PDB Cells are not rendered properly

[ravikiran]

Hi Team,

Some of the PDB cells are garbled when it is rendered in the node’s output table. We are using PbdCellFactory.create().

What I noticed is, as the size of the cell increases, the distortion is more. 1ett is rendered properly but not the other 2.

1ett - 332 K
6i49 - 756 K
7rf3 - 8.5 M

Is this a known issue?

Thanks
Ravikiran

[Martyna]

Hi @ravikiran ,

good question! I haven’t seen this before.

Did you use the node below where this happens?

Get PDB

Best,
Martyna

[Artem]

I have experienced similar issue with other data types: JSON or XML. It only happens when the cell contains a lot of data. As far as I understand this might be happening here as well.
I can see that @ravikiran uses Linux, so do I. Maybe it is a platform related issue.

In case it might be helpful, here is my config:

• Kubuntu 20.04;
• KDE Plasma 5.18.8;
• Kernel 5.4.0-132-generic.

[Martyna]

Hi @Artem
thanks for commenting on this! I will research this internally and come back to the thread as soon as I have a (hopefully) useful explanation.
Best,
Martyna

[ravikiran]

Hi Martyna,

Yes ‘Get PDB’ is the node I am using.

Thanks
Ravikiran

[ravikiran]

It only happens when the cell contains a lot of data.

Yes exactly. See my initial query where the distortion is more with size.

[ravikiran]

Thanks. Also, is that possible to add another renderer for PDB cells which just display the title/header alone? Generally the pdbs are huge in size.

[Artem]

Hello @Martyna

Just in case I took this example. I used GET Request node and simply requested https://www.instagram.com/

This is what I got:

[Martyna]

So it’s not only the file size but more the cell size that makes the issues? as you are having only one row here.

[Artem]

No, it also happens when I have multiple rows in the table. Re-scaling the cell size does not help.

[Martyna]

Hi, I can confirm we were able to reproduce this. I have created a ticket.

@ravikiran do you know of a renderer that would show less?
Would it be possible to turn this into a string and do a workaround that would filter only the top-level information? I didn’t try myself, just thinking of different ways.

Best regards,
Martyna

[ravikiran]

Dear Martyna,

do you know of a renderer that would show less?

The solution I can think of is to create a dedicated renderer (say ‘PDB Summary’) and show only the HEADER and TITLE sections. We can create a dedicated renderer from our side but since this is a general issue faced by everyone, it would be nice if KNIME can add the additional renderer and makes it default in Preferences.

Thanks
Ravikiran