Merge branch 'entailment2' into 'master'

Simplify entailment code

See merge request !97

acrepo-services-entailment/src/main/cfg/edu.amherst.acdc.services.entailment.cfg

 # Comma separated list of ontologies that should pulled in for entailment to be done on them
-rdfs.ontologies=http://purl.org/dc/terms/,http://purl.org/dc/elements/1.1/,http://id.loc.gov/ontologies/bibframe/,http://www.w3.org/2004/02/skos/core#,http://www.w3.org/2000/01/rdf-schema#
+rdfs.ontologies= \
+    http://purl.org/dc/terms/, \
+    http://www.w3.org/2004/02/skos/core#

acrepo-services-entailment/src/main/java/edu/amherst/acdc/services/entailment/EntailmentServiceImpl.java

@@ -15,8 +15,8 @@
  */
 package edu.amherst.acdc.services.entailment;
 
+import static java.util.Arrays.stream;
 import static java.util.Optional.ofNullable;
-import static java.util.stream.Collectors.toMap;
 import static org.apache.http.impl.client.HttpClientBuilder.create;
 import static org.apache.jena.rdf.model.ModelFactory.createDefaultModel;
 import static org.apache.jena.rdf.model.ModelFactory.createRDFSModel;
@@ -30,19 +30,16 @@ import static org.slf4j.LoggerFactory.getLogger;
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.InputStream;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
 import java.util.Optional;
 
 import org.apache.http.impl.client.LaxRedirectStrategy;
 import org.apache.jena.rdf.model.InfModel;
 import org.apache.jena.rdf.model.Model;
-import org.apache.jena.rdf.model.Resource;
 import org.apache.jena.rdf.model.Statement;
 import org.apache.jena.riot.Lang;
 import org.apache.jena.riot.RDFLanguages;
+import org.apache.jena.vocabulary.RDF;
+import org.apache.jena.vocabulary.RDFS;
 import org.slf4j.Logger;
 
 /**
@@ -55,7 +52,7 @@ public class EntailmentServiceImpl implements EntailmentService {
 
     private static final Lang DEFAULT_LANG = TURTLE;
 
-    private InfModel rdfsModel = createRDFSModel(createDefaultModel());
+    private InfModel schema = createRDFSModel(createDefaultModel());
 
     static {
         setDefaultHttpClient(create().setRedirectStrategy(new LaxRedirectStrategy()).build());
@@ -71,71 +68,40 @@ public class EntailmentServiceImpl implements EntailmentService {
     public EntailmentServiceImpl(final String ontologies) {
         LOGGER.info("EntailmentServiceImpl: ontologies: {}", ontologies);
 
-        Arrays.stream(ontologies.split(","))
-            .peek(ont -> LOGGER.info("adding to rdfs model: {}", ont))
-            .map(String::trim)
-            .forEach(ont -> read(rdfsModel, ont));
+        stream(ontologies.split(",")).peek(ont -> LOGGER.info("adding to rdfs model: {}", ont))
+            .map(String::trim).forEach(ont -> read(schema, ont));
     }
 
     @Override
     public InputStream getEntailedTriples(final String subject, final InputStream input,
-        final String contentType, final String acceptType) {
+            final String contentType, final String acceptType) {
 
         final Model model = createDefaultModel();
-
         read(model, input, contentTypeToLang(contentType.split(";")[0]));
 
-        // perform RDFS entailment over it by creating a RDFSModel
-        final InfModel fullModel = createRDFSModel(model);
-
-        // add the requested ontologies to the model, which does RDFS entailment over them.
-        fullModel.add(rdfsModel);
-
-        final Model entailed = fullModel.difference(rdfsModel);
+        final Model entailed = createDefaultModel();
         entailed.setNsPrefixes(model);
 
-        final Resource subjectResource = entailed.getResource(subject);
-        final List<Statement> props = subjectResource.listProperties().toList();
+        createRDFSModel(schema, model).listStatements()
+            // We don't care about rdfs:Class and rdfs:Resource types
+            .filterDrop(s -> isRdfsClass(s) || isRdfsResource(s))
+            .filterDrop(t -> schema.contains(t.getSubject(), null))
+            .forEachRemaining(entailed::add);
 
-        final Model newResourceModel = createDefaultModel();
-        newResourceModel.add(subjectResource.listProperties().toList());
+        final ByteArrayOutputStream baos = new ByteArrayOutputStream();
+        write(baos, entailed, getRdfLanguage(acceptType.split(";")[0]).orElse(DEFAULT_LANG));
+        return new ByteArrayInputStream(baos.toByteArray());
+    }
 
-        final Map<String,String> prefixMap = getPrefixMap(newResourceModel, entailed.getNsPrefixMap());
-        newResourceModel.setNsPrefixes(prefixMap);
+    private boolean isRdfsClass(final Statement stmt) {
+        return stmt.getPredicate().equals(RDF.type) && stmt.getResource().equals(RDFS.Class);
+    }
 
