JC_INSERT issue

ChemAxon 60ee1f1328

11-05-2005 14:28:56

> Any ideas about why the error message below is thrown on running


> JC_INSERT would be very helpful!


>


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


> java.io.FileNotFoundException:


> http://hporacle9i.chem.ox.ac.uk:6969/jchemstreams/misc


> ORA-06512: at "JCHEM3.JCHEM_CORE_PKG", line 5


> ORA-06512: at "JCHEM3.JC_INSERT", line 5

ChemAxon aa7c50abf8

11-05-2005 15:58:41

This may be a transient error due to a transient problem in the 'jchemstreams' context. Tomcat is still listening at hporacle9i.chem.ox.ac.uk:6969. If it were not, a more specific error message would be generated.





Please, do the following:





(1) Check the URL http://hporacle9i.chem.ox.ac.uk:6969/jchemstreams with your browser. The entry page to the JChem Cartridge administration GUI should be displayed. If it is not, then nothing is supposed to work in JChem Cartridge (not only jc_insert).





(2) Check the URL http://hporacle9i.chem.ox.ac.uk:6969/jchemstreams/misc with your browser. If it is a blank page, jc_insert should work again. If a 404 error ("The requested resource (/jchemstreams/misc) is not available.") is displayed, then try to restart the 'jchemstreams' context (or the entire Tomcat instance).





Let me know what you found.

ChemAxon 60ee1f1328

12-05-2005 13:24:19

Both conditions (1) and (2) are satisfied.


Unfortunately the problem does still exist.





The call below does not work, where as previously many similar calls have worked fine - the error message is the same.





MarvinSketch will accept the smiles below and convert to graph with no issues - so presumably no problem with the smiles string.





begin


jc_insert ('C1(OC(=O)C=CN-1C-c2(cc(C#N)c(O)c(Cl)c2))C(-c3(cnccc3))=O','smile','JCHEMPROPERTIES','false','false');


end;


/

ChemAxon 60ee1f1328

12-05-2005 13:28:45

simpler calls cause the same issue.





begin


jc_insert ('CCCl','smile','JChemproperties','false','false');


end;


/





Please be aware this is version 2.3.4 and so this may already be a known issue?

ChemAxon 60ee1f1328

12-05-2005 13:42:06

further to this, running the following for a known table





select *


from definitely_exists


where jc_equals ('Cc1[nH]c2c(Br)cc(F)cc2c1CCNC(=S)NCCc3ccccc3',cd_smiles) = 1;





yields the error message





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


oracle.jdbc.driver.OracleSQLException: ORA-00903: invalid table name


ORA-06512: at "JCHEM3.JCHEM_CORE_PKG", line 5


ORA-06512: at "JCHEM3.EQUALS_FUNC", line 32

ChemAxon aa7c50abf8

12-05-2005 13:44:14

I can insert the same molecules in my JChem environment version 2.3.4 without problem.





Please, could you upload the <tomcat-home>/logs/catalina.out file (or relevant portions of it).





Do I understand correctly that you first get the error message as you insert those particular molecules and then you can successfully insert other molecules in the same database session?

ChemAxon aa7c50abf8

12-05-2005 13:52:05

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


oracle.jdbc.driver.OracleSQLException: ORA-00903: invalid table name


ORA-06512: at "JCHEM3.JCHEM_CORE_PKG", line 5


ORA-06512: at "JCHEM3.EQUALS_FUNC", line 32
More information about this problem is output into the database session's trace file in the <ORACLE_HOME>/admin/<DBNAME>/udump directory. Please, could you post this trace file or relevant portions of it?

ChemAxon 60ee1f1328

12-05-2005 14:03:39

As far as I can see JC_INSERT is not working for any given SMILES.





However the attached catalina.out file does have a considerable amount of warning information and so hopefully this will help determine what is missing?

ChemAxon aa7c50abf8

12-05-2005 14:07:34

I guess you forgot the attachement.

ChemAxon 60ee1f1328

12-05-2005 14:10:26

attached is a trace file from today.

ChemAxon 60ee1f1328

12-05-2005 14:10:49

yes sorry

ChemAxon 60ee1f1328

12-05-2005 14:15:56

catalina.out

ChemAxon aa7c50abf8

13-05-2005 08:24:04

I still cannot see your attachment. I attached something so you can see how it looks like when there is an attachment to a posting. (I hope I manage to do the attaching myself. :-) )





First, you have to enter the path to the file that you want to attach in the "Filename" field (underneath the "Message body" edit box).





Then you have to push the "Add Attachment" button (orange of color) next to the "File Comment" edit box (which itself is below the "Filename" edit box).





If you then display a preview of the message currently being edited (by pressing the "Preview" button) you can see your message (on top of the page) and immediately below it a box containing to rows showing your current attachments to the message.

ChemAxon 60ee1f1328

13-05-2005 08:29:10

And the answer is...





Changes I made for security purposes to server.xml has caused this issue...





<Valve className="org.apache.catalina.valves.RemoteAddrValve" allow="x,y" /> under any <Engine>, <Host> and <Context> will cause this problem, good that this has been identified, bad that I cannot implement security at this level without intefering with the Cartridge functions.





Thanks for all your help...

ChemAxon aa7c50abf8

13-05-2005 08:50:32

I would still be interested to know exactly what was the problem. I have never used the RemoteAddrValve parameter, but based on the Tomcat documentation I would presume it should work with JChem Cartridge to restrict access to Tomcat. You just have to specify that your Oracle host also should have access to Tomcat. (If Tomcat and Oracle are on the same machine, then "localhost" must be specified in addition to other permitted hosts.)

ChemAxon 60ee1f1328

13-05-2005 09:36:11

I have tried adding the ipaddress of my localhost to





<Valve className="org.apache.catalina.valves.RemoteAddrValve" allow="x,y"





I have also tried adding the string "localhost" and the machine name rather than ip address to





<Valve className="org.apache.catalina.valves.RemoteHostValve" allow="x,y"





I have tried both the above for all combinations of <Engine>,<Host> and <Context> but alas inclusion of any of the above causes a "not available" error when attempting to check the JChemstreams URL.

ChemAxon 60ee1f1328

13-05-2005 11:00:22

IPtables and building a firewall layer into our Linux server is the next option I am going to investigate, so that the security is not embedded at the application level at all - Thanks Karl!

ChemAxon 60ee1f1328

13-05-2005 11:13:17

I also retract an earlier statement and modify to:





If the <Valve> tags are included in <Context> alone then all the cartridge functionality work fine and a level of security retained.





Cheers!