sbml-svn Mailing List for Systems Biology Markup Language (SBML)

Revision: 12725
          http://sbml.svn.sourceforge.net/sbml/?rev=12725&view=rev
Author:   luciansmith
Date:     2011-01-31 21:19:08 +0000 (Mon, 31 Jan 2011)

Log Message:
-----------
After some tests, I decided that '2' was too large--it would fail in ~7% of the time.  With .2, it only fails <0.00001% of the time.

Modified Paths:
--------------
    trunk/test-suite/cases/semantic/00962/00962-antimony.txt
    trunk/test-suite/cases/semantic/00962/00962-sbml-l3v1.xml

Modified: trunk/test-suite/cases/semantic/00962/00962-antimony.txt
===================================================================
--- trunk/test-suite/cases/semantic/00962/00962-antimony.txt	2011-01-30 12:39:01 UTC (rev 12724)
+++ trunk/test-suite/cases/semantic/00962/00962-antimony.txt	2011-01-31 21:19:08 UTC (rev 12725)
@@ -8,7 +8,7 @@
   Qinc: at time - reset >= 0.01: Q = Q + 0.01, reset = time;
   Rinc: at time - reset >= 0.01: R = R + 0.01, reset = time;
   maxcheck: at(abs(Q-R)>maxdiff): maxdiff = abs(Q-R);
-  error_check: at (time>=99) && (maxdiff < 2) : error = 1;
+  error_check: at (time>=99) && (maxdiff < .2) : error = 1;
 
   // Variable initializations:
   reset = 0;

Modified: trunk/test-suite/cases/semantic/00962/00962-sbml-l3v1.xml
===================================================================
--- trunk/test-suite/cases/semantic/00962/00962-sbml-l3v1.xml	2011-01-30 12:39:01 UTC (rev 12724)
+++ trunk/test-suite/cases/semantic/00962/00962-sbml-l3v1.xml	2011-01-31 21:19:08 UTC (rev 12725)
@@ -158,7 +158,7 @@
               <apply>
                 <lt/>
                 <ci> maxdiff </ci>
-                <cn type="integer"> 2 </cn>
+                <cn> .2 </cn>
               </apply>
             </apply>
           </math>


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Revision: 12724
          http://sbml.svn.sourceforge.net/sbml/?rev=12724&view=rev
Author:   sarahkeating
Date:     2011-01-30 12:39:01 +0000 (Sun, 30 Jan 2011)

Log Message:
-----------
applied same fix for linux

Modified Paths:
--------------
    trunk/libsbml/src/bindings/matlab/install.m

Modified: trunk/libsbml/src/bindings/matlab/install.m
===================================================================
--- trunk/libsbml/src/bindings/matlab/install.m	2011-01-30 12:32:20 UTC (rev 12723)
+++ trunk/libsbml/src/bindings/matlab/install.m	2011-01-30 12:39:01 UTC (rev 12724)
@@ -297,7 +297,7 @@
           error('libsbml.so could not be found');
       else
         lib{1} = lib{2};
-        addDir(lib{1});
+        bin_dir = new_bin_dir;
       end;
   end;
   


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Revision: 12723
          http://sbml.svn.sourceforge.net/sbml/?rev=12723&view=rev
Author:   sarahkeating
Date:     2011-01-30 12:32:20 +0000 (Sun, 30 Jan 2011)

Log Message:
-----------
Second try for installing

Modified Paths:
--------------
    trunk/libsbml/src/bindings/matlab/install.m

Modified: trunk/libsbml/src/bindings/matlab/install.m
===================================================================
--- trunk/libsbml/src/bindings/matlab/install.m	2011-01-29 13:25:26 UTC (rev 12722)
+++ trunk/libsbml/src/bindings/matlab/install.m	2011-01-30 12:32:20 UTC (rev 12723)
@@ -111,7 +111,8 @@
       disp('checking for TranslateSBML');
       M = TranslateSBML('test.xml');
     catch
-      disp('Installation failed - need to build TranslateSBML');
+      disp(sprintf('Installation failed - MATLAB cannot find all the libraries\n%s', ...
+          'Add the path to the libraries to your matlab path'));
       success = 0;
     end;
 
@@ -121,7 +122,8 @@
         disp('checking OutputSBML');
         OutputSBML(M, outFile);
       catch
-        disp('Installation failed - need to build OutputSBML');
+      disp(sprintf('Installation failed - MATLAB cannot find all the libraries\n%s', ...
+          'Add the path to the libraries to your matlab path'));
         success = 0;
       end;
     end;
@@ -189,7 +191,7 @@
           error('libsbml.dylib could not be found');
       else
         lib{1} = lib{2};
-        addDir(lib{1});
+        bin_dir = new_bin_dir;
       end;
   end;
   
@@ -216,7 +218,8 @@
       disp('checking for TranslateSBML');
       M = TranslateSBML('test.xml');
     catch
-      disp('Installation failed - need to build TranslateSBML');
+      disp(sprintf('Installation failed - MATLAB cannot find all the libraries\n%s', ...
+          'Add the path to the libraries to your matlab path'));
       success = 0;
     end;
 
@@ -226,7 +229,8 @@
         disp('checking OutputSBML');
         OutputSBML(M, outFile);
       catch
-        disp('Installation failed - need to build OutputSBML');
+      disp(sprintf('Installation failed - MATLAB cannot find all the libraries\n%s', ...
+          'Add the path to the libraries to your matlab path'));
         success = 0;
       end;
     end;
@@ -319,7 +323,8 @@
       disp('checking for TranslateSBML');
       M = TranslateSBML('test.xml');
     catch
-      disp('Installation failed - need to build TranslateSBML');
+      disp(sprintf('Installation failed - MATLAB cannot find all the libraries\n%s', ...
+          'Add the path to the libraries to your matlab path'));
       success = 0;
     end;
 
@@ -329,7 +334,8 @@
         disp('checking OutputSBML');
         OutputSBML(M, outFile);
       catch
-        disp('Installation failed - need to build OutputSBML');
+      disp(sprintf('Installation failed - MATLAB cannot find all the libraries\n%s', ...
+          'Add the path to the libraries to your matlab path'));
         success = 0;
       end;
     end;


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Revision: 12722
          http://sbml.svn.sourceforge.net/sbml/?rev=12722&view=rev
Author:   sarahkeating
Date:     2011-01-29 13:25:26 +0000 (Sat, 29 Jan 2011)

Log Message:
-----------
if libsbml not installed in usr/local probably need to add the path to matlab

Modified Paths:
--------------
    trunk/libsbml/src/bindings/matlab/install.m

Modified: trunk/libsbml/src/bindings/matlab/install.m
===================================================================
--- trunk/libsbml/src/bindings/matlab/install.m	2011-01-29 13:18:00 UTC (rev 12721)
+++ trunk/libsbml/src/bindings/matlab/install.m	2011-01-29 13:25:26 UTC (rev 12722)
@@ -189,6 +189,7 @@
           error('libsbml.dylib could not be found');
       else
         lib{1} = lib{2};
+        addDir(lib{1});
       end;
   end;
   
@@ -292,6 +293,7 @@
           error('libsbml.so could not be found');
       else
         lib{1} = lib{2};
+        addDir(lib{1});
       end;
   end;
   


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Revision: 12721
          http://sbml.svn.sourceforge.net/sbml/?rev=12721&view=rev
Author:   sarahkeating
Date:     2011-01-29 13:18:00 +0000 (Sat, 29 Jan 2011)

Log Message:
-----------
updated for linux

Modified Paths:
--------------
    trunk/libsbml/src/bindings/matlab/install.m

Modified: trunk/libsbml/src/bindings/matlab/install.m
===================================================================
--- trunk/libsbml/src/bindings/matlab/install.m	2011-01-29 13:04:15 UTC (rev 12720)
+++ trunk/libsbml/src/bindings/matlab/install.m	2011-01-29 13:18:00 UTC (rev 12721)
@@ -295,44 +295,76 @@
       end;
   end;
   
-  % check that the include directory exists
-  include_dir = [root, filesep, 'include'];
-  disp(sprintf('Checking for the %s directory ...', include_dir));
-  if (exist(include_dir, 'dir') ~= 7)
-    error (sprintf('%s not found\n%s', include_dir, ...
-      'the libSBML source tree expects this directory to exist'));
-  end;
-  
+  addDir(pwd);
+ 
   if (ismatlab)
+    this_dir = pwd;
     % install the files
-    inc_flag = ['-I', include_dir];
-    installMexFiles(inc_flag, lib{1});
+    try
+      M = TranslateSBML('test.xml');
+    catch
+      cd(bin_dir);
+      try
+        M = TranslateSBML('test.xml');
+        cd(this_dir);
+      catch
+        cd(this_dir);
+      end;
+    end;
+    
+    success = 1;
+    try
+      disp('checking for TranslateSBML');
+      M = TranslateSBML('test.xml');
+    catch
+      disp('Installation failed - need to build TranslateSBML');
+      success = 0;
+    end;
 
-  else
-    disp('install on octave');
-  end;
+    outFile = [tempdir, filesep, 'test-out.xml'];
+    if (success == 1)
+      try
+        disp('checking OutputSBML');
+        OutputSBML(M, outFile);
+      catch
+        disp('Installation failed - need to build OutputSBML');
+        success = 0;
+      end;
+    end;
+    
+    if (success == 1)
+      disp ('running tests for TranslateSBML');
+      cd test;
+      pass = testBinding(1);
+      cd ..;
+      if (pass == 0)
+        disp('TranslateSBML successful');
+      else
+        disp('Binding present but problem detected. Seek help.');
+        success = 0;
+      end;
+    end;
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% runs the mex command for windows and matlab
-% the messy file handle stuff is because this seems to be the best way to 
-% be able to pass arguments to the function
-function installMexFiles(include, library)
+    if (success == 1)
+      disp('running tests for OutputSBML');
+      cd test;
+      pass = testOutput(tempdir);
+      cd ..;
+      if (pass == 0)
+        disp('OutputSBML successful');
+      else
+        disp('Output function present but problem detected. Seek help.');
+        success = 0;
+      end;
+    end;
 
-  fhandle = @mex;
-  disp('Building TranslateSBML ...');
-  feval(fhandle, 'TranslateSBML.c', include, library);
-  disp('Building OutputSBML ...');
-  feval(fhandle, 'OutputSBML.c', include, library);
+    if (success == 1)
+      disp ('Installation completed');
+    end;
+   
 
-  transFile = strcat('TranslateSBML.', mexext());
-  outFile = strcat('OutputSBML.', mexext());
-
-  if ((exist(transFile) == 3 && ...
-      exist(outFile) == 3))      
-    disp(sprintf('%s\n%s', 'Build successful', ...
-      'Now run the install script which will install and test the files'));
   else
-    disp('Build failed');
+    disp('install on octave');
   end;
   
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


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Revision: 12720
          http://sbml.svn.sourceforge.net/sbml/?rev=12720&view=rev
Author:   sarahkeating
Date:     2011-01-29 13:04:15 +0000 (Sat, 29 Jan 2011)

Log Message:
-----------
added code that runs on MacOS

Modified Paths:
--------------
    trunk/libsbml/src/bindings/matlab/install.m

Modified: trunk/libsbml/src/bindings/matlab/install.m
===================================================================
--- trunk/libsbml/src/bindings/matlab/install.m	2011-01-29 11:44:25 UTC (rev 12719)
+++ trunk/libsbml/src/bindings/matlab/install.m	2011-01-29 13:04:15 UTC (rev 12720)
@@ -1,7 +1,11 @@
 function install
 
+
   [detected_os, matlab, root] = determine_system();
 
+  % check to see whether the executable exist
+  checkForExecutables();
+
   switch detected_os
     case 0
       install_win(matlab, root);
@@ -188,19 +192,75 @@
       end;
   end;
   
-  % check that the include directory exists
-  include_dir = [root, filesep, 'include'];
-  disp(sprintf('Checking for the %s directory ...', include_dir));
-  if (exist(include_dir, 'dir') ~= 7)
-    error (sprintf('%s not found\n%s', include_dir, ...
-      'the libSBML source tree expects this directory to exist'));
-  end;
+  addDir(pwd);
+
   
   if (ismatlab)
+    this_dir = pwd;
     % install the files
-    inc_flag = ['-I', include_dir];
-    installMexFiles(inc_flag, lib{1});
+    try
+      M = TranslateSBML('test.xml');
+    catch
+      cd(bin_dir);
+      try
+        M = TranslateSBML('test.xml');
+        cd(this_dir);
+      catch
+        cd(this_dir);
+      end;
+    end;
+    
+    success = 1;
+    try
+      disp('checking for TranslateSBML');
+      M = TranslateSBML('test.xml');
+    catch
+      disp('Installation failed - need to build TranslateSBML');
+      success = 0;
+    end;
 
+    outFile = [tempdir, filesep, 'test-out.xml'];
+    if (success == 1)
+      try
+        disp('checking OutputSBML');
+        OutputSBML(M, outFile);
+      catch
+        disp('Installation failed - need to build OutputSBML');
+        success = 0;
+      end;
+    end;
+    
+    if (success == 1)
+      disp ('running tests for TranslateSBML');
+      cd test;
+      pass = testBinding(1);
+      cd ..;
+      if (pass == 0)
+        disp('TranslateSBML successful');
+      else
+        disp('Binding present but problem detected. Seek help.');
+        success = 0;
+      end;
+    end;
+
+    if (success == 1)
+      disp('running tests for OutputSBML');
+      cd test;
+      pass = testOutput(tempdir);
+      cd ..;
+      if (pass == 0)
+        disp('OutputSBML successful');
+      else
+        disp('Output function present but problem detected. Seek help.');
+        success = 0;
+      end;
+    end;
+
+    if (success == 1)
+      disp ('Installation completed');
+    end;
+   
+
   else
     disp('install on octave');
   end;
@@ -274,7 +334,9 @@
   else
     disp('Build failed');
   end;
-
+  
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% add directory to the matlab path
 function addDir(name)
 
   disp(sprintf('adding %s to the path', name));
@@ -282,4 +344,23 @@
   if (savepath ~= 0)
     error(sprintf('adding %s failed', name));
   end;
-  
\ No newline at end of file
+
+  
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% check for executables and that they are right ones
+function checkForExecutables()  
+  transFile = strcat('TranslateSBML.', mexext());
+  outFile = strcat('OutputSBML.', mexext());
+
+  if (~(exist(transFile) == 3 && ...
+      exist(outFile) == 3))     
+    error(sprintf('%s\n%s', 'Executables not found', ...
+      'Run the buid script to build the relevant files'));
+  else
+      % they exist are the the right ones
+      if (~((strcmp(which(transFile), [pwd, filesep, transFile])) && ...
+            (strcmp(which(outFile), [pwd, filesep, outFile]))))     
+          error(sprintf('%s\n%s', 'Other executables from other installations found', ...
+            'Run the buid script to build the relevant files for this installation'));
+      end;
+  end;


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Revision: 12719
          http://sbml.svn.sourceforge.net/sbml/?rev=12719&view=rev
Author:   sarahkeating
Date:     2011-01-29 11:44:25 +0000 (Sat, 29 Jan 2011)

Log Message:
-----------
minor tweaks for new build/install process

Modified Paths:
--------------
    trunk/libsbml/src/bindings/matlab/OutputSBML.c
    trunk/libsbml/src/bindings/matlab/test/testBinding.m
    trunk/libsbml/src/bindings/matlab/test/testOutput.m

Added Paths:
-----------
    trunk/libsbml/src/bindings/matlab/build.m
    trunk/libsbml/src/bindings/matlab/install.m

Modified: trunk/libsbml/src/bindings/matlab/OutputSBML.c
===================================================================
--- trunk/libsbml/src/bindings/matlab/OutputSBML.c	2011-01-29 00:18:57 UTC (rev 12718)
+++ trunk/libsbml/src/bindings/matlab/OutputSBML.c	2011-01-29 11:44:25 UTC (rev 12719)
@@ -540,12 +540,15 @@
 
   /* write the SBML document to the filename specified */
 	nStatus = writeSBML(sbmlDocument, pacFilename);
-	mexPrintf("Document written\n");
 
 	if (nStatus != 1)
 	{
 		mexErrMsgTxt("Failed to write file");
 	}
+  else
+  {
+    mexPrintf("Document written\n");
+  }
 	
 	/* free any memory allocated */
 	mxFree(pacNotes);

Added: trunk/libsbml/src/bindings/matlab/build.m
===================================================================
--- trunk/libsbml/src/bindings/matlab/build.m	                        (rev 0)
+++ trunk/libsbml/src/bindings/matlab/build.m	2011-01-29 11:44:25 UTC (rev 12719)
@@ -0,0 +1,252 @@
+function build
+
+  [detected_os, matlab, root] = determine_system();
+
+  switch detected_os
+    case 0
+      build_win(matlab, root);
+    case 1
+      build_mac(matlab, root);
+    case 2
+      build_linux(matlab, root);
+    otherwise
+      error('OS not recognised');
+  end;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% check what we are using
+function [detected_os, matlab, root] = determine_system
+
+  disp('Checking system ...');
+  disp('Looking at software ...');
+  % matlab = [0, 1]
+  %     0 - octave
+  %     1 - matlab
+  if (strcmp(isoctave(), '0'))
+    matlab = 1;
+    disp('MATLAB detected');
+  else
+    matlab = 0;
+    disp('Octave detected');
+  end;
+
+  disp('Looking at OS ...');
+  % detected_os = [0, 1, 2]
+  %      0 - windows
+  %      1 - mac
+  %      2 - unix
+  if (ispc())
+    detected_os = 0;
+    disp('Windows OS detected');
+  elseif(ismac())
+    detected_os = 1;
+    disp('Mac OS detected');
+  elseif(isunix())
+    detected_os = 2;
+    disp('Linux OS detected');
+  else
+    error('Unable to establish operating system');
+  end;
+
+  disp('Checking directory structure ...');
+  % need to check which directory we are in
+  % if we are in the src directory we should 
+  % be in directory ../src/bindings/matlab
+  [remain, first] = fileparts(pwd);
+  [remain1, second] = fileparts(remain);
+  [remain2, third] = fileparts(remain1);
+
+  if (~strcmp(first, 'matlab'))
+    report_incorrect_dir(pwd, '/src/bindings/matlab');
+  elseif (~strcmp(second, 'bindings'))
+    report_incorrect_dir(pwd, '/src/bindings/matlab');
+  elseif (~strcmp(third, 'src'))
+    report_incorrect_dir(pwd, '/src/bindings/matlab');
+  else
+    root = remain2;
+    disp('Expected directory structure found');
+  end;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% tell user we are in the wrong location
+function report_incorrect_dir(this_dir, expected)
+
+  message = sprintf('You are in directory %s \nbut should be in %s', this_dir, expected);
+  error(message);
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% build on windows
+function build_win(ismatlab, root)
+
+  % check that the win/bin directory exists
+  bin_dir = [root, filesep, 'win', filesep, 'bin'];
+  disp(sprintf('Checking for the %s directory ...', bin_dir));
+  if (exist(bin_dir, 'dir') ~= 7)
+    error (sprintf('%s not found\n%s', bin_dir, ...
+      'the libSBML source tree expects this directory to exist'));
+  else
+    disp('Checking for libraries ...');
+    % check that the library files are all there
+    lib{1} = [bin_dir, filesep, 'libsbml.lib'];
+    lib{2} = [bin_dir, filesep, 'libsbml.dll'];
+    lib{3} = [bin_dir, filesep, 'libxml2.lib'];
+    lib{4} = [bin_dir, filesep, 'libxml2.dll'];
+    lib{5} = [bin_dir, filesep, 'iconv.lib'];
+    lib{6} = [bin_dir, filesep, 'iconv.dll'];
+    lib{7} = [bin_dir, filesep, 'bzip2.lib'];
+    lib{8} = [bin_dir, filesep, 'bzip2.dll'];
+
+    found = 1;
+    for i = 1:8
+      if (exist(lib{i}) ~= 0)
+        disp(sprintf('%s found', lib{i}));
+      else
+        disp(sprintf('%s not found', lib{i}));
+        found = 0;
+      end;
+    end; 
+    
+    if (found == 0)
+      error (sprintf('Not all dependencies could be found\n%s%s', ...
+      'the libSBML source tree expects the dependencies to be in ', bin_dir));
+    else
+      disp('All dependencies found');
+    end;
+  end;
+  
+  % check that the include directory exists
+  include_dir = [root, filesep, 'include'];
+  disp(sprintf('Checking for the %s directory ...', include_dir));
+  if (exist(include_dir, 'dir') ~= 7)
+    error (sprintf('%s not found\n%s', include_dir, ...
+      'the libSBML source tree expects this directory to exist'));
+  end;
+  
+  if (ismatlab)
+    % build the files
+    inc_flag = ['-I', include_dir];
+    buildMexFiles(inc_flag, lib{1});
+
+  else
+    % TO DO
+    disp('Build on octave');
+  end;
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% build on mac
+function build_mac(ismatlab, root)
+
+  % check that libsbml is in usr/local/lib directory
+  bin_dir = [];
+
+  for i=1:length(strfind(pwd, filesep))
+      bin_dir = [bin_dir, '..', filesep];
+  end;
+  bin_dir = [bin_dir, 'usr', filesep, 'local', filesep, 'lib'];
+  disp('Checking for libraries ...');
+  % check that the library files are all there
+  lib{1} = [bin_dir, filesep, 'libsbml.dylib'];
+  if (exist(lib{1}) == 0)
+      disp('libsbml.dylib could not be found');
+      new_bin_dir = input(sprintf('\n\n%s\n%s\n%s\n%s', ...
+          'The build process assumes that libsbml', ...
+          'has been installed at usr/local', ...
+          'if libsbml.dylib is in another directory please enter the ', ...
+          'full path to reach the directory from this directory: '), 's');
+      lib{2} = [new_bin_dir, filesep, 'libsbml.dylib'];
+      
+      if (exist(lib{2}) == 0)
+          error('libsbml.dylib could not be found');
+      else
+        lib{1} = lib{2};
+      end;
+  end;
+  
+  % check that the include directory exists
+  include_dir = [root, filesep, 'include'];
+  disp(sprintf('Checking for the %s directory ...', include_dir));
+  if (exist(include_dir, 'dir') ~= 7)
+    error (sprintf('%s not found\n%s', include_dir, ...
+      'the libSBML source tree expects this directory to exist'));
+  end;
+  
+  if (ismatlab)
+    % build the files
+    inc_flag = ['-I', include_dir];
+    buildMexFiles(inc_flag, lib{1});
+
+  else
+    disp('Build on octave');
+  end;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% build on linux
+function build_linux(ismatlab, root)
+
+  % check that libsbml is in usr/local/lib directory
+  bin_dir = [];
+
+  for i=1:length(strfind(pwd, filesep))
+      bin_dir = [bin_dir, '..', filesep];
+  end;
+  bin_dir = [bin_dir, 'usr', filesep, 'local', filesep, 'lib'];
+  disp('Checking for libraries ...');
+  % check that the library files are all there
+  lib{1} = [bin_dir, filesep, 'libsbml.so'];
+  if (exist(lib{1}) == 0)
+      disp('libsbml.so could not be found');
+      new_bin_dir = input(sprintf('\n\n%s\n%s\n%s\n%s', ...
+          'The build process assumes that libsbml', ...
+          'has been installed at usr/local', ...
+          'if libsbml.so is in another directory please enter the ', ...
+          'full path to reach the directory from this directory: '), 's');
+      lib{2} = [new_bin_dir, filesep, 'libsbml.so'];
+      
+      if (exist(lib{2}) == 0)
+          error('libsbml.so could not be found');
+      else
+        lib{1} = lib{2};
+      end;
+  end;
+  
+  % check that the include directory exists
+  include_dir = [root, filesep, 'include'];
+  disp(sprintf('Checking for the %s directory ...', include_dir));
+  if (exist(include_dir, 'dir') ~= 7)
+    error (sprintf('%s not found\n%s', include_dir, ...
+      'the libSBML source tree expects this directory to exist'));
+  end;
+  
+  if (ismatlab)
+    % build the files
+    inc_flag = ['-I', include_dir];
+    buildMexFiles(inc_flag, lib{1});
+
+  else
+    disp('Build on octave');
+  end;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% runs the mex command for windows and matlab
+% the messy file handle stuff is because this seems to be the best way to 
+% be able to pass arguments to the function
+function buildMexFiles(include, library)
+
+  fhandle = @mex;
+  disp('Building TranslateSBML ...');
+  feval(fhandle, 'TranslateSBML.c', include, library);
+  disp('Building OutputSBML ...');
+  feval(fhandle, 'OutputSBML.c', include, library);
+
+  transFile = strcat('TranslateSBML.', mexext());
+  outFile = strcat('OutputSBML.', mexext());
+
+  if ((exist(transFile) == 3 && ...
+      exist(outFile) == 3))      
+    disp(sprintf('%s\n%s', 'Build successful', ...
+      'Now run the install script which will install and test the files'));
+  else
+    disp('Build failed');
+  end;
+

Added: trunk/libsbml/src/bindings/matlab/install.m
===================================================================
--- trunk/libsbml/src/bindings/matlab/install.m	                        (rev 0)
+++ trunk/libsbml/src/bindings/matlab/install.m	2011-01-29 11:44:25 UTC (rev 12719)
@@ -0,0 +1,285 @@
+function install
+
+  [detected_os, matlab, root] = determine_system();
+
+  switch detected_os
+    case 0
+      install_win(matlab, root);
+    case 1
+      install_mac(matlab, root);
+    case 2
+      install_linux(matlab, root);
+    otherwise
+      error('OS not recognised');
+  end;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% check what we are using
+function [detected_os, matlab, root] = determine_system
+
+  disp('Checking system ...');
+  disp('Looking at software ...');
+  % matlab = [0, 1]
+  %     0 - octave
+  %     1 - matlab
+  if (strcmp(isoctave(), '0'))
+    matlab = 1;
+    disp('MATLAB detected');
+  else
+    matlab = 0;
+    disp('Octave detected');
+  end;
+
+  disp('Looking at OS ...');
+  % detected_os = [0, 1, 2]
+  %      0 - windows
+  %      1 - mac
+  %      2 - unix
+  if (ispc())
+    detected_os = 0;
+    disp('Windows OS detected');
+  elseif(ismac())
+    detected_os = 1;
+    disp('Mac OS detected');
+  elseif(isunix())
+    detected_os = 2;
+    disp('Linux OS detected');
+  else
+    error('Unable to establish operating system');
+  end;
+
+  disp('Checking directory structure ...');
+  % need to check which directory we are in
+  % if we are in the src directory we should 
+  % be in directory ../src/bindings/matlab
+  [remain, first] = fileparts(pwd);
+  [remain1, second] = fileparts(remain);
+  [remain2, third] = fileparts(remain1);
+
+  if (~strcmp(first, 'matlab'))
+    report_incorrect_dir(pwd, '/src/bindings/matlab');
+  elseif (~strcmp(second, 'bindings'))
+    report_incorrect_dir(pwd, '/src/bindings/matlab');
+  elseif (~strcmp(third, 'src'))
+    report_incorrect_dir(pwd, '/src/bindings/matlab');
+  else
+    root = remain2;
+    disp('Expected directory structure found');
+  end;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% tell user we are in the wrong location
+function report_incorrect_dir(this_dir, expected)
+
+  message = sprintf('You are in directory %s \nbut should be in %s', this_dir, expected);
+  error(message);
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% install on windows
+function install_win(ismatlab, root)
+
+  bin_dir = [root, filesep, 'win', filesep, 'bin'];
+  if (exist(bin_dir, 'dir') ~= 7)
+    %dir doesnot exist prompt
+    error('should not be here');
+  else
+    addDir(pwd);
+    addDir(bin_dir);
+  end;
+  
+  if (ismatlab)
+    this_dir = pwd;
+    % install the files
+    try
+      M = TranslateSBML('test.xml');
+    catch
+      cd(bin_dir);
+      try
+        M = TranslateSBML('test.xml');
+        cd(this_dir);
+      catch
+        cd(this_dir);
+      end;
+    end;
+    
+    success = 1;
+    try
+      disp('checking for TranslateSBML');
+      M = TranslateSBML('test.xml');
+    catch
+      disp('Installation failed - need to build TranslateSBML');
+      success = 0;
+    end;
+
+    outFile = [tempdir, filesep, 'test-out.xml'];
+    if (success == 1)
+      try
+        disp('checking OutputSBML');
+        OutputSBML(M, outFile);
+      catch
+        disp('Installation failed - need to build OutputSBML');
+        success = 0;
+      end;
+    end;
+    
+    if (success == 1)
+      disp ('running tests for TranslateSBML');
+      cd test;
+      pass = testBinding(1);
+      cd ..;
+      if (pass == 0)
+        disp('TranslateSBML successful');
+      else
+        disp('Binding present but problem detected. Seek help.');
+        success = 0;
+      end;
+    end;
+
+    if (success == 1)
+      disp('running tests for OutputSBML');
+      cd test;
+      pass = testOutput(tempdir);
+      cd ..;
+      if (pass == 0)
+        disp('OutputSBML successful');
+      else
+        disp('Output function present but problem detected. Seek help.');
+        success = 0;
+      end;
+    end;
+
+    if (success == 1)
+      disp ('Installation completed');
+    end;
+   
+  else
+    % TO DO
+    disp('install on octave');
+  end;
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% install on mac
+function install_mac(ismatlab, root)
+
+  % check that libsbml is in usr/local/lib directory
+  bin_dir = [];
+
+  for i=1:length(strfind(pwd, filesep))
+      bin_dir = [bin_dir, '..', filesep];
+  end;
+  bin_dir = [bin_dir, 'usr', filesep, 'local', filesep, 'lib'];
+  disp('Checking for libraries ...');
+  % check that the library files are all there
+  lib{1} = [bin_dir, filesep, 'libsbml.dylib'];
+  if (exist(lib{1}) == 0)
+      disp('libsbml.dylib could not be found');
+      new_bin_dir = input(sprintf('\n\n%s\n%s\n%s\n%s', ...
+          'The install process assumes that libsbml', ...
+          'has been installed at usr/local', ...
+          'if libsbml.dylib is in another directory please enter the ', ...
+          'full path to reach the directory from this directory: '), 's');
+      lib{2} = [new_bin_dir, filesep, 'libsbml.dylib'];
+      
+      if (exist(lib{2}) == 0)
+          error('libsbml.dylib could not be found');
+      else
+        lib{1} = lib{2};
+      end;
+  end;
+  
+  % check that the include directory exists
+  include_dir = [root, filesep, 'include'];
+  disp(sprintf('Checking for the %s directory ...', include_dir));
+  if (exist(include_dir, 'dir') ~= 7)
+    error (sprintf('%s not found\n%s', include_dir, ...
+      'the libSBML source tree expects this directory to exist'));
+  end;
+  
+  if (ismatlab)
+    % install the files
+    inc_flag = ['-I', include_dir];
+    installMexFiles(inc_flag, lib{1});
+
+  else
+    disp('install on octave');
+  end;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% install on linux
+function install_linux(ismatlab, root)
+
+  % check that libsbml is in usr/local/lib directory
+  bin_dir = [];
+
+  for i=1:length(strfind(pwd, filesep))
+      bin_dir = [bin_dir, '..', filesep];
+  end;
+  bin_dir = [bin_dir, 'usr', filesep, 'local', filesep, 'lib'];
+  disp('Checking for libraries ...');
+  % check that the library files are all there
+  lib{1} = [bin_dir, filesep, 'libsbml.so'];
+  if (exist(lib{1}) == 0)
+      disp('libsbml.so could not be found');
+      new_bin_dir = input(sprintf('\n\n%s\n%s\n%s\n%s', ...
+          'The install process assumes that libsbml', ...
+          'has been installed at usr/local', ...
+          'if libsbml.so is in another directory please enter the ', ...
+          'full path to reach the directory from this directory: '), 's');
+      lib{2} = [new_bin_dir, filesep, 'libsbml.so'];
+      
+      if (exist(lib{2}) == 0)
+          error('libsbml.so could not be found');
+      else
+        lib{1} = lib{2};
+      end;
+  end;
+  
+  % check that the include directory exists
+  include_dir = [root, filesep, 'include'];
+  disp(sprintf('Checking for the %s directory ...', include_dir));
+  if (exist(include_dir, 'dir') ~= 7)
+    error (sprintf('%s not found\n%s', include_dir, ...
+      'the libSBML source tree expects this directory to exist'));
+  end;
+  
+  if (ismatlab)
+    % install the files
+    inc_flag = ['-I', include_dir];
+    installMexFiles(inc_flag, lib{1});
+
+  else
+    disp('install on octave');
+  end;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% runs the mex command for windows and matlab
+% the messy file handle stuff is because this seems to be the best way to 
+% be able to pass arguments to the function
+function installMexFiles(include, library)
+
+  fhandle = @mex;
+  disp('Building TranslateSBML ...');
+  feval(fhandle, 'TranslateSBML.c', include, library);
+  disp('Building OutputSBML ...');
+  feval(fhandle, 'OutputSBML.c', include, library);
+
+  transFile = strcat('TranslateSBML.', mexext());
+  outFile = strcat('OutputSBML.', mexext());
+
+  if ((exist(transFile) == 3 && ...
+      exist(outFile) == 3))      
+    disp(sprintf('%s\n%s', 'Build successful', ...
+      'Now run the install script which will install and test the files'));
+  else
+    disp('Build failed');
+  end;
+
+function addDir(name)
+
+  disp(sprintf('adding %s to the path', name));
+  addpath(name);
+  if (savepath ~= 0)
+    error(sprintf('adding %s failed', name));
+  end;
+  
\ No newline at end of file

Modified: trunk/libsbml/src/bindings/matlab/test/testBinding.m
===================================================================
--- trunk/libsbml/src/bindings/matlab/test/testBinding.m	2011-01-29 00:18:57 UTC (rev 12718)
+++ trunk/libsbml/src/bindings/matlab/test/testBinding.m	2011-01-29 11:44:25 UTC (rev 12719)
@@ -31,7 +31,7 @@
   Totalfail = Totalfail + testReadFlags;
 end;
 if (install == 0)
-  Totalfail = Totalfail + testOutput;
+  Totalfail = Totalfail + testOutput('Out-test1');
 end;
 disp ('************************************');
 disp('Overall tests:');

Modified: trunk/libsbml/src/bindings/matlab/test/testOutput.m
===================================================================
--- trunk/libsbml/src/bindings/matlab/test/testOutput.m	2011-01-29 00:18:57 UTC (rev 12718)
+++ trunk/libsbml/src/bindings/matlab/test/testOutput.m	2011-01-29 11:44:25 UTC (rev 12719)
@@ -1,4 +1,4 @@
-function fail = testOutput
+function fail = testOutput(outdir)
 
 %  Filename    :   TestOutput.m
 %  Description :
@@ -21,8 +21,8 @@
 % and also available online as http://sbml.org/software/sbmltoolbox/license.html
 %----------------------------------------------------------------------- -->
 
-if (~isdir('Out-test'))
-mkdir ('Out-test');
+if (~isdir(outdir))
+mkdir (outdir);
 end;
 
 if exist('OCTAVE_VERSION')
@@ -35,7 +35,7 @@
     end;
   end;
 else
-  files = dir('test-data/*.xml');
+  files = dir(['test-data', filesep, '*.xml']);
 end;
 
 fail = 0;
@@ -52,10 +52,10 @@
   elseif (strcmp(files(i).name, 'convertedFormulasL2.xml') && exist('OCTAVE_VERSION'))
     %do nothing
   else
-    model = TranslateSBML(sprintf('test-data/%s', files(i).name));
+    model = TranslateSBML(['test-data', filesep, files(i).name]);
     if (~isempty(model))
-      OutputSBML(model, sprintf('Out-test/%s', files(i).name));
-      if (compareFiles(sprintf('test-data/%s', files(i).name), sprintf('Out-test/%s', files(i).name)))
+      OutputSBML(model, [outdir, filesep, files(i).name]);
+      if (compareFiles(['test-data', filesep, files(i).name], [outdir, filesep, files(i).name]))
         disp(sprintf('Output of %s failed', files(i).name));
         fail = fail + 1;
       end;


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 12718
          http://sbml.svn.sourceforge.net/sbml/?rev=12718&view=rev
Author:   fbergmann
Date:     2011-01-29 00:18:57 +0000 (Sat, 29 Jan 2011)

Log Message:
-----------
- modified to generate some rudimentary C# documentation. See also the mail to the team. 

