MIRIAM resources are now owned by the root container.

copasi/MIRIAM/CMIRIAMResource.cpp

@@ -69,10 +69,10 @@ void CMIRIAMResources::isCitation(void * pData, void * /* pCallee */)
 // static
 bool CMIRIAMResources::isCitation(const std::string & uri)
 {
-  size_t Index = CRootContainer::getConfiguration()->getRecentMIRIAMResources().getMIRIAMResourceIndex(uri);
+  size_t Index = CRootContainer::getMiriamResources().getMIRIAMResourceIndex(uri);
 
   if (Index != C_INVALID_INDEX &&
-      CRootContainer::getConfiguration()->getRecentMIRIAMResources().getMIRIAMResource(Index).getMIRIAMCitation())
+      CRootContainer::getMiriamResources().getMIRIAMResource(Index).getMIRIAMCitation())
     {
       return true;
     }

copasi/MIRIAMUI/CQMiriamWidget.cpp

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 - 2024 by Pedro Mendes, Rector and Visitors of the
+// Copyright (C) 2019 - 2025 by Pedro Mendes, Rector and Visitors of the
 // University of Virginia, University of Heidelberg, and University
 // of Connecticut School of Medicine.
 // All rights reserved.
@@ -505,7 +505,7 @@ void CQMiriamWidget::updateResourcesList()
 {
   // Build the list of known resources
   assert(CRootContainer::getDatamodelList()->size() > 0);
-  const CMIRIAMResources *pResource = &CRootContainer::getConfiguration()->getRecentMIRIAMResources();
+  const CMIRIAMResources *pResource = &CRootContainer::getMiriamResources();
   QMap< QString, QString > ResourceMap;
   QMap< QString, QString > ReferenceMap;
   size_t i, imax = pResource->getResourceList().size();

copasi/UI/CQPreferenceDialog.cpp

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 by Pedro Mendes, Rector and Visitors of the
+// Copyright (C) 2019 - 2025 by Pedro Mendes, Rector and Visitors of the
 // University of Virginia, University of Heidelberg, and University
 // of Connecticut School of Medicine.
 // All rights reserved.
@@ -36,7 +36,6 @@
 #define COL_NAME 0
 #define COL_VALUE 1
 
-
 #include <QApplication>
 
 /*
@@ -66,8 +65,6 @@ CQPreferenceDialog::~CQPreferenceDialog()
     {
       delete mpConfiguration;
       mpConfiguration = NULL;
-      // restore pointer to miriam resources
-      CMIRIAMResourceObject::setMIRIAMResources(&CRootContainer::getConfiguration()->getRecentMIRIAMResources());
     }
 }
 
@@ -80,7 +77,6 @@ CQPreferenceDialog::~CQPreferenceDialog()
 #include <QFile>
 #include <QFormLayout>
 
-
 void CQPreferenceDialog::slotPropertyChanged()
 {
   auto widget = dynamic_cast<QWidget*>(sender());
@@ -93,7 +89,7 @@ void CQPreferenceDialog::slotPropertyChanged()
 
   if (auto edit = dynamic_cast<QLineEdit*>(widget))
   {
-    parameter->setValue(edit->text().toStdString());    
+    parameter->setValue(edit->text().toStdString());
   }
   else if (auto edit = dynamic_cast<QCheckBox*>(widget))
   {
@@ -107,7 +103,7 @@ void CQPreferenceDialog::slotPropertyChanged()
 
 void CQPreferenceDialog::initTabsFromSettings(QSettings& settings)
 {
-  // the ini file will have groups for each tab, each tab should 
+  // the ini file will have groups for each tab, each tab should
   // have a form layout with the name of the setting as the key
   // and the value as the value
 
@@ -125,7 +121,7 @@ void CQPreferenceDialog::initTabsFromSettings(QSettings& settings)
     tab->setLayout(layout);
     tabWidget->insertTab(0, tab, mainGroup);
 
