently than I did, but the way I got past that was to comment out the bean for grammatrixexporterimpl in these two files before I ran Maven:
ctakes-ytex-res/src/main/resources/org/apache/ctakes/beans-kernel.xml
ctakes-ytex-res/target/classes/org/apache/ctakes/beans-kernel.xml

Sean

-----Original Message-----
From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
Sent: Friday, March 03, 2017 11:43 AM
To: dev@ctakes.apache.org
Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?

I'm running 3.2.3 and tried to get it running. However, it fails with the output below.

Did you face this as well? Is the line:
	Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods the issue here?

Could you share what your team did to make ytex running? I'm working at the Phillips University in Marburg, Germany, Department for rare and orphan diseases. We're a small team of students, physicians and developers commited to make use of supporting systems for differential diagnosis.



03 Mar 2017 17:33:20  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2f162cc0: defining beans [ytexApplicationContext]; root of factory hierarchy Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" failed.  (Descriptor: file:/Users/leandermelms/coding/ctakes-server/desc/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml)
	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
	at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
	at de.dfki.lt.ctakes.Server$.main(Server.scala:35)
	at de.dfki.lt.ctakes.Server.main(Server.scala)
Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml], factory key [ytexApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ytexApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-server/target/ctakes-server-0.1.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
	at org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
	at org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:65)
	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
	... 15 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ytexApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-server/target/ctakes-server-0.1.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:288)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1035)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:939)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
	... 18 more
Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:162)
	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:110)
	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:280)
	... 31 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:527)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
	... 33 more
Caused by: org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:262)
	at org.springframework.beans.CachedIntrospectionResults.forClass(CachedIntrospectionResults.java:149)
	at org.springframework.beans.BeanWrapperImpl.getCachedIntrospectionResults(BeanWrapperImpl.java:324)
	at org.springframework.beans.BeanWrapperImpl.getPropertyDescriptors(BeanWrapperImpl.java:331)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.filterPropertyDescriptorsForDependencyCheck(AbstractAutowireCapableBeanFactory.java:1242)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1101)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
	... 48 more
Caused by: java.beans.IntrospectionException: type mismatch between read and write methods
	at java.beans.PropertyDescriptor.findPropertyType(PropertyDescriptor.java:661)
	at java.beans.PropertyDescriptor.setReadMethod(PropertyDescriptor.java:257)
	at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:282)
	at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:180)
	at org.springframework.beans.ExtendedBeanInfo.<init>(ExtendedBeanInfo.java:100)
	at org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:224)
	... 54 more


Leander
> On 3 Mar 2017, at 17:25, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
> 
> ed to work with Java 8 so manual intervention is not needed.  It would be nice if the instructions mentioned the bin.xml and the pom to include the database resources you may need.  I am sure, some database(s) jars cannot be included because of licensing concerns.
> 
> We are working with 3.2.2 version of cTAKES and the group is working to release 3.2.3, so I don't know what has already been included.
> 
> We were able to get YTEX started but it is still not fully functional.

Re: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by Leander Melms <Me...@students.uni-marburg.de>.

PS: I fired up https://github.com/dirkweissenborn/ctakes-server <https://github.com/dirkweissenborn/ctakes-server> - I think the issue is related to the repo. Sorry for that.

> On 3 Mar 2017, at 17:43, Leander Melms <Me...@students.uni-marburg.de> wrote:
> 
> mismatch between read and write methods

RE: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by "Dunlop, Joyce (HP)" <Jo...@va.gov>.

If you search for GramMatrixExporter in the archive history for this email address you can see my solution.


-----Original Message-----
From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
Sent: Friday, March 03, 2017 10:43 AM
To: dev@ctakes.apache.org
Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?

I'm running 3.2.3 and tried to get it running. However, it fails with the output below.

Did you face this as well? Is the line:
	Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods the issue here?

Could you share what your team did to make ytex running? I'm working at the Phillips University in Marburg, Germany, Department for rare and orphan diseases. We're a small team of students, physicians and developers commited to make use of supporting systems for differential diagnosis.



03 Mar 2017 17:33:20  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2f162cc0: defining beans [ytexApplicationContext]; root of factory hierarchy Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" failed.  (Descriptor: file:/Users/leandermelms/coding/ctakes-server/desc/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml)
	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
	at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
	at de.dfki.lt.ctakes.Server$.main(Server.scala:35)
	at de.dfki.lt.ctakes.Server.main(Server.scala)
Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml], factory key [ytexApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ytexApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-server/target/ctakes-server-0.1.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
	at org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
	at org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:65)
	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
	... 15 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ytexApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-server/target/ctakes-server-0.1.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:288)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1035)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:939)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
	... 18 more
Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:162)
	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:110)
	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:280)
	... 31 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:527)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
	... 33 more
Caused by: org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:262)
	at org.springframework.beans.CachedIntrospectionResults.forClass(CachedIntrospectionResults.java:149)
	at org.springframework.beans.BeanWrapperImpl.getCachedIntrospectionResults(BeanWrapperImpl.java:324)
	at org.springframework.beans.BeanWrapperImpl.getPropertyDescriptors(BeanWrapperImpl.java:331)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.filterPropertyDescriptorsForDependencyCheck(AbstractAutowireCapableBeanFactory.java:1242)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1101)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
	... 48 more
Caused by: java.beans.IntrospectionException: type mismatch between read and write methods
	at java.beans.PropertyDescriptor.findPropertyType(PropertyDescriptor.java:661)
	at java.beans.PropertyDescriptor.setReadMethod(PropertyDescriptor.java:257)
	at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:282)
	at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:180)
	at org.springframework.beans.ExtendedBeanInfo.<init>(ExtendedBeanInfo.java:100)
	at org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:224)
	... 54 more


Leander
> On 3 Mar 2017, at 17:25, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
> 
> ed to work with Java 8 so manual intervention is not needed.  It would be nice if the instructions mentioned the bin.xml and the pom to include the database resources you may need.  I am sure, some database(s) jars cannot be included because of licensing concerns.
> 
> We are working with 3.2.2 version of cTAKES and the group is working to release 3.2.3, so I don't know what has already been included.
> 
> We were able to get YTEX started but it is still not fully functional.

Re: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by Leander Melms <Me...@students.uni-marburg.de>.

I'm running 3.2.3 and tried to get it running. However, it fails with the output below.

Did you face this as well? Is the line:
	Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
the issue here?

Could you share what your team did to make ytex running? I'm working at the Phillips University in Marburg, Germany, Department for rare and orphan diseases. We're a small team of students, physicians and developers commited to make use of supporting systems for differential diagnosis.



03 Mar 2017 17:33:20  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2f162cc0: defining beans [ytexApplicationContext]; root of factory hierarchy
Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" failed.  (Descriptor: file:/Users/leandermelms/coding/ctakes-server/desc/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml)
	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
	at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
	at de.dfki.lt.ctakes.Server$.main(Server.scala:35)
	at de.dfki.lt.ctakes.Server.main(Server.scala)
Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml], factory key [ytexApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ytexApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-server/target/ctakes-server-0.1.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
	at org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
	at org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:65)
	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
	... 15 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ytexApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-server/target/ctakes-server-0.1.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:288)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1035)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:939)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
	... 18 more
Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:162)
	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:110)
	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:280)
	... 31 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:527)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
	... 33 more
Caused by: org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
	at org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:262)
	at org.springframework.beans.CachedIntrospectionResults.forClass(CachedIntrospectionResults.java:149)
	at org.springframework.beans.BeanWrapperImpl.getCachedIntrospectionResults(BeanWrapperImpl.java:324)
	at org.springframework.beans.BeanWrapperImpl.getPropertyDescriptors(BeanWrapperImpl.java:331)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.filterPropertyDescriptorsForDependencyCheck(AbstractAutowireCapableBeanFactory.java:1242)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1101)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
	... 48 more
Caused by: java.beans.IntrospectionException: type mismatch between read and write methods
	at java.beans.PropertyDescriptor.findPropertyType(PropertyDescriptor.java:661)
	at java.beans.PropertyDescriptor.setReadMethod(PropertyDescriptor.java:257)
	at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:282)
	at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:180)
	at org.springframework.beans.ExtendedBeanInfo.<init>(ExtendedBeanInfo.java:100)
	at org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:224)
	... 54 more


Leander
> On 3 Mar 2017, at 17:25, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
> 
> ed to work with Java 8 so manual intervention is not needed.  It would be nice if the instructions mentioned the bin.xml and the pom to include the database resources you may need.  I am sure, some database(s) jars cannot be included because of licensing concerns.
> 
> We are working with 3.2.2 version of cTAKES and the group is working to release 3.2.3, so I don't know what has already been included.
> 
> We were able to get YTEX started but it is still not fully functional.

RE: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by "Dunlop, Joyce (HP)" <Jo...@va.gov>.

I think long term the code just needs to be upgraded to work with Java 8 so manual intervention is not needed.  It would be nice if the instructions mentioned the bin.xml and the pom to include the database resources you may need.  I am sure, some database(s) jars cannot be included because of licensing concerns.

We are working with 3.2.2 version of cTAKES and the group is working to release 3.2.3, so I don't know what has already been included.

We were able to get YTEX started but it is still not fully functional.



-----Original Message-----
From: Leander Melms [mailto:Melms@students.uni-marburg.de]
Sent: Friday, March 03, 2017 10:15 AM
To: dev@ctakes.apache.org
Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?

Joyce,

I was finally able to run the YTEX database install! Although it only took 5 mins and most of the tables are still empty. But this is a huge success. Thank you for your time and help! I would not have been able to get it running without your guidance.

I wondered if we should rewrite the guide for Java 8. I could summarize the steps you've outlined for the community.

Do you have any resources and/or experiance for ytex web? Did you managed to get it running?


Again, thank you for the help. Really made my day!

Leander


> On 3 Mar 2017, at 16:38, Leander Melms <Me...@students.Uni-Marburg.DE> wrote:
>
> I'm following allong the guide at https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation>, which is the db install. I'm stuck at 7) Execute the setup script.
>
> It is able to connect to the DB. Later on, it fails through with the
> error.  It happens after
>
> nohup ../../ant -f build-setup.xml all > setup.out 2>&1 & tail -f
> setup.out
>
> Leander
>> On 3 Mar 2017, at 16:25, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>>
>> Remind me ... are you getting the error when you try to start YTEX web or run the YTEX database install?
>>
>> -----Original Message-----
>> From: Leander Melms [mailto:Melms@students.uni-marburg.de]
>> Sent: Friday, March 03, 2017 9:15 AM
>> To: dev@ctakes.apache.org
>> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
>>
>> Yes it is - I've got ehcache-core-2.4.6.jar in the lib folder. Any ideas why ctakes can't find it?
>>
>>
>>> On 3 Mar 2017, at 16:04, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>>>
>>> You are right id does not need to be the parent pom if it was already included in the YTEX pom.
>>>
>>> Did you verify the ehcache-core jar is in the lib folder after you compile and package?
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Leander Melms [mailto:Melms@students.uni-marburg.de]
>>> Sent: Friday, March 03, 2017 8:59 AM
>>> To: dev@ctakes.apache.org
>>> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
>>>
>>> Joyce,
>>>
>>> I've added
>>>
>>>             <dependency>
>>>                     <groupId>net.sf.ehcache</groupId>
>>>                     <artifactId>ehcache-core</artifactId>
>>>                     <version>2.4.6</version>
>>>             </dependency>
>>>
>>> to my pom file at the root dir. It is already included in the pom.xml of ./ctakes-ytex. It felt wrong, but I gave it a shot resulting in the same error. Where do I have to add the ehcache-core dependency?
>>>
>>> Leander
>>>
>>>
>>>> On 3 Mar 2017, at 15:16, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>>>>
>>>> Leander,
>>>> You are still making progress.
>>>>
>>>> Your next issue is...
>>>>
>>>> nested exception is java.lang.ClassNotFoundException:
>>>> org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>>
>>>> It cannot find ehcache
>>>>
>>>> My pom has ehcache-core version 2.4.6
>>>>
>>>> Joyce
>>>>
>>>> -----Original Message-----
>>>> From: Leander Melms [mailto:Melms@students.uni-marburg.de]
>>>> Sent: Thursday, March 02, 2017 4:41 PM
>>>> To: dev@ctakes.apache.org
>>>> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
>>>>
>>>> I've modified the bin.xml accordingly and hibernate, weka and the mysql connector are now available in the classpath! Thank you for your help. I really appreciate that!
>>>>
>>>> But still, I'm getting the same output like before, complaining about BeanCreationException: Error creating bean with name 'kernelApplicationContext', BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext] and so on.
>>>>
>>>> Any ideas what I'm doing wrong?
>>>>
>>>> [java] 02 Mar 2017 23:34:42  WARN ClassPathXmlApplicationContext -
>>>> Exception encountered during context initialization - cancelling
>>>> refresh attempt:
>>>> org.springframework.beans.factory.BeanCreationException: Error
>>>> creating bean with name 'kernelApplicationContext' defined in URL
>>>> [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes
>>>> -ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernel
>>>> BeanRefContext.xml]: Instantiation of bean failed; nested exception
>>>> is org.springframework.beans.BeanInstantiationException: Could not
>>>> instantiate bean class
>>>> [org.springframework.context.support.ClassPathXmlApplicationContext
>>>> ]: Constructor threw exception; nested exception is
>>>> org.springframework.beans.factory.CannotLoadBeanClassException:
>>>> Cannot find class
>>>> [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for
>>>> bean with name 'cacheManager' defined in class path resource
>>>> [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is
>>>> java.lang.ClassNotFoundException:
>>>> org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>>  [java] 02 Mar 2017 23:34:42  INFO DefaultListableBeanFactory -
>>>> Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7ed7259e: defining beans [kernelApplicationContext]; root of factory hierarchy  [java] Exception in thread "main" java.lang.ExceptionInInitializerError
>>>>  [java]    at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
>>>>  [java]    at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
>>>>  [java] Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>>  [java]    at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
>>>>  [java]    at org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:29)
>>>>  [java]    ... 2 more
>>>>  [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>>  [java]    at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285)
>>>>  [java]    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1077)
>>>>  [java]    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:981)
>>>>  [java]    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
>>>>  [java]    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
>>>>  [java]    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
>>>>  [java]    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
>>>>  [java]    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
>>>>  [java]    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
>>>>  [java]    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
>>>>  [java]    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>>>>  [java]    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>>>>  [java]    at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
>>>>  [java]    at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
>>>>  [java]    ... 3 more
>>>>  [java] Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>>  [java]    at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
>>>>  [java]    at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:121)
>>>>  [java]    at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:277)
>>>>  [java]    ... 16 more
>>>>  [java] Caused by: org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>>  [java]    at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1278)
>>>>  [java]    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.predictBeanType(AbstractAutowireCapableBeanFactory.java:573)
>>>>  [java]    at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:1347)
>>>>  [java]    at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:913)
>>>>  [java]    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:619)
>>>>  [java]    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>>>>  [java]    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>>>>  [java]    at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
>>>>  [java]    at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
>>>>  [java]    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>>>>  [java]    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>>>>  [java]    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>>>>  [java]    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>>>>  [java]    at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:148)
>>>>  [java]    ... 18 more
>>>>  [java] Caused by: java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>>  [java]    at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>>>  [java]    at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>>  [java]    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>>>  [java]    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>>  [java]    at org.springframework.util.ClassUtils.forName(ClassUtils.java:268)
>>>>  [java]    at org.springframework.beans.factory.support.AbstractBeanDefinition.resolveBeanClass(AbstractBeanDefinition.java:419)
>>>>  [java]    at org.springframework.beans.factory.support.AbstractBeanFactory.doResolveBeanClass(AbstractBeanFactory.java:1299)
>>>>  [java]    at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1270)
>>>>  [java]    ... 31 more
>>>>
>>>> BUILD FAILED
>>>>
>>>> Leander
>>>>> On 2 Mar 2017, at 22:45, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>>>>>
>>>>> hibernate
>>>>
>>>>
>>>
>>>
>>
>>
>

