#4567 - Add support for a generic CAS RDF export format

- Switch from Jena to RDF4J

inception/inception-io-rdf/src/main/java/de/tudarmstadt/ukp/inception/io/rdf/RdfReader.java

@@ -129,9 +129,9 @@ private void step() throws IOException
                                         .stripCompressionExtension(res.getLocation()))
                                 .orElse(RDFXML);
                         model = Rio.parse(is, res.getLocation().toString(), format);
-                    }                    
-                    
-                    contextIterator = model.filter(null, RDF.TYPE, vf.createIRI(RdfCas.TYPE_VIEW)).iterator();
+                    }
+
+                    contextIterator = model.filter(null, RDF.TYPE, RdfCas.TYPE_VIEW).iterator();
                 }
                 else {
                     // No more files to read

inception/inception-io-rdf/src/main/java/de/tudarmstadt/ukp/inception/io/rdf/RdfWriter.java

@@ -49,8 +49,6 @@ public class RdfWriter
     /**
      * Specify the suffix of output files. Default value <code>.ttl</code>. The file format will be
      * chosen depending on the file suffice.
-     * 
-     * @see RDFLanguages
      */
     public static final String PARAM_FILENAME_EXTENSION = ComponentParameters.PARAM_FILENAME_EXTENSION;
     @ConfigurationParameter(name = PARAM_FILENAME_EXTENSION, mandatory = true, defaultValue = ".ttl")
@@ -61,20 +59,20 @@ public class RdfWriter
     private Set<String> iriFeatures;
 
     private Uima2Rdf uima2rdf;
-    
+
     @Override
     public void initialize(UimaContext aContext) throws ResourceInitializationException
     {
         super.initialize(aContext);
-        
+
         uima2rdf = new Uima2Rdf(iriFeatures);
     }
-    
+
     @Override
     public void process(JCas aJCas) throws AnalysisEngineProcessException
     {
         var model = new DynamicModelFactory().createEmptyModel();
-        
+
         try {
             uima2rdf.convert(aJCas, model);
         }
@@ -83,10 +81,8 @@ public void process(JCas aJCas) throws AnalysisEngineProcessException
         }
 
         try (var docOS = getOutputStream(aJCas, filenameSuffix)) {
-            var format = Rio
-                    .getParserFormatForFileName(filenameSuffix)
-                    .orElse(RDFXML);
-            Rio.write(model, docOS, format);            
+            var format = Rio.getParserFormatForFileName(filenameSuffix).orElse(RDFXML);
+            Rio.write(model, docOS, format);
         }
         catch (Exception e) {
             throw new AnalysisEngineProcessException(e);

inception/inception-io-rdf/src/main/java/de/tudarmstadt/ukp/inception/io/rdf/internal/BasicIRI.java

@@ -0,0 +1,46 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The Technische Universität Darmstadt 
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *  
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.rdf.internal;
+
+import org.eclipse.rdf4j.model.base.AbstractIRI;
+
+public class BasicIRI extends AbstractIRI
+{
+    private static final long serialVersionUID = 4794310809421877727L;
+
+    private final String namespace;
+    private final String localName;
+
+    public BasicIRI(String aNamespace, String aLocalName)
+    {
+        namespace = aNamespace;
+        localName = aLocalName;
+    }
+
+    @Override
+    public String getNamespace()
+    {
+        return namespace;
+    }
+
+    @Override
+    public String getLocalName()
+    {
+        return localName;
+    }
+}

inception/inception-io-rdf/src/main/java/de/tudarmstadt/ukp/inception/io/rdf/internal/Rdf2Uima.java

@@ -17,10 +17,19 @@
  */
 package de.tudarmstadt.ukp.inception.io.rdf.internal;
 
