ArrayIndexOutOfBounds exception on RXN to RInChi node

Groups Cheminformatics
1

@swebb

Hi,

I am trying to use the RXN to RInChi node, but get an ArrayIndexOutOfBounds exception. See attached workflow and log. The strange thing is that I was under the impression it worked before. Any idea how to fix this?

log.txt (344.1 KB)

RInChi_problem
RInChi_problem1152Ă—648 73.6 KB

Thanks for your help in advance.

Regards,
dstefane

2

Hi @dstefane

Sorry you’ve had an issue. Let’s see if we can work out what’s going on.

As an aside, there’s probably no point doing the parallel chunk on the Rxn to RInChi node the underlying dll will only be able to process 1 reaction at a time anyway.

Can you double check that you’ve selected a column and than hit ok on the dialog? The error might be a classic case of forgetting to check a column was actually selected which results in trying to get the column name as position -1 which would throw this exception. Opening the dialog and selecting close/cancel because if looks ok isn’t sufficient, it’s important to hit ok.

Unfortunately I don’t see anything in the log from a quick skim, are you able to share an example failing reaction input table with me?

Cheers

Sam

3

Hi Sam,

thanks for your quick reply. Actally, there was a column selected and I did it now again and started the workflow. Let’s see if anything changes. My impression yesterday was that the workflow actually started and broke after some time. I’ll kep you updated on the outcome.

Regarding the parallel chunks, my impression without them - which was my first attempt - was that nothing started du to my large data set, i.e. the node shew “executing” but no processed lline numbers.

Thanks again,
dstefane

4

It should fail immediately if my hunch is correct. If it takes a while to fail then there’s something else going wrong in the code that I’ll need to fix.

I’ll have a look for anything obvious.

EDIT: It looks like if something unexpected happens and it throws an exception other than a RinchiException then this could happen. I will update the node tomorrow to catch additional exception types.

Cheers

Sam

5

I’ve update the node in the trunk build so instead of crashing it will hopefully return missing cells when an issue is found.

The nodes can be installed from: http://update.knime.com/community-contributions/trunk in about 10 minutes time.

The builds for version 4 are still running.

Let me know if this fixes the issue? If not we’ll try something else.

Cheers

Sam

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6

@swebb

Hi Sam,

thanks for your help so far. My second run completed successfully. I am not sure what made it fail at the first run, because there was definitely the right column chosen. The only thing I did afterwards was to select another column, go back and select the right one, hit apply and run the work flow to completion.

Thanks and best regards,
dstefane

2 Likes