UniProt Parser - Null pointer exception caused by uniprot_config.properties

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UniProt Parser - Null pointer exception caused by uniprot_config.properties

Anthony C. Smith
Hello,

I've been helping James with the update to MitoMiner and I've have been having trouble with the trunk version of the UniProt source.

I have a problem when setting which identifiers to use for genes, specifically with malaria (36329). After I set the uniprot_config.properties  (such as to ORF or primary) and integrate the uniprot source for malaria I get a null pointer exception when the first UniProt entry of the file is being read (see below). Other taxons work fine.

If I use a test dataset from cow, which contains one entry, it works fine for cow. If I change the taxon id of the same datafile to mouse it also works fine. If I change it to malaria I get the null pointer. The entries in uniprot_config.properties are identical for all three taxons e.g:

9913.uniqueField = symbol
9913.symbol.name = primary

Therefore the datafile looks valid, but the malaria taxon itself appears to be causing the problem. Any ideas?

Thanks,

Anthony

Dr Anthony C. Smith
Bioinformatics group
MRC Mitochondrial Biology Unit
Wellcome Trust / MRC Building
Hills Road, Cambridge, UK
CB2 0XY
www.mrc-mbu.cam.ac.uk/research/bioinformatics



[integrate] java.lang.NullPointerException
[integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.resolveGene(UniprotConverter.java:1016)
[integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.createGene(UniprotConverter.java:888)
[integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processGene(UniprotConverter.java:860)
[integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processEntry(UniprotConverter.java:647)
[integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.endElement(UniprotConverter.java:479)
[integrate] at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
[integrate] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
[integrate] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
[integrate] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
[integrate] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
[integrate] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
[integrate] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
[integrate] at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
[integrate] at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
[integrate] at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
[integrate] at org.intermine.util.SAXParser.parse(SAXParser.java:59)
[integrate] at org.intermine.util.SAXParser.parse(SAXParser.java:42)
[integrate] at org.intermine.bio.dataconversion.UniprotConverter.processFiles(UniprotConverter.java:149)
[integrate] at org.intermine.bio.dataconversion.UniprotConverter.process(UniprotConverter.java:113)
[integrate] at org.intermine.task.DirectoryConverterTask.execute(DirectoryConverterTask.java:104)
[integrate] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
[integrate] at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
[integrate] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[integrate] at java.lang.reflect.Method.invoke(Method.java:616)
[integrate] at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
[integrate] at org.apache.tools.ant.Task.perform(Task.java:348)
[integrate] at org.apache.tools.ant.Target.execute(Target.java:390)
[integrate] at org.apache.tools.ant.Target.performTasks(Target.java:411)
[integrate] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
[integrate] at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
[integrate] at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
[integrate] at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
[integrate] at org.intermine.task.Integrate.performAction(Integrate.java:223)
[integrate] at org.intermine.task.Integrate.performAction(Integrate.java:135)
[integrate] at org.intermine.task.Integrate.execute(Integrate.java:127)
[integrate] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
[integrate] at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
[integrate] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[integrate] at java.lang.reflect.Method.invoke(Method.java:616)
[integrate] at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
[integrate] at org.apache.tools.ant.Task.perform(Task.java:348)
[integrate] at org.apache.tools.ant.Target.execute(Target.java:390)
[integrate] at org.apache.tools.ant.Target.performTasks(Target.java:411)
[integrate] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
[integrate] at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
[integrate] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
[integrate] at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
[integrate] at org.apache.tools.ant.Main.runBuild(Main.java:801)
[integrate] at org.apache.tools.ant.Main.startAnt(Main.java:218)
[integrate] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
[integrate] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
     [null] Exiting /intermine/intermine_0_97/bio/sources/uniprot/build.xml.

