Re: [intact-developers] Digest for intact-developers@googlegroups.com - 2 Messages in 1 Topic

[Dominik Mertens]

Hi Bruno,

the parent in the pom.xml file says version 41 of the intact-hibernate-master, as you said. I would have been very surprised since i did a complete new checkout of the intact-kickstart project.

Here´s the output of the dependency:tree command:

[INFO] Scanning for projects...
[INFO] Searching repository for plugin with prefix: 'dependency'.
[INFO] ------------------------------------------------------------------------
[INFO] Building IntAct Sites :: Kickstart
[INFO]    task-segment: [dependency:tree]
[INFO] ------------------------------------------------------------------------
[INFO] [dependency:tree {execution: default-cli}]
[INFO] uk.ac.ebi.intact.maven:intact-kickstart:jar:1.0-SNAPSHOT
[INFO] +- uk.ac.ebi.intact.core:intact-core:jar:2.5.0:compile
[INFO] |  +- uk.ac.ebi.intact.commons:intact-commons:jar:2.1.7:compile
[INFO] |  |  \- org.apache.geronimo.javamail:geronimo-javamail_1.4_mail:jar:1.2:compile
[INFO] |  |     \- org.apache.geronimo.javamail:geronimo-javamail_1.4_provider:jar:1.2:compile
[INFO] |  +- uk.ac.ebi.intact.core:intact-annotations:jar:2.5.0:compile
[INFO] |  +- uk.ac.ebi.intact.core:intact-apt:jar:2.5.0:compile
[INFO] |  |  +- velocity:velocity-dep:jar:1.4:compile
[INFO] |  |  \- sun.jdk:tools:jar:1.5.0:system
[INFO] |  +- xerces:xercesImpl:jar:2.8.1:compile
[INFO] |  |  \- xml-apis:xml-apis:jar:1.3.03:compile
[INFO] |  +- commons-net:commons-net:jar:1.4.1:compile
[INFO] |  |  \- oro:oro:jar:2.0.8:compile
[INFO] |  +- com.google.guava:guava:jar:r06:compile
[INFO] |  +- org.slf4j:slf4j-api:jar:1.6.1:compile
[INFO] |  +- org.slf4j:slf4j-log4j12:jar:1.6.1:compile
[INFO] |  +- log4j:log4j:jar:1.2.15:compile
[INFO] |  |  +- javax.mail:mail:jar:1.4:compile
[INFO] |  |  +- com.sun.jdmk:jmxtools:jar:1.2.1:compile
[INFO] |  |  \- com.sun.jmx:jmxri:jar:1.2.1:compile
[INFO] |  +- commons-logging:commons-logging:jar:1.1.1:compile
[INFO] |  +- commons-lang:commons-lang:jar:2.4:compile
[INFO] |  +- commons-beanutils:commons-beanutils:jar:1.7.0:compile
[INFO] |  +- commons-dbcp:commons-dbcp:jar:1.2.2:compile
[INFO] |  |  \- commons-pool:commons-pool:jar:1.3:compile
[INFO] |  +- antlr:antlr:jar:2.7.7:compile
[INFO] |  +- joda-time:joda-time:jar:1.6:compile
[INFO] |  +- joda-time:joda-time-hibernate:jar:1.2:compile
[INFO] |  +- net.sf.ehcache:ehcache:jar:1.3.0:compile
[INFO] |  |  +- net.sf.jsr107cache:jsr107cache:jar:1.0:compile
[INFO] |  |  \- backport-util-concurrent:backport-util-concurrent:jar:3.0:compile
[INFO] |  +- org.springframework:spring-tx:jar:3.0.3.RELEASE:compile
[INFO] |  |  +- aopalliance:aopalliance:jar:1.0:compile
[INFO] |  |  +- org.springframework:spring-beans:jar:3.0.3.RELEASE:compile
[INFO] |  |  +- org.springframework:spring-context:jar:3.0.3.RELEASE:compile
[INFO] |  |  |  \- org.springframework:spring-expression:jar:3.0.3.RELEASE:compile
[INFO] |  |  \- org.springframework:spring-core:jar:3.0.3.RELEASE:compile
[INFO] |  +- org.springframework:spring-orm:jar:3.0.3.RELEASE:compile
[INFO] |  |  \- org.springframework:spring-jdbc:jar:3.0.3.RELEASE:compile
[INFO] |  +- org.springframework:spring-aop:jar:3.0.3.RELEASE:compile
[INFO] |  |  \- org.springframework:spring-asm:jar:3.0.3.RELEASE:compile
[INFO] |  +- org.springframework:spring-aspects:jar:3.0.3.RELEASE:compile
[INFO] |  |  +- org.springframework:spring-context-support:jar:3.0.3.RELEASE:compile
[INFO] |  |  \- org.springframework:spring-test:jar:3.0.3.RELEASE:compile
[INFO] |  +- org.aspectj:aspectjrt:jar:1.6.8:compile
[INFO] |  \- org.aspectj:aspectjweaver:jar:1.6.8:compile
[INFO] +- uk.ac.ebi.intact.dataexchange.psimi:intact-psixml-exchange:jar:2.1.2:compile
[INFO] |  +- uk.ac.ebi.intact.dataexchange.psimi:intact-psixml-converters:jar:2.1.2:compile
[INFO] |  |  \- psidev.psi.mi:psi25-xml:jar:1.7.8:compile
[INFO] |  |     +- psidev.psi.tools:xxindex:jar:0.6:compile
[INFO] |  |     |  +- org.apache.commons:com.springsource.org.apache.commons.io:jar:1.4.0:compile
[INFO] |  |     |  \- cpdetector:cpdetector:jar:1.0.7:compile
[INFO] |  |     |     +- org.antlr:com.springsource.antlr:jar:2.7.7:compile
[INFO] |  |     |     +- jargs:jargs:jar:1.0:compile
[INFO] |  |     |     \- org.mozilla.intl:chardet:jar:1.0:compile
[INFO] |  |     +- org.apache.servicemix.specs:org.apache.servicemix.specs.jaxb-api-2.1:jar:1.2.0:compile
[INFO] |  |     +- org.apache.servicemix.bundles:org.apache.servicemix.bundles.jaxb-impl:jar:2.1.6_1:compile
