Bug: Build freezes on prepare_release (mondo-ingest-edit.owl-obo-report.tsv)

[joeflack4]

Overview

I'm running the build PR #601. However it has frozen 3 times on the same step.

Background

The first two times I ran it, I accidentally closed my macbook and put it to sleep. The first time, myself, the second time, I had the screen at a 45 degree angle, and later it was closed, so I assume it was my cats. Anyway, I thought that it going to sleep might have caused the issue.

I ran it a third time though; been running for 8+ hours, and has not went to sleep. It's using CPU, but IDK what it's doing. I assume it's stuck in an infinite loop.

Screenshot: Docker Stats tab

Each time, it freezes on this command:

robot --catalog catalog-v001.xml report -i tmp/merged-mondo-ingest-edit.owl  --profile profile.txt --fail-on None --print 5 -o reports/mondo-ingest-edit.owl-obo-report.tsv

This is the goal for reports/mondo-ingest-edit.owl-obo-report.tsv, which runs at the end of the build as part of prepare_release.

Logs

• Log for run 1
• Log for run 2
• Log for run 3

Just for comparison, here's a snippet from the log before and after this goal runs, taken from my recent build on the "intelligent refresh" PR.

Log from different build for comparison

# intelligent refresh context
robot --catalog catalog-v001.xml template \
	--template external/nando-mappings.robot.tsv \
	--prefix "orcid: https://orcid.org/" \
 	annotate \
			--ontology-iri http://purl.obolibrary.org/obo/mondo/external/nord.robot.owl \
			--version-iri http://purl.obolibrary.org/obo/mondo/external/2024-06-26/nord.robot.owl \
			-o external/nando-mappings.robot.owl
robot --catalog catalog-v001.xml template \
	--template external/ordo-subsets.robot.tsv \
	--prefix "orcid: https://orcid.org/" \
 	annotate \
			--ontology-iri http://purl.obolibrary.org/obo/mondo/external/nord.robot.owl \
			--version-iri http://purl.obolibrary.org/obo/mondo/external/2024-06-26/nord.robot.owl \
			-o external/ordo-subsets.robot.owl
ODK Makefile v1.5-dev
ODK Image v1.5-dev
ROBOT version 1.9.5
Ammonite REPL & Script-Runner, 2.5.9
DOSDP-Tools v0.19.3
Konclude v0.7.0-1138
Jena v4.9.0
Relation-Graph v2.3.2
Ontology Access Kit v0.6.6
Repository is up-to-date.
robot --catalog catalog-v001.xml reason --input tmp/mondo-ingest-preprocess.owl --reasoner ELK --equivalent-classes-allowed asserted-only \
	--exclude-tautologies structural --output test.owl && rm test.owl
robot --catalog catalog-v001.xml verify -i tmp/mondo-ingest-preprocess.owl --queries ../sparql/properties-as-annotation-and-object-violation.sparql ../sparql/ordo-mapping-annotations-violation.sparql -O reports
PASS Rule ../sparql/properties-as-annotation-and-object-violation.sparql: 0 violation(s)
PASS Rule ../sparql/ordo-mapping-annotations-violation.sparql: 0 violation(s)
robot --catalog catalog-v001.xml report -i tmp/merged-mondo-ingest-edit.owl  --profile profile.txt --fail-on None --print 5 -o reports/mondo-ingest-edit.owl-obo-report.tsv
Violations: 593254
-----------------
ERROR:      60708
WARN:       503787
INFO:       28759

First 5 violations:
ERROR	deprecated_class_reference	http://id.who.int/icd/entity/1000312374	rdfs:subClassOf	http://id.who.int/icd/entity/1345372703
ERROR	deprecated_class_reference	http://id.who.int/icd/entity/1001085090	rdfs:subClassOf	http://id.who.int/icd/entity/583310882
ERROR	deprecated_class_reference	http://id.who.int/icd/entity/1002125483	rdfs:subClassOf	http://id.who.int/icd/entity/794078271
ERROR	deprecated_class_reference	http://id.who.int/icd/entity/1002411765	rdfs:subClassOf	http://id.who.int/icd/entity/309514703
ERROR	deprecated_class_reference	http://id.who.int/icd/entity/1002515350	rdfs:subClassOf	http://id.who.int/icd/entity/460984650
robot --catalog catalog-v001.xml merge -i mondo-ingest.owl convert -f ofn -o tmp/validate.ofn

ODK versions

All these builds ran on ODK latest. It is up to date. From what I can see, it hasn't changed in about a month.

ROBOT versions

I see that during prepare_release, it prints out various versions of software. ODK latest is currently on ROBOT version 1.9.5, but dev is on 1.9.6, so I wonder if 1.9.5 has some bug relevant here which 1.9.6 has fixed.

Things tried, but failed

Changing ODK to dev

I just realized that we recently changed ODK from dev to latest on develop:

• ODK dev --> latest (develop) #579
  We have not yet done that on main (ODK dev --> latest (main) #580).

I do believe that this is the first build that I / we have run since then. All the builds I've done in the last month and I'm not sure how much further back have been on dev.

So I'm going to run this on ODK dev now and see how that does.

edit: Update: tried this and didn't work.

Possible cause & solution

QC check causes crazy / endless loop

Nico:

I deactived 99% of the report check in mondo ingest, as it is totally redundant. Try again running the build for #601

Nico (slack):

there is a QC check that looks for overlap between exact synonyms and label. Could be that the respective sparql query just became method because all labels now had an exact synonym with the same name

[matentzn]

I deactived 99% of the report check in mondo ingest, as it is totally redundant. Try again running the build for #601