BUILD FAILED
/intermine/intermine_0_97/imbuild/integrate.xml:54: The following error occurred while executing this line:
/intermine/intermine_0_97/bio/sources/uniprot/build.xml:24: java.lang.RuntimeException: java.lang.NullPointerException
        at org.intermine.bio.dataconversion.UniprotConverter.processFiles(UniprotConverter.java:152)
        at org.intermine.bio.dataconversion.UniprotConverter.process(UniprotConverter.java:113)
        at org.intermine.task.DirectoryConverterTask.execute(DirectoryConverterTask.java:104)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:616)
        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:1360)
        at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
        at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
        at org.intermine.task.Integrate.performAction(Integrate.java:223)
        at org.intermine.task.Integrate.performAction(Integrate.java:135)
        at org.intermine.task.Integrate.execute(Integrate.java:127)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:616)
        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:1360)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
        at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
        at org.apache.tools.ant.Main.runBuild(Main.java:801)
        at org.apache.tools.ant.Main.startAnt(Main.java:218)
        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.NullPointerException
        at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.resolveGene(UniprotConverter.java:1016)
        at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.createGene(UniprotConverter.java:888)
        at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processGene(UniprotConverter.java:860)
        at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processEntry(UniprotConverter.java:647)
        at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.endElement(UniprotConverter.java:479)
        at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
        at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
        at org.intermine.util.SAXParser.parse(SAXParser.java:59)
        at org.intermine.util.SAXParser.parse(SAXParser.java:42)
        at org.intermine.bio.dataconversion.UniprotConverter.processFiles(UniprotConverter.java:149)
        ... 33 more













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Re: UniProt Parser - Null pointer exception caused by uniprot_config.properties

Anthony C. Smith
Hi,

I figured it out. The taxon was missing from bio/core/main/resources/organism_config.properties.

Thanks,

Anthony


On 25 Jul 2011, at 12:09, Anthony C. Smith wrote:

> Hello,
>
> I've been helping James with the update to MitoMiner and I've have been having trouble with the trunk version of the UniProt source.
>
> I have a problem when setting which identifiers to use for genes, specifically with malaria (36329). After I set the uniprot_config.properties  (such as to ORF or primary) and integrate the uniprot source for malaria I get a null pointer exception when the first UniProt entry of the file is being read (see below). Other taxons work fine.
>
> If I use a test dataset from cow, which contains one entry, it works fine for cow. If I change the taxon id of the same datafile to mouse it also works fine. If I change it to malaria I get the null pointer. The entries in uniprot_config.properties are identical for all three taxons e.g:
>
> 9913.uniqueField = symbol
> 9913.symbol.name = primary
>
> Therefore the datafile looks valid, but the malaria taxon itself appears to be causing the problem. Any ideas?
>
> Thanks,
>
> Anthony
>
> Dr Anthony C. Smith
> Bioinformatics group
> MRC Mitochondrial Biology Unit
> Wellcome Trust / MRC Building
> Hills Road, Cambridge, UK
> CB2 0XY
> www.mrc-mbu.cam.ac.uk/research/bioinformatics
>
>
>
> [integrate] java.lang.NullPointerException
> [integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.resolveGene(UniprotConverter.java:1016)
> [integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.createGene(UniprotConverter.java:888)
> [integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processGene(UniprotConverter.java:860)
> [integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processEntry(UniprotConverter.java:647)
> [integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.endElement(UniprotConverter.java:479)
> [integrate] at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
> [integrate] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
> [integrate] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
> [integrate] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
> [integrate] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> [integrate] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> [integrate] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
> [integrate] at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
> [integrate] at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
> [integrate] at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
> [integrate] at org.intermine.util.SAXParser.parse(SAXParser.java:59)