[INFO] |  |     +- javax.activation:com.springsource.javax.activation:jar:1.1.1:compile
[INFO] |  |     \- javax.xml.stream:com.springsource.javax.xml.stream:jar:1.0.1:compile
[INFO] |  +- uk.ac.ebi.intact.dataexchange:intact-enricher:jar:2.1.2:compile
[INFO] |  |  +- uk.ac.ebi.intact.bridges:intact-picr:jar:2.1.3:compile
[INFO] |  |  |  \- com.sun.xml.ws:jaxws-tools:jar:2.1.7:compile
[INFO] |  |  +- uk.ac.ebi.intact.bridges:intact-citexplore:jar:2.1.3:compile
[INFO] |  |  +- uk.ac.ebi.intact.bridges.coredep:intact-cdb:jar:2.1.3:compile
[INFO] |  |  +- uk.ac.ebi.intact.bridges:intact-taxonomy:jar:2.1.3:compile
[INFO] |  |  +- uk.ac.ebi.intact.bridges:intact-uniprot:jar:2.1.3:compile
[INFO] |  |  |  \- uk.ac.ebi.uniprot.kraken:uniprotjapi:jar:2011.10:compile
[INFO] |  |  |     \- commons-httpclient:commons-httpclient:jar:3.0.1:compile
[INFO] |  |  +- uk.ac.ebi.chebi.webapps.chebiWS.client:chebiWS-client:jar:2.0:compile
[INFO] |  |  |  \- com.sun.xml.ws:jaxws-rt:jar:2.1.7:compile
[INFO] |  |  |     +- com.sun.xml.stream.buffer:streambuffer:jar:0.9:compile
[INFO] |  |  |     +- com.sun.org.apache.xml.internal:resolver:jar:20050927:compile
[INFO] |  |  |     \- org.jvnet:mimepull:jar:1.3:compile
[INFO] |  |  +- com.sun.xml.bind:jaxb-impl:jar:2.1.7:compile
[INFO] |  |  \- javax.xml.bind:jaxb-api:jar:2.1:compile
[INFO] |  +- org.hibernate:hibernate:jar:3.2.6.ga:compile
[INFO] |  +- asm:asm:jar:2.2.3:compile
[INFO] |  +- org.hibernate:hibernate-annotations:jar:3.3.1.GA:compile
[INFO] |  |  \- org.hibernate:ejb3-persistence:jar:1.0.1.GA:compile
[INFO] |  +- javassist:javassist:jar:3.7.1.GA:compile
[INFO] |  \- c3p0:c3p0:jar:0.9.1.2:compile
[INFO] +- uk.ac.ebi.intact.dataexchange.psimi:intact-psimitab:jar:2.1.2:compile
[INFO] |  +- psidev.psi.mi:psimitab:jar:1.7.8:compile
[INFO] |  |  +- org.apache.commons:com.springsource.org.apache.commons.collections:jar:3.2.1:compile
[INFO] |  |  \- org.apache.commons:com.springsource.org.apache.commons.lang:jar:2.4.0:compile
[INFO] |  +- psidev.psi.mi:psimitab-search:jar:1.7.8:compile
[INFO] |  |  \- org.apache.lucene:com.springsource.org.apache.lucene:jar:2.3.2:compile
[INFO] |  +- uk.ac.ebi.intact.util:intact-ols:jar:2.0-beta-10:compile
[INFO] |  |  \- uk.ac.ebi.pride:ols-client:jar:1.13:compile
[INFO] |  |     +- org.apache.axis:axis-jaxrpc:jar:1.4:compile
[INFO] |  |     +- org.apache.axis:axis-saaj:jar:1.4:compile
[INFO] |  |     \- soap:soap:jar:2.3.1:compile
[INFO] |  \- uk.ac.ebi.intact.bridges:intact-ontologies:jar:2.1.3:compile
[INFO] |     +- org.apache.lucene:lucene-core:jar:2.3.2:compile
[INFO] |     \- commons-io:commons-io:jar:1.4:compile
[INFO] +- uk.ac.ebi.intact.dataexchange.psimi:intact-psimitab-converters:jar:2.1.2:compile
[INFO] |  \- uk.ac.ebi.intact.commons:irefindex-seguid:jar:2.1.7:compile
[INFO] +- uk.ac.ebi.intact.dataexchange:intact-cvutils:jar:2.1.2:compile
[INFO] |  +- org.geneontology:obo:jar:2.000-beta38:compile
[INFO] |  |  \- org.geneontology:bbop:jar:2.000-beta38:compile
[INFO] |  +- org.geneontology:oboedit:jar:1.101:runtime
[INFO] |  |  \- org.geneontology:org.geneontology:jar:1.101:runtime
[INFO] |  +- uk.ac.ebi:ols:jar:1.14.1:compile
[INFO] |  |  +- commons-discovery:commons-discovery:jar:0.4:compile
[INFO] |  |  +- org.apache.axis:axis:jar:1.4:compile
[INFO] |  |  +- javax.xml:jaxrpc-api:jar:1.1:compile
[INFO] |  |  \- wsdl4j:wsdl4j:jar:1.6.1:compile
[INFO] |  \- net.sf.opencsv:opencsv:jar:1.8:compile
[INFO] +- org.hupo.psi.mi.psicquic:psicquic-client:jar:1.3:compile
[INFO] |  +- com.sun.xml:com.springsource.com.sun.xml.fastinfoset:jar:1.2.2:compile
[INFO] |  +- org.apache.servicemix.specs:org.apache.servicemix.specs.stax-api-1.0:jar:1.0.0:compile
[INFO] |  +- org.apache.cxf:cxf-bundle:jar:2.2.3:compile
[INFO] |  |  +- org.apache.geronimo.specs:geronimo-annotation_1.0_spec:jar:1.1.1:compile
[INFO] |  |  +- org.apache.geronimo.specs:geronimo-stax-api_1.0_spec:jar:1.0.1:compile
[INFO] |  |  +- org.apache.ws.commons.schema:XmlSchema:jar:1.4.5:compile
[INFO] |  |  +- org.apache.velocity:velocity:jar:1.5:compile
[INFO] |  |  +- com.sun.xml.bind:jaxb-xjc:jar:2.1.12:compile
[INFO] |  |  +- javax.xml.soap:saaj-api:jar:1.3:compile
[INFO] |  |  +- org.apache.geronimo.specs:geronimo-activation_1.1_spec:jar:1.0.2:compile
[INFO] |  |  +- org.codehaus.woodstox:wstx-asl:jar:3.2.8:compile
[INFO] |  |  +- org.apache.neethi:neethi:jar:2.0.4:compile
[INFO] |  |  +- org.apache.geronimo.specs:geronimo-javamail_1.4_spec:jar:1.6:compile