-        final ByteArrayOutputStream nbs = new ByteArrayOutputStream();
-        write(nbs, newResourceModel, getRdfLanguage(acceptType.split(";")[0]).orElse(DEFAULT_LANG));
-        return new ByteArrayInputStream(nbs.toByteArray());
+    private boolean isRdfsResource(final Statement stmt) {
+        return stmt.getPredicate().equals(RDF.type) && stmt.getResource().equals(RDFS.Resource);
     }
 
     private Optional<Lang> getRdfLanguage(final String contentType) {
         return ofNullable(contentType).map(RDFLanguages::contentTypeToLang);
     }
-
-    private Map<String,String> getPrefixMap(final Model model, final Map<String,String> prefixes) {
-        final List<Statement> props = model.listStatements().toList();
-
-        final Map<String,String> modelPrefixes = new HashMap<>();
-
-        final Map<String,String> flip_prefixes =
-          prefixes.entrySet().stream().collect(toMap(Map.Entry::getValue, Map.Entry::getKey, (key1, key2) -> key1));
-
-        LOGGER.debug("There are {} properties on resource", props.size());
-
-        props.forEach(statement -> {
-            final String pred_prefix = statement.getPredicate().getNameSpace();
-            if (flip_prefixes.containsKey(pred_prefix)) {
-                modelPrefixes.put(flip_prefixes.get(pred_prefix), pred_prefix);
-            }
-            if (statement.getObject().isResource()) {
-              final String obj_prefix = statement.getResource().getNameSpace();
-              if (flip_prefixes.containsKey(obj_prefix)) {
-                  modelPrefixes.put(flip_prefixes.get(obj_prefix), obj_prefix);
-              }
-            }
-        });
-
-        return modelPrefixes;
-
-    }
 }

acrepo-services-entailment/src/main/resources/OSGI-INF/blueprint/entailment-service.xml

@@ -9,7 +9,7 @@
 
   <cm:property-placeholder persistent-id="edu.amherst.acdc.services.entailment" update-strategy="reload" >
     <cm:default-properties>
-      <cm:property name="rdfs.ontologies" value=""/>
+      <cm:property name="rdfs.ontologies" value="http://purl.org/dc/terms/,http://www.w3.org/2004/02/skos/core#"/>
     </cm:default-properties>
   </cm:property-placeholder>
 

acrepo-services-entailment/src/test/java/edu/amherst/acdc/services/entailment/EntailmentServiceTest.java

@@ -19,15 +19,17 @@ import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.apache.jena.rdf.model.ModelFactory.createDefaultModel;
 import static org.apache.jena.riot.RDFDataMgr.read;
 import static org.apache.jena.riot.Lang.JSONLD;
-import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import static org.slf4j.LoggerFactory.getLogger;
 
 import java.io.InputStream;
 import java.io.IOException;
 import java.io.StringWriter;
+import java.util.List;
+
 import org.apache.commons.io.IOUtils;
 import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.Resource;
 import org.junit.Test;
 import org.slf4j.Logger;
 /**
@@ -59,9 +61,9 @@ public class EntailmentServiceTest {
         final String str = sw.toString();
 
         LOGGER.debug("string is : '{}'", str);
-        assertFalse(str.equals(""));
-        assertTrue(str.contains("rdfs:Resource") && str.contains("skos:Concept"));
-        assertTrue(str.contains("skos:broaderTransitive") && str.contains("skos:semanticRelation"));
+        assertTrue(str.contains("skos:Concept"));
+        assertTrue(str.contains("skos:broaderTransitive"));
+        assertTrue(str.contains("skos:semanticRelation"));
     }
 
     @Test
@@ -73,8 +75,7 @@ public class EntailmentServiceTest {
         final String str = sw.toString();
 
         LOGGER.debug("string is : '{}'", str);
-        assertFalse(str.equals(""));
-        assertTrue(str.contains("rdfs:Resource") && str.contains("rdfs:label"));
+        assertTrue(str.contains("rdfs:label"));
     }
 
     @Test
@@ -86,9 +87,11 @@ public class EntailmentServiceTest {
         final String str = sw.toString();
 
         LOGGER.debug("string is : '{}'", str);
-        assertFalse(str.equals(""));
-        assertTrue(str.contains("dc:rights") && str.contains("dc:title") && str.contains("dc:description"));
-        assertFalse(str.contains("dcterms:rights") && str.contains("dcterms:title"));
+        assertTrue(str.contains("http://purl.org/dc/elements/1.1/rights"));
+        assertTrue(str.contains("http://purl.org/dc/elements/1.1/title"));
+        assertTrue(str.contains("http://purl.org/dc/elements/1.1/description"));
+        assertTrue(str.contains("dcterms:rights"));
+        assertTrue(str.contains("dcterms:title"));
     }
 
     @Test
@@ -100,7 +103,6 @@ public class EntailmentServiceTest {
         final String str = sw.toString();
 
         LOGGER.debug("string is : '{}'", str);
-        assertFalse(str.equals(""));
         assertTrue(str.contains("@prefix ex:"));
     }
 
@@ -112,7 +114,7 @@ public class EntailmentServiceTest {
         final Model model = createDefaultModel();
 
         read(model, is, JSONLD);
-        final String res = model.listSubjects().next().getURI();
-        assertTrue(res.equals("http://localhost:8080/fcrepo/rest/test"));
+        final List<String> res = model.listSubjects().mapWith(Resource::getURI).toList();
+        assertTrue(res.contains("http://localhost:8080/fcrepo/rest/test"));
     }
 }