Invalid target: Molecule cannot be imported

Hi, all.

We use JChem 5.7.0.0 in 10.2.0.5 RAC Database (x86_64).

Whil import simple (maybe uneseless) structures we've gor error message:

ORA-29875: failed in the execution of the ODCIINDEXINSERT routine

ORA-29532: Java call terminated by uncaught Java exception: java.rmi.RemoteException: Error while getting the next hits; 

nested exception is: 

        java.rmi.ServerException: RemoteException occurred in server thread; nested exception is: 

        chemaxon.jchem.cartridge.rmi.StructureFormatException: Invalid target: Molecule cannot be imported

ORA-06512: at "JCHEM_PORTAL.JCHEM_CLOB_PKG", line 112

ORA-06512: at "JCHEM_PORTAL.JC_IDXTYPE_IM", line 843


Pavel

Hi Pavel,

Please, could you tell me how (with which parameters) the index was created?

Thanks,

Peter

Sure, Peter.

CREATE INDEX md_u_structs_i_j ON md_user_structs (structure) INDEXTYPE IS jchem_portal.jc_idxtype

  PARAMETERS ('structureType=anyStructures,fp_size=32,fp_bit=2,pat_length=6,duplicateFiltering=y')

/

ALTER TABLE md_u_structs_i_j_jcx MODIFY (cd_formula varchar2(4000))

/

 

Column STRUCTURE in MD_USER_STRUCTS table has CLOB type.

Pavel

Thank you, Pavel!

There appears to be a structure already in the table with wich the mol importer cannot cope for some reason. There should be a SEVERE entry in jchem/cartridge/logs/jcart?.log (probably jcart1.log) which lists the problematic structure. (I expect this entry to have a two-part Java stack trace with the second part listing the problematic structure.) Please, could you send me the structure, if it is not too confidential?

Thank you,

Peter

pkovacs wrote:

Thank you, Pavel! There appears to be a structure already in the table with wich the mol importer cannot cope for some reason. There should be a SEVERE entry in jchem/cartridge/logs/jcart?.log (probably jcart1.log) which lists the problematic structure. (I expect this entry to have a two-part Java stack trace with the second part listing the problematic structure.) Please, could you send me the structure, if it is not too confidential? Thank you, Peter

Sure, Peter.

Mols are in attachement.

Thank you, Pavel!

I was so far unable to reproduce the problem. I was trying to insert the structures in this order:

 

          mdu_-1498618579.mol,

          mdu_-157027505.mol,

          mdu_-563586511.mol

and tried puttig the JChem index and executing alter table on an empty table as well as on a table already containing mdu_-1498618579.mol. I invariably got DuplicateStructureException as expected. Can you spot anything that I should do differently in my test case?

Also, can you, please, provide the full Java stack trace for the error? Perhaps, we can extract something useful from it.

Thanks

Peter

 

There is no such issue in 11g (11.2.0.3 RAC).

So, forget about it.

I think it was some combination of circumstances.

Pavel.