[sbml-svn] SF.net SVN: sbml:[21163] branches/libsbml-experimental

[<sar...@us...>]

Revision: 21163
          http://sourceforge.net/p/sbml/code/21163
Author:   sarahkeating
Date:     2014-09-27 12:23:47 +0000 (Sat, 27 Sep 2014)
Log Message:
-----------
Merged revision(s) 21155-21161 from trunk/libsbml:

Modified Paths:
--------------
    branches/libsbml-experimental/CMakeLists.txt
    branches/libsbml-experimental/NEWS.txt
    branches/libsbml-experimental/src/sbml/SBase.cpp
    branches/libsbml-experimental/src/sbml/SBase.h
    branches/libsbml-experimental/src/sbml/packages/comp/sbml/Submodel.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/util/CompFlatteningConverter.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/util/CompFlatteningConverter.h
    branches/libsbml-experimental/src/sbml/packages/comp/util/test/TestRunner.c
    branches/libsbml-experimental/src/sbml/test/TestSBMLDocument.c

Added Paths:
-----------
    branches/libsbml-experimental/src/sbml/packages/comp/util/test/TestCompFlatteningConverterStripPackage.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/util/test/test-data/test_external_flat_strip/

Property Changed:
----------------
    branches/libsbml-experimental/

Index: branches/libsbml-experimental
===================================================================
--- branches/libsbml-experimental	2014-09-27 12:12:15 UTC (rev 21162)
+++ branches/libsbml-experimental	2014-09-27 12:23:47 UTC (rev 21163)

Property changes on: branches/libsbml-experimental
___________________________________________________________________
Modified: svn:mergeinfo
## -2,4 +2,4 ##
 /branches/libsbml-4:9056-10118
 /branches/libsbml-5-conversion:14155-14227
 /branches/libsbml-ast-plugin:16251-19654
-/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19829,19831-21154
+/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19829,19831-21161
\ No newline at end of property
Modified: branches/libsbml-experimental/CMakeLists.txt
===================================================================
--- branches/libsbml-experimental/CMakeLists.txt	2014-09-27 12:12:15 UTC (rev 21162)
+++ branches/libsbml-experimental/CMakeLists.txt	2014-09-27 12:23:47 UTC (rev 21163)
@@ -805,10 +805,27 @@
                 if(${flag_var} MATCHES "/MD")
                     string(REGEX REPLACE "/MD" "/MT" ${flag_var} "${${flag_var}}")
                 endif(${flag_var} MATCHES "/MD")
+								
             endforeach(flag_var)
         add_definitions( -D_MT)
         endif(WITH_STATIC_RUNTIME)
 
+		# CMake no longer creates PDB files for static libraries after 2.8.11
+		# so we store debug information in the object files instead
+		if (${CMAKE_VERSION} VERSION_GREATER "2.8.11")
+            foreach(flag_var
+                CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
+                CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO
+                CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
+                CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
+
+                if(${flag_var} MATCHES "/Zi")
+				    STRING(REPLACE "/Zi"  "/Z7" "${flag_var}" "${${flag_var}}")
+                endif(${flag_var} MATCHES "/Zi")
+
+            endforeach(flag_var)		  
+		endif()
+		
         file(GLOB WIN32_BINARIES ${LIBSBML_DEPENDENCY_DIR}/bin/*.dll)
         INSTALL(FILES ${WIN32_BINARIES} DESTINATION bin)
         file(GLOB WIN32_DEPENDENCIES ${LIBSBML_DEPENDENCY_DIR}/lib/*.lib)

Modified: branches/libsbml-experimental/NEWS.txt
===================================================================
--- branches/libsbml-experimental/NEWS.txt	2014-09-27 12:12:15 UTC (rev 21162)
+++ branches/libsbml-experimental/NEWS.txt	2014-09-27 12:23:47 UTC (rev 21163)
@@ -8,10 +8,21 @@
 STABLE RELEASE
 
 * New features
+
+  - There is now an interface for JavaScript.  This has been tested
+    on all platforms.  Building requires SWIG version 3.0.2 or greater 
+    and depends on node-gyp.  Feedback on this would be greatly
+    appreciated.
 	
