[New] Initial implementation of RetrievePrefixModule

s-pipes-core/src/main/java/cz/cvut/spipes/modules/AbstractModule.java

@@ -414,14 +414,24 @@ protected RDFNode getEffectiveValue(@NotNull Property valueProperty) {
         }
     }
 
-    protected ExecutionContext createOutputContext(boolean isReplace, Model inputModel, Model computedModel) {
+    /**
+     * Helper method to creates output execution context considering isReplace flag
+     * indicating if newly computed model should replace input model of the module
+     * or be appended to it.
+     * @param isReplace if true replace input model otherwise append to it.
+     * @param computedModel model to be reflected in final output of this module.
+     * @return Output execution context to be returned by this module.
+     */
+    protected ExecutionContext createOutputContext(boolean isReplace, Model computedModel) {
         if (isReplace) {
             return ExecutionContextFactory.createContext(computedModel);
         } else {
             if (AuditConfig.isEnabled() || ExecutionConfig.getEnvironment().equals(Environment.development)) {
                 LOG.debug("Saving module's computed output to file {}.", saveModelToTemporaryFile(computedModel));
             }
-            return ExecutionContextFactory.createContext(JenaUtils.createUnion(inputModel, computedModel));
+            return ExecutionContextFactory.createContext(
+                JenaUtils.createUnion(executionContext.getDefaultModel(), computedModel)
+            );
         }
     }
 

s-pipes-core/src/main/java/cz/cvut/spipes/modules/ApplyConstructModule.java

@@ -157,7 +157,7 @@ public ExecutionContext executeSelf() {
             nNew = inferredInSingleIterationModel.size();
         }
 
-        return this.createOutputContext(isReplace, defaultModel, inferredModel);
+        return this.createOutputContext(isReplace, inferredModel);
     }
 
     @Override

s-pipes-core/src/main/java/cz/cvut/spipes/modules/RetrievePrefixesModule.java

@@ -0,0 +1,68 @@
+package cz.cvut.spipes.modules;
+
+import cz.cvut.spipes.constants.KBSS_MODULE;
+import cz.cvut.spipes.constants.SML;
+import cz.cvut.spipes.engine.ExecutionContext;
+import cz.cvut.spipes.manager.OntoDocManager;
+import cz.cvut.spipes.manager.OntologyDocumentManager;
+import org.apache.jena.assembler.JA;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.vocabulary.RDF;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class RetrievePrefixesModule extends AbstractModule {
+    private static final Logger LOG = LoggerFactory.getLogger(RetrievePrefixesModule.class.getName());
+
+    private static String TYPE_URI = KBSS_MODULE.getURI() + "retrieve-prefixes";
+
+    //sml:replace
+    private boolean isReplace;
+
+    //TODO refactor -> should be part of execution context
+    OntologyDocumentManager ontologyDocumentManager = OntoDocManager.getInstance();
+
+    @Override
+    ExecutionContext executeSelf() {
+        Model outputModel = ModelFactory.createDefaultModel();
+
+        for (String ontologyUri : ontologyDocumentManager.getRegisteredOntologyUris()) {
+
+            Resource ontology = outputModel.createResource(ontologyUri);
+
+            ontologyDocumentManager.getOntology(ontologyUri).getNsPrefixMap().forEach((key, value) -> {
+                Resource singlePrefixMapping = outputModel.createResource();
+
+                outputModel.add(ontology, JA.prefixMapping, singlePrefixMapping);
+
+                outputModel.add(
+                    singlePrefixMapping, RDF.type, JA.SinglePrefixMapping
+                );
+                outputModel.add(
+                    singlePrefixMapping, JA.prefix, key
+                );
+                outputModel.add(
+                    singlePrefixMapping, JA.namespace, value
+                );
+            });
+        }
+
+        return this.createOutputContext(isReplace, outputModel);
+    }
+
+    @Override
+    public String getTypeURI() {
+        return TYPE_URI;
+    }
+
+    @Override
+    public void loadConfiguration() {
+        isReplace = this.getPropertyValue(SML.replace, false);
+    }
+
+    void setOntologyDocumentManager(OntologyDocumentManager ontologyDocumentManager) {
+        this.ontologyDocumentManager = ontologyDocumentManager;
+    }
+}

s-pipes-core/src/test/java/cz/cvut/spipes/modules/RetrievePrefixesModuleTest.java

