jcman error

Hi,





What could be causing the following error upon trying to upgrade to JChem 3.2.2?

Code:

[root@v20z-031 bin]# ./jcman java.sql.SQLException: Stream has already been closed         at oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:134)         at oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:179)         at oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:269)         at oracle.jdbc.dbaccess.DBDataSetImpl.getStreamItem(DBDataSetImpl.java:1598)         at oracle.jdbc.driver.OracleStatement.getBytesInternal(OracleStatement.java:3501)         at oracle.jdbc.driver.OracleStatement.getBytesValue(OracleStatement.java:4793)         at oracle.jdbc.driver.OracleStatement.getObjectValue(OracleStatement.java:5973)         at oracle.jdbc.driver.OracleStatement.getObjectValue(OracleStatement.java:5892)         at oracle.jdbc.driver.OracleResultSetImpl.getObject(OracleResultSetImpl.java:765)         at chemaxon.util.DatabaseTools.readBytesOrString(DatabaseTools.java:213)         at chemaxon.util.DatabaseTools.readBytes(DatabaseTools.java:168)         at chemaxon.util.DatabaseTools.readBytes(DatabaseTools.java:141)         at chemaxon.jchem.db.Regenerator.getNextMolData(Regenerator.java:119)         at chemaxon.jchem.db.Regenerator.access$100(Regenerator.java:24)         at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:71)

-- Bob

Hi Bob,





Could you specify the environment where this error has occured?


(e.g. which was the version whereof you tried to upgrade, which was the type of column in your table, do you use special table column, ...)





Best regards,


Edvard

I'll contact the people who actually tried to do the upgrade and get them to respond.

Many of these Java errors occur during regenerating tables for jchem.2006.08.25; upgrade to jchem 3.2.3 fails utterly, hanging part-way through regeneration.





We have one extra field, called MOL_NAME, which is declared as VARCHAR(80). It is apparently placed after field CD_FP24 in the tables.





This problem did not occur at our UK site, by the way, but at the site of our clients, who are using similar software: Java 1.5, Oracle 9.2.

I am working with Bob on this upgrade and can provide you with most of the details. Well except for the information on the column types and any special tables questions.





Current environment:


JChem 3.1.3, Marvin 4.0.4


Database server: Oracle 9.2.0.5 (running on Solaris 9)


Java: 1.5.0_09


Oracle client: 9.2.0.6


Linux: RH AS 4.3





Attempting to upgrade to Jchem 3.2.3.





When I run the jcman to do upgrade (I used the GUI so I can see progress). I see the normal popup (after I provided credentials to DB connection) about detecting older tables (EPOCH.MISC_MOLECUES_V1, EPOCH.MOLECULES1_V1, EPOCH.USER_MISC_MOLECULES_V1, EPOCH.USER_MOLECULES1_V1). I click Yes to initiate regeneration.





The regen starts and I immediately get the Java error that Bob pasted. But the regen continues for a bit of time. Then it just hangs. The progress bar just sits at the same molecule count value. I think I left it run for 30+ minutes and the molecule count value never changed (the remaining time just kept increasing).





-Henry

Hi Henry,





Could you give me your JDBC driver version?


In addition, it would be good to know which type of your CD_STRUCTURE column in JChem 3.1.3.





Best regards,


Edvard

Well I am using the jdbc driver that is included with Oracle client 9.2.0.6.





As for CD_STRUCTURE information, are you asking for the field type in the database? If I run describe on the four tables that the upgrade says it will regen I get the following:





CD_STRUCTURE NOT NULL LONG RAW








-Henry

To be more explicit here is my CLASSPATH setting when I run upgrade.





CLASSPATH=/xncpkgs/oracle-9.2.0.6/jdbc/lib/ojdbc14.jar:/xncpkgs/oracle-9.2.0.6/jdbc/lib/nls_charset12.jar

Thank you for informative responses, we try to reproduce the error in a similar environment.


The last question: How many processors are working in that machines? (Where oracle server is running, and your client)





Edvard

Oracle server: Two 450Mhz UltraSparc II Sun E220


Oracle client: Two 2GHz Dual Core AMD Opteron

Hi Henry,





I have tried to reproduce the error, but it has not occured yet.


You should try to change your JDBC driver to version 10.2.0 and regenerate your table again.


You can find it here: http://www.oracle.com/technology/tech/java/sqlj_jdbc/index.html


Inform me of your results please!





Edvard