Modified Paths:
--------------
    branches/libsbml-5/src/bindings/swig/swigdoc.py

Modified: branches/libsbml-5/src/bindings/swig/swigdoc.py
===================================================================
--- branches/libsbml-5/src/bindings/swig/swigdoc.py	2011-01-27 13:53:44 UTC (rev 12717)
+++ branches/libsbml-5/src/bindings/swig/swigdoc.py	2011-01-29 00:18:57 UTC (rev 12718)
@@ -1,11 +1,12 @@
 #!/usr/bin/env python
 #
 # @file   swigdoc.py
-# @brief  Creates documentation for Java, Python, and Perl.
+# @brief  Creates documentation for C#, Java, Python, and Perl.
 # @author Ben Bornstein
 # @author Christoph Flamm
 # @author Akiya Jouraku
 # @author Michael Hucka
+# @author Frank Bergmann
 #
 # $Id: swigdoc.py 10124 2009-08-28 12:04:51Z sarahkeating $
 # $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/src/bindings/swig/swigdoc.py $
@@ -459,6 +460,8 @@
 
   if language == 'java':  
     target = 'libsbmlConstants#'
+  elif language == 'csharp':  
+    target = 'libsbml.libsbml.#'
   elif language == 'python':
     target = 'libsbml.'
   else:
@@ -554,6 +557,14 @@
 
 
 
+def translateCSharpCrossRef (match):
+  prior = match.group(1)
+  classname = match.group(2)
+  method = match.group(3)
+  return prior + '<see cref="' + classname + '.' + method + '"/>'
+
+
+
 def translatePythonCrossRef (match):
   prior = match.group(1)
   classname = match.group(2)
@@ -587,12 +598,24 @@
   trailing     = match.group(3)
 
   if leading != '%' and leading != '(':
-    return leading + '{@link ' + classname + '}' + trailing
+	return leading + '{@link ' + classname + '}' + trailing
   else:
     return leading + classname + trailing
 
 
 
+def translateClassRefCSharp (match):
+  leading      = match.group(1)
+  classname    = match.group(2)
+  trailing     = match.group(3)
+
+  if leading != '%' and leading != '(':
+	return leading + '<see cref="' + classname + '"/>' + trailing
+  else:
+    return leading + classname + trailing
+
+
+
 def sanitizeForHTML (docstring, language):
   """sanitizeForHTML (docstring, language) -> docstring
 
@@ -605,6 +628,8 @@
   p = re.compile('@if\s+(java|python|perl|clike|notcpp)\s+(.+?)@endif', re.DOTALL)
   if language == 'java':
     docstring = p.sub(translateIfJava, docstring)
+  elif language == 'csharp':
+    docstring = p.sub(translateIfJava, docstring)
   elif language == 'perl':
     docstring = p.sub(translateIfPerl, docstring)
   elif language == 'python':
@@ -688,12 +713,18 @@
   # done better (e.g., by not hard-wiring the class names).
 
   p = re.compile(r'(\W)(' + '|'.join(libsbmlclasses) + r')\b([^:])', re.DOTALL)
-  docstring = p.sub(translateClassRef, docstring)
+  if language == 'csharp':
+    docstring = p.sub(translateClassRefCSharp, docstring)
+  else:
+    docstring = p.sub(translateClassRef, docstring)
 
   # Massage Java method cross-references.
 
   p = re.compile('(\s+)(\S+?)::(\w+\s*\([^)]*?\))', re.MULTILINE)
-  docstring = p.sub(translateJavaCrossRef, docstring)
+  if language == 'csharp':
+    docstring = p.sub(translateCSharpCrossRef, docstring)
+  else:
+    docstring = p.sub(translateJavaCrossRef, docstring)
 
   # Take out any left-over quotes, because Javadoc doesn't have the %foo
   # quoting mechanism.
@@ -787,6 +818,196 @@
 
 
 
+def rewriteDocstringForCSharp (docstring):
+  """rewriteDocstringForCSharp (docstring) -> docstring
+
+  Performs some mimimal C#-specific sanitizations on the
+  C++/Doxygen docstring.
+  """
+
+  docstring = rewriteCommonReferences(docstring, 'java')  
+
+  # Get rid of the /** ... */ and leading *'s.
+  docstring = docstring.replace('/**', '').replace('*/', '').replace('*', ' ')
+
+  # Get rid of indentation
+  p = re.compile('^\s+(\S*\s*)', re.MULTILINE)
+  docstring = p.sub(r'\1', docstring)
+
+  # Get rid of paragraph indentation not caught by the code above.
+  p = re.compile('^[ \t]+(\S)', re.MULTILINE)
+  docstring = p.sub(r'\1', docstring)
+  
+  # Preliminary: rewrite some of the data type references to equivalent
+  # C# types.  (Note: this rewriting affects only the documentation
+  # comments inside classes & methods, not the method signatures.)
+
+  docstring = docstring.replace(r'const char *', 'string ')
+  docstring = docstring.replace(r'const char* ', 'string ')
+  docstring = docstring.replace(r'an unsigned int', 'a long integer')
+  docstring = docstring.replace(r'unsigned int', 'long')
+  docstring = docstring.replace(r'const std::string&', 'string')
+  docstring = docstring.replace(r'const std::string', 'string')
+  docstring = docstring.replace(r'std::string', 'string')
+  docstring = docstring.replace(r'const ', '')
+  docstring = docstring.replace(r'NULL', 'null')
+
+  # Also use Java syntax instead of "const XMLNode*" etc.
+
+  p = re.compile(r'const (%?)(' + '|'.join(libsbmlclasses) + r') ?(\*|&)', re.DOTALL)
+  docstring = p.sub(javafyClassRef, docstring)  
+  p = re.compile(r'(%?)(' + '|'.join(libsbmlclasses) + r') ?(\*|&)', re.DOTALL)
+  docstring = p.sub(javafyClassRef, docstring)  
+
+  # Do the big work.
+
+  docstring = sanitizeForHTML(docstring, 'csharp')
+
+  # Fix up for a problem introduced by sanitizeForHTML -- should fix
+  # properly some day.
+
+  p = re.compile('(@see\s+[\w ,(]*){@link\s+([^}]+?)}')
+  docstring = p.sub(r'\1\2', docstring)
+
+  # Inside of @see, change double colons to pound signs.
+
+  docstring = re.sub('(@see\s+\w+)::', r'\1#', docstring)
+
+  # The syntax for @see is slightly different: method names need to have a
+  # leading pound sign character.  This particular bit of code only handles
+  # a single @see foo(), which means the docs have to be written that way.
+  # Maybe someday in the future it should be expanded to handle
+  # @see foo(), bar(), etc., but I don't have time right now to do it.
+
+  docstring = re.sub('(@see\s+)([\w:.]+)\(', r'\1#\2(', docstring)
+
+  # Remove the '*' character that Javadoc doesn't want to see in @see's.
+  # (This doesn't make a difference; javadoc still can't match up the refs.)
+
+  #  p = re.compile('@see[\s\w.:,()#]+[*][\s\w.:,()*#]')
+  #  docstring = p.sub(removeStar, docstring)
+
+  # The syntax for @link is vastly different.
+  
+  p = re.compile('@link([\s/*]+[\w\s,.:#()*]+[\s/*]+[\w():#]+[\s/*]*)@endlink', re.DOTALL)
+  docstring = p.sub(r'<see cref="\1"/>', docstring)
+
+  p = re.compile('{@link\s(\w+)}', re.DOTALL)
+  docstring = p.sub(r'<see cref="\1"/>', docstring)
+  
+  # this is too broad unfortunately ...   
+  # p = re.compile('@see\s[#](\w+\(.*\))', re.MULTILINE)
+  #docstring = p.sub(r'<see cref="\1"/>', docstring)
+  p = re.compile('@see\s[#](\w+\(\))', re.MULTILINE)
+  docstring = p.sub(r'<see cref="\1"/>', docstring)
+  p = re.compile('@see\s[#](\w+\(\w+\s+\w+\))', re.MULTILINE)
+  docstring = p.sub(r'<see cref="\1"/>', docstring)
+  
+  p = re.compile('@see\s+(\w+)', re.MULTILINE)
+  docstring = p.sub(r'<see cref="\1"/>', docstring)
+  
+  
+  
+  #cleanup 
+  p = re.compile('@see\s(<see.*/>)', re.MULTILINE)
+  docstring = p.sub(r'\1', docstring)
+  
+  
+  # mark parameters (TODO: figure out correct boundaries!)
+  p = re.compile('@param\s+(\w+)\s(.+?)$', re.MULTILINE)
+  docstring = p.sub(r'<param name="\1">\2</param>', docstring)
+  
+  # mark return statements (TODO: figure out correct boundaries!)
+  p = re.compile('@return\s+(.+?)$', re.MULTILINE)
+  docstring = p.sub(r'<returns>\1</returns>', docstring) 
+  
+  # mark all notes
+  p = re.compile('@note\s+(.+?)$', re.DOTALL)
+  docstring = p.sub(r'<remarks>\1</remarks>', docstring) 
+  p = re.compile('@docnote\s+(.+?)$', re.DOTALL)
+  docstring = p.sub(r'<remarks>\1</remarks>', docstring) 
+  
+  # some things are marked as 'code' but are not code samples
+  p = re.compile('<code>("*\.*\w+\,*"*)</code>', re.DOTALL)
+  docstring = p.sub(r'<c>\1</c>', docstring) 
+  
+  
+  # replace libsbmlConstants# by libsbml.libsbml.
+  p = re.compile('\s*libsbmlConstants#', re.DOTALL)
+  docstring = p.sub(r'F:libsbml.libsbml.', docstring) 
+  p = re.compile('(libsbml.\w+\_\w+)\s\w+\_\w+', re.DOTALL)
+  docstring = p.sub(r'\1', docstring)   
+  
+  p = re.compile('\s*libsbmlConstants.', re.DOTALL)
+  docstring = p.sub(r'libsbml.libsbml.', docstring) 
+  
+  #delete variable names (one argument)
+  p = re.compile('\((\w+)\s+\w+\)', re.DOTALL)
+  docstring = p.sub(r'(\1)', docstring) 
+  
+  #delete variable names (two arguments)
+  p = re.compile('\((\w+\s*)\w+(,\s*\w+)\s*\w+\)', re.DOTALL)
+  docstring = p.sub(r'(\1\2)', docstring) 
+  
+  #delete variable names (three arguments)
+  p = re.compile('\((\w+\s*)\w+(,\s*\w+)\s*\w+(,\s*\w+)\s*\w+\)', re.DOTALL)
+  docstring = p.sub(r'(\1\2\3)', docstring) 
+  
+  # fix issues
+  docstring = docstring.replace('<see cref="libsbml"/>', "libsbml")  
+  docstring = docstring.replace('<see cref="libsbml.libsbml./>', '<see cref="libsbml.libsbml"/>')  
+  docstring = docstring.replace('<a href="#<see cref="SBasePlugin"/>', '<a href="#SBasePlugin')  
+  docstring = docstring.replace('<!---------------------------------------------------------------------- -->', '')
+  docstring = docstring.replace('<!-- leave this next break as-is to work around some doxygen bug -->', '')
+  docstring = docstring.replace('(string &uri)"/>', '(string)"/>')
+  docstring = docstring.replace('/sub> < t<sub>', '/sub> &lt; t<sub>')
+  docstring = docstring.replace('</sub> <\n', '</sub> &lt;\n')
+  
+  # fix spaces in link s
+  p = re.compile('\s+"/>', re.DOTALL)
+  docstring = p.sub(r'"/>', docstring) 
+  
+  # Outside of @see and other constructs, dot is used to reference members
+  # instead of C++'s double colon.
+
+  docstring = docstring.replace(r'::', '.')
+
+  # Need to escape the quotation marks:
+
+  docstring = docstring.replace('"', "'")
+  docstring = docstring.replace(r"'", r"\'")  
+  
+  # XMLDocs are confused by some of the HTML tags
+  # pre should be marked as code
+  docstring = docstring.replace('<pre>', '<code>')  
+  docstring = docstring.replace('</pre>', '</code>')  
+  
+  # HACK: XMLDoc needs XHTML ... however many tags are not closed currently
+  #       so lets replace them for now ...
+  docstring = docstring.replace('<p>', '<br/><br/>')  
+  docstring = docstring.replace('</p>', '')  
+  docstring = docstring.replace('<li>', '<br/>* ')
+  docstring = docstring.replace('</li>', '')
+  docstring = docstring.replace('<br>', '<br/>')
+  
+  # some tags are not valid to be used in XML doc. 
+  docstring = docstring.replace('&ndash;', '-')
+  docstring = docstring.replace('&mdash;', '-')
+  docstring = docstring.replace('&nbsp;', ' ')
+  
+  
+  docstring = docstring.replace('boolean', 'bool')
+  
+  
+  # prefix lines by C# XML Comment mark 
+  docstring = docstring.replace('\n', '\n\t/// ')
+  # surround document in a summary tag
+  docstring = '\n\t///<summary>' + docstring + '\n\t///</summary>\n'
+  
+  return docstring
+
+
+
 def indentVerbatimForPython (match):
   text = match.group()
 
@@ -954,6 +1175,8 @@
         continue
       if language == 'java':
         docstring = rewriteDocstringForJava(m.docstring)
+      elif language == 'csharp':
+        docstring = rewriteDocstringForCSharp(m.docstring)
       elif language == 'perl':
         docstring = rewriteDocstringForPerl(m.docstring)  
       ostream.write(formatMethodDocString(language, m.name, cclass.name, docstring, m.args))
@@ -966,6 +1189,9 @@
   if language == 'java':
     pre  = '%javamethodmodifiers'
     post = ' public'
+  if language == 'csharp':
+    pre  = '%csmethodmodifiers'
+    post = ' public'
   elif language == 'perl':
     pre  = '=item'
     post = ''
@@ -993,6 +1219,8 @@
 
   if language == 'java':
     doc = rewriteDocstringForJava(docstring)
+  elif language == 'csharp':
+    doc = rewriteDocstringForCSharp(docstring)
   elif language == 'python':
     doc = rewriteDocstringForPython(docstring)
   elif language == 'perl':
@@ -1006,7 +1234,10 @@
     pre = '%typemap(javaimports) '
     docstring = rewriteDocstringForJava(docstring)    
     output = pre + classname + ' "\n' + docstring + '"\n\n'
-
+  elif language == 'csharp':
+    pre = '%typemap(csimports) '
+    docstring = rewriteDocstringForCSharp(docstring)    
+    output = pre + classname + ' "\n using System;\n using System.Runtime.InteropServices;\n\n' + docstring + '"\n\n'    
   elif language == 'python':
     pre = '%feature("docstring") '
     docstring = rewriteDocstringForPython(docstring)
@@ -1059,12 +1290,12 @@
 
 
 def main (args):
-  """usage: swigdoc.py [java | python | perl] -Ipath -Dpath libsbml.i output.i
+  """usage: swigdoc.py [csharp | java | python | perl] -Ipath -Dpath libsbml.i output.i
 
-  java | python | perl  generate docstrings for this language module.
-  path                  is the path to the libsbml src/ directory.
-  libsbml.i             is the master libsbml SWIG interface file.
-  output.i              is the file to output the SWIG docstrings.
+  csharp |java | python | perl  generate docstrings for this language module.
+  path                          is the path to the libsbml src/ directory.
+  libsbml.i                     is the master libsbml SWIG interface file.
+  output.i                      is the file to output the SWIG docstrings.
   """
 
   if len(args) != 6:


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Revision: 12717
          http://sbml.svn.sourceforge.net/sbml/?rev=12717&view=rev
Author:   sarahkeating
Date:     2011-01-27 13:53:44 +0000 (Thu, 27 Jan 2011)

Log Message:
-----------
added further ignore functions

Modified Paths:
--------------
    trunk/libsbml/dev/utilities/translateTests/translateTests.pl

Modified: trunk/libsbml/dev/utilities/translateTests/translateTests.pl
===================================================================
--- trunk/libsbml/dev/utilities/translateTests/translateTests.pl	2011-01-27 04:19:51 UTC (rev 12716)
+++ trunk/libsbml/dev/utilities/translateTests/translateTests.pl	2011-01-27 13:53:44 UTC (rev 12717)
@@ -177,6 +177,7 @@
   test_MathMLFormatter_semantics_url             => 0,
   test_MathMLFormatter_ci_definitionURL          => 0,
   test_ASTNode_replaceArgument                   => 0,
+  test_ASTNode_accessWithNULL                    => 0,
   test_SBase_addCVTerms_newBag                   => 0,
   test_Date_setHoursOffset_neg_arg               => 0,
   test_Date_setOffsetSign                        => 0,


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Revision: 12716
          http://sbml.svn.sourceforge.net/sbml/?rev=12716&view=rev
Author:   mhucka
Date:     2011-01-27 04:19:51 +0000 (Thu, 27 Jan 2011)

Log Message:
-----------
Minor fixes for doxygen.

Modified Paths:
--------------
    trunk/libsbml/src/annotation/ModelHistory.h
    trunk/libsbml/src/sbml/SBMLError.h
    trunk/libsbml/src/sbml/SBMLVisitor.h

Modified: trunk/libsbml/src/annotation/ModelHistory.h
===================================================================
--- trunk/libsbml/src/annotation/ModelHistory.h	2011-01-27 04:10:01 UTC (rev 12715)
+++ trunk/libsbml/src/annotation/ModelHistory.h	2011-01-27 04:19:51 UTC (rev 12716)
@@ -288,11 +288,11 @@
    * below for further explanations.  (Default value used if this argument
    * is not given: @c 0.)
    * 
-   * @param hours offset an unsigned integer representing the time zone's
+   * @param hoursOffset an unsigned integer representing the time zone's
    * hour offset from GMT.  (Default value used if this argument is not
    * given: @c 0.)
    * 
-   * @param minute offset an unsigned integer representing the time zone's
+   * @param minutesOffset an unsigned integer representing the time zone's
    * minute offset from GMT.  (Default value used if this argument is not
    * given: @c 0.)
    *

Modified: trunk/libsbml/src/sbml/SBMLError.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLError.h	2011-01-27 04:10:01 UTC (rev 12715)
+++ trunk/libsbml/src/sbml/SBMLError.h	2011-01-27 04:19:51 UTC (rev 12716)
@@ -584,9 +584,9 @@
  ,  /*!< No units for 1D Compartment */
  , TwoDimensionalCompartmentUnits        = 20512 /*!< No units for 2D Compartment */
  , ThreeDimensionalCompartmentUnits      = 20513 /*!< No units for 3D Compartment */
- , AllowedAttributesOnCompartment        = 20517 /*!< Invalid attribute on <compartment> */
- , NoUnitsOnCompartment                  = 20518 /*!< No units for <compartment> */
- , InvalidSpeciesCompartmentRef          = 20601 /*!< Invalid <code>compartment</code> reference */
+ , AllowedAttributesOnCompartment        = 20517 /*!< Invalid attribute on <code>&lt;compartment&gt;</code> */
+ , NoUnitsOnCompartment                  = 20518 /*!< No units for <code>&lt;compartment&gt;</code> */
+ , InvalidSpeciesCompartmentRef          = 20601 /*!< Invalid <code>&lt;compartment&gt;</code> reference */
  , HasOnlySubsNoSpatialUnits             = 20602 /*!< No <code>spatialSizeUnits</code> permitted if <code>hasOnlySubstanceUnits</code>=<code>true</code> */
  , NoSpatialUnitsInZeroD                 = 20603 /*!< No <code>spatialSizeUnits</code> permitted if compartment is zero-dimensional */
  , NoConcentrationInZeroD                = 20604 /*!< No <code>initialConcentration</code> permitted if compartment is zero-dimensional */
@@ -603,7 +603,7 @@
  , SpatialSizeUnitsRemoved               = 20615 /*!< Attribute <code>spatialSizeUnits</code> not supported in this Level+Version of SBML */
  , SubstanceUnitsOnSpecies               = 20616 /*!< No substance units for Species */
  , ConversionFactorOnSpecies             = 20617 /*!< Invalid conversionFactor attribute */
- , AllowedAttributesOnSpecies            = 20623 /*!< Invalid attribute on <species&gt;</code> */
+ , AllowedAttributesOnSpecies            = 20623 /*!< Invalid attribute on <code>&lt;species&gt;</code> */
  , InvalidParameterUnits                 = 20701 /*!< Invalid value for <code>units</code> in parameter definition */
  , ParameterUnits                        = 20702 /*!< No units for parameter */
  , ConversionFactorMustConstant          = 20705 /*!< ConversionFactor must be constant parameter */
@@ -620,46 +620,46 @@
  , RepeatedRule10304                     = 20905 /*!<  */
  , CircularRuleDependency                = 20906 /*!< Circular dependency involving rules and reactions */
  ,  /*!< Rule must contain one math element */
- , AllowedAttributesOnAssignRule         = 20908 /*!< Invalid attribute on <assignmentRule> */
- , AllowedAttributesOnRateRule           = 20909 /*!< Invalid attribute on <rateRule> */
- , AllowedAttributesOnAlgRule            = 20910 /*!< Invalid attribute on <algebraicRule> */
+ , AllowedAttributesOnAssignRule         = 20908 /*!< Invalid attribute on <code>&lt;assignmentRule&gt;</code> */
+ , AllowedAttributesOnRateRule           = 20909 /*!< Invalid attribute on <code>&lt;rateRule&gt;</code> */
+ , AllowedAttributesOnAlgRule            = 20910 /*!< Invalid attribute on <code>&lt;algebraicRule&gt;</code> */
  , ConstraintMathNotBoolean              = 21001 /*!< Non-boolean math expression in constraint definition */
  , IncorrectOrderInConstraint            = 21002 /*!< Incorrect order of elements in constraint definition */
  , ConstraintNotInXHTMLNamespace         = 21003 /*!< Constraint message is not in XHTML XML namespace */
  , ConstraintContainsXMLDecl             = 21004 /*!< XML declarations not permitted in constraint messages */
  , ConstraintContainsDOCTYPE             = 21005 /*!< XML <code>DOCTYPE</code> not permitted in constraint messages */
  , InvalidConstraintContent              = 21006 /*!< Invalid content for constraint message */
- ,  /*!< Only one math element on <constraint> */
- ,  /*!< Only one message element on <constraint> */
- , AllowedAttributesOnConstraint         = 21009 /*!< Invalid attribute on <constraint> */
+ ,  /*!< Only one math element on <code>&lt;constraint&gt;</code> */
+ ,  /*!< Only one message element on <code>&lt;constraint&gt;</code> */
+ , AllowedAttributesOnConstraint         = 21009 /*!< Invalid attribute on <code>&lt;constraint&gt;</code> */
  , NoReactantsOrProducts                 = 21101 /*!< Cannot have a reaction with neither reactants nor products */
  , IncorrectOrderInReaction              = 21102 /*!< Incorrect ordering of components in reaction definition */
  , EmptyListInReaction                   = 21103 /*!< Reaction components, if present, cannot be empty */
  , InvalidReactantsProductsList          = 21104 /*!< Invalid element in list of reactants or products */
  , InvalidModifiersList                  = 21105 /*!< Invalid element in list of modifiers */
- ,  /*!< Only one of subelement on <reaction> */
- , CompartmentOnReaction                 = 21107 /*!< Invalid compartment attribute on <reaction> */
- , AllowedAttributesOnReaction           = 21110 /*!< Invalid attribute on <reaction> */
+ ,  /*!< Only one of subelement on <code>&lt;reaction&gt;</code> */
+ , CompartmentOnReaction                 = 21107 /*!< Invalid compartment attribute on <code>&lt;reaction&gt;</code> */
+ , AllowedAttributesOnReaction           = 21110 /*!< Invalid attribute on <code>&lt;reaction&gt;</code> */
  , InvalidSpeciesReference               = 21111 /*!< Invalid <code>species</code> value in species reference */
  , RepeatedRule20611                     = 21112 /*!<  */
  , BothStoichiometryAndMath              = 21113 /*!< Cannot use both <code>stoichiometry</code> and <code>&lt;stoichiometryMath&gt;</code> simultaneously */
- , AllowedAttributesOnSpeciesReference   = 21116 /*!< Invalid attribute on <speciesReference> */
- , AllowedAttributesOnModifier           = 21117 /*!< Invalid attribute on <modifierSpeciesReference> */
+ , AllowedAttributesOnSpeciesReference   = 21116 /*!< Invalid attribute on <code>&lt;speciesReference&gt;</code> */
+ , AllowedAttributesOnModifier           = 21117 /*!< Invalid attribute on <code>&lt;modifierSpeciesReference&gt;</code> */
  , UndeclaredSpeciesRef                  = 21121 /*!< Undeclared species referenced in kinetic law formula */
  , IncorrectOrderInKineticLaw            = 21122 /*!< Incorrect ordering of components in kinetic law definition */
  , EmptyListInKineticLaw                 = 21123 /*!< The list of parameters component, if present, cannot be empty */
  , NonConstantLocalParameter             = 21124 /*!< Parameters local to a kinetic law must have <code>constant</code>=<code>true</code> */
  , SubsUnitsNoLongerValid                = 21125 /*!< <code>substanceUnits</code> not supported in this Level+Version of SBML */
  , TimeUnitsNoLongerValid                = 21126 /*!< <code>timeUnits</code> not supported in this Level+Version of SBML */
- ,  /*!< Only one listOfLocalParameters permitted on <kineticLaw> */
+ ,  /*!< Only one listOfLocalParameters permitted on <code>&lt;kineticLaw&gt;</code> */
  ,  /*!< Only LocalParameters allowed in ListOfLocalParameters */
  , AllowedAttributesOnListOfLocalParam   = 21129 /*!< Invalid attribute on <code>&lt;listOfLocalParameters&gt;</code> */
- ,  /*!< Only one math element on <kineticLaw> */
+ ,  /*!< Only one math element on <code>&lt;kineticLaw&gt;</code> */
  , UndeclaredSpeciesInStoichMath         = 21131 /*!< Undeclared species referenced in <code>&lt;stoichiometryMath&gt;</code> formula */
- , AllowedAttributesOnKineticLaw         = 21132 /*!< Invalid attribute on <kineticLaw> */
+ , AllowedAttributesOnKineticLaw         = 21132 /*!< Invalid attribute on <code>&lt;kineticLaw&gt;</code> */
  , AllowedAttributesOnListOfSpeciesRef   = 21150 /*!< Invalid attribute on <code>&lt;listOfSpeciesReferences&gt;</code> */
  , AllowedAttributesOnListOfMods         = 21151 /*!< Invalid attribute on <code>&lt;listofModifiers&gt;</code> */
- , AllowedAttributesOnLocalParameter     = 21172 /*!< Invalid attribute on <localParameter> */
+ , AllowedAttributesOnLocalParameter     = 21172 /*!< Invalid attribute on <code>&lt;localParameter&gt;</code> */
  , MissingTriggerInEvent                 = 21201 /*!< Missing trigger in event definition */
  , TriggerMathNotBoolean                 = 21202 /*!< Non-boolean math expression in trigger definition */
  , MissingEventAssignment                = 21203 /*!< Missing event assignment in event definition */
@@ -672,19 +672,19 @@
  , InvalidEventAssignmentVariable        = 21211 /*!< Invalid value for <code>variable</code> in event assignment */
  , EventAssignmentForConstantEntity      = 21212 /*!< Cannot assign to a constant component in an event assignment */
  ,  /*!< EventAssignment must have one math element */
- , AllowedAttributesOnEventAssignment    = 21214 /*!< Invalid attribute on <eventAssignment> */
- ,  /*!< Event can only have one <delay> */
+ , AllowedAttributesOnEventAssignment    = 21214 /*!< Invalid attribute on <code>&lt;eventAssignment&gt;</code> */
+ ,  /*!< Event can only have one <code>&lt;delay&gt;</code> */
  ,  /*!< Event can only have one <code>&lt;listOfEventAssignments&gt;</code> */
- ,  /*!< <code>&lt;listOfEventAssignments&gt;</code> can only have <eventAssignment> */
+ ,  /*!< <code>&lt;listOfEventAssignments&gt;</code> can only have <code>&lt;eventAssignment&gt;</code> */
  , AllowedAttributesOnListOfEventAssign  = 21224 /*!< Invalid attribute on <code>&lt;listOfEventAssignments&gt;</code> */
- , AllowedAttributesOnEvent              = 21225 /*!< Invalid attribute on <event> */
- , AllowedAttributesOnTrigger            = 21226 /*!< Invalid attribute on <trigger> */
- , AllowedAttributesOnDelay              = 21227 /*!< Invalid attribute on <delay> */
- , PersistentNotBoolean                  = 21228 /*!< Persistent attribute on <trigger> must be boolean */
- , InitialValueNotBoolean                = 21229 /*!< InitialValue attribute on <trigger> must be boolean */
- ,  /*!< Event can only have one <priority> */
+ , AllowedAttributesOnEvent              = 21225 /*!< Invalid attribute on <code>&lt;event&gt;</code> */
+ , AllowedAttributesOnTrigger            = 21226 /*!< Invalid attribute on <code>&lt;trigger&gt;</code> */
+ , AllowedAttributesOnDelay              = 21227 /*!< Invalid attribute on <code>&lt;delay&gt;</code> */
+ , PersistentNotBoolean                  = 21228 /*!< Persistent attribute on <code>&lt;trigger&gt;</code> must be boolean */
+ , InitialValueNotBoolean                = 21229 /*!< InitialValue attribute on <code>&lt;trigger&gt;</code> must be boolean */
+ ,  /*!< Event can only have one <code>&lt;priority&gt;</code> */
  ,  /*!< Priority must have one math element */
- , AllowedAttributesOnPriority           = 21232 /*!< Invalid attribute on <priority> */
+ , AllowedAttributesOnPriority           = 21232 /*!< Invalid attribute on <code>&lt;priority&gt;</code> */
 
 
  , GeneralWarningNotSpecified            = 29999 /*!< Unknown error */
@@ -719,7 +719,7 @@
  , NoSBOTermsInL1                        = 91013 /*!< SBML Level&nbsp;1 does not support the <code>sboTerm</code> attribute */
  , StrictUnitsRequiredInL1               = 91014 /*!< SBML Level&nbsp;1 requires strict unit consistency */
  , ConversionFactorNotInL1               = 91015 /*!< SBML Level&nbsp;1 does not support the <code>conversionFactor</code> attribute */
- , CompartmentNotOnL1Reaction            = 91016 /*!< SBML Level&nbsp;1 does not support the <code>compartment</code> attribute on a <Reaction> */
+ , CompartmentNotOnL1Reaction            = 91016 /*!< SBML Level&nbsp;1 does not support the <code>compartment</code> attribute on a <code>&lt;reaction&gt;</code> */
  , ExtentUnitsNotSubstance               = 91017 /*!< Conversion to SBML Level&nbsp;1 requires that <code>extent</code> units be a variant of substance */
 
   /* L2v1 compatability */
@@ -736,7 +736,7 @@
  , StoichiometryMathNotYetSupported      = 92010 /*!< Conversion to StoichiometryMath not yet supported */
  , PrioirtyLostFromL3                    = 92011 /*!< SBML Level&nbsp;2 Version&nbsp;1 does not support priority */
  , NonPersistentNotSupported             = 92012 /*!< SBML Level&nbsp;2 Version&nbsp;1 does not support the <code>persistent</code> attribute */
- , InitialValueFalseEventNotSupported    = 92013 /*!< SBML Level&nbsp;2 Version&nbsp;1 does not support an <code>initialValue</code> of <code>false</code> for a <Trigger> */
+ , InitialValueFalseEventNotSupported    = 92013 /*!< SBML Level&nbsp;2 Version&nbsp;1 does not support an <code>initialValue</code> of <code>false</code> for a <code>&lt;trigger&gt;</code> */
 
  /*!< SBML Level&nbsp;2 Version&nbsp;1 requires strict unit consistency */
 
@@ -812,7 +812,7 @@
 
  , NoTimeSymbolInFunctionDef             = 99301 /*!< <code>&lt;csymbol&gt;</code> for <code>time</code> used within the <code>&lt;math&gt;</code> of a function definition */
 
- , NoBodyInFunctionDef                   = 99302 /*!< There must be a body within the <math> of a function definition */
+ , NoBodyInFunctionDef                   = 99302 /*!< There must be a body within the <code>&lt;math&gt;</code> of a function definition */
 
   /* These are internal errors that reverts to 10501. */
 

Modified: trunk/libsbml/src/sbml/SBMLVisitor.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLVisitor.h	2011-01-27 04:10:01 UTC (rev 12715)
+++ trunk/libsbml/src/sbml/SBMLVisitor.h	2011-01-27 04:19:51 UTC (rev 12716)
@@ -138,11 +138,12 @@
    * Pattern</i></a> to perform operations on ListOf objects.
    *
    * @param x the ListOf object to visit.
+   *
+   * @param type the object type code.
    */
   virtual void visit (const ListOf       &x, SBMLTypeCode_t type);
 
 
-
   /**
    * Interface method for using the <a target="_blank" 
    * href="http://en.wikipedia.org/wiki/Design_pattern_(computer_science)"><i>Visitor
@@ -440,6 +441,9 @@
    * Pattern</i></a> to perform operations on ListOf objects.
    *
    * @param x the ListOf object to visit.
+   *
+   * @param type the object type code.
+   *
    */
   virtual void leave (const ListOf &x, SBMLTypeCode_t type);
 };


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Revision: 12715
          http://sbml.svn.sourceforge.net/sbml/?rev=12715&view=rev
Author:   mhucka
Date:     2011-01-27 04:10:01 +0000 (Thu, 27 Jan 2011)

Log Message:
-----------
Futzing to make doxygen happy.