@@ -0,0 +1,95 @@
+package cz.cvut.spipes.modules;
+
+import cz.cvut.spipes.engine.ExecutionContext;
+import cz.cvut.spipes.engine.ExecutionContextFactory;
+import cz.cvut.spipes.manager.OntologyDocumentManager;
+import org.apache.jena.ontology.OntDocumentManager;
+import org.apache.jena.ontology.OntModel;
+import org.apache.jena.ontology.OntModelSpec;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.shared.PrefixMapping;
+import org.apache.jena.util.FileManager;
+import org.apache.jena.util.FileUtils;
+import org.apache.jena.vocabulary.OWL;
+import org.apache.jena.vocabulary.RDF;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+
+import java.io.InputStream;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+
+import static org.mockito.BDDMockito.given;
+import static org.mockito.Mockito.doReturn;
+
+@ExtendWith(MockitoExtension.class)
+class RetrievePrefixesModuleTest {
+
+    @Mock
+    OntologyDocumentManager ontoDocManager;
+
+    private final static String[] ontologyResourcePaths = new String[]{
+        "/manager/import-closure/indirect-import.ttl",
+        "/manager/import-closure/direct-import.ttl"
+    };
+
+    HashMap<String, OntModel> uri2ontModel;
+
+    @BeforeEach
+    void setUp() {
+        uri2ontModel = new LinkedHashMap<>();
+        for (String ontologyPath : ontologyResourcePaths) {
+            OntModel model = loadOntModel(ontologyPath);
+            String iri = getOntologyIri(model);
+            uri2ontModel.put(
+                iri,
+                model
+            );
+        }
+    }
+
+    @Test
+    void testExecuteSelf() {
+        given(ontoDocManager.getRegisteredOntologyUris()).willReturn(uri2ontModel.keySet());
+        uri2ontModel.forEach((key, value) -> {
+            doReturn(value).when(ontoDocManager).getOntology(key);
+        });
+
+        ExecutionContext inputExecutionContext = ExecutionContextFactory.createEmptyContext();
+
+        RetrievePrefixesModule retrievePrefixesModule = new RetrievePrefixesModule();
+        retrievePrefixesModule.setOntologyDocumentManager(ontoDocManager);
+        retrievePrefixesModule.setInputContext(inputExecutionContext);
+        ExecutionContext outputExecutionContext = retrievePrefixesModule.executeSelf();
+
+        outputExecutionContext.getDefaultModel().write(System.out, FileUtils.langTurtle, null);
+    }
+
+
+    private static String getOntologyIri(OntModel model) {
+        return model.listResourcesWithProperty(RDF.type, OWL.Ontology).nextResource().toString();
+    }
+
+    private static OntModel loadOntModel(String resourcePath) {
+        InputStream is = RetrievePrefixesModuleTest.class.getResourceAsStream(resourcePath);
+
+        if (is == null) {
+            throw new IllegalArgumentException("Resource " + resourcePath + " not found.");
+        }
+        return loadOntModel(is);
+    }
+
+    private static OntModel loadOntModel(InputStream inputStream) {
+        OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
+
+        OntDocumentManager dm = OntDocumentManager.getInstance();
+        dm.setFileManager(FileManager.get());
+
+        ontModel.read(inputStream, null, FileUtils.langTurtle);
+        dm.loadImports(ontModel);
+        return ontModel;
+    }
+}

s-pipes-modules/module-form/src/main/java/cz/cvut/spipes/modules/ConstructFormMetadataModule.java

