IO: use Boost library for reading/writing configuration files

Author: andrea-iob

CMakeLists.txt

@@ -593,7 +593,7 @@ if (BITPIT_ENABLE_MPI)
 endif()
 set(OPERATORS_EXTERNAL_DEPS "")
 set(CONTAINERS_EXTERNAL_DEPS "")
-set(IO_EXTERNAL_DEPS "LibXml2;RapidJSON")
+set(IO_EXTERNAL_DEPS "Boost")
 set(COMMUNICATIONS_EXTERNAL_DEPS "MPI")
 set(LA_EXTERNAL_DEPS "PETSc")
 set(SA_EXTERNAL_DEPS "")
@@ -831,39 +831,6 @@ if (${_LAPACKE_index} GREATER -1)
 endif()
 unset(_LAPACKE_index)
 
-list(FIND EXTERNAL_DEPS "LibXml2" _LibXml2_index)
-if (${_LibXml2_index} GREATER -1)
-    find_package(LibXml2 REQUIRED)
-
-    list (INSERT BITPIT_EXTERNAL_DEPENDENCIES 0 "LibXml2")
-    list (INSERT BITPIT_EXTERNAL_VARIABLES_LIBRARIES 0 "LIBXML2_LIBRARIES")
-    list (INSERT BITPIT_EXTERNAL_VARIABLES_INCLUDE_DIRS 0 "LIBXML2_INCLUDE_DIR")
-endif()
-unset(_LibXml2_index)
-
-list(FIND EXTERNAL_DEPS "RapidJSON" _RapidJSON_index)
-if (${_RapidJSON_index} GREATER -1)
-    find_package(RapidJSON 1.1.0 QUIET)
-    mark_as_advanced(RapidJSON_DIR)
-
-    if (RapidJSON_FOUND)
-        # RapidJSON library has been found
-        target_compile_definitions(${BITPIT_LIBRARY} PUBLIC "BITPIT_ENABLE_RAPIDJSON=1")
-
-        list (INSERT BITPIT_EXTERNAL_DEPENDENCIES 0 "RapidJSON")
-        list (INSERT BITPIT_EXTERNAL_VARIABLES_INCLUDE_DIRS 0 "RAPIDJSON_INCLUDE_DIRS")
-
-        # Activate std::string RapidJSON compliancy
-        target_compile_definitions(${BITPIT_LIBRARY} PUBLIC "RAPIDJSON_HAS_STDSTRING=1")
-    else()
-        # RapidJSON library has not been found
-        target_compile_definitions(${BITPIT_LIBRARY} PUBLIC "BITPIT_ENABLE_RAPIDJSON=0")
-
-        message(STATUS "RapidJSON library not found, JSON support will be disabled.")
-    endif()
-endif()
-unset(_RapidJSON_index)
-
 list(FIND EXTERNAL_DEPS "PETSc" _PETSc_index)
 if (${_PETSc_index} GREATER -1)
     list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/external/PETSc/cmake")
@@ -890,15 +857,20 @@ if (${_PETSc_index} GREATER -1)
 endif()
 unset(_PETSc_index)
 
-list(FIND EXTERNAL_DEPS "BoostTest" _BoostTest_index)
-if (${_BoostTest_index} GREATER -1)
+list(FIND EXTERNAL_DEPS "Boost" _Boost_index)
+if (${_Boost_index} GREATER -1)
     set(BOOST_COMPONENTS "")
+    list(FIND EXTERNAL_DEPS "BoostTest" _BoostTest_index)
     if(${_BoostTest_index} GREATER -1)
         LIST(APPEND BOOST_COMPONENTS "unit_test_framework")
     endif()
     string (REPLACE ";" " " BOOST_COMPONENTS_STRING "${BOOST_COMPONENTS}")
 
-    FIND_PACKAGE(Boost 1.40 COMPONENTS "${BOOST_COMPONENTS_STRING}" REQUIRED)
+    if ("${BOOST_COMPONENTS}" STREQUAL "")
+        FIND_PACKAGE(Boost 1.40 REQUIRED)
+    else ()
+        FIND_PACKAGE(Boost 1.40 COMPONENTS "${BOOST_COMPONENTS_STRING}" REQUIRED)
+    endif ()
 
     list (INSERT BITPIT_EXTERNAL_DEPENDENCIES 0 "Boost")
     list (INSERT BITPIT_EXTERNAL_VARIABLES_LIBRARIES 0 "Boost_LIBRARIES")

INSTALL.md

@@ -9,14 +9,10 @@ bitpit depends on
 * (optionally) MPI implementation. It has been tested with OpenMPI >= 1.6.5.
 