Modified Paths:
--------------
    trunk/libsbml/src/annotation/CVTerm.h

Modified: trunk/libsbml/src/annotation/CVTerm.h
===================================================================
--- trunk/libsbml/src/annotation/CVTerm.h	2011-01-27 03:49:59 UTC (rev 12714)
+++ trunk/libsbml/src/annotation/CVTerm.h	2011-01-27 04:10:01 UTC (rev 12715)
@@ -245,8 +245,9 @@
    * QualifierType_t#BIOLOGICAL_QUALIFIER BIOLOGICAL_QUALIFIER@endlink.  If
    * an explicit value for @p type is not given, this method defaults to
    * using @link QualifierType_t#UNKNOWN_QUALIFIER
-   * UNKNOWN_QUALIFIER@endlink.  The @if clike #QualifierType_t@endif@if
-   * java qualifier type code@endif type value can be set later using the
+   * UNKNOWN_QUALIFIER@endlink.  The
+   * @if clike #QualifierType_t@endif@if java qualifier type code@endif 
+   * type value can be set later using the
    * CVTerm::setQualifierType(@if java int type@endif) method.
    *
    * Different BioModels.net qualifier elements encode different types of


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Revision: 12714
          http://sbml.svn.sourceforge.net/sbml/?rev=12714&view=rev
Author:   mhucka
Date:     2011-01-27 03:49:59 +0000 (Thu, 27 Jan 2011)

Log Message:
-----------
Added a note about blank namespaces.

Modified Paths:
--------------
    trunk/libsbml/docs/src/libsbml-issues.html

Modified: trunk/libsbml/docs/src/libsbml-issues.html
===================================================================
--- trunk/libsbml/docs/src/libsbml-issues.html	2011-01-27 02:52:06 UTC (rev 12713)
+++ trunk/libsbml/docs/src/libsbml-issues.html	2011-01-27 03:49:59 UTC (rev 12714)
@@ -107,6 +107,14 @@
 XML constructs inside <code>&lt;notes&gt;</code> and
 <code>&lt;annotation&gt;</code> elements).</li>
 
+<li style="margin-bottom: 1em">Some versions of libxml2 behave incorrectly
+when given a blank namespace (e.g., the use of <code>xmlns=" "</code>, with
+a space character).  Versions of libxml prior 2.7.7 will report this as an
+invalid or undefined XML namespace, but in fact a namespace URI containing
+a single space is valid (albeit not a very useful one).  This highlights
+another issue: different versions of the underlying XML parsers may behave
+differently in the face of unusual (though not necessarily illegal) inputs.
+
 </ol>
 
 


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Revision: 12713
          http://sbml.svn.sourceforge.net/sbml/?rev=12713&view=rev
Author:   mhucka
Date:     2011-01-27 02:52:06 +0000 (Thu, 27 Jan 2011)

Log Message:
-----------
Use the new HTML table.

Modified Paths:
--------------
    trunk/libsbml/docs/src/libsbml-math.txt

Modified: trunk/libsbml/docs/src/libsbml-math.txt
===================================================================
--- trunk/libsbml/docs/src/libsbml-math.txt	2011-01-27 02:41:54 UTC (rev 12712)
+++ trunk/libsbml/docs/src/libsbml-math.txt	2011-01-27 02:52:06 UTC (rev 12713)
@@ -21,8 +21,7 @@
 The figure also shows the corresponding MathML 2.0 "content"
 representation:
 
-@image html astnode-illustration.jpg "Example AST representation of a mathematical expression."
-@image latex astnode-illustration.jpg "Example AST representation of a mathematical expression."
+@htmlinclude astnode-illustration.html
 
 The following are noteworthy about the AST representation in libSBML:
 


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Revision: 12712
          http://sbml.svn.sourceforge.net/sbml/?rev=12712&view=rev
Author:   mhucka
Date:     2011-01-27 02:41:54 +0000 (Thu, 27 Jan 2011)

Log Message:
-----------
Made the bug report statement more concise.

Modified Paths:
--------------
    trunk/libsbml/docs/src/libsbml-communications.html

Modified: trunk/libsbml/docs/src/libsbml-communications.html
===================================================================
--- trunk/libsbml/docs/src/libsbml-communications.html	2011-01-26 22:43:40 UTC (rev 12711)
+++ trunk/libsbml/docs/src/libsbml-communications.html	2011-01-27 02:41:54 UTC (rev 12712)
@@ -4,19 +4,18 @@
 
 <h2>Reporting bugs and other problems</h2>
 
-<p> We invite you to report bugs and other problems using the issue
-tracker for libSBML on SourceForge.  The following URL will take you
-there directly: <a target="_blank"
+<p> Please report problems and other issues using the issue tracker for
+libSBML on SourceForge: <a target="_blank"
 href="http://sbml.org/Software/libSBML/issue-tracker">http://sbml.org/Software/libSBML/issue-tracker</a>.
 
 <p> You can also report problems on the <a target="_blank"
 href="http://www.sbml.org/Forums">sbml-interoperability</a> mailing list
-(see next section).  This may even have advantages, such as that other
-people may also have experienced the issue and offer a workaround more
+(see next section).  This may have advantages, such as that other people
+may also have experienced the same issue and offer a workaround more
 quickly than the libSBML developers can respond.
 
-<p> Finally, if you want to contact the libSBML developers, you can email
-them at <a
+<p> Finally, if you want to contact the libSBML developers directly, you
+can email them at <a
 href="mailto:lib...@ca...">lib...@ca...</a>.
 
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 12711
          http://sbml.svn.sourceforge.net/sbml/?rev=12711&view=rev
Author:   mhucka
Date:     2011-01-26 22:43:40 +0000 (Wed, 26 Jan 2011)

Log Message:
-----------
Fixed a doc formatting glitch.

Modified Paths:
--------------
    trunk/libsbml/src/xml/XMLNode.h

Modified: trunk/libsbml/src/xml/XMLNode.h
===================================================================
--- trunk/libsbml/src/xml/XMLNode.h	2011-01-26 18:43:35 UTC (rev 12710)
+++ trunk/libsbml/src/xml/XMLNode.h	2011-01-26 22:43:40 UTC (rev 12711)
@@ -32,10 +32,10 @@
  *
  * An XMLNode can contain any number of children.  Each child is another
  * XMLNode, thereby forming a tree.  The methods XMLNode::getNumChildren()
- * and @if clike XMLNode::getChild() can be used to access the
- * tree structure starting from a given node. @endif@if java XMLNode::getChild(long n)
- * can be used to access the tree structure starting from a given node.
- * @endif
+ * and @if clike XMLNode::getChild() can be used to access the tree
+ * structure starting from a given node. @endif@if java
+ * XMLNode::getChild(long n) can be used to access the tree structure
+ * starting from a given node.  @endif
  *
  * Each XMLNode is subclassed from XMLToken, and thus has the same methods
  * available as XMLToken.  These methods include XMLToken::getNamespaces(),
@@ -62,7 +62,7 @@
  * The returned XMLNode object by XMLNode::convertStringToXMLNode(@if java String xml@endif)
  * is a dummy root (container) XMLNode if the given XML string has two or
  * more top-level elements (e.g.,
- * "<code>&lt;p&gt;...&lt;/p&gt;&lt;p&gt;...&lt;/p&gt;</code>"). In the
+ * &quot;<code>&lt;p&gt;...&lt;/p&gt;&lt;p&gt;...&lt;/p&gt;</code>&quot;). In the
  * dummy root node, each top-level element in the given XML string is
  * contained as a child XMLNode. XMLToken::isEOF() can be used to identify
  * if the returned XMLNode object is a dummy node or not.  Here is an
@@ -72,7 +72,7 @@
                                                                                          
 std::string str = "..."; 
 XMLNode* xn = XMLNode::convertStringToXMLNode(str);                                      
-if (xn == NULL)
+if ( xn == NULL )
 {                                                                                      
   // returned value is null (error)                                                    
   ...
@@ -80,7 +80,7 @@
 else if ( xn->isEOF() )                                                                 
 {                                                                                      
   // root node is a dummy node                                                         
-  for (int i=0; i < xn->getNumChildren(); i++)                                          
+  for ( int i = 0; i < xn->getNumChildren(); i++ )                                          
   {                                                                                    
     // access to each child node of the dummy node.                                    
     XMLNode& xnChild = xn->getChild(i);                                                  
@@ -97,7 +97,7 @@
 
 String str = "...";
 XMLNode xn = XMLNode.convertStringToXMLNode(str);
-if (xn == null)
+if ( xn == null )
 {
   // returned value is null (error)
   ...
@@ -105,7 +105,7 @@
 else if ( xn.isEOF() )
 {
   // root node is a dummy node
-  for (int i=0; i < xn.getNumChildren(); i++)
+  for ( int i = 0; i < xn.getNumChildren(); i++ )
   {
     // access to each child node of the dummy node.
     XMLNode xnChild = xn.getChild(i);


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 12705
          http://sbml.svn.sourceforge.net/sbml/?rev=12705&view=rev
Author:   sarahkeating
Date:     2011-01-26 16:38:13 +0000 (Wed, 26 Jan 2011)

Log Message:
-----------
updated for new test in annotation/test directory

Modified Paths:
--------------
    trunk/libsbml/src/bindings/python/test/annotation/TestRDFAnnotationC.py
    trunk/libsbml/src/bindings/python/test/annotation/TestValidation.py
    trunk/libsbml/src/bindings/ruby/test/annotation/TestRDFAnnotationC.rb
    trunk/libsbml/src/bindings/ruby/test/annotation/TestValidation.rb

Modified: trunk/libsbml/src/bindings/python/test/annotation/TestRDFAnnotationC.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/annotation/TestRDFAnnotationC.py	2011-01-26 16:10:23 UTC (rev 12704)
+++ trunk/libsbml/src/bindings/python/test/annotation/TestRDFAnnotationC.py	2011-01-26 16:38:13 UTC (rev 12705)
@@ -1,236 +1,245 @@
-#
-# @file    TestRDFAnnotationC.py
-# @brief   RDFAnnotation parser unit tests
-#
-# @author  Akiya Jouraku (Python conversion)
-# @author  Sarah Keating 
-#
-# $Id$
-# $HeadURL$
-#
-# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
-#
-# DO NOT EDIT THIS FILE.
-#
-# This file was generated automatically by converting the file located at
-# src/annotation/test/TestRDFAnnotationC.c
-# using the conversion program dev/utilities/translateTests/translateTests.pl.
-# Any changes made here will be lost the next time the file is regenerated.
-#
-# -----------------------------------------------------------------------------
-# This file is part of libSBML.  Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
-# Copyright 2005-2010 California Institute of Technology.
-# Copyright 2002-2005 California Institute of Technology and
-#                     Japan Science and Technology Corporation.
-# 
-# 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/libsbml/license.html
-# -----------------------------------------------------------------------------
-
-import sys
-import unittest
-import libsbml
-
-
-class TestRDFAnnotationC(unittest.TestCase):
-
-  global d
-  d = None
-  global m
-  m = None
-
-  def setUp(self):
-    filename = "../../annotation/test/test-data/annotation.xml"
-    self.d = libsbml.readSBML(filename)
-    self.m = self.d.getModel()
-    pass  
-
-  def tearDown(self):
-    _dummyList = [ self.d ]; _dummyList[:] = []; del _dummyList
-    pass  
-
-  def test_RDFAnnotation_C_delete(self):
-    obj = self.m.getCompartment(0)
-    node = libsbml.RDFAnnotationParser.parseCVTerms(obj)
-    n1 = libsbml.RDFAnnotationParser.deleteRDFAnnotation(node)
-    self.assert_( n1.getNumChildren() == 0 )
-    self.assert_((  "annotation" == n1.getName() ))
-    _dummyList = [ node ]; _dummyList[:] = []; del _dummyList
-    pass  
-
-  def test_RDFAnnotation_C_getModelHistory(self):
-    self.assert_( (self.m == None) == False )
-    history = self.m.getModelHistory()
-    self.assert_( history != None )
-    mc = history.getCreator(0)
-    self.assert_((  "Le Novere" == mc.getFamilyName() ))
-    self.assert_((  "Nicolas" == mc.getGivenName() ))
-    self.assert_((  "le...@eb..." == mc.getEmail() ))
-    self.assert_((  "EMBL-EBI" == mc.getOrganisation() ))
-    date = history.getCreatedDate()
-    self.assert_( date.getYear() == 2005 )
-    self.assert_( date.getMonth() == 2 )
-    self.assert_( date.getDay() == 2 )
-    self.assert_( date.getHour() == 14 )
-    self.assert_( date.getMinute() == 56 )
-    self.assert_( date.getSecond() == 11 )
-    self.assert_( date.getSignOffset() == 0 )
-    self.assert_( date.getHoursOffset() == 0 )
-    self.assert_( date.getMinutesOffset() == 0 )
-    self.assert_((  "2005-02-02T14:56:11Z" == date.getDateAsString() ))
-    date = history.getModifiedDate()
-    self.assert_( date.getYear() == 2006 )
-    self.assert_( date.getMonth() == 5 )
-    self.assert_( date.getDay() == 30 )
-    self.assert_( date.getHour() == 10 )
-    self.assert_( date.getMinute() == 46 )
-    self.assert_( date.getSecond() == 2 )
-    self.assert_( date.getSignOffset() == 0 )
-    self.assert_( date.getHoursOffset() == 0 )
-    self.assert_( date.getMinutesOffset() == 0 )
-    self.assert_((  "2006-05-30T10:46:02Z" == date.getDateAsString() ))
-    pass  
-
-  def test_RDFAnnotation_C_parseCVTerms(self):
-    obj = self.m.getCompartment(0)
-    node = libsbml.RDFAnnotationParser.parseCVTerms(obj)
-    self.assert_( node.getNumChildren() == 1 )
-    rdf = node.getChild(0)
-    self.assert_((  "RDF" == rdf.getName() ))
-    self.assert_((  "rdf" == rdf.getPrefix() ))
-    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() ))
-    self.assert_( rdf.getNumChildren() == 1 )
-    desc = rdf.getChild(0)
-    self.assert_((  "Description" == desc.getName() ))
-    self.assert_((  "rdf" == desc.getPrefix() ))
-    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() ))
-    self.assert_( desc.getNumChildren() == 1 )
-    is1 = desc.getChild(0)
-    self.assert_((  "is" == is1.getName() ))
-    self.assert_((  "bqbiol" == is1.getPrefix() ))
-    self.assert_( is1.getNumChildren() == 1 )
-    Bag = is1.getChild(0)
-    self.assert_((  "Bag" == Bag.getName() ))
-    self.assert_((  "rdf" == Bag.getPrefix() ))
-    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI() ))
-    self.assert_( Bag.getNumChildren() == 4 )
-    li = Bag.getChild(0)
-    self.assert_((  "li" == li.getName() ))
-    self.assert_((  "rdf" == li.getPrefix() ))
-    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() ))
-    self.assert_( li.getNumChildren() == 0 )
-    li1 = Bag.getChild(1)
-    self.assert_((  "li" == li1.getName() ))
-    self.assert_((  "rdf" == li1.getPrefix() ))
-    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li1.getURI() ))
-    self.assert_( li1.getNumChildren() == 0 )
-    li2 = Bag.getChild(2)
-    self.assert_((  "li" == li2.getName() ))
-    self.assert_((  "rdf" == li2.getPrefix() ))
-    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li2.getURI() ))
-    self.assert_( li2.getNumChildren() == 0 )
-    li3 = Bag.getChild(3)
-    self.assert_((  "li" == li3.getName() ))
-    self.assert_((  "rdf" == li3.getPrefix() ))
-    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li3.getURI() ))
-    self.assert_( li3.getNumChildren() == 0 )
-    _dummyList = [ node ]; _dummyList[:] = []; del _dummyList
-    pass  
-
-  def test_RDFAnnotation_C_parseModelHistory(self):
-    node = libsbml.RDFAnnotationParser.parseModelHistory(self.m)
-    self.assert_( node.getNumChildren() == 1 )
-    rdf = node.getChild(0)
-    self.assert_((  "RDF" == rdf.getName() ))
-    self.assert_((  "rdf" == rdf.getPrefix() ))
-    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() ))
-    self.assert_( rdf.getNumChildren() == 1 )
-    desc = rdf.getChild(0)
-    self.assert_((  "Description" == desc.getName() ))
-    self.assert_((  "rdf" == desc.getPrefix() ))
-    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() ))
-    self.assert_( desc.getNumChildren() == 3 )
-    creator = desc.getChild(0)
-    self.assert_((  "creator" == creator.getName() ))
-    self.assert_((  "dc" == creator.getPrefix() ))
-    self.assert_((  "http://purl.org/dc/elements/1.1/" == creator.getURI() ))
-    self.assert_( creator.getNumChildren() == 1 )
-    Bag = creator.getChild(0)
-    self.assert_((  "Bag" == Bag.getName() ))
-    self.assert_((  "rdf" == Bag.getPrefix() ))
-    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI() ))
-    self.assert_( Bag.getNumChildren() == 1 )
-    li = Bag.getChild(0)
-    self.assert_((  "li" == li.getName() ))
-    self.assert_((  "rdf" == li.getPrefix() ))
-    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() ))
-    self.assert_( li.getNumChildren() == 3 )
-    N = li.getChild(0)
-    self.assert_((  "N" == N.getName() ))
-    self.assert_((  "vCard" == N.getPrefix() ))
-    self.assert_((  "http://www.w3.org/2001/vcard-rdf/3.0#" == N.getURI() ))
-    self.assert_( N.getNumChildren() == 2 )
-    Family = N.getChild(0)
-    self.assert_((  "Family" == Family.getName() ))
-    self.assert_((  "vCard" == Family.getPrefix() ))
-    self.assert_((  "http://www.w3.org/2001/vcard-rdf/3.0#" == Family.getURI() ))
-    self.assert_( Family.getNumChildren() == 1 )
-    Given = N.getChild(1)
-    self.assert_((  "Given" == Given.getName() ))
-    self.assert_((  "vCard" == Given.getPrefix() ))
-    self.assert_((  "http://www.w3.org/2001/vcard-rdf/3.0#" == Given.getURI() ))
-    self.assert_( Given.getNumChildren() == 1 )
-    EMAIL = li.getChild(1)
-    self.assert_((  "EMAIL" == EMAIL.getName() ))
-    self.assert_((  "vCard" == EMAIL.getPrefix() ))
-    self.assert_((  "http://www.w3.org/2001/vcard-rdf/3.0#" == EMAIL.getURI() ))
-    self.assert_( EMAIL.getNumChildren() == 1 )
-    ORG = li.getChild(2)
-    self.assert_((  "ORG" == ORG.getName() ))
-    self.assert_((  "vCard" == ORG.getPrefix() ))
-    self.assert_((  "http://www.w3.org/2001/vcard-rdf/3.0#" == ORG.getURI() ))
-    self.assert_( ORG.getNumChildren() == 1 )
-    Orgname = ORG.getChild(0)
-    self.assert_((  "Orgname" == Orgname.getName() ))
-    self.assert_((  "vCard" == Orgname.getPrefix() ))
-    self.assert_((  "http://www.w3.org/2001/vcard-rdf/3.0#" == Orgname.getURI() ))
-    self.assert_( Orgname.getNumChildren() == 1 )
-    created = desc.getChild(1)
-    self.assert_((  "created" == created.getName() ))
-    self.assert_((  "dcterms" == created.getPrefix() ))
-    self.assert_((  "http://purl.org/dc/terms/" == created.getURI() ))
-    self.assert_( created.getNumChildren() == 1 )
-    cr_date = created.getChild(0)
-    self.assert_((  "W3CDTF" == cr_date.getName() ))
-    self.assert_((  "dcterms" == cr_date.getPrefix() ))
-    self.assert_((  "http://purl.org/dc/terms/" == cr_date.getURI() ))
-    self.assert_( cr_date.getNumChildren() == 1 )
-    modified = desc.getChild(2)
-    self.assert_((  "modified" == modified.getName() ))
-    self.assert_((  "dcterms" == modified.getPrefix() ))
-    self.assert_((  "http://purl.org/dc/terms/" == modified.getURI() ))
-    self.assert_( modified.getNumChildren() == 1 )
-    mo_date = created.getChild(0)
-    self.assert_((  "W3CDTF" == mo_date.getName() ))
-    self.assert_((  "dcterms" == mo_date.getPrefix() ))
-    self.assert_((  "http://purl.org/dc/terms/" == mo_date.getURI() ))
-    self.assert_( mo_date.getNumChildren() == 1 )
-    _dummyList = [ node ]; _dummyList[:] = []; del _dummyList
-    pass  
-
-def suite():
-  suite = unittest.TestSuite()
-  suite.addTest(unittest.makeSuite(TestRDFAnnotationC))
-
-  return suite
-
-if __name__ == "__main__":
-  if unittest.TextTestRunner(verbosity=1).run(suite()).wasSuccessful() :
-    sys.exit(0)
-  else:
-    sys.exit(1)
+#
+# @file    TestRDFAnnotationC.py
+# @brief   RDFAnnotation parser unit tests
+#
+# @author  Akiya Jouraku (Python conversion)
+# @author  Sarah Keating 
+#
+# $Id$
+# $HeadURL$
+#
+# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
+#
+# DO NOT EDIT THIS FILE.
+#
+# This file was generated automatically by converting the file located at
+# src/annotation/test/TestRDFAnnotationC.c
+# using the conversion program dev/utilities/translateTests/translateTests.pl.
+# Any changes made here will be lost the next time the file is regenerated.
+#
+# -----------------------------------------------------------------------------
+# This file is part of libSBML.  Please visit http://sbml.org for more
+# information about SBML, and the latest version of libSBML.
+#
+# Copyright 2005-2010 California Institute of Technology.
+# Copyright 2002-2005 California Institute of Technology and
+#                     Japan Science and Technology Corporation.
+# 
+# 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/libsbml/license.html
+# -----------------------------------------------------------------------------
+
+import sys
+import unittest
+import libsbml
+
+
+class TestRDFAnnotationC(unittest.TestCase):
+
+  global d
+  d = None
+  global m
+  m = None
+
+  def setUp(self):
+    filename = "../../annotation/test/test-data/annotation.xml"
+    self.d = libsbml.readSBML(filename)
+    self.m = self.d.getModel()
+    pass  
+
+  def tearDown(self):
+    _dummyList = [ self.d ]; _dummyList[:] = []; del _dummyList
+    pass  
+
+  def test_RDFAnnotation_C_accessWithNULL(self):
+    self.assert_( libsbml.RDFAnnotationParser.createCVTerms(None) == None )
+    self.assert_( libsbml.RDFAnnotationParser.createRDFDescription(None) == None )
+    self.assert_( libsbml.RDFAnnotationParser.deleteRDFAnnotation(None) == None )
+    self.assert_( libsbml.RDFAnnotationParser.parseCVTerms(None) == None )
+    self.assert_( libsbml.RDFAnnotationParser.parseModelHistory(None) == None )
+    libsbml.RDFAnnotationParser.parseRDFAnnotation(None,None)
+    pass  
+
+  def test_RDFAnnotation_C_delete(self):
+    obj = self.m.getCompartment(0)
+    node = libsbml.RDFAnnotationParser.parseCVTerms(obj)
+    n1 = libsbml.RDFAnnotationParser.deleteRDFAnnotation(node)
+    self.assert_( n1.getNumChildren() == 0 )
+    self.assert_((  "annotation" == n1.getName() ))
+    _dummyList = [ node ]; _dummyList[:] = []; del _dummyList
+    pass  
+
+  def test_RDFAnnotation_C_getModelHistory(self):
+    self.assert_( (self.m == None) == False )
+    history = self.m.getModelHistory()
+    self.assert_( history != None )
+    mc = history.getCreator(0)
+    self.assert_((  "Le Novere" == mc.getFamilyName() ))
+    self.assert_((  "Nicolas" == mc.getGivenName() ))
+    self.assert_((  "le...@eb..." == mc.getEmail() ))
+    self.assert_((  "EMBL-EBI" == mc.getOrganisation() ))
+    date = history.getCreatedDate()
+    self.assert_( date.getYear() == 2005 )
+    self.assert_( date.getMonth() == 2 )
+    self.assert_( date.getDay() == 2 )
+    self.assert_( date.getHour() == 14 )
+    self.assert_( date.getMinute() == 56 )
+    self.assert_( date.getSecond() == 11 )
+    self.assert_( date.getSignOffset() == 0 )
+    self.assert_( date.getHoursOffset() == 0 )
+    self.assert_( date.getMinutesOffset() == 0 )
+    self.assert_((  "2005-02-02T14:56:11Z" == date.getDateAsString() ))
+    date = history.getModifiedDate()
+    self.assert_( date.getYear() == 2006 )
+    self.assert_( date.getMonth() == 5 )
+    self.assert_( date.getDay() == 30 )
+    self.assert_( date.getHour() == 10 )
+    self.assert_( date.getMinute() == 46 )
+    self.assert_( date.getSecond() == 2 )
+    self.assert_( date.getSignOffset() == 0 )
+    self.assert_( date.getHoursOffset() == 0 )
+    self.assert_( date.getMinutesOffset() == 0 )
+    self.assert_((  "2006-05-30T10:46:02Z" == date.getDateAsString() ))
+    pass  
+
+  def test_RDFAnnotation_C_parseCVTerms(self):
+    obj = self.m.getCompartment(0)
+    node = libsbml.RDFAnnotationParser.parseCVTerms(obj)
+    self.assert_( node.getNumChildren() == 1 )
+    rdf = node.getChild(0)
+    self.assert_((  "RDF" == rdf.getName() ))
+    self.assert_((  "rdf" == rdf.getPrefix() ))
+    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() ))
+    self.assert_( rdf.getNumChildren() == 1 )
+    desc = rdf.getChild(0)
+    self.assert_((  "Description" == desc.getName() ))
+    self.assert_((  "rdf" == desc.getPrefix() ))
+    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() ))
+    self.assert_( desc.getNumChildren() == 1 )
+    is1 = desc.getChild(0)
+    self.assert_((  "is" == is1.getName() ))
+    self.assert_((  "bqbiol" == is1.getPrefix() ))
+    self.assert_( is1.getNumChildren() == 1 )
+    Bag = is1.getChild(0)
+    self.assert_((  "Bag" == Bag.getName() ))
+    self.assert_((  "rdf" == Bag.getPrefix() ))
+    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI() ))
+    self.assert_( Bag.getNumChildren() == 4 )
+    li = Bag.getChild(0)
+    self.assert_((  "li" == li.getName() ))
+    self.assert_((  "rdf" == li.getPrefix() ))
+    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() ))
+    self.assert_( li.getNumChildren() == 0 )
+    li1 = Bag.getChild(1)
+    self.assert_((  "li" == li1.getName() ))
+    self.assert_((  "rdf" == li1.getPrefix() ))
+    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li1.getURI() ))
+    self.assert_( li1.getNumChildren() == 0 )
+    li2 = Bag.getChild(2)
+    self.assert_((  "li" == li2.getName() ))
+    self.assert_((  "rdf" == li2.getPrefix() ))
+    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li2.getURI() ))
+    self.assert_( li2.getNumChildren() == 0 )
+    li3 = Bag.getChild(3)
+    self.assert_((  "li" == li3.getName() ))
+    self.assert_((  "rdf" == li3.getPrefix() ))
+    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li3.getURI() ))
+    self.assert_( li3.getNumChildren() == 0 )
+    _dummyList = [ node ]; _dummyList[:] = []; del _dummyList
+    pass  
+
+  def test_RDFAnnotation_C_parseModelHistory(self):
+    node = libsbml.RDFAnnotationParser.parseModelHistory(self.m)
+    self.assert_( node.getNumChildren() == 1 )
+    rdf = node.getChild(0)
+    self.assert_((  "RDF" == rdf.getName() ))
+    self.assert_((  "rdf" == rdf.getPrefix() ))
+    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() ))
+    self.assert_( rdf.getNumChildren() == 1 )
+    desc = rdf.getChild(0)
+    self.assert_((  "Description" == desc.getName() ))
+    self.assert_((  "rdf" == desc.getPrefix() ))
+    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() ))
+    self.assert_( desc.getNumChildren() == 3 )
+    creator = desc.getChild(0)
+    self.assert_((  "creator" == creator.getName() ))
+    self.assert_((  "dc" == creator.getPrefix() ))
+    self.assert_((  "http://purl.org/dc/elements/1.1/" == creator.getURI() ))
+    self.assert_( creator.getNumChildren() == 1 )
+    Bag = creator.getChild(0)
+    self.assert_((  "Bag" == Bag.getName() ))
+    self.assert_((  "rdf" == Bag.getPrefix() ))
+    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI() ))
+    self.assert_( Bag.getNumChildren() == 1 )
+    li = Bag.getChild(0)
+    self.assert_((  "li" == li.getName() ))
+    self.assert_((  "rdf" == li.getPrefix() ))
+    self.assert_((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() ))
+    self.assert_( li.getNumChildren() == 3 )
+    N = li.getChild(0)
+    self.assert_((  "N" == N.getName() ))
+    self.assert_((  "vCard" == N.getPrefix() ))
+    self.assert_((  "http://www.w3.org/2001/vcard-rdf/3.0#" == N.getURI() ))
+    self.assert_( N.getNumChildren() == 2 )
+    Family = N.getChild(0)
+    self.assert_((  "Family" == Family.getName() ))
+    self.assert_((  "vCard" == Family.getPrefix() ))
+    self.assert_((  "http://www.w3.org/2001/vcard-rdf/3.0#" == Family.getURI() ))
+    self.assert_( Family.getNumChildren() == 1 )
+    Given = N.getChild(1)
+    self.assert_((  "Given" == Given.getName() ))
+    self.assert_((  "vCard" == Given.getPrefix() ))
+    self.assert_((  "http://www.w3.org/2001/vcard-rdf/3.0#" == Given.getURI() ))
+    self.assert_( Given.getNumChildren() == 1 )
+    EMAIL = li.getChild(1)
+    self.assert_((  "EMAIL" == EMAIL.getName() ))
+    self.assert_((  "vCard" == EMAIL.getPrefix() ))
+    self.assert_((  "http://www.w3.org/2001/vcard-rdf/3.0#" == EMAIL.getURI() ))
+    self.assert_( EMAIL.getNumChildren() == 1 )
+    ORG = li.getChild(2)
+    self.assert_((  "ORG" == ORG.getName() ))
+    self.assert_((  "vCard" == ORG.getPrefix() ))
+    self.assert_((  "http://www.w3.org/2001/vcard-rdf/3.0#" == ORG.getURI() ))
+    self.assert_( ORG.getNumChildren() == 1 )
+    Orgname = ORG.getChild(0)
+    self.assert_((  "Orgname" == Orgname.getName() ))
+    self.assert_((  "vCard" == Orgname.getPrefix() ))
+    self.assert_((  "http://www.w3.org/2001/vcard-rdf/3.0#" == Orgname.getURI() ))
+    self.assert_( Orgname.getNumChildren() == 1 )
+    created = desc.getChild(1)
+    self.assert_((  "created" == created.getName() ))
+    self.assert_((  "dcterms" == created.getPrefix() ))
+    self.assert_((  "http://purl.org/dc/terms/" == created.getURI() ))
+    self.assert_( created.getNumChildren() == 1 )
+    cr_date = created.getChild(0)
+    self.assert_((  "W3CDTF" == cr_date.getName() ))
+    self.assert_((  "dcterms" == cr_date.getPrefix() ))
+    self.assert_((  "http://purl.org/dc/terms/" == cr_date.getURI() ))
+    self.assert_( cr_date.getNumChildren() == 1 )
+    modified = desc.getChild(2)
+    self.assert_((  "modified" == modified.getName() ))
+    self.assert_((  "dcterms" == modified.getPrefix() ))
+    self.assert_((  "http://purl.org/dc/terms/" == modified.getURI() ))
+    self.assert_( modified.getNumChildren() == 1 )
+    mo_date = created.getChild(0)
+    self.assert_((  "W3CDTF" == mo_date.getName() ))
+    self.assert_((  "dcterms" == mo_date.getPrefix() ))
+    self.assert_((  "http://purl.org/dc/terms/" == mo_date.getURI() ))
+    self.assert_( mo_date.getNumChildren() == 1 )
+    _dummyList = [ node ]; _dummyList[:] = []; del _dummyList
+    pass  
+
+def suite():
+  suite = unittest.TestSuite()
+  suite.addTest(unittest.makeSuite(TestRDFAnnotationC))
+
+  return suite
+
+if __name__ == "__main__":
+  if unittest.TextTestRunner(verbosity=1).run(suite()).wasSuccessful() :
+    sys.exit(0)
+  else:
+    sys.exit(1)

