abbreviate namespace names in concept ids with prefix mappings.

histream-maven-plugin/src/main/java/de/sekmi/histream/maven/OntologyMojo.java

@@ -57,6 +57,9 @@ public class OntologyMojo extends AbstractMojo {
 	@Parameter(defaultValue="${project}", readonly=true, required=true)
 	MavenProject project;
 
+	@Parameter
+	Map<String, String> prefixes;
+
 	private void logWarning(String message){
 		getLog().warn(message);
 	}
@@ -117,6 +120,17 @@ public class OntologyMojo extends AbstractMojo {
 		} catch (RepositoryException | IOException e) {
 			throw new MojoExecutionException("Unable to load ontology", e);
 		}
+		if( prefixes != null ){
+			String[] ns = new String[prefixes.size()];
+			String[] pr = new String[ns.length];
+			int i=0;
+			for( String key : prefixes.keySet() ){
+				pr[i] = key;
+				ns[i] = prefixes.get(key);
+				i++;
+			}			
+			store.setNamespacePrefixes(ns, pr);
+		}
 		
 		try {
 			SQLGenerator gen = new SQLGenerator(metaSQL, dataSQL, map, overwrite);

histream-maven-plugin/src/test/java/de/sekmi/histream/maven/TestOntologyMojo.java

@@ -3,6 +3,7 @@ package de.sekmi.histream.maven;
 import java.io.File;
 import java.io.InputStream;
 import java.net.URL;
+import java.util.Collections;
 import java.util.Properties;
 
 import org.apache.maven.shared.model.fileset.FileSet;
@@ -23,8 +24,9 @@ public class TestOntologyMojo {
 		mojo.destination = new File("target/i2b2-aktin");
 		mojo.properties = new Properties();
 		mojo.overwrite = true;
+		mojo.prefixes = Collections.singletonMap("a", "http://aktin.org/skos-cda#");
 		try( InputStream in = getClass().getResourceAsStream("/ontology.properties") ){
-			mojo.properties.load(in);			
+			mojo.properties.load(in);
 		}
 				
 		mojo.execute();

histream-skos/src/main/java/de/sekmi/histream/ontology/skos/ConceptImpl.java

@@ -49,7 +49,7 @@ public class ConceptImpl implements Concept {
 	}
 	
 	public String toString(){
-		return res.toString();
+		return getID();
 	}
 
 	@Override
@@ -135,8 +135,13 @@ public class ConceptImpl implements Concept {
 	@Override
 	public String getID() {
 		URI me = (URI)res;
-		// TODO: use better namespace prefix instead of hashcode
-		return Integer.toHexString(me.getNamespace().hashCode())+":"+me.getLocalName();
+		String prefix = store.getNamespacePrefix(me.getNamespace());
+		if( prefix == null ){
+			// backward compatibility. this breaks the Ontology.getConceptById call.
+			// TODO: use better namespace prefix instead of hashcode
+			prefix = Integer.toHexString(me.getNamespace().hashCode());
+		}
+		return prefix + ":" +me.getLocalName();
 	}
 	
 	

histream-skos/src/main/java/de/sekmi/histream/ontology/skos/HIStreamOntology.java

@@ -32,6 +32,7 @@ public class HIStreamOntology {
 		DWH_ECMASCRIPT = f.createURI(DWH_NAMESPACE, "ECMAScript");
 		DWH_HAS_PART = f.createURI(DWH_NAMESPACE, "hasPart"); // TODO use correct names/URIs
 		DWH_IS_PART_OF = f.createURI(DWH_NAMESPACE, "isPartOf"); // XXX see above
+		// dwh:hasPart rdfs:subPropertyOf http://www.ontologydesignpatterns.org/ont/dul/DUL.owl#hasPart
 		
 	}
 }

histream-skos/src/main/java/de/sekmi/histream/ontology/skos/Store.java

@@ -49,7 +49,8 @@ public class Store implements Ontology, Plugin {
 	private Resource inferredContext;
 	// SKOS scheme to enforce unique notations
 	private Resource scheme;
-	private Map<String, String> namespaceShortener;
+	private String[] registeredPrefixes;
+	private String[] registeredNamespaces;
 	
