Merge pull request #190 from kbss-cvut/retrieve-prefix

Update documentation and test for retrieve prefix module
kbss-cvut · Aug 6, 2023 · 744aa84 · 744aa84
2 parents 2e6a281 + 1f97020
commit 744aa84
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diff --git a/s-pipes-core/src/main/java/cz/cvut/spipes/modules/RetrievePrefixesModule.java b/s-pipes-core/src/main/java/cz/cvut/spipes/modules/RetrievePrefixesModule.java
@@ -13,6 +13,40 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+/**
+ * Module returns prefix mappings of all loaded scripts.
+ * Individual mappings are represented by following graph pattern:
+ *
+ * @prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
+ *
+ * ?ontology ja:prefixMapping 
+ *      [ a ja:SinglePrefixMapping ;
+ *          ja:namespace ?namespaceIRI ;
+ *          ja:prefix ?prefix ]
+ * .
+ *
+ * As an example let's assume we loaded only one script:
+ *
+ * @prefix : <http://example.org/> .
+ * @prefix owl: <http://www.w3.org/2002/07/owl#> .
+ *
+ * :my-ontology a owl:Ontology .
+ *
+ *
+ * The output of this module for the example script would be:
+ *
+ * @prefix : <http://example.org/> .
+ * @prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
+ *
+ * :my-ontology ja:prefixMapping 
+ *      [ a ja:SinglePrefixMapping ;
+ *          ja:namespace "http://example.org/" ;
+ *          ja:prefix "" ],
+ *      [ a ja:SinglePrefixMapping ;
+ *          ja:namespace "http://www.w3.org/2002/07/owl#" ;
+ *          ja:prefix "owl" ] 
+* .
+ */
 public class RetrievePrefixesModule extends AbstractModule {
     private static final Logger LOG = LoggerFactory.getLogger(RetrievePrefixesModule.class.getName());
 
@@ -38,13 +72,13 @@ ExecutionContext executeSelf() {
                 outputModel.add(ontology, JA.prefixMapping, singlePrefixMapping);
 
                 outputModel.add(
-                    singlePrefixMapping, RDF.type, JA.SinglePrefixMapping
+                        singlePrefixMapping, RDF.type, JA.SinglePrefixMapping
                 );
                 outputModel.add(
-                    singlePrefixMapping, JA.prefix, key
+                        singlePrefixMapping, JA.prefix, key
                 );
                 outputModel.add(
-                    singlePrefixMapping, JA.namespace, value
+                        singlePrefixMapping, JA.namespace, value
                 );
             });
         }

diff --git a/s-pipes-core/src/main/java/cz/cvut/spipes/util/JenaUtils.java b/s-pipes-core/src/main/java/cz/cvut/spipes/util/JenaUtils.java
@@ -1,14 +1,5 @@
 package cz.cvut.spipes.util;
 
-import java.io.ByteArrayInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-import java.util.stream.Stream;
 import org.apache.commons.codec.digest.DigestUtils;
 import org.apache.jena.graph.compose.MultiUnion;
 import org.apache.jena.rdf.model.Model;
@@ -18,9 +9,19 @@
 import org.apache.jena.util.FileUtils;
 import org.apache.jena.vocabulary.OWL;
 import org.apache.jena.vocabulary.RDF;
+import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.List;
+import java.util.stream.Stream;
+
 public class JenaUtils {
 
     private static Logger LOG = LoggerFactory.getLogger(JenaUtils.class);
@@ -105,11 +106,11 @@ public static Model createUnion(Model... model) {
         return outputModel;
     }
 
-    public static void saveModelToTemporaryFile(Model model) {
+    public static void saveModelToTemporaryFile(@NotNull Model model) {
         try {
             Path file = Files.createTempFile("model-output-", ".ttl");
             LOG.debug("Saving model to temporary file " + file.toString() + " ...");
-            model.write(new FileOutputStream(file.toFile()), FileUtils.langTurtle);
+            model.write(Files.newOutputStream(file.toFile().toPath()), FileUtils.langTurtle);
         } catch (IOException e) {
             e.printStackTrace();
         }

diff --git a/s-pipes-core/src/test/java/cz/cvut/spipes/modules/RetrievePrefixesModuleTest.java b/s-pipes-core/src/test/java/cz/cvut/spipes/modules/RetrievePrefixesModuleTest.java
@@ -6,6 +6,7 @@
 import org.apache.jena.ontology.OntDocumentManager;
 import org.apache.jena.ontology.OntModel;
 import org.apache.jena.ontology.OntModelSpec;
+import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.util.FileManager;
 import org.apache.jena.util.FileUtils;
@@ -16,11 +17,17 @@
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.mockito.Mock;
 import org.mockito.junit.jupiter.MockitoExtension;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.InputStream;
+import java.net.URISyntaxException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 
+import static cz.cvut.spipes.test.JenaTestUtils.assertIsomorphic;
 import static org.mockito.BDDMockito.given;
 import static org.mockito.Mockito.doReturn;
 
