Merge pull request #117 from balhoff/protege-fixes

Improvements to Protege plugin and OWL API interface implementation

build.sbt

@@ -1,9 +1,8 @@
-
 lazy val owlapiVersion = "4.5.17"
 
 lazy val commonSettings = Seq(
   organization := "org.geneontology",
-  version := "1.0.3",
+  version := "1.0.4",
   licenses := Seq("BSD-3-Clause" -> url("https://opensource.org/licenses/BSD-3-Clause")),
   homepage := Some(url("https://github.com/balhoff/whelk")),
   crossScalaVersions := Seq("2.12.11", "2.13.3"),
@@ -38,27 +37,28 @@ lazy val testSettings = Seq(
   libraryDependencies ++= Seq("com.lihaoyi" %% "utest" % "0.7.5" % Test)
 )
 
-lazy val parentProject = project.in(file("."))
+lazy val parentProject = project
+  .in(file("."))
   .settings(commonSettings)
-  .settings(
-    name := "whelk-project",
-    skip in publish := true)
+  .settings(name := "whelk-project", skip in publish := true)
   .aggregate(
     core,
     owlapi,
     protege
   )
 
-lazy val core = project.in(file("modules/core"))
+lazy val core = project
+  .in(file("modules/core"))
   .settings(commonSettings)
   .settings(testSettings)
   .settings(publishSettings)
   .settings(
     name := "whelk",
-    description := "Whelk reasoner core",
+    description := "Whelk reasoner core"
   )
 
-lazy val owlapi = project.in(file("modules/owlapi"))
+lazy val owlapi = project
+  .in(file("modules/owlapi"))
   .dependsOn(core)
   .enablePlugins(JavaAppPackaging)
   .settings(commonSettings)
@@ -69,29 +69,31 @@ lazy val owlapi = project.in(file("modules/owlapi"))
     description := "Whelk reasoner OWL API bindings",
     mainClass in Compile := Some("org.geneontology.whelk.Main"),
     libraryDependencies ++= Seq(
-      "net.sourceforge.owlapi" % "owlapi-distribution" % owlapiVersion,
-      "org.phenoscape" %% "scowl" % "1.3.4",
-      "org.semanticweb.elk" % "elk-owlapi" % "0.4.3" % Test,
+      "net.sourceforge.owlapi" % "owlapi-distribution"    % owlapiVersion,
+      "org.phenoscape"        %% "scowl"                  % "1.3.4",
+      "org.semanticweb.elk"    % "elk-owlapi"             % "0.4.3"     % Test,
       "net.sourceforge.owlapi" % "org.semanticweb.hermit" % "1.4.0.432" % Test,
-      "net.sourceforge.owlapi" % "jfact" % "4.0.4" % Test
+      "net.sourceforge.owlapi" % "jfact"                  % "4.0.4"     % Test
     )
   )
 
 def isJarToEmbed(file: java.io.File): Boolean = file.getName match {
-  case name if name startsWith "scala" => true
-  case _                               => false
+  case name if (name startsWith "scala") || (name startsWith "scowl") => true
+  case _ => false
 }
 
-lazy val protege = project.in(file("modules/protege"))
+lazy val protege = project
+  .in(file("modules/protege"))
   .dependsOn(owlapi)
   .enablePlugins(SbtOsgi)
   .settings(commonSettings)
   .settings(
     skip in publish := true,
-    name := "whelk-protege",
+    name := "Whelk reasoner Protege plugin",
     description := "Whelk reasoner Protégé plugin",
     // Bundle-Version is set to the version by default.
     OsgiKeys.bundleSymbolicName := "org.geneontology.whelk;singleton:=true",
+    OsgiKeys.bundleActivator := Some("org.protege.editor.owl.ProtegeOWL"),
     // Include the packages specified by privatePackage in the bundle.
     OsgiKeys.privatePackage := Seq("org.geneontology.*"),
     OsgiKeys.exportPackage := Seq("!*"),
@@ -105,7 +107,7 @@ lazy val protege = project.in(file("modules/protege"))
     ),
     libraryDependencies ++= Seq(
       "net.sourceforge.owlapi" % "owlapi-distribution" % owlapiVersion % Provided,
-      "edu.stanford.protege" % "protege-editor-core" % "5.2.0" % Provided,
-      "edu.stanford.protege" % "protege-editor-owl" % "5.2.0" % Provided
+      "edu.stanford.protege"   % "protege-editor-core" % "5.2.0"       % Provided,
+      "edu.stanford.protege"   % "protege-editor-owl"  % "5.2.0"       % Provided
     )
   )

