Set up test suite for pipeline

[Shalsh23]

Tests should include data validation tests for critical steps in the pipeline.

[johnbradley]

I am working on running a validation test for the test/test1 data in branch small-testing-dataset. I converted the test1-bio-ontologies-merged.ofn to test1-bio-ontologies-merged.ttl since the Makefile now expects the bio-ontologies-merged file to be ttl format. I added a script (based on https://github.com/phenoscape/pipeline/pull/120) to run the Makefile on the test data (make build/phenex-data+tbox.ttl). The script can be run like so: sbatch test/run-test1.sh.

[johnbradley]

To create test1-bio-ontologies-merged.ttl I ran:

robot convert --input test1-bio-ontologies-merged.ofn --output test1-bio-ontologies-merged.ttl

When running the make command it failed in two places where similar looking errors:

ROBOT_JAVA_ARGS=-Xmx80G robot remove -i build/bio-ontologies-merged.ttl --axioms 'disjoint' --trim true \
remove --term 'owl:Nothing' --trim true \
reason \
--reasoner ELK \
--axiom-generators "SubClass EquivalentClass" \
--exclude-duplicate-axioms true \
--exclude-tautologies structural \
convert --format ttl \
-o build/bio-ontologies-classified.ttl.tmp \
&& mv build/bio-ontologies-classified.ttl.tmp build/bio-ontologies-classified.ttl
2022-03-04 16:55:43,070 ERROR org.obolibrary.robot.ReasonOperation 
- Reference violations found: 20367 - reasoning may be incomplete
2022-03-04 16:55:43,078 ERROR org.obolibrary.robot.ReasonOperation 
- Reference violation: InvalidReferenceViolation [axiom=ObjectPropertyAssertion(<http://purl.org/oban/association_has_subject> <http://purl.phenoscape.org/homology/annotation/7070f44509b5be2eef18ac0a5cf70aaeb101b0fa> <http://purl.phenoscape.org/homology/annotation/7070f44509b5be2eef18ac0a5cf70aaeb101b0fa#structure1>), referencedObject=<http://purl.org/oban/association_has_subject>, category=DANGLING]
2022-03-04 16:55:43,078 ERROR org.obolibrary.robot.ReasonOperation 
- Reference violation: InvalidReferenceViolation [axiom=EquivalentClasses(<http://purl.obolibrary.org/obo/GO_0010132> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/GO_0009058> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0004008> <http://purl.obolibrary.org/obo/CHEBI_27826>)) ), referencedObject=<http://purl.obolibrary.org/obo/CHEBI_27826>, category=DANGLING]
...

ROBOT_JAVA_ARGS=-Xmx80G robot reason \
-i build/phenoscape-kb-tbox.ofn \
--reasoner ELK \
--axiom-generators "SubClass EquivalentClass" \
--exclude-duplicate-axioms true \
--exclude-tautologies structural \
convert --format ofn \
-o build/phenoscape-kb-tbox-classified-pre-absence-reasoning.ofn.tmp \
&& mv build/phenoscape-kb-tbox-classified-pre-absence-reasoning.ofn.tmp build/phenoscape-kb-tbox-classified-pre-absence-rea
soning.ofn
2022-03-04 18:11:07,451 ERROR org.obolibrary.robot.ReasonOperation 
- Reference violations found: 613 - reasoning may be incomplete
2022-03-04 18:11:07,456 ERROR org.obolibrary.robot.ReasonOperation 
- Reference violation: InvalidReferenceViolation [axiom=ObjectPropertyAssertion(<http://purl.org/oban/association_has_object> <http://purl.phenoscape.org/homology/annotation/db65f4ecde03a8e6960f8b1a2cab9cb20bdd009b> <http://purl.phenoscape.org/homology/annotation/db65f4ecde03a8e6960f8b1a2cab9cb20bdd009b#structure2>), referencedObject=<http://purl.org/oban/association_has_object>, category=DANGLING]
2022-03-04 18:11:07,456 ERROR org.obolibrary.robot.ReasonOperation 
- Reference violation: InvalidReferenceViolation [axiom=EquivalentClasses(<http://purl.obolibrary.org/obo/MP_0008404> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001549> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/GO_0005623>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002503> <http://purl.obolibrary.org/obo/CHEBI_25255>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002573> <http://purl.obolibrary.org/obo/PATO_0000460>))) ), referencedObject=<http://purl.obolibrary.org/obo/GO_0005623>, category=DEPRECATED]
2022-03-04 18:11:07,457 ERROR org.obolibrary.robot.ReasonOperation - Reference violation: InvalidReferenceViolation [axiom=ObjectPropertyAssertion(<http://purl.org/oban/association_has_predicate> <http://purl.phenoscape.org/homology/annotation/cc6b22a81727d5c33458b7565e4494d4cade81d9> <http://purl.obolibrary.org/obo/RO_HOM0000007>), referencedObject=<http://purl.org/oban/association_has_predicate>, category=DANGLING]
...

@balhoff Any idea what I might have wrong here?