Handle missing columns and empty table cells by omitting outputs which require those values

[balhoff]

No description provided.

[balhoff]

@matentzn @dosumis This PR covers both empty cells and missing columns. The behavior I implemented is to simply not emit any output which depend on a missing value. So this works for OWL class references as well as data values. If you have for example a text definition which uses 2 variables, if both are present, it will be output.

Test YAML: https://github.com/INCATools/dosdp-tools/blob/510a0714770b2ab416d2c7e57646b39b9abc1359/src/test/resources/org/monarchinitiative/dosdp/missing_values_test.yaml

Test TSV: https://github.com/INCATools/dosdp-tools/blob/510a0714770b2ab416d2c7e57646b39b9abc1359/src/test/resources/org/monarchinitiative/dosdp/missing_values_test.tsv

Test output:

EquivalentClasses(<http://purl.obolibrary.org/obo/EX_0003> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_arm> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_part_of> <http://purl.obolibrary.org/obo/VTO_Holothuroidea>)) )
AnnotationAssertion(<http://purl.obolibrary.org/obo/RO_never_in_taxon> <http://purl.obolibrary.org/obo/EX_0001> <http://purl.obolibrary.org/obo/VTO_Holothuroidea>)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/EX_0001> "Term 0001"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/EX_0001> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_arm> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_part_of> <http://purl.obolibrary.org/obo/VTO_Holothuroidea>)) )
AnnotationAssertion(<http://purl.obolibrary.org/obo/RO_never_in_taxon> <http://purl.obolibrary.org/obo/EX_0005> <http://purl.obolibrary.org/obo/VTO_Holothuroidea>)
AnnotationAssertion(<http://purl.obolibrary.org/obo/RO_never_in_taxon> <http://purl.obolibrary.org/obo/EX_0003> <http://purl.obolibrary.org/obo/VTO_Holothuroidea>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/EX_0005> "a synonym for this term"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/EX_0005> "Term 0005"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/EX_0005> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_arm> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_part_of> <http://purl.obolibrary.org/obo/VTO_Holothuroidea>)) )
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/EX_0002> "Term 0002 Arm two and then one"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/EX_0002> "Term 0002"^^xsd:string)
AnnotationAssertion(<http://purl.obolibrary.org/obo/RO_never_in_taxon> <http://purl.obolibrary.org/obo/EX_0002> <http://purl.obolibrary.org/obo/VTO_Holothuroidea>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/EX_0001> "a synonym for this term"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/EX_0002> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_arm> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_part_of> <http://purl.obolibrary.org/obo/VTO_Holothuroidea>)) )
AnnotationAssertion(<http://purl.obolibrary.org/obo/RO_never_in_taxon> <http://purl.obolibrary.org/obo/EX_0004> <http://purl.obolibrary.org/obo/VTO_Holothuroidea>)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/EX_0001> "Term 0001 Arm two and then one"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/EX_0004> "Term 0004"^^xsd:string)