@@ -4,7 +4,6 @@
 import cz.cvut.spipes.constants.KBSS_MODULE;
 import cz.cvut.spipes.constants.SML;
 import cz.cvut.spipes.engine.ExecutionContext;
-import cz.cvut.spipes.engine.ExecutionContextFactory;
 import org.apache.commons.codec.digest.DigestUtils;
 import org.apache.jena.rdf.model.*;
 import org.apache.jena.vocabulary.RDF;
@@ -68,11 +67,7 @@ ExecutionContext executeSelf() {
             q -> processFormEntity(q, null, constructedModel)
         );
 
-        if (isReplace) {
-            return ExecutionContextFactory.createContext(constructedModel);
-        } else {
-            return ExecutionContextFactory.createContext(ModelFactory.createUnion(constructedModel, inpModel));
-        }
+        return createOutputContext(isReplace, constructedModel);
     }
 
     public boolean isReplace() {

s-pipes-modules/module-form/src/main/java/cz/cvut/spipes/modules/ConstructTextualViewModule.java

@@ -10,7 +10,6 @@
 import cz.cvut.spipes.constants.KBSS_MODULE;
 import cz.cvut.spipes.constants.SML;
 import cz.cvut.spipes.engine.ExecutionContext;
-import cz.cvut.spipes.engine.ExecutionContextFactory;
 import cz.cvut.spipes.form.JenaFormUtils;
 import cz.cvut.spipes.form.JopaPersistenceUtils;
 import org.apache.jena.rdf.model.Model;
@@ -88,11 +87,7 @@ ExecutionContext executeSelf() {
             );
         }
 
-        if (isReplace) {
-            return ExecutionContextFactory.createContext(constructedModel);
-        } else {
-            return ExecutionContextFactory.createContext(ModelFactory.createUnion(constructedModel, inpModel));
-        }
+        return createOutputContext(isReplace, constructedModel);
     }
 
     public boolean isSerializeUnansweredQuestions() {

s-pipes-modules/module-form/src/main/java/cz/cvut/spipes/modules/FetchPossibleValuesModule.java

@@ -5,7 +5,6 @@
 import cz.cvut.spipes.constants.KBSS_MODULE;
 import cz.cvut.spipes.constants.SML;
 import cz.cvut.spipes.engine.ExecutionContext;
-import cz.cvut.spipes.engine.ExecutionContextFactory;
 import cz.cvut.spipes.form.JenaFormUtils;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
@@ -70,11 +69,7 @@ ExecutionContext executeSelf() {
             }
         );
 
-        if (isReplace) {
-            return ExecutionContextFactory.createContext(constructedModel);
-        } else {
-            return ExecutionContextFactory.createContext(ModelFactory.createUnion(constructedModel, inpModel));
-        }
+        return createOutputContext(isReplace, constructedModel);
     }
 
     public String getPossibleValuesQuery(Resource question) {

s-pipes-modules/module-form/src/main/java/cz/cvut/spipes/modules/MergeFormMetadataModule.java

@@ -5,7 +5,6 @@
 import cz.cvut.spipes.constants.KBSS_MODULE;
 import cz.cvut.spipes.constants.SML;
 import cz.cvut.spipes.engine.ExecutionContext;
-import cz.cvut.spipes.engine.ExecutionContextFactory;
 import cz.cvut.spipes.form.JenaFormUtils;
 import org.apache.commons.codec.digest.DigestUtils;
 import org.apache.jena.rdf.model.Model;
@@ -69,11 +68,7 @@ ExecutionContext executeSelf() {
             }
         );
 
