fix: change serialization string to lang (#50)

* fix: change serialization string to lang

* fix: rename

* fix: use name to serialization

pom.xml

@@ -8,7 +8,7 @@
   <name>Wings OPM Mapper</name>
   <packaging>jar</packaging>
   <description>Wings OPM (Open Provenance Model) Mapper</description>
-  <version>1.2.8</version>
+  <version>2.0.0</version>
 
   <properties>
     <log4j.version>2.16.0</log4j.version>
@@ -179,7 +179,7 @@
     <dependency>
       <groupId>com.fasterxml.jackson.core</groupId>
       <artifactId>jackson-databind</artifactId>
-      <version>2.9.0</version>
+      <version>2.8.10</version>
     </dependency>
   </dependencies>
 

src/main/java/edu/isi/kcap/wings/opmm/Catalog.java

@@ -16,6 +16,7 @@
 import org.apache.jena.rdf.model.Statement;
 import org.apache.jena.rdf.model.StmtIterator;
 import org.apache.jena.rdf.model.impl.ResourceImpl;
+import org.apache.jena.riot.Lang;
 
 /**
  * Class designed to deal with the versioning of new catalog entities.
@@ -532,7 +533,7 @@ private String getCatalogTypeForObject(Resource wingsObjType) {
      * @param directory FOLDER path where to export the catalog
      * @throws IOException
      */
-    public String exportCatalog(String directory, String serialization) throws IOException {
+    public String exportCatalog(String directory, Lang serialization) throws IOException {
         String exportPath;
         // create directory if it does not exist
         File dir;
@@ -590,7 +591,7 @@ public static void main(String[] args) throws IOException {
                         " is " + c.getCatalogTypeForComponentInstanceURI(
                                 "http://www.wings-workflows.org/wings-omics-portal/export/users/alyssa/DataAbstractions/components/library.owl#SNPcaller-Polyphred"));
 
-        c.exportCatalog(null, "RDF/XML");
+        c.exportCatalog(null, Lang.RDFXML);
         System.out.println("Catalog exported");
 
         // note: local tests have been performed by modifying the catalog manually.

src/main/java/edu/isi/kcap/wings/opmm/Mapper.java

@@ -2,6 +2,9 @@
 
 import java.io.FileNotFoundException;
 import java.io.IOException;
+
+import org.apache.jena.riot.Lang;
+
 import edu.isi.kcap.wings.opmm.DataTypes.Links;
 import edu.isi.kcap.wings.opmm.DataTypes.ProvenanceResponseSchema;
 import edu.isi.kcap.wings.opmm.Publisher.TriplesPublisher;
@@ -35,17 +38,17 @@ public static ProvenanceResponseSchema main(String domain,
                                 filePublisher, workflowPublisher);
                 exportExecution(executionDestinationFilePath, workflowPublisher.serialization, response,
                                 executionExport);
-                        exportExpandedTemplate(expandedTemplateDestinationFilePath, workflowPublisher.serialization,
-                                        response,
-                                        executionExport);
+                exportExpandedTemplate(expandedTemplateDestinationFilePath, workflowPublisher.serialization,
+                                response,
+                                executionExport);
                 WorkflowTemplateExport templateExport = executionExport.getConcreteTemplateExport();
-                        exportAbstractTemplate(abstractFilePath, workflowPublisher.serialization, response,
-                                        templateExport);
+                exportAbstractTemplate(abstractFilePath, workflowPublisher.serialization, response,
+                                templateExport);
                 exportCatalog(catalogRepository, catalogPublisher.serialization, response, catalog);
                 return response;
         }
 
-        private static void exportCatalog(String catalogRepository, String serialization,
+        private static void exportCatalog(String catalogRepository, Lang serialization,
                         ProvenanceResponseSchema response,
                         Catalog catalog) throws IOException {
                 // Export the catalog
@@ -59,7 +62,7 @@ private static void exportCatalog(String catalogRepository, String serialization
                 response.setCatalog(links);
         }
 
-        private static void exportExpandedTemplate(String expandedTemplateDestinationFilePath, String serialization,
+        private static void exportExpandedTemplate(String expandedTemplateDestinationFilePath, Lang serialization,
                         ProvenanceResponseSchema response, WorkflowExecutionExport executionExport) throws IOException {
                 String expandedTemplateGraphUri = executionExport.getConcreteTemplateExport().exportAsOPMW(
                                 expandedTemplateDestinationFilePath,
@@ -74,7 +77,7 @@ private static void exportExpandedTemplate(String expandedTemplateDestinationFil
                 response.setWorkflowExpandedTemplate(links);
         }
 