+import static de.tudarmstadt.ukp.inception.io.rdf.internal.RdfCas.NS_RDFCAS;
+import static de.tudarmstadt.ukp.inception.io.rdf.internal.RdfCas.SCHEME_UIMA;
+import static de.tudarmstadt.ukp.inception.io.rdf.internal.RdfCas.PROP_INDEXED_IN;
+import static de.tudarmstadt.ukp.inception.io.rdf.internal.RdfCas.PROP_SOFA_ID;
+import static de.tudarmstadt.ukp.inception.io.rdf.internal.RdfCas.PROP_SOFA_MIME_TYPE;
+import static de.tudarmstadt.ukp.inception.io.rdf.internal.RdfCas.PROP_SOFA_STRING;
+import static de.tudarmstadt.ukp.inception.io.rdf.internal.RdfCas.TYPE_FEATURE_STRUCTURE;
+import static de.tudarmstadt.ukp.inception.io.rdf.internal.RdfCas.TYPE_VIEW;
+import static org.apache.commons.lang3.StringUtils.substringAfterLast;
+
 import java.util.HashMap;
 import java.util.Map;
 
-import org.apache.commons.lang3.StringUtils;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.CASException;
 import org.apache.uima.cas.FeatureStructure;
@@ -31,7 +40,6 @@
 import org.eclipse.rdf4j.model.Model;
 import org.eclipse.rdf4j.model.Resource;
 import org.eclipse.rdf4j.model.Statement;
-import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
 import org.eclipse.rdf4j.model.vocabulary.RDF;
 
 import de.tudarmstadt.ukp.dkpro.core.api.metadata.type.DocumentMetaData;
@@ -40,27 +48,21 @@ public class Rdf2Uima
 {
     public static void convert(Model aModel, Statement aContext, JCas aJCas) throws CASException
     {
-        var vf = SimpleValueFactory.getInstance();
         var m = aModel;
 
-        // Set up names
-        var tView = vf.createIRI(RdfCas.TYPE_VIEW);
-        var tFeatureStructure = vf.createIRI(RdfCas.TYPE_FEATURE_STRUCTURE);
-        var pIndexedIn = vf.createIRI(RdfCas.PROP_INDEXED_IN);
-
         var fsIndex = new HashMap<Resource, FeatureStructure>();
 
         // Convert the views/SofAs
         var viewIndex = new HashMap<Resource, JCas>();
-        for (var view : aModel.filter(null, RDF.TYPE, tView).subjects()) {
+        for (var view : aModel.filter(null, RDF.TYPE, TYPE_VIEW).subjects()) {
             var viewJCas = convertView(aModel, view, aJCas);
             viewIndex.put(view, viewJCas);
             fsIndex.put(view, viewJCas.getSofa());
         }
 
         // Convert the FSes but without setting their feature values yet - we cannot fill
         // the feature values just set because some of them may point to FSes not yet created
-        var fses = m.filter(null, RDF.TYPE, tFeatureStructure).subjects();
+        var fses = m.filter(null, RDF.TYPE, TYPE_FEATURE_STRUCTURE).subjects().toArray(Resource[]::new);
         for (var fs : fses) {
             var uimaFS = initFS(aModel, fs, aJCas);
             fsIndex.put(fs, uimaFS);
@@ -73,7 +75,7 @@ public static void convert(Model aModel, Statement aContext, JCas aJCas) throws
 
         // Finally add the FSes to the indexes of the respective views
         for (var fs : fses) {
-            for (var indexedIn : aModel.filter(fs, pIndexedIn, null).objects()) {
+            for (var indexedIn : aModel.filter(fs, PROP_INDEXED_IN, null).objects()) {
                 var viewJCas = viewIndex.get(indexedIn);
                 viewJCas.addFsToIndexes(fsIndex.get(fs));
             }
@@ -82,17 +84,10 @@ public static void convert(Model aModel, Statement aContext, JCas aJCas) throws
 
     public static JCas convertView(Model aModel, Resource aView, JCas aJCas) throws CASException
     {
-        var vf = SimpleValueFactory.getInstance();
-
-        // Set up names
-        var pSofaID = vf.createIRI(RdfCas.PROP_SOFA_ID);
-        var pSofaString = vf.createIRI(RdfCas.PROP_SOFA_STRING);
-        var pSofaMimeType = vf.createIRI(RdfCas.PROP_SOFA_MIME_TYPE);
-
         // Get the values
-        var viewName = aModel.filter(aView, pSofaID, null).objects().iterator().next().stringValue();
-        var sofaString = aModel.filter(aView, pSofaString, null).objects().iterator().next().stringValue();
-        var sofaMimeType = aModel.filter(aView, pSofaMimeType, null).objects().iterator().next().stringValue();
+        var viewName = aModel.filter(aView, PROP_SOFA_ID, null).objects().iterator().next().stringValue();
+        var sofaString = aModel.filter(aView, PROP_SOFA_STRING, null).objects().iterator().next().stringValue();
+        var sofaMimeType = aModel.filter(aView, PROP_SOFA_MIME_TYPE, null).objects().iterator().next().stringValue();
 
