Merge branch 'develop' into feature/dudes/statistics-log-csv-outpout

examples/ObjectCatalog/Base.hpp

@@ -5,7 +5,7 @@
  * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
  * Copyright (c) 2018-2024 TotalEnergies
  * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
- * Copyright (c) 2023-2024 Chevron 
+ * Copyright (c) 2023-2024 Chevron
  * Copyright (c) 2019-     GEOS/GEOSX Contributors
  * All rights reserved
  *
@@ -46,7 +46,7 @@ class Parameter
 class Base
 {
 public:
-  Base( int junk, double const & junk2, Parameter& pbv )
+  Base( int junk, double const & junk2, Parameter & pbv )
   {
     GEOS_LOG( "calling Base constructor with arguments (" << junk << " " << junk2 << ")" );
   }
@@ -56,14 +56,20 @@ class Base
     GEOS_LOG( "calling Base destructor" );
   }
 
-  using CatalogInterface = dataRepository::CatalogInterface< Base, int, double const &, Parameter& >;
-  static CatalogInterface::CatalogType& getCatalog()
+  using CatalogInterface = dataRepository::CatalogInterface< Base, int, double const &, Parameter & >;
+  static CatalogInterface::CatalogType & getCatalog()
   {
     static CatalogInterface::CatalogType catalog;
     return catalog;
   }
 
   virtual std::string const getName() const = 0;
+
+  static DataContext const & getDataContext()
+  {
+    static DataFileContext const context = DataFileContext( "Base Test Class", __FILE__, __LINE__ );
+    return context;
+  }
 };
 
 #endif

examples/ObjectCatalog/main.cpp

@@ -5,7 +5,7 @@
  * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
  * Copyright (c) 2018-2024 TotalEnergies
  * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
- * Copyright (c) 2023-2024 Chevron 
+ * Copyright (c) 2023-2024 Chevron
  * Copyright (c) 2019-     GEOS/GEOSX Contributors
  * All rights reserved
  *
@@ -31,10 +31,14 @@ int main( int argc, char *argv[] )
 
 
   GEOS_LOG( "Attempting to create a Derived1 object" );
-  std::unique_ptr<Base> derived1 = Base::CatalogInterface::Factory( "derived1", junk, junk2, param );
+  std::unique_ptr< Base > derived1 = Base::CatalogInterface::factory( "derived1",
+                                                                      Base::getDataContext(),
+                                                                      junk, junk2, param );
   GEOS_LOG( "Attempting to create a Derived2 object" );
-  std::unique_ptr<Base> derived2 = Base::CatalogInterface::Factory( "derived2", junk, junk3, param );
+  std::unique_ptr< Base > derived2 = Base::CatalogInterface::factory( "derived2",
+                                                                      Base::getDataContext(),
+                                                                      junk, junk3, param );
 
-  Base::CatalogInterface::catalog_cast<Derived1>( *(derived2.get()));
+  Base::CatalogInterface::catalog_cast< Derived1 >( *(derived2.get()));
   GEOS_LOG( "EXITING MAIN" );
 }

src/coreComponents/common/format/StringUtilities.hpp

@@ -88,7 +88,7 @@ string join( CONTAINER const & container, S const & delim = S() )
  * @return a string containing input values concatenated with a delimiter
  */
 template< typename IT, typename S, typename LAMBDA >
-string joinLamda( IT first, IT last, S const & delim, LAMBDA formattingFunc )
+string joinLambda( IT first, IT last, S const & delim, LAMBDA formattingFunc )
 {
   if( first == last )
   {
@@ -114,9 +114,9 @@ string joinLamda( IT first, IT last, S const & delim, LAMBDA formattingFunc )
  * @return a string containing input values concatenated with a delimiter
  */
 template< typename CONTAINER, typename S, typename LAMBDA >
-string joinLamda( CONTAINER const & container, S const & delim, LAMBDA formattingFunc )
+string joinLambda( CONTAINER const & container, S const & delim, LAMBDA formattingFunc )
 {
-  return joinLamda( std::begin( container ), std::end( container ), delim, formattingFunc );
+  return joinLambda( std::begin( container ), std::end( container ), delim, formattingFunc );
 }
 
