export to svg contains viewBox information

CHANGELOG

 minerva (12.2.0~beta.2) unstable; urgency=medium
+  * Bug fix: export to svg contains viewBox info (#716) 
   * Bug fix: import from sbml with layout could crash when two elements 
     occupied the exact same position (#717) 
   * Bug fix: overlays added via API couldn't be visualized after refresh (#718) 

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/SvgImageGenerator.java

 package lcsb.mapviewer.converter.graphics;
 
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.io.OutputStreamWriter;
 
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
 import org.apache.batik.dom.GenericDOMImplementation;
 import org.apache.batik.svggen.SVGGraphics2D;
 import org.apache.batik.svggen.SVGGraphics2DIOException;
 import org.w3c.dom.DOMImplementation;
 import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.common.exception.NotImplementedException;
 
 /**
  * This class implements SVG generator for the image object.This class uses
@@ -21,6 +24,11 @@ import org.w3c.dom.Document;
  * 
  */
 public class SvgImageGenerator extends AbstractImageGenerator {
+  
+  /**
+   * Root dom element. We need it to be able to provide viewBox.
+   */
+  private Element root;
 
 	@Override
 	protected void createImageObject(final double width, final double height) {
@@ -32,14 +40,17 @@ public class SvgImageGenerator extends AbstractImageGenerator {
 		String svgNS = "http://www.w3.org/2000/svg";
 		Document document = domImpl.createDocument(svgNS, "svg", null);
 
-		// Create an instance of the SVG Generator.
-		setGraphics(new SVGGraphics2D(document));
+        // Create an instance of the SVG Generator.
+		SVGGraphics2D graphics =new SVGGraphics2D(document);
+		root = graphics.getRoot();
+        root.setAttributeNS(null, "viewBox", "0 0 "+(int)width+" "+(int)height);
+		setGraphics(graphics);
 
 	}
 
 	@Override
-	public void saveToFileImplementation(final String fileName) throws SVGGraphics2DIOException {
-		((SVGGraphics2D) getGraphics()).stream(fileName);
+	public void saveToFileImplementation(final String fileName) throws IOException {
+	  saveToOutputStreamImplementation(new FileOutputStream(fileName));
 	}
 
 	/**
@@ -63,8 +74,9 @@ public class SvgImageGenerator extends AbstractImageGenerator {
 
 	@Override
 	public void saveToOutputStreamImplementation(OutputStream os) throws IOException {
-		((SVGGraphics2D) getGraphics()).stream(new OutputStreamWriter(os));
-
+	  //for some reason if you remove this line either viewbox is not define or content is not there
+	  ((SVGGraphics2D) getGraphics()).getRoot(root);
+	  ((SVGGraphics2D) getGraphics()).stream(root, new OutputStreamWriter(os));
 	}
 
 	@Override

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java

@@ -19,6 +19,7 @@ import lcsb.mapviewer.converter.graphics.placefinder.AllPlaceFinderTest;
 		MapGeneratorTest.class,
 		NormalImageGeneratorTest.class,
 		PdfImageGeneratorTest.class,
+		SvgImageGeneratorTest.class
 
 })
 public class AllGraphicsTests {

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/SvgImageGeneratorTest.java

+package lcsb.mapviewer.converter.graphics;
+
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayOutputStream;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+
+public class SvgImageGeneratorTest extends GraphicsTestFunctions {
+
+  @Before
+  public void setUp() throws Exception {
+  }
+
+  @After
+  public void tearDown() throws Exception {
+  }
+
+  @Test
+  public void testSaveToFile() throws Exception {
+    try {
+      Model model = createCompartmentModel();
+
+      SvgImageGenerator sig = new SvgImageGenerator(new AbstractImageGenerator.Params().model(model));
+
+      ByteArrayOutputStream output = new ByteArrayOutputStream();
+      sig.saveToOutputStream(output);
+
+      assertTrue(output.toString().contains("viewBox"));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  private Model createCompartmentModel() {
+    Model model = new ModelFullIndexed(null);
+    model.setWidth(526);
+    model.setHeight(346);
+    Complex alias = new Complex("1");
+    alias.setName("a");
+    alias.setX(300);
+    alias.setY(90);
+    alias.setWidth(100);
+    alias.setHeight(50);
+    model.addElement(alias);
+
+    return model;
+  }
+
+}