   - The facility of using the data members of objects as attributes
     in python has been extended to work with Python version 3.
-
+    
+  - The SBMLDocument class now has an 'isSetModel()' function.
+  
+  - There is a new writSBMLToStdString() function that returns a 
+    std::string rather than a const char *. This facilitates cleaner
+    memory management.
+  
   - 'comp' package-specific updates:
   - 'fbc' package-specific updates:
   - 'layout' package-specific updates:
@@ -72,6 +83,10 @@
 
 * New features
 
+  Code for the Dynamic Structures ('dyn') package has been added. 
+  This reflects the draft specification dated August 8 2014.
+  
+
   - 'arrays' package-specific updates:
   - 'distrib' package-specific updates:
   - 'groups' package-specific updates:
@@ -96,7 +111,9 @@
       Thanks to Gerard Weatherby for reporting it.
 
   - 'spatial' package-specific bug fixes:
-
+  
+    - The spatial code has been updated in line with the specification
+      Release 0.88 dated September 2014.
 		   
 ====================================================================
 5.10.2 (2014-07-17)

Modified: branches/libsbml-experimental/src/sbml/SBase.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/SBase.cpp	2014-09-27 12:12:15 UTC (rev 21162)
+++ branches/libsbml-experimental/src/sbml/SBase.cpp	2014-09-27 12:23:47 UTC (rev 21163)
@@ -3020,6 +3020,14 @@
 }
 
 
+SBasePlugin*
+SBase::getDisabledPlugin(unsigned int n)
+{
+  if (n>=getNumDisabledPlugins()) return NULL;
+  return mDisabledPlugins[n];
+}
+
+
 /*
  * Returns a plugin object (extenstion interface) of package extension
  * with the given package name or URI.
@@ -3036,6 +3044,13 @@
 }
 
 
+const SBasePlugin*
+SBase::getDisabledPlugin(unsigned int n) const
+{
+  return const_cast<SBase*>(this)->getDisabledPlugin(n);
+}
+
+
 /*
  * Returns the number of plugin objects of package extensions.
  *

Modified: branches/libsbml-experimental/src/sbml/SBase.h
===================================================================
--- branches/libsbml-experimental/src/sbml/SBase.h	2014-09-27 12:12:15 UTC (rev 21162)
+++ branches/libsbml-experimental/src/sbml/SBase.h	2014-09-27 12:23:47 UTC (rev 21163)
@@ -2658,6 +2658,40 @@
 
 
   /**
+   * Returns the nth disabled plug-in object (extension interface) for an SBML Level&nbsp;3
+   * package extension.
+   *
+   * @copydetails doc_what_are_plugins
+   *
+   * @param n the index of the disabled plug-in to return
+   *
+   * @return the nth disabled plug-in object (the libSBML extension interface) of a
+   * package extension.
+   *
+   * @see getNumDisabledPlugins()
+   * @see getPlugin(@if java String@else const std::string& package@endif)
+   */
+  SBasePlugin* getDisabledPlugin(unsigned int n);
+
+
+  /**
+   * Returns the nth disabled plug-in object (extension interface) for an SBML Level&nbsp;3
+   * package extension.
+   *
+   * @copydetails doc_what_are_plugins
+   *
+   * @param n the index of the disabled plug-in to return
+   *
+   * @return the nth disabled plug-in object (the libSBML extension interface) of a
+   * package extension.
+   *
+   * @see getNumDisabledPlugins()
+   * @see getPlugin(@if java String@else const std::string& package@endif)
+   */
+  const SBasePlugin* getDisabledPlugin(unsigned int n) const;
+
+
+  /**
    * Returns the number of plug-in objects (extenstion interfaces) for SBML
    * Level&nbsp;3 package extensions known.
    *

Modified: branches/libsbml-experimental/src/sbml/packages/comp/sbml/Submodel.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/comp/sbml/Submodel.cpp	2014-09-27 12:12:15 UTC (rev 21162)
+++ branches/libsbml-experimental/src/sbml/packages/comp/sbml/Submodel.cpp	2014-09-27 12:23:47 UTC (rev 21163)
@@ -922,20 +922,26 @@
   mInstantiatedModel->connectToParent(this);
   mInstantiatedModel->setSBMLDocument(origdoc);
   mInstantiatedModel->enablePackage(getPackageURI(), getPrefix(), true);
+  CompModelPlugin* instmodplug = 
+    static_cast<CompModelPlugin*>(mInstantiatedModel->getPlugin(getPrefix()));
+  if (instmodplug == NULL)
+  {
+    mInstantiatedModel->enablePackageInternal(getPackageURI(), getPrefix(), true);
+  }
 