Modified: trunk/libsbml/src/bindings/python/test/annotation/TestValidation.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/annotation/TestValidation.py	2011-01-26 16:10:23 UTC (rev 12704)
+++ trunk/libsbml/src/bindings/python/test/annotation/TestValidation.py	2011-01-26 16:38:13 UTC (rev 12705)
@@ -1,170 +1,186 @@
-#
-# @file    TestValidation.py
-# @brief   Validation of Date ModelCreator and ModelHistory unit tests
-#
-# @author  Akiya Jouraku (Python conversion)
-# @author  Sarah Keating 
-#
-# $Id$
-# $HeadURL$
-#
-# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
-#
-# DO NOT EDIT THIS FILE.
-#
-# This file was generated automatically by converting the file located at
-# src/annotation/test/TestValidation.cpp
-# using the conversion program dev/utilities/translateTests/translateTests.pl.
-# Any changes made here will be lost the next time the file is regenerated.
-#
-# -----------------------------------------------------------------------------
-# This file is part of libSBML.  Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
-# Copyright 2005-2010 California Institute of Technology.
-# Copyright 2002-2005 California Institute of Technology and
-#                     Japan Science and Technology Corporation.
-# 
-# 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/libsbml/license.html
-# -----------------------------------------------------------------------------
-
-import sys
-import unittest
-import libsbml
-
-
-class TestValidation(unittest.TestCase):
-
-
-  def test_Validation_CVTerm1(self):
-    cv = libsbml.CVTerm()
-    self.assert_( cv != None )
-    self.assertEqual( False, (cv.hasRequiredAttributes()) )
-    cv.setQualifierType(libsbml.MODEL_QUALIFIER)
-    self.assertEqual( False, (cv.hasRequiredAttributes()) )
-    cv.setModelQualifierType(libsbml.BQM_IS)
-    self.assertEqual( False, (cv.hasRequiredAttributes()) )
-    cv.addResource("ggg")
-    self.assertEqual( True, (cv.hasRequiredAttributes()) )
-    cv = None
-    pass  
-
-  def test_Validation_CVTerm2(self):
-    cv = libsbml.CVTerm()
-    self.assert_( cv != None )
-    self.assertEqual( False, (cv.hasRequiredAttributes()) )
-    cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
-    self.assertEqual( False, (cv.hasRequiredAttributes()) )
-    cv.setBiologicalQualifierType(libsbml.BQB_IS)
-    self.assertEqual( False, (cv.hasRequiredAttributes()) )
-    cv.addResource("ggg")
-    self.assertEqual( True, (cv.hasRequiredAttributes()) )
-    cv = None
-    pass  
-
-  def test_Validation_Date1(self):
-    date = libsbml.Date(200,12,30,12,15,45,1,2,0)
-    self.assert_( date != None )
-    self.assertEqual( False, (date.representsValidDate()) )
-    date = None
-    pass  
-
-  def test_Validation_Date2(self):
-    date = libsbml.Date(2007,14,30,12,15,45,1,2,0)
-    self.assert_( date != None )
-    self.assertEqual( False, (date.representsValidDate()) )
-    date = None
-    pass  
-
-  def test_Validation_Date3(self):
-    date = libsbml.Date("Jan 12")
-    self.assert_( date != None )
-    self.assertEqual( False, (date.representsValidDate()) )
-    date = None
-    pass  
-
-  def test_Validation_Date4(self):
-    date = libsbml.Date(2007,12,30,12,15,45,1,2,0)
-    self.assert_( date != None )
-    self.assertEqual( True, date.representsValidDate() )
-    date = None
-    pass  
-
-  def test_Validation_ModelCreator(self):
-    mc = libsbml.ModelCreator()
-    self.assert_( mc != None )
-    self.assertEqual( False, (mc.hasRequiredAttributes()) )
-    mc.setEmail("k123")
-    self.assertEqual( False, (mc.hasRequiredAttributes()) )
-    mc.setFamilyName("Keating")
-    self.assertEqual( False, (mc.hasRequiredAttributes()) )
-    mc.setGivenName("Sarah")
-    self.assertEqual( True, mc.hasRequiredAttributes() )
-    mc = None
-    pass  
-
-  def test_Validation_ModelHistory1(self):
-    mh = libsbml.ModelHistory()
-    self.assert_( mh != None )
-    self.assertEqual( False, (mh.hasRequiredAttributes()) )
-    date = libsbml.Date(2007,12,30,12,15,45,1,2,0)
-    mh.setCreatedDate(date)
-    self.assertEqual( False, (mh.hasRequiredAttributes()) )
-    mh.setModifiedDate(date)
-    self.assertEqual( False, (mh.hasRequiredAttributes()) )
-    mc = libsbml.ModelCreator()
-    mc.setFamilyName("Keating")
-    mc.setGivenName("Sarah")
-    mh.addCreator(mc)
-    self.assertEqual( True, mh.hasRequiredAttributes() )
-    mh = None
-    pass  
-
-  def test_Validation_ModelHistory2(self):
-    mh = libsbml.ModelHistory()
-    self.assert_( mh != None )
-    self.assertEqual( False, (mh.hasRequiredAttributes()) )
-    date = libsbml.Date(200,12,30,12,15,45,1,2,0)
-    mh.setCreatedDate(date)
-    self.assertEqual( False, (mh.hasRequiredAttributes()) )
-    mh.setModifiedDate(date)
-    self.assertEqual( False, (mh.hasRequiredAttributes()) )
-    mc = libsbml.ModelCreator()
-    mc.setFamilyName("Keating")
-    mc.setGivenName("Sarah")
-    mh.addCreator(mc)
-    self.assertEqual( False, (mh.hasRequiredAttributes()) )
-    mh = None
-    pass  
-
-  def test_Validation_ModelHistory3(self):
-    mh = libsbml.ModelHistory()
-    self.assert_( mh != None )
-    self.assertEqual( False, (mh.hasRequiredAttributes()) )
-    date = libsbml.Date(2007,12,30,12,15,45,1,2,0)
-    mh.setCreatedDate(date)
-    self.assertEqual( False, (mh.hasRequiredAttributes()) )
-    mh.setModifiedDate(date)
-    self.assertEqual( False, (mh.hasRequiredAttributes()) )
-    mc = libsbml.ModelCreator()
-    mc.setFamilyName("Keating")
-    mh.addCreator(mc)
-    self.assertEqual( False, (mh.hasRequiredAttributes()) )
-    mh = None
-    pass  
-
-def suite():
-  suite = unittest.TestSuite()
-  suite.addTest(unittest.makeSuite(TestValidation))
-
-  return suite
-
-if __name__ == "__main__":
-  if unittest.TextTestRunner(verbosity=1).run(suite()).wasSuccessful() :
-    sys.exit(0)
-  else:
-    sys.exit(1)
+#
+# @file    TestValidation.py
+# @brief   Validation of Date ModelCreator and ModelHistory unit tests
+#
+# @author  Akiya Jouraku (Python conversion)
+# @author  Sarah Keating 
+#
+# $Id$
+# $HeadURL$
+#
+# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
+#
+# DO NOT EDIT THIS FILE.
+#
+# This file was generated automatically by converting the file located at
+# src/annotation/test/TestValidation.cpp
+# using the conversion program dev/utilities/translateTests/translateTests.pl.
+# Any changes made here will be lost the next time the file is regenerated.
+#
+# -----------------------------------------------------------------------------
+# This file is part of libSBML.  Please visit http://sbml.org for more
+# information about SBML, and the latest version of libSBML.
+#
+# Copyright 2005-2010 California Institute of Technology.
+# Copyright 2002-2005 California Institute of Technology and
+#                     Japan Science and Technology Corporation.
+# 
+# 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/libsbml/license.html
+# -----------------------------------------------------------------------------
+
+import sys
+import unittest
+import libsbml
+
+
+class TestValidation(unittest.TestCase):
+
+
+  def test_Validation_CVTerm1(self):
+    cv = libsbml.CVTerm()
+    self.assert_( cv != None )
+    self.assertEqual( False, (cv.hasRequiredAttributes()) )
+    cv.setQualifierType(libsbml.MODEL_QUALIFIER)
+    self.assertEqual( False, (cv.hasRequiredAttributes()) )
+    cv.setModelQualifierType(libsbml.BQM_IS)
+    self.assertEqual( False, (cv.hasRequiredAttributes()) )
+    cv.addResource("ggg")
+    self.assertEqual( True, (cv.hasRequiredAttributes()) )
+    cv = None
+    pass  
+
+  def test_Validation_CVTerm2(self):
+    cv = libsbml.CVTerm()
+    self.assert_( cv != None )
+    self.assertEqual( False, (cv.hasRequiredAttributes()) )
+    cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
+    self.assertEqual( False, (cv.hasRequiredAttributes()) )
+    cv.setBiologicalQualifierType(libsbml.BQB_IS)
+    self.assertEqual( False, (cv.hasRequiredAttributes()) )
+    cv.addResource("ggg")
+    self.assertEqual( True, (cv.hasRequiredAttributes()) )
+    cv = None
+    pass  
+
+  def test_Validation_Date1(self):
+    date = libsbml.Date(200,12,30,12,15,45,1,2,0)
+    self.assert_( date != None )
+    self.assertEqual( False, (date.representsValidDate()) )
+    date = None
+    pass  
+
+  def test_Validation_Date2(self):
+    date = libsbml.Date(2007,14,30,12,15,45,1,2,0)
+    self.assert_( date != None )
+    self.assertEqual( False, (date.representsValidDate()) )
+    date = None
+    pass  
+
+  def test_Validation_Date3(self):
+    date = libsbml.Date("Jan 12")
+    self.assert_( date != None )
+    self.assertEqual( False, (date.representsValidDate()) )
+    date = None
+    pass  
+
+  def test_Validation_Date4(self):
+    date = libsbml.Date(2007,12,30,12,15,45,1,2,0)
+    self.assert_( date != None )
+    self.assertEqual( True, date.representsValidDate() )
+    date = None
+    pass  
+
+  def test_Validation_Date_Default(self):
+    date1 = libsbml.Date()
+    date2 = libsbml.Date("")
+    self.assert_( date1.getYear() == date2.getYear() )
+    self.assert_( date1.getMonth() == date2.getMonth() )
+    self.assert_( date1.getDay() == date2.getDay() )
+    self.assert_( date1.getHour() == date2.getHour() )
+    self.assert_( date1.getMinute() == date2.getMinute() )
+    self.assert_( date1.getSecond() == date2.getSecond() )
+    self.assert_( date1.getSignOffset() == date2.getSignOffset() )
+    self.assert_( date1.getHoursOffset() == date2.getHoursOffset() )
+    self.assert_( date1.getMinutesOffset() == date2.getMinutesOffset() )
+    date1 = None
+    date2 = None
+    pass  
+
+  def test_Validation_ModelCreator(self):
+    mc = libsbml.ModelCreator()
+    self.assert_( mc != None )
+    self.assertEqual( False, (mc.hasRequiredAttributes()) )
+    mc.setEmail("k123")
+    self.assertEqual( False, (mc.hasRequiredAttributes()) )
+    mc.setFamilyName("Keating")
+    self.assertEqual( False, (mc.hasRequiredAttributes()) )
+    mc.setGivenName("Sarah")
+    self.assertEqual( True, mc.hasRequiredAttributes() )
+    mc = None
+    pass  
+
+  def test_Validation_ModelHistory1(self):
+    mh = libsbml.ModelHistory()
+    self.assert_( mh != None )
+    self.assertEqual( False, (mh.hasRequiredAttributes()) )
+    date = libsbml.Date(2007,12,30,12,15,45,1,2,0)
+    mh.setCreatedDate(date)
+    self.assertEqual( False, (mh.hasRequiredAttributes()) )
+    mh.setModifiedDate(date)
+    self.assertEqual( False, (mh.hasRequiredAttributes()) )
+    mc = libsbml.ModelCreator()
+    mc.setFamilyName("Keating")
+    mc.setGivenName("Sarah")
+    mh.addCreator(mc)
+    self.assertEqual( True, mh.hasRequiredAttributes() )
+    mh = None
+    pass  
+
+  def test_Validation_ModelHistory2(self):
+    mh = libsbml.ModelHistory()
+    self.assert_( mh != None )
+    self.assertEqual( False, (mh.hasRequiredAttributes()) )
+    date = libsbml.Date(200,12,30,12,15,45,1,2,0)
+    mh.setCreatedDate(date)
+    self.assertEqual( False, (mh.hasRequiredAttributes()) )
+    mh.setModifiedDate(date)
+    self.assertEqual( False, (mh.hasRequiredAttributes()) )
+    mc = libsbml.ModelCreator()
+    mc.setFamilyName("Keating")
+    mc.setGivenName("Sarah")
+    mh.addCreator(mc)
+    self.assertEqual( False, (mh.hasRequiredAttributes()) )
+    mh = None
+    pass  
+
+  def test_Validation_ModelHistory3(self):
+    mh = libsbml.ModelHistory()
+    self.assert_( mh != None )
+    self.assertEqual( False, (mh.hasRequiredAttributes()) )
+    date = libsbml.Date(2007,12,30,12,15,45,1,2,0)
+    mh.setCreatedDate(date)
+    self.assertEqual( False, (mh.hasRequiredAttributes()) )
+    mh.setModifiedDate(date)
+    self.assertEqual( False, (mh.hasRequiredAttributes()) )
+    mc = libsbml.ModelCreator()
+    mc.setFamilyName("Keating")
+    mh.addCreator(mc)
+    self.assertEqual( False, (mh.hasRequiredAttributes()) )
+    mh = None
+    pass  
+
+def suite():
+  suite = unittest.TestSuite()
+  suite.addTest(unittest.makeSuite(TestValidation))
+
+  return suite
+
+if __name__ == "__main__":
+  if unittest.TextTestRunner(verbosity=1).run(suite()).wasSuccessful() :
+    sys.exit(0)
+  else:
+    sys.exit(1)

Modified: trunk/libsbml/src/bindings/ruby/test/annotation/TestRDFAnnotationC.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/annotation/TestRDFAnnotationC.rb	2011-01-26 16:10:23 UTC (rev 12704)
+++ trunk/libsbml/src/bindings/ruby/test/annotation/TestRDFAnnotationC.rb	2011-01-26 16:38:13 UTC (rev 12705)
@@ -1,217 +1,226 @@
-# @file    TestRDFAnnotationC.rb
-# @brief   RDFAnnotation parser unit tests
-#
-# @author  Akiya Jouraku (Ruby conversion)
-# @author  Sarah Keating 
-#
-# $Id$
-# $HeadURL$
-#
-# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
-#
-# DO NOT EDIT THIS FILE.
-#
-# This file was generated automatically by converting the file located at
-# src/annotation/test/TestRDFAnnotationC.c
-# using the conversion program dev/utilities/translateTests/translateTests.pl.
-# Any changes made here will be lost the next time the file is regenerated.
-#
-# -----------------------------------------------------------------------------
-# This file is part of libSBML.  Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
-# Copyright 2005-2010 California Institute of Technology.
-# Copyright 2002-2005 California Institute of Technology and
-#                     Japan Science and Technology Corporation.
-# 
-# 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/libsbml/license.html
-# -----------------------------------------------------------------------------
-require 'test/unit'
-require 'libSBML'
-
-class TestRDFAnnotationC < Test::Unit::TestCase
-
-  def setup
-    filename = "../../annotation/test/test-data/annotation.xml"
-    @@d = LibSBML::readSBML(filename)
-    @@m = @@d.getModel()
-  end
-
-  def teardown
-    @@d = nil
-  end
-
-  def test_RDFAnnotation_C_delete
-    obj = @@m.getCompartment(0)
-    node = LibSBML::RDFAnnotationParser.parseCVTerms(obj)
-    n1 = LibSBML::RDFAnnotationParser.deleteRDFAnnotation(node)
-    assert( n1.getNumChildren() == 0 )
-    assert ((  "annotation" == n1.getName() ))
-    node = nil
-  end
-
-  def test_RDFAnnotation_C_getModelHistory
-    assert( !( @@m == nil) )
-    history = @@m.getModelHistory()
-    assert( history != nil )
-    mc = history.getCreator(0)
-    assert ((  "Le Novere" == mc.getFamilyName() ))
-    assert ((  "Nicolas" == mc.getGivenName() ))
-    assert ((  "le...@eb..." == mc.getEmail() ))
-    assert ((  "EMBL-EBI" == mc.getOrganisation() ))
-    date = history.getCreatedDate()
-    assert( date.getYear() == 2005 )
-    assert( date.getMonth() == 2 )
-    assert( date.getDay() == 2 )
-    assert( date.getHour() == 14 )
-    assert( date.getMinute() == 56 )
-    assert( date.getSecond() == 11 )
-    assert( date.getSignOffset() == 0 )
-    assert( date.getHoursOffset() == 0 )
-    assert( date.getMinutesOffset() == 0 )
-    assert ((  "2005-02-02T14:56:11Z" == date.getDateAsString() ))
-    date = history.getModifiedDate()
-    assert( date.getYear() == 2006 )
-    assert( date.getMonth() == 5 )
-    assert( date.getDay() == 30 )
-    assert( date.getHour() == 10 )
-    assert( date.getMinute() == 46 )
-    assert( date.getSecond() == 2 )
-    assert( date.getSignOffset() == 0 )
-    assert( date.getHoursOffset() == 0 )
-    assert( date.getMinutesOffset() == 0 )
-    assert ((  "2006-05-30T10:46:02Z" == date.getDateAsString() ))
-  end
-
-  def test_RDFAnnotation_C_parseCVTerms
-    obj = @@m.getCompartment(0)
-    node = LibSBML::RDFAnnotationParser.parseCVTerms(obj)
-    assert( node.getNumChildren() == 1 )
-    rdf = node.getChild(0)
-    assert ((  "RDF" == rdf.getName() ))
-    assert ((  "rdf" == rdf.getPrefix() ))
-    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() ))
-    assert( rdf.getNumChildren() == 1 )
-    desc = rdf.getChild(0)
-    assert ((  "Description" == desc.getName() ))
-    assert ((  "rdf" == desc.getPrefix() ))
-    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() ))
-    assert( desc.getNumChildren() == 1 )
-    is1 = desc.getChild(0)
-    assert ((  "is" == is1.getName() ))
-    assert ((  "bqbiol" == is1.getPrefix() ))
-    assert( is1.getNumChildren() == 1 )
-    bag = is1.getChild(0)
-    assert ((  "Bag" == bag.getName() ))
-    assert ((  "rdf" == bag.getPrefix() ))
-    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == bag.getURI() ))
-    assert( bag.getNumChildren() == 4 )
-    li = bag.getChild(0)
-    assert ((  "li" == li.getName() ))
-    assert ((  "rdf" == li.getPrefix() ))
-    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() ))
-    assert( li.getNumChildren() == 0 )
-    li1 = bag.getChild(1)
-    assert ((  "li" == li1.getName() ))
-    assert ((  "rdf" == li1.getPrefix() ))
-    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li1.getURI() ))
-    assert( li1.getNumChildren() == 0 )
-    li2 = bag.getChild(2)
-    assert ((  "li" == li2.getName() ))
-    assert ((  "rdf" == li2.getPrefix() ))
-    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li2.getURI() ))
-    assert( li2.getNumChildren() == 0 )
-    li3 = bag.getChild(3)
-    assert ((  "li" == li3.getName() ))
-    assert ((  "rdf" == li3.getPrefix() ))
-    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li3.getURI() ))
-    assert( li3.getNumChildren() == 0 )
-    node = nil
-  end
-
-  def test_RDFAnnotation_C_parseModelHistory
-    node = LibSBML::RDFAnnotationParser.parseModelHistory(@@m)
-    assert( node.getNumChildren() == 1 )
-    rdf = node.getChild(0)
-    assert ((  "RDF" == rdf.getName() ))
-    assert ((  "rdf" == rdf.getPrefix() ))
-    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() ))
-    assert( rdf.getNumChildren() == 1 )
-    desc = rdf.getChild(0)
-    assert ((  "Description" == desc.getName() ))
-    assert ((  "rdf" == desc.getPrefix() ))
-    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() ))
-    assert( desc.getNumChildren() == 3 )
-    creator = desc.getChild(0)
-    assert ((  "creator" == creator.getName() ))
-    assert ((  "dc" == creator.getPrefix() ))
-    assert ((  "http://purl.org/dc/elements/1.1/" == creator.getURI() ))
-    assert( creator.getNumChildren() == 1 )
-    bag = creator.getChild(0)
-    assert ((  "Bag" == bag.getName() ))
-    assert ((  "rdf" == bag.getPrefix() ))
-    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == bag.getURI() ))
-    assert( bag.getNumChildren() == 1 )
-    li = bag.getChild(0)
-    assert ((  "li" == li.getName() ))
-    assert ((  "rdf" == li.getPrefix() ))
-    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() ))
-    assert( li.getNumChildren() == 3 )
-    n = li.getChild(0)
-    assert ((  "N" == n.getName() ))
-    assert ((  "vCard" == n.getPrefix() ))
-    assert ((  "http://www.w3.org/2001/vcard-rdf/3.0#" == n.getURI() ))
-    assert( n.getNumChildren() == 2 )
-    family = n.getChild(0)
-    assert ((  "Family" == family.getName() ))
-    assert ((  "vCard" == family.getPrefix() ))
-    assert ((  "http://www.w3.org/2001/vcard-rdf/3.0#" == family.getURI() ))
-    assert( family.getNumChildren() == 1 )
-    given = n.getChild(1)
-    assert ((  "Given" == given.getName() ))
-    assert ((  "vCard" == given.getPrefix() ))
-    assert ((  "http://www.w3.org/2001/vcard-rdf/3.0#" == given.getURI() ))
-    assert( given.getNumChildren() == 1 )
-    email = li.getChild(1)
-    assert ((  "EMAIL" == email.getName() ))
-    assert ((  "vCard" == email.getPrefix() ))
-    assert ((  "http://www.w3.org/2001/vcard-rdf/3.0#" == email.getURI() ))
-    assert( email.getNumChildren() == 1 )
-    org = li.getChild(2)
-    assert ((  "ORG" == org.getName() ))
-    assert ((  "vCard" == org.getPrefix() ))
-    assert ((  "http://www.w3.org/2001/vcard-rdf/3.0#" == org.getURI() ))
-    assert( org.getNumChildren() == 1 )
-    orgname = org.getChild(0)
-    assert ((  "Orgname" == orgname.getName() ))
-    assert ((  "vCard" == orgname.getPrefix() ))
-    assert ((  "http://www.w3.org/2001/vcard-rdf/3.0#" == orgname.getURI() ))
-    assert( orgname.getNumChildren() == 1 )
-    created = desc.getChild(1)
-    assert ((  "created" == created.getName() ))
-    assert ((  "dcterms" == created.getPrefix() ))
-    assert ((  "http://purl.org/dc/terms/" == created.getURI() ))
-    assert( created.getNumChildren() == 1 )
-    cr_date = created.getChild(0)
-    assert ((  "W3CDTF" == cr_date.getName() ))
-    assert ((  "dcterms" == cr_date.getPrefix() ))
-    assert ((  "http://purl.org/dc/terms/" == cr_date.getURI() ))
-    assert( cr_date.getNumChildren() == 1 )
-    modified = desc.getChild(2)
-    assert ((  "modified" == modified.getName() ))
-    assert ((  "dcterms" == modified.getPrefix() ))
-    assert ((  "http://purl.org/dc/terms/" == modified.getURI() ))
-    assert( modified.getNumChildren() == 1 )
-    mo_date = created.getChild(0)
-    assert ((  "W3CDTF" == mo_date.getName() ))
-    assert ((  "dcterms" == mo_date.getPrefix() ))
-    assert ((  "http://purl.org/dc/terms/" == mo_date.getURI() ))
-    assert( mo_date.getNumChildren() == 1 )
-    node = nil
-  end
-
-end
+# @file    TestRDFAnnotationC.rb
+# @brief   RDFAnnotation parser unit tests
+#
+# @author  Akiya Jouraku (Ruby conversion)
+# @author  Sarah Keating 
+#
+# $Id$
+# $HeadURL$
+#
+# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
+#
+# DO NOT EDIT THIS FILE.
+#
+# This file was generated automatically by converting the file located at
+# src/annotation/test/TestRDFAnnotationC.c
+# using the conversion program dev/utilities/translateTests/translateTests.pl.
+# Any changes made here will be lost the next time the file is regenerated.
+#
+# -----------------------------------------------------------------------------
+# This file is part of libSBML.  Please visit http://sbml.org for more
+# information about SBML, and the latest version of libSBML.
+#
+# Copyright 2005-2010 California Institute of Technology.
+# Copyright 2002-2005 California Institute of Technology and
+#                     Japan Science and Technology Corporation.
+# 
+# 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/libsbml/license.html
+# -----------------------------------------------------------------------------
+require 'test/unit'
+require 'libSBML'
+
+class TestRDFAnnotationC < Test::Unit::TestCase
+
+  def setup
+    filename = "../../annotation/test/test-data/annotation.xml"
+    @@d = LibSBML::readSBML(filename)
+    @@m = @@d.getModel()
+  end
+
+  def teardown
+    @@d = nil
+  end
+
+  def test_RDFAnnotation_C_accessWithNULL
+    assert( LibSBML::RDFAnnotationParser.createCVTerms(nil) == nil )
+    assert( LibSBML::RDFAnnotationParser.createRDFDescription(nil) == nil )
+    assert( LibSBML::RDFAnnotationParser.deleteRDFAnnotation(nil) == nil )
+    assert( LibSBML::RDFAnnotationParser.parseCVTerms(nil) == nil )
+    assert( LibSBML::RDFAnnotationParser.parseModelHistory(nil) == nil )
+    LibSBML::RDFAnnotationParser.parseRDFAnnotation(nil,nil)
+  end
+
+  def test_RDFAnnotation_C_delete
+    obj = @@m.getCompartment(0)
+    node = LibSBML::RDFAnnotationParser.parseCVTerms(obj)
+    n1 = LibSBML::RDFAnnotationParser.deleteRDFAnnotation(node)
+    assert( n1.getNumChildren() == 0 )
+    assert ((  "annotation" == n1.getName() ))
+    node = nil
+  end
+
+  def test_RDFAnnotation_C_getModelHistory
+    assert( !( @@m == nil) )
+    history = @@m.getModelHistory()
+    assert( history != nil )
+    mc = history.getCreator(0)
+    assert ((  "Le Novere" == mc.getFamilyName() ))
+    assert ((  "Nicolas" == mc.getGivenName() ))
+    assert ((  "le...@eb..." == mc.getEmail() ))
+    assert ((  "EMBL-EBI" == mc.getOrganisation() ))
+    date = history.getCreatedDate()
+    assert( date.getYear() == 2005 )
+    assert( date.getMonth() == 2 )
+    assert( date.getDay() == 2 )
+    assert( date.getHour() == 14 )
+    assert( date.getMinute() == 56 )
+    assert( date.getSecond() == 11 )
+    assert( date.getSignOffset() == 0 )
+    assert( date.getHoursOffset() == 0 )
+    assert( date.getMinutesOffset() == 0 )
+    assert ((  "2005-02-02T14:56:11Z" == date.getDateAsString() ))
+    date = history.getModifiedDate()
+    assert( date.getYear() == 2006 )
+    assert( date.getMonth() == 5 )
+    assert( date.getDay() == 30 )
+    assert( date.getHour() == 10 )
+    assert( date.getMinute() == 46 )
+    assert( date.getSecond() == 2 )
+    assert( date.getSignOffset() == 0 )
+    assert( date.getHoursOffset() == 0 )
+    assert( date.getMinutesOffset() == 0 )
+    assert ((  "2006-05-30T10:46:02Z" == date.getDateAsString() ))
+  end
+
+  def test_RDFAnnotation_C_parseCVTerms
+    obj = @@m.getCompartment(0)
+    node = LibSBML::RDFAnnotationParser.parseCVTerms(obj)
+    assert( node.getNumChildren() == 1 )
+    rdf = node.getChild(0)
+    assert ((  "RDF" == rdf.getName() ))
+    assert ((  "rdf" == rdf.getPrefix() ))
+    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() ))
+    assert( rdf.getNumChildren() == 1 )
+    desc = rdf.getChild(0)
+    assert ((  "Description" == desc.getName() ))
+    assert ((  "rdf" == desc.getPrefix() ))
+    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() ))
+    assert( desc.getNumChildren() == 1 )
+    is1 = desc.getChild(0)
+    assert ((  "is" == is1.getName() ))
+    assert ((  "bqbiol" == is1.getPrefix() ))
+    assert( is1.getNumChildren() == 1 )
+    bag = is1.getChild(0)
+    assert ((  "Bag" == bag.getName() ))
+    assert ((  "rdf" == bag.getPrefix() ))
+    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == bag.getURI() ))
+    assert( bag.getNumChildren() == 4 )
+    li = bag.getChild(0)
+    assert ((  "li" == li.getName() ))
+    assert ((  "rdf" == li.getPrefix() ))
+    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() ))
+    assert( li.getNumChildren() == 0 )
+    li1 = bag.getChild(1)
+    assert ((  "li" == li1.getName() ))
+    assert ((  "rdf" == li1.getPrefix() ))
+    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li1.getURI() ))
+    assert( li1.getNumChildren() == 0 )
+    li2 = bag.getChild(2)
+    assert ((  "li" == li2.getName() ))
+    assert ((  "rdf" == li2.getPrefix() ))
+    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li2.getURI() ))
+    assert( li2.getNumChildren() == 0 )
+    li3 = bag.getChild(3)
+    assert ((  "li" == li3.getName() ))
+    assert ((  "rdf" == li3.getPrefix() ))
+    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li3.getURI() ))
+    assert( li3.getNumChildren() == 0 )
+    node = nil
+  end
+
+  def test_RDFAnnotation_C_parseModelHistory
+    node = LibSBML::RDFAnnotationParser.parseModelHistory(@@m)
+    assert( node.getNumChildren() == 1 )
+    rdf = node.getChild(0)
+    assert ((  "RDF" == rdf.getName() ))
+    assert ((  "rdf" == rdf.getPrefix() ))
+    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() ))
+    assert( rdf.getNumChildren() == 1 )
+    desc = rdf.getChild(0)
+    assert ((  "Description" == desc.getName() ))
+    assert ((  "rdf" == desc.getPrefix() ))
+    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() ))
+    assert( desc.getNumChildren() == 3 )
+    creator = desc.getChild(0)
+    assert ((  "creator" == creator.getName() ))
+    assert ((  "dc" == creator.getPrefix() ))
+    assert ((  "http://purl.org/dc/elements/1.1/" == creator.getURI() ))
+    assert( creator.getNumChildren() == 1 )
+    bag = creator.getChild(0)
+    assert ((  "Bag" == bag.getName() ))
+    assert ((  "rdf" == bag.getPrefix() ))
+    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == bag.getURI() ))
+    assert( bag.getNumChildren() == 1 )
+    li = bag.getChild(0)
+    assert ((  "li" == li.getName() ))
+    assert ((  "rdf" == li.getPrefix() ))
+    assert ((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() ))
+    assert( li.getNumChildren() == 3 )
+    n = li.getChild(0)
+    assert ((  "N" == n.getName() ))
+    assert ((  "vCard" == n.getPrefix() ))
+    assert ((  "http://www.w3.org/2001/vcard-rdf/3.0#" == n.getURI() ))
+    assert( n.getNumChildren() == 2 )
+    family = n.getChild(0)
+    assert ((  "Family" == family.getName() ))
+    assert ((  "vCard" == family.getPrefix() ))
+    assert ((  "http://www.w3.org/2001/vcard-rdf/3.0#" == family.getURI() ))
+    assert( family.getNumChildren() == 1 )
+    given = n.getChild(1)
+    assert ((  "Given" == given.getName() ))
+    assert ((  "vCard" == given.getPrefix() ))
+    assert ((  "http://www.w3.org/2001/vcard-rdf/3.0#" == given.getURI() ))
+    assert( given.getNumChildren() == 1 )
+    email = li.getChild(1)
+    assert ((  "EMAIL" == email.getName() ))
+    assert ((  "vCard" == email.getPrefix() ))
+    assert ((  "http://www.w3.org/2001/vcard-rdf/3.0#" == email.getURI() ))
+    assert( email.getNumChildren() == 1 )
+    org = li.getChild(2)
+    assert ((  "ORG" == org.getName() ))
+    assert ((  "vCard" == org.getPrefix() ))
+    assert ((  "http://www.w3.org/2001/vcard-rdf/3.0#" == org.getURI() ))
+    assert( org.getNumChildren() == 1 )
+    orgname = org.getChild(0)
+    assert ((  "Orgname" == orgname.getName() ))
+    assert ((  "vCard" == orgname.getPrefix() ))
+    assert ((  "http://www.w3.org/2001/vcard-rdf/3.0#" == orgname.getURI() ))
+    assert( orgname.getNumChildren() == 1 )
+    created = desc.getChild(1)
+    assert ((  "created" == created.getName() ))
+    assert ((  "dcterms" == created.getPrefix() ))
+    assert ((  "http://purl.org/dc/terms/" == created.getURI() ))
+    assert( created.getNumChildren() == 1 )
+    cr_date = created.getChild(0)
+    assert ((  "W3CDTF" == cr_date.getName() ))
+    assert ((  "dcterms" == cr_date.getPrefix() ))
+    assert ((  "http://purl.org/dc/terms/" == cr_date.getURI() ))
+    assert( cr_date.getNumChildren() == 1 )
+    modified = desc.getChild(2)
+    assert ((  "modified" == modified.getName() ))
+    assert ((  "dcterms" == modified.getPrefix() ))
+    assert ((  "http://purl.org/dc/terms/" == modified.getURI() ))
+    assert( modified.getNumChildren() == 1 )
+    mo_date = created.getChild(0)
+    assert ((  "W3CDTF" == mo_date.getName() ))
+    assert ((  "dcterms" == mo_date.getPrefix() ))
+    assert ((  "http://purl.org/dc/terms/" == mo_date.getURI() ))
+    assert( mo_date.getNumChildren() == 1 )
+    node = nil
+  end
+
+end

