jsbml-svn Mailing List for JSBML (Page 2)

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Revision: 2488
          http://sourceforge.net/p/jsbml/code/2488
Author:   niko-rodrigue
Date:     2016-03-15 11:55:55 +0000 (Tue, 15 Mar 2016)
Log Message:
-----------
added some tests to check that the JSBML reader and writers work properly with UTF-8 characters

Modified Paths:
--------------
    trunk/build.xml
    trunk/modules/tidy/src/org/sbml/jsbml/TidySBMLWriter.java
    trunk/modules/tidy/tidy-build.properties
    trunk/test/org/sbml/jsbml/test/AllTests.java

Added Paths:
-----------
    trunk/test/org/sbml/jsbml/test/UTF8Tests.java

Modified: trunk/build.xml
===================================================================

--- trunk/build.xml	2016-03-09 14:35:44 UTC (rev 2487)
+++ trunk/build.xml	2016-03-15 11:55:55 UTC (rev 2488)
@@ -211,7 +211,7 @@
 	<target
 	  name="compile"
 	  description="Compiles the test directory"
-	  depends="prepare-src, package"
+	  depends="prepare-src, package, prepare-tidy"
 	>
 		<javac srcdir="${test.src.dir}"
            destdir="${build.dest}"
@@ -619,7 +619,33 @@
 
 	</target>
 
+	<!-- =================================================================== -->
+	<!-- Build a single jsbml module                                         -->
+	<!-- =================================================================== -->
+	<target
+	  name="prepare-tidy"
+	  depends="init"
+	  description="Build the tidy jsbml module"
+	>
 
+		<echo>Module jsbml-tidy</echo>
+
+		<ant dir="${tidy.module.base.dir}" inheritAll="false" inheritRefs="false">
+					<target name="clean" />
+					<target name="jar" />
+		</ant>
+
+		<copy todir="${build.src}">
+			<fileset dir="${tidy.module.base.dir}/build/src" />
+		</copy>
+		<copy todir="${build.dir}">
+			<fileset dir="${tidy.module.base.dir}/build/" includes="*.jar" />
+			<fileset dir="${tidy.module.base.dir}/lib/" includes="*.jar" />
+		</copy>
+
+	</target>
+
+
 	<!-- =================================================================== -->
 	<!-- Build the jsbml extensions/packages                                   -->
 	<!-- =================================================================== -->

Modified: trunk/modules/tidy/src/org/sbml/jsbml/TidySBMLWriter.java
===================================================================
--- trunk/modules/tidy/src/org/sbml/jsbml/TidySBMLWriter.java	2016-03-09 14:35:44 UTC (rev 2487)
+++ trunk/modules/tidy/src/org/sbml/jsbml/TidySBMLWriter.java	2016-03-15 11:55:55 UTC (rev 2488)
@@ -79,6 +79,7 @@
     tidy.setWraplen(200);
     tidy.setWrapAttVals(false);
     tidy.setWrapScriptlets(true);
+    tidy.setLiteralAttribs(true);
     tidy.setXmlOut(true);
     tidy.setXmlSpace(true);
     tidy.setXmlTags(true);

Modified: trunk/modules/tidy/tidy-build.properties
===================================================================
--- trunk/modules/tidy/tidy-build.properties	2016-03-09 14:35:44 UTC (rev 2487)
+++ trunk/modules/tidy/tidy-build.properties	2016-03-15 11:55:55 UTC (rev 2488)
@@ -1,6 +1,6 @@
 
 tidy.Name=Tidy SBMLWriter
 tidy.name=jsbml-tidy
-tidy.version=1.2
+tidy.version=1.2.1
 tidy.groupId=org.sbml.jsbml.modules
-tidy.artifactId=jsbml_modules_tidy
+tidy.artifactId=jsbml-tidy

