Things to do after migration?

I've migrated production data into development database. Problem is, the cartridge is not working in development database after migration. Did I miss out anything? How do I check?

Thanks.

How did you migrate? Exported and reimported the tables?

What do you mean by "not working"? Is there an error message you get, or the search results you get are unepxected?

Which JChem version is this?

Hi Peter,

Yes, I exported and re-imported the data. I didnt export the jchem owner schema. Just one schema which use the cartridge. So there should be no configuration needed to be changed right?

select JCHEM_CORE_PKG.GETENVIRONMENT() from dual;

JCHEM_CORE_PKG.GETENVIRONMENT()                                                 
--------------------------------------------------------------------------------
Oracle environment:                                                             
Oracle Database 10g Enterprise Edition Release 10.2.0.5.0 - 64bi                
PL/SQL Release 10.2.0.5.0 - Production                                          
CORE    10.2.0.5.0    Production                                                      
TNS for Linux: Version 10.2.0.5.0 - Production                                  
NLSRTL Version 10.2.0.5.0 - Production                                          
                                                                                
JChem Server environment:                                                       
Java VM vendor: Sun Microsystems Inc.                                           
Java version: 1.6.0_20                                                          
Java VM version: 16.3-b01                                                       
JChem version: 5.2.6                                                            
JChem Index version: 5020400                                                    
JDBC driver version: 11.1.0.7.0-Production                                      
    

The search are working, just the inserts are not.

Exception Details: Oracle.DataAccess.Client.OracleException:
ORA-29532: Java call terminated by uncaught Java exception:
java.sql.SQLException: Statement 'INSERT INTO CHEMDB.COMPOUND (cd_id,
cd_structure, cd_smiles, cd_formula, cd_molweight, cd_hash, cd_flags,
cd_timestamp, cd_fp1, cd_fp2, cd_fp3, cd_fp4, cd_fp5, cd_fp6, cd_fp7,
cd_fp8, cd_fp9, cd_fp10, cd_fp11, cd_fp12, cd_fp13, cd_fp14, cd_fp15,
cd_fp16, LOGP, LIPINSKY, ACCEPTORCOUNT, PSA, DONORCOUNT,
ROTATABLEBONDCOUNT)  VALUES(?, empty_blob(), ?, ?, ?, ?, ?, SYSDATE, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)' failed
for structure '
 Marvin  07231214572D          

 6  6  0  0  0  0            999 V2000
  -1.7089    1.7973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -2.4234    1.3848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -2.4234    0.5598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -1.7089    0.1473    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -0.9945    0.5598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -0.9945    1.3848    0.0000 C   0  0  0

Please, could you copy paste the corresponding error message and Java stack from the Oracle session trace file (to be found in the udump directory)?

Thanks

Peter

Hi Peter,

Sorry to trouble you, we've figured out where the problem lies. Nothing to do with the cartridge. Thanks for your help.

I have another question though, I've a need to change our database character set from WE8ISO8859P1 to AL32UTF8. Do you know if this poses any problem for chemaxon cartridge installed in the database? Also we are planning to upgrade the database from 10.2 to 11.2.0.3. Is the cartridge supported on this version of oracle?

Thanks.

Cheers,
Samantha

Hi Samantha,

I am glad you have one trouble less.

JChem Cartridge supports both AL32UTF8 and Oracle 11.2.0.3 in general.

The JChem Cartridge version you have was tested with AL32UTF8.

That version was, I suspect, not tested with Oracle 11.2, as Oracle 11.2 was released, I suspect, after JChem 5.2.6 was released. I am positive that JChem 5.2.6 was tested with Oracle 11.1, though. Having said that, I expect your JChem Cartridge version to work with Oracle 11.2.

