error in Import sdf file

User afeef30056

03-08-2007 11:19:55

Hi Tim,

i had a structure database, but there was something wrong in it because of a wrong sdf. So, first i truncated the structure table then i tried to re import my sdf file into the existing table in order to not loose my custom view. But the import from file process gets in error on many rows, this is the message i got:
java.lang.ClassCastException: org.apache.commons.dbcp.DelegatingResultSet
IJC version is the 2.0M5 on linux



ChemAxon fa971619eb

03-08-2007 12:22:43

This possbily looks like a bizare oracle specific bug that I found last week, but without further information I can't be sure. Can you dig out the full details of the exception from the logs so that I can confirm this.

Assuming it is the case then we have it fixed in the current version that we expect to release early next weeek. Will this be OK for you?


User afeef30056

06-08-2007 06:38:59

Hi tim,

the problem persists also if I completely delete the table from application, it seems there is a bug in the new release from ijc during the import from file to oracle.

The error log shows a bad null molecule, but of course the empty structure option was allowed.

ChemAxon fa971619eb

06-08-2007 07:43:50

This looks like one of the Oracle related bugs that we have fixed recently. It relates to inserting large structures into the database.

We will have the 2.0 release out this week that will resolve this.

If you want an immediate fix then you can try updating from this update center:

Set this as your update center by using Tools->Plugins and then going to the Settings tab.

Note: this update center was created for internal testing and is not an official update. But the version it contains should be very close to the final 2.0 version. Also note that the updates are not recognised as being digitally signed, and you are warned about this during the update.


User afeef30056

07-08-2007 09:49:58

Hi Tim

i have not yet tried with the update posted previously but i also got errors importing from text files to a standard database table

ChemAxon fa971619eb

07-08-2007 09:54:50

Are you able to send me these files so that I can test with the 2.0 version that is about to be released?

Please send them privately to tdudgeon at if you are able to do so.