Modified: trunk/test/org/sbml/jsbml/test/AllTests.java
===================================================================
--- trunk/test/org/sbml/jsbml/test/AllTests.java	2016-03-09 14:35:44 UTC (rev 2487)
+++ trunk/test/org/sbml/jsbml/test/AllTests.java	2016-03-15 11:55:55 UTC (rev 2488)
@@ -44,7 +44,7 @@
 @RunWith(value=Suite.class)
 @SuiteClasses(value={Tests.class, LibsbmlCompatibilityTests.class, LayoutJUnitTests.class, RenderJUnitTests.class,
   UnregisterPackageTests.class, ArraysJUnitTests.class, DisablePackageTests.class, TestL3Dyn.class,
-  PackageVersionTests.class, CompJUnitTests.class})
+  PackageVersionTests.class, CompJUnitTests.class, UTF8Tests.class})
 public class AllTests {
 
   /**

Added: trunk/test/org/sbml/jsbml/test/UTF8Tests.java
===================================================================
--- trunk/test/org/sbml/jsbml/test/UTF8Tests.java	                        (rev 0)
+++ trunk/test/org/sbml/jsbml/test/UTF8Tests.java	2016-03-15 11:55:55 UTC (rev 2488)
@@ -0,0 +1,268 @@
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2016 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ * 
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+
+package org.sbml.jsbml.test;
+
+import java.io.File;
+import java.io.IOException;
+
+import javax.xml.stream.XMLStreamException;
+
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.SBMLException;
+import org.sbml.jsbml.SBMLReader;
+import org.sbml.jsbml.SBMLWriter;
+import org.sbml.jsbml.TidySBMLWriter;
+
+
+public class UTF8Tests {
+
+  /**
+   * 
+   */
+  private SBMLDocument doc;
+  /**
+   * 
+   */
+  private Model m;
+  
+  private final static String chineseUTF8 = "份非常简";
+  
+  private final static String cyrilicUTF8 = "name utf-8: ¥¢®¶ÅÑëЉЍ ϓ Ϡ Ж Ѣ Ѩ  о҉"; //  𐍈 does not seems to be supported properly
+
+  private String utf8Model = "<?xml version='1.0' encoding='UTF-8' standalone='no'?>\n"
+      + "<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" level=\"3\" version=\"1\">\n"
+      + "  <model id=\"model\" name=\"" + cyrilicUTF8 + "\">\n"
+      + "<notes>\n<p xmlns=\"http://www.w3.org/1999/xhtml\">\n<pre>"
+      + "U+00A2  ¢ c2 a2 CENT SIGN\n"
+      + "U+00A3  £ c2 a3 POUND SIGN\n"
+      + "U+00A4  ¤ c2 a4 CURRENCY SIGN\n"
+      + "U+00A5  ¥ c2 a5 YEN SIGN\n"
+      + "U+00A6  ¦ c2 a6 BROKEN BAR\n"
+      + "U+00A7  § c2 a7 SECTION SIGN\n"
+      + "U+00A9  © c2 a9 COPYRIGHT SIGN\n"
+      + "U+00AA  ª c2 aa FEMININE ORDINAL INDICATOR\n"
+      + "U+00AB  « c2 ab LEFT-POINTING DOUBLE ANGLE QUOTATION MARK\n"
+      + "U+00AC  ¬ c2 ac NOT SIGN\n"
+      + "U+00AE  ® c2 ae REGISTERED SIGN\n"
+      + "U+00B0  ° c2 b0 DEGREE SIGN\n"
+      + "U+00B1  ± c2 b1 PLUS-MINUS SIGN\n"
+      + "U+00B2  ² c2 b2 SUPERSCRIPT TWO\n"
+      + "U+00B3  ³ c2 b3 SUPERSCRIPT THREE\n"
+      + "U+00B5  µ c2 b5 MICRO SIGN\n"
+      + "U+00B6  ¶ c2 b6 PILCROW SIGN\n"