[INFO] |  |  +- com.sun.xml.fastinfoset:FastInfoset:jar:1.2.7:compile
[INFO] |  |  +- org.apache.geronimo.specs:geronimo-ws-metadata_2.0_spec:jar:1.1.2:compile
[INFO] |  |  +- org.apache.geronimo.specs:geronimo-jaxws_2.1_spec:jar:1.0:compile
[INFO] |  |  +- xml-resolver:xml-resolver:jar:1.2:compile
[INFO] |  |  +- com.sun.xml.messaging.saaj:saaj-impl:jar:1.3.2:compile
[INFO] |  |  +- org.apache.xmlbeans:xmlbeans:jar:2.4.0:compile
[INFO] |  |  +- org.springframework:spring-web:jar:2.5.5:compile
[INFO] |  |  +- org.mortbay.jetty:jetty:jar:6.1.19:compile
[INFO] |  |  +- org.mortbay.jetty:jetty-util:jar:6.1.19:compile
[INFO] |  |  +- org.slf4j:slf4j-jdk14:jar:1.5.8:runtime
[INFO] |  |  +- org.apache.geronimo.specs:geronimo-servlet_2.5_spec:jar:1.2:compile
[INFO] |  |  +- org.apache.geronimo.specs:geronimo-jms_1.1_spec:jar:1.1.1:compile
[INFO] |  |  +- org.springframework:spring-jms:jar:2.5.5:compile
[INFO] |  |  +- org.codehaus.jra:jra:jar:1.0-alpha-4:compile
[INFO] |  |  +- rhino:js:jar:1.7R1:compile
[INFO] |  |  +- javax.ws.rs:jsr311-api:jar:1.0:compile
[INFO] |  |  +- org.apache.abdera:abdera-core:jar:0.4.0-incubating:compile
[INFO] |  |  +- org.apache.abdera:abdera-i18n:jar:0.4.0-incubating:compile
[INFO] |  |  +- commons-codec:commons-codec:jar:1.3:compile
[INFO] |  |  +- org.apache.abdera:abdera-parser:jar:0.4.0-incubating:compile
[INFO] |  |  +- org.apache.ws.commons.axiom:axiom-impl:jar:1.2.7:compile
[INFO] |  |  +- org.apache.ws.commons.axiom:axiom-api:jar:1.2.7:compile
[INFO] |  |  +- jaxen:jaxen:jar:1.1:compile
[INFO] |  |  |  \- xom:xom:jar:1.0:compile
[INFO] |  |  |     +- xerces:xmlParserAPIs:jar:2.6.2:compile
[INFO] |  |  |     \- com.ibm.icu:icu4j:jar:2.6.1:compile
[INFO] |  |  +- org.apache.abdera:abdera-extensions-json:jar:0.4.0-incubating:compile
[INFO] |  |  +- org.apache.abdera:abdera-extensions-main:jar:0.4.0-incubating:compile
[INFO] |  |  +- org.codehaus.jettison:jettison:jar:1.1:compile
[INFO] |  |  +- org.apache.ws.security:wss4j:jar:1.5.8:compile
[INFO] |  |  +- org.apache.santuario:xmlsec:jar:1.4.3:compile
[INFO] |  |  +- xalan:xalan:jar:2.7.1:compile
[INFO] |  |  +- xalan:serializer:jar:2.7.1:compile
[INFO] |  |  \- org.bouncycastle:bcprov-jdk15:jar:1.43:runtime
[INFO] |  +- javax.wsdl:com.springsource.javax.wsdl:jar:1.6.1:compile
[INFO] |  +- org.apache.xml:com.springsource.org.apache.xml.security:jar:1.4.2:compile
[INFO] |  |  +- org.apache.log4j:com.springsource.org.apache.log4j:jar:1.2.15:compile
[INFO] |  |  \- org.apache.xalan:com.springsource.org.apache.xalan:jar:2.7.0:compile
[INFO] |  |     +- org.apache.xerces:com.springsource.org.apache.xerces:jar:2.8.1:compile
[INFO] |  |     |  +- org.apache.xml:com.springsource.org.apache.xml.resolver:jar:1.2.0:compile
[INFO] |  |     |  \- org.apache.xmlcommons:com.springsource.org.apache.xmlcommons:jar:1.3.3:compile
[INFO] |  |     \- org.apache.bcel:com.springsource.org.apache.bcel:jar:5.1.0:compile
[INFO] |  |        \- org.apache.regexp:com.springsource.org.apache.regexp:jar:1.5.0:compile
[INFO] |  +- org.objectweb.asm:com.springsource.org.objectweb.asm:jar:3.1.0:compile
[INFO] |  \- org.bouncycastle:com.springsource.org.bouncycastle.jce:jar:1.39.0:compile
[INFO] +- org.jvnet.staxex:stax-ex:jar:1.2:compile
[INFO] |  +- javax.xml.stream:stax-api:jar:1.0:compile
[INFO] |  \- javax.activation:activation:jar:1.1:compile
[INFO] +- postgresql:postgresql:jar:8.2-504.jdbc3:compile
[INFO] +- com.h2database:h2:jar:1.2.121:compile
[INFO] +- commons-collections:commons-collections:jar:3.2:compile
[INFO] +- org.hibernate:hibernate-core:jar:3.6.0-intact.2:compile
[INFO] |  +- dom4j:dom4j:jar:1.6.1:compile
[INFO] |  +- org.hibernate:hibernate-commons-annotations:jar:3.2.0.Final:compile
[INFO] |  +- org.hibernate.javax.persistence:hibernate-jpa-2.0-api:jar:1.0.0.Final:compile
[INFO] |  \- javax.transaction:jta:jar:1.1:compile
[INFO] +- org.hibernate:hibernate-entitymanager:jar:3.6.0-intact:compile
[INFO] +- cglib:cglib-nodep:jar:2.2:compile
[INFO] +- org.hibernate:hibernate-validator:jar:4.1.0.Final:compile
[INFO] |  \- javax.validation:validation-api:jar:1.0.0.GA:compile
[INFO] \- junit:junit:jar:4.3.1:test (scope not updated to compile)
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESSFUL
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 5 seconds
[INFO] Finished at: Fri Oct 21 11:33:53 CEST 2011
[INFO] Final Memory: 36M/364M
[INFO] ------------------------------------------------------------------------

