Hi Giovanni,
I think I found a bug in the offending class. Can you copy the attached
file to this directory:
YTEX_HOME\resources\org\apache\ctakes\ytex\
And retry?
Thanks!
VJ
On Thu, Nov 20, 2014 at 4:16 PM, Giovanni Di Santo <[email protected]>
wrote:
> Hi,
> I have tried to install YTEX in another machine and the same exception is
> thrown during the installation. The output is slightly different:
> http://pastebin.com/gVhSFYKp.
> I suppose I make some mistakes during the installation process.
> When in the ytes installation guide is written to copy "over" my
> installation I use a command like "cp -R /directory_fo_copy/* /ctakes_home".
> Is there any already ready ytex version that I can download and use for
> Linux?
>
> I don't really now what could be the problem and I need to test the
> Semantic Similarity feature.
>
> Best regards
>
> Giovanni
>
> 2014-11-12 0:05 GMT+01:00 Kim Ebert <[email protected]>:
>
>> Adding developer mailing list, as I'm not sure what is causing your error.
>>
>> Kim Ebert
>> 1.801.669.7342
>> Perfect Search Corp
>> http://www.perfectsearchcorp.com/
>>
>> On 10/29/2014 11:57 AM, Giovanni Di Santo wrote:
>> > Hi,
>> > I'm trying to install ytex. I've followed the instructions provided
>> > here
>> > https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
>> > but the installing process stops and raises an Excpetion
>> > java.lang.ExceptionInInitializerError.
>> > More precisely I receive that output: http://pastebin.com/PrWyBxhx .
>> > I'm using cTakes 3.2 and the I've installed locally on a mysql db the
>> > umls 2014AA version.
>> >
>> > Best regards,
>> >
>> > Giovanni
>>
>>
>
<?xml version="1.0" encoding="UTF-8"?>
<!--
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or more contributor license agreements. See the NOTICE file
distributed with this work for additional information
regarding copyright ownership. The ASF licenses this file
to you under the Apache License, Version 2.0 (the
"License"); you may not use this file except in compliance
with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing,
software distributed under the License is distributed on an
"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
KIND, either express or implied. See the License for the
specific language governing permissions and limitations
under the License.
-->
<beans xmlns="http://www.springframework.org/schema/beans";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xmlns:aop="http://www.springframework.org/schema/aop";
xmlns:tx="http://www.springframework.org/schema/tx";
xsi:schemaLocation="
http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-2.5.xsd
http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop-2.5.xsd";>
<!-- ensure that the above transactional advice runs for any execution of
an operation defined by the FooService interface -->
<aop:config>
<aop:pointcut id="daoOperation"
expression="execution(* org.apache.ctakes.ytex.kernel.dao.*Dao.*(..))" />
<aop:pointcut id="umlsDaoOperation"
expression="execution(* org.apache.ctakes.ytex.umls.dao.*Dao.*(..))" />
<aop:pointcut id="exporterOperation"
expression="execution(* org.apache.ctakes.ytex.*.*Exporter*.*(..))" />
<aop:pointcut id="wekaImporter"
expression="execution(* org.apache.ctakes.ytex.weka.WekaResultsImporterImpl.*(..))" />
<aop:pointcut id="mapperOperation"
expression="execution(* org.apache.ctakes.ytex.uima.mapper.*.*(..))" />
<aop:pointcut id="treeOperation"
expression="execution(* org.apache.ctakes.ytex.kernel.tree.*Tree*.*.*(..))" />
<aop:pointcut id="utilOperation"
expression="execution(* org.apache.ctakes.ytex.kernel.KernelUtil*.*(..))" />
