Fbc v3 matlab

.github/workflows/matlab.yml

@@ -0,0 +1,63 @@
+name: Matlab (ubuntu) build and test
+
+on: [push]
+
+env:
+  MATLAB_VERSION: R2021a
+  CC: gcc-9
+  CXX: g++-9
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v3
+
+    - uses: seanmiddleditch/gha-setup-ninja@master
+
+    - name: Set up MATLAB
+      uses: matlab-actions/setup-matlab@v1
+      # with:
+      #   release: ${{ env.MATLAB_VERSION }}
+
+    - name: Install Ubuntu dependencies
+      shell: bash
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y check ccache
+        git clone https://github.com/libexpat/libexpat
+        cmake -G Ninja -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DEXPAT_BUILD_TESTS=OFF -DEXPAT_BUILD_TOOLS=OFF -DEXPAT_BUILD_EXAMPLES=OFF -DEXPAT_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=./dependencies -B libexpat -S libexpat/expat 
+        cmake --build libexpat
+        cmake --install libexpat
+
+    - name: Create Build Environment
+      run: cmake -E make_directory ${{runner.workspace}}/build
+
+    # - name: Setup tmate session
+    #   uses: mxschmitt/action-tmate@v3
+
+    - name: Configure
+      shell: bash
+      working-directory: ${{runner.workspace}}/build
+      run: |
+        cmake $GITHUB_WORKSPACE \
+        -G "Ninja" \
+        -DCMAKE_BUILD_TYPE=Debug \
+        -DWITH_CHECK=ON \
+        -DWITH_LIBXML=OFF \
+        -DWITH_EXPAT=ON \
+        -DWITH_MATLAB=ON \
+        -DWITH_STABLE_PACKAGES=ON 
+
+    - name: Build
+      working-directory: ${{runner.workspace}}/build
+      shell: bash
+      run: |
+        cmake --build . --config Debug --target matlab_binding_TranslateSBML
+        cmake --build . --config Debug --target matlab_binding_OutputSBML
+
+    - name: Run Test
+      uses: matlab-actions/run-command@v1
+      with:
+        command: cd('../build/src/bindings/matlab/test'); runTests

.github/workflows/octave.yml

@@ -42,7 +42,7 @@ jobs:
       working-directory: ${{runner.workspace}}/build
       shell: bash
       run: |
-          cmake -DCMAKE_INSTALL_PREFIX=${{runner.workspace}}/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DWITH_BZIP2=ON -DWITH_CHECK=OFF -DWITH_EXPAT=ON -DWITH_LIBXML=OFF -DWITH_OCTAVE=ON $GITHUB_WORKSPACE
+          cmake -DCMAKE_INSTALL_PREFIX=${{runner.workspace}}/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DWITH_BZIP2=ON -DWITH_CHECK=OFF -DWITH_EXPAT=ON -DWITH_LIBXML=OFF -DWITH_OCTAVE=ON -DWITH_STABLE_PACKAGES=ON $GITHUB_WORKSPACE
 
     - name: Build
       working-directory: ${{runner.workspace}}/build

src/bindings/matlab/CMakeLists.txt

@@ -33,6 +33,19 @@
 
 if(WITH_MATLAB)
 SET(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}" ${CMAKE_MODULE_PATH}) 
+
+if (NOT MATLAB_ROOT_PATH)
+  # try and find matlab in path
+  find_program(MATLAB_COMMAND NAMES matlab matlab.exe)
+  if (MATLAB_COMMAND)
+    # if we have it in the path, it will be of form <matlab_version>/bin/matlab, 
+    # so take the DIRECTORY component twice
+    get_filename_component(MATLAB_BIN_PATH ${MATLAB_COMMAND} DIRECTORY)
+    get_filename_component(MATLAB_ROOT ${MATLAB_BIN_PATH} DIRECTORY)
+    set(MATLAB_ROOT_PATH ${MATLAB_ROOT} CACHE STRING "Matlab root directory" FORCE)
+  endif()
+endif()
+
 find_package(Matlab)
 
 # on windows let us build the library using MSVC, on Linux and OS X we choose
@@ -124,12 +137,7 @@ file(GLOB matlab_scripts "${CMAKE_CURRENT_SOURCE_DIR}/../matlab/*.m"
 install(FILES ${matlab_scripts} DESTINATION ${MATLAB_PACKAGE_INSTALL_DIR})
 
 # add test cases
-if (WITH_CHECK)
-
-	add_subdirectory(test)	
-
-endif()
-
+add_subdirectory(test)	
 
 endif()
 

src/bindings/matlab/OutputSBML.cpp

@@ -193,7 +193,7 @@ dealWithAnomalies(SBMLDocument* sbmlDocument, GV& gv)
 
