Added is_format_of property to format property missing test

edamontology · Oct 13, 2022 · 9be1a8d · 9be1a8d
1 parent ec6cdd5
commit 9be1a8d
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Showing 4 changed files with 53 additions and 7 deletions.
diff --git a/caseologue/caseologue.py b/caseologue/caseologue.py
@@ -976,16 +976,27 @@ def test_object_relation_obsolete(self):
     def test_format_property_missing(self):
 
         """
-        Checks the no mandatory property for format are missing (documentation).
+        Checks the no mandatory property for format are missing (documentation,is_format_of). To make sure not to miss the inhereted "is_format_of" property from parent concept, a CONSTRUCT query is used to add the missing triplets to the graph. 
 
             > SPARQL query available `here  <https://github.com/edamontology/edam-validation/blob/main/caseologue/queries/format_property_missing.rq>`_
         """
+        construct = "queries/is_format_of_construct.rq"
+        with open(construct, "r") as f:
+            construct_term = f.read()
+
+        results_update = self.edam_graph.query(construct_term)
+        for r in results_update:
+            update_edam=self.edam_graph.add((r[0],r[1],r[2]))
 
+        f.close()
         query = "queries/format_property_missing.rq"
         with open(query, "r") as f:
             query_term = f.read()
+        if len(results_update)!=0:
+            results = update_edam.query(query_term)
+        else:
+            results = self.edam_graph.query(query_term)
 
-        results = self.edam_graph.query(query_term)
         nb_err = len(results)
         f.close()
 

diff --git a/caseologue/queries/format_property_missing.rq b/caseologue/queries/format_property_missing.rq
@@ -11,9 +11,17 @@ SELECT ?entity ?label ?property WHERE
 
     ?entity rdfs:subClassOf+ edam:format_1915 .
     ?entity rdfs:label ?label .
-
-     VALUES ?property { edam:documentation               
-                        }
-    FILTER NOT EXISTS {?entity ?property ?value .}
-
+    {
+        VALUES ?property { edam:documentation }
+        FILTER NOT EXISTS {?entity ?property ?value .}
+    }
+    UNION
+    {
+        VALUES ?property { edam:is_format_of }
+        FILTER NOT EXISTS {    
+            ?entity rdfs:subClassOf ?restriction . 
+            ?restriction rdf:type owl:Restriction ; 
+                owl:onProperty ?property  ; 
+                owl:someValuesFrom ?data.}
+    }
 }ORDER BY ?entity
diff --git a/caseologue/queries/format_property_missing_test_data.owl b/caseologue/queries/format_property_missing_test_data.owl
@@ -77,6 +77,12 @@
 
     <owl:Class rdf:about="http://edamontology.org/format_1975">
         <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2305"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
+                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <created_in>beta12orEarlier</created_in>
         <ontology_used rdf:resource="http://www.sequenceontology.org/"/>
         <oboInOwl:hasDbXref rdf:resource="https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md"/>

diff --git a/caseologue/queries/is_format_of_construct.rq b/caseologue/queries/is_format_of_construct.rq
@@ -0,0 +1,21 @@
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+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 oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX edam:<http://edamontology.org/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+CONSTRUCT { 
+    ?children_format rdfs:subClassOf ?restriction . 
+    ?restriction rdf:type owl:Restriction ; 
+            owl:onProperty edam:is_format_of  ; 
+            owl:someValuesFrom ?data. 
+}
+WHERE {
+    ?parent_format rdfs:subClassOf ?restriction . 
+    ?restriction rdf:type owl:Restriction ; 
+            owl:onProperty edam:is_format_of  ; 
+            owl:someValuesFrom ?data.
+    ?children_format rdfs:subClassOf+ ?parent_format .
+    }