Update test workflow

- Create workflow annotations from robot report

.github/workflows/test.yml

@@ -25,7 +25,16 @@ jobs:
     container: obolibrary/odklite
     steps:
       - uses: actions/checkout@v4
+
       - run: check-rdfxml gfo-light.owl
       - run: check-rdfxml modules/gfo-base.owl
+
       - run: robot reason --input gfo-light.owl
       - run: robot reason --input modules/gfo-base.owl
+
+      # - run: |
+      #     result=$(robot report --input gfo-light.owl --profile qc_report/profile.txt)
+      #     echo "::notice file=gfo-light.owl::$result"
+      - run: |
+          result=$(robot report --input modules/gfo-base.owl --profile qc_report/profile.txt)
+          echo "::notice file=modules/gfo-base.owl::$result"

qc_report/missing_definition.sparql

@@ -0,0 +1,24 @@
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+
+SELECT DISTINCT ?entity ?property ?value WHERE {
+  VALUES ?property { skos:definition }
+  ?entity ?any ?o
+  FILTER NOT EXISTS { ?entity ?property ?value }
+  FILTER NOT EXISTS { ?entity a owl:Ontology }
+  FILTER NOT EXISTS { ?entity a owl:NamedIndividual }
+  FILTER NOT EXISTS { ?entity owl:deprecated true }
+  FILTER EXISTS {
+    ?entity ?prop2 ?object .
+    FILTER (?prop2 != rdf:type)
+    FILTER (?prop2 != owl:equivalentClass)
+    FILTER (?prop2 != owl:disjointWith)
+    FILTER (?prop2 != owl:equivalentProperty)
+    FILTER (?prop2 != owl:sameAs)
+    FILTER (?prop2 != owl:differentFrom)
+    FILTER (?prop2 != owl:inverseOf)
+  }
+  FILTER (!isBlank(?entity)) }
+ORDER BY ?entity

qc_report/profile.txt

@@ -0,0 +1,29 @@
+WARN	annotation_whitespace
+ERROR	deprecated_boolean_datatype
+WARN	deprecated_class_reference
+ERROR	deprecated_property_reference
+ERROR	duplicate_definition
+WARN	duplicate_exact_synonym
+WARN	duplicate_label_synonym
+ERROR	duplicate_label
+WARN	duplicate_scoped_synonym
+WARN	equivalent_pair
+WARN	equivalent_class_axiom_no_genus
+ERROR	illegal_use_of_built_in_vocabulary
+WARN	invalid_xref
+ERROR	label_formatting
+ERROR	label_whitespace
+INFO	lowercase_definition
+WARN	file:./qc_report/missing_definition.sparql
+ERROR	missing_label
+WARN	missing_obsolete_label
+ERROR	missing_ontology_description
+ERROR	missing_ontology_license
+ERROR	missing_ontology_title
+WARN	missing_subset_declaration
+WARN	missing_synonymtype_declaration
+ERROR	misused_obsolete_label
+ERROR	misused_replaced_by
+WARN	multiple_equivalent_classes
+ERROR	multiple_equivalent_class_definitions
+WARN	invalid_entity_uri