     // the gene product associations in fbc v2
     unsigned int vers = StructureFields::readUint(gv.modelArray, "fbc_version", 0, gv);
-    if (vers == 2)
+    if (vers > 1)
     {
       addGeneProductAssociations(sbmlDocument, gv);
     }

src/bindings/matlab/StructureFields.cpp

@@ -8,6 +8,10 @@
 #include <sbml/math/ASTNode.h>
 #include <sbml/extension/SBasePlugin.h>
 #include <sbml/extension/SBMLExtensionRegistry.h>
+#ifdef USE_FBC
+#include <sbml/packages/fbc/sbml/FbcAssociation.h>
+#endif // USE_FBC
+
 
 
 #ifdef USE_OCTAVE
@@ -233,6 +237,22 @@ StructureFields::populateFields()
   mxDestroyArray(mxOutputs[2]);
   mxDestroyArray(mxOutputs[3]);
 
+
+  // get structure returns fieldnames, default values and value types
+  // fieldnames are an array of arrays giving values for several aspects of the structure 
+  // 		SBMLfieldnames = { {'typecode','','',0,0}, ...
+  //{'metaid', 'metaid', '', 1, 20}, ...
+  //{'notes', 'notes', '', 1, 1}, ...
+  //{'annotation', 'annotation', '', 1, 2}, ...
+  //{'formula', 'formula', '', 1, 5}, ...
+  //{'variable', 'variable', '', 1, 20}, ...
+  //{'species', 'species', '', 1, 20}, ...
+  //{'compartment', 'compartment', '', 1, 20}, ...
+  //{'name', 'name', '', 1, 20}, ...
+  //{'units', 'units', '', 1, 20}, ...
+  //
+  //{name of the field, sbml name, prefix, is sbml attribute, type enum}
+
   for (unsigned int i = 0; i < nNumberFields; ++i)
   {
     FieldValues_t field;
@@ -383,13 +403,19 @@ StructureFields::getValueType(unsigned int i, const std::string& id)
 
 void
 StructureFields::createStructure(const std::string& functionId, SBase* base, 
-                                 bool usePlugin, const std::string& prefix)
+                                 bool usePlugin_cs, const std::string& prefix)
 {
   std::string fieldname;
   unsigned int total_no = base->getNumObjects(sbmlTC);
-  if (usePlugin)
+  if (usePlugin_cs && total_no == 0)
   {
     total_no = base->getPlugin(prefix)->getNumObjects(sbmlTC);
+    // we may have an SBase plugin
+    if (total_no == 0)
+    {
+      SBase * sbase = static_cast<SBase*>(base);
+      total_no = sbase->getPlugin(prefix)->getNumObjects(sbmlTC);
+    }
   }
   mwSize dims[2] = {1, total_no};
 
@@ -407,7 +433,7 @@ StructureFields::createStructure(const std::string& functionId, SBase* base,
   for (unsigned int i = 0; i < total_no; ++i)
   {
     SBase* child = base->getObject(sbmlTC, i);
-    if (usePlugin)
+    if (usePlugin_cs)
     {
       child = base->getPlugin(prefix)->getObject(sbmlTC, i);
     }
@@ -429,7 +455,7 @@ StructureFields::populateStructure(const std::string& functionId, SBase* base, u
     FieldValues_t field = mFields.at(i);
     type = field.type;
     nameType = field.fieldnameType;
-    bool usePlugin = usingPlugin(field.prefix, base);
+    bool usePlugin_ps = usingPlugin(field.prefix, base, field.fieldName);
 
     if (type == TYPE_ELEMENT)
     {
@@ -442,7 +468,7 @@ StructureFields::populateStructure(const std::string& functionId, SBase* base, u
           break;
       default:
           StructureFields *sf = new StructureFields(field.sbmlName, gv);
-          sf->createStructure(functionId + ":" + field.fieldName, base, usePlugin, field.prefix);
+          sf->createStructure(functionId + ":" + field.fieldName, base, usePlugin_ps, field.prefix);
           mxSetField(mxStructure, index, field.fieldName.c_str(), mxDuplicateArray(sf->getStructure()));
           sf->freeStructureMemory();
           delete sf;
@@ -455,7 +481,7 @@ StructureFields::populateStructure(const std::string& functionId, SBase* base, u
     }
     else
     {
-      addStructureField(functionId, base, index, field, usePlugin);
+      addStructureField(functionId, base, index, field, usePlugin_ps);
     }
 
