Merge pull request #427 from rctauber/filter_update

Add support for domain and range selectors
ontodev · Feb 4, 2019 · edcbf51 · edcbf51
2 parents 7b14de4 + 1fe61ad
commit edcbf51
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Showing 2 changed files with 67 additions and 18 deletions.
diff --git a/docs/remove.md b/docs/remove.md
@@ -47,6 +47,8 @@ Relation type selections provide the ability to select which terms to remove bas
 6. `equivalents`
 7. `types`
 8. `instances`
+9. `domains`
+10. `ranges`
 
 #### Entity Types
 

diff --git a/robot-core/src/main/java/org/obolibrary/robot/RelatedObjectsHelper.java b/robot-core/src/main/java/org/obolibrary/robot/RelatedObjectsHelper.java
@@ -87,15 +87,7 @@ public static Set<OWLAxiom> getAnnotationAxioms(OWLOntology ontology, Set<OWLObj
   public static Set<OWLAxiom> getCompleteAxioms(
       OWLOntology ontology, Set<OWLObject> objects, Set<Class<? extends OWLAxiom>> axiomTypes) {
     Set<OWLAxiom> axioms = new HashSet<>();
-
-    Set<IRI> iris = new HashSet<>();
-    for (OWLObject object : objects) {
-      if (OWLNamedObject.class.isInstance(object)) {
-        OWLNamedObject namedObject = (OWLNamedObject) object;
-        iris.add(namedObject.getIRI());
-      }
-    }
-
+    Set<IRI> iris = getIRIs(objects);
     for (OWLAxiom axiom : ontology.getAxioms()) {
       if (OntologyHelper.extendsAxiomTypes(axiom, axiomTypes)) {
         // Check both the full annotated axiom and axiom without annotations (if annotated)
@@ -146,15 +138,7 @@ public static Set<OWLAxiom> getCompleteAxioms(
   public static Set<OWLAxiom> getPartialAxioms(
       OWLOntology ontology, Set<OWLObject> objects, Set<Class<? extends OWLAxiom>> axiomTypes) {
     Set<OWLAxiom> axioms = new HashSet<>();
-
-    Set<IRI> iris = new HashSet<>();
-    for (OWLObject object : objects) {
-      if (OWLNamedObject.class.isInstance(object)) {
-        OWLNamedObject namedObject = (OWLNamedObject) object;
-        iris.add(namedObject.getIRI());
-      }
-    }
-
+    Set<IRI> iris = getIRIs(objects);
     for (OWLAxiom axiom : ontology.getAxioms()) {
       if (OntologyHelper.extendsAxiomTypes(axiom, axiomTypes)) {
         if (axiom instanceof OWLAnnotationAssertionAxiom) {
@@ -284,6 +268,10 @@ public static Set<OWLObject> select(
       return objects;
     } else if (selector.equals("types")) {
       return selectTypes(ontology, objects);
+    } else if (selector.equals("ranges")) {
+      return selectRanges(ontology, objects);
+    } else if (selector.equals("domains")) {
+      return selectDomains(ontology, objects);
     } else if (selector.contains("=")) {
       return selectPattern(ontology, ioHelper, objects, selector);
     } else {
@@ -447,6 +435,27 @@ public static Set<OWLObject> selectDescendants(OWLOntology ontology, Set<OWLObje
     return relatedObjects;
   }
 
+  /**
+   * Given an ontology and a set of objects, return all domains of any properties in the set.
+   *
+   * @param ontology OWLOntology to retrieve domains from
+   * @param objects OWLObjects to retrieve domains of
+   * @return set of domains of the starting set
+   */
+  public static Set<OWLObject> selectDomains(OWLOntology ontology, Set<OWLObject> objects) {
+    Set<OWLObject> relatedObjects = new HashSet<>();
+    for (OWLObject object : objects) {
+      if (object instanceof OWLAnnotationProperty) {
+        relatedObjects.addAll(EntitySearcher.getDomains((OWLAnnotationProperty) object, ontology));
+      } else if (object instanceof OWLDataProperty) {
+        relatedObjects.addAll(EntitySearcher.getDomains((OWLDataProperty) object, ontology));
+      } else if (object instanceof OWLObjectProperty) {
+        relatedObjects.addAll(EntitySearcher.getDomains((OWLObjectProperty) object, ontology));
+      }
+    }
+    return relatedObjects;
+  }
+
   /**
    * Given an ontology and a set of objects, return all equivalent objects of the starting set.
    *
@@ -588,6 +597,27 @@ public static Set<OWLObject> selectProperties(Set<OWLObject> objects) {
     return relatedObjects;
   }
 
+  /**
+   * Given an ontology and a set of objects, return all ranges of any properties in the set.
+   *
+   * @param ontology OWLOntology to retrieve ranges from
+   * @param objects OWLObjects to retrieve ranges of
+   * @return set of ranges of the starting set
+   */
+  public static Set<OWLObject> selectRanges(OWLOntology ontology, Set<OWLObject> objects) {
+    Set<OWLObject> relatedObjects = new HashSet<>();
+    for (OWLObject object : objects) {
+      if (object instanceof OWLAnnotationProperty) {
+        relatedObjects.addAll(EntitySearcher.getRanges((OWLAnnotationProperty) object, ontology));
+      } else if (object instanceof OWLDataProperty) {
+        relatedObjects.addAll(EntitySearcher.getRanges((OWLDataProperty) object, ontology));
+      } else if (object instanceof OWLObjectProperty) {
+        relatedObjects.addAll(EntitySearcher.getRanges((OWLObjectProperty) object, ontology));
+      }
+    }
+    return relatedObjects;
+  }
+
   /**
    * Given an ontology and a set of objects, return a set of all the types of the individuals in
    * that set.
@@ -718,6 +748,23 @@ protected static Set<OWLAnnotation> getAnnotations(
     }
   }
 
+  /**
+   * Given a set of OWLObjects, return the set of IRIs for those objects.
+   *
+   * @param objects OWLObjects to get IRIs of
+   * @return IRIs of the given objects
+   */
+  private static Set<IRI> getIRIs(Set<OWLObject> objects) {
+    Set<IRI> iris = new HashSet<>();
+    for (OWLObject object : objects) {
+      if (object instanceof OWLNamedObject) {
+        OWLNamedObject namedObject = (OWLNamedObject) object;
+        iris.add(namedObject.getIRI());
+      }
+    }
+    return iris;
+  }
+
   /**
    * Given an OWL ontology, an annotation property, and an annotation value (in regex pattern form),
    * return a set of OWLAnnotations that have values matching the regex value.