+      + "U+00B9  ¹ c2 b9 SUPERSCRIPT ONE\n"
+      + "U+00BA  º c2 ba MASCULINE ORDINAL INDICATOR\n"
+      + "U+00BB  » c2 bb RIGHT-POINTING DOUBLE ANGLE QUOTATION MARK\n"
+      + "U+00BC  ¼ c2 bc VULGAR FRACTION ONE QUARTER\n"
+      + "U+00BD  ½ c2 bd VULGAR FRACTION ONE HALF\n"
+      + "U+00BE  ¾ c2 be VULGAR FRACTION THREE QUARTERS\n"
+      + "U+00BF  ¿ c2 bf INVERTED QUESTION MARK\n"
+      + "U+00C0  À c3 80 LATIN CAPITAL LETTER A WITH GRAVE\n"
+      + "U+00C1  Á c3 81 LATIN CAPITAL LETTER A WITH ACUTE\n"
+      + "U+00C2  Â c3 82 LATIN CAPITAL LETTER A WITH CIRCUMFLEX\n"
+      + "U+00C3  Ã c3 83 LATIN CAPITAL LETTER A WITH TILDE\n"
+      + "U+00C4  Ä c3 84 LATIN CAPITAL LETTER A WITH DIAERESIS\n"
+      + "U+00C5  Å c3 85 LATIN CAPITAL LETTER A WITH RING ABOVE\n"
+      + "U+00C6  Æ c3 86 LATIN CAPITAL LETTER AE\n"
+      + "U+00C7  Ç c3 87 LATIN CAPITAL LETTER C WITH CEDILLA\n"
+      + "U+00C8  È c3 88 LATIN CAPITAL LETTER E WITH GRAVE\n"
+      + "U+00C9  É c3 89 LATIN CAPITAL LETTER E WITH ACUTE\n"
+      + "U+00CA  Ê c3 8a LATIN CAPITAL LETTER E WITH CIRCUMFLEX\n"
+      + "U+00CB  Ë c3 8b LATIN CAPITAL LETTER E WITH DIAERESIS\n"
+      + "U+00CC  Ì c3 8c LATIN CAPITAL LETTER I WITH GRAVE\n"
+      + "U+00CD  Í c3 8d LATIN CAPITAL LETTER I WITH ACUTE\n"
+      + "U+00CE  Î c3 8e LATIN CAPITAL LETTER I WITH CIRCUMFLEX\n"
+      + "U+00CF  Ï c3 8f LATIN CAPITAL LETTER I WITH DIAERESIS\n"
+      + "U+00D0  Ð c3 90 LATIN CAPITAL LETTER ETH\n"
+      + "U+00D1  Ñ c3 91 LATIN CAPITAL LETTER N WITH TILDE\n"
+      + "U+00D2  Ò c3 92 LATIN CAPITAL LETTER O WITH GRAVE\n"
+      + "U+00D3  Ó c3 93 LATIN CAPITAL LETTER O WITH ACUTE\n"
+      + "U+00D4  Ô c3 94 LATIN CAPITAL LETTER O WITH CIRCUMFLEX\n"
+      + "U+00D5  Õ c3 95 LATIN CAPITAL LETTER O WITH TILDE\n"
+      + "U+00D6  Ö c3 96 LATIN CAPITAL LETTER O WITH DIAERESIS\n"
+      + "U+00D7  × c3 97 MULTIPLICATION SIGN\n"
+      + "U+00D8  Ø c3 98 LATIN CAPITAL LETTER O WITH STROKE\n"
+      + "U+00D9  Ù c3 99 LATIN CAPITAL LETTER U WITH GRAVE\n"
+      + "U+00DA  Ú c3 9a LATIN CAPITAL LETTER U WITH ACUTE\n"
+      + "U+00DB  Û c3 9b LATIN CAPITAL LETTER U WITH CIRCUMFLEX\n"
+      + "U+00DC  Ü c3 9c LATIN CAPITAL LETTER U WITH DIAERESIS\n"
+      + "U+00DD  Ý c3 9d LATIN CAPITAL LETTER Y WITH ACUTE\n"
+      + "U+00DE  Þ c3 9e LATIN CAPITAL LETTER THORN\n"
+      + "U+00DF  ß c3 9f LATIN SMALL LETTER SHARP S\n"
+      + "U+00E0  à c3 a0 LATIN SMALL LETTER A WITH GRAVE\n"
+      + "U+00E1  á c3 a1 LATIN SMALL LETTER A WITH ACUTE\n"
+      + "U+00E2  â c3 a2 LATIN SMALL LETTER A WITH CIRCUMFLEX\n"
+      + "U+00E3  ã c3 a3 LATIN SMALL LETTER A WITH TILDE\n"
+      + "U+00E4  ä c3 a4 LATIN SMALL LETTER A WITH DIAERESIS\n"
+      + "U+00E5  å c3 a5 LATIN SMALL LETTER A WITH RING ABOVE\n"
+      + "U+00E6  æ c3 a6 LATIN SMALL LETTER AE\n"
+      + "U+00E7  ç c3 a7 LATIN SMALL LETTER C WITH CEDILLA\n"