   }
@@ -651,7 +677,7 @@ StructureFields::getCVTermsStructure(SBase* base)
 void
 StructureFields::addStructureField(const std::string& functionId, SBase* base,
   unsigned int index, FieldValues_t field,
-  bool usePlugin)
+  bool usePlugin_sf)
 {
   std::string value;
   int ivalue;
@@ -663,23 +689,23 @@ StructureFields::addStructureField(const std::string& functionId, SBase* base,
   case TYPE_UNKNOWN:
 
   case TYPE_CHAR:
-    value = getStringValue(functionId, base, field, usePlugin);
+    value = getStringValue(functionId, base, field, usePlugin_sf);
     mxSetField(mxStructure, index, field.fieldName.c_str(), mxCreateString(value.c_str()));
     break;
   case TYPE_BOOL:
-    bvalue = getBoolValue(functionId, base, field, usePlugin);
+    bvalue = getBoolValue(functionId, base, field, usePlugin_sf);
     mxSetField(mxStructure, index, field.fieldName.c_str(), CreateIntScalar(bvalue));
     break;
   case TYPE_UINT:
-    uvalue = getUintValue(functionId, base, field, usePlugin);
+    uvalue = getUintValue(functionId, base, field, usePlugin_sf);
     mxSetField(mxStructure, index, field.fieldName.c_str(), CreateIntScalar(uvalue));
     break;
   case TYPE_INT:
-    ivalue = getIntValue(functionId, base, field, usePlugin);
+    ivalue = getIntValue(functionId, base, field, usePlugin_sf);
     mxSetField(mxStructure, index, field.fieldName.c_str(), CreateIntScalar(ivalue));
     break;
   case TYPE_DOUBLE:
-    dvalue = getDoubleValue(functionId, base, field, usePlugin);
+    dvalue = getDoubleValue(functionId, base, field, usePlugin_sf);
     mxSetField(mxStructure, index, field.fieldName.c_str(), mxCreateDoubleScalar(dvalue));
     break;
   case TYPE_ELEMENT:
@@ -1104,7 +1130,7 @@ StructureFields::dealWithRateOfSymbol(ASTNode* math)
 // general need to know function
 
 bool 
-StructureFields::usingPlugin(const std::string& prefix, SBase* base)
+StructureFields::usingPlugin(const std::string& prefix, SBase* base, const std::string& name)
 {
   bool usePlugin = false;
   if (prefix.size() > 0)
@@ -1113,10 +1139,17 @@ StructureFields::usingPlugin(const std::string& prefix, SBase* base)
     {
       usePlugin = true;
     }
-    else if (base != NULL && base->getPlugin(prefix) != NULL)
+    // need to account for a sbase plugin from same pkg which will be on all elements
+    else if (base != NULL && base->getPackageName() != prefix) // THIS FIXES BUT WONT READ 
+    {
+      usePlugin = true;
+    }
+#ifdef USE_FBC
+    if (name == "fbc_keyValuePair" || name == "fbc_kvp_xmlns")
     {
       usePlugin = true;
     }
+#endif
   }
 
   return usePlugin;
@@ -1244,7 +1277,7 @@ StructureFields::addChildElement(FieldValues_t field, unsigned int index)
   if (mxChild == NULL) return;
   else if (n == 0) return;
 
-  bool usePlugin = usingPlugin(field.prefix);
+  bool usePlugin = usingPlugin(field.prefix, NULL, field.fieldName.c_str());
 
   for (unsigned int i = 0; i < n; ++i)
   {
@@ -1358,7 +1391,7 @@ StructureFields::setAttribute(FieldValues_t field,
   unsigned int uvalue;
   bool bvalue;
   double dvalue;
-  bool usePlugin = usingPlugin(field.prefix);
+  bool usePlugin = usingPlugin(field.prefix, NULL, field.fieldName);
   const ASTNode *ast = NULL;
 
   switch(field.type)

src/bindings/matlab/StructureFields.h

@@ -32,7 +32,7 @@ class StructureFields
   void addAttributes(const std::string& functionId, unsigned int index = 0, 
                      unsigned int total_no = 0);
 
-  void createStructure(const std::string& functionId, SBase* base, bool usePlugin = false, 
+  void createStructure(const std::string& functionId, SBase* base, bool usePlugin_cs = false, 
                        const std::string& prefix = "");
 
   const std::string& getTypeCode() const { return sbmlTC; };
@@ -60,7 +60,7 @@ class StructureFields
                          unsigned int index);
 
   void addStructureField(const std::string& functionId, SBase* base,
-    unsigned int index, FieldValues_t field, bool usePlugin);
+    unsigned int index, FieldValues_t field, bool usePlugin_sf);
 
   void addChildElement(FieldValues_t field, unsigned int index);
 
@@ -140,7 +140,7 @@ class StructureFields
                        unsigned int index, unsigned int total_no);
 
 
-  bool usingPlugin(const std::string& prefix, SBase* base = NULL);
+  bool usingPlugin(const std::string& prefix, SBase* base = NULL, const std::string& name = "" );
 
   mxArray* getNamespacesStructure();
 

src/bindings/matlab/TranslateSBML.cpp

@@ -248,6 +248,11 @@ mexFunction (int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
   GV gv;
   // we have not made persistent memory
   gv.freeMemory = false;
+
+  // default values
+  gv.fbcUsingId = false;
+  gv.fbcAddGeneProducts = true;
+
   std::ostringstream numErrs;
   /* determine whether we are in octave or matlab */
   unsigned int usingOctave = determinePlatform(gv);