Modified: trunk/libsbml/src/bindings/ruby/test/annotation/TestValidation.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/annotation/TestValidation.rb	2011-01-26 16:10:23 UTC (rev 12704)
+++ trunk/libsbml/src/bindings/ruby/test/annotation/TestValidation.rb	2011-01-26 16:38:13 UTC (rev 12705)
@@ -1,155 +1,171 @@
-# @file    TestValidation.rb
-# @brief   Validation of Date ModelCreator and ModelHistory unit tests
-#
-# @author  Akiya Jouraku (Ruby conversion)
-# @author  Sarah Keating 
-#
-# $Id$
-# $HeadURL$
-#
-# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
-#
-# DO NOT EDIT THIS FILE.
-#
-# This file was generated automatically by converting the file located at
-# src/annotation/test/TestValidation.cpp
-# using the conversion program dev/utilities/translateTests/translateTests.pl.
-# Any changes made here will be lost the next time the file is regenerated.
-#
-# -----------------------------------------------------------------------------
-# This file is part of libSBML.  Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
-# Copyright 2005-2010 California Institute of Technology.
-# Copyright 2002-2005 California Institute of Technology and
-#                     Japan Science and Technology Corporation.
-# 
-# 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/libsbml/license.html
-# -----------------------------------------------------------------------------
-require 'test/unit'
-require 'libSBML'
-
-class TestValidation < Test::Unit::TestCase
-
-  def test_Validation_CVTerm1
-    cv = LibSBML::CVTerm.new()
-    assert( cv != nil )
-    assert_equal false, (cv.hasRequiredAttributes())
-    cv.setQualifierType(LibSBML::MODEL_QUALIFIER)
-    assert_equal false, (cv.hasRequiredAttributes())
-    cv.setModelQualifierType(LibSBML::BQM_IS)
-    assert_equal false, (cv.hasRequiredAttributes())
-    cv.addResource("ggg")
-    assert_equal true, (cv.hasRequiredAttributes())
-    cv = nil
-  end
-
-  def test_Validation_CVTerm2
-    cv = LibSBML::CVTerm.new()
-    assert( cv != nil )
-    assert_equal false, (cv.hasRequiredAttributes())
-    cv.setQualifierType(LibSBML::BIOLOGICAL_QUALIFIER)
-    assert_equal false, (cv.hasRequiredAttributes())
-    cv.setBiologicalQualifierType(LibSBML::BQB_IS)
-    assert_equal false, (cv.hasRequiredAttributes())
-    cv.addResource("ggg")
-    assert_equal true, (cv.hasRequiredAttributes())
-    cv = nil
-  end
-
-  def test_Validation_Date1
-    date = LibSBML::Date.new(200,12,30,12,15,45,1,2,0)
-    assert( date != nil )
-    assert_equal false, (date.representsValidDate())
-    date = nil
-  end
-
-  def test_Validation_Date2
-    date = LibSBML::Date.new(2007,14,30,12,15,45,1,2,0)
-    assert( date != nil )
-    assert_equal false, (date.representsValidDate())
-    date = nil
-  end
-
-  def test_Validation_Date3
-    date = LibSBML::Date.new("Jan 12")
-    assert( date != nil )
-    assert_equal false, (date.representsValidDate())
-    date = nil
-  end
-
-  def test_Validation_Date4
-    date = LibSBML::Date.new(2007,12,30,12,15,45,1,2,0)
-    assert( date != nil )
-    assert_equal true, date.representsValidDate()
-    date = nil
-  end
-
-  def test_Validation_ModelCreator
-    mc = LibSBML::ModelCreator.new()
-    assert( mc != nil )
-    assert_equal false, (mc.hasRequiredAttributes())
-    mc.setEmail("k123")
-    assert_equal false, (mc.hasRequiredAttributes())
-    mc.setFamilyName("Keating")
-    assert_equal false, (mc.hasRequiredAttributes())
-    mc.setGivenName("Sarah")
-    assert_equal true, mc.hasRequiredAttributes()
-    mc = nil
-  end
-
-  def test_Validation_ModelHistory1
-    mh = LibSBML::ModelHistory.new()
-    assert( mh != nil )
-    assert_equal false, (mh.hasRequiredAttributes())
-    date = LibSBML::Date.new(2007,12,30,12,15,45,1,2,0)
-    mh.setCreatedDate(date)
-    assert_equal false, (mh.hasRequiredAttributes())
-    mh.setModifiedDate(date)
-    assert_equal false, (mh.hasRequiredAttributes())
-    mc = LibSBML::ModelCreator.new()
-    mc.setFamilyName("Keating")
-    mc.setGivenName("Sarah")
-    mh.addCreator(mc)
-    assert_equal true, mh.hasRequiredAttributes()
-    mh = nil
-  end
-
-  def test_Validation_ModelHistory2
-    mh = LibSBML::ModelHistory.new()
-    assert( mh != nil )
-    assert_equal false, (mh.hasRequiredAttributes())
-    date = LibSBML::Date.new(200,12,30,12,15,45,1,2,0)
-    mh.setCreatedDate(date)
-    assert_equal false, (mh.hasRequiredAttributes())
-    mh.setModifiedDate(date)
-    assert_equal false, (mh.hasRequiredAttributes())
-    mc = LibSBML::ModelCreator.new()
-    mc.setFamilyName("Keating")
-    mc.setGivenName("Sarah")
-    mh.addCreator(mc)
-    assert_equal false, (mh.hasRequiredAttributes())
-    mh = nil
-  end
-
-  def test_Validation_ModelHistory3
-    mh = LibSBML::ModelHistory.new()
-    assert( mh != nil )
-    assert_equal false, (mh.hasRequiredAttributes())
-    date = LibSBML::Date.new(2007,12,30,12,15,45,1,2,0)
-    mh.setCreatedDate(date)
-    assert_equal false, (mh.hasRequiredAttributes())
-    mh.setModifiedDate(date)
-    assert_equal false, (mh.hasRequiredAttributes())
-    mc = LibSBML::ModelCreator.new()
-    mc.setFamilyName("Keating")
-    mh.addCreator(mc)
-    assert_equal false, (mh.hasRequiredAttributes())
-    mh = nil
-  end
-
-end
+# @file    TestValidation.rb
+# @brief   Validation of Date ModelCreator and ModelHistory unit tests
+#
+# @author  Akiya Jouraku (Ruby conversion)
+# @author  Sarah Keating 
+#
+# $Id$
+# $HeadURL$
+#
+# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
+#
+# DO NOT EDIT THIS FILE.
+#
+# This file was generated automatically by converting the file located at
+# src/annotation/test/TestValidation.cpp
+# using the conversion program dev/utilities/translateTests/translateTests.pl.
+# Any changes made here will be lost the next time the file is reg...
 
[truncated message content]

Revision: 12707
          http://sbml.svn.sourceforge.net/sbml/?rev=12707&view=rev
Author:   mhucka
Date:     2011-01-26 18:26:02 +0000 (Wed, 26 Jan 2011)

Log Message:
-----------
Added another common text fragment file.

Modified Paths:
--------------
    trunk/libsbml/docs/src/Makefile.in

Added Paths:
-----------
    trunk/libsbml/docs/src/common-text/cvterm-common-description-text.html

Modified: trunk/libsbml/docs/src/Makefile.in
===================================================================
--- trunk/libsbml/docs/src/Makefile.in	2011-01-26 18:24:53 UTC (rev 12706)
+++ trunk/libsbml/docs/src/Makefile.in	2011-01-26 18:26:02 UTC (rev 12707)
@@ -95,6 +95,7 @@
         common-text/comment-set-methods.html                 \
         common-text/compartment-size-recommendations.html    \
         common-text/compartment-size-restrictions.html       \
+	common-text/cvterm-common-description-text.html      \
         common-text/id-syntax.html                           \
         common-text/math-functions.html                      \
         common-text/math-precedence-table.html               \

Added: trunk/libsbml/docs/src/common-text/cvterm-common-description-text.html
===================================================================
--- trunk/libsbml/docs/src/common-text/cvterm-common-description-text.html	                        (rev 0)
+++ trunk/libsbml/docs/src/common-text/cvterm-common-description-text.html	2011-01-26 18:26:02 UTC (rev 12707)
@@ -0,0 +1,25 @@
+The RDF element used in the SBML format for referring to external
+entities is <code>&lt;rdf:Description&gt;</code>, with a
+<code>&lt;rdf:Bag&gt;</code> element inside of it containing one or
+more <code>&lt;rdf:li&gt;</code> elements.  The following template
+illustrates the structure:
+<DIV class="fragment">
+&lt;rdf:Description rdf:about=&quot;#<span style="border-bottom: 1px solid black">meta id</span>&quot;&gt;<br>
+&nbsp;&nbsp;<span style="background-color: #ddd; border-bottom: 2px dotted #888">HISTORY</span><br>
+&nbsp;&nbsp;&lt;<span style="background-color: #bbb">RELATION_ELEMENT</span>&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:Bag&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:li rdf:resource=&quot;<span style="background-color: #d0d0ee">resource URI</span>&quot; /&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #edd">...</span><br>
+&nbsp;&nbsp;&nbsp;&nbsp;&lt;/rdf:Bag&gt;<br>
+&nbsp;&nbsp;&lt;/<span style="background-color: #bbb">RELATION_ELEMENT</span>&gt;<br>
+&nbsp;&nbsp;<span style="background-color: #edd">...</span><br>
+&lt;/rdf:Description&gt;<br>
+</div>
+In the template above, the placeholder <span class="code"
+style="border-bottom: 1px solid black">meta id</span> stands for the
+element's meta identifier, which is a field available on all SBML
+components derived from the SBase base object class.  The <span
+style="border-bottom: 2px dotted #888">dotted</span> portions are
+optional, and the ellipses <span class="code" style="background-color:
+#edd">...</span> are placeholders for zero or more elements of the
+same form as the immediately preceding element.


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 12708
          http://sbml.svn.sourceforge.net/sbml/?rev=12708&view=rev
Author:   mhucka
Date:     2011-01-26 18:27:00 +0000 (Wed, 26 Jan 2011)

Log Message:
-----------
Massive documentation enhancement.

Modified Paths:
--------------
    trunk/libsbml/src/annotation/CVTerm.h

Modified: trunk/libsbml/src/annotation/CVTerm.h
===================================================================
--- trunk/libsbml/src/annotation/CVTerm.h	2011-01-26 18:26:02 UTC (rev 12707)
+++ trunk/libsbml/src/annotation/CVTerm.h	2011-01-26 18:27:00 UTC (rev 12708)
@@ -26,29 +26,133 @@
  *
  * @htmlinclude not-sbml-warning.html
  *
- * CVTerm is a libSBML construct used as part of the libSBML support for
- * annotations conforming to the guidelines specified by MIRIAM ("Minimum
- * Information Requested in the Annotation of biochemical Models").  The
- * general scheme is as follows.  A set of RDF-based annotations attached
- * to a given SBML <code>&lt;annotation&gt;</code> element are read by
- * RDFAnnotationParser and converted into a list of CVTerm objects.  Each
- * CVTerm object instance stores the following components of an annotation:
+ * The SBML Level&nbsp;2 and Level&nbsp;3 specifications define a simple
+ * format for annotating models when (a) referring to controlled vocabulary
+ * terms and database identifiers that define and describe biological and
+ * biochemical entities, and (b) describing the creator of a model and its
+ * modification history.  This SBML format is a concrete syntax that
+ * conforms to the guidelines of MIRIAM ("Minimum Information Requested in
+ * the Annotation of biochemical Models", <i>Nature Biotechnology</i>,
+ * vol. 23, no. 12, Dec. 2005).  The format uses a subset of W3C RDF (<a
+ * target="_blank" href="http://www.w3.org/RDF/">Resource Description
+ * Format</a>).  In order to help application developers work with
+ * annotations in this format, libSBML provides several helper classes that
+ * provide higher-level interfaces to the data elements; these classes
+ * include CVTerm, ModelCreator, ModelHistory, RDFAnnotationParser, and
+ * Date.
+ *
+ * @section annotation-parts Components of an SBML annotation
+ *
+ * The SBML annotation format consists of RDF-based content placed inside
+ * an <code>&lt;annotation&gt;</code> element attached to an SBML component
+ * such as Species, Compartment, etc.  The following template illustrates
+ * the different parts of SBML annotations in XML form:
  * 
+<div class="fragment">
+&lt;<span style="background-color: #bbb">SBML_ELEMENT</span> <span style="background-color: #d0eed0">+++</span> metaid=&quot;<span style="border-bottom: 1px solid black">meta id</span>&quot; <span style="background-color: #d0eed0">+++</span>&gt;<br>
+&nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
+&nbsp;&nbsp;&lt;annotation&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
+&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:dc="http://purl.org/dc/elements/1.1/"<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:dcterm="http://purl.org/dc/terms/"<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#"<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:bqmodel="http://biomodels.net/model-qualifiers/" &gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:Description rdf:about=&quot;#<span style="border-bottom: 1px solid black">meta id</span>&quot;&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #ddd; border-bottom: 2px dotted #888">HISTORY</span><br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;<span style="background-color: #bbb">RELATION_ELEMENT</span>&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:Bag&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:li rdf:resource=&quot;<span style="background-color: #d0d0ee">URI</span>&quot; /&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #edd">...</span><br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;/rdf:Bag&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;/<span style="background-color: #bbb">RELATION_ELEMENT</span>&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #edd">...</span><br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;/rdf:Description&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
+&nbsp;&nbsp;&nbsp;&nbsp;&lt;/rdf:RDF&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
+&nbsp;&nbsp;&lt;/annotation&gt;<br>
+&nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
+&lt;/<span style="background-color: #bbb">SBML_ELEMENT</span>&gt;<br>
+</div>
+ * 
+ * In the template above, the placeholder
+ * <span class="code" style="background-color: #bbb">SBML_ELEMENT</span> stands for
+ * the XML tag name of an SBML model component (e.g., <code>model</code>,
+ * <code>reaction</code>, etc.) and the placeholder 
+ * <span class="code" style="border-bottom: 1px solid black">meta id</span>
+ * stands for the element's meta identifier, which is a field available
+ * on all SBML components derived from the SBase base object class.
+ * The <span style="border-bottom: 2px dotted #888">dotted</span>
+ * portions are optional, the symbol
+ * <span class="code" style="background-color: #d0eed0">+++</span> is a placeholder
+ * for either no content or valid XML content that is not defined by
+ * the annotation scheme, and the ellipses
+ * <span class="code" style="background-color: #edd">...</span>
+ * are placeholders for zero or more elements of the same form as the
+ * immediately preceding element.  The optional content
+ * <span class="code" style="background-color: #ddd; border-bottom: 2px dotted #888">HISTORY</span>
+ * is a creation and modification history; in libSBML, this is stored
+ * using ModelHistory objects.
+ *
+ * The placeholder <span class="code" style="background-color: #bbb">RELATION_ELEMENT</span>
+ * refers to a BioModels.net qualifier element name.  This is an element in
+ * either the XML namespace
+ * <code>"http://biomodels.net/model-qualifiers"</code> (for model
+ * qualifiers) or <code>"http://biomodels.net/biology-qualifiers"</code>
+ * (for biological qualifier).  The <span class="code" style="background-color: #d0d0ee">URI</span>
+ * is a required data value that uniquely identifies a resource and
+ * data within that resource to which the annotation refers.  (Since
+ * a URI is only a label, not an address, applications will often
+ * want a means of looking up the resource to which the URI refers.
+ * Providing the facilities for doing this is the purpose of
+ * <a target="_blank" href="http://biomodels.net/miriam">MIRIAM Resources</a>.)
+ *
+ * The relation-resource pairs above are the "controlled vocabulary" terms
+ * that which CVTerm is designed to store and manipulate.  The next section
+ * describes these parts in more detail.  For more information about
+ * SBML annotations in general, please refer to Section&nbsp;6 in the
+ * SBML Level&nbsp;2 (Versions 2&ndash;4) or Level&nbsp;3 specification
+ * documents.
+ * 
+ *
+ * @section cvterm-parts The parts of a CVTerm
+ * 
+ * Annotations that refer to controlled vocabularies are managed in libSBML
+ * using CVTerm objects.  A set of RDF-based annotations attached to a
+ * given SBML <code>&lt;annotation&gt;</code> element are read by
+ * RDFAnnotationParser and converted into a list of these CVTerm objects.
+ * Each CVTerm object instance stores the following components of an
+ * annotation:
+ * 
  * <ul>
- * <li>The qualifier, which can be a MIRIAM "biological qualifier", a
- * "model qualifier", or an unknown qualifier (as far as the CVTerm class
- * is concerned).  Qualifiers are used in MIRIAM to indicate the nature of
- * the relationship between the object being annotated and the resource.
- * In CVTerm, the qualifiers can be manipulated using the methods
- * CVTerm::getQualifierType(),
- * CVTerm::setQualifierType(@if java int type@endif),
- * and related methods.
+ *
+ * <li>The @em qualifier, which can be a BioModels.net "biological
+ * qualifier", a BioModels.net "model qualifier", or an unknown qualifier
+ * (as far as the CVTerm class is concerned).  Qualifiers are used in
+ * MIRIAM to indicate the nature of the relationship between the object
+ * being annotated and the resource.  In CVTerm, the qualifiers can be
+ * manipulated using the methods CVTerm::getQualifierType(),
+ * CVTerm::setQualifierType(@if java int type@endif), and related methods.
  * 
- * <li>The resource, represent by a URI (note: not a URL).  In CVTerm, the
+ * <li>The @em resource, represented by a URI (which, we must remind
+ * developers, is not the same as a URL).  In the CVTerm class, the
  * resource component can be manipulated using the methods
- * CVTerm::addResource(@if java String resource@endif)
- * and CVTerm::removeResource(@if java String resource@endif).
+ * CVTerm::addResource(@if java String resource@endif) and
+ * CVTerm::removeResource(@if java String resource@endif).
+ *
  * </ul>
+ *
+ * Note that a CVTerm contains a single qualifier, but possibly more than
+ * one resource.  This corresponds to the possibility of an annotation
+ * pointing to multiple resources yet having the same BioModels.net
+ * qualifier.  The CVTerm object class supports this by supporting a list
+ * of resources.
+ *
+ * Detailed explanations of the qualifiers defined by BioModels.net can be
+ * found at <a target="_blank"
+ * href="http://biomodels.net/qualifiers">http://biomodels.net/qualifiers</a>.
  */
 
 #ifndef CVTerm_h
@@ -114,17 +218,43 @@
 public:
 
   /**
-   * Creates a new CVTerm, optionally with the given @if clike #QualifierType_t@endif@if java qualifier type code@endif value
+   * Creates an empty CVTerm, optionally with the given
+   * @if clike #QualifierType_t@endif@if java qualifier type code@endif value
    * @p type.
    *
-   * The possible qualifier types are @link QualifierType_t#MODEL_QUALIFIER MODEL_QUALIFIER@endlink 
-   * and @link QualifierType_t#BIOLOGICAL_QUALIFIER BIOLOGICAL_QUALIFIER@endlink.  If an explicit
-   * value for @p type is not given, this method defaults to using
-   * @link QualifierType_t#UNKNOWN_QUALIFIER UNKNOWN_QUALIFIER@endlink.  The
-   * @if clike #QualifierType_t@endif@if java qualifier type code@endif type
-   * value can be set later using the CVTerm::setQualifierType(@if java int type@endif)
-   * method.
+   * The SBML Level&nbsp;2 and Level&nbsp;3 specifications define a simple
+   * format for annotating models when (a) referring to controlled
+   * vocabulary terms and database identifiers that define and describe
+   * biological and biochemical entities, and (b) describing the creator of
+   * a model and its modification history.  The annotation content is
+   * stored in <code>&lt;annotation&gt;</code> elements attached to
+   * individual SBML elements.  The format for storing the content inside
+   * SBML <code>&lt;annotation&gt;</code> elements is a subset of W3C RDF
+   * (<a target="_blank" href="http://www.w3.org/RDF/">Resource Description
+   * Format</a>) expressed in XML.  The CVTerm class provides a programming
+   * interface for working directly with controlled vocabulary term ("CV
+   * term") objects without having to deal directly with the XML form.
+   * When libSBML reads in an SBML model containing RDF annotations, it
+   * parses those annotations into a list of CVTerm objects, and when
+   * writing a model, it parses the CVTerm objects back into the
+   * appropriate SBML <code>&lt;annotation&gt;</code> structure.
    *
+   * This method creates an empty CVTerm object.  The possible qualifier
+   * types usable as values of @p type are @link
+   * QualifierType_t#MODEL_QUALIFIER MODEL_QUALIFIER@endlink and @link
+   * QualifierType_t#BIOLOGICAL_QUALIFIER BIOLOGICAL_QUALIFIER@endlink.  If
+   * an explicit value for @p type is not given, this method defaults to
+   * using @link QualifierType_t#UNKNOWN_QUALIFIER
+   * UNKNOWN_QUALIFIER@endlink.  The @if clike #QualifierType_t@endif@if
+   * java qualifier type code@endif type value can be set later using the
+   * CVTerm::setQualifierType(@if java int type@endif) method.
+   *
+   * Different BioModels.net qualifier elements encode different types of
+   * relationships.  Please refer to the SBML specification or the <a
+   * target="_blank" href="http://biomodels.net/qualifiers/">BioModels.net
+   * qualifiers web page</a> for an explanation of the meaning of these
+   * different qualifiers.
+   *
    * @param type a @if clike #QualifierType_t@endif@if java qualifier type code@endif value
    *
    * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
@@ -135,14 +265,32 @@
   /**
    * Create a new CVTerm from the given XMLNode.
    *
-   * In libSBML, RDF annotations on a model component are stored as a list
-   * of CVTerm ("controlled vocabulary term") objects.  This allows the
-   * user to interact with the CVTerm objects directly.  When LibSBML reads
-   * in a model containing RDFAnnotation, it parses them into a list of
-   * CVTerm objects, and when writing a model, it parses the CVTerm objects
-   * into the appropriate SBML <code>&lt;annotation&gt;</code> structure.
+   * The SBML Level&nbsp;2 and Level&nbsp;3 specifications define a simple
+   * format for annotating models when (a) referring to controlled
+   * vocabulary terms and database identifiers that define and describe
+   * biological and biochemical entities, and (b) describing the creator of
+   * a model and its modification history.  The annotation content is
+   * stored in <code>&lt;annotation&gt;</code> elements attached to
+   * individual SBML elements.  The format for storing the content inside
+   * SBML <code>&lt;annotation&gt;</code> elements is a subset of W3C RDF
+   * (<a target="_blank" href="http://www.w3.org/RDF/">Resource Description
+   * Format</a>) expressed in XML.  The CVTerm class provides a programming
+   * interface for working directly with controlled vocabulary term ("CV
+   * term") objects without having to deal directly with the XML form.
+   * When libSBML reads in an SBML model containing RDF annotations, it
+   * parses those annotations into a list of CVTerm objects, and when
+   * writing a model, it parses the CVTerm objects back into the
+   * appropriate SBML <code>&lt;annotation&gt;</code> structure.
    * 
-   * This method creates a CVTerm from the XMLNode object supplied.
+   * This method creates a CVTerm object from the XMLNode object @p node.
+   * Recall that XMLNode is a node in an XML tree of elements, and each
+   * such element can be placed in a namespace.  This constructor looks for
+   * the element to be in the XML namespaces
+   * <code>"http://biomodels.net/model-qualifiers"</code> (for
+   * model qualifiers) and
+   * <code>"http://biomodels.net/biology-qualifiers"</code> (for
+   * biological qualifier), and if they are, creates CVTerm objects for
+   * the result.
    *
    * @param node an %XMLNode representing a CVTerm.
    *
@@ -159,7 +307,7 @@
 
 
   /**
-   * Copy constructor; creates a copy of a CVTerm.
+   * Copy constructor; creates a copy of a CVTerm object.
    * 
    * @param orig the CVTerm instance to copy.
    */
@@ -182,10 +330,38 @@
 
   /**
    * Returns the qualifier type code for this CVTerm object.
+   *
+   * @htmlinclude cvterm-common-description-text.html
+   *
+   * The placeholder <span class="code" style="background-color:
+   * #bbb">RELATION_ELEMENT</span> refers to a BioModels.net qualifier
+   * element name.  This is an element in either the XML namespace
+   * <code>"http://biomodels.net/model-qualifiers"</code> (for model
+   * qualifiers) or <code>"http://biomodels.net/biology-qualifiers"</code>
+   * (for biological qualifier).  The present method returns a code
+   * identifying which one of these two relationship namespaces is being
+   * used; any other qualifier in libSBML is considered unknown (as far as
+   * the CVTerm class is concerned).  Consequently, this method will return
+   * one of the following values:
    * 
+   * @li @link QualifierType_t#MODEL_QUALIFIER MODEL_QUALIFIER@endlink
+   * @li @link QualifierType_t#BIOLOGICAL_QUALIFIER BIOLOGICAL_QUALIFIER@endlink
+   * @li @link QualifierType_t#UNKNOWN_QUALIFIER UNKNOWN_QUALIFIER@endlink
+   *
+   * The specific relationship of this CVTerm to the enclosing SBML object
+   * can be determined using the CVTerm methods such as
+   * getModelQualifierType() and getBiologicalQualifierType().  Callers
+   * will typically want to use the present method to find out which one of
+   * the @em other two methods to call to find out the specific
+   * relationship.
+   *
    * @return the @if clike #QualifierType_t@endif@if java qualifier type code@endif value of this object or
    * @link QualifierType_t#UNKNOWN_QUALIFIER UNKNOWN_QUALIFIER@endlink
    * (the default).
+   *
+   * @see getResources()
+   * @see getModelQualifierType()
+   * @see getBiologicalQualifierType()
    */
   QualifierType_t getQualifierType();
 
@@ -193,6 +369,28 @@
   /**
    * Returns the model qualifier type code for this CVTerm object.
    * 
+   * @htmlinclude cvterm-common-description-text.html
+   *
+   * The placeholder <span class="code" style="background-color:
+   * #bbb">RELATION_ELEMENT</span> refers to a BioModels.net qualifier
+   * element name.  This is an element in either the XML namespace
+   * <code>"http://biomodels.net/model-qualifiers"</code> (for model
+   * qualifiers) or <code>"http://biomodels.net/biology-qualifiers"</code>
+   * (for biological qualifier).  Callers will typically use
+   * getQualifierType() to find out the type of qualifier relevant to this
+   * particular CVTerm object, then if it is a @em model qualifier, use the
+   * present method to determine the specific qualifier.  The set of known
+   * model qualifiers is, at the time of this libSBML release, the
+   * following:
+   *
+   * @li @link ModelQualifierType_t#BQM_IS BQM_IS@endlink
+   * @li @link ModelQualifierType_t#BQM_IS_DESCRIBED_BY BQM_IS_DESCRIBED_BY@endlink
+   * @li @link ModelQualifierType_t#BQM_IS_DERIVED_FROM BQM_IS_DERIVED_FROM@endlink
+   *
+   * Any other BioModels.net qualifier found in the model is considered
+   * unknown by libSBML and reported as
+   * @link ModelQualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@endlink.
+   *
    * @return the @if clike #ModelQualifierType_t@endif@if java model qualifier type code@endif value of this object or
    * @link ModelQualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@endlink
    * (the default).
@@ -203,6 +401,37 @@
   /**
    * Returns the biological qualifier type code for this CVTerm object.
    * 
+   * @htmlinclude cvterm-common-description-text.html
+   *
+   * The placeholder <span class="code" style="background-color:
+   * #bbb">RELATION_ELEMENT</span> refers to a BioModels.net qualifier
+   * element name.  This is an element in either the XML namespace
+   * <code>"http://biomodels.net/model-qualifiers"</code> (for model
+   * qualifiers) or <code>"http://biomodels.net/biology-qualifiers"</code>
+   * (for biological qualifier).  Callers will typically use
+   * getQualifierType() to find out the type of qualifier relevant to this
+   * particular CVTerm object, then if it is a @em biological qualifier,
+   * use the present method to determine the specific qualifier.  The set
+   * of known biological qualifiers is, at the time of this libSBML
+   * release, the following:
+   *
+   * @li @link BiolQualifierType_t#BQB_IS BQB_IS@endlink
+   * @li @link BiolQualifierType_t#BQB_HAS_PART BQB_HAS_PART@endlink
+   * @li @link BiolQualifierType_t#BQB_IS_PART_OF BQB_IS_PART_OF@endlink
+   * @li @link BiolQualifierType_t#BQB_IS_VERSION_OF BQB_IS_VERSION_OF@endlink
+   * @li @link BiolQualifierType_t#BQB_HAS_VERSION BQB_HAS_VERSION@endlink
+   * @li @link BiolQualifierType_t#BQB_IS_HOMOLOG_TO BQB_IS_HOMOLOG_TO@endlink
+   * @li @link BiolQualifierType_t#BQB_IS_DESCRIBED_BY BQB_IS_DESCRIBED_BY@endlink
+   * @li @link BiolQualifierType_t#BQB_IS_ENCODED_BY BQB_IS_ENCODED_BY@endlink
+   * @li @link BiolQualifierType_t#BQB_ENCODES BQB_ENCODES@endlink
+   * @li @link BiolQualifierType_t#BQB_OCCURS_IN BQB_OCCURS_IN@endlink
+   * @li @link BiolQualifierType_t#BQB_HAS_PROPERTY BQB_HAS_PROPERTY@endlink
+   * @li @link BiolQualifierType_t#BQB_IS_PROPERTY_OF BQB_IS_PROPERTY_OF@endlink
+   *
+   * Any other BioModels.net qualifier found in the model is considered
+   * unknown by libSBML and reported as
+   * @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink.
+   *
    * @return the @if clike #BiolQualifierType_t@endif@if java biology qualifier type code@endif value of this object or
    * @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink
    * (the default).
@@ -211,9 +440,26 @@
 
 
   /**
-   * Returns the resources for this CVTerm object.
+   * Returns the resource references for this CVTerm object.
+   *
+   * @htmlinclude cvterm-common-description-text.html
+   *
+   * The <span class="code" style="background-color: #d0d0ee">resource
+   * URI</span> values shown in the template above are stored internally in
+   * CVTerm objects using an XMLAttributes object.  Each attribute stored
+   * inside the XMLAttributes will have the same name (specifically,
+   * &quot;<code>rdf:resource</code>&quot;) but a different value, and the
+   * value will be a <span class="code" style="background-color:
+   * #d0d0ee">resource URI</span> shown in the XML template above.
+   *
+   * A valid CVTerm entity must always have at least one resource and
+   * a value for the relationship qualifier.
    * 
    * @return the XMLAttributes that store the resources of this CVTerm.
+   *
+   * @see getQualifierType()
+   * @see addResource()
+   * @see getResourceURI()
    */
   XMLAttributes * getResources(); 
 
@@ -221,7 +467,24 @@
   /**
    * Returns the resources for this CVTerm object.
    * 
+   * @htmlinclude cvterm-common-description-text.html
+   *
+   * The <span class="code" style="background-color: #d0d0ee">resource
+   * URI</span> values shown in the template above are stored internally in
+   * CVTerm objects using an XMLAttributes object.  Each attribute stored
+   * inside the XMLAttributes will have the same name (specifically,
+   * &quot;<code>rdf:resource</code>&quot;) but a different value, and the
+   * value will be a <span class="code" style="background-color:
+   * #d0d0ee">resource URI</span> shown in the XML template above.
+   *
+   * A valid CVTerm entity must always have at least one resource and
+   * a value for the relationship qualifier.
+   * 
    * @return the XMLAttributes that store the resources of this CVTerm.
+   *
+   * @see getQualifierType()
+   * @see addResource()
+   * @see getResourceURI()
    */
   const XMLAttributes * getResources() const; 
 
@@ -229,23 +492,46 @@
   /**
    * Returns the number of resources for this CVTerm object.
    * 
+   * @htmlinclude cvterm-common-description-text.html
+   *
+   * The fragment above illustrates that there can be more than one
+   * resource referenced by a given relationship annotation (i.e., the
+   * <span class="code" style="background-color: #d0d0ee">resource
+   * URI</span> values associated with a particular <span class="code"
+   * style="background-color: #bbb">RELATION_ELEMENT</span>).  The present
+   * method returns a count of the resources stored in this CVTerm object.
+   *
    * @return the number of resources in the set of XMLAttributes
    * of this CVTerm.
+   *
+   * @see getResources()
+   * @see getResourceURI()
    */
   unsigned int getNumResources(); 
 
   
   /**
-   * Returns the value of the nth resource for this CVTerm object.
+   * Returns the value of the <em>n</em>th resource for this CVTerm object.
    *
+   * @htmlinclude cvterm-common-description-text.html
+   *
+   * The fragment above illustrates that there can be more than one
+   * resource referenced by a given relationship annotation (i.e., the
+   * <span class="code" style="background-color: #d0d0ee">resource
+   * URI</span> values associated with a particular <span class="code"
+   * style="background-color: #bbb">RELATION_ELEMENT</span>).  LibSBML
+   * stores all resource URIs in a single CVTerm object for a given
+   * relationship.  Callers can use getNumResources() to find out how many
+   * resources are stored in this CVTerm object, then call this method to
+   * retrieve the <em>n</em>th resource URI.
+   * 
    * @param n the index of the resource to query
    *
    * @return string representing the value of the nth resource
    * in the set of XMLAttributes of this CVTerm.
    *
-   * @note Since the values of the resource attributes in a CVTerm are
-   * URIs, this is a convenience method to facilitate interaction with the
-   * CVTerm class.
+   * @see getNumResources()
+   * @see getQualifierType()
    */
   std::string getResourceURI(unsigned int n); 
 