+      + "U+00E8  è c3 a8 LATIN SMALL LETTER E WITH GRAVE\n"
+      + "U+00E9  é c3 a9 LATIN SMALL LETTER E WITH ACUTE\n"
+      + "U+00EA  ê c3 aa LATIN SMALL LETTER E WITH CIRCUMFLEX\n"
+      + "U+00EB  ë c3 ab LATIN SMALL LETTER E WITH DIAERESIS\n"
+      + "U+00EC  ì c3 ac LATIN SMALL LETTER I WITH GRAVE\n"
+      + "U+00ED  í c3 ad LATIN SMALL LETTER I WITH ACUTE\n"
+      + "U+00EE  î c3 ae LATIN SMALL LETTER I WITH CIRCUMFLEX\n"
+      + "U+00EF  ï c3 af LATIN SMALL LETTER I WITH DIAERESIS\n"
+      + "U+00F0  ð c3 b0 LATIN SMALL LETTER ETH\n"
+      + "U+00F1  ñ c3 b1 LATIN SMALL LETTER N WITH TILDE\n"
+      + "U+00F2  ò c3 b2 LATIN SMALL LETTER O WITH GRAVE\n"
+      + "U+00F3  ó c3 b3 LATIN SMALL LETTER O WITH ACUTE\n"
+      + "U+00F4  ô c3 b4 LATIN SMALL LETTER O WITH CIRCUMFLEX\n"
+      + "U+00F5  õ c3 b5 LATIN SMALL LETTER O WITH TILDE\n"
+      + "U+00F6  ö c3 b6 LATIN SMALL LETTER O WITH DIAERESIS\n"
+      + "U+00F7  ÷ c3 b7 DIVISION SIGN\n"
+      + "U+00F8  ø c3 b8 LATIN SMALL LETTER O WITH STROKE\n"
+      + "U+00F9  ù c3 b9 LATIN SMALL LETTER U WITH GRAVE\n"
+      + "U+00FA  ú c3 ba LATIN SMALL LETTER U WITH ACUTE\n"
+      + "U+00FB  û c3 bb LATIN SMALL LETTER U WITH CIRCUMFLEX\n"
+      + "U+00FC  ü c3 bc LATIN SMALL LETTER U WITH DIAERESIS\n"
+      + "U+00FD  ý c3 bd LATIN SMALL LETTER Y WITH ACUTE\n"
+      + "U+00FE  þ c3 be LATIN SMALL LETTER THORN\n"
+      + "U+00FF  ÿ c3 bf LATIN SMALL LETTER Y WITH DIAERESIS\n"
+      + "这是一份非常简单的说明书…"
+      + "</pre></p></notes>\n"
+      + "</model>"
+      + "</sbml>";
+
+  /**
+   * 
+   */
+  @BeforeClass public static void initialSetUp() {}
+
+
+  /**
+   * 
+   */
+  @Before public void setUp() {
+    doc = new SBMLDocument(3, 1);
+
+    m = doc.createModel("test");
+    m.setName(cyrilicUTF8);
+    try {
+      m.appendNotes("<p xmlns=\"http://www.w3.org/1999/xhtml\">" + chineseUTF8 + " ÆÈÖßæ</p>");
+    } catch (XMLStreamException e) {
+      e.printStackTrace();
+      Assert.fail();
+    }
+    
+    m.createCompartment("cell");
+    m.createSpecies("S1");
+    m.createSpecies("S2");
+
+
+  }
+
+
+  /**
+   * Checks that the reading/writing from a String keep properly the UTF-8 characters.
+   */
+  @Test public void testModelString() {
+    try {
+      SBMLDocument d = new SBMLReader().readSBMLFromString(utf8Model);
+
+      String docStr = new SBMLWriter().writeSBMLToString(d);
+      
+      Assert.assertTrue(cyrilicUTF8.equals(d.getModel().getName()));      
+      Assert.assertTrue(docStr.contains(chineseUTF8));
+      Assert.assertTrue(docStr.contains(cyrilicUTF8));
+      Assert.assertTrue(docStr.contains("æ"));
+      Assert.assertTrue(docStr.contains("Ø"));
+      Assert.assertTrue(docStr.contains("÷"));
+      Assert.assertTrue(docStr.contains("©"));
+      
+      d = new SBMLReader().readSBMLFromString(utf8Model);
