[Biojava-l] Question about xml results

[Mark Fortner]

Also, double-check the encoding you're using, and the encoding returned
from the method.  The message that goes with that Oracle exception is:
ORA-29532
- java call terminated by uncaught java exception. Which suggests that the
underlying exception hasn't been caught.  Try adding some code around your
persistence call and see if you can trap the underlying exception.  It may
give you more insight into the problem.

Cheers,

Mark



On Fri, Aug 9, 2013 at 1:13 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:

> Maybe try an oracle mailing list, since it's a SQLException (although the
> polish error message doesn't help me).
>
> My only advice is to separate out the potential problems:
> 1) Serialize the AFPChain to a string, and make sure that looks right and
> doesn't raise exceptions
> 2) Make sure that you can store strings to your clob column.
>
> The first part should work fine in BioJava, so I'm guessing it's a problem
> with the second part. From your past emails I feel that a careful read
> through the Oracle manual might be worth your time.
>
> -Spencer
>
>
> On Wed, Aug 7, 2013 at 5:14 AM, Radomir Adamek
> <radomir.adamek at hotmail.com>wrote:
>
> > Hi, i changed return type to clob and that didn`t resolve my problem. I`m
> > getting new exception:
> >
> > SQL Error: ORA-29532: wywołanie Javy zatrzymane przez nieprzechwycony
> > wyjątek Javy: java.sql.SQLException: Nie udało się przekształcić w
> > reprezentację wewnętrzną: <AFPChain name1="1a1d" name2="1a06"
> > method="jFatCat_rigid" version="1.0" alnLength="172" blockNum="1"
> > gapLen="107" optLength="65" totalLenIni="48" alignScore="41,53"
> > chainRmsd="12,23" identity="0,0465" normAlignScore="-0,72"
> > probability="8.94e-01" similarity="0,0988" similarity1="45"
> > similarity2="23" totalRmsdIni="12,23" totalRmsdOpt="5,57" ca1Length="146"
> > ca2Length="279" afpNum="10778" alignScoreUpdate="41,00" time="16185">
> >   <block blockNr="0" blockSize="6" blockScore="41,53" blockRmsd="12,23"
> > blockGap="60">
> >     <eqr eqrNr="0" pdbres1="10" chain1="A" pdbres2="29" chain2="A" />
> >     <eqr eqrNr="1" pdbres1="11" chain1="A" pdbres2="30" chain2="A" />
> >     <eqr eqrNr="2" pdbres1="12" chain1="A" pdbres2="31" chain2="A" />
> >     <eqr eqrNr="3" pdbres1="13" chain1="A" pdbres2="32" chain2="A" />
> >     <eqr eqrNr="4" pdbres1="14" chain1="A" pdbres2="33" chain2="A" />
> >     <eqr eqrNr="5" pdbres1="27" chain1="
> > ORA-06512: przy "SYSTEM.FATCAT_PROCEDURE", linia 1
> >
> > Maybe someone have similar problem with writing xml result to oracle clob
> > column??
> >
> > ------------------------------
> > From: sbliven at ucsd.edu
> > Date: Thu, 1 Aug 2013 17:05:14 -0700
> > Subject: Re: [Biojava-l] Question about xml results
> > To: andreas at sdsc.edu
> > CC: radomir.adamek at hotmail.com; biojava-l at lists.open-bio.org
> >
> >
> > How many characters did you specify for your VARCHAR2 column? XML can be
> a
> > bit verbose, and it's possible that it simply won't fit in the column. In
> > that case you can use a CLOB column instead.
> >
> >
> >
> > On Mon, Jul 29, 2013 at 1:19 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> >
> > Can you give us some code snippets to comment on?
> >
> > Andreas
> >
> >
> > On Mon, Jul 29, 2013 at 12:00 AM, Radomir Adamek <
> > radomir.adamek at hotmail.com
> > > wrote:
> >
> > > Hi, i have a problem with method AFPChainXMLConverter.toXML. I found
> that
> > > method is returning string. I`m trying to save that XML string in
> Oracle
> > > database as varchar2 column and i`m getting error with inconsistent
> > > datatype. Could someone help me or explain what i`m doing wrong? Best
> > > regards,Radomir
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> >
>
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