<aop:pointcut id="corpusEvaluatorOperation"
expression="execution(* org.apache.ctakes.ytex.kernel.*EvaluatorImpl.*(..))" />
<aop:advisor advice-ref="txAdvice" pointcut-ref="exporterOperation" />
<aop:advisor advice-ref="txAdvice" pointcut-ref="mapperOperation" />
<aop:advisor advice-ref="txAdvice" pointcut-ref="wekaImporter" />
<aop:advisor advice-ref="txAdvice" pointcut-ref="daoOperation" />
<aop:advisor advice-ref="txAdvice" pointcut-ref="umlsDaoOperation" />
<aop:advisor advice-ref="txAdvice" pointcut-ref="treeOperation" />
<aop:advisor advice-ref="txAdvice" pointcut-ref="utilOperation" />
<aop:advisor advice-ref="txAdvice" pointcut-ref="corpusEvaluatorOperation" />
</aop:config>
<bean id="kernelEvaluationDao"
class="org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl">
<property name="sessionFactory" ref="sessionFactory" />
<property name="transactionManager" ref="transactionManager" />
</bean>
<bean id="conceptDao" class="org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl">
<property name="ytexProperties" ref="ytexProperties" />
<property name="dataSource" ref="dataSource" />
<property name="intrinsicInfoContentEvaluator" ref="intrinsicInfoContentEvaluator" />
</bean>
<bean id="umlsDao" class="org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl">
<property name="sessionFactory" ref="sessionFactory" />
</bean>
<bean id="wekaBagOfWordsExporter" class="org.apache.ctakes.ytex.weka.WekaBagOfWordsExporterImpl">
<property name="dataSource" ref="dataSource" />
<property name="transactionManager" ref="transactionManager" />
</bean>
<bean id="documentResultInstanceImporter"
class="org.apache.ctakes.ytex.weka.DocumentResultInstanceImporter">
<property name="sessionFactory" ref="sessionFactory" />
</bean>
<bean id="wekaResultsImporter" class="org.apache.ctakes.ytex.weka.WekaResultsImporterImpl">
<property name="docResultInstanceImporter" ref="documentResultInstanceImporter" />
<property name="sessionFactory" ref="sessionFactory" />
</bean>
<!-- <bean id="corpusDao" class="org.apache.ctakes.ytex.kernel.dao.CorpusDaoImpl">
<property name="sessionFactory" ref="sessionFactory" /> </bean> -->
<bean id="classifierEvaluationDao"
class="org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl">
<property name="sessionFactory" ref="sessionFactory" />
</bean>
<bean id="libSVMGramMatrixExporter"
class="org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl">
<property name="dataSource" ref="dataSource" />
<property name="kernelEvaluationDao" ref="kernelEvaluationDao" />
<property name="transactionManager" ref="transactionManager" />
<property name="libsvmUtil" ref="libsvmUtil" />
<property name="kernelUtil" ref="kernelUtil" />
</bean>
<bean id="rGramMatrixExporter" class="org.apache.ctakes.ytex.R.RGramMatrixExporterImpl">
<property name="kernelEvaluationDao" ref="kernelEvaluationDao" />
<property name="kernelUtil" ref="kernelUtil" />
<property name="instanceDataExporter" ref="instanceDataExporter" />
</bean>
<bean id="libsvmUtil" class="org.apache.ctakes.ytex.libsvm.LibSVMUtilImpl">
<property name="dataSource" ref="dataSource" />
</bean>
<bean id="instanceTreeBuilder"
class="org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilderImpl">
<property name="dataSource" ref="dataSource" />
</bean>
<bean id="abstractNormKernel" abstract="true"
class="org.apache.ctakes.ytex.kernel.evaluator.NormKernel"
init-method="init">
<property name="cacheManager" ref="cacheManager" />
</bean>
<bean id="equalityKernel" class="org.apache.ctakes.ytex.kernel.evaluator.EqualityKernel">
</bean>
<bean id="atttributeProductKernel"
class="org.apache.ctakes.ytex.kernel.evaluator.AttributeProductKernel">
</bean>