Any idea? I already checked if it could be a Maven version issue, but with Maven2 and Maven3 it did not work... as far as ai remember  i ran into this problem about months ago, and intact-kickstart did only work with maven2. But i´m not 100% sure...

Thanks for your efforts!

Cheers,
Dominik


Am 21.10.2011 11:09, schrieb intact-d...@googlegroups.com:

  Today's Topic Summary

Group: http://groups.google.com/group/intact-developers/topics

• intact-kickstart seems not to work any more [2 Updates]

 intact-kickstart seems not to work any more

"dominik...@biologie.uni-freiburg.de" <dominik...@biologie.uni-freiburg.de> Oct 20 10:45AM -0700  

Hi Bruno,
 
thanks for the quick reply and your effort!
 
I checked out the whole intact-kickstart again and for different
reasons it did not work... Have you checked the intact-kickstart
after your changes?
The project compiles fine, but when starting the class
"CreateDatabase" it give me the following exception:
"nested exception is java.lang.NoSuchMethodError:
javax.persistence.spi.PersistenceUnitInfo.getValidationMode()Ljavax/
persistence/ValidationMode;"
 
I just copied the "hibernate-jpa-2.0-api-1.0.1.Final.jar" in order to
remove the error, and just ran into a new one:
 
Exception in thread "main"
org.springframework.beans.factory.BeanCreationException: Error
creating bean with name
'org.springframework.dao.annotation.PersistenceExceptionTranslationPostProcessor#0'
defined in class path resource [META-INF/base.spring.xml]:
Initialization of bean failed; nested exception is
org.springframework.beans.factory.BeanCreationException: Error
creating bean with name 'entityManagerFactory' defined in class path
resource [META-INF/base.spring.xml]: Invocation of init method failed;
nested exception is java.lang.ArrayStoreException:
sun.reflect.annotation.EnumConstantNotPresentExceptionProxy
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:291)
at
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:
222)
at
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:
288)
at
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
194)
at
org.springframework.context.support.AbstractApplicationContext.registerBeanPostProcessors(AbstractApplicationContext.java:
710)
at
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:
410)
at
org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:
139)
at
org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:
105)
at
uk.ac.ebi.intact.core.context.IntactContext.initContext(IntactContext.java:
172)
at
uk.ac.ebi.intact.core.context.IntactContext.initContext(IntactContext.java:
138)
at uk.ac.ebi.intact.kickstart.ExportToFasta.main(ExportToFasta.java:
39)
 
 
When running intact-kickstart on netbeans instead of eclipse, i get a
more precise error message:
error: in class file uk\ac\ebi\intact\model\Experiment.class(uk\ac\ebi
\intact\model:Experiment.class): unknown enum constant
javax.persistence.CascadeType.DETACH
error: in class file uk\ac\ebi\intact\model\Experiment.class(uk\ac\ebi
\intact\model:Experiment.class): unknown enum constant
org.hibernate.annotations.CascadeType.DETACH
error: in class file uk\ac\ebi\intact\model\Experiment.class(uk\ac\ebi
\intact\model:Experiment.class): unknown enum constant
org.hibernate.annotations.CascadeType.DETACH
error: in class file uk\ac\ebi\intact\model\Publication.class(uk\ac\ebi
\intact\model:Publication.class): unknown enum constant
org.hibernate.annotations.CascadeType.DETACH
error: in class file uk\ac\ebi\intact\model\Publication.class(uk\ac\ebi
\intact\model:Publication.class): unknown enum constant
javax.persistence.CascadeType.DETACH
 
And netbeans is right! ;-) The cascadeType.DETACH is not supported in
the older hibernate.anotations libraries included in intact-kickstart.
When i tried to import the newer ones containing CascadeType.DETACH,
i ran into several compatibility issues, so i guess some library
updates weren´t done in conjunction with some others...
 
Can you help me out in this issue? When i checked out the intact-
kickstart months ago, it worked fine with just few modifications, but
now i just see ugly exceptions ;-)
 
Cheers,
Dominik
 
 
 


 

Bruno Aranda <bruno...@gmail.com> Oct 21 09:43AM +0100  

Hi,
 
It is responding as if you hadn't updated the main pom.xml file. I am
running a few checks, but could you run the command
 
mvn dependency:tree
 
in the command line so I can compare the exact dependencies? You seem oto
have problems with the jpa/hibernate dependencies. Could you check that the
parent in the pom.xml file says version 41 of the intact-hibernate-master?
 
Tell me how that works!
 
Bruno
 
On 20 October 2011 18:45, dominik...@biologie.uni-freiburg.de <


 

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-- 
Dominik Mertens, M.Sc. Bioinf.

Center for Biological Systems Analysis (ZBSA)
Albert-Ludwigs-Universitaet Freiburg
Habsburgerstr. 49
79104 Freiburg im Breisgau, Germany

Phone:     +49 761 203-97166
Fax:       +49 761 203-97172
Email:     dominik...@biologie.uni-freiburg.de

[Bruno Aranda]

Uhm, interestingly, this problem happens on Eclipse, but not on IntelliJ IDEA, which is our favourite tool. I will investigate, probably this being related to the order in which the classpath is handled/loaded by the different IDEs... Trying to a class directly with Maven fails as well. Time to investigate...

Cheers,

Bruno

PS We use Maven 3 by default

[Arnaud Ceol]

Hi,

I won't resolve the problem here, but just add a short comment that may help in some cases : when working with eclipse, you may have to run the eclipse plugin for maven, ie: mvn eclipse:clean eclipse:eclipse, and then refresh the workspace.

best,

Arnaud

On 10/21/2011 12:46 PM, Bruno Aranda wrote:

Uhm, interestingly, this problem happens on Eclipse, but not on IntelliJ IDEA, which is our favourite tool. I will investigate, probably this being related to the order in which the classpath is handled/loaded by the different IDEs... Trying to a class directly with Maven fails as well. Time to investigate...

e

[Bruno Aranda]

Hi, I have fixed the problem.

There was one dependency on the kickstart that was relying on an old version of hibernate - one that was a bundle. Hence they were repeated classes in the classpath. I have updated the version for the dependencies and everything seems to work in eclipse as well...

Cheers,

Bruno

[dominik...@biologie.uni-freiburg.de]

Hi Bruno,

thanks again for the quick reply, now i can start intact-kickstart in
eclipse.

However, when i tried to create the database (postgres) again and
tried to import th controlled vocabularies, i realized that only 38
rows in ia_controlledvocab, about 900 were expected... Therfore, when
trying to run the ImportPsiData file it crashes.
I tested all possibilities, creating the database:

postgres=# CREATE DATABASE "intact-db" with owner = intact encoding =
'SQL_ASCII
'tablespace = pg_default template=template0;

and without the SCL_ASCII encoding (pgadmin complained about it...)
I tried to create the schema with the intact-kickstart running
CreateDatabase, ImportControlledVocabularies and ImportPsiData, but i
got several error messages.