Re: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by Leander Melms <Me...@students.uni-marburg.de>.

Joyce,

I was finally able to run the YTEX database install! Although it only took 5 mins and most of the tables are still empty. But this is a huge success. Thank you for your time and help! I would not have been able to get it running without your guidance.

I wondered if we should rewrite the guide for Java 8. I could summarize the steps you've outlined for the community.

Do you have any resources and/or experiance for ytex web? Did you managed to get it running?


Again, thank you for the help. Really made my day!

Leander


> On 3 Mar 2017, at 16:38, Leander Melms <Me...@students.Uni-Marburg.DE> wrote:
> 
> I'm following allong the guide at https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation>, which is the db install. I'm stuck at 7) Execute the setup script.
> 
> It is able to connect to the DB. Later on, it fails through with the error.  It happens after
> 
> nohup ../../ant -f build-setup.xml all > setup.out 2>&1 &
> tail -f setup.out
> 
> Leander
>> On 3 Mar 2017, at 16:25, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>> 
>> Remind me ... are you getting the error when you try to start YTEX web or run the YTEX database install?
>> 
>> -----Original Message-----
>> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
>> Sent: Friday, March 03, 2017 9:15 AM
>> To: dev@ctakes.apache.org
>> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
>> 
>> Yes it is - I've got ehcache-core-2.4.6.jar in the lib folder. Any ideas why ctakes can't find it?
>> 
>> 
>>> On 3 Mar 2017, at 16:04, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>>> 
>>> You are right id does not need to be the parent pom if it was already included in the YTEX pom.
>>> 
>>> Did you verify the ehcache-core jar is in the lib folder after you compile and package?
>>> 
>>> 
>>> 
>>> -----Original Message-----
>>> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
>>> Sent: Friday, March 03, 2017 8:59 AM
>>> To: dev@ctakes.apache.org
>>> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
>>> 
>>> Joyce,
>>> 
>>> I've added 
>>> 
>>> 		<dependency>
>>> 			<groupId>net.sf.ehcache</groupId>
>>> 			<artifactId>ehcache-core</artifactId>
>>> 			<version>2.4.6</version>
>>> 		</dependency>
>>> 
>>> to my pom file at the root dir. It is already included in the pom.xml of ./ctakes-ytex. It felt wrong, but I gave it a shot resulting in the same error. Where do I have to add the ehcache-core dependency?
>>> 
>>> Leander
>>> 
>>> 
>>>> On 3 Mar 2017, at 15:16, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>>>> 
>>>> Leander,
>>>> You are still making progress.  
>>>> 
>>>> Your next issue is...
>>>> 
>>>> nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>> 
>>>> It cannot find ehcache
>>>> 
>>>> My pom has ehcache-core version 2.4.6
>>>> 
>>>> Joyce
>>>> 
>>>> -----Original Message-----
>>>> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
>>>> Sent: Thursday, March 02, 2017 4:41 PM
>>>> To: dev@ctakes.apache.org
>>>> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
>>>> 
>>>> I've modified the bin.xml accordingly and hibernate, weka and the mysql connector are now available in the classpath! Thank you for your help. I really appreciate that!
>>>> 
>>>> But still, I'm getting the same output like before, complaining about BeanCreationException: Error creating bean with name 'kernelApplicationContext', BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext] and so on.
>>>> 
>>>> Any ideas what I'm doing wrong?
>>>> 
>>>> [java] 02 Mar 2017 23:34:42  WARN ClassPathXmlApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>>  [java] 02 Mar 2017 23:34:42  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7ed7259e: defining beans [kernelApplicationContext]; root of factory hierarchy
>>>>  [java] Exception in thread "main" java.lang.ExceptionInInitializerError
>>>>  [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
>>>>  [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
>>>>  [java] Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>>  [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
>>>>  [java] 	at org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:29)
>>>>  [java] 	... 2 more
>>>>  [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>>  [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285)
>>>>  [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1077)
>>>>  [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:981)
>>>>  [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
>>>>  [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
>>>>  [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
>>>>  [java] 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
>>>>  [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
>>>>  [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
>>>>  [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
>>>>  [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>>>>  [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>>>>  [java] 	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
>>>>  [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
>>>>  [java] 	... 3 more
>>>>  [java] Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>>  [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
>>>>  [java] 	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:121)
>>>>  [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:277)
>>>>  [java] 	... 16 more
>>>>  [java] Caused by: org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>>  [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1278)
>>>>  [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.predictBeanType(AbstractAutowireCapableBeanFactory.java:573)
>>>>  [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:1347)
>>>>  [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:913)
>>>>  [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:619)
>>>>  [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>>>>  [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>>>>  [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
>>>>  [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
>>>>  [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>>>>  [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>>>>  [java] 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>>>>  [java] 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>>>>  [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:148)
>>>>  [java] 	... 18 more
>>>>  [java] Caused by: java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>>  [java] 	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>>>  [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>>  [java] 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>>>  [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>>  [java] 	at org.springframework.util.ClassUtils.forName(ClassUtils.java:268)
>>>>  [java] 	at org.springframework.beans.factory.support.AbstractBeanDefinition.resolveBeanClass(AbstractBeanDefinition.java:419)
>>>>  [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doResolveBeanClass(AbstractBeanFactory.java:1299)
>>>>  [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1270)
>>>>  [java] 	... 31 more
>>>> 
>>>> BUILD FAILED
>>>> 
>>>> Leander
>>>>> On 2 Mar 2017, at 22:45, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>>>>> 
>>>>> hibernate
>>>> 
>>>> 
>>> 
>>> 
>> 
>> 
>

Re: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by Leander Melms <Me...@students.uni-marburg.de>.

I'm following allong the guide at https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation>, which is the db install. I'm stuck at 7) Execute the setup script.

It is able to connect to the DB. Later on, it fails through with the error.  It happens after

nohup ../../ant -f build-setup.xml all > setup.out 2>&1 &
tail -f setup.out

 Leander
> On 3 Mar 2017, at 16:25, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
> 
> Remind me ... are you getting the error when you try to start YTEX web or run the YTEX database install?
> 
> -----Original Message-----
> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
> Sent: Friday, March 03, 2017 9:15 AM
> To: dev@ctakes.apache.org
> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
> 
> Yes it is - I've got ehcache-core-2.4.6.jar in the lib folder. Any ideas why ctakes can't find it?
> 
> 
>> On 3 Mar 2017, at 16:04, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>> 
>> You are right id does not need to be the parent pom if it was already included in the YTEX pom.
>> 
>> Did you verify the ehcache-core jar is in the lib folder after you compile and package?
>> 
>> 
>> 
>> -----Original Message-----
>> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
>> Sent: Friday, March 03, 2017 8:59 AM
>> To: dev@ctakes.apache.org
>> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
>> 
>> Joyce,
>> 
>> I've added 
>> 
>> 		<dependency>
>> 			<groupId>net.sf.ehcache</groupId>
>> 			<artifactId>ehcache-core</artifactId>
>> 			<version>2.4.6</version>
>> 		</dependency>
>> 
>> to my pom file at the root dir. It is already included in the pom.xml of ./ctakes-ytex. It felt wrong, but I gave it a shot resulting in the same error. Where do I have to add the ehcache-core dependency?
>> 
>> Leander
>> 
>> 
>>> On 3 Mar 2017, at 15:16, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>>> 
>>> Leander,
>>> You are still making progress.  
>>> 
>>> Your next issue is...
>>> 
>>> nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>> 
>>> It cannot find ehcache
>>> 
>>> My pom has ehcache-core version 2.4.6
>>> 
>>> Joyce
>>> 
>>> -----Original Message-----
>>> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
>>> Sent: Thursday, March 02, 2017 4:41 PM
>>> To: dev@ctakes.apache.org
>>> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
>>> 
>>> I've modified the bin.xml accordingly and hibernate, weka and the mysql connector are now available in the classpath! Thank you for your help. I really appreciate that!
>>> 
>>> But still, I'm getting the same output like before, complaining about BeanCreationException: Error creating bean with name 'kernelApplicationContext', BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext] and so on.
>>> 
>>> Any ideas what I'm doing wrong?
>>> 
>>> [java] 02 Mar 2017 23:34:42  WARN ClassPathXmlApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>   [java] 02 Mar 2017 23:34:42  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7ed7259e: defining beans [kernelApplicationContext]; root of factory hierarchy
>>>   [java] Exception in thread "main" java.lang.ExceptionInInitializerError
>>>   [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
>>>   [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
>>>   [java] Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>   [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
>>>   [java] 	at org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:29)
>>>   [java] 	... 2 more
>>>   [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>   [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285)
>>>   [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1077)
>>>   [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:981)
>>>   [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
>>>   [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
>>>   [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
>>>   [java] 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
>>>   [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
>>>   [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
>>>   [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
>>>   [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>>>   [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>>>   [java] 	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
>>>   [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
>>>   [java] 	... 3 more
>>>   [java] Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>   [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
>>>   [java] 	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:121)
>>>   [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:277)
>>>   [java] 	... 16 more
>>>   [java] Caused by: org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>   [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1278)
>>>   [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.predictBeanType(AbstractAutowireCapableBeanFactory.java:573)
>>>   [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:1347)
>>>   [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:913)
>>>   [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:619)
>>>   [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>>>   [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>>>   [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
>>>   [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
>>>   [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>>>   [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>>>   [java] 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>>>   [java] 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>>>   [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:148)
>>>   [java] 	... 18 more
>>>   [java] Caused by: java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>>   [java] 	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>>   [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>   [java] 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>>   [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>   [java] 	at org.springframework.util.ClassUtils.forName(ClassUtils.java:268)
>>>   [java] 	at org.springframework.beans.factory.support.AbstractBeanDefinition.resolveBeanClass(AbstractBeanDefinition.java:419)
>>>   [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doResolveBeanClass(AbstractBeanFactory.java:1299)
>>>   [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1270)
>>>   [java] 	... 31 more
>>> 
>>> BUILD FAILED
>>> 
>>> Leander
>>>> On 2 Mar 2017, at 22:45, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>>>> 
>>>> hibernate
>>> 
>>> 
>> 
>> 
> 
>

RE: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by "Dunlop, Joyce (HP)" <Jo...@va.gov>.

Remind me ... are you getting the error when you try to start YTEX web or run the YTEX database install?

-----Original Message-----
From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
Sent: Friday, March 03, 2017 9:15 AM
To: dev@ctakes.apache.org
Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?

Yes it is - I've got ehcache-core-2.4.6.jar in the lib folder. Any ideas why ctakes can't find it?


