superstructure search fails

superstructure search does not seem to work.








SQL> select cpd_sid,jc_smiles from cpd where jc_Compare(jc_smiles,'c1ccccc1', 't:r')=1;


select cpd_Sid,jc_smiles from cpd where jc_Compare(jc_smiles,'c1ccccc1', 't:r')=1


*


ERROR at line 1:


ORA-29902: error in executing ODCIIndexStart() routine


ORA-29532: Java call terminated by uncaught Java exception:


java.lang.RuntimeException: The following exception has been thrown by the


servlet:


Exception: null


ORA-06512: at "JCHEM_CARTRIDGE.JCHEM_CORE_PKG", line 0


ORA-06512: at "JCHEM_CARTRIDGE.JC_IDXTYPE_IM", line 323


ORA-06512: at line 1





SQL> select jchem_core_pkg.getenvironment() from dual;





JCHEM_CORE_PKG.GETENVIRONMENT()


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


Oracle9i Enterprise Edition Release 9.2.0.7.0 - Production


PL/SQL Release 9.2.0.7.0 - Production


CORE 9.2.0.7.0 Production


TNS for Linux: Version 9.2.0.7.0 - Production


NLSRTL Version 9.2.0.7.0 - Production


NLSRTL Version 9.2.0.7.0 - Production


JChem version in the database: 3.1.5


JChem version in the Tomcat server: 3.1.5


java.vm.version: 1.4.2_11-b06


java.vm.vendor: Sun Microsystems Inc.


Apache Tomcat/5.0.19





JCHEM_CORE_PKG.GETENVIRONMENT()


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


Major JDBC version in Tomcat: 10


Minor JDBC version in Tomcat: 2

Please, could you post the stack trace from the Tomcat log?





Thanks





Peter

java.lang.NullPointerException


at java.lang.String.<init>(String.java:346)


at chemaxon.jchem.db.JChemSearch.retrieveBatchAndSearch(JChemSearch.java:3401)


at chemaxon.jchem.db.JChemSearch.searchInDB(JChemSearch.java:3344)


at chemaxon.jchem.db.JChemSearch.search1(JChemSearch.java:2118)


at chemaxon.jchem.db.JChemSearch.search(JChemSearch.java:1909)


at chemaxon.jchem.db.JChemSearch.setRunning(JChemSearch.java:1796)


at chemaxon.jchem.db.JChemSearch.run(JChemSearch.java:1816)


at chemaxon.jchem.cartridge.servlets.JChemCached.run(JChemCached.java:851)


at chemaxon.jchem.cartridge.servlets.JChemCached.doSearch(JChemCached.java:808)


at chemaxon.jchem.cartridge.servlets.JChemCached.doPerform(JChemCached.java:610)


at chemaxon.jchem.cartridge.servlets.JChemCached.process(JChemCached.java:137)


at chemaxon.jchem.cartridge.servlets.JChemServletBase.doPost(JChemServletBase.java:232)


at javax.servlet.http.HttpServlet.service(HttpServlet.java:763)


at javax.servlet.http.HttpServlet.service(HttpServlet.java:856)


at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:284)


at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:204)


at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:257)


at org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:151)


at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:567)


at org.apache.catalina.core.StandardContextValve.invokeInternal(StandardContextValve.java:245)


at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:199)


at org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:151)


at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:567)


at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:184)


at org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:151)


at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:164)


at org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:149)


at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:567)


at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:156)


at org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:151)


at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:567)


at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:972)


at org.apache.coyote.tomcat5.CoyoteAdapter.service(CoyoteAdapter.java:206)


at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:833)


at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processConnection(Http11Protocol.java:732)


at org.apache.tomcat.util.net.TcpWorkerThread.runIt(PoolTcpEndpoint.java:619)


at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:688)


at java.lang.Thread.run(Thread.java:534)

This is a bug in JChem Cartridge. It will be fixed in the next JChem release.





Thank you for reporting it.





Peter

Some additional information on the nature of the bug:





The superstructure search problem only occurs if there are one or more NULL values in the structure column of the indexed table.





Szilard

SQL> select cpd_sid from cpd where jc_smiles is null;





CPD_SID


----------


3834778





SQL> delete from cpd where cpd_sid=3834778;





1 row deleted.





SQL> select cpd_sid from cpd where jc_compare(jc_smiles,'c1ccccc1','t:r')=1;


select cpd_sid from cpd where jc_compare(jc_smiles,'c1ccccc1','t:r')=1


*


ERROR at line 1:


ORA-29902: error in executing ODCIIndexStart() routine


ORA-29532: Java call terminated by uncaught Java exception:


java.lang.RuntimeException: The following exception has been thrown by the


servlet:


Exception: null


ORA-06512: at "JCHEM_CARTRIDGE.JCHEM_CORE_PKG", line 0


ORA-06512: at "JCHEM_CARTRIDGE.JC_IDXTYPE_IM", line 323


ORA-06512: at line 1








SQL> select count(*) from cpd where jc_smiles is null;





COUNT(*)


----------


0

Please, commit your work and try searching thereafter.

Good, forgot that part. Works as you suggested.

The bug is fixed in JChem 3.2 which has recently been released.