Trillian updates

checkstyle-suppressions.xml

@@ -9,7 +9,7 @@
   <suppress checks="AbbreviationAsWordInName" files="UID\.java" />
 
   <!-- examples suppressions -->
-  <suppress checks="LineLength" files="ExampleDataObjects.java|ExampleRdl.java|ExampleAssociations.java" />
+  <suppress checks="LineLength" files="ExampleDataObjects.java|ExampleRdl.java|ExampleAssociations.java|MagmaCoreService.java" />
   <suppress checks="MethodLength" files="ExampleDataObjects.java" />
 
   <!-- hqdm-core suppressions -->

core/src/main/java/module-info.java

@@ -29,6 +29,7 @@
     requires transitive uk.gov.gchq.magmacore.hqdm.rdf;
 
     exports uk.gov.gchq.magmacore.service;
+    exports uk.gov.gchq.magmacore.service.dto;
     exports uk.gov.gchq.magmacore.service.transformation;
     exports uk.gov.gchq.magmacore.exception;
     exports uk.gov.gchq.magmacore.util;

core/src/main/java/uk/gov/gchq/magmacore/database/MagmaCoreDatabase.java

@@ -14,12 +14,18 @@
 
 package uk.gov.gchq.magmacore.database;
 
+import java.io.InputStream;
 import java.io.PrintStream;
 import java.util.List;
 
+import org.apache.jena.riot.Lang;
+
+import uk.gov.gchq.magmacore.database.query.QueryResultList;
 import uk.gov.gchq.magmacore.hqdm.model.Thing;
 import uk.gov.gchq.magmacore.hqdm.rdf.iri.HqdmIri;
 import uk.gov.gchq.magmacore.hqdm.rdf.iri.IRI;
+import uk.gov.gchq.magmacore.service.transformation.DbCreateOperation;
+import uk.gov.gchq.magmacore.service.transformation.DbDeleteOperation;
 
 /**
  * Interface defining CRUD operations and generic queries for Magma Core data collections.
@@ -63,6 +69,13 @@ public interface MagmaCoreDatabase {
      */
     void create(Thing object);
 
+    /**
+     * Apply a set of creates to the database.
+     *
+     * @param creates a {@link List} of {@link DbDeleteOperation}
+     */
+    void create(List<DbCreateOperation> creates);
+
     /**
      * Update an existing entity within the collection.
      *
@@ -77,6 +90,13 @@ public interface MagmaCoreDatabase {
      */
     void delete(Thing object);
 
+    /**
+     * Apply a set of deletes to the database.
+     *
+     * @param deletes a {@link List} of {@link DbDeleteOperation}
+     */
+    void delete(List<DbDeleteOperation> deletes);
+
     /**
      * Find object(s) that have a specific object associated with them.
      *
@@ -118,4 +138,44 @@ public interface MagmaCoreDatabase {
      * @param out Output stream to dump to.
      */
     void dump(PrintStream out);
+
+    /**
+     * Write the database as TTL using the {@link PrintStream} and {@link org.apache.jena.riot.Lang}.
+     *
+     * @param out      a {@link PrintStream}
+     * @param language a {@link Lang}
+     */
+    void dump(final PrintStream out, final Lang language);
+
+    /**
+     * Import data into the model.
+     *
+     * @param in       {@link InputStream} to read from.
+     * @param language RDF language syntax to output data as.
+     */
+    void load(final InputStream in, final Lang language);
+
+    /**
+     * Perform a SPARQL query on the dataset.
+     *
+     * @param sparqlQueryString SPARQL query to execute.
+     * @return Results of the query.
+     */
+    QueryResultList executeQuery(final String sparqlQueryString);
+
+    /**
+     * Convert a {@link QueryResultList} to a {@link List} of {@link Thing}.
+     *
+     * @param queryResultsList {@link QueryResultList}
+     * @return a {@link List} of {@link Thing}
+     */
+    List<Thing> toTopObjects(final QueryResultList queryResultsList);
+
+    /**
+     * Execute a CONSTRUCT query.
+     *
+     * @param query a CONSTRUCT query {@link String}
+     * @return a {@link List} of {@link Thing}
+     */
+    List<Thing> executeConstruct(final String query);
 }

core/src/main/java/uk/gov/gchq/magmacore/database/MagmaCoreJenaDatabase.java

@@ -14,6 +14,7 @@
 
 package uk.gov.gchq.magmacore.database;
 