> On 3 Mar 2017, at 16:04, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
> 
> You are right id does not need to be the parent pom if it was already included in the YTEX pom.
> 
> Did you verify the ehcache-core jar is in the lib folder after you compile and package?
> 
> 
> 
> -----Original Message-----
> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
> Sent: Friday, March 03, 2017 8:59 AM
> To: dev@ctakes.apache.org
> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
> 
> Joyce,
> 
> I've added 
> 
> 		<dependency>
> 			<groupId>net.sf.ehcache</groupId>
> 			<artifactId>ehcache-core</artifactId>
> 			<version>2.4.6</version>
> 		</dependency>
> 
> to my pom file at the root dir. It is already included in the pom.xml of ./ctakes-ytex. It felt wrong, but I gave it a shot resulting in the same error. Where do I have to add the ehcache-core dependency?
> 
> Leander
> 
> 
>> On 3 Mar 2017, at 15:16, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>> 
>> Leander,
>> You are still making progress.  
>> 
>> Your next issue is...
>> 
>> nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>> 
>> It cannot find ehcache
>> 
>> My pom has ehcache-core version 2.4.6
>> 
>> Joyce
>> 
>> -----Original Message-----
>> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
>> Sent: Thursday, March 02, 2017 4:41 PM
>> To: dev@ctakes.apache.org
>> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
>> 
>> I've modified the bin.xml accordingly and hibernate, weka and the mysql connector are now available in the classpath! Thank you for your help. I really appreciate that!
>> 
>> But still, I'm getting the same output like before, complaining about BeanCreationException: Error creating bean with name 'kernelApplicationContext', BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext] and so on.
>> 
>> Any ideas what I'm doing wrong?
>> 
>> [java] 02 Mar 2017 23:34:42  WARN ClassPathXmlApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 02 Mar 2017 23:34:42  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7ed7259e: defining beans [kernelApplicationContext]; root of factory hierarchy
>>    [java] Exception in thread "main" java.lang.ExceptionInInitializerError
>>    [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
>>    [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
>>    [java] Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
>>    [java] 	at org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:29)
>>    [java] 	... 2 more
>>    [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1077)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:981)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
>>    [java] 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
>>    [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
>>    [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>>    [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>>    [java] 	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
>>    [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
>>    [java] 	... 3 more
>>    [java] Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
>>    [java] 	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:121)
>>    [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:277)
>>    [java] 	... 16 more
>>    [java] Caused by: org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1278)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.predictBeanType(AbstractAutowireCapableBeanFactory.java:573)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:1347)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:913)
>>    [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:619)
>>    [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>>    [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>>    [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
>>    [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
>>    [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>>    [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>>    [java] 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>>    [java] 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>>    [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:148)
>>    [java] 	... 18 more
>>    [java] Caused by: java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>    [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>    [java] 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>    [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>    [java] 	at org.springframework.util.ClassUtils.forName(ClassUtils.java:268)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanDefinition.resolveBeanClass(AbstractBeanDefinition.java:419)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doResolveBeanClass(AbstractBeanFactory.java:1299)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1270)
>>    [java] 	... 31 more
>> 
>> BUILD FAILED
>> 
>> Leander
>>> On 2 Mar 2017, at 22:45, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>>> 
>>> hibernate
>> 
>> 
> 
>

Re: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by Leander Melms <Me...@students.uni-marburg.de>.

Yes it is - I've got ehcache-core-2.4.6.jar in the lib folder. Any ideas why ctakes can't find it?


> On 3 Mar 2017, at 16:04, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
> 
> You are right id does not need to be the parent pom if it was already included in the YTEX pom.
> 
> Did you verify the ehcache-core jar is in the lib folder after you compile and package?
> 
> 
> 
> -----Original Message-----
> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
> Sent: Friday, March 03, 2017 8:59 AM
> To: dev@ctakes.apache.org
> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
> 
> Joyce,
> 
> I've added 
> 
> 		<dependency>
> 			<groupId>net.sf.ehcache</groupId>
> 			<artifactId>ehcache-core</artifactId>
> 			<version>2.4.6</version>
> 		</dependency>
> 
> to my pom file at the root dir. It is already included in the pom.xml of ./ctakes-ytex. It felt wrong, but I gave it a shot resulting in the same error. Where do I have to add the ehcache-core dependency?
> 
> Leander
> 
> 
>> On 3 Mar 2017, at 15:16, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>> 
>> Leander,
>> You are still making progress.  
>> 
>> Your next issue is...
>> 
>> nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>> 
>> It cannot find ehcache
>> 
>> My pom has ehcache-core version 2.4.6
>> 
>> Joyce
>> 
>> -----Original Message-----
>> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
>> Sent: Thursday, March 02, 2017 4:41 PM
>> To: dev@ctakes.apache.org
>> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
>> 
>> I've modified the bin.xml accordingly and hibernate, weka and the mysql connector are now available in the classpath! Thank you for your help. I really appreciate that!
>> 
>> But still, I'm getting the same output like before, complaining about BeanCreationException: Error creating bean with name 'kernelApplicationContext', BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext] and so on.
>> 
>> Any ideas what I'm doing wrong?
>> 
>> [java] 02 Mar 2017 23:34:42  WARN ClassPathXmlApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 02 Mar 2017 23:34:42  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7ed7259e: defining beans [kernelApplicationContext]; root of factory hierarchy
>>    [java] Exception in thread "main" java.lang.ExceptionInInitializerError
>>    [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
>>    [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
>>    [java] Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
>>    [java] 	at org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:29)
>>    [java] 	... 2 more
>>    [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1077)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:981)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
>>    [java] 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
>>    [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
>>    [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>>    [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>>    [java] 	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
>>    [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
>>    [java] 	... 3 more
>>    [java] Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
>>    [java] 	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:121)
>>    [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:277)
>>    [java] 	... 16 more
>>    [java] Caused by: org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1278)
>>    [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.predictBeanType(AbstractAutowireCapableBeanFactory.java:573)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:1347)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:913)
>>    [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:619)
>>    [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>>    [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>>    [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
>>    [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
>>    [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>>    [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>>    [java] 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>>    [java] 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>>    [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:148)
>>    [java] 	... 18 more
>>    [java] Caused by: java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>>    [java] 	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>    [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>    [java] 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>    [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>    [java] 	at org.springframework.util.ClassUtils.forName(ClassUtils.java:268)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanDefinition.resolveBeanClass(AbstractBeanDefinition.java:419)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doResolveBeanClass(AbstractBeanFactory.java:1299)
>>    [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1270)
>>    [java] 	... 31 more
>> 
>> BUILD FAILED
>> 
>> Leander
>>> On 2 Mar 2017, at 22:45, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>>> 
>>> hibernate
>> 
>> 
> 
>

RE: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by "Dunlop, Joyce (HP)" <Jo...@va.gov>.

You are right id does not need to be the parent pom if it was already included in the YTEX pom.

Did you verify the ehcache-core jar is in the lib folder after you compile and package?



-----Original Message-----
From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
Sent: Friday, March 03, 2017 8:59 AM
To: dev@ctakes.apache.org
Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?

Joyce,

I've added 

		<dependency>
			<groupId>net.sf.ehcache</groupId>
			<artifactId>ehcache-core</artifactId>
			<version>2.4.6</version>
		</dependency>

to my pom file at the root dir. It is already included in the pom.xml of ./ctakes-ytex. It felt wrong, but I gave it a shot resulting in the same error. Where do I have to add the ehcache-core dependency?

Leander


> On 3 Mar 2017, at 15:16, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
> 
> Leander,
> You are still making progress.  
> 
> Your next issue is...
> 
> nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
> 
> It cannot find ehcache
> 
> My pom has ehcache-core version 2.4.6
> 
> Joyce
> 
> -----Original Message-----
> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
> Sent: Thursday, March 02, 2017 4:41 PM
> To: dev@ctakes.apache.org
> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
> 
> I've modified the bin.xml accordingly and hibernate, weka and the mysql connector are now available in the classpath! Thank you for your help. I really appreciate that!
> 
> But still, I'm getting the same output like before, complaining about BeanCreationException: Error creating bean with name 'kernelApplicationContext', BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext] and so on.
> 
> Any ideas what I'm doing wrong?
> 
> [java] 02 Mar 2017 23:34:42  WARN ClassPathXmlApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>     [java] 02 Mar 2017 23:34:42  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7ed7259e: defining beans [kernelApplicationContext]; root of factory hierarchy
>     [java] Exception in thread "main" java.lang.ExceptionInInitializerError
>     [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
>     [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
>     [java] Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>     [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
>     [java] 	at org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:29)
>     [java] 	... 2 more
>     [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>     [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285)
>     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1077)
>     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:981)
>     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
>     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
>     [java] 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
>     [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
>     [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>     [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>     [java] 	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
>     [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
>     [java] 	... 3 more
>     [java] Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>     [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
>     [java] 	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:121)
>     [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:277)
>     [java] 	... 16 more
>     [java] Caused by: org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1278)
>     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.predictBeanType(AbstractAutowireCapableBeanFactory.java:573)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:1347)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:913)
>     [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:619)
>     [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>     [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>     [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
>     [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
>     [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>     [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>     [java] 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>     [java] 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>     [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:148)
>     [java] 	... 18 more
>     [java] Caused by: java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>     [java] 	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>     [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>     [java] 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>     [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>     [java] 	at org.springframework.util.ClassUtils.forName(ClassUtils.java:268)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanDefinition.resolveBeanClass(AbstractBeanDefinition.java:419)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doResolveBeanClass(AbstractBeanFactory.java:1299)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1270)
>     [java] 	... 31 more
> 
> BUILD FAILED
> 
> Leander
>> On 2 Mar 2017, at 22:45, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>> 
>> hibernate
> 
>

Re: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by Leander Melms <Me...@students.uni-marburg.de>.

Joyce,

I've added 

		<dependency>
			<groupId>net.sf.ehcache</groupId>
			<artifactId>ehcache-core</artifactId>
			<version>2.4.6</version>
		</dependency>

to my pom file at the root dir. It is already included in the pom.xml of ./ctakes-ytex. It felt wrong, but I gave it a shot resulting in the same error. Where do I have to add the ehcache-core dependency?

Leander


> On 3 Mar 2017, at 15:16, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
> 
> Leander,
> You are still making progress.  
> 
> Your next issue is...
> 
> nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
> 
> It cannot find ehcache
> 
> My pom has ehcache-core version 2.4.6
> 
> Joyce
> 
> -----Original Message-----
> From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
> Sent: Thursday, March 02, 2017 4:41 PM
> To: dev@ctakes.apache.org
> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
> 
> I've modified the bin.xml accordingly and hibernate, weka and the mysql connector are now available in the classpath! Thank you for your help. I really appreciate that!
> 
> But still, I'm getting the same output like before, complaining about BeanCreationException: Error creating bean with name 'kernelApplicationContext', BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext] and so on.
> 
> Any ideas what I'm doing wrong?
> 
> [java] 02 Mar 2017 23:34:42  WARN ClassPathXmlApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>     [java] 02 Mar 2017 23:34:42  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7ed7259e: defining beans [kernelApplicationContext]; root of factory hierarchy
>     [java] Exception in thread "main" java.lang.ExceptionInInitializerError
>     [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
>     [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
>     [java] Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>     [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
>     [java] 	at org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:29)
>     [java] 	... 2 more
>     [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>     [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285)
>     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1077)
>     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:981)
>     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
>     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
>     [java] 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
>     [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
>     [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>     [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>     [java] 	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
>     [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
>     [java] 	... 3 more
>     [java] Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>     [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
>     [java] 	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:121)
>     [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:277)
>     [java] 	... 16 more
>     [java] Caused by: org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1278)
>     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.predictBeanType(AbstractAutowireCapableBeanFactory.java:573)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:1347)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:913)
>     [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:619)
>     [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
>     [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
>     [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
>     [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
>     [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>     [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>     [java] 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>     [java] 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>     [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:148)
>     [java] 	... 18 more
>     [java] Caused by: java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
>     [java] 	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>     [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>     [java] 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>     [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>     [java] 	at org.springframework.util.ClassUtils.forName(ClassUtils.java:268)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanDefinition.resolveBeanClass(AbstractBeanDefinition.java:419)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doResolveBeanClass(AbstractBeanFactory.java:1299)
>     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1270)
>     [java] 	... 31 more
> 
> BUILD FAILED
> 
> Leander
>> On 2 Mar 2017, at 22:45, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>> 
>> hibernate
> 
>

RE: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by "Dunlop, Joyce (HP)" <Jo...@va.gov>.

Leander,
You are still making progress.  

Your next issue is...

nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean

It cannot find ehcache

My pom has ehcache-core version 2.4.6

Joyce

-----Original Message-----
From: Leander Melms [mailto:Melms@students.uni-marburg.de] 
Sent: Thursday, March 02, 2017 4:41 PM
To: dev@ctakes.apache.org
Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?

I've modified the bin.xml accordingly and hibernate, weka and the mysql connector are now available in the classpath! Thank you for your help. I really appreciate that!

But still, I'm getting the same output like before, complaining about BeanCreationException: Error creating bean with name 'kernelApplicationContext', BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext] and so on.

Any ideas what I'm doing wrong?

[java] 02 Mar 2017 23:34:42  WARN ClassPathXmlApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
     [java] 02 Mar 2017 23:34:42  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7ed7259e: defining beans [kernelApplicationContext]; root of factory hierarchy
     [java] Exception in thread "main" java.lang.ExceptionInInitializerError
     [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
     [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
     [java] Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
     [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
     [java] 	at org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:29)
     [java] 	... 2 more
     [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
     [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1077)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:981)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
     [java] 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
     [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
     [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
     [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
     [java] 	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
     [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
     [java] 	... 3 more
     [java] Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
     [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
     [java] 	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:121)
     [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:277)
     [java] 	... 16 more
     [java] Caused by: org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1278)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.predictBeanType(AbstractAutowireCapableBeanFactory.java:573)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:1347)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:913)
     [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:619)
     [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
     [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
     [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
     [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
     [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
     [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
     [java] 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
     [java] 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
     [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:148)
     [java] 	... 18 more
     [java] Caused by: java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
     [java] 	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
     [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
     [java] 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
     [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
     [java] 	at org.springframework.util.ClassUtils.forName(ClassUtils.java:268)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanDefinition.resolveBeanClass(AbstractBeanDefinition.java:419)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doResolveBeanClass(AbstractBeanFactory.java:1299)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1270)
     [java] 	... 31 more

BUILD FAILED

Leander
> On 2 Mar 2017, at 22:45, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
> 
> hibernate

Re: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by Leander Melms <Me...@students.uni-marburg.de>.

I've modified the bin.xml accordingly and hibernate, weka and the mysql connector are now available in the classpath! Thank you for your help. I really appreciate that!

But still, I'm getting the same output like before, complaining about BeanCreationException: Error creating bean with name 'kernelApplicationContext', BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext] and so on.