@@ -300,45 +586,109 @@
 
 
   /**
-   * Adds a resource to the CVTerm.
+   * Adds a resource reference to this CVTerm object.
    *
-   * @param resource string representing the resource; e.g.,
+   * The SBML Level&nbsp;2 and Level&nbsp;3 specifications define a simple
+   * standardized format for annotating models with references to
+   * controlled vocabulary terms and database identifiers that define and
+   * describe biological and biochemical entities.  This annotation format
+   * consists of RDF-based content placed inside an
+   * <code>&lt;annotation&gt;</code> element attached to an SBML component
+   * such as Species, Compartment, etc.
+   *
+   * The specific RDF element used in this SBML format for referring to
+   * external entities is <code>&lt;rdf:Description&gt;</code>, with a
+   * <code>&lt;rdf:Bag&gt;</code> element inside of it containing one or
+   * more <code>&lt;rdf:li&gt;</code> elements.  Each such element refers
+   * to a data item in an external resource; the resource and data item are
+   * together identified uniquely using a URI.  The following template
+   * illustrates the structure:
+   *
+<DIV class="fragment">
+&lt;rdf:Description rdf:about=&quot;#<span style="border-bottom: 1px solid black">meta id</span>&quot;&gt;<br>
+&nbsp;&nbsp;<span style="background-color: #ddd; border-bottom: 2px dotted #888">HISTORY</span><br>
+&nbsp;&nbsp;&lt;<span style="background-color: #bbb">RELATION_ELEMENT</span>&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:Bag&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:li rdf:resource=&quot;<span style="background-color: #d0d0ee">resource URI</span>&quot; /&gt;<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #edd">...</span><br>
+&nbsp;&nbsp;&nbsp;&nbsp;&lt;/rdf:Bag&gt;<br>
+&nbsp;&nbsp;&lt;/<span style="background-color: #bbb">RELATION_ELEMENT</span>&gt;<br>
+&nbsp;&nbsp;<span style="background-color: #edd">...</span><br>
+&lt;/rdf:Description&gt;<br>
+</div>
+   *
+   * In the template above, the placeholder <span class="code"
+   * style="border-bottom: 1px solid black">meta id</span> stands for the
+   * element's meta identifier, which is a field available on all SBML
+   * components derived from the SBase base object class.  The <span
+   * style="border-bottom: 2px dotted #888">dotted</span> portions are
+   * optional, and the ellipses <span class="code" style="background-color:
+   * #edd">...</span> are placeholders for zero or more elements of the
+   * same form as the immediately preceding element.  The placeholder <span
+   * class="code" style="background-color: #bbb">RELATION_ELEMENT</span>
+   * refers to a BioModels.net qualifier element name.  This is an element
+   * in either the XML namespace
+   * <code>"http://biomodels.net/model-qualifiers"</code> (for model
+   * qualifiers) or <code>"http://biomodels.net/biology-qualifiers"</code>
+   * (for biological qualifier).
+   *
+   * The <span class="code" style="background-color: #d0d0ee">resource
+   * URI</span> is a required data value that uniquely identifies a
+   * resource and data within that resource to which the annotation refers.
+   * The present method allows callers to add a reference to a resource URI
+   * with the same relationship to the enclosing SBML object.  (In other
+   * words, the argument to this method is a <span class="code"
+   * style="background-color: #d0d0ee">resource URI</span> as shown in the
+   * XML fragment above.)  Resources are stored in this CVTerm object
+   * within an XMLAttributes object.
+   * 
+   * The relationship of this CVTerm to the enclosing SBML object can be
+   * determined using the CVTerm methods such as getModelQualifierType()
+   * and getBiologicalQualifierType().
+   *
+   * @param resource a string representing the URI of the resource and data
+   * item being referenced; e.g.,
    * <code>"http://www.geneontology.org/#GO:0005892"</code>.
    *
-   * @note This method adds the name <code>"rdf:resource"</code> to the
-   * attribute prior to adding it to the resources in this CVTerm object.
-   *
-   * @return integer value indicating success/failure of the
-   * function. The possible values
-   * returned by this function are:
+   * @return integer value indicating success/failure of the call. The
+   * possible values returned by this function are:
    * @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
    * @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED@endlink
+   *
+   * @see getResources()
+   * @see removeResource()
+   * @see getQualifierType()
+   * @see getModelQualifierType()
+   * @see getBiologicalQualifierType()
    */
   int addResource(const std::string& resource);
 
 
   /**
-   * Removes a resource from the CVTerm.
+   * Removes a resource URI from the set of resources stored in this CVTerm
+   * object.
    *
-   * @param resource string representing the resource; e.g.,
-   * <code>"http://www.geneontology.org/#GO:0005892"</code>.
+   * @param resource a string representing the resource URI to remove;
+   * e.g., <code>"http://www.geneontology.org/#GO:0005892"</code>.
    *
    * @return integer value indicating success/failure of the
    * function. The possible values
    * returned by this function are:
    * @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
    * @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
+   *
+   * @see addResource();
    */
   int removeResource(std::string resource);
   
 
   /**
-   * Predicate returning @c true if all the
-   * required elements for this Rule object have been set.
+   * Predicate returning @c true if all the required elements for this
+   * CVTerm object have been set.
    *
    * @note The required attributes for a CVTerm are:
-   * @li qualifierType and appropriate biologicalQualifierType or 
-   * @li modelQualifierType and at least one resource.
+   * @li a <em>qualifier type</em>, which can be either a model qualifier or a biological qualifier
+   * @li at least one resource
    */ 
   bool hasRequiredAttributes();
 


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Revision: 12709
          http://sbml.svn.sourceforge.net/sbml/?rev=12709&view=rev
Author:   mhucka
Date:     2011-01-26 18:27:40 +0000 (Wed, 26 Jan 2011)

Log Message:
-----------
Small correction to a statement.

Modified Paths:
--------------
    trunk/libsbml/src/annotation/RDFAnnotation.h

Modified: trunk/libsbml/src/annotation/RDFAnnotation.h
===================================================================
--- trunk/libsbml/src/annotation/RDFAnnotation.h	2011-01-26 18:27:00 UTC (rev 12708)
+++ trunk/libsbml/src/annotation/RDFAnnotation.h	2011-01-26 18:27:40 UTC (rev 12709)
@@ -32,8 +32,8 @@
  * ("Minimum Information Requested in the Annotation of biochemical
  * Models", <i>Nature Biotechnology</i>, vol. 23, no. 12, Dec. 2005).
  * Section 6 of the SBML Level&nbsp;2 and Level&nbsp;3 specification
- * documents defines a recommended way of encoding MIRIAM information as
- * RDF annotations in SBML.  The general scheme is as follows.  A set of
+ * documents defines a recommended way of encoding MIRIAM information using
+ * a subset of RDF in SBML.  The general scheme is as follows.  A set of
  * RDF-based annotations attached to a given SBML
  * <code>&lt;annotation&gt;</code> element are read by RDFAnnotationParser
  * and converted into a list of CVTerm objects.  There


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Revision: 12706
          http://sbml.svn.sourceforge.net/sbml/?rev=12706&view=rev
Author:   mhucka
Date:     2011-01-26 18:24:53 +0000 (Wed, 26 Jan 2011)

Log Message:
-----------
Removed some stray doxygen comment starters that caused comments to be
merged into the intended documentation.

Modified Paths:
--------------
    trunk/libsbml/src/annotation/CVTerm.cpp

Modified: trunk/libsbml/src/annotation/CVTerm.cpp
===================================================================
--- trunk/libsbml/src/annotation/CVTerm.cpp	2011-01-26 16:38:13 UTC (rev 12705)
+++ trunk/libsbml/src/annotation/CVTerm.cpp	2011-01-26 18:24:53 UTC (rev 12706)
@@ -189,9 +189,9 @@
 
 
 
-/**
-  * clones the CVTerm
-  */  
+/*
+ * clones the CVTerm
+ */  
 CVTerm* CVTerm::clone() const
 {
     CVTerm* term=new CVTerm(*this);
@@ -330,7 +330,7 @@
 }
 
   
-/**
+ /*
   * adds a resource to the term
   */
 int 
@@ -347,7 +347,7 @@
 }
 
 
-/**
+ /*
   * removes a resource to the term
   */
 int 
@@ -379,7 +379,7 @@
   return result;
 }
 
-/** @cond doxygen-libsbml-internal */
+ /* @cond doxygen-libsbml-internal */
 bool 
 CVTerm::hasRequiredAttributes()
 {


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Revision: 12710
          http://sbml.svn.sourceforge.net/sbml/?rev=12710&view=rev
Author:   sarahkeating
Date:     2011-01-26 18:43:35 +0000 (Wed, 26 Jan 2011)

Log Message:
-----------
The $cat variable was not correctly identifying the directory. I replaced the code with the if statement that is used to find the CurTestDir variable which does work.

Modified Paths:
--------------
    trunk/libsbml/dev/utilities/translateTests/translateTests.pl

Modified: trunk/libsbml/dev/utilities/translateTests/translateTests.pl
===================================================================
--- trunk/libsbml/dev/utilities/translateTests/translateTests.pl	2011-01-26 18:27:40 UTC (rev 12709)
+++ trunk/libsbml/dev/utilities/translateTests/translateTests.pl	2011-01-26 18:43:35 UTC (rev 12710)
@@ -3420,7 +3420,7 @@
   my ($file) = @_;
   my $cat = 'sbml';
 
-  $cat = $1 if ( $file =~ m|/src/([^/]*)/| ); 
+  $cat = $1 if ( $file =~ m| (\w+)/test/ |x ); 
   $file =~ s/.*\///;
   my $ofile = $file;
 


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Revision: 12704
          http://sbml.svn.sourceforge.net/sbml/?rev=12704&view=rev
Author:   sarahkeating
Date:     2011-01-26 16:10:23 +0000 (Wed, 26 Jan 2011)

Log Message:
-----------
updated for new test in annotation/test directory

Modified Paths:
--------------
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestRDFAnnotationC.java
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestValidation.java

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestRDFAnnotationC.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestRDFAnnotationC.java	2011-01-26 15:38:37 UTC (rev 12703)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestRDFAnnotationC.java	2011-01-26 16:10:23 UTC (rev 12704)
@@ -1,363 +1,373 @@
-/*
- * @file    TestRDFAnnotationC.java
- * @brief   RDFAnnotation parser unit tests
- *
- * @author  Akiya Jouraku (Java conversion)
- * @author  Sarah Keating 
- *
- * $Id$
- * $HeadURL$
- *
- * ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
- *
- * DO NOT EDIT THIS FILE.
- *
- * This file was generated automatically by converting the file located at
- * src/annotation/test/TestRDFAnnotationC.c
- * using the conversion program dev/utilities/translateTests/translateTests.pl.
- * Any changes made here will be lost the next time the file is regenerated.
- *
- * -----------------------------------------------------------------------------
- * This file is part of libSBML.  Please visit http://sbml.org for more
- * information about SBML, and the latest version of libSBML.
- *
- * Copyright 2005-2010 California Institute of Technology.
- * Copyright 2002-2005 California Institute of Technology and
- *                     Japan Science and Technology Corporation.
- * 
- * 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/libsbml/license.html
- * -----------------------------------------------------------------------------
- */
-
-package org.sbml.libsbml.test.annotation;
-
-import org.sbml.libsbml.*;
-
-import java.io.File;
-import java.lang.AssertionError;
-
-public class TestRDFAnnotationC {
-
-  static void assertTrue(boolean condition) throws AssertionError
-  {
-    if (condition == true)
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-
-  static void assertEquals(Object a, Object b) throws AssertionError
-  {
-    if ( (a == null) && (b == null) )
-    {
-      return;
-    }
-    else if ( (a == null) || (b == null) )
-    {
-      throw new AssertionError();
-    }
-    else if (a.equals(b))
-    {
-      return;
-    }
-
-    throw new AssertionError();
-  }
-
-  static void assertNotEquals(Object a, Object b) throws AssertionError
-  {
-    if ( (a == null) && (b == null) )
-    {
-      throw new AssertionError();
-    }
-    else if ( (a == null) || (b == null) )
-    {
-      return;
-    }
-    else if (a.equals(b))
-    {
-      throw new AssertionError();
-    }
-  }
-
-  static void assertEquals(boolean a, boolean b) throws AssertionError
-  {
-    if ( a == b )
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-
-  static void assertNotEquals(boolean a, boolean b) throws AssertionError
-  {
-    if ( a != b )
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-
-  static void assertEquals(int a, int b) throws AssertionError
-  {
-    if ( a == b )
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-
-  static void assertNotEquals(int a, int b) throws AssertionError
-  {
-    if ( a != b )
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-  private SBMLDocument d;
-  private Model m;
-
-  protected void setUp() throws Exception
-  {
-    String filename = "../../annotation/test/test-data/annotation.xml";
-    d = libsbml.readSBML(filename);
-    m = d.getModel();
-  }
-
-  protected void tearDown() throws Exception
-  {
-    d = null;
-  }
-
-  public void test_RDFAnnotation_C_delete()
-  {
-    SBase obj = m.getCompartment(0);
-    XMLNode node = RDFAnnotationParser.parseCVTerms(obj);
-    XMLNode n1 = RDFAnnotationParser.deleteRDFAnnotation(node);
-    assertTrue( n1.getNumChildren() == 0 );
-    assertTrue(n1.getName().equals( "annotation"));
-    node = null;
-  }
-
-  public void test_RDFAnnotation_C_getModelHistory()
-  {
-    assertTrue( ! (m == null) );
-    ModelHistory history = m.getModelHistory();
-    assertTrue( history != null );
-    ModelCreator mc = history.getCreator(0);
-    assertTrue(mc.getFamilyName().equals( "Le Novere"));
-    assertTrue(mc.getGivenName().equals( "Nicolas"));
-    assertTrue(mc.getEmail().equals( "le...@eb..."));
-    assertTrue(mc.getOrganisation().equals( "EMBL-EBI"));
-    Date date = history.getCreatedDate();
-    assertTrue( date.getYear() == 2005 );
-    assertTrue( date.getMonth() == 2 );
-    assertTrue( date.getDay() == 2 );
-    assertTrue( date.getHour() == 14 );
-    assertTrue( date.getMinute() == 56 );
-    assertTrue( date.getSecond() == 11 );
-    assertTrue( date.getSignOffset() == 0 );
-    assertTrue( date.getHoursOffset() == 0 );
-    assertTrue( date.getMinutesOffset() == 0 );
-    assertTrue(date.getDateAsString().equals( "2005-02-02T14:56:11Z"));
-    date = history.getModifiedDate();
-    assertTrue( date.getYear() == 2006 );
-    assertTrue( date.getMonth() == 5 );
-    assertTrue( date.getDay() == 30 );
-    assertTrue( date.getHour() == 10 );
-    assertTrue( date.getMinute() == 46 );
-    assertTrue( date.getSecond() == 2 );
-    assertTrue( date.getSignOffset() == 0 );
-    assertTrue( date.getHoursOffset() == 0 );
-    assertTrue( date.getMinutesOffset() == 0 );
-    assertTrue(date.getDateAsString().equals( "2006-05-30T10:46:02Z"));
-  }
-
-  public void test_RDFAnnotation_C_parseCVTerms()
-  {
-    SBase obj = m.getCompartment(0);
-    XMLNode node = RDFAnnotationParser.parseCVTerms(obj);
-    assertTrue( node.getNumChildren() == 1 );
-    XMLNode rdf = node.getChild(0);
-    assertTrue(rdf.getName().equals( "RDF"));
-    assertTrue(rdf.getPrefix().equals( "rdf"));
-    assertTrue(rdf.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
-    assertTrue( rdf.getNumChildren() == 1 );
-    XMLNode desc = rdf.getChild(0);
-    assertTrue(desc.getName().equals( "Description"));
-    assertTrue(desc.getPrefix().equals( "rdf"));
-    assertTrue(desc.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
-    assertTrue( desc.getNumChildren() == 1 );
-    XMLNode is1 = desc.getChild(0);
-    assertTrue(is1.getName().equals( "is"));
-    assertTrue(is1.getPrefix().equals( "bqbiol"));
-    assertTrue( is1.getNumChildren() == 1 );
-    XMLNode Bag = is1.getChild(0);
-    assertTrue(Bag.getName().equals( "Bag"));
-    assertTrue(Bag.getPrefix().equals( "rdf"));
-    assertTrue(Bag.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
-    assertTrue( Bag.getNumChildren() == 4 );
-    XMLNode li = Bag.getChild(0);
-    assertTrue(li.getName().equals( "li"));
-    assertTrue(li.getPrefix().equals( "rdf"));
-    assertTrue(li.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
-    assertTrue( li.getNumChildren() == 0 );
-    XMLNode li1 = Bag.getChild(1);
-    assertTrue(li1.getName().equals( "li"));
-    assertTrue(li1.getPrefix().equals( "rdf"));
-    assertTrue(li1.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
-    assertTrue( li1.getNumChildren() == 0 );
-    XMLNode li2 = Bag.getChild(2);
-    assertTrue(li2.getName().equals( "li"));
-    assertTrue(li2.getPrefix().equals( "rdf"));
-    assertTrue(li2.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
-    assertTrue( li2.getNumChildren() == 0 );
-    XMLNode li3 = Bag.getChild(3);
-    assertTrue(li3.getName().equals( "li"));
-    assertTrue(li3.getPrefix().equals( "rdf"));
-    assertTrue(li3.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
-    assertTrue( li3.getNumChildren() == 0 );
-    node = null;
-  }
-
-  public void test_RDFAnnotation_C_parseModelHistory()
-  {
-    XMLNode node = RDFAnnotationParser.parseModelHistory(m);
-    assertTrue( node.getNumChildren() == 1 );
-    XMLNode rdf = node.getChild(0);
-    assertTrue(rdf.getName().equals( "RDF"));
-    assertTrue(rdf.getPrefix().equals( "rdf"));
-    assertTrue(rdf.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
-    assertTrue( rdf.getNumChildren() == 1 );
-    XMLNode desc = rdf.getChild(0);
-    assertTrue(desc.getName().equals( "Description"));
-    assertTrue(desc.getPrefix().equals( "rdf"));
-    assertTrue(desc.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
-    assertTrue( desc.getNumChildren() == 3 );
-    XMLNode creator = desc.getChild(0);
-    assertTrue(creator.getName().equals( "creator"));
-    assertTrue(creator.getPrefix().equals( "dc"));
-    assertTrue(creator.getURI().equals( "http://purl.org/dc/elements/1.1/"));
-    assertTrue( creator.getNumChildren() == 1 );
-    XMLNode Bag = creator.getChild(0);
-    assertTrue(Bag.getName().equals( "Bag"));
-    assertTrue(Bag.getPrefix().equals( "rdf"));
-    assertTrue(Bag.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
-    assertTrue( Bag.getNumChildren() == 1 );
-    XMLNode li = Bag.getChild(0);
-    assertTrue(li.getName().equals( "li"));
-    assertTrue(li.getPrefix().equals( "rdf"));
-    assertTrue(li.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
-    assertTrue( li.getNumChildren() == 3 );
-    XMLNode N = li.getChild(0);
-    assertTrue(N.getName().equals( "N"));
-    assertTrue(N.getPrefix().equals( "vCard"));
-    assertTrue(N.getURI().equals( "http://www.w3.org/2001/vcard-rdf/3.0#"));
-    assertTrue( N.getNumChildren() == 2 );
-    XMLNode Family = N.getChild(0);
-    assertTrue(Family.getName().equals( "Family"));
-    assertTrue(Family.getPrefix().equals( "vCard"));
-    assertTrue(Family.getURI().equals( "http://www.w3.org/2001/vcard-rdf/3.0#"));
-    assertTrue( Family.getNumChildren() == 1 );
-    XMLNode Given = N.getChild(1);
-    assertTrue(Given.getName().equals( "Given"));
-    assertTrue(Given.getPrefix().equals( "vCard"));
-    assertTrue(Given.getURI().equals( "http://www.w3.org/2001/vcard-rdf/3.0#"));
-    assertTrue( Given.getNumChildren() == 1 );
-    XMLNode EMAIL = li.getChild(1);
-    assertTrue(EMAIL.getName().equals( "EMAIL"));
-    assertTrue(EMAIL.getPrefix().equals( "vCard"));
-    assertTrue(EMAIL.getURI().equals( "http://www.w3.org/2001/vcard-rdf/3.0#"));
-    assertTrue( EMAIL.getNumChildren() == 1 );
-    XMLNode ORG = li.getChild(2);
-    assertTrue(ORG.getName().equals( "ORG"));
-    assertTrue(ORG.getPrefix().equals( "vCard"));
-    assertTrue(ORG.getURI().equals( "http://www.w3.org/2001/vcard-rdf/3.0#"));
-    assertTrue( ORG.getNumChildren() == 1 );
-    XMLNode Orgname = ORG.getChild(0);
-    assertTrue(Orgname.getName().equals( "Orgname"));
-    assertTrue(Orgname.getPrefix().equals( "vCard"));
-    assertTrue(Orgname.getURI().equals( "http://www.w3.org/2001/vcard-rdf/3.0#"));
-    assertTrue( Orgname.getNumChildren() == 1 );
-    XMLNode created = desc.getChild(1);
-    assertTrue(created.getName().equals( "created"));
-    assertTrue(created.getPrefix().equals( "dcterms"));
-    assertTrue(created.getURI().equals( "http://purl.org/dc/terms/"));
-    assertTrue( created.getNumChildren() == 1 );
-    XMLNode cr_date = created.getChild(0);
-    assertTrue(cr_date.getName().equals( "W3CDTF"));
-    assertTrue(cr_date.getPrefix().equals( "dcterms"));
-    assertTrue(cr_date.getURI().equals( "http://purl.org/dc/terms/"));
-    assertTrue( cr_date.getNumChildren() == 1 );
-    XMLNode modified = desc.getChild(2);
-    assertTrue(modified.getName().equals( "modified"));
-    assertTrue(modified.getPrefix().equals( "dcterms"));
-    assertTrue(modified.getURI().equals( "http://purl.org/dc/terms/"));
-    assertTrue( modified.getNumChildren() == 1 );
-    XMLNode mo_date = created.getChild(0);
-    assertTrue(mo_date.getName().equals( "W3CDTF"));
-    assertTrue(mo_date.getPrefix().equals( "dcterms"));
-    assertTrue(mo_date.getURI().equals( "http://purl.org/dc/terms/"));
-    assertTrue( mo_date.getNumChildren() == 1 );
-    node = null;
-  }
-
-  /**
-   * Loads the SWIG-generated libSBML Java module when this class is
-   * loaded, or reports a sensible diagnostic message about why it failed.
-   */
-  static
-  {
-    String varname;
-    String shlibname;
-
-    if (System.getProperty("mrj.version") != null)
-    {
-      varname = "DYLD_LIBRARY_PATH";    // We're on a Mac.
-      shlibname = "libsbmlj.jnilib and/or libsbml.dylib";
-    }
-    else
-    {
-      varname = "LD_LIBRARY_PATH";      // We're not on a Mac.
-      shlibname = "libsbmlj.so and/or libsbml.so";
-    }
-
-    try
-    {
-      System.loadLibrary("sbmlj");
-      // For extra safety, check that the jar file is in the classpath.
-      Class.forName("org.sbml.libsbml.libsbml");
-    }
-    catch (SecurityException e)
-    {
-      e.printStackTrace();
-      System.err.println("Could not load the libSBML library files due to a"+
-                         " security exception.\n");
-      System.exit(1);
-    }
-    catch (UnsatisfiedLinkError e)
-    {
-      e.printStackTrace();
-      System.err.println("Error: could not link with the libSBML library files."+
-                         " It is likely\nyour " + varname +
-                         " environment variable does not include the directories\n"+
-                         "containing the " + shlibname + " library files.\n");
-      System.exit(1);
-    }
-    catch (ClassNotFoundException e)
-    {
-      e.printStackTrace();
-      System.err.println("Error: unable to load the file libsbmlj.jar."+
-                         " It is likely\nyour -classpath option and CLASSPATH" +
-                         " environment variable\n"+
-                         "do not include the path to libsbmlj.jar.\n");
-      System.exit(1);
-    }
-  }
-}
+/*
+ * @file    TestRDFAnnotationC.java
+ * @brief   RDFAnnotation parser unit tests
+ *
+ * @author  Akiya Jouraku (Java conversion)
+ * @author  Sarah Keating 
+ *
+ * $Id$
+ * $HeadURL$
+ *
+ * ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
+ *
+ * DO NOT EDIT THIS FILE.
+ *
+ * This file was generated automatically by converting the file located at
+ * src/annotation/test/TestRDFAnnotationC.c
+ * using the conversion program dev/utilities/translateTests/translateTests.pl.
+ * Any changes made here will be lost the next time the file is regenerated.
+ *
+ * -----------------------------------------------------------------------------
+ * This file is part of libSBML.  Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright 2005-2010 California Institute of Technology.
+ * Copyright 2002-2005 California Institute of Technology and
+ *                     Japan Science and Technology Corporation.
+ * 
+ * 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/libsbml/license.html
+ * -----------------------------------------------------------------------------
+ */
+
+package org.sbml.libsbml.test.annotation;
+
+import org.sbml.libsbml.*;
+
+import java.io.File;
+import java.lang.AssertionError;
+
+public class TestRDFAnnotationC {
+
+  static void assertTrue(boolean condition) throws AssertionError
+  {
+    if (condition == true)
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+
+  static void assertEquals(Object a, Object b) throws AssertionError
+  {
+    if ( (a == null) && (b == null) )
+    {
+      return;
+    }
+    else if ( (a == null) || (b == null) )
+    {
+      throw new AssertionError();
+    }
+    else if (a.equals(b))
+    {
+      return;
+    }
+
+    throw new AssertionError();
+  }
+
+  static void assertNotEquals(Object a, Object b) throws AssertionError
+  {
+    if ( (a == null) && (b == null) )
+    {
+      throw new AssertionError();
+    }
+    else if ( (a == null) || (b == null) )
+    {
+      return;
+    }
+    else if (a.equals(b))
+    {
+      throw new AssertionError();
+    }
+  }
+
+  static void assertEquals(boolean a, boolean b) throws AssertionError
+  {
+    if ( a == b )
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+
+  static void assertNotEquals(boolean a, boolean b) throws AssertionError
+  {
+    if ( a != b )
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+
+  static void assertEquals(int a, int b) throws AssertionError
+  {
+    if ( a == b )
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+
+  static void assertNotEquals(int a, int b) throws AssertionError
+  {
+    if ( a != b )
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+  private SBMLDocument d;
+  private Model m;
+
+  protected void setUp() throws Exception
+  {
+    String filename = "../../annotation/test/test-data/annotation.xml";
+    d = libsbml.readSBML(filename);
+    m = d.getModel();
+  }
+
+  protected void tearDown() throws Exception
+  {
+    d = null;
+  }
+
+  public void test_RDFAnnotation_C_accessWithNULL()
+  {
+    assertTrue( RDFAnnotationParser.createCVTerms(null) == null );
+    assertTrue( RDFAnnotationParser.createRDFDescription(null) == null );
+    assertTrue( RDFAnnotationParser.deleteRDFAnnotation(null) == null );
+    assertTrue( RDFAnnotationParser.parseCVTerms(null) == null );
+    assertTrue( RDFAnnotationParser.parseModelHistory(null) == null );
+    RDFAnnotationParser.parseRDFAnnotation(null,null);
+  }
+
+  public void test_RDFAnnotation_C_delete()
+  {
+    SBase obj = m.getCompartment(0);
+    XMLNode node = RDFAnnotationParser.parseCVTerms(obj);
+    XMLNode n1 = RDFAnnotationParser.deleteRDFAnnotation(node);
+    assertTrue( n1.getNumChildren() == 0 );
+    assertTrue(n1.getName().equals( "annotation"));
+    node = null;
+  }
+
+  public void test_RDFAnnotation_C_getModelHistory()
+  {
+    assertTrue( ! (m == null) );
+    ModelHistory history = m.getModelHistory();
+    assertTrue( history != null );
+    ModelCreator mc = history.getCreator(0);
+    assertTrue(mc.getFamilyName().equals( "Le Novere"));
+    assertTrue(mc.getGivenName().equals( "Nicolas"));
+    assertTrue(mc.getEmail().equals( "le...@eb..."));
+    assertTrue(mc.getOrganisation().equals( "EMBL-EBI"));
+    Date date = history.getCreatedDate();
+    assertTrue( date.getYear() == 2005 );
+    assertTrue( date.getMonth() == 2 );
+    assertTrue( date.getDay() == 2 );
+    assertTrue( date.getHour() == 14 );
+    assertTrue( date.getMinute() == 56 );
+    assertTrue( date.getSecond() == 11 );
+    assertTrue( date.getSignOffset() == 0 );
+    assertTrue( date.getHoursOffset() == 0 );
+    assertTrue( date.getMinutesOffset() == 0 );
+    assertTrue(date.getDateAsString().equals( "2005-02-02T14:56:11Z"));
+    date = history.getModifiedDate();
+    assertTrue( date.getYear() == 2006 );
+    assertTrue( date.getMonth() == 5 );
+    assertTrue( date.getDay() == 30 );
+    assertTrue( date.getHour() == 10 );
+    assertTrue( date.getMinute() == 46 );
+    assertTrue( date.getSecond() == 2 );
+    assertTrue( date.getSignOffset() == 0 );
+    assertTrue( date.getHoursOffset() == 0 );
+    assertTrue( date.getMinutesOffset() == 0 );
+    assertTrue(date.getDateAsString().equals( "2006-05-30T10:46:02Z"));
+  }
+
+  public void test_RDFAnnotation_C_parseCVTerms()
+  {
+    SBase obj = m.getCompartment(0);
+    XMLNode node = RDFAnnotationParser.parseCVTerms(obj);
+    assertTrue( node.getNumChildren() == 1 );
+    XMLNode rdf = node.getChild(0);
+    assertTrue(rdf.getName().equals( "RDF"));
+    assertTrue(rdf.getPrefix().equals( "rdf"));
+    assertTrue(rdf.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+    assertTrue( rdf.getNumChildren() == 1 );
+    XMLNode desc = rdf.getChild(0);
+    assertTrue(desc.getName().equals( "Description"));
+    assertTrue(desc.getPrefix().equals( "rdf"));
+    assertTrue(desc.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+    assertTrue( desc.getNumChildren() == 1 );
+    XMLNode is1 = desc.getChild(0);
+    assertTrue(is1.getName().equals( "is"));
+    assertTrue(is1.getPrefix().equals( "bqbiol"));
+    assertTrue( is1.getNumChildren() == 1 );
+    XMLNode Bag = is1.getChild(0);
+    assertTrue(Bag.getName().equals( "Bag"));
+    assertTrue(Bag.getPrefix().equals( "rdf"));
+    assertTrue(Bag.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+    assertTrue( Bag.getNumChildren() == 4 );
+    XMLNode li = Bag.getChild(0);
+    assertTrue(li.getName().equals( "li"));
+    assertTrue(li.getPrefix().equals( "rdf"));
+    assertTrue(li.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+    assertTrue( li.getNumChildren() == 0 );
+    XMLNode li1 = Bag.getChild(1);
+    assertTrue(li1.getName().equals( "li"));
+    assertTrue(li1.getPrefix().equals( "rdf"));
+    assertTrue(li1.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+    assertTrue( li1.getNumChildren() == 0 );
+    XMLNode li2 = Bag.getChild(2);
+    assertTrue(li2.getName().equals( "li"));
+    assertTrue(li2.getPrefix().equals( "rdf"));
+    assertTrue(li2.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+    assertTrue( li2.getNumChildren() == 0 );
+    XMLNode li3 = Bag.getChild(3);
+    assertTrue(li3.getName().equals( "li"));
+    assertTrue(li3.getPrefix().equals( "rdf"));
+    assertTrue(li3.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+    assertTrue( li3.getNumChildren() == 0 );
+    node = null;
+  }
+
+  public void test_RDFAnnotation_C_parseModelHistory()
+  {
+    XMLNode node = RDFAnnotationParser.parseModelHistory(m);
+    assertTrue( node.getNumChildren() == 1 );
+    XMLNode rdf = node.getChild(0);
+    assertTrue(rdf.getName().equals( "RDF"));
+    assertTrue(rdf.getPrefix().equals( "rdf"));
+    assertTrue(rdf.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+    assertTrue( rdf.getNumChildren() == 1 );
+    XMLNode desc = rdf.getChild(0);
+    assertTrue(desc.getName().equals( "Description"));
+    assertTrue(desc.getPrefix().equals( "rdf"));
+    assertTrue(desc.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+    assertTrue( desc.getNumChildren() == 3 );
+    XMLNode creator = desc.getChild(0);
+    assertTrue(creator.getName().equals( "creator"));
+    assertTrue(creator.getPrefix().equals( "dc"));
+    assertTrue(creator.getURI().equals( "http://purl.org/dc/elements/1.1/"));
+    assertTrue( creator.getNumChildren() == 1 );
+    XMLNode Bag = creator.getChild(0);
+    assertTrue(Bag.getName().equals( "Bag"));
+    assertTrue(Bag.getPrefix().equals( "rdf"));
+    assertTrue(Bag.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+    assertTrue( Bag.getNumChildren() == 1 );
+    XMLNode li = Bag.getChild(0);
+    assertTrue(li.getName().equals( "li"));
+    assertTrue(li.getPrefix().equals( "rdf"));
+    assertTrue(li.getURI().equals( "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+    assertTrue( li.getNumChildren() == 3 );
+    XMLNode N = li.getChild(0);
+    assertTrue(N.getName().equals( "N"));
+    assertTrue(N.getPrefix().equals( "vCard"));
+    assertTrue(N.getURI().equals( "http://www.w3.org/2001/vcard-rdf/3.0#"));
+    assertTrue( N.getNumChildren() == 2 );
+    XMLNode Family = N.getChild(0);
+    assertTrue(Family.getName().equals( "Family"));
+    assertTrue(Family.getPrefix().equals( "vCard"));
+    assertTrue(Family.getURI().equals( "http://www.w3.org/2001/vcard-rdf/3.0#"));
+    assertTrue( Family.getNumChildren() == 1 );
+    XMLNode Given = N.getChild(1);
+    assertTrue(Given.getName().equals( "Given"));
+    assertTrue(Given.getPrefix().equals( "vCard"));
+    assertTrue(Given.getURI().equals( "http://www.w3.org/2001/vcard-rdf/3.0#"));
+    assertTrue( Given.getNumChildren() == 1 );
+    XMLNode EMAIL = li.getChild(1);
+    assertTrue(EMAIL.getName().equals( "EMAIL"));
+    assertTrue(EMAIL.getPrefix().equals( "vCard"));
+    assertTrue(EMAIL.getURI().equals( "http://www.w3.org/2001/vcard-rdf/3.0#"));
+    assertTrue( EMAIL.getNumChildren() == 1 );
+    XMLNode ORG = li.getChild(2);
+    assertTrue(ORG.getName().equals( "ORG"));
+    assertTrue(ORG.getPrefix().equals( "vCard"));
+    assertTrue(ORG.getURI().equals( "http://www.w3.org/2001/vcard-rdf/3.0#"));
+    assertTrue( ORG.getNumChildren() == 1 );
+    XMLNode Orgname = ORG.getChild(0);
+    assertTrue(Orgname.getName().equals( "Orgname"));
+    assertTrue(Orgname.getPrefix().equals( "vCard"));
+    assertTrue(Orgname.getURI().equals( "http://www.w3.org/2001/vcard-rdf/3.0#"));
+    assertTrue( Orgname.getNumChildren() == 1 );
+    XMLNode created = desc.getChild(1);
+    assertTrue(created.getName().equals( "created"));
+    assertTrue(created.getPrefix().equals( "dcterms"));
+    assertTrue(created.getURI().equals( "http://purl.org/dc/terms/"));
+    assertTrue( created.getNumChildren() == 1 );
+    XMLNode cr_date = created.getChild(0);
+    assertTrue(cr_date.getName().equals( "W3CDTF"));
+    assertTrue(cr_date.getPrefix().equals( "dcterms"));
+    assertTrue(cr_date.getURI().equals( "http://purl.org/dc/terms/"));
+    assertTrue( cr_date.getNumChildren() == 1 );
+    XMLNode modified = desc.getChild(2);
+    assertTrue(modified.getName().equals( "modified"));
+    assertTrue(modified.getPrefix().equals( "dcterms"));
+    assertTrue(modified.getURI().equals( "http://purl.org/dc/terms/"));
+    assertTrue( modified.getNumChildren() == 1 );
+    XMLNode mo_date = created.getChild(0);
+    assertTrue(mo_date.getName().equals( "W3CDTF"));
+    assertTrue(mo_date.getPrefix().equals( "dcterms"));
+    assertTrue(mo_date.getURI().equals( "http://purl.org/dc/terms/"));
+    assertTrue( mo_date.getNumChildren() == 1 );
+    node = null;
+  }
+
+  /**
+   * Loads the SWIG-generated libSBML Java module when this class is
+   * loaded, or reports a sensible diagnostic message about why it failed.
+   */
+  static
+  {
+    String varname;
+    String shlibname;
+
+    if (System.getProperty("mrj.version") != null)
+    {
+      varname = "DYLD_LIBRARY_PATH";    // We're on a Mac.
+      shlibname = "libsbmlj.jnilib and/or libsbml.dylib";
+    }
+    else
+    {
+      varname = "LD_LIBRARY_PATH";      // We're not on a Mac.
+      shlibname = "libsbmlj.so and/or libsbml.so";
+    }
+
+    try
+    {
+      System.loadLibrary("sbmlj");
+      // For extra safety, check that the jar file is in the classpath.
+      Class.forName("org.sbml.libsbml.libsbml");
+    }
+    catch (SecurityException e)
+    {
+      e.printStackTrace();
+      System.err.println("Could not load the libSBML library files due to a"+
+                         " security exception.\n");
+      System.exit(1);
+    }
+    catch (UnsatisfiedLinkError e)
+    {
+      e.printStackTrace();
+      System.err.println("Error: could not link with the libSBML library files."+
+                         " It is likely\nyour " + varname +
+                         " environment variable does not include the directories\n"+
+                         "containing the " + shlibname + " library files.\n");
+      System.exit(1);
+    }
+    catch (ClassNotFoundException e)
+    {
+      e.printStackTrace();
+      System.err.println("Error: unable to load the file libsbmlj.jar."+
+                         " It is likely\nyour -classpath option and CLASSPATH" +
+                         " environment variable\n"+
+                         "do not include the path to libsbmlj.jar.\n");
+      System.exit(1);
+    }
+  }
+}