Best regards,

Peter

Hi Peter,

We have a need to re-install the database on a new server. I did a complete database recovery. After complete recovery, a SELECT JCHEM_CORE_PKG.GETENVIRONMENT() FROM DUAL shows this;

JCHEM_CORE_PKG.GETENVIRONMENT()                                                 
--------------------------------------------------------------------------------
Oracle environment:                                                             
Oracle Database 11g Enterprise Edition Release 11.2.0.3.0 - 64bit Production    
PL/SQL Release 11.2.0.3.0 - Production                                          
CORE    11.2.0.3.0    Production                                                      
TNS for Linux: Version 11.2.0.3.0 - Production                                  
NLSRTL Version 11.2.0.3.0 - Production                                          
                                                                                
JChem Server environment:                                                       
Java VM vendor: Sun Microsystems Inc.                                           
Java version: 1.6.0_20                                                          
Java VM version: 16.3-b01                                                       
JChem version: 5.2.6                                                            
JChem Index version: 5020400                                                    
JDBC driver version: 11.1.0.7.0-Production                                      
                                                                                
                                                                                
1 row selected.

But when we execute other functions like jc_compare, there are only nulls.

Do we have to re-install jchem cartridge, or can we just copy over the relevant files? & what are the relevant files to copy?

Thanks.

Samantha

Hi Samantha,

If you use plain structure tables (as opposed to JCB structure tables), it is possible that the ROWIDs have been changed during recovery which may explain that JC_COMPARE returns no hits. If this is the case, rebuilding the indices may help.

If you use JCB structure tables, I don't have much idea what may have gone wrong. In this case, I recommend the uninstall and reinstall JChem Cartridge.

Regards,

Peter

Hi Peter

I received the following error after I migrated the database to another server.

ORA-29532: Java call terminated by uncaught Java exception: java.rmi.ServerException: RemoteException occurred in server thread; nested exception is:
    java.rmi.RemoteException: Inconsistent oracle.server.host setting for JChemServer: ora-dev.etc.a-star.edu.sg resolves to ora-dev.etc.a-star.edu.sg/172.24.22.113, but client oracle server is hosted on 172.24.22.54 (which resolves to /172.24.22.54)

Any idea where do I change the oracle.server.host setting?

Thanks.

Regards,

Samantha

Hi,

You can change it in the jcart.properties file which is located in the jchermsite/cartridge/conf directory.

Regards,

Tamas

Hi,

I changed the settings, I execute the same statement & I receive the following error:

ORA-29532: Java call terminated by uncaught Java exception: java.lang.Exception: Problem connecting to JChemServer: rmi://172.24.22.111:1099: Connection refused

Hi Samantha,

Is the IP address of the host where the JChem Cartridge server is running 172.24.22.111?

Peter

yes

And the JChem Cartridge server is listening on the 1099 port?

P.

yes

Please, try the following:

1. Login on the Oracle server

2. Start telnet like this: telnet 172.24.22.111 1099

What output do you get?

P.

I dont have telnet installed in my linux server.

Is there any other way I can check?

Thanks.

ftp

leeyc$ telnet 172.24.22.111 1099
Trying 172.24.22.111...
Connected to 172.24.22.111.
Escape character is '^]'.
####sr4chemaxon.jchem.cartridge.rmi.impl.DirectoryImpl_Stubxrjava.rmi.server.RemoteStub########xrjava.rmi.server.RemoteObject####
                                                 a3xpw6
172.24.22.111#####*#########<####xConnection closed by foreign host.

Hmm, I expected this to also give "Connection refused"...  Please, could you post the full error message (I think a PL/SQL stack trace should be part of the message). You get the "Connection refused" error message, when you are trying to execute SELECT JCHEM_CORE_PKG.GETENVIRONMENT() FROM DUAL, correct?

I understand that you could get the configuration with the second database server (mentioned in your post of Wed Jan 09, 2013) working. Is this correct? Are you aware of any difference between that second server and this third server which might affect networking behaviour? Are there firewalls running on the servers and if there are, is there any difference between their configurations? Is the configuration of the Oracle database itself any different on this newest database server than on the previous one?

Also, it appears that we are a step back compared to Mon Jan 28, 2013. The error message you reported in your post on Mon Jan 28, 2013, is generated after the Oracle stored procedure successfully connects to the JChem Cartridge server. This new error message is, however, about the Oracle stored procedure not even being able to connect to the JChem Cartridge server. Please, could you post the modifications you made to the jchem/cartridge/jcart.properties file?

Thanks,

Pete