         // Instantiate the view/SofA
         var view = JCasUtil.getView(aJCas, viewName, true);
@@ -107,10 +102,10 @@ public static FeatureStructure initFS(Model aModel, Resource aFS, JCas aJCas)
 
         // Figure out the UIMA type - there can be only one type per FS
         var types = aModel.filter(aFS, RDF.TYPE, null).objects();
-        types.removeIf(res -> res.stringValue().startsWith(RdfCas.NS_RDFCAS));
+        types.removeIf(res -> res.stringValue().startsWith(NS_RDFCAS));
         assert types.size() == 1;
         var type = CasUtil.getType(cas,
-                types.iterator().next().stringValue().substring(RdfCas.NS_UIMA.length()));
+                types.iterator().next().stringValue().substring(SCHEME_UIMA.length()));
 
         FeatureStructure fs;
         if (type.getName().equals(DocumentMetaData.class.getName())) {
@@ -135,7 +130,7 @@ public static FeatureStructure convertFS(Model aModel, Resource aFS, JCas aJCas,
                 continue;
             }
 
-            var featureName = StringUtils.substringAfterLast(stmt.getPredicate().stringValue(), "-");
+            var featureName = substringAfterLast(stmt.getPredicate().stringValue(), "-");
             var uimaFeat = fs.getType().getFeatureByBaseName(featureName);
 
             // Cannot update start/end of document annotation because that FS is already indexed, so
@@ -149,7 +144,7 @@ public static FeatureStructure convertFS(Model aModel, Resource aFS, JCas aJCas,
             if (uimaFeat.getRange().isPrimitive()) {
                 Literal literal = null;
                 if (stmt.getObject().isLiteral()) {
-                    literal = (Literal) stmt;
+                    literal = (Literal) stmt.getObject();
                 }
 
                 switch (uimaFeat.getRange().getName()) {

inception/inception-io-rdf/src/main/java/de/tudarmstadt/ukp/inception/io/rdf/internal/RdfCas.java

@@ -18,6 +18,7 @@
 package de.tudarmstadt.ukp.inception.io.rdf.internal;
 
 import org.apache.uima.cas.CAS;
+import org.eclipse.rdf4j.model.IRI;
 
 /**
  * RDF CAS vocabulary.
@@ -27,19 +28,18 @@ public class RdfCas
     public static final String PREFIX_RDFCAS = "rdfcas";
 
     public static final String NS_RDFCAS = "http://uima.apache.org/rdf/cas#";
-    public static final String NS_UIMA = "uima:";
+    public static final String SCHEME_UIMA = "uima:";
 
-    public static final String PROP_VIEW = NS_RDFCAS + "view";
-    public static final String PROP_INDEXED_IN = NS_RDFCAS + "indexedIn";
+    public static final IRI PROP_VIEW = new BasicIRI(NS_RDFCAS, "view");
+    public static final IRI PROP_INDEXED_IN =new BasicIRI(NS_RDFCAS, "indexedIn");
 
-    // public static final String TYPE_CAS = NS_RDFCAS + "CAS";
-    public static final String TYPE_VIEW = NS_RDFCAS + "View";
-    public static final String TYPE_FEATURE_STRUCTURE = NS_RDFCAS + "FeatureStructure";
+    public static final IRI TYPE_VIEW = new BasicIRI(NS_RDFCAS, "View");
+    public static final IRI TYPE_FEATURE_STRUCTURE = new BasicIRI(NS_RDFCAS, "FeatureStructure");
 