+import java.io.InputStream;
 import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -29,7 +30,10 @@
 import org.apache.jena.query.QueryFactory;
 import org.apache.jena.query.QuerySolution;
 import org.apache.jena.query.ResultSet;
+import org.apache.jena.rdf.model.Literal;
 import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.Property;
 import org.apache.jena.rdf.model.RDFNode;
 import org.apache.jena.rdf.model.Resource;
 import org.apache.jena.rdf.model.Statement;
@@ -51,6 +55,8 @@
 import uk.gov.gchq.magmacore.hqdm.rdf.iri.IRI;
 import uk.gov.gchq.magmacore.hqdm.rdf.iri.IriBase;
 import uk.gov.gchq.magmacore.hqdm.rdf.util.Pair;
+import uk.gov.gchq.magmacore.service.transformation.DbCreateOperation;
+import uk.gov.gchq.magmacore.service.transformation.DbDeleteOperation;
 
 /**
  * Apache Jena triplestore to store HQDM objects as RDF triples either as an in-memory Jena dataset
@@ -165,10 +171,44 @@ public Thing get(final IRI iri) {
      */
     @Override
     public void create(final Thing object) {
-        final Resource resource = dataset.getDefaultModel().createResource(object.getId());
+        final Model defaultModel = dataset.getDefaultModel();
 
-        object.getPredicates().forEach((iri, predicates) -> predicates.forEach(predicate -> resource
-                .addProperty(dataset.getDefaultModel().createProperty(iri.toString()), predicate.toString())));
+        final Resource resource = defaultModel.createResource(object.getId());
+
+        object.getPredicates().forEach((iri, predicates) -> predicates.forEach(value -> {
+            if (value instanceof IRI) {
+                final Resource valueResource = defaultModel.createResource(value.toString());
+                resource.addProperty(defaultModel.createProperty(iri.toString()), valueResource);
+            } else {
+                resource.addProperty(defaultModel.createProperty(iri.toString()), value.toString());
+            }
+        }));
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public void create(final List<DbCreateOperation> creates) {
+        final Model forCreation = ModelFactory.createDefaultModel();
+
+        creates.forEach(create -> {
+            final Resource s = forCreation.createResource(create.subject.getIri());
+            final Property p = forCreation.createProperty(create.predicate.getIri());
+            final Object value = create.object;
+
+            final RDFNode o;
+            if (value instanceof IRI) {
+                o = forCreation.createResource(value.toString());
+            } else {
+                o = forCreation.createLiteral(value.toString());
+            }
+            forCreation.add(forCreation.createStatement(s, p, o));
+        });
+
+        final Model model = dataset.getDefaultModel();
+
+        model.add(forCreation);
     }
 
     /**
@@ -188,6 +228,33 @@ public void delete(final Thing object) {
         executeUpdate(String.format("delete {<%s> ?p ?o} WHERE {<%s> ?p ?o}", object.getId(), object.getId()));
     }
 
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public void delete(final List<DbDeleteOperation> deletes) {
+        final Model forDeletion = ModelFactory.createDefaultModel();
+
+        deletes.forEach(delete -> {
+            final Resource s = forDeletion.createResource(delete.subject.getIri());
+            final Property p = forDeletion.createProperty(delete.predicate.getIri());
+            final Object value = delete.object;
+
+            final RDFNode o;
+            if (value instanceof IRI) {
+                o = forDeletion.createResource(value.toString());
+            } else {
+                o = forDeletion.createLiteral(value.toString());
+            }
+
+            forDeletion.add(forDeletion.createStatement(s, p, o));
+        });
+
+        final Model model = dataset.getDefaultModel();
+
+        model.remove(forDeletion);
+    }
+
     /**
      * {@inheritDoc}
      */
@@ -233,6 +300,22 @@ public List<Thing> findByPredicateIriAndStringCaseInsensitive(final IRI predicat
         return toTopObjects(list);
     }
 