-  // enable any packages that were enabled on the doc
-  //for (unsigned int n = 0; n < origdoc->getNumPlugins(); n++)
-  //{
-  //  SBasePlugin * plugin = origdoc->getPlugin(n);
-  //  
-  //  mInstantiatedModel->enablePackage(plugin->getURI(),
-  //                                    plugin->getPrefix(), true);
-  //}
+  // disable any packages that were disabled on the rootdoc
+  for (unsigned int n = 0; n < rootdoc->getNumDisabledPlugins(); n++)
+  {
+    SBasePlugin * plugin = rootdoc->getDisabledPlugin(n);
+    
+    mInstantiatedModel->enablePackageInternal(plugin->getURI(),
+                                      plugin->getPrefix(), false);
+  }
   
   CompModelPlugin* origmodplug = 
     static_cast<CompModelPlugin*>(rootdoc->getModel()->getPlugin(getPrefix()));
 
-  CompModelPlugin* instmodplug = 
+  instmodplug = 
     static_cast<CompModelPlugin*>(mInstantiatedModel->getPlugin(getPrefix()));
   
   if (instmodplug == NULL)

Modified: branches/libsbml-experimental/src/sbml/packages/comp/util/CompFlatteningConverter.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/comp/util/CompFlatteningConverter.cpp	2014-09-27 12:12:15 UTC (rev 21162)
+++ branches/libsbml-experimental/src/sbml/packages/comp/util/CompFlatteningConverter.cpp	2014-09-27 12:23:47 UTC (rev 21163)
@@ -39,6 +39,7 @@
 #include <sbml/packages/comp/common/CompExtensionTypes.h>
 #include <sbml/SBMLWriter.h>
 #include <sbml/SBMLReader.h>
+#include <sbml/util/IdList.h>
 
 #ifdef __cplusplus
 
@@ -111,6 +112,8 @@
     "specify whether to abort if any unflattenable packages are encountered");
   prop.addOption("stripUnflattenablePackages", true, 
     "specify whether to strip any unflattenable packages ignored by 'abortIfUnflattenable'");
+  prop.addOption("stripPackages", "", 
+    "comma separated list of packages to be stripped before flattening is attempted");
   return prop;
 }
 
@@ -149,7 +152,14 @@
     return LIBSBML_OPERATION_SUCCESS;
   }
 
-  // look at the document and work out the status of any packages
+  // strip packages as instructed by user
+  int success = stripPackages();
+  if (success != LIBSBML_OPERATION_SUCCESS)
+  {
+    return LIBSBML_OPERATION_FAILED;
+  }
+
+  // look at the document and work out the status of any remaining packages
   mPackageValues.clear();
   analyseDocument();
 
@@ -639,6 +649,27 @@
 }
 
 
+const std::string& 
+CompFlatteningConverter::getPackagesToStrip() const
+{
+	static std::string empty = "";
+
+  if (getProperties() == NULL)
+  {
+    return empty;
+  }
+  else if (getProperties()->hasOption("stripPackages") == false)
+  {
+    return empty;
+  }
+  else
+  {
+    return getProperties()->getValue("stripPackages");
+  }
+}
+
+
+
 void
 CompFlatteningConverter::stripUnflattenablePackages()
 {
@@ -723,6 +754,53 @@
   }
 }
 
+int
+CompFlatteningConverter::stripPackages()
+{
+  IdList pkgsToStrip(getPackagesToStrip());
+
+  unsigned int num = pkgsToStrip.size();
+
+  if (num == 0)
+  {
+    return LIBSBML_OPERATION_SUCCESS;
+  }
+
+  XMLNamespaces *ns = mDocument->getSBMLNamespaces()->getNamespaces();
+  for (int i = 0; i < ns->getLength(); i++)
+  {
+    std::string nsURI = ns->getURI(i);
+    std::string package = ns->getPrefix(i);
+    if (package.empty() == true)
+    {
+      continue;
+    }
+    else if (pkgsToStrip.contains(package) == true)
+    {
+      mDocument->enablePackage(nsURI, package, false);
+      mDisabledPackages.insert(make_pair(nsURI, package));
+    }
+  }
+
+  unsigned int count = 0;
+  for (unsigned int i = 0; i < num; i++)
+  {
+    if (mDocument->isPackageEnabled(pkgsToStrip.at(i)) == false)
+    {
+      count++;
+    }
+  }
+
+  if (num == count)
+  {
+    return LIBSBML_OPERATION_SUCCESS;
+  }
+  else
+  {
+    return LIBSBML_OPERATION_FAILED;
+  }
+}
+
 bool
 CompFlatteningConverter::canBeFlattened()
 {

