Something error in the Executing of W8 Protein Data Acquisition , TeachOpenCADD workflow

KNIME Server
1

running the PDB connector query executer in Step 1, W8:
ERROR PDB Connector Query Executor 0:24:280 Execute failed: java.util.concurrent.ExecutionException: java.io.IOException: Error retrieving query - Response code 400 - ‘{
“status” : 400,
“message” : “Invalid request to the [ text ] service: search is not enabled on [ chem_comp.type ] attribute”,
“link” : “ReDoc”
}’

2

Hi @kuc626

thanks for reporting this issue on the forum.
I’m afraid I’m not familiar with the PDB. However, a status 400 response suggests that some settings were wrong. Do you have a similar example that worked, to which you can compare the current setup?

It would also be very interesting to know what KNIME version you are using and maybe you could give instructions on how to reproduce the issue you experienced.

Kind regards
Marvin

3

Hi, Marvin!
I’ve tried both knime versions 4.3 and 4.4, but they still show the same error.

4

Hm, I’m afraid the workflow isn’t working for me either. Maybe @Vernalis has an idea what might have changed recently and how to get everything working again?

We’re talking about the PDB Connector Query Executor – KNIME Hub node in W8 of

Kind regards
Marvin

2 Likes
5

Hi Marvin,

This relates to some heavy changes to the remote RESTful API around 6 weeks ago (see PDB Connector Issues) - Some of the queries (full text, and most things relating to chemical components) were moved to a separate search service with the RESTful API which broke any query involving any of those search types.

I have pushed an updated version which managed to fix this in the node without breaking any queries. That fix is available as of yesterday in the stable build for KNIME versions 4.1, 4.2 and 4.3. There are a few issues I need to work through with Gabriel - hopefully next week - to get them available in the 4.4 release channel and nightly builds.

Hopefully those should fix the problems.

Steve

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6

Fantastic! Thank you Steve for clarifying (at lightning speed :D)

@kuc626 if you start your 4.3 version of KNIME, you should be able to update via File > Update KNIME…

Kind regards
Marvin

2 Likes
7

No problem - I just confirmed that it works in KNIME 4.3 with the update applied :slight_smile: (Phew!!!)

Steve

2 Likes