> 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
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).
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
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?
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?
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?
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.
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.
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.)
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.
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!
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