Any ideas what I'm doing wrong?

[java] 02 Mar 2017 23:34:42  WARN ClassPathXmlApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
     [java] 02 Mar 2017 23:34:42  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7ed7259e: defining beans [kernelApplicationContext]; root of factory hierarchy
     [java] Exception in thread "main" java.lang.ExceptionInInitializerError
     [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
     [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
     [java] Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
     [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
     [java] 	at org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:29)
     [java] 	... 2 more
     [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
     [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1077)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:981)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
     [java] 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
     [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
     [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
     [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
     [java] 	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
     [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
     [java] 	... 3 more
     [java] Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
     [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
     [java] 	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:121)
     [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:277)
     [java] 	... 16 more
     [java] Caused by: org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.springframework.cache.ehcache.EhCacheManagerFactoryBean] for bean with name 'cacheManager' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1278)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.predictBeanType(AbstractAutowireCapableBeanFactory.java:573)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:1347)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:913)
     [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:619)
     [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
     [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
     [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
     [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
     [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
     [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
     [java] 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
     [java] 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
     [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:148)
     [java] 	... 18 more
     [java] Caused by: java.lang.ClassNotFoundException: org.springframework.cache.ehcache.EhCacheManagerFactoryBean
     [java] 	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
     [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
     [java] 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
     [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
     [java] 	at org.springframework.util.ClassUtils.forName(ClassUtils.java:268)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanDefinition.resolveBeanClass(AbstractBeanDefinition.java:419)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doResolveBeanClass(AbstractBeanFactory.java:1299)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1270)
     [java] 	... 31 more

BUILD FAILED

Leander
> On 2 Mar 2017, at 22:45, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
> 
> hibernate

RE: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by "Dunlop, Joyce (HP)" <Jo...@va.gov>.

Leander,

Looks like you are getting closer.     Have you made hibernate available?

Hibernate / Database jars were in the resources zips that are no longer available.

I believe I modified the bin.xml file in the ctake-distribution to change the excludes

From my bin.xml file:   I am using MS SQL server so I commented out the excludes for hibernate and ms sql server
....
                   <excludes>
                        <exclude>net.sourceforge.ctakesresources:*</exclude>
                        <!-- exclude assertion and lvg - they still need to be unpacked and not read from classpath yet -->
                        <exclude>org.apache.ctakes:ctakes-assertion-res</exclude>
                        <exclude>org.apache.ctakes:ctakes-lvg-res</exclude>
                <!-- Exclude fast-res - it should be unpacked in the resources directory -->
                <exclude>org.apache.ctakes:ctakes-dictionary-lookup-fast-res</exclude>
                <!-- exclude non-asf compliant dependencies used by ytex -->
                <!--  <exclude>org.hibernate:*</exclude>
                <exclude>nz.ac.waikato.cms.weka:*</exclude> -->
                <exclude>mysql:*</exclude>
                <!-- <exclude>com.microsoft.sqlserver:*</exclude> -->
                <exclude>oracle.jdbc:*</exclude>
                </excludes>
....

You may also look at the POM Files for hibernate and make sure it is not commented out too.

Thanks,
Joyce


-----Original Message-----
From: Leander Melms [mailto:Melms@students.Uni-Marburg.DE]
Sent: Thursday, March 02, 2017 3:36 PM
To: dev@ctakes.apache.org
Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?

Hello Joyce,

thank you for the fast reply. I've updated the POM and replaced all *-2.5.xsd and *-2.0.xsd with 3.2. Still no luck.

I couldn't make sense of it and was hoping for hints to solve this.

The output says that it can't load
- bean 'kernelApplicationContext' in kernelBeanRefContext.xml
- 'txAdvice' defined in class path resource org/apache/ctakes/ytex/beans-datasource.xml
...

Full error log:

[java] 02 Mar 2017 22:28:11  WARN ClassPathXmlApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
     [java] 02 Mar 2017 22:28:11  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2145b572: defining beans [kernelApplicationContext]; root of factory hierarchy
     [java] Exception in thread "main" java.lang.ExceptionInInitializerError
     [java]     at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
     [java]     at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
     [java] Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
     [java]     at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
     [java]     at org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:29)
     [java]     ... 2 more
     [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
     [java]     at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285)
     [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1077)
     [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:981)
     [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
     [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
     [java]     at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
     [java]     at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
     [java]     at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
     [java]     at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
     [java]     at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
     [java]     at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
     [java]     at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
     [java]     at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
     [java]     at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
     [java]     ... 3 more
     [java] Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
     [java]     at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
     [java]     at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:121)
     [java]     at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:277)
     [java]     ... 16 more
     [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
     [java]     at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:334)
     [java]     at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
     [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1419)
     [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1160)
     [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
     [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
     [java]     at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
     [java]     at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
     [java]     at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
     [java]     at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
     [java]     at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
     [java]     at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
     [java]     at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
     [java]     at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
     [java]     at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
     [java]     at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
     [java]     at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
     [java]     at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
     [java]     at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
     [java]     at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:148)
     [java]     ... 18 more
     [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
     [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1039)
     [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:985)
     [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
     [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
     [java]     at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
     [java]     at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
     [java]     at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
     [java]     at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
     [java]     at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
     [java]     ... 37 more
     [java] Caused by: java.lang.NoClassDefFoundError: org/hibernate/HibernateException
     [java]     at java.lang.Class.getDeclaredConstructors0(Native Method)
     [java]     at java.lang.Class.privateGetDeclaredConstructors(Class.java:2671)
     [java]     at java.lang.Class.getConstructor0(Class.java:3075)
     [java]     at java.lang.Class.getDeclaredConstructor(Class.java:2178)
     [java]     at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:78)
     [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1032)
     [java]     ... 45 more
     [java] Caused by: java.lang.ClassNotFoundException: org.hibernate.HibernateException
     [java]     at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
     [java]     at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
     [java]     at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
     [java]     at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
     [java]     ... 51 more