-        if (isReplace) {
-            return ExecutionContextFactory.createContext(constructedModel);
-        } else {
-            return ExecutionContextFactory.createContext(ModelFactory.createUnion(constructedModel, inpModel));
-        }
+        return createOutputContext(isReplace, constructedModel);
     }
 
     public boolean isReplace() {

s-pipes-modules/module-nlp/src/main/java/cz/cvut/spipes/modules/SUTimeModuleNew.java

@@ -3,52 +3,35 @@
 import cz.cvut.spipes.constants.KBSS_MODULE;
 import cz.cvut.spipes.constants.SML;
 import cz.cvut.spipes.engine.ExecutionContext;
-import cz.cvut.spipes.engine.ExecutionContextFactory;
 import cz.cvut.spipes.sutime.AnnforModel;
 import cz.cvut.spipes.sutime.DescriptorModel;
 import cz.cvut.spipes.util.JenaUtils;
 import cz.cvut.spipes.util.QueryUtils;
 import edu.stanford.nlp.ling.CoreAnnotations;
 import edu.stanford.nlp.ling.CoreLabel;
-import edu.stanford.nlp.pipeline.Annotation;
-import edu.stanford.nlp.pipeline.AnnotationPipeline;
-import edu.stanford.nlp.pipeline.POSTaggerAnnotator;
-import edu.stanford.nlp.pipeline.TokenizerAnnotator;
-import edu.stanford.nlp.pipeline.WordsToSentencesAnnotator;
+import edu.stanford.nlp.pipeline.*;
 import edu.stanford.nlp.time.TimeAnnotations;
 import edu.stanford.nlp.time.TimeAnnotator;
 import edu.stanford.nlp.time.TimeExpression;
 import edu.stanford.nlp.util.CoreMap;
-import java.io.IOException;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.time.format.DateTimeFormatter;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.GregorianCalendar;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Properties;
 import org.apache.jena.query.Query;
 import org.apache.jena.query.QueryFactory;
 import org.apache.jena.query.QuerySolution;
-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.ReifiedStatement;
-import org.apache.jena.rdf.model.Resource;
-import org.apache.jena.rdf.model.ResourceFactory;
+import org.apache.jena.rdf.model.*;
 import org.apache.jena.vocabulary.RDF;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.topbraid.spin.arq.ARQFactory;
 import org.topbraid.spin.model.Construct;
 import org.topbraid.spin.vocabulary.SP;
 
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.*;
+
 
 public class SUTimeModuleNew extends AbstractModule {
 
@@ -157,11 +140,7 @@ public ExecutionContext executeSelf() {
             inferredModel = JenaUtils.createUnion(inferredModel, inferredInSingleIterationModel);
         }
 
-        if (isReplace) {
-            return ExecutionContextFactory.createContext(inferredModel);
-        } else {
-            return ExecutionContextFactory.createContext(ModelFactory.createUnion(defaultModel, inferredModel));
-        }
+        return createOutputContext(isReplace, inferredModel);
     }
 
     private Model analyzeModel(Model m) {

s-pipes-modules/module-sparql-endpoint/src/main/java/cz/cvut/spipes/modules/ApplyConstructAbstractModule.java

@@ -3,7 +3,6 @@
 import cz.cvut.spipes.constants.KBSS_MODULE;
 import cz.cvut.spipes.constants.SML;
 import cz.cvut.spipes.engine.ExecutionContext;
-import cz.cvut.spipes.engine.ExecutionContextFactory;
 import cz.cvut.spipes.util.JenaUtils;
 import cz.cvut.spipes.util.QueryUtils;
 import org.apache.jena.query.Query;
@@ -155,11 +154,7 @@ public ExecutionContext executeSelf() {
             }
         }
 
-        if (isReplace) {
-            return ExecutionContextFactory.createContext(inferredModel);
-        } else {
-            return ExecutionContextFactory.createContext(ModelFactory.createUnion(defaultModel, inferredModel));
-        }
+        return createOutputContext(isReplace, inferredModel);
     }
 
     protected String substituteQueryMarkers(int currentIteration, String queryStr) {