Modified: branches/libsbml-experimental/src/sbml/packages/comp/util/CompFlatteningConverter.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/comp/util/CompFlatteningConverter.h	2014-09-27 12:12:15 UTC (rev 21162)
+++ branches/libsbml-experimental/src/sbml/packages/comp/util/CompFlatteningConverter.h	2014-09-27 12:23:47 UTC (rev 21163)
@@ -254,6 +254,8 @@
 
 private:
 
+  int stripPackages();
+
   int reconstructDocument(Model* flatmodel); 
 
   int reconstructDocument(Model* flatmodel, 
@@ -277,6 +279,8 @@
 
   bool getAbortForNone() const;
 
+  const std::string& getPackagesToStrip() const;
+
   bool canBeFlattened();
 
   void restoreNamespaces();

Copied: branches/libsbml-experimental/src/sbml/packages/comp/util/test/TestCompFlatteningConverterStripPackage.cpp (from rev 21161, trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningConverterStripPackage.cpp)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/comp/util/test/TestCompFlatteningConverterStripPackage.cpp	                        (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/comp/util/test/TestCompFlatteningConverterStripPackage.cpp	2014-09-27 12:23:47 UTC (rev 21163)
@@ -0,0 +1,572 @@
+/**
+ * \file    TestCompFlatteningConverterStripPackage.cpp
+ * \brief   Implementation of the Tests for the Comp flattening converter
+ * \author  Frank T. Bergmann
+ * 
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML.  Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2013-2014 jointly by the following organizations:
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ *     3. University of Heidelberg, Heidelberg, Germany
+ * 
+ * Copyright 2011-2012 jointly by the following organizations:
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation.  A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ * ---------------------------------------------------------------------- -->*/
+
+#include <sbml/common/common.h>
+
+#include <sbml/packages/comp/common/CompExtensionTypes.h>
+
+#include <sbml/conversion/SBMLConverterRegistry.h>
+#include <sbml/SBMLReader.h>
+#include <sbml/SBMLTypes.h>
+
+#include <string>
+
+#include <check.h>
+
+using namespace std;
+
+LIBSBML_CPP_NAMESPACE_USE
+
+
+std::string writeSBMLToStringSafe1(const SBMLDocument* doc)
+{
+  char* modelC = writeSBMLToString(doc);
+  std::string model(modelC);
+  free(modelC);
+  return model;
+}
+
+
+BEGIN_C_DECLS
+
+extern char *TestDataDirectory;
+
+void TestPair(std::string file1, std::string file2, std::string pkgToStrip,
+              unsigned int numErrors = 0)
+{
+  std::string filename(TestDataDirectory);
+  std::string dir("test_external_flat_strip/");
+
+  ConversionProperties props;
+  
+  props.addOption("flatten comp");
+  props.addOption("basePath", filename);
+  props.addOption("performValidation", true);
+  props.addOption("stripPackages", pkgToStrip);
+  props.addOption("abortIfUnflattenable", "none");
+
+  SBMLConverter* converter = SBMLConverterRegistry::getInstance().
+                                                    getConverterFor(props);
+  
+  // load document
+  std::string cfile = filename + dir + file1;  
+  SBMLDocument* doc = readSBMLFromFile(cfile.c_str());
+
+  // fail if there is no model (readSBMLFromFile always returns a valid doc)
+  fail_unless(doc->getModel() != NULL);
+
+  fail_unless(doc->getErrorLog()->getNumFailsWithSeverity(LIBSBML_SEV_ERROR) 
+                                                          == numErrors);
+
+  converter->setDocument(doc);
+  int result = converter->convert();
+
+  // fail if conversion was not valid
+  fail_unless(result == LIBSBML_OPERATION_SUCCESS);
+
+  std::string newModel = writeSBMLToStringSafe1(doc);
+  
+  std::string ffile = filename + dir + file2;
+  SBMLDocument* fdoc = readSBMLFromFile(ffile.c_str());
+  std::string flatModel = writeSBMLToStringSafe1(fdoc);
+
+  fail_unless(flatModel == newModel);
+
+  delete doc;
+  delete fdoc;
+  delete converter;
+}
+
+
+void TestPairDiffDir(std::string file1, std::string file2, 
+                     std::string pkgToStrip,
+                     unsigned int numErrors = 0)
+{
+  std::string filename(TestDataDirectory);
+
+  ConversionProperties props;
+  
+  props.addOption("flatten comp");
+  props.addOption("basePath", filename);
+  props.addOption("performValidation", true);
+  props.addOption("stripPackages", pkgToStrip);
+  props.addOption("abortIfUnflattenable", "none");
+
+  SBMLConverter* converter = SBMLConverterRegistry::getInstance().
+                                                    getConverterFor(props);
+  
+  // load document
+  std::string cfile = filename + file1;  