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestValidation.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestValidation.java	2011-01-26 15:38:37 UTC (rev 12703)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestValidation.java	2011-01-26 16:10:23 UTC (rev 12704)
@@ -1,303 +1,320 @@
-/*
- * @file    TestValidation.java
- * @brief   Validation of Date ModelCreator and ModelHistory unit tests
- *
- * @author  Akiya Jouraku (Java conversion)
- * @author  Sarah Keating 
- *
- * $Id$
- * $HeadURL$
- *
- * ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
- *
- * DO NOT EDIT THIS FILE.
- *
- * This file was generated automatically by converting the file located at
- * src/annotation/test/TestValidation.cpp
- * using the conversion program dev/utilities/translateTests/translateTests.pl.
- * Any changes made here will be lost the next time the file is regenerated.
- *
- * -----------------------------------------------------------------------------
- * This file is part of libSBML.  Please visit http://sbml.org for more
- * information about SBML, and the latest version of libSBML.
- *
- * Copyright 2005-2010 California Institute of Technology.
- * Copyright 2002-2005 California Institute of Technology and
- *                     Japan Science and Technology Corporation.
- * 
- * 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/libsbml/license.html
- * -----------------------------------------------------------------------------
- */
-
-package org.sbml.libsbml.test.annotation;
-
-import org.sbml.libsbml.*;
-
-import java.io.File;
-import java.lang.AssertionError;
-
-public class TestValidation {
-
-  static void assertTrue(boolean condition) throws AssertionError
-  {
-    if (condition == true)
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-
-  static void assertEquals(Object a, Object b) throws AssertionError
-  {
-    if ( (a == null) && (b == null) )
-    {
-      return;
-    }
-    else if ( (a == null) || (b == null) )
-    {
-      throw new AssertionError();
-    }
-    else if (a.equals(b))
-    {
-      return;
-    }
-
-    throw new AssertionError();
-  }
-
-  static void assertNotEquals(Object a, Object b) throws AssertionError
-  {
-    if ( (a == null) && (b == null) )
-    {
-      throw new AssertionError();
-    }
-    else if ( (a == null) || (b == null) )
-    {
-      return;
-    }
-    else if (a.equals(b))
-    {
-      throw new AssertionError();
-    }
-  }
-
-  static void assertEquals(boolean a, boolean b) throws AssertionError
-  {
-    if ( a == b )
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-
-  static void assertNotEquals(boolean a, boolean b) throws AssertionError
-  {
-    if ( a != b )
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-
-  static void assertEquals(int a, int b) throws AssertionError
-  {
-    if ( a == b )
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-
-  static void assertNotEquals(int a, int b) throws AssertionError
-  {
-    if ( a != b )
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-
-  public void test_Validation_CVTerm1()
-  {
-    CVTerm cv = new CVTerm();
-    assertTrue( cv != null );
-    assertEquals( false, (cv.hasRequiredAttributes()) );
-    cv.setQualifierType(libsbml.MODEL_QUALIFIER);
-    assertEquals( false, (cv.hasRequiredAttributes()) );
-    cv.setModelQualifierType(libsbml.BQM_IS);
-    assertEquals( false, (cv.hasRequiredAttributes()) );
-    cv.addResource("ggg");
-    assertEquals( true, (cv.hasRequiredAttributes()) );
-    cv = null;
-  }
-
-  public void test_Validation_CVTerm2()
-  {
-    CVTerm cv = new CVTerm();
-    assertTrue( cv != null );
-    assertEquals( false, (cv.hasRequiredAttributes()) );
-    cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER);
-    assertEquals( false, (cv.hasRequiredAttributes()) );
-    cv.setBiologicalQualifierType(libsbml.BQB_IS);
-    assertEquals( false, (cv.hasRequiredAttributes()) );
-    cv.addResource("ggg");
-    assertEquals( true, (cv.hasRequiredAttributes()) );
-    cv = null;
-  }
-
-  public void test_Validation_Date1()
-  {
-    Date date = new Date(200,12,30,12,15,45,1,2,0);
-    assertTrue( date != null );
-    assertEquals( false, (date.representsValidDate()) );
-    date = null;
-  }
-
-  public void test_Validation_Date2()
-  {
-    Date date = new Date(2007,14,30,12,15,45,1,2,0);
-    assertTrue( date != null );
-    assertEquals( false, (date.representsValidDate()) );
-    date = null;
-  }
-
-  public void test_Validation_Date3()
-  {
-    Date date = new Date("Jan 12");
-    assertTrue( date != null );
-    assertEquals( false, (date.representsValidDate()) );
-    date = null;
-  }
-
-  public void test_Validation_Date4()
-  {
-    Date date = new Date(2007,12,30,12,15,45,1,2,0);
-    assertTrue( date != null );
-    assertEquals( true, date.representsValidDate() );
-    date = null;
-  }
-
-  public void test_Validation_ModelCreator()
-  {
-    ModelCreator mc = new ModelCreator();
-    assertTrue( mc != null );
-    assertEquals( false, (mc.hasRequiredAttributes()) );
-    mc.setEmail("k123");
-    assertEquals( false, (mc.hasRequiredAttributes()) );
-    mc.setFamilyName("Keating");
-    assertEquals( false, (mc.hasRequiredAttributes()) );
-    mc.setGivenName("Sarah");
-    assertEquals( true, mc.hasRequiredAttributes() );
-    mc = null;
-  }
-
-  public void test_Validation_ModelHistory1()
-  {
-    ModelHistory mh = new ModelHistory();
-    assertTrue( mh != null );
-    assertEquals( false, (mh.hasRequiredAttributes()) );
-    Date date = new Date(2007,12,30,12,15,45,1,2,0);
-    mh.setCreatedDate(date);
-    assertEquals( false, (mh.hasRequiredAttributes()) );
-    mh.setModifiedDate(date);
-    assertEquals( false, (mh.hasRequiredAttributes()) );
-    ModelCreator mc = new ModelCreator();
-    mc.setFamilyName("Keating");
-    mc.setGivenName("Sarah");
-    mh.addCreator(mc);
-    assertEquals( true, mh.hasRequiredAttributes() );
-    mh = null;
-  }
-
-  public void test_Validation_ModelHistory2()
-  {
-    ModelHistory mh = new ModelHistory();
-    assertTrue( mh != null );
-    assertEquals( false, (mh.hasRequiredAttributes()) );
-    Date date = new Date(200,12,30,12,15,45,1,2,0);
-    mh.setCreatedDate(date);
-    assertEquals( false, (mh.hasRequiredAttributes()) );
-    mh.setModifiedDate(date);
-    assertEquals( false, (mh.hasRequiredAttributes()) );
-    ModelCreator mc = new ModelCreator();
-    mc.setFamilyName("Keating");
-    mc.setGivenName("Sarah");
-    mh.addCreator(mc);
-    assertEquals( false, (mh.hasRequiredAttributes()) );
-    mh = null;
-  }
-
-  public void test_Validation_ModelHistory3()
-  {
-    ModelHistory mh = new ModelHistory();
-    assertTrue( mh != null );
-    assertEquals( false, (mh.hasRequiredAttributes()) );
-    Date date = new Date(2007,12,30,12,15,45,1,2,0);
-    mh.setCreatedDate(date);
-    assertEquals( false, (mh.hasRequiredAttributes()) );
-    mh.setModifiedDate(date);
-    assertEquals( false, (mh.hasRequiredAttributes()) );
-    ModelCreator mc = new ModelCreator();
-    mc.setFamilyName("Keating");
-    mh.addCreator(mc);
-    assertEquals( false, (mh.hasRequiredAttributes()) );
-    mh = null;
-  }
-
-  /**
-   * Loads the SWIG-generated libSBML Java module when this class is
-   * loaded, or reports a sensible diagnostic message about why it failed.
-   */
-  static
-  {
-    String varname;
-    String shlibname;
-
-    if (System.getProperty("mrj.version") != null)
-    {
-      varname = "DYLD_LIBRARY_PATH";    // We're on a Mac.
-      shlibname = "libsbmlj.jnilib and/or libsbml.dylib";
-    }
-    else
-    {
-      varname = "LD_LIBRARY_PATH";      // We're not on a Mac.
-      shlibname = "libsbmlj.so and/or libsbml.so";
-    }
-
-    try
-    {
-      System.loadLibrary("sbmlj");
-      // For extra safety, check that the jar file is in the classpath.
-      Class.forName("org.sbml.libsbml.libsbml");
-    }
-    catch (SecurityException e)
-    {
-      e.printStackTrace();
-      System.err.println("Could not load the libSBML library files due to a"+
-                         " security exception.\n");
-      System.exit(1);
-    }
-    catch (UnsatisfiedLinkError e)
-    {
-      e.printStackTrace();
-      System.err.println("Error: could not link with the libSBML library files."+
-                         " It is likely\nyour " + varname +
-                         " environment variable does not include the directories\n"+
-                         "containing the " + shlibname + " library files.\n");
-      System.exit(1);
-    }
-    catch (ClassNotFoundException e)
-    {
-      e.printStackTrace();
-      System.err.println("Error: unable to load the file libsbmlj.jar."+
-                         " It is likely\nyour -classpath option and CLASSPATH" +
-                         " environment variable\n"+
-                         "do not include the path to libsbmlj.jar.\n");
-      System.exit(1);
-    }
-  }
-}
+/*
+ * @file    TestValidation.java
+ * @brief   Validation of Date ModelCreator and ModelHistory unit tests
+ *
+ * @author  Akiya Jouraku (Java conversion)
+ * @author  Sarah Keating 
+ *
+ * $Id$
+ * $HeadURL$
+ *
+ * ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
+ *
+ * DO NOT EDIT THIS FILE.
+ *
+ * This file was generated automatically by converting the file located at
+ * src/annotation/test/TestValidation.cpp
+ * using the conversion program dev/utilities/translateTests/translateTests.pl.
+ * Any changes made here will be lost the next time the file is regenerated.
+ *
+ * -----------------------------------------------------------------------------
+ * This file is part of libSBML.  Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright 2005-2010 California Institute of Technology.
+ * Copyright 2002-2005 California Institute of Technology and
+ *                     Japan Science and Technology Corporation.
+ * 
+ * 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/libsbml/license.html
+ * -----------------------------------------------------------------------------
+ */
+
+package org.sbml.libsbml.test.annotation;
+
+import org.sbml.libsbml.*;
+
+import java.io.File;
+import java.lang.AssertionError;
+
+public class TestValidation {
+
+  static void assertTrue(boolean condition) throws AssertionError
+  {
+    if (condition == true)
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+
+  static void assertEquals(Object a, Object b) throws AssertionError
+  {
+    if ( (a == null) && (b == null) )
+    {
+      return;
+    }
+    else if ( (a == null) || (b == null) )
+    {
+      throw new AssertionError();
+    }
+    else if (a.equals(b))
+    {
+      return;
+    }
+
+    throw new AssertionError();
+  }
+
+  static void assertNotEquals(Object a, Object b) throws AssertionError
+  {
+    if ( (a == null) && (b == null) )
+    {
+      throw new AssertionError();
+    }
+    else if ( (a == null) || (b == null) )
+    {
+      return;
+    }
+    else if (a.equals(b))
+    {
+      throw new AssertionError();
+    }
+  }
+
+  static void assertEquals(boolean a, boolean b) throws AssertionError
+  {
+    if ( a == b )
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+
+  static void assertNotEquals(boolean a, boolean b) throws AssertionError
+  {
+    if ( a != b )
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+
+  static void assertEquals(int a, int b) throws AssertionError
+  {
+    if ( a == b )
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+
+  static void assertNotEquals(int a, int b) throws AssertionError
+  {
+    if ( a != b )
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+
+  public void test_Validation_CVTerm1()
+  {
+    CVTerm cv = new CVTerm();
+    assertTrue( cv != null );
+    assertEquals( false, (cv.hasRequiredAttributes()) );
+    cv.setQualifierType(libsbml.MODEL_QUALIFIER);
+    assertEquals( false, (cv.hasRequiredAttributes()) );
+    cv.setModelQualifierType(libsbml.BQM_IS);
+    assertEquals( false, (cv.hasRequiredAttributes()) );
+    cv.addResource("ggg");
+    assertEquals( true, (cv.hasRequiredAttributes()) );
+    cv = null;
+  }
+
+  public void test_Validation_CVTerm2()
+  {
+    CVTerm cv = new CVTerm();
+    assertTrue( cv != null );
+    assertEquals( false, (cv.hasRequiredAttributes()) );
+    cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER);
+    assertEquals( false, (cv.hasRequiredAttributes()) );
+    cv.setBiologicalQualifierType(libsbml.BQB_IS);
+    assertEquals( false, (cv.hasRequiredAttributes()) );
+    cv.addResource("ggg");
+    assertEquals( true, (cv.hasRequiredAttributes()) );
+    cv = null;
+  }
+
+  public void test_Validation_Date1()
+  {
+    Date date = new Date(200,12,30,12,15,45,1,2,0);
+    assertTrue( date != null );
+    assertEquals( false, (date.representsValidDate()) );
+    date = null;
+  }
+
+  public void test_Validation_Date2()
+  {
+    Date date = new Date(2007,14,30,12,15,45,1,2,0);
+    assertTrue( date != null );
+    assertEquals( false, (date.representsValidDate()) );
+    date = null;
+  }
+
+  public void test_Validation_Date3()
+  {
+    Date date = new Date("Jan 12");
+    assertTrue( date != null );
+    assertEquals( false, (date.representsValidDate()) );
+    date = null;
+  }
+
+  public void test_Validation_Date4()
+  {
+    Date date = new Date(2007,12,30,12,15,45,1,2,0);
+    assertTrue( date != null );
+    assertEquals( true, date.representsValidDate() );
+    date = null;
+  }
+
+  public void test_Validation_Date_Default()
+  {
+    Date date1 = new Date();
+    Date date2 = new Date("");
+    assertTrue( date1.getYear() == (date2.getYear()) );
+    assertTrue( date1.getMonth() == (date2.getMonth()) );
+    assertTrue( date1.getDay() == (date2.getDay()) );
+    assertTrue( date1.getHour() == (date2.getHour()) );
+    assertTrue( date1.getMinute() == (date2.getMinute()) );
+    assertTrue( date1.getSecond() == (date2.getSecond()) );
+    assertTrue( date1.getSignOffset() == (date2.getSignOffset()) );
+    assertTrue( date1.getHoursOffset() == (date2.getHoursOffset()) );
+    assertTrue( date1.getMinutesOffset() == (date2.getMinutesOffset()) );
+    date1 = null;
+    date2 = null;
+  }
+
+  public void test_Validation_ModelCreator()
+  {
+    ModelCreator mc = new ModelCreator();
+    assertTrue( mc != null );
+    assertEquals( false, (mc.hasRequiredAttributes()) );
+    mc.setEmail("k123");
+    assertEquals( false, (mc.hasRequiredAttributes()) );
+    mc.setFamilyName("Keating");
+    assertEquals( false, (mc.hasRequiredAttributes()) );
+    mc.setGivenName("Sarah");
+    assertEquals( true, mc.hasRequiredAttributes() );
+    mc = null;
+  }
+
+  public void test_Validation_ModelHistory1()
+  {
+    ModelHistory mh = new ModelHistory();
+    assertTrue( mh != null );
+    assertEquals( false, (mh.hasRequiredAttributes()) );
+    Date date = new Date(2007,12,30,12,15,45,1,2,0);
+    mh.setCreatedDate(date);
+    assertEquals( false, (mh.hasRequiredAttributes()) );
+    mh.setModifiedDate(date);
+    assertEquals( false, (mh.hasRequiredAttributes()) );
+    ModelCreator mc = new ModelCreator();
+    mc.setFamilyName("Keating");
+    mc.setGivenName("Sarah");
+    mh.addCreator(mc);
+    assertEquals( true, mh.hasRequiredAttributes() );
+    mh = null;
+  }
+
+  public void test_Validation_ModelHistory2()
+  {
+    ModelHistory mh = new ModelHistory();
+    assertTrue( mh != null );
+    assertEquals( false, (mh.hasRequiredAttributes()) );
+    Date date = new Date(200,12,30,12,15,45,1,2,0);
+    mh.setCreatedDate(date);
+    assertEquals( false, (mh.hasRequiredAttributes()) );
+    mh.setModifiedDate(date);
+    assertEquals( false, (mh.hasRequiredAttributes()) );
+    ModelCreator mc = new ModelCreator();
+    mc.setFamilyName("Keating");
+    mc.setGivenName("Sarah");
+    mh.addCreator(mc);
+    assertEquals( false, (mh.hasRequiredAttributes()) );
+    mh = null;
+  }
+
+  public void test_Validation_ModelHistory3()
+  {
+    ModelHistory mh = new ModelHistory();
+    assertTrue( mh != null );
+    assertEquals( false, (mh.hasRequiredAttributes()) );
+    Date date = new Date(2007,12,30,12,15,45,1,2,0);
+    mh.setCreatedDate(date);
+    assertEquals( false, (mh.hasRequiredAttributes()) );
+    mh.setModifiedDate(date);
+    assertEquals( false, (mh.hasRequiredAttributes()) );
+    ModelCreator mc = new ModelCreator();
+    mc.setFamilyName("Keating");
+    mh.addCreator(mc);
+    assertEquals( false, (mh.hasRequiredAttributes()) );
+    mh = null;
+  }
+
+  /**
+   * Loads the SWIG-generated libSBML Java module when this class is
+   * loaded, or reports a sensible diagnostic message about why it failed.
+   */
+  static
+  {
+    String varname;
+    String shlibname;
+
+    if (System.getProperty("mrj.version") != null)
+    {
+      varname = "DYLD_LIBRARY_PATH";    // We're on a Mac.
+      shlibname = "libsbmlj.jnilib and/or libsbml.dylib";
+    }
+    else
+    {
+      varname = "LD_LIBRARY_PATH";      // We're not on a Mac.
+      shlibname = "libsbmlj.so and/or libsbml.so";
+    }
+
+    try
+    {
+      System.loadLibrary("sbmlj");
+      // For extra safety, check that the jar file is in the classpath.
+      Class.forName("org.sbml.libsbml.libsbml");
+    }
+    catch (SecurityException e)
+    {
+      e.printStackTrace();
+      System.err.println("Could not load the libSBML library files due to a"+
+                         " security exception.\n");
+      System.exit(1);
+    }
+    catch (UnsatisfiedLinkError e)
+    {
+      e.printStackTrace();
+      System.err.println("Error: could not link with the libSBML library files."+
+                         " It is likely\nyour " + varname +
+                         " environment variable does not include the directories\n"+
+                         "containing the " + shlibname + " library files.\n");
+      System.exit(1);
+    }
+    catch (ClassNotFoundException e)
+    {
+      e.printStackTrace();
+      System.err.println("Error: unable to load the file libsbmlj.jar."+
+                         " It is likely\nyour -classpath option and CLASSPATH" +
+                         " environment variable\n"+
+                         "do not include the path to libsbmlj.jar.\n");
+      System.exit(1);
+    }
+  }
+}


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 12703
          http://sbml.svn.sourceforge.net/sbml/?rev=12703&view=rev
Author:   sarahkeating
Date:     2011-01-26 15:38:37 +0000 (Wed, 26 Jan 2011)

Log Message:
-----------
updated for new test in annotation/test directory

Modified Paths:
--------------
    trunk/libsbml/dev/utilities/translateTests/translateTests.pl

Modified: trunk/libsbml/dev/utilities/translateTests/translateTests.pl
===================================================================
--- trunk/libsbml/dev/utilities/translateTests/translateTests.pl	2011-01-26 15:37:25 UTC (rev 12702)
+++ trunk/libsbml/dev/utilities/translateTests/translateTests.pl	2011-01-26 15:38:37 UTC (rev 12703)
@@ -26,7 +26,7 @@
 
 (my $myname = $0) =~ s,.*[\/\\],,;
 my $usage = <<EOF;
-Usage: $myname [-d output_dir] [-h] [-r|-p|-j|-c] ctest_file [ ctest_file2 ... ]
+Usage: $myname [-o output_dir] [-h] [-r|-p|-j|-c] ctest_file [ ctest_file2 ... ]
   -r : Converts given C/C++ test files into Ruby scripts (*Default*)
   -p : Converts given C/C++ test files into Python scripts 
   -j : Converts given C/C++ test files into Java files
@@ -138,6 +138,7 @@
   addFormulaUnitsData    => 0,
   getInternalId          => 0,
   setInternalId          => 0,
+  parseRDFAnnotationWithModelHistory => 0,
 );
 
 my %IgnoreTestFunc = (
@@ -180,9 +181,13 @@
   test_Date_setHoursOffset_neg_arg               => 0,
   test_Date_setOffsetSign                        => 0,
   test_Date_ConstructorException                 => 0,
+  test_Date_accessWithNULL                       => 0,
   test_ModelCreator_ConstructorException         => 0,
+  test_ModelCreator_accessWithNULL               => 0,
   test_ModelHistory_ConstructorException         => 0,
+  test_ModelHistory_accessWithNULL               => 0,
   test_CVTerm_ConstructorException               => 0,
+  test_CVTerm_accessWithNULL                     => 0,
   test_Model_copyConstructor                     => 0,
   test_Model_assignmentOperator                  => 0,
   test_Model_clone                               => 0,


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 12702
          http://sbml.svn.sourceforge.net/sbml/?rev=12702&view=rev
Author:   sarahkeating
Date:     2011-01-26 15:37:25 +0000 (Wed, 26 Jan 2011)

Log Message:
-----------
updated tests in line with current annotation/test directory

Modified Paths:
--------------
    trunk/libsbml/src/bindings/csharp/test/annotation/TestRDFAnnotationC.cs
    trunk/libsbml/src/bindings/csharp/test/annotation/TestValidation.cs

