ChEMBLdb Connector - Connexion FAILED

KNIME Analytics Platform
1

Hello everybody,

Everytime I try to extract ChEMBL data with "ChEMBLdb Connector", I get an error message saying :

WARN  ChEMBLdb Connector   0:11       The XML URL may be invalid: Connection timed out
ERROR ChEMBLdb Connector   0:11       Execute failed: Cannot get table: container is not closed.
WARN  ChEMBLdb Connector Input 0:12       The XML URL may be invalid: Connection timed out
WARN  ChEMBLdb Connector Input 0:12       Node created an empty data table.

I have correctly set up my "Network Connections". I don't understand why am I getting this error message ? Can you help me ?

Best Regards,

Baptiste CANAULT

 

2

Hi Baptiste,

Could you try pasting this into your web browser? What happens?

https://www.ebi.ac.uk/chembl/api/data/activity

Thanks,

Jon

3

Hello Jon,

When I paste this into my web browser, I get this message :

"This XML file does not appear to have any style information associated with it. The document tree is shown below."

And I see XML page : <response><activities><activity><activity_comment/> ...

Is it normal ?

Baptiste

 

4

Hi Baptiste,

That sounds normal, and means that you can rule out a network issue from your machine. Are you using the latest version of the ChEMBL connectors?

One other test you could do is to use the REST, 'Get Resource' node with the URL I gave above. Does that work?

Best,

Jon

5

Hi Jon,

I try to install the latest version of KNIME (3.0.0) but without success.

Get Resource solution : ERROR GET Resource         2:6        Execute failed: Error when trying to submit request: java.net.ConnectException: Connection timed out


Thanks,

Baptiste

 

 

6

Hi Baptiste,

Best to use KNIME 2.12.1 for testing. In any case it looks like a network issue since the GET Resouce node also fails.

I guess that this means that you are behind some kind of proxy and you'll need to go to File > Preferences and setup the proxy in KNIME.

Best,

Jon

7

Hi Jon,

With 2.12.2 :  ERROR     GET Resource                       Execute failed: Invalid URL: https://www.ebi.ac.uk/chembl/api/data/activity.

I am connected to internet and I set up correctly my proxy connexion because the nodes "ChEBI" work fine. What is most surprising is that "ChEMBL" nodes have stopped to work in the last month or so.

Regards,

Baptiste

 

8

Hi Baptiste,

Just to note that the question was answered here: https://tech.knime.org/forum/embl-ebi/chembldb-connector-connexion-failed

Best,

Jon