 Some additional dependencies are required for building specific modules
-* libxml2 and its development headers are needed when compiling the 'IO'
+* boost and its development headers are needed when compiling the 'IO'
   module (please note that the 'IO' module is a dependecies for many other
   bitpit modules, the only modules that do not depend on 'IO' are the low
-  level modules like 'operators', 'containers', 'LA', and 'SA'). Moreover,
-  json support is automatically enabled if RapidJSON (version 1.1.0) libraries  
-  are installed on the system (https://github.com/Tencent/rapidjson): this is
-  a completely optional requirement, IO module will compile and work fine
-  with the only xml support too;   
+  level modules like 'operators', 'containers', 'LA', and 'SA').
 * blas, lapack, and lapacke are needed when compiling 'CG', 'RBF', and 'POD'
   modules.
 

README_WINDOWS.md

@@ -17,12 +17,10 @@ This is a short guide to set a bitpit compliant 64bit Windows environment using
   - mingw-w64-x86_64-toolchain
   - mingw-w64-x86_64-lapack
   - mingw-w64-x86_64-msmpi
-  - mingw-w64-x86_64-libxml2
   - mingw-w64-x86_64-cmake
   - mingw-w64-x86_64-qt5 (optional, but needed to run cmake-gui. Consider 1.22 GB to install it.)
   - mingw-w64-x86_64-doxygen (to generate Doxygen documentation)
   - mingw-w64-x86_64-graphviz (to generate Doxygen documentation)
-  - mingw-w64-x86_64-rapidjson (to enable JSON I/O support on IO module)
 
 - <B>Microsoft MPI</B>: MSMpiSetup.exe or msmpisdk.msi (downloadable for free from https://www.microsoft.com/ searching for "MicrosoftMPI v x.x.x". Here the exact version x.x.x must be compliant with the version of MinGW64 package mingw-w64-x86_64-msmpi. See MSMPI section in procedure chapter for details)
 
@@ -200,22 +198,6 @@ user@machine MINGW64 ~
 > pacman -S mingw-w64-x86_64-lapack
 ```
 
-**__LIBMXL2__**
-
-Install *libxml2* with:
-```bash
-user@machine MINGW64 ~
-> pacman -S mingw-w64-x86_64-libxml2
-```
-
-**__RAPIDJSON__**
-
-If JSON support on IO module is required, install *rapidjson* with:
-```bash
-user@machine MINGW64 ~
-> pacman -S mingw-w64-x86_64-rapidjson
-```
-
 **__PETSc__**
 
 _PETSc_ can be installed on the MSYS2/MinGW64 environment in two ways:

THIRDPARTIES.md

@@ -81,37 +81,6 @@
   ```
 </details>
 
-## libxml2
-<details>
-  <summary>See License</summary>
-
-  ```
-  Except where otherwise noted in the source code (e.g. the files hash.c,
-  list.c and the trio files, which are covered by a similar licence but
-  with different Copyright notices) all the files are:
-
-   Copyright (C) 1998-2012 Daniel Veillard.  All Rights Reserved.
-
-  Permission is hereby granted, free of charge, to any person obtaining a copy
-  of this software and associated documentation files (the "Software"), to deal
-  in the Software without restriction, including without limitation the rights
-  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-  copies of the Software, and to permit persons to whom the Software is fur-
-  nished to do so, subject to the following conditions:
-
-  The above copyright notice and this permission notice shall be included in
-  all copies or substantial portions of the Software.
-
-  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FIT-
-  NESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
-  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-  THE SOFTWARE.
-  ```
-</details>
-
 ## METIS
 <details>
   <summary>See License</summary>
@@ -252,18 +221,3 @@
   This license DOES NOT apply to any software that may be obtained via the download-package option of the PETSc configuration. Each of those packages are covered by their own licenses.
   ```
 </details>
-
-## RAPIDJSON
-<details>
-  <summary>See License</summary>
-
-  ```
-  Copyright (C) 2015 THL A29 Limited, a Tencent company, and Milo Yip.  All rights reserved.
-
-  Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
-
-  The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
-
-  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-  ```
-</details>

environments/ubuntu/Dockerfile

@@ -11,12 +11,10 @@ RUN sed -i "s/htt[p|ps]:\/\/archive.ubuntu.com\/ubuntu\//mirror:\/\/mirrors.ubun
         liblapack-dev  \
         liblapacke-dev \
         mpich \
-        libxml2-dev \
         libmetis-dev \
         git \
         wget \
-        python3 \
-        rapidjson-dev
+        python3
 