Leander

> On 2 Mar 2017, at 21:00, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>
> Hello Leander,
> The error your reporting is most likely related to a version conflict.
> I had to make the following changes to upgrade the spring version.
>
> POM Moderations:
> Property -
>        <spring.version>3.2.18.RELEASE</spring.version>
> Dependencies -
>                        <dependency>
>                                <groupId>org.springframework</groupId>
>                                <artifactId>spring-core</artifactId>
>                                <version>${spring.version}</version>
>                        </dependency>
>                        <dependency>
>                                <groupId>org.springframework</groupId>
>                                <artifactId>spring-context</artifactId>
>                                <version>${spring.version}</version>
>                        </dependency>
>                        <dependency>
>                                <groupId>org.springframework</groupId>
>                                <artifactId>spring-context-support</artifactId>
>                                <version>${spring.version}</version>
>                        </dependency>
>                        <dependency>
>                                <groupId>org.springframework</groupId>
>                                <artifactId>spring-web</artifactId>
>                                <version>${spring.version}</version>
>                        </dependency>
>                        <dependency>
>                                <groupId>org.springframework</groupId>
>                                <artifactId>spring-jdbc</artifactId>
>                                <version>${spring.version}</version>
>                        </dependency>
>                        <dependency>
>                                <groupId>org.springframework</groupId>
>                                <artifactId>spring-orm</artifactId>
>                                <version>${spring.version}</version>
>                        </dependency>
>                        <dependency>
>                                <groupId>org.springframework</groupId>
>                                <artifactId>spring-aop</artifactId>
>                                <version>${spring.version}</version>
>                        </dependency>
>
> Modified xsi:schemaLocation(s):
>
>        Look for 2.5.xsd or 2.0.xsd references and change to 3.2.xsd
>        Example:
>                spring-aop-2.5.xsd to spring-aop-3.2.xsd
>
> Thanks,
> Joyce
>
>
> -----Original Message-----
> From: Leander Melms [mailto:Melms@students.uni-marburg.de]
> Sent: Thursday, March 02, 2017 12:23 PM
> To: dev@ctakes.apache.org
> Subject: [EXTERNAL] Re: YTEX User Inferace Users?
>
> Hi Sean and Joyce,
>
> I'm trying hard to get ytex running as well. I've followed each step you've outlined but I'm somewhat stuck now.
>
> What I did:
>
> - Tried to compile and run with Java 7 --> not working
> - Tried to compile and run with Java 8 --> not working
> - Tried to update Spring to 3.2.18.RELEASE in pom.xml
>
>      <dependency>
>        <groupId>org.springframework</groupId>
>        <artifactId>spring-core</artifactId>
>        <version>3.2.18.RELEASE</version>
>      </dependency>
>      <dependency>
>        <groupId>org.springframework</groupId>
>        <artifactId>spring-context</artifactId>
>        <version>3.2.18.RELEASE</version>
>      </dependency>
>      <dependency>
>        <groupId>org.springframework</groupId>
>        <artifactId>spring-web</artifactId>
>        <version>3.2.18.RELEASE</version>
>      </dependency>
>      <dependency>
>
> leading to the Exception in thread "main"
> java.lang.IncompatibleClassChangeError: class
> org.springframework.core.LocalVariableTableParameterNameDiscoverer$Par
> ameterNameDiscoveringVisitor has interface
> org.springframework.asm.ClassVisitor as super class
>
> Could you briefly describe what you did to get ytex running? Any help is greatly appreciated.
>
>
> Leander
>
>
>> On 13 Feb 2017, at 17:41, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>>
>> Is there anyone on this email list that is using the YTEX web interface?
>>
>> Thanks for the information Sean!
>>
>> Joyce
>>
>> -----Original Message-----
>> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
>> Sent: Monday, February 13, 2017 10:26 AM
>> To: Dunlop, Joyce (HP)
>> Cc: dev@ctakes.apache.org
>> Subject: [EXTERNAL] RE: YTEX setup notes
>>
>> Our main interest in YTEX is the database reader and consumer that it comes with. That is probably a smaller subset of its functionality but it was a good source for those. We are still working on implementation, but we plan to run an annotation pipeline on the new notes we get each day and store the resulting annotations in our database. The notes will be read from a database, parceled out in chunks to several processes, annotated, and consumed by the database consumer.
>>
>> Sean
>>
>> -----Original Message-----
>> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
>> Sent: Monday, February 13, 2017 11:17 AM
>> To: Mullane, Sean *HS
>> Cc: dev@ctakes.apache.org
>> Subject: RE: YTEX setup notes
>>
>> Hi Sean,
>>
>> I will have to check with the VA Researchers to find out what they planned to for the ytex web.
>> So you don't use YTEX web interface but you do use ytex correct?  Could you share the steps in a typical process you run for YTEX?
>>
>> Thanks,
>> Joyce
>>
>> -----Original Message-----
>> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
>> Sent: Monday, February 13, 2017 7:59 AM
>> To: Dunlop, Joyce (HP)
>> Cc: dev@ctakes.apache.org
>> Subject: [EXTERNAL] RE: YTEX setup notes
>>
>> Hi Joyce,
>>
>> I wound up solving the error by commenting out the bean definition in ctakes-ytex-res/src/main/resources/org/apache/ctakes/beans-kernel.xml and ctakes-ytex-res/target/classes/org/apache/ctakes/beans-kernel.xml, which resolved that error. I think it was deprecated anyway.
>>
>> I did run into another error where I didn't have LookupDesc_SNOMED.xml in the directory path. Added it from the ctakes-src files solved that problem and got it working on Java 8 for us.
>>
>> I haven't tried using the web interface - we don't have any plans to use it. Can I ask what you want to use it for? I'm not really familiar with what it does.
>>
>> Thanks,
>> Sean
>>
>> -----Original Message-----
>> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
>> Sent: Friday, February 10, 2017 3:57 PM
>> To: Mullane, Sean *HS
>> Subject: RE: YTEX setup notes
>>
>> Hi Sean,
>>
>> We had to change the return type from BagOfWordsExporter to WekaBagOfWordsExporter in that file.
>>
>> From:
>>      public BagOfWordsExporter getBagOfWordsExporter() {
>>              return bagOfWordsExporter;
>>      }
>>
>> To:
>>      public WekaBagOfWordsExporter getBagOfWordsExporter() {
>>              return bagOfWordsExporter;
>>      }
>>
>> We have still not be able to get the YTEX web interface to work.  The YTEX application starts up and we are able to access through the URL:  http://localhost:8080/semanticSim.jsf - We see 4 tabs but nothing seems functional.  Is there something we are still missing?  We found references to rest services - are they called separate from the YTEX UI?
>>
>> Any clue would be appreciated.
>>
>> Thanks,
>> Joyce
>>
>> PS:  I think there was one other code change to get Java 8 working, so if you get another error just shoot it over and I should have the answer.
>>
>>
>>
>>
>>
>>
>> -----Original Message-----
>> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
>> Sent: Monday, February 06, 2017 3:33 PM
>> To: Dunlop, Joyce (HP)
>> Cc: dev@ctakes.apache.org
>> Subject: [EXTERNAL] RE: YTEX setup notes
>>
>> Joyce,
>>
>> I haven't been able to find further documentation. It seems it is somewhat out of date and some of the Yale sources have been taken down.
>>
>> In your feedback on my YTEX setup notes, I'm finding that when I try to run YTEX using Java 8 I get an error related to org.apache.ctakes.ytex.weka.GramMatrixExporterImpl. When I run it on Java 7 I get no errors. You mentioned that upgrading to Spring 3.2 solved an issue for you. How did you do that - did you change the Maven build file to pull in the newer version or did you do something else to get the newer Spring version? I'm hoping that will resolve the Java 8 issue here.
>>
>> Thanks,
>> Sean
>>
>> -----Original Message-----
>> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
>> Sent: Friday, February 03, 2017 4:26 PM
>> To: Mullane, Sean *HS
>> Cc: dev@ctakes.apache.org
>> Subject: RE: YTEX setup notes
>>
>> Sean/others,
>>
>> Do you by chance have any of the documentation produced by Yale tucked away locally?
>>
>> I see quite a few dead links that seem to go back to demo's and documents on cTakes site.
>>
>> Examples:
>> The demo similarity web app is available under
>> http://informatics.med.yale.edu/ytex.web;
>>
>> http://ytex.googlecode.com/svn/trunk/projects/nlm.wsd/doc/YTEX%20Sema
>> ntic%20Similarity%20Measures.pdf
>>
>> Thanks,
>> Joyce
>>
>> -----Original Message-----
>> From: Dunlop, Joyce (HP)
>> Sent: Monday, January 30, 2017 8:27 PM
>> To: 'Mullane, Sean *HS'; dev@ctakes.apache.org
>> Subject: RE: YTEX setup notes
>>
>> Sean M,
>> This is perfect!
>>
>> Thanks,
>> Joyce
>>
>> -----Original Message-----
>> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
>> Sent: Monday, January 30, 2017 3:06 PM
>> To: Dunlop, Joyce (HP); dev@ctakes.apache.org
>> Subject: [EXTERNAL] RE: YTEX setup notes
>>
>> Joyce,
>>
>> Thanks for the notes. I'm glad to see you had success using Java 8 - I'll have to try that.
>>
>> To answer your question about table contents, see below for the rowcounts in the YTEX tables after in my installation. Apologies in advance for the formatting:
>>
>> tablename     tot_cnt
>> anno_base             0
>> anno_base_sequence    1
>> anno_contain          0
>> anno_date             0
>> anno_link             0
>> anno_markable 0
>> anno_med_event        0
>> anno_mm_acronym       0
>> anno_mm_candidate     0
>> anno_mm_cuiconcept    0
>> anno_mm_negation      0
>> anno_mm_utterance     0
>> anno_named_entity     0
>> anno_ontology_concept 0
>> anno_segment          0
>> anno_sentence 0
>> anno_token            0
>> anno_treebank_node    0
>> classifier_eval               0
>> classifier_eval_ir    0
>> classifier_eval_semil 0
>> classifier_eval_svm   0
>> classifier_instance_eval      0
>> classifier_instance_eval_prob 0
>> corpus_doc            0
>> corpus_label          0
>> cv_best_svm           0
>> cv_fold                       0
>> cv_fold_instance      0
>> document              0
>> feature_eval          0
>> feature_parchd        0
>> feature_rank          0
>> fracture_demo         31
>> hibernate_sequences   1
>> hotspot               0
>> hotspot_instance      0
>> hotspot_sentence      0
>> kernel_eval           0
>> kernel_eval_instance  0
>> ref_named_entity_regex        0
>> ref_segment_regex     0
>> ref_stopword          360
>> ref_uima_type         38
>> tfidf_doclength       0
>> umls_aui_fword        6902003
>> v_snomed_fword_lookup 1374810
>>
>> Sean
>>
>> -----Original Message-----
>> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
>> Sent: Friday, January 27, 2017 10:12 AM
>> To: dev@ctakes.apache.org
>> Subject: YTEX setup notes
>>
>> Hi Sean M,
>>
>> Notes from :
>> Step
>> -The Needed to add sqljdbc4.jar to CTAKES_HOME/lib probably need to happen after -3. Install cTAKES "as usual"
>>
>> -Java 7 is throwing errors because Spring needs to be upgraded to at least 3.2.
>> --It looks like Spring was previously upgraded from 2.5 to 3.1, but spring context files -  xsi:schemaLocation were not previous upgraded and remained 2.5.
>>
>> -We have been able to successful run the script with JAVA 8 after upgrading Spring to 3.2.18-Release from the 3.1/2.5 version.   We also upgraded the version of Jetty.
>>
>> -Step 7 which I think you list as 8 below to execute the setup script. It looks like it has mostly been successful but I do have a few errors at the bottom related to the database password we chose which had an & (AMP) character is being parsed on the & character.
>>
>> 3 tables that are showing errors related to the amp characters:
>> -ref_uima_type.xml
>> -fracture_demo.xml
>> -stopword.xml
>>
>> 2 tables are the only table will significant record counts:
>> -umls_aui_fword
>> -v_snomed_fword_lookup
>>
>> 2 other table seem to have one row inserted.
>>
>> The question I have is when this step completes how many of the tables should have data?
>>
>> Thanks again.
>> Joyce
>>
>>
>>
>>
>> -----Original Message-----
>> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
>> Sent: Tuesday, January 17, 2017 12:33 PM
>> To: dev@ctakes.apache.org
>> Subject: [EXTERNAL] RE: New to CTAKES
>>
>> Sean M,
>>
>> I will try to work through the process this tomorrow.
>>
>> Thanks!
>>
>> Joyce
>>
>> -----Original Message-----
>> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
>> Sent: Tuesday, January 17, 2017 11:10 AM
>> To: dev@ctakes.apache.org
>> Subject: [EXTERNAL] RE: New to CTAKES
>>
>> Joyce,
>>
>> This may help, here are some notes I put together when installing YTEX in our Windows/SQL Server test environment. I didn't build from source here, this is just installation (including UMLS). I'm working on writing up these instructions more thoroughly so if you use this please let me know if you find any points of improvement.
>>
>> Requirements and steps to set up YTEX These notes refer to the
>> installation instructions at
>> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
>> 1. They suggest installing UMLS in our database
>>      Follow instructions here to install UMLS: https://cwiki.apache.org/confluence/display/CTAKES/UMLS+MS+SQL+Server+Installation
>>      -http://groups.csail.mit.edu/medg/projects/text/Load_UMLS_mysql.html is useful when installing from .zip file. The mmsys.zip file needs to be unzipped to access the run64.bat file but also needs to be present as a .zip file for the run64.bat file to read from.
>> 2. Create a database user and schema for use with YTEX 3. Load UMLS into database
>>      -Needed to create ytex.properties file from examples files in the developer/source version of cTAKES
>>      -Needed to change path in ctakes.profile to match version name of CTAKES_HOME directory
>>      -Needed to add sqljdbc4.jar to CTAKES_HOME/lib and sqljdbc_auth.dll to C:\Program Files\Java\jre_Version\bin
>>      -Needed to open port 1433 for TCP/IP traffic and clear dynamic ports
>>      -Need to change table definitions as follows to install UMLS-2016AB:
>>              MRCONSO.CODE varchar(75) -- was varchar(50)
>>              MRDEF.DEF varchar(max) -- was varchar(4000)
>>              MRSAB.VSAB varchar(24) -- was varchar(20)
>>              MRSAT.ATN varchar(64) -- was varchar(50)
>>              MRSAT.ATV varchar(max) -- was varchar(4000) 3. Install cTAKES "as usual"
>> 4. Download and unzip ctakes-ytex-lib-3.1.2-SNAPSHOT.zip 'over' your installation.
>>      -I believe this step is deprecated - skip to step 6 5. Unzip YTEX Resources (Optional - UTS login required)
>>      -I believe this step is deprecated - skip to step 6
>>      -may be needed for concept graphs and dictionary lookup table for NER 6. Fix the path references in shell script to match your environment 7. Create CTAKES_HOME\resources\org\apache\ctakes\ytex\ytex.properties and specify database connection parameters.
>> 8. Execute the setup script
>>      -Need to use Java 7 - Java 8 errors out
>>      -If SQL errors encountered, appenders can be added to log4j.xml
>> to collect SQL queries
>>
>> Sean
>>
>> -----Original Message-----
>> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
>> Sent: Tuesday, January 17, 2017 11:57 AM
>> To: dev@ctakes.apache.org
>> Subject: RE: New to CTAKES
>>
>> Hi Joyce,
>>
>> If you are building from source then you should not need to manually download the resources.  Maven should be doing it for you.  Well, that is the behavior of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
>>
>> Otherwise, I think that if the latest was the 3.2.1.1 then that is probably the most appropriate for the 3.2.2 release if you want all of the resources.
>>
>> As for building and deploying ytex, I don't have any advice.  Perhaps some ytex power-user out there can help.
>>
>> Sean
>>
>> -----Original Message-----
>> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
>> Sent: Tuesday, January 17, 2017 11:25 AM
>> To: dev@ctakes.apache.org
>> Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
>> Subject: New to CTAKES
>>
>> Good Morning,
>>
>> I am trying to set up a development environment using the source release of 3.2.2.
>>
>> Reading though the documentation on
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
>>
>> Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e=  into your ctakes-dictionary-lookup-res project.
>>
>> ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is available for download.  Is there a 3.2.2 version of the resources?
>>
>> After reading some of the posts from the email box, and reading the documentation on the site above.  It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.
>>
>> Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?
>>
>> Thanks,
>> Joyce
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>

Re: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by Leander Melms <Me...@students.Uni-Marburg.DE>.

Hello Joyce,

thank you for the fast reply. I've updated the POM and replaced all *-2.5.xsd and *-2.0.xsd with 3.2. Still no luck.

I couldn't make sense of it and was hoping for hints to solve this.

The output says that it can't load 
- bean 'kernelApplicationContext' in kernelBeanRefContext.xml
- 'txAdvice' defined in class path resource org/apache/ctakes/ytex/beans-datasource.xml
...

Full error log:

[java] 02 Mar 2017 22:28:11  WARN ClassPathXmlApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
     [java] 02 Mar 2017 22:28:11  INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2145b572: defining beans [kernelApplicationContext]; root of factory hierarchy
     [java] Exception in thread "main" java.lang.ExceptionInInitializerError
     [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
     [java] 	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
     [java] Caused by: org.springframework.beans.factory.access.BootstrapException: Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
     [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
     [java] 	at org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:29)
     [java] 	... 2 more
     [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
     [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1077)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:981)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
     [java] 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
     [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
     [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
     [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
     [java] 	at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
     [java] 	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
     [java] 	... 3 more
     [java] Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
     [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
     [java] 	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:121)
     [java] 	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:277)
     [java] 	... 16 more
     [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
     [java] 	at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:334)
     [java] 	at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1419)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1160)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
     [java] 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
     [java] 	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
     [java] 	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
     [java] 	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
     [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
     [java] 	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
     [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
     [java] 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
     [java] 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
     [java] 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
     [java] 	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:148)
     [java] 	... 18 more
     [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1039)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:985)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
     [java] 	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
     [java] 	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
     [java] 	at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
     [java] 	... 37 more
     [java] Caused by: java.lang.NoClassDefFoundError: org/hibernate/HibernateException
     [java] 	at java.lang.Class.getDeclaredConstructors0(Native Method)
     [java] 	at java.lang.Class.privateGetDeclaredConstructors(Class.java:2671)
     [java] 	at java.lang.Class.getConstructor0(Class.java:3075)
     [java] 	at java.lang.Class.getDeclaredConstructor(Class.java:2178)
     [java] 	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:78)
     [java] 	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1032)
     [java] 	... 45 more
     [java] Caused by: java.lang.ClassNotFoundException: org.hibernate.HibernateException
     [java] 	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
     [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
     [java] 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
     [java] 	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
     [java] 	... 51 more


