[InterMine Dev] error in model - help with debugging

Jayaraman, Pushkala pjayaraman at mcw.edu
Wed Mar 13 20:43:29 GMT 2013


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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