@@ -30,9 +37,11 @@ class RetrievePrefixesModuleTest {
     @Mock
     OntologyDocumentManager ontoDocManager;
 
+    private static final Logger LOG = LoggerFactory.getLogger(RetrievePrefixesModuleTest.class);
+
     private final static String[] ontologyResourcePaths = new String[]{
-        "/manager/import-closure/indirect-import.ttl",
-        "/manager/import-closure/direct-import.ttl"
+            "/manager/import-closure/indirect-import.ttl",
+            "/manager/import-closure/direct-import.ttl"
     };
 
     HashMap<String, OntModel> uri2ontModel;
@@ -44,14 +53,14 @@ void setUp() {
             OntModel model = loadOntModel(ontologyPath);
             String iri = getOntologyIri(model);
             uri2ontModel.put(
-                iri,
-                model
+                    iri,
+                    model
             );
         }
     }
 
     @Test
-    void executeSelfReturnPrefixes() {
+    void executeSelfReturnPrefixes() throws URISyntaxException {
         given(ontoDocManager.getRegisteredOntologyUris()).willReturn(uri2ontModel.keySet());
         uri2ontModel.forEach((key, value) -> {
             doReturn(value).when(ontoDocManager).getOntology(key);
@@ -64,9 +73,13 @@ void executeSelfReturnPrefixes() {
         retrievePrefixesModule.setInputContext(inputExecutionContext);
         ExecutionContext outputExecutionContext = retrievePrefixesModule.executeSelf();
 
-        outputExecutionContext.getDefaultModel().write(System.out, FileUtils.langTurtle, null);
-    }
+        Model actualModel = outputExecutionContext.getDefaultModel();
 
+        Model expectedModel = ModelFactory.createDefaultModel()
+                .read(getFilePath("module/retrieve-prefixes/expected-output.ttl").toString());
+
+        assertIsomorphic(actualModel, expectedModel);
+    }
 
     private static String getOntologyIri(OntModel model) {
         return model.listResourcesWithProperty(RDF.type, OWL.Ontology).nextResource().toString();
@@ -91,4 +104,9 @@ private static OntModel loadOntModel(InputStream inputStream) {
         dm.loadImports(ontModel);
         return ontModel;
     }
+
+
+    public Path getFilePath(String fileName) throws URISyntaxException {
+        return Paths.get(getClass().getResource("/" + fileName).toURI());
+    }
 }
diff --git a/s-pipes-core/src/test/resources/module/retrieve-prefixes/expected-output.ttl b/s-pipes-core/src/test/resources/module/retrieve-prefixes/expected-output.ttl
@@ -0,0 +1,39 @@
+@prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
+
+<http://onto.fel.cvut.cz/ontologies/test/direct-import-test> ja:prefixMapping [ a ja:SinglePrefixMapping ;
+            ja:namespace "http://onto.fel.cvut.cz/ontologies/test/loading-test#" ;
+            ja:prefix "" ],
+        [ a ja:SinglePrefixMapping ;
+            ja:namespace "http://www.w3.org/2002/07/owl#" ;
+            ja:prefix "owl" ],
+        [ a ja:SinglePrefixMapping ;
+            ja:namespace "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
+            ja:prefix "rdf" ],
+        [ a ja:SinglePrefixMapping ;
+            ja:namespace "http://www.w3.org/XML/1998/namespace" ;
+            ja:prefix "xml" ],
+        [ a ja:SinglePrefixMapping ;
+            ja:namespace "http://www.w3.org/2001/XMLSchema#" ;
+            ja:prefix "xsd" ],
+        [ a ja:SinglePrefixMapping ;
+            ja:namespace "http://www.w3.org/2000/01/rdf-schema#" ;
+            ja:prefix "rdfs" ] .
+
+<http://onto.fel.cvut.cz/ontologies/test/indirect-import-test> ja:prefixMapping [ a ja:SinglePrefixMapping ;
+            ja:namespace "http://www.w3.org/XML/1998/namespace" ;
+            ja:prefix "xml" ],
+        [ a ja:SinglePrefixMapping ;
+            ja:namespace "http://www.w3.org/2001/XMLSchema#" ;
+            ja:prefix "xsd" ],
+        [ a ja:SinglePrefixMapping ;
+            ja:namespace "http://www.w3.org/2000/01/rdf-schema#" ;
+            ja:prefix "rdfs" ],
+        [ a ja:SinglePrefixMapping ;
+            ja:namespace "http://onto.fel.cvut.cz/ontologies/test/loading-test#" ;
+            ja:prefix "" ],
+        [ a ja:SinglePrefixMapping ;
+            ja:namespace "http://www.w3.org/2002/07/owl#" ;
+            ja:prefix "owl" ],
+        [ a ja:SinglePrefixMapping ;
+            ja:namespace "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
+            ja:prefix "rdf" ] .
diff --git a/s-pipes-modules/module-tabular/src/test/java/cz/cvut/spipes/modules/TabularModuleTest.java b/s-pipes-modules/module-tabular/src/test/java/cz/cvut/spipes/modules/TabularModuleTest.java
@@ -7,7 +7,6 @@
 import cz.cvut.spipes.exception.ResourceNotUniqueException;
 import cz.cvut.spipes.modules.exception.TableSchemaException;
 import cz.cvut.spipes.test.JenaTestUtils;
-import cz.cvut.spipes.util.JenaUtils;
 import cz.cvut.spipes.util.StreamResourceUtils;
 import org.apache.jena.rdf.model.*;
 import org.junit.jupiter.api.BeforeEach;
@@ -18,14 +17,16 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.*;
+import java.io.IOException;
 import java.net.URISyntaxException;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.Arrays;
 import java.util.List;
 
