I got this to work. The solution is to call the set_config function which can
be done as:
select set_config('rdkit.do_chiral_sss', 'true', false);
This can be done using JDBC statements apis
From: Webster Homer <webster.ho...@milliporesigma.com>
Sent: Friday, November 15, 2019 12:18 PM
To: Greg Landrum <greg.land...@gmail.com>
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] RD Kit Cartridge setting do_chiral_sss flag with
Java JDBC
I do not believe so. In psql the set statement actually sets a variable in the
database session. It’s not SQL. The PostgreSQL Jdbc BaseDataSource class does
have methods to set session properties. The problem I discovered is that the
DataSource returned by the JNDI lookup does not extend BaseDataSource. JNDI is
a Java technology that allows the database link configuration to be separate
from the code. It allows us to be able to change the database user, password,
host, etc without modifying the application code. This is provided by the
application server.
I think my solution is simply to default the do_chiral_sss to true. My only
concern with that is it could increase the overhead on the search.
I think I can set the default on the JDBC URL. It will not be something that
the application can modify though. If that is not acceptable I can provide an
alternative to JNDI, but our administrators won’t like it. However if I use the
PosgreSQL DataSource class for this I will need to use their connection pooling
DataSource which is not recommended for production even by Postgresql
Regards,
Webster
From: Greg Landrum <greg.land...@gmail.com<mailto:greg.land...@gmail.com>>
Sent: Friday, November 15, 2019 10:16 AM
To: Webster Homer
<webster.ho...@milliporesigma.com<mailto:webster.ho...@milliporesigma.com>>
Cc:
rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] RD Kit Cartridge setting do_chiral_sss flag with
Java JDBC
Hi Webster,
I am, unfortunately, not familiar enough with the way JDBC works to be able to
help here.
Isn't there some way you can execute the raw SQL command: "set
rdkit.do_chiral_sss=true"?
On Thu, Nov 14, 2019 at 9:41 PM Webster Homer
<webster.ho...@milliporesigma.com<mailto:webster.ho...@milliporesigma.com>>
wrote:
I’m trying to understand how to set the rdkit.do_chiral_sss in Java.
I would like to call RD Kit structure search from a Java application. However
the way RD Kit depends upon setting some values in Postgresql via SET seems to
be hard to do using JDBC. I am using JBoss Wildfly to host the application.
The normal way to set up the database connection is via JNDI.
It is not clear how to set the rdkit.do_chiral_sss variable for the search via
JDBC.
This does not work
Context initCtx = new InitialContext();
ds = (DataSource) initCtx.lookup("java:/jdbc/rdkit-sss");
if (ds instanceof BaseDataSource) { // never true
BaseDataSource bds = (BaseDataSource)ds;
bds.setProperty("rdkit.do_chiral_sss",
structureSearchRequest.isStereoSearch()? "true" : "false");
} else {
logger.error("Cannot set RD Kit session variables");
}
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