-    public static final String PROP_SOFA_ID = NS_UIMA + CAS.TYPE_NAME_SOFA + '-'
-            + CAS.FEATURE_BASE_NAME_SOFAID;
-    public static final String PROP_SOFA_STRING = NS_UIMA + CAS.TYPE_NAME_SOFA + '-'
-            + CAS.FEATURE_BASE_NAME_SOFASTRING;
-    public static final String PROP_SOFA_MIME_TYPE = NS_UIMA + CAS.TYPE_NAME_SOFA + '-'
-            + CAS.FEATURE_BASE_NAME_SOFAMIME;
+    public static final IRI PROP_SOFA_ID = new BasicIRI(SCHEME_UIMA, CAS.TYPE_NAME_SOFA + '-'
+            + CAS.FEATURE_BASE_NAME_SOFAID);
+    public static final IRI PROP_SOFA_STRING = new BasicIRI(SCHEME_UIMA, CAS.TYPE_NAME_SOFA + '-'
+            + CAS.FEATURE_BASE_NAME_SOFASTRING);
+    public static final IRI PROP_SOFA_MIME_TYPE = new BasicIRI(SCHEME_UIMA, CAS.TYPE_NAME_SOFA + '-'
+            + CAS.FEATURE_BASE_NAME_SOFAMIME);
 }

inception/inception-io-rdf/src/main/java/de/tudarmstadt/ukp/inception/io/rdf/internal/Uima2Rdf.java

@@ -17,6 +17,8 @@
  */
 package de.tudarmstadt.ukp.inception.io.rdf.internal;
 
+import static de.tudarmstadt.ukp.inception.io.rdf.internal.RdfCas.PREFIX_RDFCAS;
+import static de.tudarmstadt.ukp.inception.io.rdf.internal.RdfCas.SCHEME_UIMA;
 import static java.lang.String.format;
 
 import java.util.HashSet;
@@ -31,6 +33,7 @@
 import org.apache.uima.jcas.JCas;
 import org.eclipse.rdf4j.model.IRI;
 import org.eclipse.rdf4j.model.Model;
+import org.eclipse.rdf4j.model.Namespace;
 import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
 import org.eclipse.rdf4j.model.vocabulary.RDF;
 import de.tudarmstadt.ukp.clarin.webanno.diag.CasDoctorUtils;
@@ -56,9 +59,9 @@ public void convert(JCas aJCas, Model aTarget) throws CASException
     {
         // Set up prefix mappings
         var ts = aJCas.getTypeSystem();
-        aTarget.setNamespace("cas", RdfCas.NS_UIMA + "uima.cas.");
-        aTarget.setNamespace("tcas", RdfCas.NS_UIMA + "uima.tcas.");
-        aTarget.setNamespace(RdfCas.PREFIX_RDFCAS, RdfCas.NS_RDFCAS);
+        aTarget.setNamespace("cas", SCHEME_UIMA + "uima.cas.");
+        aTarget.setNamespace("tcas", SCHEME_UIMA + "uima.tcas.");
+        aTarget.setNamespace(PREFIX_RDFCAS, RdfCas.NS_RDFCAS);
 
         // Additional prefix mappings for DKPro Core typesystems
         for (var t : ts.getProperlySubsumedTypes(ts.getTopType())) {
@@ -73,7 +76,7 @@ public void convert(JCas aJCas, Model aTarget) throws CASException
                 if (nameMatcher.group("INMODULE") != null) {
                     prefix = prefix + "-" + nameMatcher.group("INMODULE");
                 }
-                aTarget.setNamespace(prefix, RdfCas.NS_UIMA + nameMatcher.group("LONG"));
+                aTarget.setNamespace(prefix, SCHEME_UIMA + nameMatcher.group("LONG"));
             }
         }
 
@@ -87,11 +90,6 @@ private void convertView(JCas aJCas, Model aTarget)
     {
         var vf = SimpleValueFactory.getInstance();
 
-        // Set up names
-        var tView = vf.createIRI(RdfCas.TYPE_VIEW);
-        var tFeatureStructure = vf.createIRI(RdfCas.TYPE_FEATURE_STRUCTURE);
-        var pIndexedIn = vf.createIRI(RdfCas.PROP_INDEXED_IN);
-
         // Get a URI for the document
         var dmd = DocumentMetaData.get(aJCas);
         var docuri = dmd.getDocumentUri() != null ? dmd.getDocumentUri()
@@ -104,23 +102,23 @@ private void convertView(JCas aJCas, Model aTarget)
         reachable.add(aJCas.getSofa());
 
