Error importing SDF files into IJC 5.3.1

We are having import issues with the latest version of IJC (5.3.1), even on files that have been successfully imported in previous versions.

The output we get from the attempted import is:

Starting to import data...

Warning: Failed to import row 1: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 2: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 3: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 4: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 5: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 6: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 7: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 8: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 9: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 10: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 11: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 12: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 13: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 14: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 15: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 16: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 17: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 18: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 19: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 20: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 21: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 22: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 23: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 24: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Warning: Failed to import row 25: com.im.df.api.chem.MarvinStructure cannot be cast to java.lang.String 

 

Error: 

 

TOO MANY CONSECUTIVE ERRORS, TERMINATING IMPORT

 

 

Import completed in 1s.

0 entries successfully imported.

25 Errors.

Bad records can be found at

S:\Projects\....

 

 

Any advice?

Thanks for the error report. We don't know of any such errors, so could you give us a small sample file that can be used to reproduce the problem. Please send privately to tdudgeon at chemaxon dot com if necessary. This will allow us to investigate the problem.

Many thanks.

Tim

tdudgeon wrote:

Thanks for the error report. We don't know of any such errors, so could you give us a small sample file that can be used to reproduce the problem. Please send privately to tdudgeon at chemaxon dot com if necessary. This will allow us to investigate the problem. Many thanks. Tim

 

Tim:

 

SDF File attached.  I exported the Wombat demo data set from IJC 5.3.1, and I cannot re-import the exported file to a new database table.

 

As an aside, I tried to attach the .errors file as well, but it wouldn't let me.  If you would like this, I'll email it to you.

The file that you attached imported OK for me with IJC 5.3.1

Could you please attach:

1, info from the Help> About Instant JChem window.

2, the log file after a failed import. The log file can be found using: View -> Instant JChem log file

Thanks

Tim

Tim:

 

See attached.

 

-B.

Thanks for that extra information. It has helped track down the problem.

It seems that it happens when importing a structure file as a standard table (with the structures being put into a text field). Importing as a structure table is unaffected.

We will resolve the problem.

Thanks

Tim

Tim:

 

Until this is fixed, what can we do to work around it?  I know you said you were able to import the file, and right now we have two different project teams waiting for the data we need to import.

 

Thanks again.

 

-B.

Import into a structure table works fine. It seems that the bug is just related to importing a structure file as  a non-structure table. Can you confirm that this is what you are trying to do (this would be an unusual thing to do, but there might be good reasons for wanting to do so)?

Assuming so, the obvious thing to suggest is to import into a structure table instead.

If this isn't possible we can provide a fix, but it is not fully tested yet so might potentially cause other problems.

Tim

Tim:

 

I'm not following you. Are you saying we should import as a "New structure entity"?  

Hi Tim,

When we try to import our SDF file into the structure table, we get an Oracle Error that says "identifier too long". I believe that means one of the headers in the SDF file is too long for creating column names in the Oracle table. Do you know the maximum allowed length for the column names?

Yes, the only way we can reprodue the bug is by importing a structure file into a standard entity. If the file is imported into a structure entity (e.g. a JChem base table), which would be the default beahaviour, the import appears to go OK. At least that's how it seems to me. If you are seeing anythign differnt then please let me know.

I hope to upload a fix for the problem soon.

Tim

Tom,

the max length for things like table and column names in oracle is 30 characters. It would be useful to know what was too long, as we try to handle things like that, so knowing what was the cause would be useful (e.g. exactly what was considered too long).

Can you send us the log file that contains a full error report. You can find its location by looking for the "Userdir" property in the Help->About Instant JChem dialog, and then looking in the var/log directory within this location. The log files will be called messages.log or messages.log.1 etc, where ones with a number on the end are older log files (a new one is created each time IJC starts).

If you could track down the error and attach it then it will help us improve this.

Thanks

Tim

Here is a fix for the import error reported by Brian.

Please download the attached file and install it in IJC.

1. Download the file and remove the .zip expension. The actual file name will become com-im-ijc-io.nbm. Adding the .zip extension was necessary as .nbm is not allowed on the forum.

2. Open IJC.

3. Use Tools->Plugins to open the plugin manager.

4. Switch to the "Downloaded" tab and click on the "Add Plugins..." button. Locate the renamed downloaded file.

5. Click on the "Install" button.

6. Restart IJC when finished.

 

Please note that whilst this fix seems to solve the problem, but has not yet had extensive testing. I recommend installing it only for people who need the fix.

 

Tim

tdudgeon wrote:

Tom, the max length for things like table and column names in oracle is 30 characters. It would be useful to know what was too long, as we try to handle things like that, so knowing what was the cause would be useful (e.g. exactly what was considered too long). Can you send us the log file that contains a full error report. You can find its location by looking for the "Userdir" property in the Help->About Instant JChem dialog, and then looking in the var/log directory within this location. The log files will be called messages.log or messages.log.1 etc, where ones with a number on the end are older log files (a new one is created each time IJC starts). If you could track down the error and attach it then it will help us improve this. Thanks Tim

Tim:

 

It looks like IJC was choking on the SDF file name, not on any data within the file.  I have imported files with longer names in the past.  Perhaps there was a change in the last update?

Thanks again.

-Brian.

tdudgeon wrote:

Here is a fix for the import error reported by Brian. Please download the attached file and install it in IJC.   Please note that whilst this fix seems to solve the problem, but has not yet had extensive testing. I recommend installing it only for people who need the fix.   Tim

Tim:

 

Working on this now.  I'll update you when I know more.

 

Thanks,

 

-B.