The most useful for you should be this one:
CreateDatabase with Eclipse: (52 tables, 2 sequences: cv_local_seq,
intact_ac)
2011-10-25 18:01:07,006 [main] INFO (AbstractApplicationContext,456)
- Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@5dccce3c:
startup date [Tue Oct 25 18:01:06 CEST 2011]; root of context
hierarchy
2011-10-25 18:01:07,123 [main] INFO (XmlBeanDefinitionReader,315) -
Loading XML bean definitions from URL [jar:file:/C:/Users/
dominator/.m2/repository/uk/ac/ebi/intact/core/intact-core/2.5.0/
intact-core-2.5.0.jar!/META-INF/intact.spring.xml]
2011-10-25 18:01:09,679 [main] INFO (XmlBeanDefinitionReader,315) -
Loading XML bean definitions from URL [jar:file:/C:/Users/
dominator/.m2/repository/uk/ac/ebi/intact/dataexchange/psimi/intact-
psixml-exchange/2.1.3/intact-psixml-exchange-2.1.3.jar!/META-INF/
intact.spring.xml]
2011-10-25 18:01:09,732 [main] INFO (XmlBeanDefinitionReader,315) -
Loading XML bean definitions from URL [jar:file:/C:/Users/
dominator/.m2/repository/uk/ac/ebi/intact/dataexchange/intact-enricher/
2.1.3/intact-enricher-2.1.3.jar!/META-INF/intact.spring.xml]
2011-10-25 18:01:09,804 [main] INFO (XmlBeanDefinitionReader,315) -
Loading XML bean definitions from URL [jar:file:/C:/Users/
dominator/.m2/repository/uk/ac/ebi/intact/dataexchange/intact-cvutils/
2.1.3/intact-cvutils-2.1.3.jar!/META-INF/intact.spring.xml]
2011-10-25 18:01:09,915 [main] INFO (XmlBeanDefinitionReader,315) -
Loading XML bean definitions from class path resource [META-INF/
postgres-create.spring.xml]
2011-10-25 18:01:09,955 [main] INFO (XmlBeanDefinitionReader,315) -
Loading XML bean definitions from class path resource [META-INF/
base.spring.xml]
2011-10-25 18:01:10,099 [main] INFO (DefaultListableBeanFactory,612)
- Overriding bean definition for bean 'intactConfig': replacing
[Generic bean: class
[uk.ac.ebi.intact.core.config.IntactConfiguration]; 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:/C:/Users/dominator/.m2/repository/uk/ac/ebi/
intact/core/intact-core/2.5.0/intact-core-2.5.0.jar!/META-INF/
intact.spring.xml]] with [Generic bean: class
[uk.ac.ebi.intact.core.config.IntactConfiguration]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null;
defined in class path resource [META-INF/base.spring.xml]]
2011-10-25 18:01:10,101 [main] INFO (DefaultListableBeanFactory,612)
- Overriding bean definition for bean 'userContext': replacing
[Generic bean: class [uk.ac.ebi.intact.core.context.UserContext];
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:/C:/Users/
dominator/.m2/repository/uk/ac/ebi/intact/core/intact-core/2.5.0/
intact-core-2.5.0.jar!/META-INF/intact.spring.xml]] with [Generic
bean: class [uk.ac.ebi.intact.core.context.UserContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null;
defined in class path resource [META-INF/base.spring.xml]]
2011-10-25 18:01:10,883 [main] INFO (DriverManagerDataSource,153) -
Loaded JDBC driver: org.postgresql.Driver
2011-10-25 18:01:10,884 [main] INFO (AbstractApplicationContext
$BeanPostProcessorChecker,1332) - Bean 'kickstartDataSource' is not
eligible for getting processed by all BeanPostProcessors (for example:
not eligible for auto-proxying)
2011-10-25 18:01:10,920 [main] INFO (AbstractApplicationContext
$BeanPostProcessorChecker,1332) - Bean
'org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter#c970c0e'
is not eligible for getting processed by all BeanPostProcessors (for
example: not eligible for auto-proxying)
2011-10-25 18:01:10,946 [main] INFO
(LocalContainerEntityManagerFactoryBean,221) - Building JPA container
EntityManagerFactory for persistence unit 'intact-core-default'
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/C:/Users/dominator/.m2/repository/
org/slf4j/slf4j-log4j12/1.6.1/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/
StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/C:/Users/dominator/.m2/repository/
org/slf4j/slf4j-jdk14/1.5.8/slf4j-jdk14-1.5.8.jar!/org/slf4j/impl/
StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
explanation.
2011-10-25 18:01:17,447 [main] INFO (JdbcSupportLoader,79) -
Disabling contextual LOB creation as JDBC driver reported JDBC version
[3] less than 4
2011-10-25 18:01:17,450 [main] INFO (TransactionFactoryFactory,62) -
Transaction strategy: org.hibernate.transaction.JDBCTransactionFactory
2011-10-25 18:01:17,452 [main] INFO (TransactionManagerLookupFactory,
80) - No TransactionManagerLookup configured (in JTA environment, use
of read-write or transactional second-level cache is not recommended)
2011-10-25 18:01:17,498 [main] INFO (SessionFactoryImpl,200) -
building session factory
2011-10-25 18:01:19,957 [main] INFO (SessionFactoryObjectFactory,105)
- Not binding factory to JNDI, no JNDI name configured
2011-10-25 18:01:24,585 [main] ERROR (SchemaExport,386) -
Unsuccessful: create table ia_lifecycle_event (ac varchar(30) not
null, created timestamp not null, created_user varchar(30) not null,
updated timestamp not null, userstamp varchar(30) not null, deprecated
bool not null, note text, when timestamp, event_ac varchar(30) not
null, publication_ac varchar(30) not null, user_ac varchar(30) not
null, primary key (ac))
2011-10-25 18:01:24,595 [main] ERROR (SchemaExport,387) - ERROR:
syntax error at or near "when"
2011-10-25 18:01:26,496 [main] ERROR (SchemaExport,386) -
Unsuccessful: create index idx_event_who on ia_lifecycle_event
(user_ac)
2011-10-25 18:01:26,506 [main] ERROR (SchemaExport,387) - ERROR:
relation "ia_lifecycle_event" does not exist
2011-10-25 18:01:26,506 [main] ERROR (SchemaExport,386) -
Unsuccessful: create index idx_event_event on ia_lifecycle_event
(event_ac)
2011-10-25 18:01:26,506 [main] ERROR (SchemaExport,387) - ERROR:
relation "ia_lifecycle_event" does not exist
2011-10-25 18:01:26,506 [main] ERROR (SchemaExport,386) -
Unsuccessful: alter table ia_lifecycle_event add constraint
FK_LIFECYCLE_EVENT_EVENT foreign key (event_ac) references
ia_controlledvocab
2011-10-25 18:01:26,516 [main] ERROR (SchemaExport,387) - ERROR:
relation "ia_lifecycle_event" does not exist
2011-10-25 18:01:26,516 [main] ERROR (SchemaExport,386) -
Unsuccessful: alter table ia_lifecycle_event add constraint
FK_LIFECYCLE_EVENT_PUBLICATION foreign key (publication_ac) references
ia_publication
2011-10-25 18:01:26,516 [main] ERROR (SchemaExport,387) - ERROR:
relation "ia_lifecycle_event" does not exist
2011-10-25 18:01:26,516 [main] ERROR (SchemaExport,386) -
Unsuccessful: alter table ia_lifecycle_event add constraint
FK_LIFECYCLE_EVENT_USER foreign key (user_ac) references ia_user
2011-10-25 18:01:26,516 [main] ERROR (SchemaExport,387) - ERROR:
relation "ia_lifecycle_event" does not exist
2011-10-25 18:01:27,306 [main] INFO (AbstractApplicationContext
$BeanPostProcessorChecker,1332) - Bean 'entityManagerFactory' is not
eligible for getting processed by all BeanPostProcessors (for example:
not eligible for auto-proxying)
2011-10-25 18:01:27,328 [main] INFO (DefaultListableBeanFactory,549)
- Pre-instantiating singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@2db7ae22:
defining beans
