[DAS] Ensembl Dazzle for Oracle
Frank.R.Visser@gsk.com
Frank.R.Visser@gsk.com
Thu, 21 Nov 2002 11:58:04 +0000
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OK, the problem could lie with the fact that we have our reference ensembl
dataserver still in mysql, and only our DAS datasets in Oracle. If your
problem is with the reference server, my solution is not going to work.
You probably need to modify the biojava code.
However, I am very interested in getting it to work for Oracle. Is there a
chance that you can get me the Oracle schema and dataload? I would be
happy to work with you to see where the problem lies and get a working DAS
Server with Oracle reference database.
If you decide it is propriatry we are stuck, because even if I get it to
work, the chances are that my changes to the schema are slightly different
than yours, so it would still not work for you.
Frank
"Thorsten Jansen" <thorsten.jansen@lionbioscience.com>
21-Nov-2002 10:28
To: Frank.R.Visser
cc:
Subject: RE: [DAS] Ensembl Dazzle for Oracle
Hi Frank,
unfortunatly we have problems with doing this. Maybe we are using the
wrong Ensembl classes. Are you using the actual cvc-classes or the
downloadable skeleton. We hold the complete homo_sapiens_core database in
Oracle and want to access it via a DAS server. Therefor we had to change
some columnnames because the mysql-version uses names which are reserved
words in oracle. It would be great if you could provide me a list of the
classes I have to change. An example would be really helpfull.
Thanks
Thorsten
-----Original Message-----
From: Frank.R.Visser@gsk.com [mailto:Frank.R.Visser@gsk.com]
Sent: Wednesday, October 30, 2002 3:30 PM
To: jansen@lionbioscience.com
Cc: das@biodas.org; das-admin@biodas.org
Subject: Re: [DAS] Ensembl Dazzle for Oracle
I did. It is very simple, just take the 'plugin' you want to use for the
database access, and replace the mysql driver initialization with the
oracle driver initialization. Put the correct jdbc dbURL in the
dazzlecfg.xml file and it works.
If you run into trouble, let me know, and I'll send you an example.
Frank
Jansen <jansen@lionbioscience.com>
Sent by: das-admin@biodas.org
30-Oct-2002 10:51
To: das
cc:
Subject: [DAS] Ensembl Dazzle for Oracle
Hi,
is there anybody who changed the Ensembl das classes for oracle access? If
yes, what do I have to take care about?
Thanks
Thorsten Jansen
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http://biodas.org/mailman/listinfo/das
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<br><font size=2 face="Arial">OK, the problem could lie with the fact that we have our reference ensembl dataserver still in mysql, and only our DAS datasets in Oracle. If your problem is with the reference server, my solution is not going to work. You probably need to modify the biojava code.</font>
<br>
<br><font size=2 face="Arial">However, I am very interested in getting it to work for Oracle. Is there a chance that you can get me the Oracle schema and dataload? I would be happy to work with you to see where the problem lies and get a working DAS Server with Oracle reference database.</font>
<br>
<br><font size=2 face="Arial">If you decide it is propriatry we are stuck, because even if I get it to work, the chances are that my changes to the schema are slightly different than yours, so it would still not work for you. </font>
<br>
<br><font size=2 face="Arial">Frank</font>
<br>
<br>
<br>
<br>
<br>
<table width=100%>
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<td>
<td><font size=1 face="sans-serif"><b>"Thorsten Jansen" <thorsten.jansen@lionbioscience.com></b></font>
<br>
<p><font size=1 face="sans-serif">21-Nov-2002 10:28</font>
<br>
<td><font size=1 face="Arial"> </font>
<br><font size=1 face="sans-serif"> </font>
<br>
<br><font size=1 face="sans-serif"> To: Frank.R.Visser</font>
<br>
<br><font size=1 face="sans-serif"> cc: </font>
<br><font size=1 face="sans-serif"> Subject: RE: [DAS] Ensembl Dazzle for Oracle</font></table>
<br>
<br><font size=2 color=blue face="Arial">Hi Frank,</font>
<br><font size=2 color=blue face="Arial">unfortunatly we have problems with doing this. Maybe we are using the wrong Ensembl classes. Are you using the actual cvc-classes or the downloadable skeleton. We hold the complete homo_sapiens_core database in Oracle and want to access it via a DAS server. Therefor we had to change some columnnames because the mysql-version uses names which are reserved words in oracle. It would be great if you could provide me a list of the classes I have to change. An example would be really helpfull.</font>
<br><font size=3 face="Times New Roman"> </font>
<br><font size=2 color=blue face="Arial">Thanks</font>
<br><font size=2 color=blue face="Arial">Thorsten</font>
<br><font size=2 color=blue face="Arial"> </font>
<br><font size=3 face="Times New Roman"> </font>
<br><font size=2 face="Tahoma"> -----Original Message-----<b><br>
From:</b> Frank.R.Visser@gsk.com [mailto:Frank.R.Visser@gsk.com]<b><br>
Sent:</b> Wednesday, October 30, 2002 3:30 PM<b><br>
To:</b> jansen@lionbioscience.com<b><br>
Cc:</b> das@biodas.org; das-admin@biodas.org<b><br>
Subject:</b> Re: [DAS] Ensembl Dazzle for Oracle<br>
</font>
<br><font size=2 face="Arial"><br>
I did. It is very simple, just take the 'plugin' you want to use for the database access, and replace the mysql driver initialization with the oracle driver initialization. Put the correct jdbc dbURL in the dazzlecfg.xml file and it works. </font><font size=3 face="Times New Roman"><br>
</font><font size=2 face="Arial"><br>
If you run into trouble, let me know, and I'll send you an example.</font><font size=3 face="Times New Roman"> <br>
</font><font size=2 face="Arial"><br>
Frank</font><font size=3 face="Times New Roman"> <br>
<br>
</font>
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<td width=46%><font size=1 face="sans-serif"><b>Jansen <jansen@lionbioscience.com></b></font><font size=3 face="Times New Roman"> <br>
</font><font size=1 face="sans-serif"><br>
Sent by: das-admin@biodas.org</font><font size=3 face="Times New Roman"> </font>
<p><font size=1 face="sans-serif">30-Oct-2002 10:51</font><font size=3 face="Times New Roman"> </font>
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To: das</font><font size=3 face="Times New Roman"> <br>
</font><font size=1 face="sans-serif"><br>
cc: </font><font size=3 face="Times New Roman"> </font><font size=1 face="sans-serif"><br>
Subject: [DAS] Ensembl Dazzle for Oracle</font></table>
<br><font size=3 face="Times New Roman"><br>
</font><font size=2 face="Courier New"><br>
Hi,<br>
is there anybody who changed the Ensembl das classes for oracle access? If<br>
yes, what do I have to take care about?<br>
<br>
Thanks<br>
Thorsten Jansen<br>
<br>
_______________________________________________<br>
DAS mailing list<br>
DAS@biodas.org<br>
http://biodas.org/mailman/listinfo/das<br>
</font><font size=3 face="Times New Roman"><br>
<br>
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