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monarch-initiative / mondo-ingest

Coordinating the mondo-ingest with external sources
https://monarch-initiative.github.io/mondo-ingest/
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Feature data release and patch for the lexmatch generation #582

Closed matentzn closed 1 week ago

matentzn commented 1 week ago

[!note]

  • Includes #581

Build for:

Current issues

Failed with:

python3 ../scripts/sync_subclassof.py \
--outpath-added reports/doid.subclass.added.robot.tsv \
--outpath-added-obsolete reports/doid.subclass.added-obsolete.robot.tsv \
--outpath-confirmed reports/doid.subclass.confirmed.robot.tsv \
--outpath-direct-in-mondo-only reports/doid.subclass.direct-in-mondo-only.tsv \
--outpath-self-parentage tmp/doid.subclass.self-parentage.tsv \
--mondo-db-path tmp/mondo.db \
--mondo-ingest-db-path tmp/mondo-ingest.db \
--mondo-mappings-path tmp/mondo.sssom.tsv \
--onto-config-path metadata/doid.yml
Traceback (most recent call last):
  File "/work/src/ontology/../scripts/sync_subclassof.py", line 523, in <module>
    cli()
  File "/work/src/ontology/../scripts/sync_subclassof.py", line 500, in cli
    sync_subclassof(**d)
  File "/work/src/ontology/../scripts/sync_subclassof.py", line 314, in sync_subclassof
    raise ValueError(
ValueError: FATAL BUILD ERROR: Ancestors discrepancy
Detected error in consistency of sets of terms gathered from Mondo.

 1. Mondo SCR ancestors: 259069
 2. Mondo direct SCR relationships: 33833
 3. Mondo indirect SCR relationships: 225279
 Intersection (Top 5): [('MONDO:0971014', 'rdfs:subClassOf', 'MONDO:0008855'), ('MONDO:0971008', 'rdfs:subClassOf', 'MONDO:0007100'), ('MONDO:0970964', 'rdfs:subClassOf', 'MONDO:0968988'), ('MONDO:0970962', 'rdfs:subClassOf', 'MONDO:0017077'), ('MONDO:0970998', 'rdfs:subClassOf', 'MONDO:0002254')]
 "1" should be same as "2" + "3", but instead it has n less rels: 43
See also: https://github.com/monarch-initiative/mondo-ingest/issues/525

Exiting.
make[1]: *** [mondo-ingest.Makefile:544: reports/doid.subclass.confirmed.robot.tsv] Error 1
make[1]: Leaving directory '/work/src/ontology'
make: *** [mondo-ingest.Makefile:342: build-mondo-ingest-no-imports] Error 2
Command exited with non-zero status 2
### DEBUG STATS ###
Elapsed time: 3:12:51
Peak memory: 32032256 kb

Related

matentzn commented 1 week ago

I assigned this to @twhetzel to merge!

twhetzel commented 1 week ago

I also ran the build from a fresh clone of the repo (on Sat, 22-Jun) using the fix-confidence-issue-sssom branch as: sh run.sh make build-mondo-ingest -B and have the same results as this PR other than 4 different lines in the lexmatch/README.md file.

I also re-ran the build as a second test on Sunday from this same clone and other than differences in files that relate to OMIM this second test build also has the same diff result as compared to this PR. Note, there is an automatic refresh of the OMIM repo used by the mondo-ingest repo on Saturday evening so this would account for the OMIM files being different between these two test builds and OMIM is updated daily.

In both test builds, I did not encounter the ancestors ValueError issue.

With all of our reviews, this PR will be approved and merged.