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add goals to generate a mapping change diff report #7962

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merged 5 commits into from
Jul 25, 2024
Merged

add goals to generate a mapping change diff report #7962

merged 5 commits into from
Jul 25, 2024

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twhetzel
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addresses #7230

@twhetzel twhetzel requested a review from matentzn as a code owner July 14, 2024 15:03
@twhetzel twhetzel mentioned this pull request Jul 14, 2024
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matentzn requested changes Jul 18, 2024
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1 important, 1 minor suggestion

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Another thing I just saw

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@twhetzel twhetzel self-assigned this Jul 19, 2024
twhetzel and others added 3 commits July 18, 2024 21:13
@twhetzel @matentzn
Update src/ontology/mondo.Makefile
1bfd009 
Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
@twhetzel @matentzn
Update src/ontology/mondo.Makefile
5c56c7d 
Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
@twhetzel @matentzn
Update src/ontology/mondo.Makefile
d90d4e5 
Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
@matentzn matentzn mentioned this pull request Jul 19, 2024
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@twhetzel twhetzel requested a review from matentzn July 19, 2024 15:57
@twhetzel twhetzel assigned matentzn and unassigned twhetzel Jul 19, 2024
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LGTM, assuming you tried this!

@twhetzel twhetzel assigned twhetzel and unassigned matentzn Jul 19, 2024
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No, actually I have not but I will.

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twhetzel commented Jul 23, 2024
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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.

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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.

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Remove txt KGCL output
51851bb 
This output was not needed for the Mondo DIFF pipeline
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hrshdhgd commented Jul 23, 2024 •
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No handler for key: RemoveNodeFromSubset

@hrshdhgd?

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

@hrshdhgd hrshdhgd mentioned this pull request Jul 23, 2024
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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.

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twhetzel commented Jul 23, 2024 •
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@matentzn anything else that should be checked or done before merging? If nothing else is needed, can you please merge? Thank you!

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No, good to go!

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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

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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!

@twhetzel twhetzel merged commit ad86856 into master Jul 25, 2024
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@twhetzel twhetzel deleted the issue-7230 branch July 25, 2024 06:00
twhetzel added a commit that referenced this pull request Jul 26, 2024
@twhetzel @matentzn
add goals to generate a mapping change diff report (#7962)
b6c500b 
* add goals to generate a mapping change diff report

* Update src/ontology/mondo.Makefile

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

* Update src/ontology/mondo.Makefile

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

* Update src/ontology/mondo.Makefile

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

* Remove txt KGCL output

This output was not needed for the Mondo DIFF pipeline

---------

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
twhetzel added a commit that referenced this pull request Jul 31, 2024
@twhetzel @matentzn
add goals to generate a mapping change diff report (#7962)
9d73c70 
* add goals to generate a mapping change diff report

* Update src/ontology/mondo.Makefile

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

* Update src/ontology/mondo.Makefile

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

* Update src/ontology/mondo.Makefile

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

* Remove txt KGCL output

This output was not needed for the Mondo DIFF pipeline

---------

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
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