integration errors

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integration errors

James Blackshaw
Hi, I've been getting errors of "key not defined in
genomic_keyDefs.properties", even though in Intermine 0.92 and up it's
not necessary to define keys there, only in source file keydefs.
Deleting the old genomic.keydefs.properties doesn't solve this, and the
keys in question are defined in the sourcefile keydefs as:

CellularLocation.key_location=cellularLocation, evidenceType

Tissue.key_tissue=tissue

The fields tissue, cellularlocation and evidencetype are visible in the
database when I query it in psql. Any idea what's causing the errors?

-James

Error message is:
BUILD FAILED
/home/jab250/intermine_mass_copy/imbuild/integrate.xml:54: The following
error occurred while executing this line:
/home/jab250/intermine_mass_copy/imbuild/source.xml:201: Exception while
reading from: /data/datasets/mitominer/tissue/tissue.xml
     at
org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
     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.IllegalArgumentException: Primary key key_location
for class CellularLocation required by datasource ms_xml in
ms_xml_keys.properties is not defined in genomic_keyDefs.properties
     at
org.intermine.dataloader.DataLoaderHelper.getPrimaryKeys(DataLoaderHelper.java:148)
     at
org.intermine.dataloader.BaseEquivalentObjectFetcher.createPKQueriesForClass(BaseEquivalentObjectFetcher.java:285)
     at
org.intermine.dataloader.BaseEquivalentObjectFetcher.createPKQuery(BaseEquivalentObjectFetcher.java:238)
     at
org.intermine.dataloader.BaseEquivalentObjectFetcher.queryEquivalentObjects(BaseEquivalentObjectFetcher.java:195)
     at
org.intermine.dataloader.IntegrationWriterAbstractImpl.getEquivalentObjects(IntegrationWriterAbstractImpl.java:151)
     at
org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:257)
     at
org.intermine.dataloader.IntegrationWriterAbstractImpl.store(IntegrationWriterAbstractImpl.java:171)
     at
org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:80)
     at
org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
     ... 31 more



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Re: integration errors

Vallejos, Andrew
I was having problems like this with a different source.  Have you tried
entering in a garbage line into your source key_def file to see if the
file is being read properly?

-Andrew

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On
Behalf Of James Blackshaw
Sent: Monday, February 14, 2011 8:25 AM
To: Intermine
Subject: [InterMine Dev] integration errors

Hi, I've been getting errors of "key not defined in
genomic_keyDefs.properties", even though in Intermine 0.92 and up it's
not necessary to define keys there, only in source file keydefs.
Deleting the old genomic.keydefs.properties doesn't solve this, and the
keys in question are defined in the sourcefile keydefs as:

CellularLocation.key_location=cellularLocation, evidenceType

Tissue.key_tissue=tissue

The fields tissue, cellularlocation and evidencetype are visible in the
database when I query it in psql. Any idea what's causing the errors?

-James

Error message is:
BUILD FAILED
/home/jab250/intermine_mass_copy/imbuild/integrate.xml:54: The following

error occurred while executing this line:
/home/jab250/intermine_mass_copy/imbuild/source.xml:201: Exception while

reading from: /data/datasets/mitominer/tissue/tissue.xml
     at
org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.jav
a:170)
     at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
     at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:43)
     at java.lang.reflect.Method.invoke(Method.java:616)
     at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
06)
     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(SingleChe
ckExecutor.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(DelegatingMethodAccessor
Impl.java:43)
     at java.lang.reflect.Method.invoke(Method.java:616)
     at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
06)
     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(DefaultExecut
or.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.IllegalArgumentException: Primary key key_location
for class CellularLocation required by datasource ms_xml in
ms_xml_keys.properties is not defined in genomic_keyDefs.properties
     at
org.intermine.dataloader.DataLoaderHelper.getPrimaryKeys(DataLoaderHelpe
r.java:148)
     at
org.intermine.dataloader.BaseEquivalentObjectFetcher.createPKQueriesForC
lass(BaseEquivalentObjectFetcher.java:285)
     at
org.intermine.dataloader.BaseEquivalentObjectFetcher.createPKQuery(BaseE
quivalentObjectFetcher.java:238)
     at
org.intermine.dataloader.BaseEquivalentObjectFetcher.queryEquivalentObje
cts(BaseEquivalentObjectFetcher.java:195)
     at
org.intermine.dataloader.IntegrationWriterAbstractImpl.getEquivalentObje
cts(IntegrationWriterAbstractImpl.java:151)
     at
org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(Integra
tionWriterDataTrackingImpl.java:257)
     at
org.intermine.dataloader.IntegrationWriterAbstractImpl.store(Integration
WriterAbstractImpl.java:171)
     at
org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:80)
     at
org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.jav
a:160)
     ... 31 more



