Robot upgrade

.github/workflows/caseologue_robot_report.yml

@@ -30,7 +30,7 @@ jobs:
       if: always()
       run: |
         cd robot_config/
-        wget https://github.com/ontodev/robot/releases/download/v1.8.1/robot.jar
+        wget https://github.com/ontodev/robot/releases/download/v1.9.1/robot.jar
         java -jar robot.jar report --input ${{inputs.edam_path}} --output report_profile.tsv --profile report_queries.txt
 
     - name: Print report output

robot_config/README.md

@@ -1,5 +1,5 @@
 ## download .jar file 
-wget https://github.com/ontodev/robot/releases/download/v1.8.1/robot.jar
+wget https://github.com/ontodev/robot/releases/download/v1.9.1/robot.jar
 -P /usr/local/bin
 ## download shell script wrapper 
 curl https://raw.githubusercontent.com/ontodev/robot/master/bin/robot >

robot_config/deprecated_class_reference.rq

@@ -0,0 +1,61 @@
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+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#>
+
+SELECT DISTINCT ?entity ?property ?value WHERE {
+  {
+   VALUES ?property {
+     rdfs:subClassOf
+   }
+   ?entity a owl:Class;
+           owl:deprecated true ;
+           ?property ?value .
+   FILTER ( ?value NOT IN (owl:DeprecatedClass, owl:Thing) )
+  }
+  UNION
+  {
+   VALUES ?property {
+     owl:equivalentClass
+     owl:disjointWith
+   }
+   ?entity a owl:Class;
+           owl:deprecated true ;
+           ?property ?value .
+  }
+  UNION
+  {
+     VALUES ?property {
+       rdfs:subClassOf
+       owl:equivalentClass
+       owl:disjointWith
+     }
+     ?entity a owl:Class;
+             owl:deprecated true .
+     ?value ?property ?entity .
+  }
+  UNION
+  {
+   VALUES ?property {
+     owl:ObjectProperty
+     owl:DataProperty
+   }
+   ?entity a owl:Class ;
+           owl:deprecated true ;
+           ?property ?value .
+  }
+  UNION
+  {
+   VALUES ?property {
+     owl:someValuesFrom
+     owl:allValuesFrom
+   }
+   ?value a owl:Class ;
+          owl:deprecated true .
+   ?rest a owl:Restriction ;
+         ?property ?value .
+   BIND("blank node" as ?entity)
+  }
+}
+ORDER BY ?entity

robot_config/report_queries.txt

@@ -2,7 +2,7 @@ ERROR	file:./multiple_definition.rq
 ERROR	file:./boolean_datatype.rq
 ERROR	file:./duplicate_definition.rq
 WARN	file:./misused_replaced_by.rq
-ERROR	deprecated_class_reference
+ERROR	file:./deprecated_class_reference.rq
 ERROR	deprecated_property_reference
 WARN	duplicate_exact_synonym
 WARN	duplicate_label_synonym