Merge pull request #26 from phenoscape/develop

Add command line interface to negation hierarchy asserter
phenoscape · Feb 5, 2019 · a455264 · a455264
2 parents 7968fa5 + c12ebc9
commit a455264
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Showing 4 changed files with 30 additions and 29 deletions.
diff --git a/src/getscores-genes-corpus.rq b/src/getscores-genes-corpus.rq
diff --git a/src/main/scala/org/phenoscape/owl/NegationHierarchyAsserter.scala b/src/main/scala/org/phenoscape/owl/NegationHierarchyAsserter.scala
@@ -3,8 +3,28 @@ package org.phenoscape.owl
 import scala.collection.JavaConverters._
 import org.phenoscape.scowl._
 import org.semanticweb.owlapi.model._
+import org.semanticweb.owlapi.apibinding.OWLManager
+import java.io.File
+import java.io.FileOutputStream
+import scala.collection.JavaConverters._
+import org.semanticweb.owlapi.model.parameters.Imports
+
+
+object NegationHierarchyAsserter {
+
+  val factory = OWLManager.getOWLDataFactory
+  val Negates = factory.getOWLAnnotationProperty(Vocab.NEGATES)
 
-object NegationHierarchyAsserter extends OWLTask {
+
+  def main(args: Array[String]): Unit = {
+
+    val manager: OWLOntologyManager = OWLManager.createOWLOntologyManager()
+    val inputOntology: OWLOntology = manager.loadOntologyFromOntologyDocument(new File(args(0)))
+    val axioms: Set[OWLAxiom] = inputOntology.getAxioms(Imports.INCLUDED).asScala.toSet
+    val negationAxioms: Set[OWLAxiom] = assertNegationHierarchy(axioms)
+    val negationOntology: OWLOntology = manager.createOntology(negationAxioms.asJava)
+    manager.saveOntology(negationOntology, new FileOutputStream(args(1)))     //  negation axioms file
+  }
 
   def assertNegationHierarchy(axioms: Set[OWLAxiom]): Set[OWLAxiom] = {
     //  create tuples (class expressions, named classes)
@@ -44,7 +64,7 @@ object NegationHierarchyAsserter extends OWLTask {
     } yield Class(negater) SubClassOf Class(superClassOfOntClassIRI)
 
     val equivalentClassAxioms = for {
-      equivAxiom @ EquivalentClasses(_, _) <- axioms
+      equivAxiom@EquivalentClasses(_, _) <- axioms
       classes = equivAxiom.getNamedClasses.asScala
       if classes.size > 1
     } yield {
@@ -59,4 +79,5 @@ object NegationHierarchyAsserter extends OWLTask {
 
   def emptyIndex[A, B]: Map[A, Set[B]] = Map.empty.withDefaultValue(Set.empty)
 
+
 }
diff --git a/src/main/scala/org/phenoscape/owl/build/Command.scala b/src/main/scala/org/phenoscape/owl/build/Command.scala
@@ -1,6 +1,7 @@
 package org.phenoscape.owl.build
 
 import com.bigdata.rdf.store.DataLoader
+import org.phenoscape.owl.NegationHierarchyAsserter
 
 object Command extends App {
 
@@ -18,6 +19,7 @@ object Command extends App {
     case "sparql-construct"     => RunSPARQLConstruct.main(commandArgs)
     case "sparql-update"        => RunSPARQLUpdate.main(commandArgs)
     case "convert-nexml"        => ConvertNeXML.main(commandArgs)
+    case "assert-negation-hierarchy" => NegationHierarchyAsserter.main(commandArgs)
     case _ => println("""
 Valid commands are:
 

diff --git a/src/getscores-taxa-corpus.rq → src/main/sparql/get-scores.rq b/src/getscores-taxa-corpus.rq → src/main/sparql/get-scores.rq
@@ -7,14 +7,12 @@ PREFIX owlet: <http://purl.org/phenoscape/owlet/syntax#>
 PREFIX dc: <http://purl.org/dc/elements/1.1/>
 PREFIX StandardState: <http://purl.obolibrary.org/obo/CDAO_0000045>
 
-SELECT ?match ?score ?query ?query_label ?corpusprofile ?corpusprofile_label
-FROM <http://kb.phenoscape.org/>
-FROM <http://kb.phenoscape.org/sim/taxa>
+SELECT ?match ?score ?query ?corpusprofile
 WHERE
 {
 ?match ps:combined_score ?score .
-?match ps:for_query_profile/^ps:has_phenotypic_profile ?query .
-?match ps:for_corpus_profile/^ps:has_phenotypic_profile ?corpusprofile .
-?query rdfs:label ?query_label .
-?corpusprofile rdfs:label ?corpusprofile_label .
+?match ps:for_query_profile ?query .
+?match ps:for_corpus_profile  ?corpusprofile .
+
+
 }