monarch-initiative / mondo-ingest

Coordinating the mondo-ingest with external sources
https://monarch-initiative.github.io/mondo-ingest/
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Build 2024-05-22 (ran with error) #537

Closed twhetzel closed 1 month ago

twhetzel commented 1 month ago

This ended with an error status:

Traceback (most recent call last):
  File "/work/src/ontology/../scripts/sync_subclassof.py", line 502, in <module>
    cli()
  File "/work/src/ontology/../scripts/sync_subclassof.py", line 481, in cli
    sync_subclassof(**d)
  File "/work/src/ontology/../scripts/sync_subclassof.py", line 313, in sync_subclassof
    raise ValueError(
ValueError: Detected error in consistency of sets of terms gathered from Mondo.

 1. Mondo SCR ancestors: 257177
 2. Mondo direct SCR relationships: 33484
 3. Mondo indirect SCR relationships: 223743
 Intersection (Top 5): [('MONDO:0006013', 'rdfs:subClassOf', 'MONDO:0700053'), ('MONDO:0033954', 'rdfs:subClassOf', 'MONDO:0100004'), ('MONDO:0968981', 'rdfs:subClassOf', 'MONDO:0019588'), ('MONDO:0025485', 'rdfs:subClassOf', 'MONDO:0700053'), ('MONDO:0958299', 'rdfs:subClassOf', 'MONDO:0958160')]
 "1" should be same as "2" + "3", but instead it has n less rels: 50
make[1]: *** [mondo-ingest.Makefile:536: reports/doid.subclass.direct-in-mondo-only.tsv] Error 1
make[1]: Leaving directory '/work/src/ontology'
make: *** [mondo-ingest.Makefile:334: build-mondo-ingest] Error 2
Command exited with non-zero status 2
matentzn commented 1 month ago

Maybe the most sane approach is:

  1. switch error to warning as a one off
  2. run build make pr, review, merge
  3. prioritise investigating #525

The better approach would be

  1. investigating #525, fix
  2. run build make pr, review, merge

but since its unclear how much work (1) is, I would tend to do the former.