<bean id="cacheManager"
class="org.springframework.cache.ehcache.EhCacheManagerFactoryBean">
<property name="configLocation" value="classpath:org/apache/ctakes/ytex/kernel/ehcache.xml" />
</bean>
<bean id="abstractCorpusKernelEvaluator"
class="org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl">
<property name="dataSource" ref="dataSource" />
<property name="kernelEvaluationDao" ref="kernelEvaluationDao" />
<property name="transactionManager" ref="transactionManager" />
</bean>
<bean id="foldGenerator" class="org.apache.ctakes.ytex.kernel.FoldGeneratorImpl">
<property name="kernelUtil" ref="kernelUtil" />
<property name="classifierEvaluationDao" ref="classifierEvaluationDao" />
</bean>
<bean id="kernelUtil" class="org.apache.ctakes.ytex.kernel.KernelUtilImpl">
<property name="dataSource" ref="dataSource" />
<property name="transactionManager" ref="transactionManager" />
<property name="kernelEvaluationDao" ref="kernelEvaluationDao" />
<property name="classifierEvaluationDao" ref="classifierEvaluationDao" />
<property name="foldGenerator" ref="foldGenerator" />
</bean>
<bean id="baseClassifierEvaluationParser" abstract="true">
<property name="classifierEvaluationDao" ref="classifierEvaluationDao" />
</bean>
<bean id="semiLEvaluationParser" class="org.apache.ctakes.ytex.semil.SemiLEvaluationParser"
parent="baseClassifierEvaluationParser" />
<bean id="libSVMParser" class="org.apache.ctakes.ytex.libsvm.LibSVMParser"
parent="baseClassifierEvaluationParser" />
<bean id="svmLightParser" class="org.apache.ctakes.ytex.svmlight.SVMLightParser"
parent="baseClassifierEvaluationParser" />
<bean id="svmlinParser" class="org.apache.ctakes.ytex.kernel.SvmlinEvaluationParser"
parent="baseClassifierEvaluationParser" />
<bean id="ClassifierEvaluationImporter"
class="org.apache.ctakes.ytex.kernel.ClassifierEvaluationImporter">
<property name="nameToParserMap">
<map>
<entry>
<key>
<value>libsvm</value>
</key>
<ref bean="libSVMParser" />
</entry>
<entry>
<key>
<value>svmlight</value>
</key>
<ref bean="svmLightParser" />
</entry>
<entry>
<key>
<value>semil</value>
</key>
<ref bean="semiLEvaluationParser" />
</entry>
<entry>
<key>
<value>svmlin</value>
</key>
<ref bean="svmlinParser" />
</entry>
</map>
</property>
</bean>
<bean id="sparseDataExporter" class="org.apache.ctakes.ytex.kernel.SparseDataExporterImpl">
<property name="dataSource" ref="dataSource" />
<property name="txTemplateNew" ref="txTemplateNew" />
<property name="kernelUtil" ref="kernelUtil" />
<property name="nameToFormatterMap">
<map>
<entry>
<key>
<value>libsvm</value>
</key>
<ref bean="libSVMFormatterFactory" />
</entry>
<entry>
<key>
<value>sparsematrix</value>
</key>
<ref bean="sparseMatrixFormatterFactory" />
</entry>
<entry>
<key>
<value>svmlight</value>
</key>
<ref bean="svmLightFormatterFactory" />
</entry>
<entry>
<key>
<value>sgt</value>
</key>
<ref bean="sgtFormatterFactory" />
</entry>
<entry>
<key>
<value>svmlin</value>
</key>
<ref bean="svmLinFormatterFactory" />
</entry>
<entry>
<key>
<value>semil</value>
</key>
<ref bean="semiLFormatterFactory" />
</entry>
<entry>
<key>
<value>weka</value>
</key>
<ref bean="wekaFormatterFactory" />
</entry>
</map>
</property>
</bean>
<bean id="sparseDataFormatterFactory" abstract="true">
<property name="kernelUtil" ref="kernelUtil" />
</bean>
<bean id="svmLightFormatterFactory"
class="org.apache.ctakes.ytex.svmlight.SVMLightFormatterFactory"
parent="sparseDataFormatterFactory">
</bean>
<bean id="libSVMFormatterFactory" class="org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory"
parent="sparseDataFormatterFactory">
</bean>
