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

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?

[Robert Metzger]

Hi Filip,

thank you for reporting the issue. Its an issue with the AvroTypeInfo. I've
pushed a fix to the "master" branch.
If you want, you can port your program to 0.9-SNAPSHOT, there, the issue
should be fixed.

I'll also push a fix to the "release-0.8" branch if you want to keep using
the 0.8 series of Flink.

Sorry for the inconvenience.
Please let us know if you need more help getting your Flink program to work.

Best,
Robert

On Sun, Mar 15, 2015 at 2:22 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
>

[Robert Metzger]

I've just pushed a fix to my "release-0.8" branch.
If you want, you can build the version with the fix yourself:

git clone https://github.com/rmetzger/flink.git
cd flink
git checkout release-0.8
mvn clean install -DskipTests

Once that has finished, you can set the version in your pom.xml to
"0.8-SNAPSHOT" and the issues should be resolved.

I'll merge the fix to the official "release-0.8" branch at Apache once the
integration tests succeeded.


Robert


On Sun, Mar 15, 2015 at 4:56 PM, Robert Metzger <[hidden email]> wrote:

> Hi Filip,
>
> thank you for reporting the issue. Its an issue with the AvroTypeInfo.
> I've pushed a fix to the "master" branch.
> If you want, you can port your program to 0.9-SNAPSHOT, there, the issue
> should be fixed.
>
> I'll also push a fix to the "release-0.8" branch if you want to keep using
> the 0.8 series of Flink.
>
> Sorry for the inconvenience.
> Please let us know if you need more help getting your Flink program to
> work.
>
> Best,
> Robert
>
> On Sun, Mar 15, 2015 at 2:22 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
>>
>
>