-    // each group has child elements with keys: 
+    // each group has child elements with keys:
     // - name: the name of the setting
     // - type: the type of the setting
     // - parameter: the parameter of the COPASI setting to change
@@ -140,20 +136,20 @@ void CQPreferenceDialog::initTabsFromSettings(QSettings& settings)
       auto type = settings.value("type").toString();
       auto parameter = settings.value("parameter").toString();
       auto value = settings.value("value");
-      
+
       auto param_path = parameter.split(".");
       CCopasiParameter * pNode = mpConfiguration;
       for (auto paramName : param_path)
         if (pNode && dynamic_cast< CCopasiParameterGroup * >(pNode))
           pNode = dynamic_cast< CCopasiParameterGroup * >(pNode)->getParameter(paramName.toStdString());
-      
+
       auto tooltip = settings.value("tooltip").toString();
 
       if (type == "string")
       {
         auto edit = new QLineEdit(value.toString());
         edit->setToolTip(tooltip);
-        
+
         if (pNode)
           edit->setText(FROM_UTF8(pNode->getValue<std::string>()));
         layout->addRow(name, edit);
@@ -183,7 +179,7 @@ void CQPreferenceDialog::initTabsFromSettings(QSettings& settings)
 
         connect(edit, QOverload<int>::of(&QSpinBox::valueChanged), this, &CQPreferenceDialog::slotPropertyChanged);
         mWidgetToParameter[edit] = pNode;
-      }      
+      }
       else
       {
         CQMessageBox::warning(this, "Error", "Unknown type: " + type);
@@ -210,7 +206,6 @@ void CQPreferenceDialog::init()
   mpTreeView->setAdvanced(false);
   mpTreeView->pushGroup(mpConfiguration);
 
-
   // initialize other tabs from config file
   auto copasiDir = COptions::getConfigDir();
   auto preferenceConfigFile = copasiDir + "/preferences.ini";
@@ -228,11 +223,10 @@ void CQPreferenceDialog::init()
             outFile.write(file.readAll());
             outFile.close();
           }
-        file.close();        
+        file.close();
       }
   }
 
-
   QSettings settings(preferenceConfigFile.c_str(), QSettings::IniFormat, this);
   initTabsFromSettings(settings);
 }
@@ -263,8 +257,6 @@ void CQPreferenceDialog::slotBtnCancel()
 
       delete mpConfiguration;
       mpConfiguration = NULL;
-      // restore pointer to miriam resources
-      CMIRIAMResourceObject::setMIRIAMResources(&CRootContainer::getConfiguration()->getRecentMIRIAMResources());
     }
 
   done(0);

copasi/UI/copasiui3window.cpp

@@ -2664,8 +2664,6 @@ void CopasiUI3Window::slotUpdateMIRIAMFinished(bool success)
   if (success)
     {
       mpDataModelGUI->saveConfiguration(true);
-      CMIRIAMResourceObject::setMIRIAMResources(
-        &CRootContainer::getConfiguration()->getRecentMIRIAMResources());
       mpDataModelGUI->updateMIRIAMResourceContents();
       this->checkPendingMessages();
     }
@@ -2683,8 +2681,7 @@ void CopasiUI3Window::slotUpdateMIRIAM()
 
   try
     {
-      success = mpDataModelGUI->updateMIRIAM(
-                  CRootContainer::getConfiguration()->getRecentMIRIAMResources());
+      success = mpDataModelGUI->updateMIRIAM(CRootContainer::getMiriamResources());
     }
   catch (...)
     {

copasi/commandline/CConfigurationFile.cpp

@@ -27,11 +27,11 @@
 #include "CConfigurationFile.h"
 #include "COptions.h"
 
+#include "copasi/core/CRootContainer.h"
 #include "copasi/CopasiDataModel/CDataModel.h"
 #include "copasi/utilities/CVersion.h"
 #include "copasi/utilities/utility.h"
 #include "copasi/utilities/CDirEntry.h"
-#include "copasi/MIRIAM/CConstants.h"
 