 FROM bitpit-ubuntu-base AS bitpit-ubuntu-mpi
 LABEL stage=bitpit-ubuntu-mpi

src/IO/configuration.cpp

@@ -24,11 +24,7 @@
 
 
 #include "configuration.hpp"
-#include "configuration_XML.hpp"
-
-#if BITPIT_ENABLE_RAPIDJSON
-#include "configuration_JSON.hpp"
-#endif
+#include "configuration_tree.hpp"
 
 #include <stringUtils.hpp>
 
@@ -152,8 +148,7 @@ void ConfigParser::reset(const std::string &root, int version, bool multiSection
 /*!
     Read the specified configuration file.
 
-    Configuration file can be either XML or JSON files (if JSON support was
-    found at compile time).
+    Configuration can be read either from XML or JSON files.
 
     \param filename is the filename of the configuration file
     \param append controls if the configuration file will be appended to the
@@ -175,23 +170,27 @@ void ConfigParser::read(const std::string &filename, bool append)
         extension = utils::string::trim(extension);
     }
 
+    config::FileFormat fileFormat;
     if (extension == "xml" || extension == "XML") {
-        config::XML::readConfiguration(filename, m_root, m_checkVersion, m_version, this);
-#if BITPIT_ENABLE_RAPIDJSON
+        fileFormat = config::FILE_FORMAT_XML;
     } else if (extension == "json" || extension == "JSON") {
-        config::JSON::readConfiguration(filename, this);
-#endif
+        fileFormat = config::FILE_FORMAT_JSON;
     } else {
         throw std::runtime_error("ConfigParser::read - Unsupported file format");
     }
+
+    bool checkFileVersion = false;
+    if (fileFormat == config::FILE_FORMAT_XML) {
+        checkFileVersion = m_checkVersion;
+    }
+
+    config::tree::readConfiguration(filename, fileFormat, m_root, checkFileVersion, m_version, this);
 }
 
 /*!
     Write the configuration to the specified file.
 
-    Configuration file can be either XML or JSON files (if JSON support was
-    found at compile time).
-
+    Configuration can be written either to XML or JSON files.
 
     \param filename is the filename where the configuration will be written to
 */
@@ -205,16 +204,16 @@ void ConfigParser::write(const std::string &filename) const
         extension = utils::string::trim(extension);
     }
 
+    config::FileFormat fileFormat;
     if (extension == "xml" || extension == "XML") {
-        config::XML::writeConfiguration(filename, m_root, m_version, this);
-#if BITPIT_ENABLE_RAPIDJSON
+        fileFormat = config::FILE_FORMAT_XML;
     } else if (extension == "json" || extension == "JSON") {
-        bool prettify = true;
-        config::JSON::writeConfiguration(filename, this, prettify);
-#endif
+        fileFormat = config::FILE_FORMAT_JSON;
     } else {
-        throw std::runtime_error("ConfigParser::write - Unsupported file format");
+        throw std::runtime_error("ConfigParser::read - Unsupported file format");
     }
+
+    config::tree::writeConfiguration(filename, fileFormat, m_root, m_version, this);
 }
 
 /*!
@@ -332,8 +331,7 @@ namespace config {
     /*!
         Read the specified configuration file.
 
-        Configuration file can be either XML or JSON files (if JSON support was
-        found at compile time).
+        Configuration can be read either from XML or JSON files.
 
         \param filename is the filename of the configuration file
         \param append controls if the configuration file will be appended to the
@@ -348,8 +346,7 @@ namespace config {
     /*!
         Write the configuration to the specified file.
 
-        Configuration file can be either XML or JSON files (if JSON support was
-        found at compile time).
+        Configuration can be written either to XML or JSON files.
 
         \param filename is the filename where the configuration will be written to
     */

src/IO/configuration.hpp

@@ -26,7 +26,6 @@
 
 #include <memory>
 #include <string>
-#include <unordered_map>
 
 #include "configuration_config.hpp"