Problem loading uniprot source

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Problem loading uniprot source

James Blackshaw-2
Hi,
I'm having trouble loading any data from Saccharomyces pombe into
Mitominer. Uniprot entries for other organisms work fine. We've tried
changing '284812.primaryIdentifier.dbref = GeneDB_Spombe' to reference
ORF and EnsemblFungi as unique identifiers instead, but that's not
helped. Any idea what's the problem with this organism specifically?

Regards,
James



Terminal output:
======================================================================

do-compile:
      [copy] No sources found.
      [copy]  omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/build/classes is up
to date.
      [copy] org omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/build/classes/org is
up to date.
      [copy] org/intermine omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/build/classes/org/intermine
is up to date.
      [copy] org/intermine/bio omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/build/classes/org/intermine/bio
is up to date.
      [copy] org/intermine/bio/dataconversion omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/build/classes/org/intermine/bio/dataconversion
is up to date.

-post-compile:

compile:

-init-jar:
     [mkdir] Skipping
/intermine/intermine_0_97/bio/sources/uniprot/main/dist because it
already exists.

-pre-jar:

-init-presetdef-jar:
[presetdef] defining preset http://www.intermine.org/ns/im-lib-proj/1:jar

do-jar:
   [lib:jar]
org/intermine/bio/dataconversion/UniprotConfig$ConfigEntry.class omitted
as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotConfig$ConfigEntry.class
is up to date.
   [lib:jar]
org/intermine/bio/dataconversion/UniprotConfig$IdentifierConfig.class
omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotConfig$IdentifierConfig.class
is up to date.
   [lib:jar] org/intermine/bio/dataconversion/UniprotConfig.class
omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotConfig.class
is up to date.
   [lib:jar] org/intermine/bio/dataconversion/UniprotConverter$1.class
omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotConverter$1.class
is up to date.
   [lib:jar]
org/intermine/bio/dataconversion/UniprotConverter$UniprotHandler.class
omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotConverter$UniprotHandler.class
is up to date.
   [lib:jar] org/intermine/bio/dataconversion/UniprotConverter.class
omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotConverter.class
is up to date.
   [lib:jar] org/intermine/bio/dataconversion/UniprotConverter.java.zip
omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotConverter.java.zip
is up to date.
   [lib:jar] org/intermine/bio/dataconversion/UniprotEntry$Comment.class
omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotEntry$Comment.class
is up to date.
   [lib:jar] org/intermine/bio/dataconversion/UniprotEntry$Dbref.class
omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotEntry$Dbref.class
is up to date.
   [lib:jar] org/intermine/bio/dataconversion/UniprotEntry.class omitted
as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotEntry.class
is up to date.
   [lib:jar] org/intermine/bio/dataconversion/UniprotFilterTask.class
omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotFilterTask.class
is up to date.
   [lib:jar] org/intermine/bio/dataconversion/UniprotXmlFilter.class
omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotXmlFilter.class
is up to date.
   [lib:jar] org omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/
is up to date.
   [lib:jar] org/intermine omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/
is up to date.
   [lib:jar] org/intermine/bio omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/
is up to date.
   [lib:jar] org/intermine/bio/dataconversion omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/
is up to date.
   [lib:jar] uniprot_config.properties omitted as
/intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:uniprot_config.properties
is up to date.
   [lib:jar] No sources found.
   [lib:jar] No Implementation-Title set.No Implementation-Version
set.No Implementation-Vendor set.
   [lib:jar] Location: /intermine/intermine_0_97/imbuild/library.xml:142:

-post-jar:

jar:
      [null] Exiting
/intermine/intermine_0_97/bio/sources/uniprot/main/build.xml.

-define-task-classpath:

-check-task-availability:
[available] Unable to load resource
org/intermine/web/task/antlib-web.xml to set property antlib-web-available

-load-os-tasks:
      [echo] Loading objectstore tasks
parsing buildfile
jar:file:/intermine/intermine_0_97/intermine/objectstore/main/dist/intermine-objectstore.jar!/org/intermine/task/antlib-os.xml
with URI =
jar:file:/intermine/intermine_0_97/intermine/objectstore/main/dist/intermine-objectstore.jar!/org/intermine/task/antlib-os.xml
from a zip file
Trying to override old definition of task acceptance-tests
Trying to override old definition of task build-torque
Trying to override old definition of task build-db
Trying to override old definition of task db-insert-model
Trying to override old definition of task analyse-db
Trying to override old definition of task retrieve-metadata
Trying to override old definition of task model-output

-load-int-tasks:
      [echo] Loading integration tasks
parsing buildfile
jar:file:/intermine/intermine_0_97/intermine/integrate/main/dist/intermine-integrate.jar!/org/intermine/task/antlib-int.xml
with URI =
jar:file:/intermine/intermine_0_97/intermine/integrate/main/dist/intermine-integrate.jar!/org/intermine/task/antlib-int.xml
from a zip file
Trying to override old definition of task create-indexes
Trying to override old definition of task convert-file
Trying to override old definition of task convert-dir
Trying to override old definition of task convert-db
Trying to override old definition of task precompute-queries
Trying to override old definition of task summarise-objectstore
Trying to override old definition of task drop-precomputed-tables
Trying to override old definition of task insert-xml-data
Trying to override old definition of task model-merger
Trying to override old definition of task convert-fullxml-file
Trying to override old definition of task data-load
Trying to override old definition of task method-call
Trying to override old definition of task postprocessor

-load-web-tasks:
Skipped because property 'antlib-web-available' not set.