Modified: trunk/libsbml/src/bindings/csharp/test/annotation/TestRDFAnnotationC.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/annotation/TestRDFAnnotationC.cs	2011-01-26 07:30:37 UTC (rev 12701)
+++ trunk/libsbml/src/bindings/csharp/test/annotation/TestRDFAnnotationC.cs	2011-01-26 15:37:25 UTC (rev 12702)
@@ -1,321 +1,331 @@
-///  @file    TestRDFAnnotationC.cs
-///  @brief   RDFAnnotation parser unit tests
-///  @author  Frank Bergmann (Csharp conversion)
-///  @author  Akiya Jouraku (Csharp conversion)
-///  @author  Sarah Keating 
-/// 
-///  $Id$
-///  $HeadURL$
-/// 
-///  ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
-/// 
-///  DO NOT EDIT THIS FILE.
-/// 
-///  This file was generated automatically by converting the file located at
-///  src/annotation/test/TestRDFAnnotationC.c
-///  using the conversion program dev/utilities/translateTests/translateTests.pl.
-///  Any changes made here will be lost the next time the file is regenerated.
-/// 
-///  -----------------------------------------------------------------------------
-///  This file is part of libSBML.  Please visit http://sbml.org for more
-///  information about SBML, and the latest version of libSBML.
-/// 
-///  Copyright 2005-2010 California Institute of Technology.
-///  Copyright 2002-2005 California Institute of Technology and
-///                      Japan Science and Technology Corporation.
-///  
-///  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/libsbml/license.html
-///  -----------------------------------------------------------------------------
-
-
-namespace LibSBMLCSTest {
-
-  using libsbml;
-
-  using System;
-
-  using System.IO;
-
-  public class TestRDFAnnotationC {
-    public class AssertionError : System.Exception 
-    {
-      public AssertionError() : base()
-      {
-        
-      }
-    }
-
-
-    static void assertTrue(bool condition)
-    {
-      if (condition == true)
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-    static void assertEquals(object a, object b)
-    {
-      if ( (a == null) && (b == null) )
-      {
-        return;
-      }
-      else if ( (a == null) || (b == null) )
-      {
-        throw new AssertionError();
-      }
-      else if (a.Equals(b))
-      {
-        return;
-      }
-  
-      throw new AssertionError();
-    }
-
-    static void assertNotEquals(object a, object b)
-    {
-      if ( (a == null) && (b == null) )
-      {
-        throw new AssertionError();
-      }
-      else if ( (a == null) || (b == null) )
-      {
-        return;
-      }
-      else if (a.Equals(b))
-      {
-        throw new AssertionError();
-      }
-    }
-
-    static void assertEquals(bool a, bool b)
-    {
-      if ( a == b )
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-    static void assertNotEquals(bool a, bool b)
-    {
-      if ( a != b )
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-    static void assertEquals(int a, int b)
-    {
-      if ( a == b )
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-    static void assertNotEquals(int a, int b)
-    {
-      if ( a != b )
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-    private SBMLDocument d;
-    private Model m;
-
-    public void setUp()
-    {
-      string filename = "../../annotation/test/test-data/annotation.xml";
-      d = libsbml.readSBML(filename);
-      m = d.getModel();
-    }
-
-    public void tearDown()
-    {
-      d = null;
-    }
-
-    public void test_RDFAnnotation_C_delete()
-    {
-      SBase obj = m.getCompartment(0);
-      XMLNode node = RDFAnnotationParser.parseCVTerms(obj);
-      XMLNode n1 = RDFAnnotationParser.deleteRDFAnnotation(node);
-      assertTrue( n1.getNumChildren() == 0 );
-      assertTrue((  "annotation" == n1.getName() ));
-      node = null;
-    }
-
-    public void test_RDFAnnotation_C_getModelHistory()
-    {
-      assertTrue( ! (m == null) );
-      ModelHistory history = m.getModelHistory();
-      assertTrue( history != null );
-      ModelCreator mc = history.getCreator(0);
-      assertTrue((  "Le Novere" == mc.getFamilyName() ));
-      assertTrue((  "Nicolas" == mc.getGivenName() ));
-      assertTrue((  "le...@eb..." == mc.getEmail() ));
-      assertTrue((  "EMBL-EBI" == mc.getOrganisation() ));
-      Date date = history.getCreatedDate();
-      assertTrue( date.getYear() == 2005 );
-      assertTrue( date.getMonth() == 2 );
-      assertTrue( date.getDay() == 2 );
-      assertTrue( date.getHour() == 14 );
-      assertTrue( date.getMinute() == 56 );
-      assertTrue( date.getSecond() == 11 );
-      assertTrue( date.getSignOffset() == 0 );
-      assertTrue( date.getHoursOffset() == 0 );
-      assertTrue( date.getMinutesOffset() == 0 );
-      assertTrue((  "2005-02-02T14:56:11Z" == date.getDateAsString() ));
-      date = history.getModifiedDate();
-      assertTrue( date.getYear() == 2006 );
-      assertTrue( date.getMonth() == 5 );
-      assertTrue( date.getDay() == 30 );
-      assertTrue( date.getHour() == 10 );
-      assertTrue( date.getMinute() == 46 );
-      assertTrue( date.getSecond() == 2 );
-      assertTrue( date.getSignOffset() == 0 );
-      assertTrue( date.getHoursOffset() == 0 );
-      assertTrue( date.getMinutesOffset() == 0 );
-      assertTrue((  "2006-05-30T10:46:02Z" == date.getDateAsString() ));
-    }
-
-    public void test_RDFAnnotation_C_parseCVTerms()
-    {
-      SBase obj = m.getCompartment(0);
-      XMLNode node = RDFAnnotationParser.parseCVTerms(obj);
-      assertTrue( node.getNumChildren() == 1 );
-      XMLNode rdf = node.getChild(0);
-      assertTrue((  "RDF" == rdf.getName() ));
-      assertTrue((  "rdf" == rdf.getPrefix() ));
-      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() ));
-      assertTrue( rdf.getNumChildren() == 1 );
-      XMLNode desc = rdf.getChild(0);
-      assertTrue((  "Description" == desc.getName() ));
-      assertTrue((  "rdf" == desc.getPrefix() ));
-      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() ));
-      assertTrue( desc.getNumChildren() == 1 );
-      XMLNode is1 = desc.getChild(0);
-      assertTrue((  "is" == is1.getName() ));
-      assertTrue((  "bqbiol" == is1.getPrefix() ));
-      assertTrue( is1.getNumChildren() == 1 );
-      XMLNode Bag = is1.getChild(0);
-      assertTrue((  "Bag" == Bag.getName() ));
-      assertTrue((  "rdf" == Bag.getPrefix() ));
-      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI() ));
-      assertTrue( Bag.getNumChildren() == 4 );
-      XMLNode li = Bag.getChild(0);
-      assertTrue((  "li" == li.getName() ));
-      assertTrue((  "rdf" == li.getPrefix() ));
-      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() ));
-      assertTrue( li.getNumChildren() == 0 );
-      XMLNode li1 = Bag.getChild(1);
-      assertTrue((  "li" == li1.getName() ));
-      assertTrue((  "rdf" == li1.getPrefix() ));
-      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li1.getURI() ));
-      assertTrue( li1.getNumChildren() == 0 );
-      XMLNode li2 = Bag.getChild(2);
-      assertTrue((  "li" == li2.getName() ));
-      assertTrue((  "rdf" == li2.getPrefix() ));
-      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li2.getURI() ));
-      assertTrue( li2.getNumChildren() == 0 );
-      XMLNode li3 = Bag.getChild(3);
-      assertTrue((  "li" == li3.getName() ));
-      assertTrue((  "rdf" == li3.getPrefix() ));
-      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li3.getURI() ));
-      assertTrue( li3.getNumChildren() == 0 );
-      node = null;
-    }
-
-    public void test_RDFAnnotation_C_parseModelHistory()
-    {
-      XMLNode node = RDFAnnotationParser.parseModelHistory(m);
-      assertTrue( node.getNumChildren() == 1 );
-      XMLNode rdf = node.getChild(0);
-      assertTrue((  "RDF" == rdf.getName() ));
-      assertTrue((  "rdf" == rdf.getPrefix() ));
-      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() ));
-      assertTrue( rdf.getNumChildren() == 1 );
-      XMLNode desc = rdf.getChild(0);
-      assertTrue((  "Description" == desc.getName() ));
-      assertTrue((  "rdf" == desc.getPrefix() ));
-      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() ));
-      assertTrue( desc.getNumChildren() == 3 );
-      XMLNode creator = desc.getChild(0);
-      assertTrue((  "creator" == creator.getName() ));
-      assertTrue((  "dc" == creator.getPrefix() ));
-      assertTrue((  "http://purl.org/dc/elements/1.1/" == creator.getURI() ));
-      assertTrue( creator.getNumChildren() == 1 );
-      XMLNode Bag = creator.getChild(0);
-      assertTrue((  "Bag" == Bag.getName() ));
-      assertTrue((  "rdf" == Bag.getPrefix() ));
-      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI() ));
-      assertTrue( Bag.getNumChildren() == 1 );
-      XMLNode li = Bag.getChild(0);
-      assertTrue((  "li" == li.getName() ));
-      assertTrue((  "rdf" == li.getPrefix() ));
-      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() ));
-      assertTrue( li.getNumChildren() == 3 );
-      XMLNode N = li.getChild(0);
-      assertTrue((  "N" == N.getName() ));
-      assertTrue((  "vCard" == N.getPrefix() ));
-      assertTrue((  "http://www.w3.org/2001/vcard-rdf/3.0#" == N.getURI() ));
-      assertTrue( N.getNumChildren() == 2 );
-      XMLNode Family = N.getChild(0);
-      assertTrue((  "Family" == Family.getName() ));
-      assertTrue((  "vCard" == Family.getPrefix() ));
-      assertTrue((  "http://www.w3.org/2001/vcard-rdf/3.0#" == Family.getURI() ));
-      assertTrue( Family.getNumChildren() == 1 );
-      XMLNode Given = N.getChild(1);
-      assertTrue((  "Given" == Given.getName() ));
-      assertTrue((  "vCard" == Given.getPrefix() ));
-      assertTrue((  "http://www.w3.org/2001/vcard-rdf/3.0#" == Given.getURI() ));
-      assertTrue( Given.getNumChildren() == 1 );
-      XMLNode EMAIL = li.getChild(1);
-      assertTrue((  "EMAIL" == EMAIL.getName() ));
-      assertTrue((  "vCard" == EMAIL.getPrefix() ));
-      assertTrue((  "http://www.w3.org/2001/vcard-rdf/3.0#" == EMAIL.getURI() ));
-      assertTrue( EMAIL.getNumChildren() == 1 );
-      XMLNode ORG = li.getChild(2);
-      assertTrue((  "ORG" == ORG.getName() ));
-      assertTrue((  "vCard" == ORG.getPrefix() ));
-      assertTrue((  "http://www.w3.org/2001/vcard-rdf/3.0#" == ORG.getURI() ));
-      assertTrue( ORG.getNumChildren() == 1 );
-      XMLNode Orgname = ORG.getChild(0);
-      assertTrue((  "Orgname" == Orgname.getName() ));
-      assertTrue((  "vCard" == Orgname.getPrefix() ));
-      assertTrue((  "http://www.w3.org/2001/vcard-rdf/3.0#" == Orgname.getURI() ));
-      assertTrue( Orgname.getNumChildren() == 1 );
-      XMLNode created = desc.getChild(1);
-      assertTrue((  "created" == created.getName() ));
-      assertTrue((  "dcterms" == created.getPrefix() ));
-      assertTrue((  "http://purl.org/dc/terms/" == created.getURI() ));
-      assertTrue( created.getNumChildren() == 1 );
-      XMLNode cr_date = created.getChild(0);
-      assertTrue((  "W3CDTF" == cr_date.getName() ));
-      assertTrue((  "dcterms" == cr_date.getPrefix() ));
-      assertTrue((  "http://purl.org/dc/terms/" == cr_date.getURI() ));
-      assertTrue( cr_date.getNumChildren() == 1 );
-      XMLNode modified = desc.getChild(2);
-      assertTrue((  "modified" == modified.getName() ));
-      assertTrue((  "dcterms" == modified.getPrefix() ));
-      assertTrue((  "http://purl.org/dc/terms/" == modified.getURI() ));
-      assertTrue( modified.getNumChildren() == 1 );
-      XMLNode mo_date = created.getChild(0);
-      assertTrue((  "W3CDTF" == mo_date.getName() ));
-      assertTrue((  "dcterms" == mo_date.getPrefix() ));
-      assertTrue((  "http://purl.org/dc/terms/" == mo_date.getURI() ));
-      assertTrue( mo_date.getNumChildren() == 1 );
-      node = null;
-    }
-
-  }
-}
+///  @file    TestRDFAnnotationC.cs
+///  @brief   RDFAnnotation parser unit tests
+///  @author  Frank Bergmann (Csharp conversion)
+///  @author  Akiya Jouraku (Csharp conversion)
+///  @author  Sarah Keating 
+/// 
+///  $Id$
+///  $HeadURL$
+/// 
+///  ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
+/// 
+///  DO NOT EDIT THIS FILE.
+/// 
+///  This file was generated automatically by converting the file located at
+///  src/annotation/test/TestRDFAnnotationC.c
+///  using the conversion program dev/utilities/translateTests/translateTests.pl.
+///  Any changes made here will be lost the next time the file is regenerated.
+/// 
+///  -----------------------------------------------------------------------------
+///  This file is part of libSBML.  Please visit http://sbml.org for more
+///  information about SBML, and the latest version of libSBML.
+/// 
+///  Copyright 2005-2010 California Institute of Technology.
+///  Copyright 2002-2005 California Institute of Technology and
+///                      Japan Science and Technology Corporation.
+///  
+///  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/libsbml/license.html
+///  -----------------------------------------------------------------------------
+
+
+namespace LibSBMLCSTest {
+
+  using libsbml;
+
+  using System;
+
+  using System.IO;
+
+  public class TestRDFAnnotationC {
+    public class AssertionError : System.Exception 
+    {
+      public AssertionError() : base()
+      {
+        
+      }
+    }
+
+
+    static void assertTrue(bool condition)
+    {
+      if (condition == true)
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+    static void assertEquals(object a, object b)
+    {
+      if ( (a == null) && (b == null) )
+      {
+        return;
+      }
+      else if ( (a == null) || (b == null) )
+      {
+        throw new AssertionError();
+      }
+      else if (a.Equals(b))
+      {
+        return;
+      }
+  
+      throw new AssertionError();
+    }
+
+    static void assertNotEquals(object a, object b)
+    {
+      if ( (a == null) && (b == null) )
+      {
+        throw new AssertionError();
+      }
+      else if ( (a == null) || (b == null) )
+      {
+        return;
+      }
+      else if (a.Equals(b))
+      {
+        throw new AssertionError();
+      }
+    }
+
+    static void assertEquals(bool a, bool b)
+    {
+      if ( a == b )
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+    static void assertNotEquals(bool a, bool b)
+    {
+      if ( a != b )
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+    static void assertEquals(int a, int b)
+    {
+      if ( a == b )
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+    static void assertNotEquals(int a, int b)
+    {
+      if ( a != b )
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+    private SBMLDocument d;
+    private Model m;
+
+    public void setUp()
+    {
+      string filename = "../../annotation/test/test-data/annotation.xml";
+      d = libsbml.readSBML(filename);
+      m = d.getModel();
+    }
+
+    public void tearDown()
+    {
+      d = null;
+    }
+
+    public void test_RDFAnnotation_C_accessWithNULL()
+    {
+      assertTrue( RDFAnnotationParser.createCVTerms(null) == null );
+      assertTrue( RDFAnnotationParser.createRDFDescription(null) == null );
+      assertTrue( RDFAnnotationParser.deleteRDFAnnotation(null) == null );
+      assertTrue( RDFAnnotationParser.parseCVTerms(null) == null );
+      assertTrue( RDFAnnotationParser.parseModelHistory(null) == null );
+      RDFAnnotationParser.parseRDFAnnotation(null,null);
+    }
+
+    public void test_RDFAnnotation_C_delete()
+    {
+      SBase obj = m.getCompartment(0);
+      XMLNode node = RDFAnnotationParser.parseCVTerms(obj);
+      XMLNode n1 = RDFAnnotationParser.deleteRDFAnnotation(node);
+      assertTrue( n1.getNumChildren() == 0 );
+      assertTrue((  "annotation" == n1.getName() ));
+      node = null;
+    }
+
+    public void test_RDFAnnotation_C_getModelHistory()
+    {
+      assertTrue( ! (m == null) );
+      ModelHistory history = m.getModelHistory();
+      assertTrue( history != null );
+      ModelCreator mc = history.getCreator(0);
+      assertTrue((  "Le Novere" == mc.getFamilyName() ));
+      assertTrue((  "Nicolas" == mc.getGivenName() ));
+      assertTrue((  "le...@eb..." == mc.getEmail() ));
+      assertTrue((  "EMBL-EBI" == mc.getOrganisation() ));
+      Date date = history.getCreatedDate();
+      assertTrue( date.getYear() == 2005 );
+      assertTrue( date.getMonth() == 2 );
+      assertTrue( date.getDay() == 2 );
+      assertTrue( date.getHour() == 14 );
+      assertTrue( date.getMinute() == 56 );
+      assertTrue( date.getSecond() == 11 );
+      assertTrue( date.getSignOffset() == 0 );
+      assertTrue( date.getHoursOffset() == 0 );
+      assertTrue( date.getMinutesOffset() == 0 );
+      assertTrue((  "2005-02-02T14:56:11Z" == date.getDateAsString() ));
+      date = history.getModifiedDate();
+      assertTrue( date.getYear() == 2006 );
+      assertTrue( date.getMonth() == 5 );
+      assertTrue( date.getDay() == 30 );
+      assertTrue( date.getHour() == 10 );
+      assertTrue( date.getMinute() == 46 );
+      assertTrue( date.getSecond() == 2 );
+      assertTrue( date.getSignOffset() == 0 );
+      assertTrue( date.getHoursOffset() == 0 );
+      assertTrue( date.getMinutesOffset() == 0 );
+      assertTrue((  "2006-05-30T10:46:02Z" == date.getDateAsString() ));
+    }
+
+    public void test_RDFAnnotation_C_parseCVTerms()
+    {
+      SBase obj = m.getCompartment(0);
+      XMLNode node = RDFAnnotationParser.parseCVTerms(obj);
+      assertTrue( node.getNumChildren() == 1 );
+      XMLNode rdf = node.getChild(0);
+      assertTrue((  "RDF" == rdf.getName() ));
+      assertTrue((  "rdf" == rdf.getPrefix() ));
+      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() ));
+      assertTrue( rdf.getNumChildren() == 1 );
+      XMLNode desc = rdf.getChild(0);
+      assertTrue((  "Description" == desc.getName() ));
+      assertTrue((  "rdf" == desc.getPrefix() ));
+      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() ));
+      assertTrue( desc.getNumChildren() == 1 );
+      XMLNode is1 = desc.getChild(0);
+      assertTrue((  "is" == is1.getName() ));
+      assertTrue((  "bqbiol" == is1.getPrefix() ));
+      assertTrue( is1.getNumChildren() == 1 );
+      XMLNode Bag = is1.getChild(0);
+      assertTrue((  "Bag" == Bag.getName() ));
+      assertTrue((  "rdf" == Bag.getPrefix() ));
+      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI() ));
+      assertTrue( Bag.getNumChildren() == 4 );
+      XMLNode li = Bag.getChild(0);
+      assertTrue((  "li" == li.getName() ));
+      assertTrue((  "rdf" == li.getPrefix() ));
+      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() ));
+      assertTrue( li.getNumChildren() == 0 );
+      XMLNode li1 = Bag.getChild(1);
+      assertTrue((  "li" == li1.getName() ));
+      assertTrue((  "rdf" == li1.getPrefix() ));
+      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li1.getURI() ));
+      assertTrue( li1.getNumChildren() == 0 );
+      XMLNode li2 = Bag.getChild(2);
+      assertTrue((  "li" == li2.getName() ));
+      assertTrue((  "rdf" == li2.getPrefix() ));
+      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li2.getURI() ));
+      assertTrue( li2.getNumChildren() == 0 );
+      XMLNode li3 = Bag.getChild(3);
+      assertTrue((  "li" == li3.getName() ));
+      assertTrue((  "rdf" == li3.getPrefix() ));
+      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li3.getURI() ));
+      assertTrue( li3.getNumChildren() == 0 );
+      node = null;
+    }
+
+    public void test_RDFAnnotation_C_parseModelHistory()
+    {
+      XMLNode node = RDFAnnotationParser.parseModelHistory(m);
+      assertTrue( node.getNumChildren() == 1 );
+      XMLNode rdf = node.getChild(0);
+      assertTrue((  "RDF" == rdf.getName() ));
+      assertTrue((  "rdf" == rdf.getPrefix() ));
+      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() ));
+      assertTrue( rdf.getNumChildren() == 1 );
+      XMLNode desc = rdf.getChild(0);
+      assertTrue((  "Description" == desc.getName() ));
+      assertTrue((  "rdf" == desc.getPrefix() ));
+      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() ));
+      assertTrue( desc.getNumChildren() == 3 );
+      XMLNode creator = desc.getChild(0);
+      assertTrue((  "creator" == creator.getName() ));
+      assertTrue((  "dc" == creator.getPrefix() ));
+      assertTrue((  "http://purl.org/dc/elements/1.1/" == creator.getURI() ));
+      assertTrue( creator.getNumChildren() == 1 );
+      XMLNode Bag = creator.getChild(0);
+      assertTrue((  "Bag" == Bag.getName() ));
+      assertTrue((  "rdf" == Bag.getPrefix() ));
+      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI() ));
+      assertTrue( Bag.getNumChildren() == 1 );
+      XMLNode li = Bag.getChild(0);
+      assertTrue((  "li" == li.getName() ));
+      assertTrue((  "rdf" == li.getPrefix() ));
+      assertTrue((  "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() ));
+      assertTrue( li.getNumChildren() == 3 );
+      XMLNode N = li.getChild(0);
+      assertTrue((  "N" == N.getName() ));
+      assertTrue((  "vCard" == N.getPrefix() ));
+      assertTrue((  "http://www.w3.org/2001/vcard-rdf/3.0#" == N.getURI() ));
+      assertTrue( N.getNumChildren() == 2 );
+      XMLNode Family = N.getChild(0);
+      assertTrue((  "Family" == Family.getName() ));
+      assertTrue((  "vCard" == Family.getPrefix() ));
+      assertTrue((  "http://www.w3.org/2001/vcard-rdf/3.0#" == Family.getURI() ));
+      assertTrue( Family.getNumChildren() == 1 );
+      XMLNode Given = N.getChild(1);
+      assertTrue((  "Given" == Given.getName() ));
+      assertTrue((  "vCard" == Given.getPrefix() ));
+      assertTrue((  "http://www.w3.org/2001/vcard-rdf/3.0#" == Given.getURI() ));
+      assertTrue( Given.getNumChildren() == 1 );
+      XMLNode EMAIL = li.getChild(1);
+      assertTrue((  "EMAIL" == EMAIL.getName() ));
+      assertTrue((  "vCard" == EMAIL.getPrefix() ));
+      assertTrue((  "http://www.w3.org/2001/vcard-rdf/3.0#" == EMAIL.getURI() ));
+      assertTrue( EMAIL.getNumChildren() == 1 );
+      XMLNode ORG = li.getChild(2);
+      assertTrue((  "ORG" == ORG.getName() ));
+      assertTrue((  "vCard" == ORG.getPrefix() ));
+      assertTrue((  "http://www.w3.org/2001/vcard-rdf/3.0#" == ORG.getURI() ));
+      assertTrue( ORG.getNumChildren() == 1 );
+      XMLNode Orgname = ORG.getChild(0);
+      assertTrue((  "Orgname" == Orgname.getName() ));
+      assertTrue((  "vCard" == Orgname.getPrefix() ));
+      assertTrue((  "http://www.w3.org/2001/vcard-rdf/3.0#" == Orgname.getURI() ));
+      assertTrue( Orgname.getNumChildren() == 1 );
+      XMLNode created = desc.getChild(1);
+      assertTrue((  "created" == created.getName() ));
+      assertTrue((  "dcterms" == created.getPrefix() ));
+      assertTrue((  "http://purl.org/dc/terms/" == created.getURI() ));
+      assertTrue( created.getNumChildren() == 1 );
+      XMLNode cr_date = created.getChild(0);
+      assertTrue((  "W3CDTF" == cr_date.getName() ));
+      assertTrue((  "dcterms" == cr_date.getPrefix() ));
+      assertTrue((  "http://purl.org/dc/terms/" == cr_date.getURI() ));
+      assertTrue( cr_date.getNumChildren() == 1 );
+      XMLNode modified = desc.getChild(2);
+      assertTrue((  "modified" == modified.getName() ));
+      assertTrue((  "dcterms" == modified.getPrefix() ));
+      assertTrue((  "http://purl.org/dc/terms/" == modified.getURI() ));
+      assertTrue( modified.getNumChildren() == 1 );
+      XMLNode mo_date = created.getChild(0);
+      assertTrue((  "W3CDTF" == mo_date.getName() ));
+      assertTrue((  "dcterms" == mo_date.getPrefix() ));
+      assertTrue((  "http://purl.org/dc/terms/" == mo_date.getURI() ));
+      assertTrue( mo_date.getNumChildren() == 1 );
+      node = null;
+    }
+
+  }
+}

Modified: trunk/libsbml/src/bindings/csharp/test/annotation/TestValidation.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/annotation/TestValidation.cs	2011-01-26 07:30:37 UTC (rev 12701)
+++ trunk/libsbml/src/bindings/csharp/test/annotation/TestValidation.cs	2011-01-26 15:37:25 UTC (rev 12702)
@@ -1,261 +1,278 @@
-///  @file    TestValidation.cs
-///  @brief   Validation of Date ModelCreator and ModelHistory unit tests
-///  @author  Frank Bergmann (Csharp conversion)
-///  @author  Akiya Jouraku (Csharp conversion)
-///  @author  Sarah Keating 
-/// 
-///  $Id$
-///  $HeadURL$
-/// 
-///  ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
-/// 
-///  DO NOT EDIT THIS FILE.
-/// 
-///  This file was generated automatically by converting the file located at
-///  src/annotation/test/TestValidation.cpp
-///  using the conversion program dev/utilities/translateTests/translateTests.pl.
-///  Any changes made here will be lost the next time the file is regenerated.
-/// 
-///  -----------------------------------------------------------------------------
-///  This file is part of libSBML.  Please visit http://sbml.org for more
-///  information about SBML, and the latest version of libSBML.
-/// 
-///  Copyright 2005-2010 California Institute of Technology.
-///  Copyright 2002-2005 California Institute of Technology and
-///                      Japan Science and Technology Corporation.
-///  
-///  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/libsbml/license.html
-///  -----------------------------------------------------------------------------
-
-
-namespace LibSBMLCSTest {
-
-  using libsbml;
-
-  using System;
-
-  using System.IO;
-
-  public class TestValidation {
-    public class AssertionError : System.Exception 
-    {
-      public AssertionError() : base()
-      {
-        
-      }
-    }
-
-
-    static void assertTrue(bool condition)
-    {
-      if (condition == true)
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-    static void assertEquals(object a, object b)
-    {
-      if ( (a == null) && (b == null) )
-      {
-        return;
-      }
-      else if ( (a == null) || (b == null) )
-      {
-        throw new AssertionError();
-      }
-      else if (a.Equals(b))
-      {
-        return;
-      }
-  
-      throw new AssertionError();
-    }
-
-    static void assertNotEquals(object a, object b)
-    {
-      if ( (a == null) && (b == null) )
-      {
-        throw new AssertionError();
-      }
-      else if ( (a == null) || (b == null) )
-      {
-        return;
-      }
-      else if (a.Equals(b))
-      {
-        throw new AssertionError();
-      }
-    }
-
-    static void assertEquals(bool a, bool b)
-    {
-      if ( a == b )
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-    static void assertNotEquals(bool a, bool b)
-    {
-      if ( a != b )
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-    static void assertEquals(int a, int b)
-    {
-      if ( a == b )
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-    static void assertNotEquals(int a, int b)
-    {
-      if ( a != b )
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-
-    public void test_Validation_CVTerm1()
-    {
-      CVTerm cv = new CVTerm();
-      assertTrue( cv != null );
-      assertEquals( false, (cv.hasRequiredAttributes()) );
-      cv.setQualifierType(libsbml.MODEL_QUALIFIER);
-      assertEquals( false, (cv.hasRequiredAttributes()) );
-      cv.setModelQualifierType(libsbml.BQM_IS);
-      assertEquals( false, (cv.hasRequiredAttributes()) );
-      cv.addResource("ggg");
-      assertEquals( true, (cv.hasRequiredAttributes()) );
-      cv = null;
-    }
-
-    public void test_Validation_CVTerm2()
-    {
-      CVTerm cv = new CVTerm();
-      assertTrue( cv != null );
-      assertEquals( false, (cv.hasRequiredAttributes()) );
-      cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER);
-      assertEquals( false, (cv.hasRequiredAttributes()) );
-      cv.setBiologicalQualifierType(libsbml.BQB_IS);
-      assertEquals( false, (cv.hasRequiredAttributes()) );
-      cv.addResource("ggg");
-      assertEquals( true, (cv.hasRequiredAttributes()) );
-      cv = null;
-    }
-
-    public void test_Validation_Date1()
-    {
-      Date date = new Date(200,12,30,12,15,45,1,2,0);
-      assertTrue( date != null );
-      assertEquals( false, (date.representsValidDate()) );
-      date = null;
-    }
-
-    public void test_Validation_Date2()
-    {
-      Date date = new Date(2007,14,30,12,15,45,1,2,0);
-      assertTrue( date != null );
-      assertEquals( false, (date.representsValidDate()) );
-      date = null;
-    }
-
-    public void test_Validation_Date3()
-    {
-      Date date = new Date("Jan 12");
-      assertTrue( date != null );
-      assertEquals( false, (date.representsValidDate()) );
-      date = null;
-    }
-
-    public void test_Validation_Date4()
-    {
-      Date date = new Date(2007,12,30,12,15,45,1,2,0);
-      assertTrue( date != null );
-      assertEquals( true, date.representsValidDate() );
-      date = null;
-    }
-
-    public void test_Validation_ModelCreator()
-    {
-      ModelCreator mc = new ModelCreator();
-      assertTrue( mc != null );
-      assertEquals( false, (mc.hasRequiredAttributes()) );
-      mc.setEmail("k123");
-      assertEquals( false, (mc.hasRequiredAttributes()) );
-      mc.setFamilyName("Keating");
-      assertEquals( false, (mc.hasRequiredAttributes()) );
-      mc.setGivenName("Sarah");
-      assertEquals( true, mc.hasRequiredAttributes() );
-      mc = null;
-    }
-
-    public void test_Validation_ModelHistory1()
-    {
-      ModelHistory mh = new ModelHistory();
-      assertTrue( mh != null );
-      assertEquals( false, (mh.hasRequiredAttributes()) );
-      Date date = new Date(2007,12,30,12,15,45,1,2,0);
-      mh.setCreatedDate(date);
-      assertEquals( false, (mh.hasRequiredAttributes()) );
-      mh.setModifiedDate(date);
-      assertEquals( false, (mh.hasRequiredAttributes()) );
-      ModelCreator mc = new ModelCreator();
-      mc.setFamilyName("Keating");
-      mc.setGivenName("Sarah");
-      mh.addCreator(mc);
-      assertEquals( true, mh.hasRequiredAttributes() );
-      mh = null;
-    }
-
-    public void test_Validation_ModelHistory2()
-    {
-      ModelHistory mh = new ModelHistory();
-      assertTrue( mh != null );
-      assertEquals( false, (mh.hasRequiredAttributes()) );
-      Date date = new Date(200,12,30,12,15,45,1,2,0);
-      mh.setCreatedDate(date);
-      assertEquals( false, (mh.hasRequiredAttributes()) );
-      mh.setModifiedDate(date);
-      assertEquals( false, (mh.hasRequiredAttributes()) );
-      ModelCreator mc = new ModelCreator();
-      mc.setFamilyName("Keating");
-      mc.setGivenName("Sarah");
-      mh.addCreator(mc);
-      assertEquals( false, (mh.hasRequiredAttributes()) );
-      mh = null;
-    }
-
-    public void test_Validation_ModelHistory3()
-    {
-      ModelHistory mh = new ModelHistory();
-      assertTrue( mh != null );
-      assertEquals( false, (mh.hasRequiredAttributes()) );
-      Date date = new Date(2007,12,30,12,15,45,1,2,0);
-      mh.setCreatedDate(date);
-      assertEquals( false, (mh.hasRequiredAttributes()) );
-      mh.setModifiedDate(date);
-      assertEquals( false, (mh.hasRequiredAttributes()) );
-      ModelCreator mc = new ModelCreator();
-      mc.setFamilyName("Keating");
-      mh.addCreator(mc);
-      assertEquals( false, (mh.hasRequiredAttributes()) );
-      mh = null;
-    }
-
-  }
-}
+///  @file    TestValidation.cs
+///  @brief   Validation of Date ModelCreator and ModelHistory unit tests
+///  @author  Frank Bergmann (Csharp conversion)
+///  @author  Akiya Jouraku (Csharp conversion)
+///  @author  Sarah Keating 
+/// 
+///  $Id$
+///  $HeadURL$
+/// 
+///  ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
+/// 
+///  DO NOT EDIT THIS FILE.
+/// 
+///  This file was generated automatically by converting the file located at
+///  src/annotation/test/TestValidation.cpp
+///  using the conversion program dev/utilities/translateTests/translateTests.pl.
+///  Any changes made here will be lost the next time the file is regenerated.
+/// 
+///  -----------------------------------------------------------------------------
+///  This file is part of libSBML.  Please visit http://sbml.org for more
+///  information about SBML, and the latest version of libSBML.
+/// 
+///  Copyright 2005-2010 California Institute of Technology.
+///  Copyright 2002-2005 California Institute of Technology and
+///                      Japan Science and Technology Corporation.
+///  
+///  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/libsbml/license.html
+///  -----------------------------------------------------------------------------
+
+
+namespace LibSBMLCSTest {
+
+  using libsbml;
+
+  using System;
+
+  using System.IO;
+
+  public class TestValidation {
+    public class AssertionError : System.Exception 
+    {
+      public AssertionError() : base()
+      {
+        
+      }
+    }
+
+
+    static void assertTrue(bool condition)
+    {
+      if (condition == true)
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+    static void assertEquals(object a, object b)
+    {
+      if ( (a == null) && (b == null) )
+      {
+        return;
+      }
+      else if ( (a == null) || (b == null) )
+      {
+        throw new AssertionError();
+      }
+      else if (a.Equals(b))
+      {
+        return;
+      }
+  
+      throw new AssertionError();
+    }
+
+    static void assertNotEquals(object a, object b)
+    {
+      if ( (a == null) && (b == null) )
+      {
+        throw new AssertionError();
+      }
+      else if ( (a == null) || (b == null) )
+      {
+        return;
+      }
+      else if (a.Equals(b))
+      {
+        throw new AssertionError();
+      }
+    }
+
+    static void assertEquals(bool a, bool b)
+    {
+      if ( a == b )
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+    static void assertNotEquals(bool a, bool b)
+    {
+      if ( a != b )
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+    static void assertEquals(int a, int b)
+    {
+      if ( a == b )
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+    static void assertNotEquals(int a, int b)
+    {
+      if ( a != b )
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+
+    public void test_Validation_CVTerm1()
+    {
+      CVTerm cv = new CVTerm();
+      assertTrue( cv != null );
+      assertEquals( false, (cv.hasRequiredAttributes()) );
+      cv.setQualifierType(libsbml.MODEL_QUALIFIER);
+      assertEquals( false, (cv.hasRequiredAttributes()) );
+      cv.setModelQualifierType(libsbml.BQM_IS);
+      assertEquals( false, (cv.hasRequiredAttributes()) );
+      cv.addResource("ggg");
+      assertEquals( true, (cv.hasRequiredAttributes()) );
+      cv = null;
+    }
+
+    public void test_Validation_CVTerm2()
+    {
+      CVTerm cv = new CVTerm();
+      assertTrue( cv != null );
+      assertEquals( false, (cv.hasRequiredAttributes()) );
+      cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER);
+      assertEquals( false, (cv.hasRequiredAttributes()) );
+      cv.setBiologicalQualifierType(libsbml.BQB_IS);
+      assertEquals( false, (cv.hasRequiredAttributes()) );
+      cv.addResource("ggg");
+      assertEquals( true, (cv.hasRequiredAttributes()) );
+      cv = null;
+    }
+
+    public void test_Validation_Date1()
+    {
+      Date date = new Date(200,12,30,12,15,45,1,2,0);
+      assertTrue( date != null );
+      assertEquals( false, (date.representsValidDate()) );
+      date = null;
+    }
+
+    public void test_Validation_Date2()
+    {
+      Date date = new Date(2007,14,30,12,15,45,1,2,0);
+      assertTrue( date != null );
+      assertEquals( false, (date.representsValidDate()) );
+      date = null;
+    }
+
+    public void test_Validation_Date3()
+    {
+      Date date = new Date("Jan 12");
+      assertTrue( date != null );
+      assertEquals( false, (date.representsValidDate()) );
+      date = null;
+    }
+
+    public void test_Validation_Date4()
+    {
+      Date date = new Date(2007,12,30,12,15,45,1,2,0);
+      assertTrue( date != null );
+      assertEquals( true, date.representsValidDate() );
+      date = null;
+    }
+
+    public void test_Validation_Date_Default()
+    {
+      Date date1 = new Date();
+      Date date2 = new Date("");
+      assertTrue( date1.getYear() == date2.getYear() );
+      assertTrue( date1.getMonth() == date2.getMonth() );
+      assertTrue( date1.getDay() == date2.getDay() );
+      assertTrue( date1.getHour() == date2.getHour() );
+      assertTrue( date1.getMinute() == date2.getMinute() );
+      assertTrue( date1.getSecond() == date2.getSecond() );
+      assertTrue( date1.getSignOffset() == date2.getSignOffset() );
+      assertTrue( date1.getHoursOffset() == date2.getHoursOffset() );
+      assertTrue( date1.getMinutesOffset() == date2.getMinutesOffset() );
+      date1 = null;
+      date2 = null;
+    }
+
+    public void test_Validation_ModelCreator()
+    {
+      ModelCreator mc = new ModelCreator();
+      assertTrue( mc != null );
+      assertEquals( false, (mc.hasRequiredAttributes()) );
+      mc.setEmail("k123");
+      assertEquals( false, (mc.hasRequiredAttributes()) );
+      mc.setFamilyName("Keating");
+      assertEquals( false, (mc.hasRequiredAttributes()) );
+      mc.setGivenName("Sarah");
+      assertEquals( true, mc.hasRequiredAttributes() );
+      mc = null;
+    }
+
+    public void test_Validation_ModelHistory1()
+    {
+      ModelHistory mh = new ModelHistory();
+      assertTrue( mh != null );
+      assertEquals( false, (mh.hasRequiredAttributes()) );
+      Date date = new Date(2007,12,30,12,15,45,1,2,0);
+      mh.setCreatedDate(date);
+      assertEquals( false, (mh.hasRequiredAttributes()) );
+      mh.setModifiedDate(date);
+      assertEquals( false, (mh.hasRequiredAttributes()) );
+      ModelCreator mc = new ModelCreator();
+      mc.setFamilyName("Keating");
+      mc.setGivenName("Sarah");
+      mh.addCreator(mc);
+      assertEquals( true, mh.hasRequiredAttributes() );
+      mh = null;
+    }
+
+    public void test_Validation_ModelHistory2()
+    {
+      ModelHistory mh = new ModelHistory();
+      assertTrue( mh != null );
+      assertEquals( false, (mh.hasRequiredAttributes()) );
+      Date date = new Date(200,12,30,12,15,45,1,2,0);
+      mh.setCreatedDate(date);
+      assertEquals( false, (mh.hasRequiredAttributes()) );
+      mh.setModifiedDate(date);
+      assertEquals( false, (mh.hasRequiredAttributes()) );
+      ModelCreator mc = new ModelCreator();
+      mc.setFamilyName("Keating");
+      mc.setGivenName("Sarah");
+      mh.addCreator(mc);
+      assertEquals( false, (mh.hasRequiredAttributes()) );
+      mh = null;
+    }
+
+    public void test_Validation_ModelHistory3()
+    {
+      ModelHistory mh = new ModelHistory();
+      assertTrue( mh != null );
+      assertEquals( false, (mh.hasRequiredAttributes()) );
+      Date date = new Date(2007,12,30,12,15,45,1,2,0);
+      mh.setCreatedDate(date);
+      assertEquals( false, (mh.hasRequiredAttributes()) );
+      mh.setModifiedDate(date);
+      assertEquals( false, (mh.hasRequiredAttributes()) );
+      ModelCreator mc = new ModelCreator();
+      mc.setFamilyName("Keating");
+      mh.addCreator(mc);
+      assertEquals( false, (mh.hasRequiredAttributes()) );
+      mh = null;
+    }
+
+  }
+}


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Revision: 12701
          http://sbml.svn.sourceforge.net/sbml/?rev=12701&view=rev
Author:   luciansmith
Date:     2011-01-26 07:30:37 +0000 (Wed, 26 Jan 2011)

Log Message:
-----------
Wrong column headers (thanks, Frank!)

Modified Paths:
--------------
    trunk/test-suite/cases/semantic/00944/00944-results.csv

Modified: trunk/test-suite/cases/semantic/00944/00944-results.csv
===================================================================
--- trunk/test-suite/cases/semantic/00944/00944-results.csv	2011-01-26 04:17:03 UTC (rev 12700)
+++ trunk/test-suite/cases/semantic/00944/00944-results.csv	2011-01-26 07:30:37 UTC (rev 12701)
@@ -1,4 +1,4 @@
-time,S1,C
+time,S1,k1
 0,1,1
 0.01,1.009950496,1
 0.02,1.019803904,1


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.