-import static org.junit.jupiter.api.Assertions.*;
+import static cz.cvut.spipes.test.JenaTestUtils.assertIsomorphic;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assumptions.assumeTrue;
 
  class TabularModuleTest extends AbstractModuleTestHelper {
@@ -228,15 +229,6 @@ void executeSelfWithHTMLFileInput() throws URISyntaxException, IOException {
         }
      }
 
-    void assertIsomorphic(Model actualModel, Model expectedModel){
-        if (! actualModel.isIsomorphicWith(expectedModel)) {
-            LOG.debug("Saving actual model ... ");
-            JenaUtils.saveModelToTemporaryFile(actualModel);
-            LOG.debug("Saving expected model ... ");
-            JenaUtils.saveModelToTemporaryFile(expectedModel);
-            fail("Actual model is not isomorphic with expected model (see additional information above).");
-        }
-    }
 
     @Override
     public String getModuleName() {

diff --git a/s-pipes-test/pom.xml b/s-pipes-test/pom.xml
@@ -29,7 +29,10 @@
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-core</artifactId>
-            <version>${org.apache.jena}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-api</artifactId>
         </dependency>
     </dependencies>
 </project>
diff --git a/s-pipes-test/src/main/java/cz/cvut/spipes/test/JenaTestUtils.java b/s-pipes-test/src/main/java/cz/cvut/spipes/test/JenaTestUtils.java
@@ -7,11 +7,20 @@
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.util.FileManager;
 import org.apache.jena.util.FileUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
+import java.io.IOException;
 import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import static org.junit.jupiter.api.Assertions.fail;
 
 public class JenaTestUtils {
 
+    private static Logger LOG = LoggerFactory.getLogger(JenaTestUtils.class);
+
     public static void mapLocalSPipesDefinitionFiles() {
         OntDocumentManager dm = OntDocumentManager.getInstance();
         dm.setFileManager(FileManager.getInternal());
@@ -52,4 +61,24 @@ public static Model laodModelFromResource(String path) {
 
         return model;
     }
+
+    public static void assertIsomorphic(Model actualModel, Model expectedModel) {
+        if (!actualModel.isIsomorphicWith(expectedModel)) {
+            LOG.debug("Saving actual model ... ");
+            saveModelToTemporaryFile(actualModel);
+            LOG.debug("Saving expected model ... ");
+            saveModelToTemporaryFile(expectedModel);
+            fail("Actual model is not isomorphic with expected model (see additional information above).");
+        }
+    }
+
+    private static void saveModelToTemporaryFile(Model model) {
+        try {
+            Path file = Files.createTempFile("model-output-", ".ttl");
+            LOG.debug("Saving model to temporary file " + file.toString() + " ...");
+            model.write(Files.newOutputStream(file.toFile().toPath()), FileUtils.langTurtle);
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
 }