-load-task-taskdefs:

-init-macrodef-build-db:
  [macrodef] creating macro  
http://www.intermine.org/ns/im-task-proj/1:build-db

-init-task-xml:

-init-deps:
      [copy] uniprot-human_keys.properties omitted as
/intermine/intermine_0_97/bio/sources/uniprot/build/main/uniprot-human_keys.properties
is up to date.
      [copy] uniprot_keys.properties omitted as
/intermine/intermine_0_97/bio/sources/uniprot/build/main/uniprot_keys.properties
is up to date.
      [copy]  added as  is outdated.

-init-legacy-dag-properties:
Skipped because property 'have.file.dag' not set.

-init-legacy-properties:

-init-flags:
Property "have.file.custom.direct" has not been set
Property "have.file.custom.direct" has not been set

build-db-tgt-items:
[integrate] Our new url -> jdbc:postgresql://localhost/items-mitominer-test
[integrate] Our new url -> jdbc:postgresql://localhost/items-mitominer-test

-pre-retrieve:
Skipped because property 'use.filter' not set.

-set-custom-file-includes:

-set-custom-file-excludes:

-retrieve-tgt-from-custom-file:
Skipped because property 'have.file.custom.tgt' not set.

-retrieve-tgt-from-db:
Skipped because property 'have.db.tgt' not set.

-set-gff-seq-handler:

-retrieve-from-gff3:
Skipped because property 'have.file.gff3' not set.

-retrieve-from-obo:
Skipped because property 'have.file.obo' not set.

-set-xml-tgt-file-includes:
Skipped because property 'src.data.dir.includes' set.

-set-xml-tgt-file:

-retrieve-tgt-from-xml-file:
Skipped because property 'have.file.xml.tgt' not set.

-retrieve-tgt-from-large-xml-file:
Skipped because property 'have.large.file.xml.tgt' not set.

-retrieve-tgt-from-custom-dir-filtered:
Skipped because property 'use.filter' not set.

-retrieve-tgt-from-custom-dir-whole:
[integrate] Processing file:
/intermine/processedData/uniprot/test/284812_uniprot_sprot.xml
[integrate] <<<<KEGGECE2QC18
[integrate] <<<<KEGGEC[]
[integrate] Processing file:
/intermine/processedData/uniprot/test/284812_uniprot_trembl.xml
[integrate] <<<<KEGGECC6Y4A3
[integrate] <<<<KEGGEC[]
[integrate] java.lang.NullPointerException
[integrate]     at
org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.resolveGene(UniprotConverter.java:1027)
[integrate]     at
org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.createGene(UniprotConverter.java:899)
[integrate]     at
org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processGene(UniprotConverter.java:871)
[integrate]     at
org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processEntry(UniprotConverter.java:657)
[integrate]     at
org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.endElement(UniprotConverter.java:480)
[integrate]     at
org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
[integrate]     at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown
Source)
[integrate]     at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$UniprotHandler.resolveGene(UniprotConverter.java:1027)
     at
org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.createGene(UniprotConverter.java:899)
     at
org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processGene(UniprotConverter.java:871)
     at
org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processEntry(UniprotConverter.java:657)
     at
org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.endElement(UniprotConverter.java:480)
     at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown
Source)
     at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown
Source)
     at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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

Total time: 29 seconds

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project.xml (6K) Download Attachment
uniprot_config.properties (5K) Download Attachment
184922_uniprot_sprot.xml (137K) Download Attachment
284812_uniprot_sprot.xml (5K) Download Attachment
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Re: Problem loading uniprot source

Julie Sullivan

Hi James,

"284812_uniprot_sprot.xml" has one entry for Baker's yeast and it doesn't
have any genes.  Did you send me the file you used?  I'm guessing not as
both files loaded without error for me.

Also, the error message doesn't line up with what I have in my code:

org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.resolveGene(UniprotConverter.java:1027)

The resolveGene() method is on line 985 not 1027:

http://intermine.org/browser/branches/intermine_0_97/bio/sources/uniprot/main/src/org/intermine/bio/dataconversion/UniprotConverter.java

Can you tell me what is on line 1027?  I guess it's trying to resolve
identifiers for fly?  If so, we just might need a NULL check for
"flyResolverFactory".