 	/// XXX  namespace resolver
 	/**
@@ -142,7 +143,6 @@ public class Store implements Ontology, Plugin {
 		return count;
 	}
 	private void initializeRepo(Iterable<File> files, Iterable<URL> urls, String baseURI) throws RepositoryException, IOException{
-	    namespaceShortener = new HashMap<>();
 	    repo = new SailRepository(new MemoryStore());
 	    repo.initialize();
 		rc = repo.getConnection();
@@ -260,7 +260,50 @@ public class Store implements Ontology, Plugin {
 		}
 		
 	}
-	
+
+	public void setNamespacePrefixes(String[] namespaces, String prefixes[]){
+		// TODO order namespaces by length
+		this.registeredNamespaces = namespaces;
+		this.registeredPrefixes = prefixes;
+	}
+	private String expandIdPrefixes(String id){
+		if( registeredPrefixes == null ){
+			// no prefixes to expand
+			return id;
+		}
+		for( int i=0; i<registeredPrefixes.length; i++ ){
+			String prefix = registeredPrefixes[i] + ":";
+			if( id.length() > prefix.length() && id.startsWith(prefix) ){
+				return registeredNamespaces[i] + id.substring(prefix.length());
+			}
+		}
+		return id;
+	}
+	String getNamespacePrefix(String namespace){
+		if( registeredNamespaces == null ){
+			return null;
+		}
+		for( int i=0; i<registeredNamespaces.length; i++ ){
+			if( namespace.equals(registeredNamespaces[i]) ){
+				return registeredPrefixes[i];
+			}
+		}
+		return null;
+	}
+//	
+//	private String shortenIdNamespaces(String id){
+//		if( registeredNamespaces == null ){
+//			// no namespaces to shorten
+//			return id;
+//		}
+//		for( int i=0; i<registeredNamespaces.length; i++ ){
+//			String ns = registeredNamespaces[i];
+//			if( id.length() > ns.length() && id.startsWith(ns) ){
+//				return registeredPrefixes[i] + ":" + id.substring(ns.length());
+//			}
+//		}
+//		return id;
+//	}
 
 	@Override
 	public ConceptImpl getConceptByNotation(String id) throws OntologyException {
@@ -494,7 +537,10 @@ public class Store implements Ontology, Plugin {
 		}
 	}
 	@Override
-	public Concept getConceptById(String id) throws OntologyException {
+	public Concept getConceptById(String conceptId) throws OntologyException {
+		// lookup namespaces
+		String id = expandIdPrefixes(conceptId);
+
 		URI uri = repo.getValueFactory().createURI(id);
 		RepositoryResult<Statement> s = null;
 		ConceptImpl ci = null;

histream-skos/src/test/java/de/sekmi/histream/ontology/skos/OntologyTest.java

@@ -23,6 +23,7 @@ public class OntologyTest {
 	public void setupOntology()throws Exception{
 		store = new Store(new File("examples/test-ontology.ttl"));
 		store.setConceptScheme(NS_PREFIX+"TestScheme");
+		store.setNamespacePrefixes(new String[]{"http://sekmi.de/histream/skos/tests#"}, new String[]{"test"});
 	}
 
 	@Test
@@ -135,6 +136,16 @@ public class OntologyTest {
 		Assert.assertEquals(1,n.length);
 		Assert.assertEquals("other",n[0]);
 	}
+	@Test
+	public void verifyGetByShortIRI() throws OntologyException{
+
+		Concept c = store.getConceptById("test:OtherSub");
+		Assert.assertNotNull(c);
+		String[] n = c.getNotations();
+		Assert.assertNotNull(n);
+		Assert.assertEquals(1,n.length);
+		Assert.assertEquals("other",n[0]);
+	}
 	@After
 	public void closeOntology() throws IOException{
 		store.close();
@@ -142,6 +153,7 @@ public class OntologyTest {
 	
 	public static void main(String[] args) throws Exception{
 		try( Store store = new Store(new File("examples/test-ontology.ttl")) ){
+			store.setNamespacePrefixes(new String[]{"http://sekmi.de/histream/skos/tests#"}, new String[]{"test"});
 			store.printConceptHierarchy();
 			
 			Concept c = store.getConceptByNotation("Type");