Merge pull request #18 from phenoscape/nexml-converter

Add converter for NeXML files to OWL.

src/main/scala/org/phenoscape/owl/build/Command.scala

@@ -17,6 +17,7 @@ object Command extends App {
     case "sparql-select"        => RunSPARQLQuery.main(commandArgs)
     case "sparql-construct"     => RunSPARQLConstruct.main(commandArgs)
     case "sparql-update"        => RunSPARQLUpdate.main(commandArgs)
+    case "convert-nexml"        => ConvertNeXML.main(commandArgs)
     case _ => println("""
 Valid commands are:
 

src/main/scala/org/phenoscape/owl/build/ConvertNeXML.scala

@@ -0,0 +1,23 @@
+package org.phenoscape.owl.build
+
+import java.io.File
+
+import org.phenoscape.owl.PhenexToOWL
+import org.phenoscape.owl.PropertyNormalizer
+import org.semanticweb.owlapi.apibinding.OWLManager
+import org.semanticweb.owlapi.formats.FunctionalSyntaxDocumentFormat
+import org.semanticweb.owlapi.model.IRI
+import java.io.FileOutputStream
+
+object ConvertNeXML extends App {
+
+  val ontologyPath = args(0)
+  val nexmlFiles = args.drop(1)
+  val manager = OWLManager.createOWLOntologyManager()
+  val ontology = manager.loadOntology(IRI.create(new File(ontologyPath)))
+  nexmlFiles.foreach { file =>
+    val nexmlOnt = PropertyNormalizer.normalize(PhenexToOWL.convert(new File(file), ontology))
+    manager.saveOntology(nexmlOnt, new FunctionalSyntaxDocumentFormat(), new FileOutputStream(new File(s"$file.ofn")))
+  }
+
+}