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Re: integration errors

Richard Smith
Hi James,
As Andrew suggests it may be that it isn't actually reading the keys
file you expect.  The rules for reading keys are:

<source name="my-source-name" type="my-source">
   ...

1. look for a file called my-source-name.properties
2. look for a file called my-source.properties (the type)

And:

1. look first in MINE/integrate/resources/
2. then look in bio/source/my-source/resources

Is there another file that is shadowing the one you edited?

Cheers,
Richard.



On 14/02/2011 17:58, Vallejos, Andrew wrote:

> I was having problems like this with a different source.  Have you tried
> entering in a garbage line into your source key_def file to see if the
> file is being read properly?
>
> -Andrew
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On
> Behalf Of James Blackshaw
> Sent: Monday, February 14, 2011 8:25 AM
> To: Intermine
> Subject: [InterMine Dev] integration errors
>
> Hi, I've been getting errors of "key not defined in
> genomic_keyDefs.properties", even though in Intermine 0.92 and up it's
> not necessary to define keys there, only in source file keydefs.
> Deleting the old genomic.keydefs.properties doesn't solve this, and the
> keys in question are defined in the sourcefile keydefs as:
>
> CellularLocation.key_location=cellularLocation, evidenceType
>
> Tissue.key_tissue=tissue
>
> The fields tissue, cellularlocation and evidencetype are visible in the
> database when I query it in psql. Any idea what's causing the errors?
>
> -James
>
> Error message is:
> BUILD FAILED
> /home/jab250/intermine_mass_copy/imbuild/integrate.xml:54: The following
>
> error occurred while executing this line:
> /home/jab250/intermine_mass_copy/imbuild/source.xml:201: Exception while
>
> reading from: /data/datasets/mitominer/tissue/tissue.xml
>       at
> org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.jav
> a:170)
>       at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>       at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:43)
>       at java.lang.reflect.Method.invoke(Method.java:616)
>       at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 06)
>       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(SingleChe
> ckExecutor.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(DelegatingMethodAccessor
> Impl.java:43)
>       at java.lang.reflect.Method.invoke(Method.java:616)
>       at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 06)
>       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(DefaultExecut
> or.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.IllegalArgumentException: Primary key key_location
> for class CellularLocation required by datasource ms_xml in
> ms_xml_keys.properties is not defined in genomic_keyDefs.properties
>       at
> org.intermine.dataloader.DataLoaderHelper.getPrimaryKeys(DataLoaderHelpe
> r.java:148)
>       at
> org.intermine.dataloader.BaseEquivalentObjectFetcher.createPKQueriesForC
> lass(BaseEquivalentObjectFetcher.java:285)
>       at
> org.intermine.dataloader.BaseEquivalentObjectFetcher.createPKQuery(BaseE
> quivalentObjectFetcher.java:238)
>       at
> org.intermine.dataloader.BaseEquivalentObjectFetcher.queryEquivalentObje
> cts(BaseEquivalentObjectFetcher.java:195)
>       at
> org.intermine.dataloader.IntegrationWriterAbstractImpl.getEquivalentObje
> cts(IntegrationWriterAbstractImpl.java:151)
>       at
> org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(Integra
> tionWriterDataTrackingImpl.java:257)
>       at
> org.intermine.dataloader.IntegrationWriterAbstractImpl.store(Integration
> WriterAbstractImpl.java:171)
>       at
> org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:80)
>       at
> org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.jav
> a:160)
>       ... 31 more
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>


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