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Posted to dev@flink.apache.org by Filip Łęczycki <fi...@gmail.com> on 2015/03/15 14:22:44 UTC
Flink - Avro - AvroTypeInfo issue - Index out of bounds exception
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
Re: Flink - Avro - AvroTypeInfo issue - Index out of bounds exception
Posted by Robert Metzger <rm...@apache.org>.
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 <rm...@apache.org> 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 <fi...@gmail.com>
> 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
>>
>
>
Re: Flink - Avro - AvroTypeInfo issue - Index out of bounds exception
Posted by Robert Metzger <rm...@apache.org>.
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 <fi...@gmail.com>
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
>