Thanks
Julie

> Hi,
> I'm having trouble loading any data from Saccharomyces pombe into
> Mitominer. Uniprot entries for other organisms work fine. We've tried
> changing '284812.primaryIdentifier.dbref = GeneDB_Spombe' to reference
> ORF and EnsemblFungi as unique identifiers instead, but that's not
> helped. Any idea what's the problem with this organism specifically?
>
> Regards,
> James
>
>
>
> Terminal output:
> ======================================================================
>
> do-compile:
>       [copy] No sources found.
>       [copy]  omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/build/classes is up
> to date.
>       [copy] org omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/build/classes/org is
> up to date.
>       [copy] org/intermine omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/build/classes/org/intermine
> is up to date.
>       [copy] org/intermine/bio omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/build/classes/org/intermine/bio
> is up to date.
>       [copy] org/intermine/bio/dataconversion omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/build/classes/org/intermine/bio/dataconversion
> is up to date.
>
> -post-compile:
>
> compile:
>
> -init-jar:
>      [mkdir] Skipping
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist because it
> already exists.
>
> -pre-jar:
>
> -init-presetdef-jar:
> [presetdef] defining preset http://www.intermine.org/ns/im-lib-proj/1:jar
>
> do-jar:
>    [lib:jar]
> org/intermine/bio/dataconversion/UniprotConfig$ConfigEntry.class omitted
> as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotConfig$ConfigEntry.class
> is up to date.
>    [lib:jar]
> org/intermine/bio/dataconversion/UniprotConfig$IdentifierConfig.class
> omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotConfig$IdentifierConfig.class
> is up to date.
>    [lib:jar] org/intermine/bio/dataconversion/UniprotConfig.class
> omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotConfig.class
> is up to date.
>    [lib:jar] org/intermine/bio/dataconversion/UniprotConverter$1.class
> omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotConverter$1.class
> is up to date.
>    [lib:jar]
> org/intermine/bio/dataconversion/UniprotConverter$UniprotHandler.class
> omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotConverter$UniprotHandler.class
> is up to date.
>    [lib:jar] org/intermine/bio/dataconversion/UniprotConverter.class
> omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotConverter.class
> is up to date.
>    [lib:jar] org/intermine/bio/dataconversion/UniprotConverter.java.zip
> omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotConverter.java.zip
> is up to date.
>    [lib:jar] org/intermine/bio/dataconversion/UniprotEntry$Comment.class
> omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotEntry$Comment.class
> is up to date.
>    [lib:jar] org/intermine/bio/dataconversion/UniprotEntry$Dbref.class
> omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotEntry$Dbref.class
> is up to date.
>    [lib:jar] org/intermine/bio/dataconversion/UniprotEntry.class omitted
> as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotEntry.class
> is up to date.
>    [lib:jar] org/intermine/bio/dataconversion/UniprotFilterTask.class
> omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotFilterTask.class
> is up to date.
>    [lib:jar] org/intermine/bio/dataconversion/UniprotXmlFilter.class
> omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/UniprotXmlFilter.class
> is up to date.
>    [lib:jar] org omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/
> is up to date.
>    [lib:jar] org/intermine omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/
> is up to date.
>    [lib:jar] org/intermine/bio omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/
> is up to date.
>    [lib:jar] org/intermine/bio/dataconversion omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:org/intermine/bio/dataconversion/
> is up to date.
>    [lib:jar] uniprot_config.properties omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/main/dist/uniprot-tasks.jar:uniprot_config.properties
> is up to date.
>    [lib:jar] No sources found.
>    [lib:jar] No Implementation-Title set.No Implementation-Version
> set.No Implementation-Vendor set.
>    [lib:jar] Location: /intermine/intermine_0_97/imbuild/library.xml:142:
>
> -post-jar:
>
> jar:
>       [null] Exiting
> /intermine/intermine_0_97/bio/sources/uniprot/main/build.xml.
>
> -define-task-classpath:
>
> -check-task-availability:
> [available] Unable to load resource
> org/intermine/web/task/antlib-web.xml to set property antlib-web-available
>
> -load-os-tasks:
>       [echo] Loading objectstore tasks
> parsing buildfile
> jar:file:/intermine/intermine_0_97/intermine/objectstore/main/dist/intermine-objectstore.jar!/org/intermine/task/antlib-os.xml
> with URI =
> jar:file:/intermine/intermine_0_97/intermine/objectstore/main/dist/intermine-objectstore.jar!/org/intermine/task/antlib-os.xml
> from a zip file
> Trying to override old definition of task acceptance-tests
> Trying to override old definition of task build-torque
> Trying to override old definition of task build-db
> Trying to override old definition of task db-insert-model
