Hello,
we have a problem with the connection to a BioSQL Database.
When we start our application for the very first time and try to connect
to the Database, it throws an SQLException "Connection is closed."
After that, when we simply repeat the process, everything works fine and
one can store S
day and now the
database-update works fine.
Greetings,
Felix
--
Felix Dreher
Max-Planck-Institute for Infection Biology
Campus Charité Mitte
Department of Immunology
Mailing address: Schumannstraße 21/22
Visitors: Virchowweg 12
10117 Berlin
Germany
Tel.: +49 (0)30 28460-254 / -494
Mobile: +49
SecurityUtil.execute(SecurityUtil.java:282)
org.apache.catalina.security.SecurityUtil.doAsPrivilege(SecurityUtil.java:165)
java.security.AccessController.doPrivileged(Native Method)
com.sun.web.ui.util.UploadFilter.doFilter(UploadFilter.java:179)
Any help would be appreciated!
Thank you,
Fel
list that does?)
What happens if you put a line like:
WalkerFactory.getInstance().addTypeWithParent
(FeatureFilter.OnlyChildren.class);
somewhere in your code? I'd expect this to fail, too, but hopefully
it with give a more informative exception.
Thomas.
On 30 N
n the Server-Configuration-file is not
'globally enough' to affect all custom ClassLoader-calls.
Maybe someone has experienced something similar or knows something about
this specific Server?
Thanks,
Felix
--
Felix Dreher
Max-Planck-Institute for Infection Biology
Campus Charit
e jar-file again and
deleting and re-adding it in StudioCreator.
Greetings,
Felix
Felix Dreher wrote:
Hi,
the problem is the security-policy of the container I use for my
web-application. In this case it's the 'Sun Java System Application
Server Platform Edition 8.1'. As T
f the corresponding class:
/BioSQLSequenceDB.java/1.70/Fri Jun 10 07:48:11 2005//
Further I use the latest cvs-version of the BioSQL-script
'biosqldb-pg.sql' (it's from June 2005).
Are there any suggestions how this could be solved?
Thank you,
Felix
--
Felix Dreher
Max-Planc
ch Investigator (Bioinformatics)
Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
phone +65 6722 2973
fax +65 6722 2910
Felix Dreher <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
01/20/2006 10:45 PM
To: biojava-l@
ttacagattaca","test"));
db.addRichSequence(seq);
tx.commit();
The Namespace and the sequence are actually being saved in the database,
but the sequence is saved in the default namespace 'lcl' and not in the
new namespace 'mRNA'.
Can someone tell me what I
.id.AbstractPostInsertGenerator.getGenerated(AbstractPostInsertGenerator.java:42)
... 20 more
Thanks in advance!
Greetings,
Felix
--
Felix Dreher
Max-Planck-Institute for Infection Biology
Campus Charité Mitte
Department of Immunology
Mailing address: Schumannstraße 21/22
Visi
i-pattern'.
>
>RichSequence seq =
>(SimpleRichSequence)RichSequence.Tools.enrich(DNATools.createDNASequence("gattacagattaca","urn:local:seq"));
>
>As an aside there is no need to cast the return of enrich if you are
>assining it to a RichSequence pointe
uenceDB,
a "NoSuchMethodException" is thrown at this line.
I searched for the getMethod- method and in fact it is not present in
org.hibernate.Criteria.
So does anyone know if this is an error in the BioJava-class or in the
Hibernate-class?
Greetings,
Felix
--
Felix Dreher
Max-Planck-Institute f
change its version to 99
be.setVersion(99);
--> can't use the method setVersion(int) --> but e.g. setDescription("XYZ");
Regards,
Felix
--
Felix Dreher
Max-Planck-Institute for Infection Biology
Campus Charité Mitte
Department of Immunology
Mailing address: Schumannstra
nate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:58)
at
org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:195)
... 57 more
Any suggestions would be highly appreciated!
Regards,
Felix
--
Felix Dreher
Max-Planck-Institute for Infection Biology
Campus Charité Mitte
r database from previous testing
that may need cleaning out (although if the hibernate mapping is correct
this is not likely).
- Mark
Felix Dreher <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
03/09/2006 02:08 AM
To: biojava-l@biojava.org
cc: (bcc: Mark Schre
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