 #include "copasi/xml/parser/CXMLParser.h"
 #include "copasi/xml/CGroupXML.h"
@@ -118,7 +118,6 @@ CConfigurationFile::CConfigurationFile(const std::string & name,
   , mpRecentFiles(NULL)
   , mpRecentSBMLFiles(NULL)
   , mpRecentSEDMLFiles(NULL)
-  , mRecentMIRIAMResources("MIRIAM Resources", pParent)
   , mpApplicationFont(NULL)
   , mpValidateUnits(NULL)
   , mpDisplayIssueSeverity(NULL)
@@ -152,7 +151,6 @@ CConfigurationFile::CConfigurationFile(const CConfigurationFile & src,
   , mpRecentFiles(NULL)
   , mpRecentSBMLFiles(NULL)
   , mpRecentSEDMLFiles(NULL)
-  , mRecentMIRIAMResources(src.mRecentMIRIAMResources, pParent)
   , mpApplicationFont(NULL)
   , mpValidateUnits(NULL)
   , mpDisplayIssueSeverity(NULL)
@@ -207,13 +205,13 @@ bool CConfigurationFile::elevateChildren()
 
   if (!mpCheckForUpdates) success = false;
 
-  // We need to make sure that the contained group "MIRIAM Resources" is converted to mRecentMIRIAMResources
+  // We need to make sure that the contained group "MIRIAM Resources" is converted to CRootContainer::getMiriamResources()
   CCopasiParameterGroup *pMIRIAMResources = getGroup("MIRIAM Resources");
 
-  if (mRecentMIRIAMResources.getResourceList().size() == 0
+  if (CRootContainer::getMiriamResources().getResourceList().size() == 0
       && pMIRIAMResources != nullptr)
     {
-      mRecentMIRIAMResources = *pMIRIAMResources;
+      CRootContainer::getMiriamResources() = *pMIRIAMResources;
       removeParameter(pMIRIAMResources);
     }
 
@@ -310,11 +308,12 @@ bool CConfigurationFile::save(bool saveMiriam)
   COptions::getValue("ConfigFile", ConfigFile);
 
   std::string miriamConfigFile = ConfigFile + std::string(".miriam");
-  saveMiriam |= (!CDirEntry::exist(miriamConfigFile) && mRecentMIRIAMResources.getResourceList().size() > 0);
+  saveMiriam |= (!CDirEntry::exist(miriamConfigFile)
+                 && CRootContainer::getMiriamResources().getResourceList().size() > 0);
 
   if (saveMiriam)
     {
-      CGroupXML(mRecentMIRIAMResources).CCopasiXMLInterface::save(miriamConfigFile, CDirEntry::dirName(ConfigFile));
+      CGroupXML(CRootContainer::getMiriamResources()).CCopasiXMLInterface::save(miriamConfigFile, CDirEntry::dirName(ConfigFile));
     }
 
   bool success = CGroupXML(*this).CCopasiXMLInterface::save(ConfigFile, CDirEntry::dirName(ConfigFile));
@@ -341,12 +340,12 @@ bool CConfigurationFile::load()
       CCopasiParameterGroup MIRIAMResources("MIRIAM Resources");
 
       if (CGroupXML(MIRIAMResources).CCopasiXMLInterface::load(configMIRIAMResourceFile, configMIRIAMResourceFile))
-        mRecentMIRIAMResources = MIRIAMResources;
+        CRootContainer::getMiriamResources() = MIRIAMResources;
       else
         return false;
     }
 
-  if (mRecentMIRIAMResources.getResourceList().size() == 0)
+  if (CRootContainer::getMiriamResources().getResourceList().size() == 0)
     {
       // We load the default MIRIAM resources, which are part of the COPASI installation.
       std::string MIRIAMResourceFile;
@@ -363,11 +362,11 @@ bool CConfigurationFile::load()
           if (pGroup == nullptr)
             return false;
 
-          mRecentMIRIAMResources = *pGroup;
+          CRootContainer::getMiriamResources() = *pGroup;
 
           if (!haveConfigMiriam)
             {
-              CGroupXML(mRecentMIRIAMResources).CCopasiXMLInterface::save(configMIRIAMResourceFile, configMIRIAMResourceFile);
+              CGroupXML(CRootContainer::getMiriamResources()).CCopasiXMLInterface::save(configMIRIAMResourceFile, configMIRIAMResourceFile);
             }
         }
       else
@@ -408,16 +407,6 @@ CRecentFiles & CConfigurationFile::getRecentSEDMLFiles()
   return *mpRecentSEDMLFiles;
 }
 
