[DAS] Ensembl Dazzle for Oracle
Sicotte, Hugues (NIH/NCI)
sicotteh@mail.nih.gov
Thu, 21 Nov 2002 09:43:07 -0500
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I am in the process of enabling DAS to run off of Oracle databases.
I want to modify the DAS Pool connection code to allow it to have several
types of connections open at the same type. (at least Oracles 8.17+, MS
Access, and mysql). I think it makes sense to put all that code in one place
(a single class file)
instead of having to modify the Database loaders in many places. Right now
the database opening code
is in many places.
I'm contemplating two options.
- Loading a bunch of drivers. (easier to code.. but slower)
- Parsing the database URL string and doing a lookup among a config list
of drivers to see
if the correct driver is part of the installation. (Harder to code, but
more flexible and optimized)
I'm a beginner Java programmer, so I'm testing this outside of the DAS
framework. It'll take me some time.
If some Java Guru can do it quickly, that'd be great.
Hugues Sicotte
-----Original Message-----
From: Frank.R.Visser@gsk.com [mailto:Frank.R.Visser@gsk.com]
Sent: Thursday, November 21, 2002 6:58 AM
To: thorsten.jansen@lionbioscience.com
Cc: das@biodas.org; das-admin@biodas.org
Subject: RE: [DAS] Ensembl Dazzle for Oracle
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
_______________________________________________
DAS mailing list
DAS@biodas.org
http://biodas.org/mailman/listinfo/das
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<DIV><SPAN class=843523414-21112002><FONT face=Arial color=#0000ff size=2>I am
in the process of enabling DAS to run off of Oracle
databases.</FONT></SPAN></DIV>
<DIV><SPAN class=843523414-21112002><FONT face=Arial color=#0000ff size=2>I want
to modify the DAS Pool connection code to allow it </FONT></SPAN><SPAN
class=843523414-21112002><FONT face=Arial color=#0000ff size=2>to have several
types of connections open at the same type. (at least Oracles 8.17+, MS Access,
and </FONT></SPAN><SPAN class=843523414-21112002><FONT face=Arial color=#0000ff
size=2>mysql). I think it makes sense to put all that code in one place (a
single class file)</FONT></SPAN></DIV>
<DIV><SPAN class=843523414-21112002><FONT face=Arial color=#0000ff
size=2>instead of having to modify the Database loaders in many places. Right
now the database opening code</FONT></SPAN></DIV>
<DIV><SPAN class=843523414-21112002><FONT face=Arial color=#0000ff size=2>is in
many places.</FONT></SPAN></DIV>
<DIV><SPAN class=843523414-21112002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=843523414-21112002><FONT face=Arial color=#0000ff size=2>I'm
contemplating two options. </FONT></SPAN></DIV>
<DIV><SPAN class=843523414-21112002> <FONT face=Arial
color=#0000ff size=2>- Loading a bunch of drivers. (easier to code.. but
slower)</FONT></SPAN></DIV>
<DIV><SPAN class=843523414-21112002> <FONT face=Arial
color=#0000ff size=2>- Parsing the database URL string and doing a lookup among
a config list of drivers to see</FONT></SPAN></DIV>
<DIV><SPAN class=843523414-21112002> <FONT face=Arial
color=#0000ff size=2>if the correct driver is part of the installation. (Harder
to code, but more flexible and optimized)</FONT></SPAN></DIV>
<DIV><SPAN class=843523414-21112002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=843523414-21112002><FONT face=Arial color=#0000ff size=2>I'm a
beginner Java programmer, so I'm testing this outside of the DAS framework.
