fixing SBGNML tests

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesigner2SbgnmlConversionTest.java

@@ -16,7 +16,7 @@ import org.junit.runners.Parameterized;
 import org.junit.runners.Parameterized.Parameters;
 
 import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
 import lcsb.mapviewer.model.map.model.Model;
 
@@ -53,8 +53,8 @@ public class CellDesigner2SbgnmlConversionTest {
 	}
 
 	private void parseAndExport(Path testPath) throws Exception {
-		IConverter cellDesignerConverter = new CellDesignerXmlParser();
-		IConverter sbgnmlConverter = new SbgnmlXmlConverter();
+		Converter cellDesignerConverter = new CellDesignerXmlParser();
+		Converter sbgnmlConverter = new SbgnmlXmlConverter();
 
 		String testName = "";
 		Path tempPath = testPath;
@@ -73,7 +73,7 @@ public class CellDesigner2SbgnmlConversionTest {
 		}
 
 		String outputFile = "testFiles/sbgnmlExporterTestFiles/fromCellDesigner/".concat(testName).concat(".sbgn");
-		sbgnmlConverter.exportModelToFile(model, outputFile);
+		sbgnmlConverter.model2File(model, outputFile);
 		new File(outputFile).delete();
 	}
 

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java

@@ -13,7 +13,7 @@ import org.junit.Before;
 import org.junit.Test;
 
 import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
@@ -36,13 +36,13 @@ public class CellDesignerToSbgnTest {
   @Test
   public void testSample() throws Exception {
     try {
-      IConverter converter = new CellDesignerXmlParser();
-      IConverter converter2 = new SbgnmlXmlConverter();
+      Converter converter = new CellDesignerXmlParser();
+      Converter converter2 = new SbgnmlXmlConverter();
 
       Model model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/sample.xml"));
 
       String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
-      converter2.exportModelToFile(model, output);
+      converter2.model2File(model, output);
 
       try (FileInputStream inputStream = new FileInputStream(output)) {
         String everything = IOUtils.toString(inputStream, "UTF-8");
@@ -61,13 +61,13 @@ public class CellDesignerToSbgnTest {
   @Test
   public void testSample2() throws Exception {
     try {
-      IConverter converter = new CellDesignerXmlParser();
-      IConverter converter2 = new SbgnmlXmlConverter();
+      Converter converter = new CellDesignerXmlParser();
+      Converter converter2 = new SbgnmlXmlConverter();
 
       Model model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/bubbles.xml"));
 
       String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
-      converter2.exportModelToFile(model, output);
+      converter2.model2File(model, output);
       new File(output).delete();
     } catch (Exception e) {
       e.printStackTrace();
@@ -78,13 +78,13 @@ public class CellDesignerToSbgnTest {
   @Test
   public void testCompartmentsExport() throws Exception {
     try {
-      IConverter converter = new CellDesignerXmlParser();
-      IConverter converter2 = new SbgnmlXmlConverter();
+      Converter converter = new CellDesignerXmlParser();
+      Converter converter2 = new SbgnmlXmlConverter();
 
       Model model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/neuron.xml"));
 
       String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
-      converter2.exportModelToFile(model, output);
+      converter2.model2File(model, output);
 
       converter2.createModel(new ConverterParams().filename(output));
 
@@ -111,13 +111,13 @@ public class CellDesignerToSbgnTest {
   @Test
   public void testProteinState() throws Exception {
     try {
-      IConverter converter = new CellDesignerXmlParser();
-      IConverter converter2 = new SbgnmlXmlConverter();
+      Converter converter = new CellDesignerXmlParser();
+      Converter converter2 = new SbgnmlXmlConverter();
 
       Model model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/state.xml"));
 
       String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
-      converter2.exportModelToFile(model, output);
+      converter2.model2File(model, output);
 
       Model model2 = converter2.createModel(new ConverterParams().filename(output));
 

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java

@@ -19,6 +19,8 @@ import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.persist.DbUtils;
 import lcsb.mapviewer.persist.dao.map.ModelDao;
 
+import java.io.File;
+
 @Transactional
 @ContextConfiguration(classes = SpringSBGNMLConverterTestConfig.class)
 @RunWith(SpringJUnit4ClassRunner.class)
@@ -33,8 +35,8 @@ public class DbSerializationTest {
   private void makeDbSerializationTest(String filePath) throws Exception {
     SbgnmlXmlParser parser = new SbgnmlXmlParser();
 
-    Model model = parser
-        .createModel(new ConverterParams().filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/".concat(filePath)));
+    String fileName = "testFiles/sbgnmlParserTestFiles/sbgnmlFiles/".concat(filePath);
+    Model model = parser.createModel(fileName, new File(fileName));
 
     modelDao.add(model);
     modelDao.flush();

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java

@@ -14,7 +14,7 @@ import org.junit.runners.Parameterized;
 import org.junit.runners.Parameterized.Parameters;
 
 import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.model.map.model.Model;
 
 @RunWith(Parameterized.class)
@@ -41,11 +41,11 @@ public class SbgnmlXmlExporterTest {
 	}
 
 	private void parseAndExport(String testName) throws Exception {
-		IConverter converter = new SbgnmlXmlConverter();
+		Converter converter = new SbgnmlXmlConverter();
 
 		Model model = converter.createModel(new ConverterParams().filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/".concat(testName).concat(".sbgn")));
 
-		converter.exportModelToFile(model, File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath());
+		converter.model2File(model, File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath());
 	}
 
 	/*

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest.java

@@ -22,7 +22,7 @@ import org.junit.runners.Parameterized;
 import org.junit.runners.Parameterized.Parameters;
 
 import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
 import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
 import lcsb.mapviewer.converter.graphics.PngImageGenerator;
@@ -58,7 +58,7 @@ public class SbgnmlXmlParserTest {
     try {
       String dir = Files.createTempDirectory("sbgn-temp-images-dir").toFile().getAbsolutePath();
 
-      IConverter converter = new SbgnmlXmlConverter();
+      Converter converter = new SbgnmlXmlConverter();
 
       Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
 
@@ -72,7 +72,7 @@ public class SbgnmlXmlParserTest {
       nig.saveToFile(pngFilePath);
 
       CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
-      String xmlString = cellDesignerXmlParser.toXml(model);
+      String xmlString = cellDesignerXmlParser.model2Xml(model);
 
       String cellDesignerFilePath = dir + "/"
           .concat(filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".sbgn")))

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java

@@ -11,7 +11,7 @@ import org.junit.Test;
 
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.species.Complex;
@@ -43,7 +43,7 @@ public class SbgnmlXmlParserTest2 {
   @Test
   public void createModelWithCompartmentsTest() throws Exception {
     try {
-        IConverter converter = new SbgnmlXmlConverter();
+        Converter converter = new SbgnmlXmlConverter();
 
         Model model = converter
             .createModel(new ConverterParams().filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/elements_inside_compartment.xml"));