 /**

src/coreComponents/constitutive/ConstitutiveBase.cpp

@@ -83,7 +83,8 @@ ConstitutiveBase::deliverClone( string const & name,
                                 Group * const parent ) const
 {
   std::unique_ptr< ConstitutiveBase >
-  newModel = ConstitutiveBase::CatalogInterface::factory( this->getCatalogName(), name, parent );
+  newModel = ConstitutiveBase::CatalogInterface::factory( this->getCatalogName(), getDataContext(),
+                                                          name, parent );
 
   newModel->forWrappers( [&]( WrapperBase & wrapper )
   {

src/coreComponents/constitutive/ConstitutiveManager.cpp

@@ -44,7 +44,8 @@ ConstitutiveManager::~ConstitutiveManager()
 Group * ConstitutiveManager::createChild( string const & childKey, string const & childName )
 {
   GEOS_LOG_RANK_0( GEOS_FMT( "{}: adding {} {}", getName(), childKey, childName ) );
-  std::unique_ptr< ConstitutiveBase > material = ConstitutiveBase::CatalogInterface::factory( childKey, childName, this );
+  std::unique_ptr< ConstitutiveBase > material =
+    ConstitutiveBase::CatalogInterface::factory( childKey, getDataContext(), childName, this );
   return &registerGroup< ConstitutiveBase >( childName, std::move( material ) );
 }
 

src/coreComponents/dataRepository/DataContext.cpp

@@ -25,7 +25,7 @@ namespace dataRepository
 {
 
 
-DataContext::DataContext( string const & targetName ):
+DataContext::DataContext( string_view targetName ):
   m_targetName( targetName )
 {}
 
@@ -35,12 +35,12 @@ std::ostream & operator<<( std::ostream & os, DataContext const & ctx )
   return os;
 }
 
-DataContext::ToStringInfo::ToStringInfo( string const & targetName, string const & filePath, size_t line ):
+DataContext::ToStringInfo::ToStringInfo( string_view targetName, string_view filePath, size_t line ):
   m_targetName( targetName ),
   m_filePath( filePath ),
   m_line( line )
 {}
-DataContext::ToStringInfo::ToStringInfo( string const & targetName ):
+DataContext::ToStringInfo::ToStringInfo( string_view targetName ):
   m_targetName( targetName )
 {}
 
@@ -83,6 +83,15 @@ DataFileContext::DataFileContext( xmlWrapper::xmlNode const & targetNode,
   m_offset( attPos.offset )
 {}
 
+DataFileContext::DataFileContext( string_view targetName, string_view file, size_t line ):
+  DataContext( targetName ),
+  m_typeName( "C++ Source File" ),
+  m_filePath( file ),
+  m_line( line ),
+  m_offsetInLine( 0 ),
+  m_offset( 0 )
+{}
+
 string DataFileContext::toString() const
 {
   if( m_line != xmlWrapper::xmlDocument::npos )
@@ -95,7 +104,7 @@ string DataFileContext::toString() const
   }
   else
   {
-    return GEOS_FMT( "{} (Source file not found)", m_targetName );
+    return GEOS_FMT( "{} ({})", m_targetName, ( m_filePath.empty() ? "Source file not found" : m_filePath ) );
   }
 }
 

src/coreComponents/dataRepository/DataContext.hpp

@@ -47,7 +47,7 @@ class DataContext
    * @brief Construct a new DataContext object.
    * @param targetName the target object name
    */
-  DataContext( string const & targetName );
+  DataContext( string_view targetName );
 
   /**
    * @brief Destroy the DataContext object
@@ -95,12 +95,12 @@ class DataContext
      * @param filePath the input file path where the target is declared.
      * @param line the line in the file where the target is declared.
      */
-    ToStringInfo( string const & targetName, string const & filePath, size_t line );
+    ToStringInfo( string_view targetName, string_view filePath, size_t line );
     /**
      * @brief Construct a new ToStringInfo object from a DataContext that has no input file info.
      * @param targetName the target name.
      */
-    ToStringInfo( string const & targetName );
+    ToStringInfo( string_view targetName );
     /**
      * @return true if a location has been found to declare the target in an input file.
      */
@@ -142,6 +142,14 @@ class DataFileContext final : public DataContext
   DataFileContext( xmlWrapper::xmlNode const & targetNode, xmlWrapper::xmlAttribute const & att,
                    xmlWrapper::xmlAttributePos const & attPos );
 
