I'm glad to hear you found something that works!
On Fri, Nov 15, 2019 at 10:23 PM Webster Homer <
webster.ho...@milliporesigma.com> wrote:
> 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>
> *Sent:* Friday, November 15, 2019 10:16 AM
> *To:* Webster Homer <webster.ho...@milliporesigma.com>
> *Cc:* 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> 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");
>
> }
>
>
>
>
>
> This message and any attachment are confidential and may be privileged or
> otherwise protected from disclosure. If you are not the intended recipient,
> you must not copy this message or attachment or disclose the contents to
> any other person. If you have received this transmission in error, please
> notify the sender immediately and delete the message and any attachment
> from your system. Merck KGaA, Darmstadt, Germany and any of its
> subsidiaries do not accept liability for any omissions or errors in this
> message which may arise as a result of E-Mail-transmission or for damages
> resulting from any unauthorized changes of the content of this message and
> any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its
> subsidiaries do not guarantee that this message is free of viruses and does
> not accept liability for any damages caused by any virus transmitted
> therewith. Click http://www.merckgroup.com/disclaimer to access the
> German, French, Spanish and Portuguese versions of this disclaimer.
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
> This message and any attachment are confidential and may be privileged or
> otherwise protected from disclosure. If you are not the intended recipient,
> you must not copy this message or attachment or disclose the contents to
> any other person. If you have received this transmission in error, please
> notify the sender immediately and delete the message and any attachment
> from your system. Merck KGaA, Darmstadt, Germany and any of its
> subsidiaries do not accept liability for any omissions or errors in this
> message which may arise as a result of E-Mail-transmission or for damages
> resulting from any unauthorized changes of the content of this message and
> any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its
> subsidiaries do not guarantee that this message is free of viruses and does
> not accept liability for any damages caused by any virus transmitted
> therewith. Click http://www.merckgroup.com/disclaimer to access the
> German, French, Spanish and Portuguese versions of this disclaimer.
> This message and any attachment are confidential and may be privileged or
> otherwise protected from disclosure. If you are not the intended recipient,
> you must not copy this message or attachment or disclose the contents to
> any other person. If you have received this transmission in error, please
> notify the sender immediately and delete the message and any attachment
> from your system. Merck KGaA, Darmstadt, Germany and any of its
> subsidiaries do not accept liability for any omissions or errors in this
> message which may arise as a result of E-Mail-transmission or for damages
> resulting from any unauthorized changes of the content of this message and
> any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its
> subsidiaries do not guarantee that this message is free of viruses and does
> not accept liability for any damages caused by any virus transmitted
> therewith. Click http://www.merckgroup.com/disclaimer to access the
> German, French, Spanish and Portuguese versions of this disclaimer.
>
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