+      String tidyDocStr = new TidySBMLWriter().writeSBMLToString(d);
+
+      Assert.assertTrue(cyrilicUTF8.equals(d.getModel().getName()));      
+      Assert.assertTrue(tidyDocStr.contains(chineseUTF8));
+      Assert.assertTrue(tidyDocStr.contains(cyrilicUTF8));
+      Assert.assertTrue(tidyDocStr.contains("æ"));
+      Assert.assertTrue(tidyDocStr.contains("Ø"));
+      Assert.assertTrue(tidyDocStr.contains("÷"));
+      Assert.assertTrue(tidyDocStr.contains("©"));
+
+      d = new SBMLReader().readSBMLFromString(tidyDocStr);
+      tidyDocStr = new TidySBMLWriter().writeSBMLToString(d);
+      
+      Assert.assertTrue(cyrilicUTF8.equals(d.getModel().getName()));      
+      Assert.assertTrue(tidyDocStr.contains(chineseUTF8));
+      Assert.assertTrue(tidyDocStr.contains(cyrilicUTF8));
+      Assert.assertTrue(tidyDocStr.contains("æ"));
+      Assert.assertTrue(tidyDocStr.contains("Ø"));
+      Assert.assertTrue(tidyDocStr.contains("÷"));
+      Assert.assertTrue(tidyDocStr.contains("©"));
+      
+    } catch (XMLStreamException e) {
+      e.printStackTrace();
+      Assert.fail();
+    }
+  }
+  
+  /**
+   * Checks that the writing to a file keep properly the UTF-8 characters.
+   */
+  @Test public void testModelFile() {
+
+    try {
+      File tmpFile = File.createTempFile("utf8Tests-", ".xml");
+      File tmpFile2 = File.createTempFile("utf8Tests-", ".xml");
+      
+      new SBMLWriter().writeSBML(doc, tmpFile);
+
+      SBMLDocument d = new SBMLReader().readSBML(tmpFile);
+      
+      String docStr = new SBMLWriter().writeSBMLToString(d);
+
+      Assert.assertTrue(docStr.contains(chineseUTF8));
+      Assert.assertTrue(docStr.contains(cyrilicUTF8));
+      Assert.assertTrue(docStr.contains("ÆÈÖßæ"));
+
+      new TidySBMLWriter().writeSBMLToFile(d, tmpFile2.getAbsolutePath());
+      d = new SBMLReader().readSBML(tmpFile2);
+      String tidyDocStr = new SBMLWriter().writeSBMLToString(d);
+      
+      Assert.assertTrue(cyrilicUTF8.equals(d.getModel().getName()));      
+      Assert.assertTrue(tidyDocStr.contains(chineseUTF8));
+      Assert.assertTrue(tidyDocStr.contains(cyrilicUTF8));
+      Assert.assertTrue(tidyDocStr.contains("ÆÈÖßæ"));
+      
+    } catch (IOException e) {
+      e.printStackTrace();
+      Assert.fail();
+    } catch (SBMLException e) {
+      e.printStackTrace();
+      Assert.fail();
+    } catch (XMLStreamException e) {
+      e.printStackTrace();
+      Assert.fail();
+    }
+    
+  }
+}


Property changes on: trunk/test/org/sbml/jsbml/test/UTF8Tests.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added: svn:keywords
## -0,0 +1 ##
+Author Date Id Rev URL
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
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jsbml-svn Mailing List for JSBML (Page 2)

The Java library for working with the SBML format.

jsbml-svn — SVN commit notification list for the JSBML project.