+  SBMLDocument* doc = readSBMLFromFile(cfile.c_str());
+
+  // fail if there is no model (readSBMLFromFile always returns a valid doc)
+  fail_unless(doc->getModel() != NULL);
+
+  fail_unless(doc->getErrorLog()->getNumFailsWithSeverity(LIBSBML_SEV_ERROR) 
+                                                          == numErrors);
+
+  converter->setDocument(doc);
+  int result = converter->convert();
+
+  // fail if conversion was not valid
+  fail_unless(result == LIBSBML_OPERATION_SUCCESS);
+
+  std::string newModel = writeSBMLToStringSafe1(doc);
+  
+  std::string ffile = filename + file2;
+  SBMLDocument* fdoc = readSBMLFromFile(ffile.c_str());
+  std::string flatModel = writeSBMLToStringSafe1(fdoc);
+
+  fail_unless(flatModel == newModel);
+
+  delete doc;
+  delete fdoc;
+  delete converter;
+}
+
+
+START_TEST (test_comp_flatten_strip_fbc_submodels)
+{ 
+  // fbc in modeldefinitions within one doc
+  if (SBMLExtensionRegistry::isPackageEnabled("fbc") == true)
+  {
+    TestPairDiffDir("aggregate_fbc2.xml", 
+                    "aggregate_fbc2_flat_fbc_removed.xml", "fbc");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_fbc_submodels_1)
+{ 
+  // fbc in modeldefinitions within one doc
+  if (SBMLExtensionRegistry::isPackageEnabled("fbc") == true)
+  {
+    TestPairDiffDir("aggregate_fbc2.xml", "aggregate_fbc2_flat.xml", "");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_fbc_external)
+{ 
+  // fbc in main doc and external doc
+  if (SBMLExtensionRegistry::isPackageEnabled("fbc") == true)
+  {
+    TestPair("fbc_in_external.xml", 
+             "fbc_in_external_flat_fbc_removed.xml", "fbc");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_fbc_external_1)
+{ 
+  // fbc in main doc and external doc
+  if (SBMLExtensionRegistry::isPackageEnabled("fbc") == true)
+  {
+    TestPair("fbc_in_external.xml", "fbc_in_external_flat.xml", "");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_fbc_external_2)
+{ 
+  // fbc not in main doc but only in external doc
+  if (SBMLExtensionRegistry::isPackageEnabled("fbc") == true)
+  {
+    TestPair("fbc_in_external_only.xml", 
+             "fbc_in_external_flat_fbc_removed.xml", "fbc");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_fbc_external_3)
+{ 
+  // fbc not in main doc but only in external doc
+  // flat doc should declare fbc
+  if (SBMLExtensionRegistry::isPackageEnabled("fbc") == true)
+  {
+    TestPair("fbc_in_external_only.xml", 
+             "fbc_in_external_flat_fbc_added.xml", "");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_fbc_external_4)
+{ 
+  // comp in main doc not in external; fbc in both
+  if (SBMLExtensionRegistry::isPackageEnabled("fbc") == true)
+  {
+    TestPair("fbc_in_external_no_comp.xml", 
+             "fbc_in_external_flat_fbc_removed.xml", "fbc");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_layout_submodels)
+{ 
+  // layout in modeldefinitions within one doc
+  if (SBMLExtensionRegistry::isPackageEnabled("layout") == true)
+  {
+    TestPair("layout_in_submodels.xml", 
+             "layout_in_submodels_flat_layout_removed.xml", "layout");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_layout_submodels_1)
+{ 
+  // layout in modeldefinitions within one doc
+  if (SBMLExtensionRegistry::isPackageEnabled("layout") == true)
+  {
+    TestPairDiffDir("aggregate_layout.xml", 
+                    "aggregate_layout_flat_layout_removed.xml", "layout");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_layout_external)
+{ 
+ // layout in main doc and external doc
+  if (SBMLExtensionRegistry::isPackageEnabled("layout") == true)
+  {
+    TestPair("layout_in_external.xml", 
+             "layout_in_external_flat_layout_removed.xml", "layout");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_layout_external_1)
+{ 
+ // layout in main doc and external doc
+  if (SBMLExtensionRegistry::isPackageEnabled("layout") == true)
+  {
+    TestPair("layout_in_external.xml", "layout_in_external_flat.xml", "");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_layout_external_2)
+{ 
+  // layout not in main doc but only in external doc
+  if (SBMLExtensionRegistry::isPackageEnabled("layout") == true)
+  {
+    TestPair("layout_in_external_only.xml", 
+             "layout_in_external_flat_layout_removed.xml", "layout");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_layout_external_3)
+{ 
+  // layout not in main doc but only in external doc
+  // flat doc should declare layout
+  if (SBMLExtensionRegistry::isPackageEnabled("layout") == true)
+  {
+    TestPair("layout_in_external_only.xml", 
