[InterMine Dev] error in model - help with debugging

Julie Sullivan julie at flymine.org
Thu Mar 14 09:22:41 GMT 2013


Hi Pushkala,

I think reading this page will help you understand how the model works:

	http://intermine.readthedocs.org/en/latest/data-model/model

On 13/03/13 20:51, Jayaraman, Pushkala wrote:
> So I figured out how to make my build successful but had another question spring out of this one:
> I may have missed out reading up on some of the documentation..
> But, Is this the cardinal rule:
> Whenever we reverse-reference something we always add the tag "reference" is it?
> And when we don't reverse-reference anything we use the tag "attribute"?
>
>
> From: dev-bounces at intermine.org [mailto:dev-bounces at intermine.org] On Behalf Of Jayaraman, Pushkala
> Sent: Wednesday, March 13, 2013 3:43 PM
> To: dev at intermine.org
> Subject: [InterMine Dev] error in model - help with debugging
>
> Hello,
> I have been trying to debug this for a while. I know it is relatively simple but I would like some direction on where to begin
> I was trying to add a new class to my additions.xml file and my build failed..
> Would anyone know where to begin when the error caused is this:
>
> Caused by: org.intermine.modelproduction.ModelParserException: java.lang.IllegalArgumentException: Error - type of attribute `submissions` not defined for `org.intermine.model.bio.Project`
>
> Here is my additions.xml file:
>
>
> <?xml version="1.0"?>
> <!-- This file details any extensions needed to the data model to store data from this source, everything else is automatically generated from the model description so this is all we need to do to add to the model. -->
>
> <classes>
>          <class name="Submission" is-interface="true">
>                  <collection name="dataPoints" referenced-type="DataPoint" reverse-reference="submission"/>
>                  <attribute name="experimentDate" type="java.util.Date"/>
>                  <reference name="publication" referenced-type="Publication"/>
>                  <attribute name="title" type="java.lang.String"/>
>          </class>
>
>          <class name="DataPoint" is-interface="true">
>                  <reference name="submission" referenced-type="Submission" reverse-reference="dataPoints"/>
>          </class>
>
>          <class name="eQTL" extends="DataPoint" is-interface="true">
>                  <attribute name="reaperPValue" type="java.lang.Float"/>
>                  <reference name="submission" referenced-type="Submission" reverse-reference="dataPoints"/>
>                  <reference name="sslv" referenced-type="SimpleSequenceLengthVariation"/>
>                  <reference name="probeSet" referenced-type="ProbeSet"/>
>                  <collection name="tissueExpressions" referenced-type="Expression"/>
>                  <reference name="organism" referenced-type="Organism"/>
>          </class>
>
>          <class name="Expression" is-interface="true">
>                  <attribute name="tissue" type="java.lang.String"/>
>                  <attribute name="foldChange" type="java.lang.Float"/>
>                  <attribute name="pval" type="java.lang.Float"/>
>                  <reference name="eqtl" referenced-type="eQTL" reverse-reference="tissueExpressions"/>
>          </class>
>
>          <class name="ProbeSet" extends="SequenceCollection" is-interface="true">
>                  <collection name="eqtls" referenced-type="eQTL" reverse-reference="probeSet"/>
>          </class>
>
>          <class name="SimpleSequenceLengthVariation" is-interface="true">
>                  <collection name="eqtls" referenced-type="eQTL" reverse-reference="sslv"/>
>          </class>
>
>          <class name="Project" is-interface="true">
>                  <attribute name="name" type="java.lang.String"/>
>                  <attribute name="submissions" referenced-type="Submission"/>
>          </class>
>
> </classes>
>
>
>
>
>
>
>
> Here's the build log:
>
> BUILD FAILED
> /home/intermine/git_ratmine/intermine/imbuild/objectstore.xml:151: exception while invoking execute on org.intermine.task.ModelMergerTask
>          at org.intermine.task.MergeSourceModelsTask.execute(MergeSourceModelsTask.java:162)
>          at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>          at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>          at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>          at java.lang.reflect.Method.invoke(Method.java:597)
>          at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>          at org.apache.tools.ant.Task.perform(Task.java:348)
>          at org.apache.tools.ant.Target.execute(Target.java:390)
>          at org.apache.tools.ant.Target.performTasks(Target.java:411)
>          at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
>          at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
>          at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>          at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
>          at org.apache.tools.ant.Main.runBuild(Main.java:809)
>          at org.apache.tools.ant.Main.startAnt(Main.java:217)
>          at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>          at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
> Caused by: java.lang.reflect.InvocationTargetException
>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>          at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>          at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>          at java.lang.reflect.Method.invoke(Method.java:597)
>          at org.intermine.task.MergeSourceModelsTask.execute(MergeSourceModelsTask.java:160)
>          ... 16 more
> Caused by: Failed to parse model from input files
>          at org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:83)
>          ... 21 more
> Caused by: org.intermine.metadata.MetaDataException: Exception while merging /home/intermine/git_ratmine/intermine/bio/ratmine_bio_sources/e-qtl/e-qtl_additions.xml into /home/intermine/git_ratmine/intermine/ratmine/dbmodel/build/model/genomic_model.xml
>          at org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:46)
>          at org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:81)
>          ... 21 more
> Caused by: org.intermine.modelproduction.ModelParserException: java.lang.IllegalArgumentException: Error - type of attribute `submissions` not defined for `org.intermine.model.bio.Project`
>          at org.intermine.modelproduction.xml.InterMineModelParser.generateClassDescriptors(InterMineModelParser.java:78)
>          at org.intermine.modelproduction.ModelFileMerger.processFile(ModelFileMerger.java:65)
>          at org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:44)
>          ... 22 more
> Caused by: java.lang.IllegalArgumentException: Error - type of attribute `submissions` not defined for `org.intermine.model.bio.Project`
>          at org.intermine.modelproduction.xml.InterMineModelParser$ModelHandler.startElement(InterMineModelParser.java:120)
>          at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:501)
>          at com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:179)
>          at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1343)
>          at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2755)
>          at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648)
>          at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:511)
>          at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:808)
>          at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
>          at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:119)
>          at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
>          at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)
>          at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
>          at org.intermine.util.SAXParser.parse(SAXParser.java:59)
>          at org.intermine.util.SAXParser.parse(SAXParser.java:42)
>          at org.intermine.modelproduction.xml.InterMineModelParser.generateClassDescriptors(InterMineModelParser.java:75)
>          ... 24 more
>
> Total time: 15 seconds
> [intermine at jordan dbmodel]$ vi /home/intermine/git_ratmine/intermine/bio/ratmine_bio_sources/e-qtl/e-qtl_additions.xml
>
> Pushkala Jayaraman
> Programmer/Analyst - Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> 414-955-2229
> http://rgd.mcw.edu
>
>
>
>
>
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