+  /**
+   * @brief Constructs the file context of a Group from a C++ source file.
+   * @param targetName The name of the target Group.
+   * @param file The name of the source file.
+   * @param line The line number in the source file.
+   */
+  DataFileContext( string_view targetName, string_view file, size_t line );
+
   /**
    * @return the target object name followed by the the file and line declaring it.
    */

src/coreComponents/dataRepository/Group.cpp

@@ -135,18 +135,64 @@ string Group::getPath() const
   return noProblem.empty() ? "/" : noProblem;
 }
 
+string Group::processInputName( xmlWrapper::xmlNode const & targetNode,
+                                xmlWrapper::xmlNodePos const & targetNodePos,
+                                string_view parentNodeName,
+                                xmlWrapper::xmlNodePos const & parentNodePos,
+                                std::set< string > & siblingNames )
+{
+  GEOS_THROW_IF( targetNode.type() != xmlWrapper::xmlNodeType::node_element,
+                 GEOS_FMT( "Error in node named \"{}\" ({}): GEOS XML nodes cannot contain "
+                           "text data nor anything but XML nodes.\nErroneous content: \"{}\"\n",
+                           parentNodeName, parentNodePos.toString(),
+                           stringutilities::trimSpaces( targetNode.value() ) ),
+                 InputError );
+
+  string targetNodeName;
+  try
+  { // read & validate the name attribute
+    xmlWrapper::readAttributeAsType( targetNodeName, "name",
+                                     rtTypes::getTypeRegex< string >( rtTypes::CustomTypes::groupName ),
+                                     targetNode, string( "" ) );
+  } catch( std::exception const & ex )
+  {
+    xmlWrapper::processInputException( ex, "name", targetNode, targetNodePos );
+  }
+
+  if( targetNodeName.empty() )
+  { // if there is no name attribute, we use the node tag as a node name
+    targetNodeName = targetNode.name();
+  }
+  else
+  { // Make sure names are not duplicated by checking all previous siblings
+    GEOS_THROW_IF( siblingNames.count( targetNodeName ) != 0,
+                   GEOS_FMT( "Error at node named \"{}\" ({}): "
+                             "An XML block cannot contain children with duplicated names.\n",
+                             targetNodeName, targetNodePos.toString() ),
+                   InputError );
+    siblingNames.insert( targetNodeName );
+  }
+
+  return targetNodeName;
+}
+
 void Group::processInputFileRecursive( xmlWrapper::xmlDocument & xmlDocument,
                                        xmlWrapper::xmlNode & targetNode )
 {
-  xmlWrapper::xmlNodePos nodePos = xmlDocument.getNodePosition( targetNode );
-  processInputFileRecursive( xmlDocument, targetNode, nodePos );
+  xmlWrapper::xmlNodePos targetNodePos = xmlDocument.getNodePosition( targetNode );
+  processInputFileRecursive( xmlDocument, targetNode, targetNodePos );
 }
 void Group::processInputFileRecursive( xmlWrapper::xmlDocument & xmlDocument,
                                        xmlWrapper::xmlNode & targetNode,
-                                       xmlWrapper::xmlNodePos const & nodePos )
+                                       xmlWrapper::xmlNodePos const & targetNodePos )
 {
   xmlDocument.addIncludedXML( targetNode );
 
+  if( targetNodePos.isFound() )
+  {
+    m_dataContext = std::make_unique< DataFileContext >( targetNode, targetNodePos );
+  }
+
   // Handle the case where the node was imported from a different input file
   // Set the path prefix to make sure all relative Path variables are interpreted correctly
   string const oldPrefix = std::string( Path::getPathPrefix() );
@@ -157,40 +203,12 @@ void Group::processInputFileRecursive( xmlWrapper::xmlDocument & xmlDocument,
   }
 
