test showing that translation from sbgn 0.2 does not use proper encod…

…ing on machines with encoding different than utf-8 (for instance typical Windows machine)

org.sbgn/test/org/sbgn/SbgnUtilTest.java

@@ -0,0 +1,52 @@
+package org.sbgn;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.File;
+import java.lang.reflect.Field;
+import java.lang.reflect.Modifier;
+import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
+
+import javax.xml.bind.JAXBException;
+
+import org.junit.Test;
+import org.sbgn.bindings.Sbgn;
+
+public class SbgnUtilTest {
+
+  @Test
+  public void testUtfEncodingWithDifferentSystemFileEncoding() throws JAXBException {
+    try {
+      // modify the encoding that was taken from file.encoding system property
+      // this is done at JVM startup therefore instead of changing system property we
+      // must modify the cached value to simulate running it on the machine with
+      // ISO-8859-1 encoding
+      Field field = null;
+      for (Field f : Charset.class.getDeclaredFields()) {
+        if (f.getName().equals("defaultCharset")) {
+          field = f;
+        }
+      }
+      field.setAccessible(true);
+      Field modifiersField = Field.class.getDeclaredField("modifiers");
+      modifiersField.setAccessible(true);
+      modifiersField.setInt(field, field.getModifiers() & ~Modifier.FINAL);
+
+      field.set(null, StandardCharsets.ISO_8859_1);
+
+      try {
+        Sbgn sbgn = SbgnUtil.readFromFile(new File("test-files/PD/utf8_sbgn.0.2.sbgn"));
+        assertEquals("β", sbgn.getMap().get(0).getGlyph().get(0).getLabel().getText());
+      } finally {
+        //restore default encoding to UTF-8
+        field.set(null, StandardCharsets.UTF_8);
+      }
+
+    } catch (Exception e) {
+      e.printStackTrace();
+    }
+
+  }
+
+}

test-files/PD/utf8_sbgn.0.2.sbgn

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+    <map language="process description">
+        <glyph class="simple chemical" id="glyph_n3">
+            <label text="β"/>
+            <bbox w="140.0" h="32.0" x="75.0" y="272.53503"/>
+        </glyph>
+    </map>
+</sbgn>