add goals to generate a mapping change diff report

[twhetzel]

addresses #7230

[matentzn]

1 important, 1 minor suggestion

[matentzn]

Another thing I just saw

[matentzn]

LGTM, assuming you tried this!

[twhetzel]

No, actually I have not but I will.

[twhetzel]

If I run sh run.sh make kgcl-diff -B I get:

...
runoak -i simpleobo:tmp/mondo-released.obo diff -X simpleobo:mondo-base.obo -o reports/difference_release_base.yaml --output-type yaml
runoak -i simpleobo:tmp/mondo-released.obo diff -X simpleobo:mondo-base.obo \
-o reports/difference_release_base.tsv --output-type csv --statistics --group-by-property oio:hasOBONamespace
runoak -i simpleobo:tmp/mondo-released.obo diff -X simpleobo:mondo-base.obo -o reports/difference_release_base.md --output-type md
No handler for key: RemoveNodeFromSubset

When I tried: sh run.sh make all -B I ran into this error:

MISSING FILE ERROR file '../sparql/preprocess-module.ru' does not exist

It runs in "obolibrary/odkfull:latest" and I pulled the latest.

Edit: Each make command above resulted in failure with the error messages as posted above.

[matentzn]

No handler for key: RemoveNodeFromSubset

@hrshdhgd?

MISSING FILE ERROR file '../sparql/preprocess-module.ru' does not exist

I will track that down for the sake of identifying the leak, but in general we should never run:

sh run.sh make all -B

Always run:

sh run.sh make all -B IMP=false

Somewhere in the main pipeline there is an import dependency that should not exist anymore, but this is unrelated to this PR.

[hrshdhgd]

No handler for key: RemoveNodeFromSubset

@hrshdhgd?

Sorry about that. Somehow this got missed in oaklib. Working on a PR right now.

[twhetzel]

I ran sh run.sh make all -B IMP=false and the release process finished successfully.

I then checked reports/difference_release_base.md against the most recent Orphanet alignment for August release and OMIM Alignment for August release and the new xrefs added into Mondo are found in the new report, e.g. reports/difference_release_base.md.

[twhetzel]

@matentzn anything else that should be checked or done before merging? If nothing else is needed, can you please merge? Thank you!

[matentzn]

No, good to go!

[hrshdhgd]

No handler for key: RemoveNodeFromSubset

@hrshdhgd?

Sorry about that. Somehow this got missed in oaklib. Working on a PR right now.

oaklib v0.6.12 should take care of this

[matentzn]

Thank you @hrshdhgd

It will be a while before we will notice this change, we just updated ODK and it will be at least until October now :P thanks for fixing! @twhetzel i think we can merge this!