CellMLToSharedLibraryConverter.cpp

/*

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*/

#include "CellMLToSharedLibraryConverter.hpp"

#include <sstream>
#include <fstream>      // for std::ofstream
#include <sys/stat.h> // For mkdir()
#include <ctime>
#include <cstring> // For strerror()
#include <cerrno> // For errno

#include <boost/foreach.hpp>

#include "ChasteSyscalls.hpp"
#include "Exception.hpp"
#include "Warnings.hpp"
#include "ChasteBuildRoot.hpp"
#include "PetscTools.hpp"
#include "DynamicModelLoaderRegistry.hpp"
#include "GetCurrentWorkingDirectory.hpp"

#define IGNORE_EXCEPTIONS(code) \
    try {                       \
        code;                   \
    } catch (...) {}

#ifdef __APPLE__
//Mac OSX
const std::string CellMLToSharedLibraryConverter::msSoSuffix = "dylib";
#else
//Normal behaviour
const std::string CellMLToSharedLibraryConverter::msSoSuffix = "so";
#endif

CellMLToSharedLibraryConverter::CellMLToSharedLibraryConverter(bool preserveGeneratedSources,
                                                               std::string component)
    : mPreserveGeneratedSources(preserveGeneratedSources),
      mComponentName(component)
{
}

DynamicCellModelLoaderPtr CellMLToSharedLibraryConverter::Convert(const FileFinder& rFilePath,
                                                                  bool isCollective)
{
    DynamicCellModelLoaderPtr p_loader;
    std::string absolute_path = rFilePath.GetAbsolutePath();
    // Find out whether rFilePath is a .cellml or .so
    size_t dot_position = absolute_path.find_last_of(".");
    if (dot_position == std::string::npos || absolute_path[dot_position+1] =='/')
    {
        // Either there is no dot in the absolute path or there is one along the path (/home/user/chaste/../temp/stuff)
        EXCEPTION("File does not have an extension: " + absolute_path);
    }
    std::string extension = absolute_path.substr(dot_position+1);
    // We make a modifiable version of the const FileFinder just incase we feel like
    // amending the suffix
    FileFinder file_path_copy(rFilePath);
#ifdef __APPLE__
    if (extension == "so")
    {
        WARN_ONCE_ONLY("CellMLToSharedLibraryConverter asked to load a \".so\" file.  On this architecture it should be \".dylib\"");
        extension = "dylib";
        absolute_path.replace(dot_position+1, 5, extension);
        file_path_copy.SetPath(absolute_path,  RelativeTo::Absolute);
    }
#endif
    // Check the file exists
    if (!file_path_copy.Exists())
    {
        EXCEPTION("Dynamically loadable cell model '" + absolute_path + "' does not exist.");
    }
    if (extension == "cellml")
    {
        // Split the path into folder and leaf
        size_t slash_position = absolute_path.find_last_of("/\\");
        assert(slash_position != std::string::npos);
        std::string folder = absolute_path.substr(0, slash_position+1); // Include trailing slash
        std::string leaf = absolute_path.substr(slash_position+1, dot_position-slash_position); // Include dot
        std::string so_path = folder + "lib" + leaf + msSoSuffix;
        // Does the .so file already exist (and was it modified after the .cellml?)
        FileFinder so_file(so_path, RelativeTo::Absolute);
        if (!so_file.Exists() || rFilePath.IsNewerThan(so_file))
        {
            if (!isCollective)
            {
                EXCEPTION("Unable to convert .cellml to .so unless called collectively, due to possible race conditions.");
            }
            ConvertCellmlToSo(absolute_path, folder);
        }
        // Load the .so
        p_loader = DynamicModelLoaderRegistry::Instance()->GetLoader(so_file);
    }
    else if (extension == msSoSuffix)
    {
        // Just load the .so
        // Note that this may have been modified to .dylib
        p_loader = DynamicModelLoaderRegistry::Instance()->GetLoader(file_path_copy);
    }
    else
    {
        EXCEPTION("Unsupported extension '." + extension + "' of file '" + absolute_path + "'; must be .so, .dylib or .cellml");
    }

