From within Knime I am trying to access a mySQL-based JChem database using JChem Manager followed by JChem Search nodes. The latter complains that:
ERROR JChem Search 3:23 Execute failed: chemaxon.jchem.base.storage.PersistenceException: The structure table contains obsolete data. Please recalculate the table.
Are the Knime nodes incompatible with the JChem version?
ChemAxon/Infocom JChem Extensions Feature 4.4.0.v211500
InstantJChem 21.4.4 (LTS Helium)
The version of JChem used for the KNIME nodes (in this case, v2115 → JChem 21.15) must match the version of IJC. Thus upgrading IJC to version 21.15 should solve the problem.
(KNIME nodes are not released for every version of JChem, so it is easier to get the IJC version to match the KNIME version, rather than the other way around.)
P.S. Chemaxon support responded via a different channel earlier this week.
Hi, thanks for your troll. Could I also downgrade the nodes to match the IJC version? Or would these be incompatible with my Knime version 4.5.1. The things is that if I upgrade IJC many other users need to do this as well.
Downgrading the Chemaxon/Infocom nodes would only be a possibility if there was a release matching the version of IJC you are using. Unfortunately, there was not a ChemAxon/Infocom node build based on JChem 21.4.4, so this is not a possibility in your particular case.
A complete list of all of the Chemaxon/Infocom KNIME node releases can be found here.
Hi, 21.4.4 is a long-term support release. Imo it stands to reason that Infochem should release node versions that are compatible with LTS versions of IJC. Maybe something you can consider?