         // Set up the view itself
-        var viewUri = format("%s#%d", docuri, aJCas.getLowLevelCas().ll_getFSRef(aJCas.getSofa()));
-        var rdfView = vf.createIRI(viewUri);
-        aTarget.add(rdfView, RDF.TYPE, tView);
+        var rdfView = vf.createIRI(
+                format("%s#%d", docuri, aJCas.getLowLevelCas().ll_getFSRef(aJCas.getSofa())));
+        aTarget.add(rdfView, RDF.TYPE, RdfCas.TYPE_VIEW);
 
         for (var uimaFS : reachable) {
             var uri = format("%s#%d", docuri, aJCas.getLowLevelCas().ll_getFSRef(uimaFS));
             var rdfFS = vf.createIRI(uri);
-            aTarget.add(rdfFS, RDF.TYPE, vf.createIRI(rdfType(uimaFS.getType())));
+            aTarget.add(rdfFS, RDF.TYPE, rdfType(aTarget, uimaFS.getType()));
 
             // The SoFa is not a regular FS - do not mark it as such
             if (uimaFS != aJCas.getSofa()) {
-                aTarget.add(rdfFS, RDF.TYPE, tFeatureStructure);
+                aTarget.add(rdfFS, RDF.TYPE, RdfCas.TYPE_FEATURE_STRUCTURE);
             }
 
             // Internal UIMA information
             if (indexed.contains(uimaFS)) {
-                aTarget.add(rdfFS, pIndexedIn, rdfView);
+                aTarget.add(rdfFS, RdfCas.PROP_INDEXED_IN, rdfView);
             }
 
             // Convert features
@@ -133,7 +131,7 @@ private void convertFeatures(Model aTarget, String docuri, FeatureStructure uima
         var vf = SimpleValueFactory.getInstance();
 
         for (var uimaFeat : uimaFS.getType().getFeatures()) {
-            var rdfFeat = vf.createIRI(rdfFeature(uimaFeat));
+            var rdfFeat = rdfFeature(aTarget, uimaFeat);
             if (uimaFeat.getRange().isPrimitive()) {
                 switch (uimaFeat.getRange().getName()) {
                 case CAS.TYPE_NAME_BOOLEAN:
@@ -189,13 +187,32 @@ private static String rdfUri(String docuri, FeatureStructure uimaFS)
         return format("%s#%d", docuri, uimaFS.getCAS().getLowLevelCAS().ll_getFSRef(uimaFS));
     }
 
-    private static String rdfFeature(Feature aUimaFeature)
+    private static IRI rdfFeature(Model aModel, Feature aUimaFeature)
     {
-        return rdfType(aUimaFeature.getDomain()) + "-" + aUimaFeature.getShortName();
+        var typeIri = rdfType(aModel, aUimaFeature.getDomain());
+        return new BasicIRI(typeIri.getNamespace(),
+                typeIri.getLocalName() + "-" + aUimaFeature.getShortName());
     }
 
-    private static String rdfType(Type aUimaType)
+    private static IRI rdfType(Model aModel, Type aUimaType)
     {
-        return RdfCas.NS_UIMA + aUimaType.getName();
+        Namespace bestNs = null;
+        for (var ns : aModel.getNamespaces()) {
+            var nsName = ns.getName().substring(SCHEME_UIMA.length());
+            if (aUimaType.getName().startsWith(nsName)
+                    && (bestNs == null || nsName.length() > bestNs.getName().length())) {
+                bestNs = ns;
+            }
+        }
+
+        var vf = SimpleValueFactory.getInstance();
+        if (bestNs != null) {
+            var namespace = bestNs.getName();
+            var localName = aUimaType.getName()
+                    .substring(bestNs.getName().length() - SCHEME_UIMA.length());
+            return new BasicIRI(namespace, localName);
+        }
+
+        return vf.createIRI(SCHEME_UIMA + aUimaType.getName());
     }
 }