> [integrate] at org.intermine.util.SAXParser.parse(SAXParser.java:42)
> [integrate] at org.intermine.bio.dataconversion.UniprotConverter.processFiles(UniprotConverter.java:149)
> [integrate] at org.intermine.bio.dataconversion.UniprotConverter.process(UniprotConverter.java:113)
> [integrate] at org.intermine.task.DirectoryConverterTask.execute(DirectoryConverterTask.java:104)
> [integrate] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> [integrate] at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> [integrate] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> [integrate] at java.lang.reflect.Method.invoke(Method.java:616)
> [integrate] at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> [integrate] at org.apache.tools.ant.Task.perform(Task.java:348)
> [integrate] at org.apache.tools.ant.Target.execute(Target.java:390)
> [integrate] at org.apache.tools.ant.Target.performTasks(Target.java:411)
> [integrate] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
> [integrate] at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> [integrate] at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
> [integrate] at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
> [integrate] at org.intermine.task.Integrate.performAction(Integrate.java:223)
> [integrate] at org.intermine.task.Integrate.performAction(Integrate.java:135)
> [integrate] at org.intermine.task.Integrate.execute(Integrate.java:127)
> [integrate] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> [integrate] at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> [integrate] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> [integrate] at java.lang.reflect.Method.invoke(Method.java:616)
> [integrate] at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> [integrate] at org.apache.tools.ant.Task.perform(Task.java:348)
> [integrate] at org.apache.tools.ant.Target.execute(Target.java:390)
> [integrate] at org.apache.tools.ant.Target.performTasks(Target.java:411)
> [integrate] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
> [integrate] at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
> [integrate] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> [integrate] at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
> [integrate] at org.apache.tools.ant.Main.runBuild(Main.java:801)
> [integrate] at org.apache.tools.ant.Main.startAnt(Main.java:218)
> [integrate] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
> [integrate] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>     [null] Exiting /intermine/intermine_0_97/bio/sources/uniprot/build.xml.
>
> BUILD FAILED
> /intermine/intermine_0_97/imbuild/integrate.xml:54: The following error occurred while executing this line:
> /intermine/intermine_0_97/bio/sources/uniprot/build.xml:24: java.lang.RuntimeException: java.lang.NullPointerException
> at org.intermine.bio.dataconversion.UniprotConverter.processFiles(UniprotConverter.java:152)
> at org.intermine.bio.dataconversion.UniprotConverter.process(UniprotConverter.java:113)
> at org.intermine.task.DirectoryConverterTask.execute(DirectoryConverterTask.java:104)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
> 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:1360)
> at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
> at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
> at org.intermine.task.Integrate.performAction(Integrate.java:223)
> at org.intermine.task.Integrate.performAction(Integrate.java:135)
> at org.intermine.task.Integrate.execute(Integrate.java:127)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
> 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:1360)
> at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
> at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
> at org.apache.tools.ant.Main.runBuild(Main.java:801)
> at org.apache.tools.ant.Main.startAnt(Main.java:218)
> 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.NullPointerException
> at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.resolveGene(UniprotConverter.java:1016)
> at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.createGene(UniprotConverter.java:888)
> at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processGene(UniprotConverter.java:860)
> at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processEntry(UniprotConverter.java:647)
> at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.endElement(UniprotConverter.java:479)
> at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
> at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
> at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
> at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
> at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
> at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
> at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
> at org.intermine.util.SAXParser.parse(SAXParser.java:59)
> at org.intermine.util.SAXParser.parse(SAXParser.java:42)
> at org.intermine.bio.dataconversion.UniprotConverter.processFiles(UniprotConverter.java:149)
> ... 33 more
>
>
>
>
>
>
>
>
>
>
>
>


