I had a dream last night that this might not be necessary because of the way that semsql works. I dont know exactly what semsql does though, and now that Chris is gone it may be not possible to find out.
Here my dream:
semsql is using relationgraph under the hood (that is a fact)
RG may, all by itself, remove the red subclass axiom in the figure below, rendering the change in this PR ineffectual
In my view, nothing bad will come of this change, but we need to check manually, later down the line, if subclass assertions in mondo-edit.owl do not get support, even though it exists. We can stem that in a second round I think
Overview
This PR:
Changes the source of the subclass sync Mondo DB to a version that contains both the release and edit file axioms
This was discussed and agreed in the last tech call
Pre-merge checklist
Documentation
Was the documentation added/updated under docs/?
[ ] Yes
[X] No, updates to the docs were not necessary after careful consideration
QC
Was the full pipeline run before submitting this PR using sh run.sh make build-mondo-ingest on this branch (after
docker pull obolibrary/odkfull:dev), and no errors occurred?
[X] Yes
[ ] No, there are no functional (code-related) changes to the pipeline in the PR, so no re-run is necessary
Has the PR been sufficiently reviewed by at least 1 team member of the Mondo Technical team and all threads resolved?
[ ] Yes
[X] No
Sub-tasks
[ ] Ensure this PR is actually useful & doing what it is supposed to
As @joeflack4 determine in his comment this PR may, after all, be redundant. We need to figure out the following:
If a redundant subclass axiom exists in Mondo (red line), will we gather evidence for it?
We may have to adjust the code to handle this case if it is not, but we can put this on the list of priorities in the next quarter
I had a dream last night that this might not be necessary because of the way that semsql works. I dont know exactly what semsql does though, and now that Chris is gone it may be not possible to find out.
Here my dream:
In my view, nothing bad will come of this change, but we need to check manually, later down the line, if subclass assertions in mondo-edit.owl do not get support, even though it exists. We can stem that in a second round I think
Overview
This PR:
Pre-merge checklist
Documentation
Was the documentation added/updated under
docs/?QC
Was the full pipeline run before submitting this PR using
sh run.sh make build-mondo-ingeston this branch (afterdocker pull obolibrary/odkfull:dev), and no errors occurred?New Packages
Were any new Python packages added?
Were any other non-Python packages added?
PR Review and Conversations Resolved
Has the PR been sufficiently reviewed by at least 1 team member of the Mondo Technical team and all threads resolved?
Sub-tasks