+    /**
+     * Execute a CONSTRUCT query.
+     *
+     * @param sparqlQueryString a CONSTRUCT query {@link String}
+     * @return a {@link List} of {@link Thing}
+     */
+    public List<Thing> executeConstruct(final String sparqlQueryString) {
+        final Query query = QueryFactory.create(sparqlQueryString);
+        final QueryExecution queryExec = QueryExecutionFactory.create(query, dataset);
+
+        final Model model = queryExec.execConstruct();
+        final Query selectAllQuery = QueryFactory.create("select ?s ?p ?o where { ?s ?p ?o. }");
+        final QueryExecution selectAllQueryExec = QueryExecutionFactory.create(selectAllQuery, model);
+        return toTopObjects(getQueryResultList(selectAllQueryExec));
+    }
+
     /**
      * Perform an update query on the dataset.
      *
@@ -250,7 +333,7 @@ protected void executeUpdate(final String statement) {
      * @param sparqlQueryString SPARQL query to execute.
      * @return Results of the query.
      */
-    protected QueryResultList executeQuery(final String sparqlQueryString) {
+    public QueryResultList executeQuery(final String sparqlQueryString) {
         final Query query = QueryFactory.create(sparqlQueryString);
         final QueryExecution queryExec = QueryExecutionFactory.create(query, dataset);
         return getQueryResultList(queryExec);
@@ -282,28 +365,45 @@ private final QueryResultList getQueryResultList(final QueryExecution queryExec)
         return queryResultList;
     }
 
-    private final List<Thing> toTopObjects(final QueryResultList queryResultsList) {
-        final Map<String, List<Pair<String, String>>> objectMap = new HashMap<>();
-        final String subjectVarName = ((List<String>) queryResultsList.getVarNames()).get(0);
-        final String predicateVarName = ((List<String>) queryResultsList.getVarNames()).get(1);
-        final String objectVarName = ((List<String>) queryResultsList.getVarNames()).get(2);
+    /**
+     * Convert a {@link QueryResultList} to a {@link List} of {@link Thing}.
+     *
+     * @param queryResultsList {@link QueryResultList}
+     * @return a {@link List} of {@link Thing}
+     */
+    public final List<Thing> toTopObjects(final QueryResultList queryResultsList) {
+        final Map<RDFNode, List<Pair<Object, Object>>> objectMap = new HashMap<>();
+        final List<String> varNames = (List<String>) queryResultsList.getVarNames();
+
+        final String subjectVarName = varNames.get(0);
+        final String predicateVarName = varNames.get(1);
+        final String objectVarName = varNames.get(2);
 
         // Create a map of the triples for each unique subject IRI
         final List<QueryResult> queryResults = queryResultsList.getQueryResults();
         queryResults.forEach(queryResult -> {
-            final String subjectValue = queryResult.get(subjectVarName).toString();
-            final String predicateValue = queryResult.get(predicateVarName).toString();
-            final String objectValue = queryResult.get(objectVarName).toString();
+            final RDFNode subjectValue = queryResult.get(subjectVarName);
+            final RDFNode predicateValue = queryResult.get(predicateVarName);
+            final RDFNode objectValue = queryResult.get(objectVarName);
 
-            List<Pair<String, String>> dataModelObject = objectMap.get(subjectValue);
+            List<Pair<Object, Object>> dataModelObject = objectMap.get(subjectValue);
             if (dataModelObject == null) {
                 dataModelObject = new ArrayList<>();
                 objectMap.put(subjectValue, dataModelObject);
             }
-            dataModelObject.add(new Pair<>(predicateValue, objectValue));
+            if (objectValue instanceof Literal) {
+                dataModelObject.add(new Pair<>(new IRI(predicateValue.toString()), objectValue.toString()));
+            } else if (objectValue instanceof Resource) {
+                dataModelObject.add(new Pair<>(new IRI(predicateValue.toString()), new IRI(objectValue.toString())));
+            } else {
+                throw new RuntimeException("objectValue is of unknown type: " + objectValue.getClass());
+            }
         });
 
-        return objectMap.entrySet().stream().map(entry -> HqdmObjectFactory.create(entry.getKey(), entry.getValue()))
+        return objectMap
+                .entrySet()
+                .stream()
+                .map(entry -> HqdmObjectFactory.create(new IRI(entry.getKey().toString()), entry.getValue()))
                 .collect(Collectors.toList());
     }
 
@@ -334,4 +434,17 @@ public final void dump(final PrintStream out, final Lang language) {
         RDFDataMgr.write(out, dataset.getDefaultModel(), language);
         abort();
     }
+
+    /**
+     * Import data into the model.
+     *
+     * @param in       {@link InputStream} to read from.
+     * @param language RDF language syntax to output data as.
+     */
+    public final void load(final InputStream in, final Lang language) {
+        begin();
+        final Model model = dataset.getDefaultModel();
+        RDFDataMgr.read(model, in, language);
+        commit();
+    }
 }