It'll take me some time. </FONT></SPAN></DIV>
<DIV><SPAN class=843523414-21112002><FONT face=Arial color=#0000ff size=2>If
some Java Guru can do it quickly, that'd be great.</FONT></SPAN></DIV>
<DIV><SPAN class=843523414-21112002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=843523414-21112002><FONT face=Arial color=#0000ff size=2>Hugues
Sicotte</FONT></SPAN></DIV>
<BLOCKQUOTE>
<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B> Frank.R.Visser@gsk.com
[mailto:Frank.R.Visser@gsk.com]<BR><B>Sent:</B> Thursday, November 21, 2002
6:58 AM<BR><B>To:</B> thorsten.jansen@lionbioscience.com<BR><B>Cc:</B>
das@biodas.org; das-admin@biodas.org<BR><B>Subject:</B> RE: [DAS] Ensembl
Dazzle for Oracle<BR><BR></FONT></DIV><BR><FONT face=Arial size=2>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 face=Arial size=2>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 face=Arial size=2>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 face=Arial size=2>Frank</FONT>
<BR><BR><BR><BR><BR>
<TABLE width="100%">
<TBODY>
<TR vAlign=top>
<TD>
<TD><FONT face=sans-serif size=1><B>"Thorsten Jansen"
<thorsten.jansen@lionbioscience.com></B></FONT> <BR>
<P><FONT face=sans-serif size=1>21-Nov-2002 10:28</FONT> <BR></P>
<TD><FONT face=Arial size=1> </FONT><BR><FONT
face=sans-serif size=1>
</FONT><BR><BR><FONT face=sans-serif
size=1> To:
Frank.R.Visser</FONT> <BR><BR><FONT face=sans-serif size=1>
cc: </FONT> <BR><FONT
face=sans-serif size=1> Subject:
RE: [DAS] Ensembl Dazzle for
Oracle</FONT></TR></TBODY></TABLE><BR><BR><FONT face=Arial color=blue
size=2>Hi Frank,</FONT> <BR><FONT face=Arial color=blue size=2>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 face="Times New Roman" size=3> </FONT>
<BR><FONT face=Arial color=blue size=2>Thanks</FONT> <BR><FONT face=Arial
color=blue size=2>Thorsten</FONT> <BR><FONT face=Arial color=blue
size=2> </FONT> <BR><FONT face="Times New Roman" size=3> </FONT>
<BR><FONT face=Tahoma size=2> -----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 face=Arial size=2><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
face="Times New Roman" size=3><BR></FONT><FONT face=Arial size=2><BR>If you
run into trouble, let me know, and I'll send you an example.</FONT><FONT
face="Times New Roman" size=3> <BR></FONT><FONT face=Arial
size=2><BR>Frank</FONT><FONT face="Times New Roman" size=3> <BR><BR></FONT>
<TABLE width="100%">
<TBODY>
<TR vAlign=top>
<TD width="2%">
<TD width="46%"><FONT face=sans-serif size=1><B>Jansen
<jansen@lionbioscience.com></B></FONT><FONT face="Times New Roman"
size=3> <BR></FONT><FONT face=sans-serif size=1><BR>Sent by:
das-admin@biodas.org</FONT><FONT face="Times New Roman" size=3> </FONT>
<P><FONT face=sans-serif size=1>30-Oct-2002 10:51</FONT><FONT
face="Times New Roman" size=3> </FONT></P>
<TD width="50%"><FONT face=Arial size=1>
</FONT><FONT face=sans-serif size=1><BR>
</FONT><FONT
face="Times New Roman" size=3><BR></FONT><FONT face=sans-serif
size=1><BR> To:
das</FONT><FONT face="Times New Roman" size=3> <BR></FONT><FONT
face=sans-serif size=1><BR> cc:
</FONT><FONT face="Times New Roman" size=3> </FONT><FONT
face=sans-serif size=1><BR> Subject:
[DAS] Ensembl Dazzle for
Oracle</FONT></TR></TBODY></TABLE><BR><FONT face="Times New Roman"
size=3><BR></FONT><FONT face="Courier New" size=2><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
face="Times New Roman" size=3><BR><BR></FONT><BR><BR></BLOCKQUOTE></BODY></HTML>
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