> Trying to override old definition of task analyse-db
> Trying to override old definition of task retrieve-metadata
> Trying to override old definition of task model-output
>
> -load-int-tasks:
>       [echo] Loading integration tasks
> parsing buildfile
> jar:file:/intermine/intermine_0_97/intermine/integrate/main/dist/intermine-integrate.jar!/org/intermine/task/antlib-int.xml
> with URI =
> jar:file:/intermine/intermine_0_97/intermine/integrate/main/dist/intermine-integrate.jar!/org/intermine/task/antlib-int.xml
> from a zip file
> Trying to override old definition of task create-indexes
> Trying to override old definition of task convert-file
> Trying to override old definition of task convert-dir
> Trying to override old definition of task convert-db
> Trying to override old definition of task precompute-queries
> Trying to override old definition of task summarise-objectstore
> Trying to override old definition of task drop-precomputed-tables
> Trying to override old definition of task insert-xml-data
> Trying to override old definition of task model-merger
> Trying to override old definition of task convert-fullxml-file
> Trying to override old definition of task data-load
> Trying to override old definition of task method-call
> Trying to override old definition of task postprocessor
>
> -load-web-tasks:
> Skipped because property 'antlib-web-available' not set.
>
> -load-task-taskdefs:
>
> -init-macrodef-build-db:
>   [macrodef] creating macro
> http://www.intermine.org/ns/im-task-proj/1:build-db
>
> -init-task-xml:
>
> -init-deps:
>       [copy] uniprot-human_keys.properties omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/build/main/uniprot-human_keys.properties
> is up to date.
>       [copy] uniprot_keys.properties omitted as
> /intermine/intermine_0_97/bio/sources/uniprot/build/main/uniprot_keys.properties
> is up to date.
>       [copy]  added as  is outdated.
>
> -init-legacy-dag-properties:
> Skipped because property 'have.file.dag' not set.
>
> -init-legacy-properties:
>
> -init-flags:
> Property "have.file.custom.direct" has not been set
> Property "have.file.custom.direct" has not been set
>
> build-db-tgt-items:
> [integrate] Our new url ->
> jdbc:postgresql://localhost/items-mitominer-test
> [integrate] Our new url ->
> jdbc:postgresql://localhost/items-mitominer-test
>
> -pre-retrieve:
> Skipped because property 'use.filter' not set.
>
> -set-custom-file-includes:
>
> -set-custom-file-excludes:
>
> -retrieve-tgt-from-custom-file:
> Skipped because property 'have.file.custom.tgt' not set.
>
> -retrieve-tgt-from-db:
> Skipped because property 'have.db.tgt' not set.
>
> -set-gff-seq-handler:
>
> -retrieve-from-gff3:
> Skipped because property 'have.file.gff3' not set.
>
> -retrieve-from-obo:
> Skipped because property 'have.file.obo' not set.
>
> -set-xml-tgt-file-includes:
> Skipped because property 'src.data.dir.includes' set.
>
> -set-xml-tgt-file:
>
> -retrieve-tgt-from-xml-file:
> Skipped because property 'have.file.xml.tgt' not set.
>
> -retrieve-tgt-from-large-xml-file:
> Skipped because property 'have.large.file.xml.tgt' not set.
>
> -retrieve-tgt-from-custom-dir-filtered:
> Skipped because property 'use.filter' not set.
>
> -retrieve-tgt-from-custom-dir-whole:
> [integrate] Processing file:
> /intermine/processedData/uniprot/test/284812_uniprot_sprot.xml
> [integrate] <<<<KEGGECE2QC18
> [integrate] <<<<KEGGEC[]
> [integrate] Processing file:
> /intermine/processedData/uniprot/test/284812_uniprot_trembl.xml
> [integrate] <<<<KEGGECC6Y4A3
> [integrate] <<<<KEGGEC[]
> [integrate] java.lang.NullPointerException
> [integrate]     at
> org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.resolveGene(UniprotConverter.java:1027)
> [integrate]     at
> org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.createGene(UniprotConverter.java:899)
> [integrate]     at
> org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processGene(UniprotConverter.java:871)
> [integrate]     at
> org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processEntry(UniprotConverter.java:657)
> [integrate]     at
> org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.endElement(UniprotConverter.java:480)
> [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$UniprotHandler.resolveGene(UniprotConverter.java:1027)
>      at
> org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.createGene(UniprotConverter.java:899)
>      at
> org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processGene(UniprotConverter.java:871)
>      at
> org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.processEntry(UniprotConverter.java:657)
>      at
> org.intermine.bio.dataconversion.UniprotConverter$UniprotHandler.endElement(UniprotConverter.java:480)
>      at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown
> Source)
>      at
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown
> Source)
>      at
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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
>
> Total time: 29 seconds
> _______________________________________________
> dev mailing list
> [hidden email]
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>


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