-        private static void exportExecution(String executionDestinationFilePath, String serialization,
+        private static void exportExecution(String executionDestinationFilePath, Lang serialization,
                         ProvenanceResponseSchema response, WorkflowExecutionExport executionExport)
                         throws IOException, FileNotFoundException {
                 String executionGraphUri = executionExport.exportAsOPMW(executionDestinationFilePath, serialization);
@@ -85,7 +88,7 @@ private static void exportExecution(String executionDestinationFilePath, String
                 response.setWorkflowExecution(links);
         }
 
-        private static void exportAbstractTemplate(String abstractFilePath, String serialization,
+        private static void exportAbstractTemplate(String abstractFilePath, Lang serialization,
                         ProvenanceResponseSchema response,
                         WorkflowTemplateExport abstractTemplateExport) throws IOException {
                 if (abstractTemplateExport != null) {

src/main/java/edu/isi/kcap/wings/opmm/ModelUtils.java

@@ -17,6 +17,7 @@
 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.riot.Lang;
 import org.apache.jena.util.FileManager;
 
 /**
@@ -62,14 +63,14 @@ public static OntModel loadModel(String path) throws IllegalArgumentException {
      * @param mode    serialization to export the model in
      * @throws IOException
      */
-    public static void exportRDFFile(String outFile, OntModel model, String mode)
+    public static void exportRDFFile(String outFile, OntModel model, Lang mode)
             throws IOException, FileNotFoundException {
         if (outFile == null) {
             throw new FileNotFoundException("File not found");
         }
         OutputStream out;
         out = new FileOutputStream(outFile);
-        model.write(out, mode);
+        model.write(out, mode.getName());
         // model.write(out,"RDF/XML");
         out.close();
     }

src/main/java/edu/isi/kcap/wings/opmm/Publisher/TriplesPublisher.java

@@ -13,9 +13,12 @@
 import org.apache.http.entity.StringEntity;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClients;
+import org.apache.jena.datatypes.xsd.impl.RDFLangString;
 import org.apache.jena.query.DatasetAccessor;
 import org.apache.jena.query.DatasetAccessorFactory;
 import org.apache.jena.query.QuerySolution;
+import org.apache.jena.riot.Lang;
+import org.apache.jena.vocabulary.RDF;
 
 import edu.isi.kcap.wings.opmm.Constants;
 import edu.isi.kcap.wings.opmm.ModelUtils;
@@ -25,12 +28,12 @@ public class TriplesPublisher {
   public String queryEndpoint;
   public String graphURI = null;
   DatasetAccessor accessor;
-  public String serialization;
+  public Lang serialization;
   public String exportUrl;
 
   public TriplesPublisher(String endpointQueryURI, String endpointPostURI, String exportBaseUrl,
       String exportPrefix,
-      String serialization) {
+      Lang serialization) {
     this.updateEndpoint = endpointPostURI;
     this.queryEndpoint = endpointQueryURI;
     this.accessor = DatasetAccessorFactory.createHTTP(updateEndpoint);
@@ -53,9 +56,9 @@ private void uploadTriples(byte[] data, HttpPost request, CloseableHttpClient ht
       throws UnsupportedEncodingException, IOException, ClientProtocolException {
     ByteArrayEntity entity = new ByteArrayEntity(data);
     request.setEntity(entity);
-    if (serialization == "TTL")
+    if (serialization == Lang.TURTLE || serialization == Lang.TTL)
       request.setHeader("Content-Type", "text/turtle");
-    else if (serialization == "RDF/XML")
+    else if (serialization == Lang.RDFXML)
       request.setHeader("Content-Type", "application/rdf+xml");
     else
       throw new UnsupportedEncodingException("Serialization not supported");
@@ -114,7 +117,7 @@ public void setAccessor(DatasetAccessor accessor) {
     this.accessor = accessor;
   }
 