Leander

> On 2 Mar 2017, at 21:00, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
> 
> Hello Leander,
> The error your reporting is most likely related to a version conflict.
> I had to make the following changes to upgrade the spring version.
> 
> POM Moderations:
> Property -
>        <spring.version>3.2.18.RELEASE</spring.version>
> Dependencies -
>                        <dependency>
>                                <groupId>org.springframework</groupId>
>                                <artifactId>spring-core</artifactId>
>                                <version>${spring.version}</version>
>                        </dependency>
>                        <dependency>
>                                <groupId>org.springframework</groupId>
>                                <artifactId>spring-context</artifactId>
>                                <version>${spring.version}</version>
>                        </dependency>
>                        <dependency>
>                                <groupId>org.springframework</groupId>
>                                <artifactId>spring-context-support</artifactId>
>                                <version>${spring.version}</version>
>                        </dependency>
>                        <dependency>
>                                <groupId>org.springframework</groupId>
>                                <artifactId>spring-web</artifactId>
>                                <version>${spring.version}</version>
>                        </dependency>
>                        <dependency>
>                                <groupId>org.springframework</groupId>
>                                <artifactId>spring-jdbc</artifactId>
>                                <version>${spring.version}</version>
>                        </dependency>
>                        <dependency>
>                                <groupId>org.springframework</groupId>
>                                <artifactId>spring-orm</artifactId>
>                                <version>${spring.version}</version>
>                        </dependency>
>                        <dependency>
>                                <groupId>org.springframework</groupId>
>                                <artifactId>spring-aop</artifactId>
>                                <version>${spring.version}</version>
>                        </dependency>
> 
> Modified xsi:schemaLocation(s):
> 
>        Look for 2.5.xsd or 2.0.xsd references and change to 3.2.xsd
>        Example:
>                spring-aop-2.5.xsd to spring-aop-3.2.xsd
> 
> Thanks,
> Joyce
> 
> 
> -----Original Message-----
> From: Leander Melms [mailto:Melms@students.uni-marburg.de]
> Sent: Thursday, March 02, 2017 12:23 PM
> To: dev@ctakes.apache.org
> Subject: [EXTERNAL] Re: YTEX User Inferace Users?
> 
> Hi Sean and Joyce,
> 
> I'm trying hard to get ytex running as well. I've followed each step you've outlined but I'm somewhat stuck now.
> 
> What I did:
> 
> - Tried to compile and run with Java 7 --> not working
> - Tried to compile and run with Java 8 --> not working
> - Tried to update Spring to 3.2.18.RELEASE in pom.xml
> 
>      <dependency>
>        <groupId>org.springframework</groupId>
>        <artifactId>spring-core</artifactId>
>        <version>3.2.18.RELEASE</version>
>      </dependency>
>      <dependency>
>        <groupId>org.springframework</groupId>
>        <artifactId>spring-context</artifactId>
>        <version>3.2.18.RELEASE</version>
>      </dependency>
>      <dependency>
>        <groupId>org.springframework</groupId>
>        <artifactId>spring-web</artifactId>
>        <version>3.2.18.RELEASE</version>
>      </dependency>
>      <dependency>
> 
> leading to the Exception in thread "main" java.lang.IncompatibleClassChangeError: class org.springframework.core.LocalVariableTableParameterNameDiscoverer$ParameterNameDiscoveringVisitor has interface org.springframework.asm.ClassVisitor as super class
> 
> Could you briefly describe what you did to get ytex running? Any help is greatly appreciated.
> 
> 
> Leander
> 
> 
>> On 13 Feb 2017, at 17:41, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>> 
>> Is there anyone on this email list that is using the YTEX web interface?
>> 
>> Thanks for the information Sean!
>> 
>> Joyce
>> 
>> -----Original Message-----
>> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
>> Sent: Monday, February 13, 2017 10:26 AM
>> To: Dunlop, Joyce (HP)
>> Cc: dev@ctakes.apache.org
>> Subject: [EXTERNAL] RE: YTEX setup notes
>> 
>> Our main interest in YTEX is the database reader and consumer that it comes with. That is probably a smaller subset of its functionality but it was a good source for those. We are still working on implementation, but we plan to run an annotation pipeline on the new notes we get each day and store the resulting annotations in our database. The notes will be read from a database, parceled out in chunks to several processes, annotated, and consumed by the database consumer.
>> 
>> Sean
>> 
>> -----Original Message-----
>> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
>> Sent: Monday, February 13, 2017 11:17 AM
>> To: Mullane, Sean *HS
>> Cc: dev@ctakes.apache.org
>> Subject: RE: YTEX setup notes
>> 
>> Hi Sean,
>> 
>> I will have to check with the VA Researchers to find out what they planned to for the ytex web.
>> So you don't use YTEX web interface but you do use ytex correct?  Could you share the steps in a typical process you run for YTEX?
>> 
>> Thanks,
>> Joyce
>> 
>> -----Original Message-----
>> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
>> Sent: Monday, February 13, 2017 7:59 AM
>> To: Dunlop, Joyce (HP)
>> Cc: dev@ctakes.apache.org
>> Subject: [EXTERNAL] RE: YTEX setup notes
>> 
>> Hi Joyce,
>> 
>> I wound up solving the error by commenting out the bean definition in ctakes-ytex-res/src/main/resources/org/apache/ctakes/beans-kernel.xml and ctakes-ytex-res/target/classes/org/apache/ctakes/beans-kernel.xml, which resolved that error. I think it was deprecated anyway.
>> 
>> I did run into another error where I didn't have LookupDesc_SNOMED.xml in the directory path. Added it from the ctakes-src files solved that problem and got it working on Java 8 for us.
>> 
>> I haven't tried using the web interface - we don't have any plans to use it. Can I ask what you want to use it for? I'm not really familiar with what it does.
>> 
>> Thanks,
>> Sean
>> 
>> -----Original Message-----
>> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
>> Sent: Friday, February 10, 2017 3:57 PM
>> To: Mullane, Sean *HS
>> Subject: RE: YTEX setup notes
>> 
>> Hi Sean,
>> 
>> We had to change the return type from BagOfWordsExporter to WekaBagOfWordsExporter in that file.
>> 
>> From:
>>      public BagOfWordsExporter getBagOfWordsExporter() {
>>              return bagOfWordsExporter;
>>      }
>> 
>> To:
>>      public WekaBagOfWordsExporter getBagOfWordsExporter() {
>>              return bagOfWordsExporter;
>>      }
>> 
>> We have still not be able to get the YTEX web interface to work.  The YTEX application starts up and we are able to access through the URL:  http://localhost:8080/semanticSim.jsf - We see 4 tabs but nothing seems functional.  Is there something we are still missing?  We found references to rest services - are they called separate from the YTEX UI?
>> 
>> Any clue would be appreciated.
>> 
>> Thanks,
>> Joyce
>> 
>> PS:  I think there was one other code change to get Java 8 working, so if you get another error just shoot it over and I should have the answer.
>> 
>> 
>> 
>> 
>> 
>> 
>> -----Original Message-----
>> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
>> Sent: Monday, February 06, 2017 3:33 PM
>> To: Dunlop, Joyce (HP)
>> Cc: dev@ctakes.apache.org
>> Subject: [EXTERNAL] RE: YTEX setup notes
>> 
>> Joyce,
>> 
>> I haven't been able to find further documentation. It seems it is somewhat out of date and some of the Yale sources have been taken down.
>> 
>> In your feedback on my YTEX setup notes, I'm finding that when I try to run YTEX using Java 8 I get an error related to org.apache.ctakes.ytex.weka.GramMatrixExporterImpl. When I run it on Java 7 I get no errors. You mentioned that upgrading to Spring 3.2 solved an issue for you. How did you do that - did you change the Maven build file to pull in the newer version or did you do something else to get the newer Spring version? I'm hoping that will resolve the Java 8 issue here.
>> 
>> Thanks,
>> Sean
>> 
>> -----Original Message-----
>> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
>> Sent: Friday, February 03, 2017 4:26 PM
>> To: Mullane, Sean *HS
>> Cc: dev@ctakes.apache.org
>> Subject: RE: YTEX setup notes
>> 
>> Sean/others,
>> 
>> Do you by chance have any of the documentation produced by Yale tucked away locally?
>> 
>> I see quite a few dead links that seem to go back to demo's and documents on cTakes site.
>> 
>> Examples:
>> The demo similarity web app is available under http://informatics.med.yale.edu/ytex.web;
>> 
>> http://ytex.googlecode.com/svn/trunk/projects/nlm.wsd/doc/YTEX%20Semantic%20Similarity%20Measures.pdf
>> 
>> Thanks,
>> Joyce
>> 
>> -----Original Message-----
>> From: Dunlop, Joyce (HP)
>> Sent: Monday, January 30, 2017 8:27 PM
>> To: 'Mullane, Sean *HS'; dev@ctakes.apache.org
>> Subject: RE: YTEX setup notes
>> 
>> Sean M,
>> This is perfect!
>> 
>> Thanks,
>> Joyce
>> 
>> -----Original Message-----
>> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
>> Sent: Monday, January 30, 2017 3:06 PM
>> To: Dunlop, Joyce (HP); dev@ctakes.apache.org
>> Subject: [EXTERNAL] RE: YTEX setup notes
>> 
>> Joyce,
>> 
>> Thanks for the notes. I'm glad to see you had success using Java 8 - I'll have to try that.
>> 
>> To answer your question about table contents, see below for the rowcounts in the YTEX tables after in my installation. Apologies in advance for the formatting:
>> 
>> tablename     tot_cnt
>> anno_base             0
>> anno_base_sequence    1
>> anno_contain          0
>> anno_date             0
>> anno_link             0
>> anno_markable 0
>> anno_med_event        0
>> anno_mm_acronym       0
>> anno_mm_candidate     0
>> anno_mm_cuiconcept    0
>> anno_mm_negation      0
>> anno_mm_utterance     0
>> anno_named_entity     0
>> anno_ontology_concept 0
>> anno_segment          0
>> anno_sentence 0
>> anno_token            0
>> anno_treebank_node    0
>> classifier_eval               0
>> classifier_eval_ir    0
>> classifier_eval_semil 0
>> classifier_eval_svm   0
>> classifier_instance_eval      0
>> classifier_instance_eval_prob 0
>> corpus_doc            0
>> corpus_label          0
>> cv_best_svm           0
>> cv_fold                       0
>> cv_fold_instance      0
>> document              0
>> feature_eval          0
>> feature_parchd        0
>> feature_rank          0
>> fracture_demo         31
>> hibernate_sequences   1
>> hotspot               0
>> hotspot_instance      0
>> hotspot_sentence      0
>> kernel_eval           0
>> kernel_eval_instance  0
>> ref_named_entity_regex        0
>> ref_segment_regex     0
>> ref_stopword          360
>> ref_uima_type         38
>> tfidf_doclength       0
>> umls_aui_fword        6902003
>> v_snomed_fword_lookup 1374810
>> 
>> Sean
>> 
>> -----Original Message-----
>> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
>> Sent: Friday, January 27, 2017 10:12 AM
>> To: dev@ctakes.apache.org
>> Subject: YTEX setup notes
>> 
>> Hi Sean M,
>> 
>> Notes from :
>> Step
>> -The Needed to add sqljdbc4.jar to CTAKES_HOME/lib probably need to happen after -3. Install cTAKES "as usual"
>> 
>> -Java 7 is throwing errors because Spring needs to be upgraded to at least 3.2.
>> --It looks like Spring was previously upgraded from 2.5 to 3.1, but spring context files -  xsi:schemaLocation were not previous upgraded and remained 2.5.
>> 
>> -We have been able to successful run the script with JAVA 8 after upgrading Spring to 3.2.18-Release from the 3.1/2.5 version.   We also upgraded the version of Jetty.
>> 
>> -Step 7 which I think you list as 8 below to execute the setup script. It looks like it has mostly been successful but I do have a few errors at the bottom related to the database password we chose which had an & (AMP) character is being parsed on the & character.
>> 
>> 3 tables that are showing errors related to the amp characters:
>> -ref_uima_type.xml
>> -fracture_demo.xml
>> -stopword.xml
>> 
>> 2 tables are the only table will significant record counts:
>> -umls_aui_fword
>> -v_snomed_fword_lookup
>> 
>> 2 other table seem to have one row inserted.
>> 
>> The question I have is when this step completes how many of the tables should have data?
>> 
>> Thanks again.
>> Joyce
>> 
>> 
>> 
>> 
>> -----Original Message-----
>> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
>> Sent: Tuesday, January 17, 2017 12:33 PM
>> To: dev@ctakes.apache.org
>> Subject: [EXTERNAL] RE: New to CTAKES
>> 
>> Sean M,
>> 
>> I will try to work through the process this tomorrow.
>> 
>> Thanks!
>> 
>> Joyce
>> 
>> -----Original Message-----
>> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
>> Sent: Tuesday, January 17, 2017 11:10 AM
>> To: dev@ctakes.apache.org
>> Subject: [EXTERNAL] RE: New to CTAKES
>> 
>> Joyce,
>> 
>> This may help, here are some notes I put together when installing YTEX in our Windows/SQL Server test environment. I didn't build from source here, this is just installation (including UMLS). I'm working on writing up these instructions more thoroughly so if you use this please let me know if you find any points of improvement.
>> 
>> Requirements and steps to set up YTEX
>> These notes refer to the installation instructions at https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
>> 1. They suggest installing UMLS in our database
>>      Follow instructions here to install UMLS: https://cwiki.apache.org/confluence/display/CTAKES/UMLS+MS+SQL+Server+Installation
>>      -http://groups.csail.mit.edu/medg/projects/text/Load_UMLS_mysql.html is useful when installing from .zip file. The mmsys.zip file needs to be unzipped to access the run64.bat file but also needs to be present as a .zip file for the run64.bat file to read from.
>> 2. Create a database user and schema for use with YTEX 3. Load UMLS into database
>>      -Needed to create ytex.properties file from examples files in the developer/source version of cTAKES
>>      -Needed to change path in ctakes.profile to match version name of CTAKES_HOME directory
>>      -Needed to add sqljdbc4.jar to CTAKES_HOME/lib and sqljdbc_auth.dll to C:\Program Files\Java\jre_Version\bin
>>      -Needed to open port 1433 for TCP/IP traffic and clear dynamic ports
>>      -Need to change table definitions as follows to install UMLS-2016AB:
>>              MRCONSO.CODE varchar(75) -- was varchar(50)
>>              MRDEF.DEF varchar(max) -- was varchar(4000)
>>              MRSAB.VSAB varchar(24) -- was varchar(20)
>>              MRSAT.ATN varchar(64) -- was varchar(50)
>>              MRSAT.ATV varchar(max) -- was varchar(4000) 3. Install cTAKES "as usual"
>> 4. Download and unzip ctakes-ytex-lib-3.1.2-SNAPSHOT.zip 'over' your installation.
>>      -I believe this step is deprecated - skip to step 6 5. Unzip YTEX Resources (Optional - UTS login required)
>>      -I believe this step is deprecated - skip to step 6
>>      -may be needed for concept graphs and dictionary lookup table for NER 6. Fix the path references in shell script to match your environment 7. Create CTAKES_HOME\resources\org\apache\ctakes\ytex\ytex.properties and specify database connection parameters.
>> 8. Execute the setup script
>>      -Need to use Java 7 - Java 8 errors out
>>      -If SQL errors encountered, appenders can be added to log4j.xml to collect SQL queries
>> 
>> Sean
>> 
>> -----Original Message-----
>> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
>> Sent: Tuesday, January 17, 2017 11:57 AM
>> To: dev@ctakes.apache.org
>> Subject: RE: New to CTAKES
>> 
>> Hi Joyce,
>> 
>> If you are building from source then you should not need to manually download the resources.  Maven should be doing it for you.  Well, that is the behavior of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
>> 
>> Otherwise, I think that if the latest was the 3.2.1.1 then that is probably the most appropriate for the 3.2.2 release if you want all of the resources.
>> 
>> As for building and deploying ytex, I don't have any advice.  Perhaps some ytex power-user out there can help.
>> 
>> Sean
>> 
>> -----Original Message-----
>> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
>> Sent: Tuesday, January 17, 2017 11:25 AM
>> To: dev@ctakes.apache.org
>> Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
>> Subject: New to CTAKES
>> 
>> Good Morning,
>> 
>> I am trying to set up a development environment using the source release of 3.2.2.
>> 
>> Reading though the documentation on
>> 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
>> 
>> Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e=  into your ctakes-dictionary-lookup-res project.
>> 
>> ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is available for download.  Is there a 3.2.2 version of the resources?
>> 
>> After reading some of the posts from the email box, and reading the documentation on the site above.  It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.
>> 
>> Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?
>> 
>> Thanks,
>> Joyce
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
> 
>

RE: [EXTERNAL] Re: YTEX User Inferace Users?