modules/core/src/main/scala/org/geneontology/whelk/Reasoner.scala

@@ -60,7 +60,7 @@ final case class ReasonerState(
     // Using the regular algorithm for Bottom takes too long
     val directSuperClassesOfBottom = closureSubsBySuperclass.collect { case (superclass: AtomicConcept, subclasses) if (subclasses - Bottom - superclass).forall(_.isAnonymous) => superclass }.toSet
     val equivalentsToBottom = closureSubsBySuperclass(Bottom).collect { case subclass: AtomicConcept => subclass }
-    closureSubsBySubclass.collect {
+    (closureSubsBySubclass - Bottom).collect {
       case (c: AtomicConcept, subsumers) => c -> directSubsumers(c, subsumers + Top)
     } + (Bottom -> (equivalentsToBottom, directSuperClassesOfBottom))
   }
@@ -179,16 +179,20 @@ object Reasoner {
   private[this] def processConcept(concept: Concept, reasoner: ReasonerState): ReasonerState = {
     if (reasoner.inits(concept)) reasoner
     else {
-      val newState = `R⊤`(concept, R0(concept, reasoner.copy(inits = reasoner.inits + concept)))
+      val superClassesOfBottom = reasoner.closureSubsBySubclass.getOrElse(Bottom, Set.empty)
+      val updatedClosureSubsBySubclass = reasoner.closureSubsBySubclass.updated(Bottom, superClassesOfBottom + concept)
+      val newState = `R⊤`(concept, R0(concept, reasoner.copy(inits = reasoner.inits + concept, closureSubsBySubclass = updatedClosureSubsBySubclass)))
       newState.queueDelegates.keysIterator.foldLeft(newState) { (state, delegateKey) =>
         state.queueDelegates(delegateKey).processConcept(concept, state)
       }
     }
   }
 
+  private[this] val emptySubClassSet: Set[Concept] = Set(Bottom)
+
   private[this] def processConceptInclusion(ci: ConceptInclusion, reasoner: ReasonerState): ReasonerState = {
     val ConceptInclusion(subclass, superclass) = ci
-    val subs = reasoner.closureSubsBySuperclass.getOrElse(superclass, Set.empty)
+    val subs = reasoner.closureSubsBySuperclass.getOrElse(superclass, emptySubClassSet)
     if (subs(subclass)) reasoner else {
       val closureSubsBySuperclass = reasoner.closureSubsBySuperclass.updated(superclass, subs + subclass)
       val supers = reasoner.closureSubsBySubclass.getOrElse(subclass, Set.empty)

modules/owlapi/src/test/resources/org/geneontology/whelk/owl-reasoner-nothing-equiv.ofn

@@ -0,0 +1,47 @@
+Prefix(:=<http://example.org/>)
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(<http://example.org/>
+
+Declaration(Class(:A))
+Declaration(Class(:B))
+Declaration(Class(:BY))
+Declaration(Class(:C))
+Declaration(Class(:X))
+Declaration(Class(:Y))
+Declaration(Class(:Z))
+############################
+#   Classes
+############################
+
+# Class: :A (:A)
+
+DisjointClasses(:A :X)
+
+# Class: :B (:B)
+
+SubClassOf(:B :A)
+
+# Class: :BY (:BY)
+
+EquivalentClasses(:BY ObjectIntersectionOf(:B :Y))
+
+# Class: :C (:C)
+
+SubClassOf(:C :B)
+
+# Class: :Y (:Y)
+
+SubClassOf(:Y :X)
+
+# Class: :Z (:Z)
+
+SubClassOf(:Z :Y)
+
+
+)

modules/owlapi/src/test/scala/org/geneontology/whelk/TestOWLReasoner.scala

@@ -66,6 +66,18 @@ object TestOWLReasoner extends TestSuite {
       reasoner.getInstances(Class("http://example.org/blah"), true)
     }
 
+    "Unsatisfiable classes should be equivalent to owl:Nothing" - {
+      val manager = OWLManager.createOWLOntologyManager()
+      val ontology = manager.loadOntologyFromOntologyDocument(this.getClass.getResourceAsStream("owl-reasoner-nothing-equiv.ofn"))
+      val reasoner = new WhelkOWLReasonerFactory().createReasoner(ontology)
+      assert(reasoner.getSubClasses(Class("http://example.org/C") and Class("http://example.org/Z"), false).isEmpty)
+      assert(reasoner.getEquivalentClasses(Class("http://example.org/C") and Class("http://example.org/Z")).getEntities.asScala.toSet == Set(OWLNothing))
+      assert(reasoner.getSubClasses(Class("http://example.org/BY"), false).isEmpty)
+      assert(reasoner.getEquivalentClasses(Class("http://example.org/BY")).getEntities.asScala.toSet == Set(OWLNothing))
+      assert(reasoner.getSubClasses(OWLNothing, false).getFlattened.isEmpty)
+      assert(reasoner.getEquivalentClasses(OWLNothing).getEntities.asScala.toSet == Set(Class("http://example.org/BY")))
+    }
+
   }
 
 }

modules/protege/update.properties

@@ -1,7 +1,6 @@
 id=org.geneontology.whelk
-version=1.0
-#FIXME
-download=https://github.com/balhoff/whelk-protege/releases/download/v0.1.0.1/whelk-protege-0.1.0.1.jar
+version=1.0.4
+download=https://github.com/balhoff/whelk-protege/releases/download/v1.0.4/whelk-reasoner-protege-plugin-1.0.4.jar
 name=Whelk plug-in for Protégé
 readme=https://raw.githubusercontent.com/balhoff/whelk/master/README.md
 license=https://opensource.org/licenses/BSD-3-Clause