+             "layout_in_external_flat_layout_added.xml", "");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_layout_external_4)
+{ 
+  // comp in main doc not in external; layout in both
+  if (SBMLExtensionRegistry::isPackageEnabled("layout") == true)
+  {
+    TestPair("layout_in_external_no_comp.xml", 
+             "layout_in_external_flat_layout_removed.xml", "layout");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_unreq_unknown_submodels)
+{ 
+  // unknown unrequired package in modeldefinitions within one doc
+  TestPairDiffDir("unknown9.xml", "unknown9_flat.xml", "");
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_unreq_unknown_external)
+{ 
+  // unknown unrequired in main doc and external doc
+  TestPair("unreq_unknown_in_external.xml", "unreq_unknown_in_external_flat_unknown_removed.xml", "extra");
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_unreq_unknown_external_1)
+{ 
+  // unknown unrequired in main doc and external doc
+  TestPair("unreq_unknown_in_external.xml", "unreq_unknown_in_external_flat_unknown_removed.xml", "");
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_unreq_unknown_external_2)
+{ 
+  // unknown unrequired not in main doc but only in external doc
+  TestPair("unreq_unknown_in_external_only.xml", "unreq_unknown_in_external_flat_unknown_removed.xml", "extra");
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_unreq_unknown_external_3)
+{ 
+  // unknown unrequired not in main doc but only in external doc
+  TestPair("unreq_unknown_in_external_only.xml", "unreq_unknown_in_external_flat_unknown_removed.xml", "");
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_unreq_unknown_external_4)
+{ 
+  // comp in main doc not in external; unknown unrequired in both
+  TestPair("unreq_unknown_in_external_no_comp.xml", "unreq_unknown_in_external_flat_unknown_removed.xml", "extra");
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_req_unknown_submodels)
+{ 
+  // unknown required package in modeldefinitions within one doc
+  TestPairDiffDir("unknown10.xml", "unknown10_flat.xml", "", 1);
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_req_unknown_external)
+{ 
+  // unknown required in main doc and external doc
+  TestPair("req_unknown_in_external.xml", "req_unknown_in_external_flat_unknown_removed.xml", "extra", 1);
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_req_unknown_external_1)
+{ 
+  // unknown required in main doc and external doc
+  TestPair("req_unknown_in_external.xml", "req_unknown_in_external_flat_unknown_removed.xml", "", 1);
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_req_unknown_external_2)
+{ 
+  // unknown required not in main doc but only in external doc
+  TestPair("req_unknown_in_external_only.xml", "req_unknown_in_external_flat_unknown_removed.xml", "extra");
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_req_unknown_external_3)
+{ 
+  // unknown required not in main doc but only in external doc
+  TestPair("req_unknown_in_external_only.xml", "req_unknown_in_external_flat_unknown_removed.xml", "");
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_req_unknown_external_4)
+{ 
+  // comp in main doc not in external; unknown required in both
+  TestPair("req_unknown_in_external_no_comp.xml", "req_unknown_in_external_flat_unknown_removed.xml", "extra", 1);
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_fbc_layout_external)
+{ 
+ // fbc and layout in main doc and external doc
+  if (SBMLExtensionRegistry::isPackageEnabled("layout") == true
+    && SBMLExtensionRegistry::isPackageEnabled("fbc") == true)
+  {
+    TestPair("fbc_layout_in_external.xml", 
+             "fbc_layout_in_external_flat_both_removed.xml", "layout, fbc");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_fbc_layout_external_1)
+{ 
+ // fbc and layout in main doc and external doc
+  if (SBMLExtensionRegistry::isPackageEnabled("layout") == true
+    && SBMLExtensionRegistry::isPackageEnabled("fbc") == true)
+  {
+    TestPair("fbc_layout_in_external.xml", 
+             "fbc_layout_in_external_flat_both_removed.xml", "fbc, layout");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_fbc_layout_external_2)
+{ 
+ // fbc and layout in main doc and external doc
+  if (SBMLExtensionRegistry::isPackageEnabled("layout") == true
+    && SBMLExtensionRegistry::isPackageEnabled("fbc") == true)
+  {
+    TestPair("fbc_layout_in_external.xml", 
+             "fbc_layout_in_external_flat_fbc_removed.xml", "fbc");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_fbc_layout_external_3)
+{ 
+ // fbc and layout in main doc and external doc
