[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&nbsp;enabling DAS to run&nbsp;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>&nbsp;</DIV>
<DIV><SPAN class=843523414-21112002><FONT face=Arial color=#0000ff size=2>I'm 
contemplating two options.&nbsp;&nbsp;</FONT></SPAN></DIV>
<DIV><SPAN class=843523414-21112002>&nbsp;&nbsp;&nbsp; <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>&nbsp;&nbsp;&nbsp; <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>&nbsp;&nbsp;&nbsp; <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>&nbsp;</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>&nbsp;</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" 
        &lt;thorsten.jansen@lionbioscience.com&gt;</B></FONT> <BR>
        <P><FONT face=sans-serif size=1>21-Nov-2002 10:28</FONT> <BR></P>
      <TD><FONT face=Arial size=1>&nbsp; &nbsp; &nbsp; &nbsp; </FONT><BR><FONT 
        face=sans-serif size=1>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
        &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; </FONT><BR><BR><FONT face=sans-serif 
        size=1>&nbsp; &nbsp; &nbsp; &nbsp; To: &nbsp; &nbsp; &nbsp; 
        &nbsp;Frank.R.Visser</FONT> <BR><BR><FONT face=sans-serif size=1>&nbsp; 
        &nbsp; &nbsp; &nbsp; cc: &nbsp; &nbsp; &nbsp; &nbsp;</FONT> <BR><FONT 
        face=sans-serif size=1>&nbsp; &nbsp; &nbsp; &nbsp; Subject: &nbsp; 
        &nbsp; &nbsp; &nbsp;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. &nbsp;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>&nbsp;</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>&nbsp;</FONT> <BR><FONT face="Times New Roman" size=3>&nbsp;</FONT> 
  <BR><FONT face=Tahoma size=2>&nbsp;-----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 
        &lt;jansen@lionbioscience.com&gt;</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>&nbsp; &nbsp; &nbsp; &nbsp; 
        </FONT><FONT face=sans-serif size=1><BR>&nbsp; &nbsp; &nbsp; &nbsp; 
        &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;</FONT><FONT 
        face="Times New Roman" size=3><BR></FONT><FONT face=sans-serif 
        size=1><BR>&nbsp; &nbsp; &nbsp; &nbsp;To: &nbsp; &nbsp; &nbsp; 
        &nbsp;das</FONT><FONT face="Times New Roman" size=3> <BR></FONT><FONT 
        face=sans-serif size=1><BR>&nbsp; &nbsp; &nbsp; &nbsp;cc: &nbsp; &nbsp; 
        &nbsp; &nbsp;</FONT><FONT face="Times New Roman" size=3> </FONT><FONT 
        face=sans-serif size=1><BR>&nbsp; &nbsp; &nbsp; &nbsp;Subject: &nbsp; 
        &nbsp; &nbsp; &nbsp;[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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