ChemAxon Forum Archive » Storage & search: JChem Base and JChem Oracle Cartridge

JChem 15.4.20.0: Some structures could not be index

User e127549d9c

03-06-2015 10:10:26

Hi all,


After upgrading Jchem to version  15.4.20.0 some structures were not able to index.


Message from jchem-log


SEVERE: Error while processing ROWID=AEgH9LAJkAAIWiuAAD: chemaxon.jchem.db.UpdateHandlerException: java.lang.NullPointerException


Caused by:


java.lang.NullPointerException, 


  CDK    6/26/13,23:51

 
...


[RMI TCP Connection(9)-10.225.18.15/58]: 2015-05-31 12:27:20.764 chemaxon.jchem.cartridge.rmi.impl.RmiExceptionHandler handleError


SEVERE: chemaxon.jchem.cartridge.servlets.indexing.IndexingException: 1 structure(s) could not be indexed. Please, check the JChem Server logs.


java.util.concurrent.ExecutionException: chemaxon.jchem.cartridge.servlets.indexing.IndexingException: 1 structure(s) could not be indexed. Please, check the JChem Server logs.


        at java.util.concurrent.FutureTask.report(FutureTask.java:122)


        at java.util.concurrent.FutureTask.get(FutureTask.java:188)


        at chemaxon.jchem.cartridge.servlets.indexing.operations.AbstractAsyncIndexing.waitForProgressRefresh(AbstractAsyncIndexing.java:43)


        at chemaxon.jchem.cartridge.rmi.impl.IndexImpl.waitForProgressRefresh(IndexImpl.java:149)


        at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown Source)


        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)


        at java.lang.reflect.Method.invoke(Method.java:606)


        at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:322)


        at sun.rmi.transport.Transport$2.run(Transport.java:202)


        at sun.rmi.transport.Transport$2.run(Transport.java:199)


        at java.security.AccessController.doPrivileged(Native Method)


        at sun.rmi.transport.Transport.serviceCall(Transport.java:198)


        at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:567)


        at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:828)


        at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.access$400(TCPTransport.java:619)


        at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler$1.run(TCPTransport.java:684)


        at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler$1.run(TCPTransport.java:681)


        at java.security.AccessController.doPrivileged(Native Method)


        at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:681)


        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)


        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)


        at java.lang.Thread.run(Thread.java:745)


Caused by: chemaxon.jchem.cartridge.servlets.indexing.IndexingException: 1 structure(s) could not be indexed. Please, check the JChem Server logs.


        at chemaxon.jchem.cartridge.servlets.indexing.errorhandling.IndexingErrorHandlerImpl.checkDeferredErrors(IndexingErrorHandlerImpl.java:90)


        at chemaxon.jchem.cartridge.servlets.indexing.operations.CreateIndex.buildIndexConcurrently(CreateIndex.java:545)


        at chemaxon.jchem.cartridge.servlets.indexing.operations.CreateIndex.buildIndex(CreateIndex.java:454)


        at chemaxon.jchem.cartridge.servlets.indexing.operations.CreateIndex.executePayLoad(CreateIndex.java:116)


        at chemaxon.jchem.cartridge.servlets.indexing.operations.AbstractIndexing.executeSynch(AbstractIndexing.java:73)


        at chemaxon.jchem.cartridge.servlets.indexing.operations.AbstractAsyncIndexing$1.call(AbstractAsyncIndexing.java:65)


        at java.util.concurrent.FutureTask.run(FutureTask.java:262)


        ... 3 more

Structure:






  CDK    6/26/13,23:51






 22 24  0  0  0  0  0  0  0  0999 V2000


  543.7999  595.3185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  573.7359  578.0356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  513.8680  578.0356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  537.8000  629.3564    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0


  573.7359  543.4698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  621.6378  605.6841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  513.8680  543.4698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  543.7999  526.1828    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  612.6591  521.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0


  648.1132  583.4698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  627.6418  639.7303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  483.9319  526.1828    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  680.5925  595.2934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  660.1212  651.5498    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  601.1581  661.9489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  454.0000  543.4698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  686.5922  629.3271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  704.5079  569.7315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  567.1160  655.9449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  610.1075  695.3373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  454.0000  578.0356    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0


  739.5718  577.8873    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0


  1  2  1  0  0  0  0 


  1  3  2  0  0  0  0 


  1  4  1  0  0  0  0 


  2  5  2  0  0  0  0 


  6  2  1  1  0  0  0 


  7  3  1  0  0  0  0 


  5  8  1  0  0  0  0 


  5  9  1  0  0  0  0 


  6 10  1  0  0  0  0 


  6 11  1  0  0  0  0 


  8  7  2  0  0  0  0 


  7 12  1  0  0  0  0 


 10 13  2  0  0  0  0 


 14 11  1  0  0  0  0 


 11 15  1  6  0  0  0 


 12 16  1  0  0  0  0 


 13 17  1  0  0  0  0 


 13 18  1  0  0  0  0 


 17 14  1  0  0  0  0 


 19 15  2  0  0  0  0 


 15 20  1  0  0  0  0 


 16 21  1  0  0  0  0 


 18 22  1  0  0  0  0 


 18 22  1  0  0  0  0 


M  END

 


Environment:


JChem server environment


----------------------------------------------------------------------------------------------------


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 owner: JCHEM_GG_PORTAL


 


JChem Server environment:


Java VM vendor: Oracle Corporation


Java version: 1.7.0_75


Java VM version: 24.75-b04


JChem version: 15.4.20.0


JChem index version: 15030900


                                  
JDBC driver version: 11.2.0.3.0

to create the index we do


CREATE INDEX chem_structs_i_jchem ON chem_structs (structure) INDEXTYPE IS jc_idxtype


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

 


In result we deleted this row, successfully recreated index and inserted row back. No errors.


 


Please, can you some comment this situation. What we have to do to avoid this in the future?


We use Jchem cartridge many years. Last update was more one year ago. Maybe we need update some structures?


But on other server with the same environment on the same data in table, index was recreated without errors - it's some strange for us.


 


Regards,


Maria

ChemAxon abe887c64e

03-06-2015 13:27:18

Hi Maria,


Thank you for the report, we could reproduce the unsuccessful indexing of the structure you sent, and will be back after a deeper investigation.


Best regards,


Krisztina

ChemAxon abe887c64e

03-06-2015 15:09:16

Hi Maria,


We checked the structure in question and found it erroneous. The last two bond-defining lines consist of the same numbers (that is, the same bond is defined two times):



 18 22  1  0  0  0  0 


 18 22  1  0  0  0  0


This causes the unsuccessful indexing. If we remove one of these lines and modify the bond number from 24 to 23 in the first line


from



 22 24  0  0  0  0  0  0  0  0999 V2000


to



 22 23  0  0  0  0  0  0  0  0999 V2000


import or indexing works fine.


With which tool was this structure drawn and saved?


Thank you,


Krisztina



User e127549d9c

08-06-2015 16:14:57

Hi Krisztina,


Thank you for help! We have corrected the structure. It was created by a very old tool. 


But I have question - why Jchem saves these structures, but when we are trying to rebuild index - falls with an error. Why did he not immediately issues a message that the structure is bad?


 


Regards,


Maria

ChemAxon abe887c64e

09-06-2015 07:42:46

Hi Maria,


Thank you for the positive feedback.


Is JChem Cartridge index created on JChem tables or on standard Oracle tables  in your system?  If on JChem tables, what is the JChem version number of the old tables? (If on standard Oracle tables, JChem has no effect on what kjnd of chemical structure is stored in them.)


Best regards,


Krisztina