+  if (SBMLExtensionRegistry::isPackageEnabled("layout") == true
+    && SBMLExtensionRegistry::isPackageEnabled("fbc") == true)
+  {
+    TestPair("fbc_layout_in_external.xml", 
+             "fbc_layout_in_external_flat_layout_removed.xml", "layout");
+  }
+}
+END_TEST
+
+
+START_TEST (test_comp_flatten_strip_fbc_layout_external_4)
+{ 
+ // fbc and layout in main doc and external doc
+  if (SBMLExtensionRegistry::isPackageEnabled("layout") == true
+    && SBMLExtensionRegistry::isPackageEnabled("fbc") == true)
+  {
+    TestPair("fbc_layout_in_external.xml", 
+             "fbc_layout_in_external_flat.xml", "");
+  }
+}
+END_TEST
+
+
+Suite *
+create_suite_TestFlatteningConverterStripPackage (void)
+{ 
+  TCase *tcase = tcase_create("SBMLCompFlatteningConverterStripPackage");
+  Suite *suite = suite_create("SBMLCompFlatteningConverterStripPackage");
+  
+  // fbc in modeldefinitions within one doc
+  tcase_add_test(tcase, test_comp_flatten_strip_fbc_submodels);
+  tcase_add_test(tcase, test_comp_flatten_strip_fbc_submodels_1);
+  
+  // fbc in main doc and external doc
+  tcase_add_test(tcase, test_comp_flatten_strip_fbc_external);
+  tcase_add_test(tcase, test_comp_flatten_strip_fbc_external_1);
+  
+  // fbc not in main doc but only in external doc
+  // FAILS - fbc not removed from external references
+  //tcase_add_test(tcase, test_comp_flatten_strip_fbc_external_2);
+
+  // fbc not in main doc but only in external doc
+  // flat doc should declare fbc
+  // FAILS - fbc not declared on flat doc
+  //tcase_add_test(tcase, test_comp_flatten_strip_fbc_external_3);
+
+  // comp in main doc not in external; fbc in both
+  tcase_add_test(tcase, test_comp_flatten_strip_fbc_external_4);
+
+  // layout in modeldefinitions within one doc
+  tcase_add_test(tcase, test_comp_flatten_strip_layout_submodels);
+  tcase_add_test(tcase, test_comp_flatten_strip_layout_submodels_1);
+ 
+  // layout in main doc and external doc
+  tcase_add_test(tcase, test_comp_flatten_strip_layout_external);
+  tcase_add_test(tcase, test_comp_flatten_strip_layout_external_1);
+  
+  // layout not in main doc but only in external doc
+  tcase_add_test(tcase, test_comp_flatten_strip_layout_external_2);
+
+  // layout not in main doc but only in external doc
+  // flat doc should declare layout
+  // FAILS - layout not declared on flat doc
+  //tcase_add_test(tcase, test_comp_flatten_strip_layout_external_3);
+
+  // comp in main doc not in external; layout in both
+  tcase_add_test(tcase, test_comp_flatten_strip_layout_external_4);
+
+  // unknown unrequired package in modeldefinitions within one doc
+  tcase_add_test(tcase, test_comp_flatten_strip_unreq_unknown_submodels);
+
+  // unknown unrequired in main doc and external doc
+  tcase_add_test(tcase, test_comp_flatten_strip_unreq_unknown_external);
+  tcase_add_test(tcase, test_comp_flatten_strip_unreq_unknown_external_1);
+  
+  // unknown unrequired not in main doc but only in external doc
+  tcase_add_test(tcase, test_comp_flatten_strip_unreq_unknown_external_2);
+
+  // unknown unrequired not in main doc but only in external doc
+  tcase_add_test(tcase, test_comp_flatten_strip_unreq_unknown_external_3);
+
+  // comp in main doc not in external; unknown unrequired in both
+  tcase_add_test(tcase, test_comp_flatten_strip_unreq_unknown_external_4);
+
+  // unknown required package in modeldefinitions within one doc
+  tcase_add_test(tcase, test_comp_flatten_strip_req_unknown_submodels);
+  
+  // unknown required in main doc and external doc
+  tcase_add_test(tcase, test_comp_flatten_strip_req_unknown_external);
+  tcase_add_test(tcase, test_comp_flatten_strip_req_unknown_external_1);
+ 
+  // unknown required not in main doc but only in external doc
+  // FAILS conversion
+  //tcase_add_test(tcase, test_comp_flatten_strip_req_unknown_external_2);
+
+  // unknown required not in main doc but only in external doc
+  // FAILS conversion
+  //tcase_add_test(tcase, test_comp_flatten_strip_req_unknown_external_3);
+
+  // comp in main doc not in external; unknown required in both
+  tcase_add_test(tcase, test_comp_flatten_strip_req_unknown_external_4);
+  
+  // fbc and layout in main doc and external doc
+  tcase_add_test(tcase, test_comp_flatten_strip_fbc_layout_external);
+  tcase_add_test(tcase, test_comp_flatten_strip_fbc_layout_external_1);
+  tcase_add_test(tcase, test_comp_flatten_strip_fbc_layout_external_2);
+  tcase_add_test(tcase, test_comp_flatten_strip_fbc_layout_external_3);
+  tcase_add_test(tcase, test_comp_flatten_strip_fbc_layout_external_4);
+  
+  
+  suite_add_tcase(suite, tcase);
+
+  return suite;
+}
+
+
+END_C_DECLS
+