[institutionMerger,roleDaoImpl,userDaoImpl,preferenceDaoImpl,daoFactory,applicationDaoImpl,applicationPropertyDaoImpl,dbInfoDaoImpl,publicationDaoImpl,confidenceDaoImpl,componentConfidenceDaoImpl,componentParameterDaoImpl,experimentDaoImpl,interactionDaoImpl,interactionParameterDaoImpl,rangeDaoImpl,mineInteractionDaoImpl,aliasDaoImpl,componentDaoImpl,featureDaoImpl,proteinDaoImpl,xrefDaoImpl,lifecycleEventDaoImpl,bioSourceDaoImpl,polymerDaoImpl,institutionDaoImpl,searchableDaoImpl,interactorDaoImpl,cvObjectDaoImpl,annotationDaoImpl,userServiceImpl,simpleSearchService,configurationHandler,sequenceManager,floatPropertyConverter,shortPropertyConverter,booleanPropertyConverter,integerPropertyConverter,doublePropertyConverter,institutionPropertyConverter,longPropertyConverter,charPropertyConverter,stringPropertyConverter,correctionAssigner,lifecycleManager,releasedStatus,acceptedStatus,newStatus,readyForCheckingStatus,assignedStatus,curationInProgressStatus,readyForReleaseStatus,startStatus,acceptedOnHoldStatus,transitionCheckerAspect,intactFlushModeAspect,simpleProfiler,bulkOperationsImpl,intactContext,dataContext,lazyIntactCloner,interactorEnricher,bioSourceEnricher,cvObjectEnricher,interactionEnricher,institutionEnricher,experimentEnricher,componentEnricher,intactEntryEnricher,cvUpdaterFactory,annotationInfoDatasetService,org.springframework.context.annotation.internalConfigurationAnnotationProcessor,org.springframework.context.annotation.internalAutowiredAnnotationProcessor,org.springframework.context.annotation.internalRequiredAnnotationProcessor,org.springframework.context.annotation.internalCommonAnnotationProcessor,org.springframework.context.annotation.internalPersistenceAnnotationProcessor,org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor#0,org.springframework.aop.config.internalAutoProxyCreator,intactInitializer,userContext,intactConfig,schemaVersion,persisterHelper,corePersister,coreDeleter,finder,institutionIntact,institutionMint,institutionDip,institutionUndefined,defaultApp,psiExchange,psiEnricher,enricherConfig,enricherContext,enricherCacheManager,cvObjectFetcher,experimentFetcher,bioSourceFetcher,interactorFetcher,cvUpdater,cvExporter,org.springframework.dao.annotation.PersistenceExceptionTranslationPostProcessor#0,org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor#0,transactionManager,org.springframework.transaction.annotation.AnnotationTransactionAttributeSource#0,org.springframework.transaction.interceptor.TransactionInterceptor#0,org.springframework.transaction.config.internalTransactionAdvisor,org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor#1,entityManagerFactory,kickstartDataSource,org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0];
root of factory hierarchy
2011-10-25 18:01:31,256 [main] INFO (IntactInitializer,99) - Starting
IntAct Core module...
2011-10-25 18:01:31,257 [main] INFO (IntactInitializer,100) - Binding
context to Application: default
2011-10-25 18:01:31,688 [main] INFO (ConfigurationHandler,56) -
Loading configuration for application: default
2011-10-25 18:01:31,864 [main] INFO (ConfigurationHandler,106) -
Persisting configuration for application: default
2011-10-25 18:01:32,108 [main] INFO (IntactInitializer,110) -
Default institution: Institution: exampleInstitution
2011-10-25 18:01:32,108 [main] INFO (IntactInitializer,111) - Schema
version: 2.5.0
2011-10-25 18:01:32,108 [main] INFO (IntactInitializer,112) -
Autopersist: true
2011-10-25 18:01:32,109 [main] INFO (IntactInitializer,113) -
Configuration: [Preference{key='intactConfig.acPrefix',
value='KICKSTART'}, Preference{key='intactConfig.defaultInstitution',
value='exampleInstitution'},
Preference{key='intactConfig.localCvPrefix', value='IA'},
Preference{key='intactConfig.autoUpdateExperimentLabel',
value='false'},
Preference{key='intactConfig.autoUpdateInteractionLabel',
value='false'}, Preference{key='intactConfig.skipSchemaCheck',
value='true'}]
2011-10-25 18:01:32,110 [main] INFO (IntactInitializer,116) -
DataSources(1):
2011-10-25 18:01:32,114 [main] INFO (IntactInitializer,118) -
kickstartDataSource: url: 'jdbc:postgresql://localhost:5432/intact-
db', username: 'intact'
2011-10-25 18:01:33,694 [main] INFO (IntactInitializer,224) -
Persisting necessary CvObjects
2011-10-25 18:01:34,013 [main] INFO (SequenceManager,107) - Sequence
could not be found and it is going to be created: cv_local_seq
2011-10-25 18:01:41,825 [main] INFO (IntactInitializer,343) - Created
user role: ADMIN
2011-10-25 18:01:41,876 [main] INFO (IntactInitializer,343) - Created
user role: CURATOR
2011-10-25 18:01:41,923 [main] INFO (IntactInitializer,343) - Created
user role: REVIEWER
2011-10-25 18:01:41,964 [main] INFO (IntactInitializer,328) - After
init: found 3 role(s) in the database.
2011-10-25 18:01:42,409 [Thread-1] INFO (AbstractApplicationContext,
1002) - Closing
org.springframework.context.support.ClassPathXmlApplicationContext@5dccce3c:
startup date [Tue Oct 25 18:01:06 CEST 2011]; root of context
hierarchy
2011-10-25 18:01:42,411 [Thread-1] INFO (DefaultSingletonBeanRegistry,
422) - Destroying singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@2db7ae22:
defining beans
[institutionMerger,roleDaoImpl,userDaoImpl,preferenceDaoImpl,daoFactory,applicationDaoImpl,applicationPropertyDaoImpl,dbInfoDaoImpl,publicationDaoImpl,confidenceDaoImpl,componentConfidenceDaoImpl,componentParameterDaoImpl,experimentDaoImpl,interactionDaoImpl,interactionParameterDaoImpl,rangeDaoImpl,mineInteractionDaoImpl,aliasDaoImpl,componentDaoImpl,featureDaoImpl,proteinDaoImpl,xrefDaoImpl,lifecycleEventDaoImpl,bioSourceDaoImpl,polymerDaoImpl,institutionDaoImpl,searchableDaoImpl,interactorDaoImpl,cvObjectDaoImpl,annotationDaoImpl,userServiceImpl,simpleSearchService,configurationHandler,sequenceManager,floatPropertyConverter,shortPropertyConverter,booleanPropertyConverter,integerPropertyConverter,doublePropertyConverter,institutionPropertyConverter,longPropertyConverter,charPropertyConverter,stringPropertyConverter,correctionAssigner,lifecycleManager,releasedStatus,acceptedStatus,newStatus,readyForCheckingStatus,assignedStatus,curationInProgressStatus,readyForReleaseStatus,startStatus,acceptedOnHoldStatus,transitionCheckerAspect,intactFlushModeAspect,simpleProfiler,bulkOperationsImpl,intactContext,dataContext,lazyIntactCloner,interactorEnricher,bioSourceEnricher,cvObjectEnricher,interactionEnricher,institutionEnricher,experimentEnricher,componentEnricher,intactEntryEnricher,cvUpdaterFactory,annotationInfoDatasetService,org.springframework.context.annotation.internalConfigurationAnnotationProcessor,org.springframework.context.annotation.internalAutowiredAnnotationProcessor,org.springframework.context.annotation.internalRequiredAnnotationProcessor,org.springframework.context.annotation.internalCommonAnnotationProcessor,org.springframework.context.annotation.internalPersistenceAnnotationProcessor,org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor#0,org.springframework.aop.config.internalAutoProxyCreator,intactInitializer,userContext,intactConfig,schemaVersion,persisterHelper,corePersister,coreDeleter,finder,institutionIntact,institutionMint,institutionDip,institutionUndefined,defaultApp,psiExchange,psiEnricher,enricherConfig,enricherContext,enricherCacheManager,cvObjectFetcher,experimentFetcher,bioSourceFetcher,interactorFetcher,cvUpdater,cvExporter,org.springframework.dao.annotation.PersistenceExceptionTranslationPostProcessor#0,org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor#0,transactionManager,org.springframework.transaction.annotation.AnnotationTransactionAttributeSource#0,org.springframework.transaction.interceptor.TransactionInterceptor#0,org.springframework.transaction.config.internalTransactionAdvisor,org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor#1,entityManagerFactory,kickstartDataSource,org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0];
root of factory hierarchy
2011-10-25 18:01:42,422 [Thread-1] WARN (ConfigurationFactory,127) -
No configuration found. Configuring ehcache from ehcache-failsafe.xml
found in the classpath: jar:file:/C:/Users/dominator/.m2/repository/
net/sf/ehcache/ehcache/1.3.0/ehcache-1.3.0.jar!/ehcache-failsafe.xml
2011-10-25 18:01:42,452 [Thread-1] WARN (DisposableBeanAdapter,193) -
Invocation of destroy method failed on bean with name 'intactContext':
org.springframework.beans.factory.BeanCreationNotAllowedException:
Error creating bean with name 'configurationHandler': Singleton bean
creation not allowed while the singletons of this factory are in
destruction (Do not request a bean from a BeanFactory in a destroy
method implementation!)
2011-10-25 18:01:42,452 [Thread-1] INFO
(AbstractEntityManagerFactoryBean,406) - Closing JPA
EntityManagerFactory for persistence unit 'intact-core-default'
2011-10-25 18:01:42,452 [Thread-1] INFO (SessionFactoryImpl,925) -
closing