    return p_loader;
}

void CellMLToSharedLibraryConverter::ConvertCellmlToSo(const std::string& rCellmlFullPath,
                                                       const std::string& rCellmlFolder)
{
    FileFinder tmp_folder;
    FileFinder build_folder;

    std::string old_cwd = GetCurrentWorkingDirectory();
    // Check that the Chaste build tree exists
    FileFinder chaste_root("", RelativeTo::ChasteBuildRoot);

    if (!chaste_root.IsDir())
    {
        EXCEPTION("No Chaste build tree found at '" << chaste_root.GetAbsolutePath()
                  << "' - you need the source to use CellML models directly in Chaste.");
    }
    FileFinder component_dir(mComponentName, RelativeTo::ChasteBuildRoot);
    if (!component_dir.IsDir())
    {
        EXCEPTION("Unable to convert CellML model: required Chaste component '" << mComponentName
                  << "' does not exist in '" << chaste_root.GetAbsolutePath() << "'.");
    }
    // Try the conversion
    try
    {
        // Need to create a .so file from the CellML...
        if (PetscTools::AmMaster())
        {
            // Create a temporary folder within heart/dynamic
            std::stringstream folder_name;
            folder_name << "dynamic/tmp_" << getpid() << "_" << time(NULL);

#ifdef CHASTE_CMAKE
            tmp_folder.SetPath(component_dir.GetAbsolutePath() + "/" + folder_name.str(), RelativeTo::Absolute);
            build_folder.SetPath(component_dir.GetAbsolutePath() + "/" + folder_name.str(), RelativeTo::Absolute);
#else
            tmp_folder.SetPath(component_dir.GetAbsolutePath() + "/" + folder_name.str(), RelativeTo::Absolute);
            build_folder.SetPath(component_dir.GetAbsolutePath() + "/build/" + ChasteBuildDirName() + "/" + folder_name.str(), RelativeTo::Absolute);
#endif

            int ret = mkdir((tmp_folder.GetAbsolutePath()).c_str(), 0700);
            if (ret != 0)
            {
                EXCEPTION("Failed to create temporary folder '" << tmp_folder.GetAbsolutePath() << "' for CellML conversion: "
                          << strerror(errno));
            }

            // Copy the .cellml file (and any relevant others) into the temporary folder
            FileFinder cellml_file(rCellmlFullPath, RelativeTo::Absolute);
            FileFinder cellml_folder = cellml_file.GetParent();
            std::string cellml_leaf_name = cellml_file.GetLeafNameNoExtension();
            std::vector<FileFinder> cellml_files = cellml_folder.FindMatches(cellml_leaf_name + "*");

            BOOST_FOREACH(const FileFinder& r_cellml_file, cellml_files)
            {
                r_cellml_file.CopyTo(tmp_folder);
            }

#ifdef CHASTE_CMAKE
            std::string cmake_lists_filename = tmp_folder.GetAbsolutePath() + "/CMakeLists.txt";
            std::ofstream cmake_lists_filestream(cmake_lists_filename.c_str());
            cmake_lists_filestream << "cmake_minimum_required(VERSION 2.8.12)\n" <<
                                      "add_compile_options(-std=c++11)\n" <<
                                      "find_package(Chaste COMPONENTS " << mComponentName << ")\n" <<
                                      "chaste_do_cellml(sources " << cellml_file.GetAbsolutePath() << " " << "ON)\n" <<
                                      "set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})\n" <<
                                      "include_directories(${Chaste_THIRD_PARTY_INCLUDE_DIRS} ${Chaste_INCLUDE_DIRS})\n" <<
                                      "add_library(" << cellml_leaf_name << " SHARED " << "${sources})\n" <<
                                      "if (${CMAKE_SYSTEM_NAME} MATCHES \"Darwin\")\n" <<
                                      "   target_link_libraries(" << cellml_leaf_name << " \"-Wl,-undefined,dynamic_lookup\")\n" <<
                                      "endif()\n"
                                      //"target_link_libraries(" << cellml_leaf_name << " ${Chaste_LIBRARIES})\n"
                                      ;
            cmake_lists_filestream.close();
            std::string cmake_args = " -DCMAKE_PREFIX_PATH=" + chaste_root.GetAbsolutePath() +
                                     " -DCMAKE_BUILD_TYPE=" + ChasteBuildType() +
                                     " -DChaste_ENABLE_TESTING=OFF" +
                                     " -DBUILD_SHARED_LIBS=ON";
            EXPECT0(chdir, tmp_folder.GetAbsolutePath());
            EXPECT0(system, "cmake" + cmake_args + " .");
            EXPECT0(system, "cmake --build . --config " + ChasteBuildType());
#else
            // Change to Chaste source folder
            EXPECT0(chdir, chaste_root.GetAbsolutePath());
            // Run scons to generate C++ code and compile it to a .so
            EXPECT0(system, "scons --warn=no-all dyn_libs_only=1 build=" + ChasteBuildType() + " " + tmp_folder.GetAbsolutePath());
            if (mPreserveGeneratedSources)
            {
                // Copy the generated source (.hpp and .cpp) to the same place as the .so file is going.
                // NB. CMake does this by default
                FileFinder destination_folder_for_sources(rCellmlFolder, RelativeTo::Absolute);
                // Copy generated source code as well
                std::vector<FileFinder> generated_files = build_folder.FindMatches("*.?pp");
                BOOST_FOREACH(const FileFinder& r_generated_file, generated_files)
                {
                    r_generated_file.CopyTo(destination_folder_for_sources);
                }
            }
#endif

