abbreviate namespace names in concept ids with prefix mappings. (8b800489) · Commits · Raphael Majeed / histream

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

+14 −0

Original line number	Diff line number	Diff line
		@@ -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 −1

Original line number	Diff line number	Diff line
		@@ -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;
		@@ -23,6 +24,7 @@ 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);
		}

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

+8 −3

Original line number	Diff line number	Diff line
		@@ -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;
		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
		return Integer.toHexString(me.getNamespace().hashCode())+":"+me.getLocalName();
		prefix = Integer.toHexString(me.getNamespace().hashCode());
		}
		return prefix + ":" +me.getLocalName();
		}

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

+1 −0

Original line number	Diff line number	Diff line
		@@ -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

+50 −4

Original line number	Diff line number	Diff line
		@@ -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();
		@@ -261,6 +261,49 @@ 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;