XML reader times out

KNIME Analytics Platform
1

Hi all, 

I noticed the in KNIME 2.6 the XML Reader node fails with a time-out error much faster than its predecessor in v2.5.4.

For example I used this URL as selected file in the XML Reader node:

https://www.ebi.ac.uk/chemblws/compounds/similarity/c1[n]c2[nH]ccc2c([n]1)-c1ccccc1/70

and gives me this error:

 

ERROR XML Reader Execute failed: Read timed out

By slighly increasing the tanimoto threshold to 75 and above (i.e. reducing the length of the response) the same query works:

https://www.ebi.ac.uk/chemblws/compounds/similarity/c1[n]c2[nH]ccc2c([n]1)-c1ccccc1/75

As I said, this was definitely not the case in 2.5.4.

Is there a fix?

 

Thanks in advance,

George

ChEMBL group

 

2

We have introduced a timeout of 1 second for all readers since quite a few users complained that slow websites blocked dialogs. You can adjust the timeout by setting the Java property "knime.url.timeout" to a value in milliseconds in your knime.ini (e.g. -D.knime.url.timeout=10000).

3

Hi Thorsten,

Indeed, by adding this:

 

-Dknime.url.timeout=6000

in the knime.ini, the problem was solved.

Many thanks,

George

4

I'm not sure this is an ideal solution relying on the user to be editing the knime.ini file, it's not particularly user friendly. Is there no way of building in a timeout setting in the node dialog of the XML reader node. At least this way George could update his public workflows so they work straight out of the box.

 

Simon.

1 Like
5

I agree with "richards99"  it's not the ideal solution but it did work for me. However now I've upgrade to knime 2.7.4 it doesn't work anymore. Has there been a change?

I now implement a JPython script which does work since but obviously this is not the preferred way at all.

 

Thanks,

Peter

6

Do you have to restart KNIME when you change the knime.ini?

 

 

7

Yes.