            FileFinder so_file(tmp_folder.GetAbsolutePath() + "/lib" + cellml_leaf_name + "." + msSoSuffix, RelativeTo::Absolute);
            EXCEPT_IF_NOT(so_file.Exists());
            // CD back
            EXPECT0(chdir, old_cwd);

            // Copy the .so to the same folder as the original .cellml file
            FileFinder destination_folder(rCellmlFolder, RelativeTo::Absolute);
            so_file.CopyTo(destination_folder);

            // Delete the temporary folders
            build_folder.DangerousRemove();
            tmp_folder.DangerousRemove();
        }
    }
    catch (Exception& e)
    {
        PetscTools::ReplicateException(true);
        if (tmp_folder.IsPathSet() && tmp_folder.Exists())
        {
            if (mPreserveGeneratedSources)
            {
                // Copy any temporary files
                IGNORE_EXCEPTIONS(build_folder.CopyTo(FileFinder(rCellmlFolder + "/build/", RelativeTo::Absolute)));
                IGNORE_EXCEPTIONS(tmp_folder.CopyTo(FileFinder(rCellmlFolder + "/tmp/", RelativeTo::Absolute)));
            }
            // Delete the temporary folders
            IGNORE_EXCEPTIONS(build_folder.DangerousRemove()); // rm -r under source
            IGNORE_EXCEPTIONS(tmp_folder.DangerousRemove()); // rm -r under source
        }
        IGNORE_RET(chdir, old_cwd);
        EXCEPTION("Conversion of CellML to Chaste shared object failed. Error was: " + e.GetMessage());
    }
    // This also has the effect of a barrier, ensuring all processes wait for the
    // shared library to be created.
    PetscTools::ReplicateException(false);
}

void CellMLToSharedLibraryConverter::CreateOptionsFile(const OutputFileHandler& rHandler,
                                                       const std::string& rModelName,
                                                       const std::vector<std::string>& rArgs,
                                                       const std::string& rExtraXml)
{
    if (PetscTools::AmMaster())
    {
        out_stream p_optfile = rHandler.OpenOutputFile(rModelName + "-conf.xml");
        (*p_optfile) << "<?xml version='1.0'?>" << std::endl
                     << "<pycml_config>" << std::endl;
        if (!rArgs.empty())
        {
            (*p_optfile) << "<command_line_args>" << std::endl;
            for (unsigned i=0; i<rArgs.size(); i++)
            {
                (*p_optfile) << "<arg>" << rArgs[i] << "</arg>" << std::endl;
            }
            (*p_optfile) << "</command_line_args>" << std::endl;
        }
        (*p_optfile) << rExtraXml << "</pycml_config>" << std::endl;
        p_optfile->close();
    }
    PetscTools::Barrier("CellMLToSharedLibraryConverter::CreateOptionsFile");
}