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Re: UniProt Parser - Null pointer exception caused by uniprot_config.properties

Julie Sullivan
Hi Anthony,

Sorry you had a problem with UniProt, I am glad you found the fix!

I've updated the `organism_config.properties` file in Subversion so this is now
fixed for everyone.  I've also improved the error message so if this happens
again the cause will be a little more clear.

Thanks again,
Julie

On 07/26/2011 11:33 AM, Anthony C. Smith wrote:

> Hi,
>
> I figured it out. The taxon was missing from bio/core/main/resources/organism_config.properties.
>
> Thanks,
>
> Anthony
>
>
> On 25 Jul 2011, at 12:09, Anthony C. Smith wrote:
>
>> Hello,
>>
>> I've been helping James with the update to MitoMiner and I've have been having trouble with the trunk version of the UniProt source.
>>
>> I have a problem when setting which identifiers to use for genes, specifically with malaria (36329). After I set the uniprot_config.properties  (such as to ORF or primary) and integrate the uniprot source for malaria I get a null pointer exception when the first UniProt entry of the file is being read (see below). Other taxons work fine.
>>
>> If I use a test dataset from cow, which contains one entry, it works fine for cow. If I change the taxon id of the same datafile to mouse it also works fine. If I change it to malaria I get the null pointer. The entries in uniprot_config.properties are identical for all three taxons e.g:
>>
>> 9913.uniqueField = symbol
>> 9913.symbol.name = primary
>>
>> Therefore the datafile looks valid, but the malaria taxon itself appears to be causing the problem. Any ideas?
>>
>> Thanks,
>>
>> Anthony
>>
>> Dr Anthony C. Smith
>> Bioinformatics group
>> MRC Mitochondrial Biology Unit
>> Wellcome Trust / MRC Building
>> Hills Road, Cambridge, UK
>> CB2 0XY
>> www.mrc-mbu.cam.ac.uk/research/bioinformatics
>>
>>
>>
>> [integrate] java.lang.NullPointerException
>> [integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.resolveGene(UniprotConverter.java:1016)
>> [integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.createGene(UniprotConverter.java:888)
>> [integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processGene(UniprotConverter.java:860)
>> [integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processEntry(UniprotConverter.java:647)
>> [integrate] at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.endElement(UniprotConverter.java:479)
>> [integrate] at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
>> [integrate] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
>> [integrate] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
>> [integrate] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
>> [integrate] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
>> [integrate] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
>> [integrate] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
>> [integrate] at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
>> [integrate] at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
>> [integrate] at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
>> [integrate] at org.intermine.util.SAXParser.parse(SAXParser.java:59)
>> [integrate] at org.intermine.util.SAXParser.parse(SAXParser.java:42)
>> [integrate] at org.intermine.bio.dataconversion.UniprotConverter.processFiles(UniprotConverter.java:149)
>> [integrate] at org.intermine.bio.dataconversion.UniprotConverter.process(UniprotConverter.java:113)
>> [integrate] at org.intermine.task.DirectoryConverterTask.execute(DirectoryConverterTask.java:104)
>> [integrate] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>> [integrate] at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>> [integrate] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> [integrate] at java.lang.reflect.Method.invoke(Method.java:616)
>> [integrate] at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>> [integrate] at org.apache.tools.ant.Task.perform(Task.java:348)
>> [integrate] at org.apache.tools.ant.Target.execute(Target.java:390)
>> [integrate] at org.apache.tools.ant.Target.performTasks(Target.java:411)
>> [integrate] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
>> [integrate] at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>> [integrate] at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
>> [integrate] at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
>> [integrate] at org.intermine.task.Integrate.performAction(Integrate.java:223)
>> [integrate] at org.intermine.task.Integrate.performAction(Integrate.java:135)
>> [integrate] at org.intermine.task.Integrate.execute(Integrate.java:127)
>> [integrate] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>> [integrate] at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>> [integrate] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> [integrate] at java.lang.reflect.Method.invoke(Method.java:616)
>> [integrate] at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>> [integrate] at org.apache.tools.ant.Task.perform(Task.java:348)
>> [integrate] at org.apache.tools.ant.Target.execute(Target.java:390)
>> [integrate] at org.apache.tools.ant.Target.performTasks(Target.java:411)
>> [integrate] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
>> [integrate] at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
>> [integrate] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>> [integrate] at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
>> [integrate] at org.apache.tools.ant.Main.runBuild(Main.java:801)
>> [integrate] at org.apache.tools.ant.Main.startAnt(Main.java:218)
>> [integrate] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>> [integrate] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>      [null] Exiting /intermine/intermine_0_97/bio/sources/uniprot/build.xml.
>>
>> BUILD FAILED
>> /intermine/intermine_0_97/imbuild/integrate.xml:54: The following error occurred while executing this line:
>> /intermine/intermine_0_97/bio/sources/uniprot/build.xml:24: java.lang.RuntimeException: java.lang.NullPointerException
>> at org.intermine.bio.dataconversion.UniprotConverter.processFiles(UniprotConverter.java:152)
>> at org.intermine.bio.dataconversion.UniprotConverter.process(UniprotConverter.java:113)
>> at org.intermine.task.DirectoryConverterTask.execute(DirectoryConverterTask.java:104)
>> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> at java.lang.reflect.Method.invoke(Method.java:616)
>> 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:1360)
>> at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>> at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
>> at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
>> at org.intermine.task.Integrate.performAction(Integrate.java:223)
>> at org.intermine.task.Integrate.performAction(Integrate.java:135)
>> at org.intermine.task.Integrate.execute(Integrate.java:127)
>> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> at java.lang.reflect.Method.invoke(Method.java:616)
>> 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:1360)
>> at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
>> at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>> at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
>> at org.apache.tools.ant.Main.runBuild(Main.java:801)
>> at org.apache.tools.ant.Main.startAnt(Main.java:218)
>> 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.NullPointerException
>> at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.resolveGene(UniprotConverter.java:1016)
>> at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.createGene(UniprotConverter.java:888)
>> at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processGene(UniprotConverter.java:860)
>> at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processEntry(UniprotConverter.java:647)
>> at org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.endElement(UniprotConverter.java:479)
>> at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
>> at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
>> at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
>> at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
>> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
>> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
>> at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
>> at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
>> at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
>> at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
>> at org.intermine.util.SAXParser.parse(SAXParser.java:59)
>> at org.intermine.util.SAXParser.parse(SAXParser.java:42)
>> at org.intermine.bio.dataconversion.UniprotConverter.processFiles(UniprotConverter.java:149)
>> ... 33 more
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>
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