The new code does indeed break existing BioSQL databases. As far as I can tell it relates to the changes in the core_ontology.
To test this, I found that within my existing databases, the core_ontology terms are never used, so I removed all the core_ontology terms from the database. I then re-ran one of my DB programs, so the core ontology would be re-built, but it fails with this error.
So, is this the recommended upgrade method? (I'll have to check whether or not the core_ontology terms are used in my db's, but I don't think they are)
Cheers, Len.
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