-CMIRIAMResources & CConfigurationFile::getRecentMIRIAMResources()
-{
-  return mRecentMIRIAMResources;
-}
-
-void CConfigurationFile::setRecentMIRIAMResources(const CMIRIAMResources & miriamResources)
-{
-  mRecentMIRIAMResources = miriamResources;
-}
-
 const std::string CConfigurationFile::getApplicationFont() const
 {
   return *mpApplicationFont;

copasi/commandline/CConfigurationFile.h

@@ -230,14 +230,6 @@ class CConfigurationFile : public CCopasiParameterGroup
    */
   CRecentFiles & getRecentSEDMLFiles();
 
-  /**
-   * Retrieve the list of recent MIRIAM Resources
-   * @return CMIRIAMResources & recentMIRIAMResources
-   */
-  CMIRIAMResources & getRecentMIRIAMResources();
-
-  void setRecentMIRIAMResources(const CMIRIAMResources & miriamResources);
-
   /**
    * Retrieve the application font.
    * @return const std::string & applicationFont
@@ -494,11 +486,6 @@ class CConfigurationFile : public CCopasiParameterGroup
    */
   CRecentFiles * mpRecentSEDMLFiles;
 
-  /**
-   * A pointer to the list of MIRIAM Resources
-   */
-  CMIRIAMResources  mRecentMIRIAMResources;
-
   /**
    * A pointer to the application font
    */

copasi/core/CRootContainer.cpp

@@ -41,16 +41,17 @@ extern CRootContainer * pRootContainer;
  * The only way to create a root container is through the static init
  * method.
  */
-CRootContainer::CRootContainer(const bool & withGUI):
-  CDataContainer("Root", NULL, "CN", CDataObject::Root),
-  mKeyFactory(),
-  mpUnknownResource(NULL),
-  mpFunctionList(NULL),
-  mpUnitDefinitionList(NULL),
-  mpConfiguration(NULL),
-  mpDataModelList(NULL),
-  mWithGUI(withGUI),
-  mpUndefined(NULL)
+CRootContainer::CRootContainer(const bool & withGUI)
+  : CDataContainer("Root", NULL, "CN", CDataObject::Root)
+  , mKeyFactory()
+  , mpUnknownResource(NULL)
+  , mpMIRIAMResources(NULL)
+  , mpFunctionList(NULL)
+  , mpUnitDefinitionList(NULL)
+  , mpConfiguration(NULL)
+  , mpDataModelList(NULL)
+  , mWithGUI(withGUI)
+  , mpUndefined(NULL)
 {}
 
 // Destructor
@@ -69,6 +70,9 @@ CRootContainer::~CRootContainer()
   // delete the unkown resource
   pdelete(mpUnknownResource);
 
+  // delete the MIRIAM resources
+  pdelete(mpMIRIAMResources);
+
   // delete the model list
   pdelete(mpDataModelList);
 
@@ -126,6 +130,9 @@ void CRootContainer::initializeChildren()
   mpUnknownResource->setMIRIAMDisplayName("-- select --");
   mpUnknownResource->setMIRIAMURI("urn:miriam:unknown");
 
+  mpMIRIAMResources = new CMIRIAMResources;
+  CMIRIAMResourceObject::setMIRIAMResources(mpMIRIAMResources);
+
   mpFunctionList = new CFunctionDB("FunctionDB", this);
   mpFunctionList->load();
 
@@ -134,8 +141,6 @@ void CRootContainer::initializeChildren()
   mpConfiguration = new CConfigurationFile;
   mpConfiguration->load();
 
-  CMIRIAMResourceObject::setMIRIAMResources(&mpConfiguration->getRecentMIRIAMResources());
-
   mpUndefined = new CFunction("undefined", this);
   mpUndefined->setInfix("nan");
   mpUndefined->compile();
@@ -253,6 +258,12 @@ const CMIRIAMResource & CRootContainer::getUnknownMiriamResource()
   return *pRootContainer->mpUnknownResource;
 }
 
+// static
+CMIRIAMResources & CRootContainer::getMiriamResources()
+{
+  return *pRootContainer->mpMIRIAMResources;
+}
+
 // static
 bool CRootContainer::removeDatamodel(const CDataModel * pDatamodel)
 {