When trying to import the ControlledVocabs, the programs runs for
about 10 minutes, so i guess it does not complete successfully.

I also tried to create the schema from postgres by using the
intact-db=> \i postgres-2.0.dll
commad, but it did not work. In one schema e.g. does a ia_application
table exist (intact-kickstart i guess), in the other it didn´t (from
postgres by postgres-2.0.dll)


I did not change anything on my postgres and about some months ago i
did not have any problems to get everything running.
Any ideas?

Thank you in advance!

Cheer,
Dominik

On Oct 21, 1:29 pm, Bruno Aranda <brunoara...@gmail.com> wrote:
> Hi, I have fixed the problem.
>
> There was one dependency on the kickstart that was relying on an old version
> of hibernate - one that was a bundle. Hence they were repeated classes in
> the classpath. I have updated the version for the dependencies and
> everything seems to work in eclipse as well...
>
> Cheers,
>
> Bruno
>

> On 21 October 2011 11:55, Arnaud Ceol <arnaud.c...@gmail.com> wrote:
>
>
>
>
>
>
>
> >  Hi,
>
> > I won't resolve the problem here, but just add a short comment that may
> > help in some cases : when working with eclipse, you may have to run the

> > eclipse plugin for maven, ie: *mvn eclipse:clean eclipse:eclipse*, and

> > then refresh the workspace.
>
> > best,
>
> > Arnaud
>
> > On 10/21/2011 12:46 PM, Bruno Aranda wrote:
>
> > Uhm, interestingly, this problem happens on Eclipse, but not on IntelliJ
> > IDEA, which is our favourite tool. I will investigate, probably this being
> > related to the order in which the classpath is handled/loaded by the
> > different IDEs... Trying to a class directly with Maven fails as well. Time
> > to investigate...
> > e
> > Cheers,
>
> > Bruno
>
> > PS We use Maven 3 by default
>
> > On 21 October 2011 10:43, Dominik Mertens <

> ...
>
> read more »

[Bruno Aranda]

Hi,

I guess me updating the intact-kickstart to the latest intact-core 2.5.0 is causing more problems that I thought. Basically, it expects some new tables related to curation flows or application info.