-  public void setSerialization(String serialization) {
+  public void setSerialization(Lang serialization) {
     this.serialization = serialization;
   }
 

src/main/java/edu/isi/kcap/wings/opmm/WorkflowExecutionExport.java

@@ -12,6 +12,7 @@
 import org.apache.jena.query.ResultSet;
 import org.apache.jena.rdf.model.Literal;
 import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.riot.Lang;
 
 import edu.isi.kcap.wings.opmm.Publisher.TriplesPublisher;
 
@@ -408,7 +409,7 @@ private String getExpandedTemplateURI() {
      * @param serialization serialization of choice: RDF/XML, TTL, etc.
      * @throws IOException
      */
-    public String exportAsOPMW(String filepath, String serialization) throws IOException, FileNotFoundException {
+    public String exportAsOPMW(String filepath, Lang serialization) throws IOException, FileNotFoundException {
         if (transformedExecutionURI == null) {
             this.transform();
         }

src/main/java/edu/isi/kcap/wings/opmm/WorkflowTemplateExport.java

@@ -14,6 +14,7 @@
 import org.apache.jena.query.ResultSet;
 import org.apache.jena.rdf.model.Literal;
 import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.riot.Lang;
 
 import edu.isi.kcap.wings.opmm.Publisher.TriplesPublisher;
 
@@ -454,7 +455,7 @@ private String convertTemplateToOPMW(Individual wingsTemplate, int versionNumber
      * @return
      * @throws IOException
      */
-    public String exportAsOPMW(String filepath, String serialization) throws IOException {
+    public String exportAsOPMW(String filepath, Lang serialization) throws IOException {
         if (transformedTemplate == null) {
             this.transform();
         }
@@ -495,7 +496,7 @@ public String exportAsPPlan(String outFileDirectory, String serialization) {
      * @return URI of the template
      * @throws IOException
      */
-    public String exportAll(String outFileDirectory, String serialization) throws IOException {
+    public String exportAll(String outFileDirectory, Lang serialization) throws IOException {
         // TO DO
         System.out.println("Not done yet!");
         // this.export_as_OPMW(outFilePath, serialization);

src/test/java/opmw_mapper/MapperTest.java

@@ -7,6 +7,7 @@
 import java.util.List;
 
 import org.apache.jena.ontology.OntModel;
+import org.apache.jena.riot.Lang;
 import org.apache.jena.sparql.function.library.e;
 import org.junit.Assert;
 import org.junit.Test;
@@ -38,8 +39,8 @@ public class MapperTest {
 
         @Test
         public void testMapperTurtle() throws IOException {
-                String serialization = "TTL";
-                File targetDirectory = new File(serialization);
+                Lang serialization = Lang.TTL;
+                File targetDirectory = new File(serialization.getName());
                 if (!targetDirectory.exists()) {
                         targetDirectory.mkdir();
                 }

src/test/java/opmw_mapper/TriplePublisherTest.java

@@ -6,6 +6,7 @@
 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.riot.Lang;
 import org.apache.jena.vocabulary.OWL;
 import org.apache.jena.vocabulary.RDF;
 import org.apache.jena.vocabulary.RDFS;
@@ -23,7 +24,8 @@ public class TriplePublisherTest {
   @Test
   public void publishTriplesTestTurtle() throws IOException {
     String resourceUri = "http://example.org/example#example";
-    TriplesPublisher tp = new TriplesPublisher(queryEndpoint, updateEndpoint, graph, "", "TTL");
+    Lang serialization = Lang.TTL;
+    TriplesPublisher tp = new TriplesPublisher(queryEndpoint, updateEndpoint, graph, "", Lang.TTL);
     tp.setGraphURI(graph);
     File file = createTripleFile(resourceUri, "TTL");
     tp.publish(file);
@@ -33,7 +35,8 @@ public void publishTriplesTestTurtle() throws IOException {
   @Test
   public void publishTriplesTestRDFXML() throws IOException {
     String resourceUri = "http://example.org/example";
-    TriplesPublisher tp = new TriplesPublisher(queryEndpoint, updateEndpoint, resourceUri, "test", "RDF/XML");
+    Lang serialization = Lang.RDFXML;
+    TriplesPublisher tp = new TriplesPublisher(queryEndpoint, updateEndpoint, resourceUri, "test", serialization);
     tp.setGraphURI(graph);
     File file = createTripleFile(resourceUri, "RDF/XML");
     tp.publish(file);