<bean id="svmLinFormatterFactory" class="org.apache.ctakes.ytex.kernel.SVMLinFormatterFactory"
parent="sparseDataFormatterFactory">
</bean>
<bean id="sgtFormatterFactory" class="org.apache.ctakes.ytex.svmlight.SGTFormatterFactory"
parent="sparseDataFormatterFactory">
</bean>
<bean id="sparseMatrixFormatterFactory"
class="org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory"
parent="sparseDataFormatterFactory">
<property name="instanceDataExporter" ref="instanceDataExporter" />
</bean>
<bean id="semiLFormatterFactory" class="org.apache.ctakes.ytex.semil.SemiLFormatterFactory"
parent="sparseDataFormatterFactory">
</bean>
<bean id="wekaFormatterFactory" class="org.apache.ctakes.ytex.weka.WekaFormatterFactory"
parent="sparseDataFormatterFactory">
</bean>
<bean id="instanceDataExporter"
class="org.apache.ctakes.ytex.sparsematrix.InstanceDataExporterImpl">
</bean>
<bean id="infogainAttributeEval" class="weka.attributeSelection.InfoGainAttributeEval">
</bean>
<bean id="rankerSearch" class="weka.attributeSelection.Ranker">
</bean>
<bean id="infogainAttributeSelection" class="weka.attributeSelection.AttributeSelection">
<property name="evaluator" ref="infogainAttributeEval" />
<property name="search" ref="rankerSearch" />
</bean>
<bean id="wekaAttributeEvaluator" class="org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl">
<property name="attributeSelection" ref="infogainAttributeSelection" />
<property name="sparseDataExporter" ref="sparseDataExporter" />
<property name="classifierEvaluationDao" ref="classifierEvaluationDao" />
<property name="asEvaluation" ref="infogainAttributeEval" />
<property name="kernelUtil" ref="kernelUtil" />
</bean>
<bean id="infoContentEvaluator" class="org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl">
<property name="conceptDao" ref="conceptDao" />
<property name="classifierEvaluationDao" ref="classifierEvaluationDao" />
<property name="dataSource" ref="dataSource" />
</bean>
<bean id="intrinsicInfoContentEvaluator"
class="org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl">
<property name="conceptDao" ref="conceptDao" />
<property name="classifierEvaluationDao" ref="classifierEvaluationDao" />
</bean>
<bean id="imputedFeatureEvaluator"
class="org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl">
<property name="conceptDao" ref="conceptDao" />
<property name="dataSource" ref="dataSource" />
<property name="kernelUtil" ref="kernelUtil" />
<property name="classifierEvaluationDao" ref="classifierEvaluationDao" />
<property name="ytexProperties" ref="ytexProperties" />
<property name="infoContentEvaluator" ref="infoContentEvaluator" />
</bean>
<bean id="cytoscapeHelper" class="org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl">
<property name="conceptDao" ref="conceptDao" />
<property name="classifierEvaluationDao" ref="classifierEvaluationDao" />
<property name="umlsDao" ref="umlsDao" />
</bean>
<bean id="abstractKernelCacheAdvice"
class="org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor"
abstract="true">
<property name="cacheManager" ref="cacheManager" />
<property name="cacheKeyGenerator">
<bean
class="org.apache.ctakes.ytex.kernel.evaluator.SymmetricPairCacheKeyGenerator" />
</property>
<property name="methodName" value="evaluate" />
</bean>
<bean id="pageRankService"
class="org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl">
</bean>
<!-- <bean id="abstractKernelCacheAdvisor" class="org.springframework.aop.support.DefaultPointcutAdvisor">
<property name="pointcut"> <bean class="org.springframework.aop.support.JdkRegexpMethodPointcut">
<property name="pattern"> <value>.*evaluate.*</value> </property> </bean>
</property> </bean> -->
</beans>
