[DAS] DAS and Oracle

[Jean-Jack Riethoven]

On Tue, 28 May 2002, Scott J. Pearson wrote:

> I am trying to integrate DAS with Oracle to provide better performance
> than with MySQL. Has anyone performed this integration before? If so, I
> would appreciate any tips that you might provide.

I don't have any generic tips for you, but I did do the very minor changes
in the Dazzle code to get it to work with Oracle in stead of the default
my SQL.

>From your query I am not sure if this is what you are after (i.e.
modifying existing DAS servers to work with Oracle), but in case you are
this is what you need to do (for Dazzle).

1. Make sure Dazzle runs in an environment which is suitable for Oracle
SQL. Meaning: set the required environment variables to suit your system.
If you can run sqlplus, things should be ok.

2. Pack up the required Oracle classes into a jar file. Do not go for the
thin drivers. (some Oracle installations do not have the jar file handy,
or only the thin drivers)

3. Copy this jar file into Dazzle's WEB-INF/lib directory. (if you are
paranoid, or if more servlets use Oracle, move it into Tomcat's
/common/libs/ directory as well).

4. Modify some Java code. 

4a. Ensembl-das package:
4a1: AbstractSeqFeature.java: load oracle.jdbc.driver.OracleDriver in
place of the mm.mysql one
4a2: EnsemblHolder.java: in getEnsembl function: do the same as in 4a1

4b Ensembl package:
4b1: JDBCConnectionPool.java: disable the big SQL selects option (mySQL
tweak)

5. And build + move jars to Dazzle WEB-INF/lib

6. If you are using the same table structures as Ensembl (in their mySQL
example) then you are set to go. Else, you need some tweaking in the
Abstract...Source you are using, esp. in the select statements and
following code.

That should do the trick.

We are using modifications of the RemoteGenericSeqFeatureSource plugin
together with the Abstract class (we are using Ensembl's DAS servers as
reference, but if you have them in-house you need another adaptor).

Hope this answers some questions for you, or at least gave you some leads
if you are not using Dazzle :)

With kind regards,

Drs. Jean-Jack Riethoven

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