generate go.db (sqllite version of the GO), for use with closure tooling in oaklib

[sierra-moxon]

We need to generate a sqllite version of the GO to improve speed in calculating closures used in generating index files for GO-CAMs served by the go API.

This work includes:

• update go-ontology to use a more recent version of ODK (ODK docker image is already used in the pipeline to generate different serializations of the GO) that incorporates the backend packages (semsql, which also has rdflib and rust requirements better included via ODK than manually) that are used to generate this artifact.
• In the geneontology/go-ontology repo, add a target to generate the .db artifact like this:

%.db: %.owl
	@rm -f $*.db $*-relation-graph.tsv.gz .template.db .template.db.tmp
	semsql make $*.db
	@rm -f $*-relation-graph.tsv.gz .template.db .template.db.tmp
	@test -f $*.db || (echo "SQLite/SemSQL generation failed" && exit 1)

locally in the geneontology/go-ontology repo (with the most recent version of ODK):

% cd go-ontology/src/ontology
% wget https://purl.obolibrary.org/obo/go.owl .
% ./run.sh semsql make go.db      # run.sh is equivalent to odk.sh as documented in ODK 

This requires go.owl to be present in the directory where the make command is run. and is called like: % ./run.sh semsql make go.db which wraps a call to the running ODK docker container and runs semsql inside that docker container.

• It would be nice to run this command both on the full go.owl file, and separately on the go-base.owl file, so we have choice in artifacts to use in calculating closures (the go-base version being smaller and quicker).

• make sure the go.db is shuttled to the "products" directory of skyhook release/snapshot/etc...

[kltm]

As a temporary workaround until we have this in the main pipeline, @sierra-moxon will provide a manually created go.db (and go-basic.db) which we will try to sideload onto the next release attempt.

[kltm]

@sierra-moxon Is there a GO-CAM-in-API issue somewhere? I know I've seen it, but I'm having trouble finding it for some reason...