   // Loop over the child nodes of the targetNode
-  array1d< string > childNames;
+  std::set< string > childNames;
   for( xmlWrapper::xmlNode childNode : targetNode.children() )
   {
     xmlWrapper::xmlNodePos childNodePos = xmlDocument.getNodePosition( childNode );
-
-    // Get the child tag and name
-    string childName;
-
-    try
-    {
-      xmlWrapper::readAttributeAsType( childName, "name",
-                                       rtTypes::getTypeRegex< string >( rtTypes::CustomTypes::groupName ),
-                                       childNode, string( "" ) );
-    } catch( std::exception const & ex )
-    {
-      xmlWrapper::processInputException( ex, "name", childNode, childNodePos );
-    }
-
-    if( childName.empty() )
-    {
-      childName = childNode.name();
-    }
-    else
-    {
-      // Make sure child names are not duplicated
-      GEOS_ERROR_IF( std::find( childNames.begin(), childNames.end(), childName ) != childNames.end(),
-                     GEOS_FMT( "Error: An XML block cannot contain children with duplicated names.\n"
-                               "Error detected at node {} with name = {} ({}:l.{})",
-                               childNode.path(), childName, xmlDocument.getFilePath(),
-                               xmlDocument.getNodePosition( childNode ).line ) );
-
-      childNames.emplace_back( childName );
-    }
-
+    string const childName = processInputName( childNode, childNodePos,
+                                               getName(), targetNodePos, childNames );
     // Create children
     Group * newChild = createChild( childNode.name(), childName );
     if( newChild == nullptr )
@@ -203,7 +221,7 @@ void Group::processInputFileRecursive( xmlWrapper::xmlDocument & xmlDocument,
     }
   }
 
-  processInputFile( targetNode, nodePos );
+  processInputFile( targetNode, targetNodePos );
 
   // Restore original prefix once the node is processed
   Path::setPathPrefix( oldPrefix );
@@ -212,12 +230,6 @@ void Group::processInputFileRecursive( xmlWrapper::xmlDocument & xmlDocument,
 void Group::processInputFile( xmlWrapper::xmlNode const & targetNode,
                               xmlWrapper::xmlNodePos const & nodePos )
 {
-  if( nodePos.isFound() )
-  {
-    m_dataContext = std::make_unique< DataFileContext >( targetNode, nodePos );
-  }
-
-
   std::set< string > processedAttributes;
   for( std::pair< string const, WrapperBase * > & pair : m_wrappers )
   {
@@ -233,10 +245,10 @@ void Group::processInputFile( xmlWrapper::xmlNode const & targetNode,
     if( !xmlWrapper::isFileMetadataAttribute( attributeName ) )
     {
       GEOS_THROW_IF( processedAttributes.count( attributeName ) == 0,
-                     GEOS_FMT( "XML Node at '{}' with name={} contains unused attribute '{}'.\n"
+                     GEOS_FMT( "Error in {}: XML Node at '{}' contains unused attribute '{}'.\n"
                                "Valid attributes are:\n{}\nFor more details, please refer to documentation at:\n"
                                "http://geosx-geosx.readthedocs-hosted.com/en/latest/docs/sphinx/userGuide/Index.html",
-                               targetNode.path(), m_dataContext->toString(), attributeName,
+                               getDataContext(), targetNode.path(), attributeName,
                                dumpInputOptions() ),
                      InputError );
     }
@@ -264,11 +276,10 @@ void Group::registerDataOnMeshRecursive( Group & meshBodies )
 
 Group * Group::createChild( string const & childKey, string const & childName )
 {
-  GEOS_ERROR_IF( !(CatalogInterface::hasKeyName( childKey )),
-                 "KeyName ("<<childKey<<") not found in Group::Catalog" );
   GEOS_LOG_RANK_0( "Adding Object " << childKey<<" named "<< childName<<" from Group::Catalog." );
   return &registerGroup( childName,
-                         CatalogInterface::factory( childKey, childName, this ) );
+                         CatalogInterface::factory( childKey, getDataContext(),
+                                                    childName, this ) );
 }
 
 void Group::printDataHierarchy( integer const indent ) const