I have created a class CreateDatabaseDDL in intact-kickstart, which can be used to generate a fresh DDL for IntAct. I understand you are using a database with existing data? You have two options if this is the case:

1) Use intact-core 2.4.1 - update the intact-kickstart POM file with that version.
2) It is possible to generate manually a DDL containing the update between two intact-core versions. To do that, speficy the version of the intact-core you want to use (in this case 2.5.0 as seen in the POM file. I have added a comment in the CreateDatabaseDDL class where I explain how you can use the method SchemaUtils.generateUpdateSchemaDDLForPostgresSQL(...). You could try to run the generated SQL statements in your existing database to modify the schema manually.

Let us know if this works?

Cheers!

Bruno

[dominik...@biologie.uni-freiburg.de]

Hi Bruno,

thanks a lot, it seems to work fine now. I just changed the version of
the intact-core to 2.4.1 and this solved the issue. However, the
number of controlled vocabularies is now over 1600, so many people
seem to work on this, good to know!
I will keep working on integrating the intact software in mine and
hope to get it running soon. If i am reaching deadlock again i will
let you know ;-)

Thanks for the quick replies and the fast modifications on the
project!

Best regards,
Dominik

On Oct 26, 11:36 am, Bruno Aranda <brunoara...@gmail.com> wrote:
> Hi,
>

> I guess me updating the intact-kickstart to the latest intact-core 2.5.0 is
> causing more problems that I thought. Basically, it expects some new tables
> related to curation flows or application info.
>
> I have created a class CreateDatabaseDDL in intact-kickstart, which can be
> used to generate a fresh DDL for IntAct. I understand you are using a
> database with existing data? You have two options if this is the case:
>
> 1) Use intact-core 2.4.1 - update the intact-kickstart POM file with that
> version.
> 2) It is possible to generate manually a DDL containing the update between
> two intact-core versions. To do that, speficy the version of the intact-core
> you want to use (in this case 2.5.0 as seen in the POM file. I have added a
> comment in the CreateDatabaseDDL class where I explain how you can use the
> method SchemaUtils.generateUpdateSchemaDDLForPostgresSQL(...). You could try
> to run the generated SQL statements in your existing database to modify the
> schema manually.
>
> Let us know if this works?
>
> Cheers!
>
> Bruno
>

> On 25 October 2011 17:43, dominik.mert...@biologie.uni-freiburg.de <

> > SLF4J: Seehttp://www.slf4j.org/codes.html#multiple_bindingsfor an

> ...
>
> read more »

[dominik...@biologie.uni-freiburg.de]

Hi guys,

i got a new error when trying to export the sample data
("intact_2006-07-19.xml") by using ExportToPsiXml.java, using one of
these publicationID´s:
IntactEntry intactEntry =
IntactEntryFactory.createIntactEntry(intactContext).addPublicationId("16469704");
IntactEntry intactEntry =
IntactEntryFactory.createIntactEntry(intactContext).addPublicationId("16469705");


Exception in thread "main"
org.springframework.dao.DataIntegrityViolationException: could not
execute query; SQL [select this_.ac as ac10_7.....
.....
Caused by: org.postgresql.util.PSQLException: Bad value for type int:
MNTDLAAGKMASAACSMDPIDSFELLDLLFDRQDGILRHVELGEGWGHVKDQVLPNPDSDDFLSSILGSGDSLPSSPLWSPEGSDSGISEDLPSDPQDTPPRSGPATSPAGCHPAQPGKGPCLSYHPGNSCSTTTPGPVIQVPEASVTIDLEMWSPGGRICAEKPADPVDLSPRCNLTVKDLLLSGSSGDLQQHHLGASYLLRPGAGHCQELVLTEDEKKLLAKEGITLPTQLPLTKYEERVLKKIRRKIRNKQSAQESRKKKKEYIDGLETRMSACTAQNQELQRKVLHLEKQNLSLLEQLKKLQAIVVQSTSKSAQTGT.
at
org.postgresql.jdbc2.AbstractJdbc2ResultSet.toInt(AbstractJdbc2ResultSet.java:
2638)
at
org.postgresql.jdbc2.AbstractJdbc2ResultSet.getInt(AbstractJdbc2ResultSet.java:
1968)
at org.postgresql.jdbc3.Jdbc3ResultSet.getClob(Jdbc3ResultSet.java:
44)
at
org.postgresql.jdbc2.AbstractJdbc2ResultSet.getClob(AbstractJdbc2ResultSet.java:
373)
at org.hibernate.type.descriptor.sql.ClobTypeDescriptor
$2.doExtract(ClobTypeDescriptor.java:70)
at
org.hibernate.type.descriptor.sql.BasicExtractor.extract(BasicExtractor.java:
64)
at
org.hibernate.type.AbstractStandardBasicType.nullSafeGet(AbstractStandardBasicType.java:
254)
at
org.hibernate.type.AbstractStandardBasicType.nullSafeGet(AbstractStandardBasicType.java:
250)
at
org.hibernate.type.AbstractStandardBasicType.nullSafeGet(AbstractStandardBasicType.java:
230)
at
org.hibernate.type.AbstractStandardBasicType.hydrate(AbstractStandardBasicType.java:
331)
at
org.hibernate.persister.entity.AbstractEntityPersister.hydrate(AbstractEntityPersister.java:
2265)
at org.hibernate.loader.Loader.loadFromResultSet(Loader.java:1527)
at org.hibernate.loader.Loader.instanceNotYetLoaded(Loader.java:1455)
at org.hibernate.loader.Loader.getRow(Loader.java:1355)
at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:611)
at org.hibernate.loader.Loader.doQuery(Loader.java:829)
at
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:
274)
at org.hibernate.loader.Loader.doList(Loader.java:2533)


It´s a matter of the featureRange list as far as i know. If the ranges
are set to 0, the error disappears. When trying to importand export
other sample data, i do not get these error.
I don´t think i had this problem with the previous intact-version. I
set the intact-core to 2.4.1, but the rest is up to date.

This is not an urgent issue for me, just wanted to let you know what
is working/not working. Maybe its just due to the different version of
the intact-core.


Cheers,
Dominik


On Oct 27, 7:05 pm, "dominik.mert...@biologie.uni-freiburg.de"

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