jchem.db.Exporter produces NullPointerException

Hi,

With version  6.0.3 we have problem when use export with custom sql. Simplified test case below:

ConnectionHandler jchem_con = new ConnectionHandler();

jchem_con.setConnection(c);

jchem_con.setPropertyTable("jchemprops");

Exporter exp = new Exporter();

exp.setFormat(Transfer.SDFILE);

exp.setConnectionHandler(jchem_con);

exp.setSelectStatement("select 'CCCC' as CD_STRUCTURE, 0 as CD_ID from dual");

ByteArrayOutputStream out = new ByteArrayOutputStream();

exp.setOutputStream(out );

Integer molNumber = exp.writeAll();

Last instruction writeAll throws chemaxon.jchem.db.TransferException: Unexpected error during DB export init: null, cause NullPointerException.

We variated with setSelectStatement: used selection from registered structure table like 

select * from jsmiles_bb limit 1 or select CD_STRUCTURE,  CD_ID from jsmiles_bb limit 1

result the same..

When instead of setSelectStatement use setTableName('jsmiles_bb ') the above code works. 

We did nod find in docs any special hints except CD_STRUCTURE must be first in field list. So what's wrong?

Hi,

 

I've moved your topic to the appropriate forum. My colleauges will answer you soon.

BRs,

Peter

Hi,

Could you send us the log file with the stack trace?

Thank you,

Krisztina

code sample:

 

package org.Shop.Utils;

 

import java.io.*;

import java.sql.DriverManager;

import java.sql.PreparedStatement;

import java.sql.Connection;

import java.sql.SQLException;

import chemaxon.util.ConnectionHandler;

import chemaxon.formats.MolImporter;

import chemaxon.jchem.db.*;

public class Updater

{

 public static void main(String[] args)

    {

        try

        {

            Connection connection = DriverManager.getConnection("jdbc:mysql://spectra:3306/Shop", "root", "root");

            ConnectionHandler jchem_con = new ConnectionHandler();

            jchem_con.setConnection(connection);

            jchem_con.setPropertyTable("jchemprops");

 

            Exporter exp = new Exporter();

            exp.setFormat(Transfer.SDFILE);

            exp.setConnectionHandler(jchem_con);

            exp.setSelectStatement("select 'CCCC' as CD_STRUCTURE, 0 as CD_ID from dual");

            ByteArrayOutputStream out = new ByteArrayOutputStream();

            exp.setOutputStream(out);

            Integer molNumber = exp.writeAll();

        }

        catch (Exception ex)

        {

            ex.printStackTrace();

        }

}

result:

chemaxon.jchem.db.TransferException: Unexpected error during DB export init: null

at chemaxon.jchem.db.Exporter.init(Exporter.java:501)

at chemaxon.jchem.db.Exporter.writeAll(Exporter.java:418)

at org.Shop.Utils.Updater.main(Updater.java:491)

Caused by: java.lang.NullPointerException

at chemaxon.jchem.base.persist.impl.sql.SqlCollectionPhysicalConfiguration.getNameWithSchema(SqlCollectionPhysicalConfiguration.java:90)

at chemaxon.jchem.base.persist.impl.sql.SqlCollectionPhysicalConfiguration.getNameWithSchema(SqlCollectionPhysicalConfiguration.java:82)

at chemaxon.jchem.db.TableInfo.getTableNameWithSchema(TableInfo.java:1057)

at chemaxon.jchem.db.DatabaseProperties.tablePrefix(DatabaseProperties.java:1096)

at chemaxon.jchem.db.DatabaseProperties.getTableType(DatabaseProperties.java:1390)

at chemaxon.jchem.db.SQLToFileHandler.<init>(SQLToFileHandler.java:114)

at chemaxon.jchem.db.Exporter.init(Exporter.java:495)

... 2 more

Thank you for the details. We could reproduce the erroneous behavior. We will inform about the version number of JChem which will contain the bugfix.

Best regards,

Krisztina

Hi,

I can confirm that the fix will be released in the 6.0.4 and the 6.1 versions. The 6.0.4 version will be released in a few days time.

Regards,

Tamas

Hi,

JChem 6.0.4 has been released with the fix.

Regards,

Tamas