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From Andre Juffer <ajuf...@sun3.oulu.fi>
Subject Re: No inline metadata reader available for version 109
Date Tue, 25 Jan 2011 06:22:57 GMT
On 01/25/2011 04:50 AM, Natalia Shilenkova wrote:
> On Jan 24, 2011, at 12:27 PM, Andre Juffer wrote:
>
>> Due to an expected crash of a server, a few (3) entries in the XML database were
corrupted. All but one could be restored from backup, by deleting the affected entry and uploading
the entry from backup. In all these cases, the affected entry lost some data, causing XML
parsing errors.
>>
>> However, in one case, I receive the following error:
>>
>>   No inline metadata reader available for version 109
>>
>> This prevents me to read or write that entry in question. All actions cause the above
error message to appear. This is very unfortunate as XIndice has been extremely stable for
years now. For the backup, I also extract all entries into the separate location (in addition
to just copying the actual database), but now of course the extraction actually fails:
>>
>>
>> [WARN] XMLCompressedInput - -invalid node type : 5
>> [WARN] XMLCompressedInput - -invalid node type : 5
>> [WARN] ElementImpl - -ignored exception<java.io.EOFException>java.io.EOFException
>>         at java.io.DataInputStream.readShort(DataInputStream.java:298)
>>         at org.apache.xindice.xml.dom.ElementImpl.loadAttributes(ElementImpl.java:175)
>> .....
>> [WARN] ElementImpl - -ignored exception<java.lang.NullPointerException>java.lang.NullPointerException
>>         at org.apache.xindice.xml.dom.ElementImpl.loadAttributes(ElementImpl.java:184)
>> ...
>>
>> What would be the appropriate course of action to resolve this issue. Is there a
way to extract the binary file in another way (not XML-based) so that I manually delete the
affected entry.
>>
>> XIndice version: v1.1b5-dev
>>
>
> Andre,
>
> Are you trying to retrieve the corrupted document from the database or just delete it?
If it is the latter, then the simplest way, I think, is to create new empty collection and
load the existing documents.

Yes, I thought already that is probably the way to go. It will be 
cumbersome.
>
> Does the exception for XMLCompressedInput happen for the same collection and the same
corrupt document or for some unrelated backup collection?

The backup is fine. It was created before the crash. The entry in the db 
itself is corrupted. I manage to 'isolate' the corrupted entry such that 
users are not anymore affected.

>
> Regards,
> Natalia
>
>> --
>> Andre H. Juffer              | Phone: +358-8-553 1161
>> Biocenter Oulu and           | Fax: +358-8-553-1141
>> Department of Biochemistry   | Email: andre.juffer@oulu.fi
>> University of Oulu, Finland  | WWW: www.biochem.oulu.fi/Biocomputing/
>> StruBioCat                   | WWW: www.strubiocat.oulu.fi
>> NordProt                     | WWW: www.nordprot.org
>> Triacle Biocomputing         | WWW: www.triacle-bc.com
>
>


-- 
Andre H. Juffer              | Phone: +358-8-553 1161
Biocenter Oulu and           | Fax: +358-8-553-1141
Department of Biochemistry   | Email: andre.juffer@oulu.fi
University of Oulu, Finland  | WWW: www.biochem.oulu.fi/Biocomputing/
StruBioCat                   | WWW: www.strubiocat.oulu.fi
NordProt                     | WWW: www.nordprot.org
Triacle Biocomputing         | WWW: www.triacle-bc.com

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