Flink - Avro - AvroTypeInfo issue - Index out of bounds exception

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Flink - Avro - AvroTypeInfo issue - Index out of bounds exception

Filip Łęczycki
Hi

I have an issue while running the following line while usig flink v 0.8.1 (:
    val asdf = new AvroTypeInfo[AlignmentRecord](classOf[AlignmentRecord])

Alignment record belongs to the package :
org.bdgenomics.formats.avro.AlignmentRecord

While trying to run I am receivng following exception:

Exception in thread "main" java.lang.IndexOutOfBoundsException
at org.apache.flink.api.java.typeutils.PojoTypeInfo.getPojoFieldAt(PojoTypeInfo.java:178)
at org.apache.flink.api.java.typeutils.AvroTypeInfo.generateFieldsFromAvroSchema(AvroTypeInfo.java:52)
at org.apache.flink.api.java.typeutils.AvroTypeInfo.<init>(AvroTypeInfo.java:38)
at flinkTest.FlinkBAMReader$.main(FlinkBAMReader.scala:74)

While debugging I have noticed that the generated AvroTypeInfo class has a fields array with 42 elements, while the totalFIelds property has value 52 (please find screenshot attached) which seems to be the cause of the exception. Could you please help me o determine what may be the issue with the parser? Is this some bug in AvroTypeInfo class or the AlignmentRecord class is somehow corrupted?

Best Regards/Pozdrawiam,
Filip Łęczycki

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Re: Flink - Avro - AvroTypeInfo issue - Index out of bounds exception

Stephan Ewen
Hi!

Thanks you for reporting this.

The Apache mailing lists do not support attachments, unfortunately. To help
us fix this, can you upload the attachment (screenshot) somewhere and post
a link here?

Thanks,
Stephan


On Mon, Apr 13, 2015 at 6:25 PM, Filip Łęczycki <[hidden email]>
wrote:

> Hi
>
> I have an issue while running the following line while usig flink v 0.8.1
> (:
>     val asdf = new AvroTypeInfo[AlignmentRecord](classOf[AlignmentRecord])
>
> Alignment record belongs to the package :
> org.bdgenomics.formats.avro.AlignmentRecord
>
> http://mvnrepository.com/artifact/org.bdgenomics.bdg-formats/bdg-formats/0.4.0
>
> While trying to run I am receivng following exception:
>
> Exception in thread "main" java.lang.IndexOutOfBoundsException
> at
> org.apache.flink.api.java.typeutils.PojoTypeInfo.getPojoFieldAt(PojoTypeInfo.java:178)
> at
> org.apache.flink.api.java.typeutils.AvroTypeInfo.generateFieldsFromAvroSchema(AvroTypeInfo.java:52)
> at
> org.apache.flink.api.java.typeutils.AvroTypeInfo.<init>(AvroTypeInfo.java:38)
> at flinkTest.FlinkBAMReader$.main(FlinkBAMReader.scala:74)
>
> While debugging I have noticed that the generated AvroTypeInfo class has a
> fields array with 42 elements, while the totalFIelds property has value 52
> (please find screenshot attached) which seems to be the cause of the
> exception. Could you please help me o determine what may be the issue with
> the parser? Is this some bug in AvroTypeInfo class or the AlignmentRecord
> class is somehow corrupted?
>
> Best Regards/Pozdrawiam,
> Filip Łęczycki
>
>
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Re: Flink - Avro - AvroTypeInfo issue - Index out of bounds exception

Robert Metzger
Hi,

no need to supply us with the code. Its a known issue that has been fixed
in 0.9-milestone1.
If you can easily upgrade to 0.9-milestone1, that's the way to go.

Otherwise, you can set the version in your poms to 0.8-SNAPSHOT and you
should get a version with the fix (through Apache's Snapshot repository).

On Mon, Apr 13, 2015 at 6:28 PM, Stephan Ewen <[hidden email]> wrote:

> Hi!
>
> Thanks you for reporting this.
>
> The Apache mailing lists do not support attachments, unfortunately. To help
> us fix this, can you upload the attachment (screenshot) somewhere and post
> a link here?
>
> Thanks,
> Stephan
>
>
> On Mon, Apr 13, 2015 at 6:25 PM, Filip Łęczycki <[hidden email]>
> wrote:
>
> > Hi
> >
> > I have an issue while running the following line while usig flink v 0.8.1
> > (:
> >     val asdf = new
> AvroTypeInfo[AlignmentRecord](classOf[AlignmentRecord])
> >
> > Alignment record belongs to the package :
> > org.bdgenomics.formats.avro.AlignmentRecord
> >
> >
> http://mvnrepository.com/artifact/org.bdgenomics.bdg-formats/bdg-formats/0.4.0
> >
> > While trying to run I am receivng following exception:
> >
> > Exception in thread "main" java.lang.IndexOutOfBoundsException
> > at
> >
> org.apache.flink.api.java.typeutils.PojoTypeInfo.getPojoFieldAt(PojoTypeInfo.java:178)
> > at
> >
> org.apache.flink.api.java.typeutils.AvroTypeInfo.generateFieldsFromAvroSchema(AvroTypeInfo.java:52)
> > at
> >
> org.apache.flink.api.java.typeutils.AvroTypeInfo.<init>(AvroTypeInfo.java:38)
> > at flinkTest.FlinkBAMReader$.main(FlinkBAMReader.scala:74)
> >
> > While debugging I have noticed that the generated AvroTypeInfo class has
> a
> > fields array with 42 elements, while the totalFIelds property has value
> 52
> > (please find screenshot attached) which seems to be the cause of the
> > exception. Could you please help me o determine what may be the issue
> with
> > the parser? Is this some bug in AvroTypeInfo class or the AlignmentRecord
> > class is somehow corrupted?
> >
> > Best Regards/Pozdrawiam,
> > Filip Łęczycki
> >
> >
>