jc_insert problem (null exception thrown)

User 77bcbbb206

19-04-2005 19:55:10

Can anyone shed some light on the following trace for me? I have a client schema executing a jc_insert on a JCHEM schema on the same database instance with the web server on a different computer. I'm assuming it's some permissions issue, but I can't figure out what. I have attached the whole trace and have appended the last part to this post. Thanks in advance.





=====================


PARSING IN CURSOR #13 len=77 dep=1 uid=116 oct=3 lid=116 tim=1551892709271 hv=2281486051 ad='fe7feaa0'


select cd_id, cd_smiles from JCHEM_CARTRIDGE.RMS_STRUCTURE where cd_hash = :1


END OF STMT


PARSE #13:c=0,e=1290,p=0,cr=0,cu=0,mis=1,r=0,dep=1,og=0,tim=1551892709256


EXEC #13:c=0,e=1288,p=0,cr=0,cu=0,mis=0,r=0,dep=1,og=4,tim=1551892710814


FETCH #13:c=0,e=78,p=0,cr=1,cu=0,mis=0,r=0,dep=1,og=4,tim=1551892711336


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


Exception: null


at chemaxon.jchem.cartridge.JFunctions.checkForException(JFunctions.java:2341)


at chemaxon.jchem.cartridge.JFunctions.sendAndRecBytes(JFunctions.java:2099)


at chemaxon.jchem.cartridge.JFunctions.sendBatchForSearch(JFunctions.java:1793)


at chemaxon.jchem.cartridge.JFunctions.insertSingleMol(JFunctions.java:3076)


at chemaxon.jchem.cartridge.JFunctions.insertMol(JFunctions.java:3019)


EXEC #1:c=1170000,e=1624826,p=1,cr=606,cu=0,mis=0,r=0,dep=0,og=4,tim=1551892738532


ERROR #1:err=29532 tim=158913816


STAT #8 id=1 cnt=5 pid=0 pos=1 obj=18 op='TABLE ACCESS BY INDEX ROWID OBJ#(18) '


STAT #8 id=2 cnt=5 pid=1 pos=1 obj=36 op='INDEX UNIQUE SCAN OBJ#(36) '


STAT #10 id=1 cnt=0 pid=0 pos=1 obj=18 op='TABLE ACCESS BY INDEX ROWID OBJ#(18) '


STAT #10 id=2 cnt=0 pid=1 pos=1 obj=37 op='INDEX RANGE SCAN OBJ#(37) '

ChemAxon aa7c50abf8

20-04-2005 08:03:23

Please, could you post the corresponding stack trace from <tomcat-home>/logs/catalina.out?





My preliminary diagnosis is that you tried to insert a NULL or empty SMILES. NULL or empty SMILES are currently not supported in JChem Cartridge, but will be soon.

User 77bcbbb206

20-04-2005 15:46:48

It's going to take a few hours as this is a deployment at a client site, but I'll post the web server log file when I get it.





On line 69 in the trace file I attached is the jc_insert command that was executed (inserting benzene). I can assure you this jc_insert was not attempting to insert null.


pkovacs wrote:
Please, could you post the corresponding stack trace from <tomcat-home>/logs/catalina.out?





My preliminary diagnosis is that you tried to insert a NULL or empty SMILES. NULL or empty SMILES are currently not supported in JChem Cartridge, but will be soon.

ChemAxon aa7c50abf8

20-04-2005 16:34:47

Sorry, I did not notice you attached a trace file. Based on this trace file, the problem occurred as a perfect search was being performed on the rms_structure table. (Perfect search is executed as part of the duplicate checking specified as an argument to jc_insert.) Perfect search in this case consists of two steps: (1) an SQL statement is executed to find the structures (already existing in the target table) with a hash code matching the hash code of the structure to be inserted; (2) the structures resulting from step (1) are sent to Tomcat to undergo a full graph search comparison with the structure to be inserted. The error seems to occur during step (2) where no database operations are involved. If this is true, the source of the problem is probably not a permission issue.





I definitely need the stack trace from catalina.out.





It would be also extremely helpful to know the JChem version involved. Depending on the JChem version in question, the output of the test.sh script might also be relevant.

User 77bcbbb206

20-04-2005 16:45:32

Thank you very much for the quick reply (and the explanation). Sorry about not sending the version information. JChem 3.0.8. Apache Tomcat 4.1. Oracle 9.2.0.6. I'll get you the tomcat log as soon as I can. I think I can also get the output of the getEnv. I thought the culprit was the web server communication piece and you have confirmed that. Again. Thank you for the quick reply, I really appreciate it.
pkovacs wrote:
Sorry, I did not notice you attached a trace file. Based on this trace file, the problem occurred as a perfect search was being performed on the rms_structure table. (Perfect search is executed as part of the duplicate checking specified as an argument to jc_insert.) Perfect search in this case consists of two steps: (1) an SQL statement is executed to find the structures (already existing in the target table) with a hash code matching the hash code of the structure to be inserted; (2) the structures resulting from step (1) are sent to Tomcat to undergo a full graph search comparison with the structure to be inserted. The error seems to occur during step (2) where no database operations are involved. If this is true, the source of the problem is probably not a permission issue.





I definitely need the stack trace from catalina.out.





It would be also extremely helpful to know the JChem version involved. Depending on the JChem version in question, the output of the test.sh script might also be relevant.

User 77bcbbb206

22-04-2005 17:21:36

I've been taken out of the look for this problem as my client has agreed to fix it. I will have no more updates. The problem did have something do with the web server though. Thanks for the help.