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:[email protected]]
Sent: Thursday, March 02, 2017 3:36 PM
To: [email protected]
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) <[email protected]> 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>${spring.version}</version>
> </dependency>
>
> Modified xsi:schemaLocation(s):
>
> Look for 2.5.xsd or 2.0.xsd references and change to 3.2.xsd
> Example:
> spring-aop-2.5.xsd to spring-aop-3.2.xsd
>
> Thanks,
> Joyce
>
>
> -----Original Message-----
> From: Leander Melms [mailto:[email protected]]
> Sent: Thursday, March 02, 2017 12:23 PM
> To: [email protected]
> Subject: [EXTERNAL] Re: YTEX User Inferace Users?
>
> Hi Sean and Joyce,
>
> I'm trying hard to get ytex running as well. I've followed each step you've
> outlined but I'm somewhat stuck now.
>
> What I did:
>
> - Tried to compile and run with Java 7 --> not working
> - Tried to compile and run with Java 8 --> not working
> - Tried to update Spring to 3.2.18.RELEASE in pom.xml
>
> <dependency>
> <groupId>org.springframework</groupId>
> <artifactId>spring-core</artifactId>
> <version>3.2.18.RELEASE</version>
> </dependency>
> <dependency>
> <groupId>org.springframework</groupId>
> <artifactId>spring-context</artifactId>
> <version>3.2.18.RELEASE</version>
> </dependency>
> <dependency>
> <groupId>org.springframework</groupId>
> <artifactId>spring-web</artifactId>
> <version>3.2.18.RELEASE</version>
> </dependency>
> <dependency>
>
> leading to the Exception in thread "main"
> java.lang.IncompatibleClassChangeError: class
> org.springframework.core.LocalVariableTableParameterNameDiscoverer$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) <[email protected]> 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:[email protected]]
>> Sent: Monday, February 13, 2017 10:26 AM
>> To: Dunlop, Joyce (HP)
>> Cc: [email protected]
>> 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:[email protected]]
>> Sent: Monday, February 13, 2017 11:17 AM
>> To: Mullane, Sean *HS
>> Cc: [email protected]
>> 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:[email protected]]
>> Sent: Monday, February 13, 2017 7:59 AM
>> To: Dunlop, Joyce (HP)
>> Cc: [email protected]
>> 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:[email protected]]
>> 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:[email protected]]
>> Sent: Monday, February 06, 2017 3:33 PM
>> To: Dunlop, Joyce (HP)
>> Cc: [email protected]
>> 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:[email protected]]
>> Sent: Friday, February 03, 2017 4:26 PM
>> To: Mullane, Sean *HS
>> Cc: [email protected]
>> 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'; [email protected]
>> Subject: RE: YTEX setup notes
>>
>> Sean M,
>> This is perfect!
>>
>> Thanks,
>> Joyce
>>
>> -----Original Message-----
>> From: Mullane, Sean *HS [mailto:[email protected]]
>> Sent: Monday, January 30, 2017 3:06 PM
>> To: Dunlop, Joyce (HP); [email protected]
>> 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:[email protected]]
>> Sent: Friday, January 27, 2017 10:12 AM
>> To: [email protected]
>> 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:[email protected]]
>> Sent: Tuesday, January 17, 2017 12:33 PM
>> To: [email protected]
>> 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:[email protected]]
>> Sent: Tuesday, January 17, 2017 11:10 AM
>> To: [email protected]
>> 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:[email protected]]
>> Sent: Tuesday, January 17, 2017 11:57 AM
>> To: [email protected]
>> 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:[email protected]]
>> Sent: Tuesday, January 17, 2017 11:25 AM
>> To: [email protected]
>> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>