Modified: branches/libsbml-experimental/src/sbml/packages/comp/util/test/TestRunner.c
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/comp/util/test/TestRunner.c	2014-09-27 12:12:15 UTC (rev 21162)
+++ branches/libsbml-experimental/src/sbml/packages/comp/util/test/TestRunner.c	2014-09-27 12:23:47 UTC (rev 21163)
@@ -121,6 +121,7 @@
 Suite *create_suite_TestURIResolvers (void);
 Suite *create_suite_TestExternalModelResolving (void);
 Suite *create_suite_TestCompFlatteningNewFlags (void);
+Suite *create_suite_TestFlatteningConverterStripPackage (void);
 
 /**
  * Global.
@@ -171,6 +172,7 @@
   srunner_add_suite( runner, create_suite_TestFlatteningConverter() );
   srunner_add_suite( runner, create_suite_TestExternalModelResolving() );
   srunner_add_suite( runner, create_suite_TestCompFlatteningNewFlags() );
+  srunner_add_suite( runner, create_suite_TestFlatteningConverterStripPackage() );
 
   /* srunner_set_fork_status(runner, CK_NOFORK); */
 

Modified: branches/libsbml-experimental/src/sbml/test/TestSBMLDocument.c
===================================================================
--- branches/libsbml-experimental/src/sbml/test/TestSBMLDocument.c	2014-09-27 12:12:15 UTC (rev 21162)
+++ branches/libsbml-experimental/src/sbml/test/TestSBMLDocument.c	2014-09-27 12:23:47 UTC (rev 21163)
@@ -66,6 +66,8 @@
 
   fail_unless( SBMLDocument_getNumErrors  (d) == 0 );
 
+  fail_unless( SBMLDocument_isSetModel(d) == 0 );
+
   SBMLDocument_free(d);
 }
 END_TEST
@@ -85,6 +87,8 @@
 
   fail_unless( SBMLDocument_getNumErrors  (d) == 0 );
 
+  fail_unless( SBMLDocument_isSetModel(d) == 0 );
+
   SBMLDocument_free(d);
 }
 END_TEST
@@ -105,12 +109,14 @@
   Model_t        *mout;
 
   fail_unless(SBMLDocument_getModel(d) == NULL);
+  fail_unless( SBMLDocument_isSetModel(d) == 0 );
 
   int i = SBMLDocument_setModel(d, m1);
   fail_unless ( i == LIBSBML_OPERATION_SUCCESS );
   mout = SBMLDocument_getModel(d);
   fail_unless(mout != NULL);
   fail_unless(mout != m1);
+  fail_unless( SBMLDocument_isSetModel(d) == 1 );
 
   /* Reflexive case (pathological) */
   i = SBMLDocument_setModel(d, SBMLDocument_getModel(d));

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