[Biojava-l] Question about xml results

[Radomir Adamek]

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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