Posted by "Dunlop, Joyce (HP)" <Jo...@va.gov>.

Hello Leander,
The error your reporting is most likely related to a version conflict.
I had to make the following changes to upgrade the spring version.

POM Moderations:
Property -
        <spring.version>3.2.18.RELEASE</spring.version>
Dependencies -
                        <dependency>
                                <groupId>org.springframework</groupId>
                                <artifactId>spring-core</artifactId>
                                <version>${spring.version}</version>
                        </dependency>
                        <dependency>
                                <groupId>org.springframework</groupId>
                                <artifactId>spring-context</artifactId>
                                <version>${spring.version}</version>
                        </dependency>
                        <dependency>
                                <groupId>org.springframework</groupId>
                                <artifactId>spring-context-support</artifactId>
                                <version>${spring.version}</version>
                        </dependency>
                        <dependency>
                                <groupId>org.springframework</groupId>
                                <artifactId>spring-web</artifactId>
                                <version>${spring.version}</version>
                        </dependency>
                        <dependency>
                                <groupId>org.springframework</groupId>
                                <artifactId>spring-jdbc</artifactId>
                                <version>${spring.version}</version>
                        </dependency>
                        <dependency>
                                <groupId>org.springframework</groupId>
                                <artifactId>spring-orm</artifactId>
                                <version>${spring.version}</version>
                        </dependency>
                        <dependency>
                                <groupId>org.springframework</groupId>
                                <artifactId>spring-aop</artifactId>
                                <version>${spring.version}</version>
                        </dependency>

Modified xsi:schemaLocation(s):

        Look for 2.5.xsd or 2.0.xsd references and change to 3.2.xsd
        Example:
                spring-aop-2.5.xsd to spring-aop-3.2.xsd

Thanks,
Joyce


-----Original Message-----
From: Leander Melms [mailto:Melms@students.uni-marburg.de]
Sent: Thursday, March 02, 2017 12:23 PM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] Re: YTEX User Inferace Users?

Hi Sean and Joyce,

I'm trying hard to get ytex running as well. I've followed each step you've outlined but I'm somewhat stuck now.

What I did:

- Tried to compile and run with Java 7 --> not working
- Tried to compile and run with Java 8 --> not working
- Tried to update Spring to 3.2.18.RELEASE in pom.xml

      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-core</artifactId>
        <version>3.2.18.RELEASE</version>
      </dependency>
      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-context</artifactId>
        <version>3.2.18.RELEASE</version>
      </dependency>
      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-web</artifactId>
        <version>3.2.18.RELEASE</version>
      </dependency>
      <dependency>

leading to the Exception in thread "main" java.lang.IncompatibleClassChangeError: class org.springframework.core.LocalVariableTableParameterNameDiscoverer$ParameterNameDiscoveringVisitor has interface org.springframework.asm.ClassVisitor as super class

Could you briefly describe what you did to get ytex running? Any help is greatly appreciated.


Leander


> On 13 Feb 2017, at 17:41, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
>
> Is there anyone on this email list that is using the YTEX web interface?
>
> Thanks for the information Sean!
>
> Joyce
>
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
> Sent: Monday, February 13, 2017 10:26 AM
> To: Dunlop, Joyce (HP)
> Cc: dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: YTEX setup notes
>
> Our main interest in YTEX is the database reader and consumer that it comes with. That is probably a smaller subset of its functionality but it was a good source for those. We are still working on implementation, but we plan to run an annotation pipeline on the new notes we get each day and store the resulting annotations in our database. The notes will be read from a database, parceled out in chunks to several processes, annotated, and consumed by the database consumer.
>
> Sean
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Monday, February 13, 2017 11:17 AM
> To: Mullane, Sean *HS
> Cc: dev@ctakes.apache.org
> Subject: RE: YTEX setup notes
>
> Hi Sean,
>
> I will have to check with the VA Researchers to find out what they planned to for the ytex web.
> So you don't use YTEX web interface but you do use ytex correct?  Could you share the steps in a typical process you run for YTEX?
>
> Thanks,
> Joyce
>
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
> Sent: Monday, February 13, 2017 7:59 AM
> To: Dunlop, Joyce (HP)
> Cc: dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: YTEX setup notes
>
> Hi Joyce,
>
> I wound up solving the error by commenting out the bean definition in ctakes-ytex-res/src/main/resources/org/apache/ctakes/beans-kernel.xml and ctakes-ytex-res/target/classes/org/apache/ctakes/beans-kernel.xml, which resolved that error. I think it was deprecated anyway.
>
> I did run into another error where I didn't have LookupDesc_SNOMED.xml in the directory path. Added it from the ctakes-src files solved that problem and got it working on Java 8 for us.
>
> I haven't tried using the web interface - we don't have any plans to use it. Can I ask what you want to use it for? I'm not really familiar with what it does.
>
> Thanks,
> Sean
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Friday, February 10, 2017 3:57 PM
> To: Mullane, Sean *HS
> Subject: RE: YTEX setup notes
>
> Hi Sean,
>
> We had to change the return type from BagOfWordsExporter to WekaBagOfWordsExporter in that file.
>
> From:
>       public BagOfWordsExporter getBagOfWordsExporter() {
>               return bagOfWordsExporter;
>       }
>
> To:
>       public WekaBagOfWordsExporter getBagOfWordsExporter() {
>               return bagOfWordsExporter;
>       }
>
> We have still not be able to get the YTEX web interface to work.  The YTEX application starts up and we are able to access through the URL:  http://localhost:8080/semanticSim.jsf - We see 4 tabs but nothing seems functional.  Is there something we are still missing?  We found references to rest services - are they called separate from the YTEX UI?
>
> Any clue would be appreciated.
>
> Thanks,
> Joyce
>
> PS:  I think there was one other code change to get Java 8 working, so if you get another error just shoot it over and I should have the answer.
>
>
>
>
>
>
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
> Sent: Monday, February 06, 2017 3:33 PM
> To: Dunlop, Joyce (HP)
> Cc: dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: YTEX setup notes
>
> Joyce,
>
> I haven't been able to find further documentation. It seems it is somewhat out of date and some of the Yale sources have been taken down.
>
> In your feedback on my YTEX setup notes, I'm finding that when I try to run YTEX using Java 8 I get an error related to org.apache.ctakes.ytex.weka.GramMatrixExporterImpl. When I run it on Java 7 I get no errors. You mentioned that upgrading to Spring 3.2 solved an issue for you. How did you do that - did you change the Maven build file to pull in the newer version or did you do something else to get the newer Spring version? I'm hoping that will resolve the Java 8 issue here.
>
> Thanks,
> Sean
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Friday, February 03, 2017 4:26 PM
> To: Mullane, Sean *HS
> Cc: dev@ctakes.apache.org
> Subject: RE: YTEX setup notes
>
> Sean/others,
>
> Do you by chance have any of the documentation produced by Yale tucked away locally?
>
> I see quite a few dead links that seem to go back to demo's and documents on cTakes site.
>
> Examples:
> The demo similarity web app is available under http://informatics.med.yale.edu/ytex.web;
>
> http://ytex.googlecode.com/svn/trunk/projects/nlm.wsd/doc/YTEX%20Semantic%20Similarity%20Measures.pdf
>
> Thanks,
> Joyce
>
> -----Original Message-----
> From: Dunlop, Joyce (HP)
> Sent: Monday, January 30, 2017 8:27 PM
> To: 'Mullane, Sean *HS'; dev@ctakes.apache.org
> Subject: RE: YTEX setup notes
>
> Sean M,
> This is perfect!
>
> Thanks,
> Joyce
>
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
> Sent: Monday, January 30, 2017 3:06 PM
> To: Dunlop, Joyce (HP); dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: YTEX setup notes
>
> Joyce,
>
> Thanks for the notes. I'm glad to see you had success using Java 8 - I'll have to try that.
>
> To answer your question about table contents, see below for the rowcounts in the YTEX tables after in my installation. Apologies in advance for the formatting:
>
> tablename     tot_cnt
> anno_base             0
> anno_base_sequence    1
> anno_contain          0
> anno_date             0
> anno_link             0
> anno_markable 0
> anno_med_event        0
> anno_mm_acronym       0
> anno_mm_candidate     0
> anno_mm_cuiconcept    0
> anno_mm_negation      0
> anno_mm_utterance     0
> anno_named_entity     0
> anno_ontology_concept 0
> anno_segment          0
> anno_sentence 0
> anno_token            0
> anno_treebank_node    0
> classifier_eval               0
> classifier_eval_ir    0
> classifier_eval_semil 0
> classifier_eval_svm   0
> classifier_instance_eval      0
> classifier_instance_eval_prob 0
> corpus_doc            0
> corpus_label          0
> cv_best_svm           0
> cv_fold                       0
> cv_fold_instance      0
> document              0
> feature_eval          0
> feature_parchd        0
> feature_rank          0
> fracture_demo         31
> hibernate_sequences   1
> hotspot               0
> hotspot_instance      0
> hotspot_sentence      0
> kernel_eval           0
> kernel_eval_instance  0
> ref_named_entity_regex        0
> ref_segment_regex     0
> ref_stopword          360
> ref_uima_type         38
> tfidf_doclength       0
> umls_aui_fword        6902003
> v_snomed_fword_lookup 1374810
>
> Sean
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Friday, January 27, 2017 10:12 AM
> To: dev@ctakes.apache.org
> Subject: YTEX setup notes
>
> Hi Sean M,
>
> Notes from :
> Step
> -The Needed to add sqljdbc4.jar to CTAKES_HOME/lib probably need to happen after -3. Install cTAKES "as usual"
>
> -Java 7 is throwing errors because Spring needs to be upgraded to at least 3.2.
> --It looks like Spring was previously upgraded from 2.5 to 3.1, but spring context files -  xsi:schemaLocation were not previous upgraded and remained 2.5.
>
> -We have been able to successful run the script with JAVA 8 after upgrading Spring to 3.2.18-Release from the 3.1/2.5 version.   We also upgraded the version of Jetty.
>
> -Step 7 which I think you list as 8 below to execute the setup script. It looks like it has mostly been successful but I do have a few errors at the bottom related to the database password we chose which had an & (AMP) character is being parsed on the & character.
>
> 3 tables that are showing errors related to the amp characters:
> -ref_uima_type.xml
> -fracture_demo.xml
> -stopword.xml
>
> 2 tables are the only table will significant record counts:
> -umls_aui_fword
> -v_snomed_fword_lookup
>
> 2 other table seem to have one row inserted.
>
> The question I have is when this step completes how many of the tables should have data?
>
> Thanks again.
> Joyce
>
>
>
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Tuesday, January 17, 2017 12:33 PM
> To: dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: New to CTAKES
>
> Sean M,
>
> I will try to work through the process this tomorrow.
>
> Thanks!
>
> Joyce
>
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
> Sent: Tuesday, January 17, 2017 11:10 AM
> To: dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: New to CTAKES
>
> Joyce,
>
> This may help, here are some notes I put together when installing YTEX in our Windows/SQL Server test environment. I didn't build from source here, this is just installation (including UMLS). I'm working on writing up these instructions more thoroughly so if you use this please let me know if you find any points of improvement.
>
> Requirements and steps to set up YTEX
> These notes refer to the installation instructions at https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
> 1. They suggest installing UMLS in our database
>       Follow instructions here to install UMLS: https://cwiki.apache.org/confluence/display/CTAKES/UMLS+MS+SQL+Server+Installation
>       -http://groups.csail.mit.edu/medg/projects/text/Load_UMLS_mysql.html is useful when installing from .zip file. The mmsys.zip file needs to be unzipped to access the run64.bat file but also needs to be present as a .zip file for the run64.bat file to read from.
> 2. Create a database user and schema for use with YTEX 3. Load UMLS into database
>       -Needed to create ytex.properties file from examples files in the developer/source version of cTAKES
>       -Needed to change path in ctakes.profile to match version name of CTAKES_HOME directory
>       -Needed to add sqljdbc4.jar to CTAKES_HOME/lib and sqljdbc_auth.dll to C:\Program Files\Java\jre_Version\bin
>       -Needed to open port 1433 for TCP/IP traffic and clear dynamic ports
>       -Need to change table definitions as follows to install UMLS-2016AB:
>               MRCONSO.CODE varchar(75) -- was varchar(50)
>               MRDEF.DEF varchar(max) -- was varchar(4000)
>               MRSAB.VSAB varchar(24) -- was varchar(20)
>               MRSAT.ATN varchar(64) -- was varchar(50)
>               MRSAT.ATV varchar(max) -- was varchar(4000) 3. Install cTAKES "as usual"
> 4. Download and unzip ctakes-ytex-lib-3.1.2-SNAPSHOT.zip 'over' your installation.
>       -I believe this step is deprecated - skip to step 6 5. Unzip YTEX Resources (Optional - UTS login required)
>       -I believe this step is deprecated - skip to step 6
>       -may be needed for concept graphs and dictionary lookup table for NER 6. Fix the path references in shell script to match your environment 7. Create CTAKES_HOME\resources\org\apache\ctakes\ytex\ytex.properties and specify database connection parameters.
> 8. Execute the setup script
>       -Need to use Java 7 - Java 8 errors out
>       -If SQL errors encountered, appenders can be added to log4j.xml to collect SQL queries
>
> Sean
>
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Tuesday, January 17, 2017 11:57 AM
> To: dev@ctakes.apache.org
> Subject: RE: New to CTAKES
>
> Hi Joyce,
>
> If you are building from source then you should not need to manually download the resources.  Maven should be doing it for you.  Well, that is the behavior of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
>
> Otherwise, I think that if the latest was the 3.2.1.1 then that is probably the most appropriate for the 3.2.2 release if you want all of the resources.
>
> As for building and deploying ytex, I don't have any advice.  Perhaps some ytex power-user out there can help.
>
> Sean
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Tuesday, January 17, 2017 11:25 AM
> To: dev@ctakes.apache.org
> Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
> Subject: New to CTAKES
>
> Good Morning,
>
> I am trying to set up a development environment using the source release of 3.2.2.
>
> Reading though the documentation on
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
>
> Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e=  into your ctakes-dictionary-lookup-res project.
>
> ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is available for download.  Is there a 3.2.2 version of the resources?
>
> After reading some of the posts from the email box, and reading the documentation on the site above.  It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.
>
> Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?
>
> Thanks,
> Joyce
>
>
>
>
>
>
>
>
>
>
>
>

Re: YTEX User Inferace Users?

Posted by Leander Melms <Me...@students.uni-marburg.de>.

Hi Sean and Joyce,

I'm trying hard to get ytex running as well. I've followed each step you've outlined but I'm somewhat stuck now.

What I did:

- Tried to compile and run with Java 7 --> not working
- Tried to compile and run with Java 8 --> not working
- Tried to update Spring to 3.2.18.RELEASE in pom.xml

      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-core</artifactId>
        <version>3.2.18.RELEASE</version>
      </dependency>
      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-context</artifactId>
        <version>3.2.18.RELEASE</version>
      </dependency>
      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-web</artifactId>
        <version>3.2.18.RELEASE</version>
      </dependency>
      <dependency>

leading to the Exception in thread "main" java.lang.IncompatibleClassChangeError: class org.springframework.core.LocalVariableTableParameterNameDiscoverer$ParameterNameDiscoveringVisitor has interface org.springframework.asm.ClassVisitor as super class

Could you briefly describe what you did to get ytex running? Any help is greatly appreciated.


Leander


> On 13 Feb 2017, at 17:41, Dunlop, Joyce (HP) <Jo...@va.gov> wrote:
> 
> Is there anyone on this email list that is using the YTEX web interface?
> 
> Thanks for the information Sean!
> 
> Joyce
> 
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu] 
> Sent: Monday, February 13, 2017 10:26 AM
> To: Dunlop, Joyce (HP)
> Cc: dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: YTEX setup notes
> 
> Our main interest in YTEX is the database reader and consumer that it comes with. That is probably a smaller subset of its functionality but it was a good source for those. We are still working on implementation, but we plan to run an annotation pipeline on the new notes we get each day and store the resulting annotations in our database. The notes will be read from a database, parceled out in chunks to several processes, annotated, and consumed by the database consumer.
> 
> Sean
> 
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov] 
> Sent: Monday, February 13, 2017 11:17 AM
> To: Mullane, Sean *HS
> Cc: dev@ctakes.apache.org
> Subject: RE: YTEX setup notes
> 
> Hi Sean,
> 
> I will have to check with the VA Researchers to find out what they planned to for the ytex web. 
> So you don't use YTEX web interface but you do use ytex correct?  Could you share the steps in a typical process you run for YTEX?
> 
> Thanks,
> Joyce
> 
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu] 
> Sent: Monday, February 13, 2017 7:59 AM
> To: Dunlop, Joyce (HP)
> Cc: dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: YTEX setup notes
> 
> Hi Joyce,
> 
> I wound up solving the error by commenting out the bean definition in ctakes-ytex-res/src/main/resources/org/apache/ctakes/beans-kernel.xml and ctakes-ytex-res/target/classes/org/apache/ctakes/beans-kernel.xml, which resolved that error. I think it was deprecated anyway. 
> 
> I did run into another error where I didn't have LookupDesc_SNOMED.xml in the directory path. Added it from the ctakes-src files solved that problem and got it working on Java 8 for us.
> 
> I haven't tried using the web interface - we don't have any plans to use it. Can I ask what you want to use it for? I'm not really familiar with what it does.
> 
> Thanks,
> Sean
> 
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Friday, February 10, 2017 3:57 PM
> To: Mullane, Sean *HS
> Subject: RE: YTEX setup notes
> 
> Hi Sean,
> 
> We had to change the return type from BagOfWordsExporter to WekaBagOfWordsExporter in that file.
> 
> From:
> 	public BagOfWordsExporter getBagOfWordsExporter() {
> 		return bagOfWordsExporter;
> 	}
> 
> To:
> 	public WekaBagOfWordsExporter getBagOfWordsExporter() {
> 		return bagOfWordsExporter;
> 	}
> 
> We have still not be able to get the YTEX web interface to work.  The YTEX application starts up and we are able to access through the URL:  http://localhost:8080/semanticSim.jsf - We see 4 tabs but nothing seems functional.  Is there something we are still missing?  We found references to rest services - are they called separate from the YTEX UI? 
> 
> Any clue would be appreciated.
> 
> Thanks,
> Joyce
> 
> PS:  I think there was one other code change to get Java 8 working, so if you get another error just shoot it over and I should have the answer.
> 
> 
> 
> 
> 
> 
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
> Sent: Monday, February 06, 2017 3:33 PM
> To: Dunlop, Joyce (HP)
> Cc: dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: YTEX setup notes
> 
> Joyce,
> 
> I haven't been able to find further documentation. It seems it is somewhat out of date and some of the Yale sources have been taken down.
> 
> In your feedback on my YTEX setup notes, I'm finding that when I try to run YTEX using Java 8 I get an error related to org.apache.ctakes.ytex.weka.GramMatrixExporterImpl. When I run it on Java 7 I get no errors. You mentioned that upgrading to Spring 3.2 solved an issue for you. How did you do that - did you change the Maven build file to pull in the newer version or did you do something else to get the newer Spring version? I'm hoping that will resolve the Java 8 issue here.
> 
> Thanks,
> Sean
> 
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Friday, February 03, 2017 4:26 PM
> To: Mullane, Sean *HS
> Cc: dev@ctakes.apache.org
> Subject: RE: YTEX setup notes
> 
> Sean/others,
> 
> Do you by chance have any of the documentation produced by Yale tucked away locally?
> 
> I see quite a few dead links that seem to go back to demo's and documents on cTakes site.
> 
> Examples:
> The demo similarity web app is available under http://informatics.med.yale.edu/ytex.web;
> 
> http://ytex.googlecode.com/svn/trunk/projects/nlm.wsd/doc/YTEX%20Semantic%20Similarity%20Measures.pdf
> 
> Thanks,
> Joyce
> 
> -----Original Message-----
> From: Dunlop, Joyce (HP)
> Sent: Monday, January 30, 2017 8:27 PM
> To: 'Mullane, Sean *HS'; dev@ctakes.apache.org
> Subject: RE: YTEX setup notes
> 
> Sean M,
> This is perfect!  
> 
> Thanks,
> Joyce
> 
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
> Sent: Monday, January 30, 2017 3:06 PM
> To: Dunlop, Joyce (HP); dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: YTEX setup notes
> 
> Joyce,
> 
> Thanks for the notes. I'm glad to see you had success using Java 8 - I'll have to try that.
> 
> To answer your question about table contents, see below for the rowcounts in the YTEX tables after in my installation. Apologies in advance for the formatting:
> 
> tablename	tot_cnt
> anno_base		0
> anno_base_sequence	1
> anno_contain		0
> anno_date		0
> anno_link		0
> anno_markable	0
> anno_med_event	0
> anno_mm_acronym	0
> anno_mm_candidate	0
> anno_mm_cuiconcept	0
> anno_mm_negation	0
> anno_mm_utterance	0
> anno_named_entity	0
> anno_ontology_concept	0
> anno_segment		0
> anno_sentence	0
> anno_token		0
> anno_treebank_node	0
> classifier_eval		0
> classifier_eval_ir	0
> classifier_eval_semil	0
> classifier_eval_svm	0
> classifier_instance_eval	0
> classifier_instance_eval_prob	0
> corpus_doc		0
> corpus_label		0
> cv_best_svm		0
> cv_fold			0
> cv_fold_instance	0
> document		0
> feature_eval		0
> feature_parchd	0
> feature_rank		0
> fracture_demo		31
> hibernate_sequences	1
> hotspot		0
> hotspot_instance	0
> hotspot_sentence	0
> kernel_eval		0
> kernel_eval_instance	0
> ref_named_entity_regex	0
> ref_segment_regex	0
> ref_stopword		360
> ref_uima_type		38
> tfidf_doclength	0
> umls_aui_fword	6902003
> v_snomed_fword_lookup	1374810
> 
> Sean
> 
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Friday, January 27, 2017 10:12 AM
> To: dev@ctakes.apache.org
> Subject: YTEX setup notes
> 
> Hi Sean M, 
> 
> Notes from :
> Step
> -The Needed to add sqljdbc4.jar to CTAKES_HOME/lib probably need to happen after -3. Install cTAKES "as usual"
> 
> -Java 7 is throwing errors because Spring needs to be upgraded to at least 3.2.
> --It looks like Spring was previously upgraded from 2.5 to 3.1, but spring context files -  xsi:schemaLocation were not previous upgraded and remained 2.5.
> 
> -We have been able to successful run the script with JAVA 8 after upgrading Spring to 3.2.18-Release from the 3.1/2.5 version.   We also upgraded the version of Jetty.
> 
> -Step 7 which I think you list as 8 below to execute the setup script. It looks like it has mostly been successful but I do have a few errors at the bottom related to the database password we chose which had an & (AMP) character is being parsed on the & character.
> 
> 3 tables that are showing errors related to the amp characters:
> -ref_uima_type.xml
> -fracture_demo.xml
> -stopword.xml
> 
> 2 tables are the only table will significant record counts:
> -umls_aui_fword
> -v_snomed_fword_lookup  
> 
> 2 other table seem to have one row inserted.
> 
> The question I have is when this step completes how many of the tables should have data? 
> 
> Thanks again.
> Joyce
> 
> 
> 
> 
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Tuesday, January 17, 2017 12:33 PM
> To: dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: New to CTAKES 
> 
> Sean M,
> 
> I will try to work through the process this tomorrow.
> 
> Thanks!
> 
> Joyce
> 
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
> Sent: Tuesday, January 17, 2017 11:10 AM
> To: dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: New to CTAKES 
> 
> Joyce,
> 
> This may help, here are some notes I put together when installing YTEX in our Windows/SQL Server test environment. I didn't build from source here, this is just installation (including UMLS). I'm working on writing up these instructions more thoroughly so if you use this please let me know if you find any points of improvement.
> 
> Requirements and steps to set up YTEX
> These notes refer to the installation instructions at https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
> 1. They suggest installing UMLS in our database
> 	Follow instructions here to install UMLS: https://cwiki.apache.org/confluence/display/CTAKES/UMLS+MS+SQL+Server+Installation
> 	-http://groups.csail.mit.edu/medg/projects/text/Load_UMLS_mysql.html is useful when installing from .zip file. The mmsys.zip file needs to be unzipped to access the run64.bat file but also needs to be present as a .zip file for the run64.bat file to read from.
> 2. Create a database user and schema for use with YTEX 3. Load UMLS into database
> 	-Needed to create ytex.properties file from examples files in the developer/source version of cTAKES
> 	-Needed to change path in ctakes.profile to match version name of CTAKES_HOME directory
> 	-Needed to add sqljdbc4.jar to CTAKES_HOME/lib and sqljdbc_auth.dll to C:\Program Files\Java\jre_Version\bin
> 	-Needed to open port 1433 for TCP/IP traffic and clear dynamic ports
> 	-Need to change table definitions as follows to install UMLS-2016AB:
> 		MRCONSO.CODE varchar(75) -- was varchar(50)
> 		MRDEF.DEF varchar(max) -- was varchar(4000)
> 		MRSAB.VSAB varchar(24) -- was varchar(20)
> 		MRSAT.ATN varchar(64) -- was varchar(50)
> 		MRSAT.ATV varchar(max) -- was varchar(4000) 3. Install cTAKES "as usual"
> 4. Download and unzip ctakes-ytex-lib-3.1.2-SNAPSHOT.zip 'over' your installation.
> 	-I believe this step is deprecated - skip to step 6 5. Unzip YTEX Resources (Optional - UTS login required)
> 	-I believe this step is deprecated - skip to step 6
> 	-may be needed for concept graphs and dictionary lookup table for NER 6. Fix the path references in shell script to match your environment 7. Create CTAKES_HOME\resources\org\apache\ctakes\ytex\ytex.properties and specify database connection parameters.
> 8. Execute the setup script
> 	-Need to use Java 7 - Java 8 errors out
> 	-If SQL errors encountered, appenders can be added to log4j.xml to collect SQL queries
> 
> Sean
> 
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Tuesday, January 17, 2017 11:57 AM
> To: dev@ctakes.apache.org
> Subject: RE: New to CTAKES 
> 
> Hi Joyce,
> 
> If you are building from source then you should not need to manually download the resources.  Maven should be doing it for you.  Well, that is the behavior of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
> 
> Otherwise, I think that if the latest was the 3.2.1.1 then that is probably the most appropriate for the 3.2.2 release if you want all of the resources.
> 
> As for building and deploying ytex, I don't have any advice.  Perhaps some ytex power-user out there can help.
> 
> Sean
> 
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Tuesday, January 17, 2017 11:25 AM
> To: dev@ctakes.apache.org
> Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
> Subject: New to CTAKES 
> 
> Good Morning,
> 
> I am trying to set up a development environment using the source release of 3.2.2.
> 
> Reading though the documentation on
> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
> 
> Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e=  into your ctakes-dictionary-lookup-res project.
> 
> ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is available for download.  Is there a 3.2.2 version of the resources?
> 
> After reading some of the posts from the email box, and reading the documentation on the site above.  It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.
> 
> Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?
> 
> Thanks,
> Joyce
> 
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