CellMLToSharedLibraryConverter.cpp

/*

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*/

#include "CellMLToSharedLibraryConverter.hpp"

#include <sstream>
#include <unistd.h> // For getpid()
#include <sys/stat.h> // For mkdir()
#include <ctime>
#include <cstring> // For strerror()
#include <cerrno> // For errno

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

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();
    // Check the file exists
    if (!rFilePath.Exists())
    {
        EXCEPTION("Dynamically loadable cell model '" + absolute_path + "' does not exist.");
    }
    // Find out whether rFilePath is a .cellml or .so
    size_t dot_position = absolute_path.find_last_of(".");
    if (dot_position == std::string::npos)
    {
        EXCEPTION("File does not have an extension: " + absolute_path);
    }
    std::string extension = absolute_path.substr(dot_position+1);
    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 + "so";
        // 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, leaf);
        }
        // Load the .so
        p_loader = DynamicModelLoaderRegistry::Instance()->GetLoader(so_file);
    }
    else if (extension == "so")
    {
        // Just load the .so
        p_loader = DynamicModelLoaderRegistry::Instance()->GetLoader(rFilePath);
    }
    else
    {
        EXCEPTION("Unsupported extension '." + extension + "' of file '" + absolute_path + "'; must be .so or .cellml");
    }

    return p_loader;
}

void CellMLToSharedLibraryConverter::ConvertCellmlToSo(const std::string& rCellmlFullPath,
                                                       const std::string& rCellmlFolder,
                                                       const std::string& rModelLeafName)
{
    std::string tmp_folder, build_folder;
    std::string old_cwd = GetCurrentWorkingDirectory();
    // Check that the Chaste source tree exists
    FileFinder chaste_root("", RelativeTo::ChasteSourceRoot);
    if (!chaste_root.IsDir())
    {
        EXCEPTION("No Chaste source tree found at '" << chaste_root.GetAbsolutePath()
                  << "' - you need the source to use CellML models directly in Chaste.");
    }
    FileFinder component_dir(mComponentName, RelativeTo::ChasteSourceRoot);
    if (!component_dir.IsDir())
    {
        EXCEPTION("Unable to convert CellML model: required Chaste component '" << mComponentName
                  << "' does not exist in '" << ChasteBuildRootDir() << "'.");
    }
    // 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);
            tmp_folder = component_dir.GetAbsolutePath() + "/" + folder_name.str();
            build_folder = component_dir.GetAbsolutePath() + "/build/" + ChasteBuildDirName() + "/" + folder_name.str();
            int ret = mkdir(tmp_folder.c_str(), 0700);
            if (ret != 0)
            {
                EXCEPTION("Failed to create temporary folder '" << tmp_folder << "' for CellML conversion: "
                          << strerror(errno));
            }
            // Copy the .cellml file (and any relevant others) into the temporary folder
            size_t dot_pos = rCellmlFullPath.rfind('.');
            std::string cellml_base = rCellmlFullPath.substr(0, dot_pos);
            EXPECT0(system, "cp " + cellml_base + "* " + tmp_folder);
            // If there's a config file, copy that too
            std::string config_path = rCellmlFullPath.substr(0, rCellmlFullPath.length() - 7) + "-conf.xml";
            if (FileFinder(config_path, RelativeTo::Absolute).Exists())
            {
                EXPECT0(system, "cp " + config_path + " " + tmp_folder);
            }
            // Change to Chaste source folder
            EXPECT0(chdir, ChasteBuildRootDir());
            // 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);
            EXCEPT_IF_NOT(FileFinder(tmp_folder + "/lib" + rModelLeafName + "so", RelativeTo::Absolute).Exists());
            // CD back
            EXPECT0(chdir, old_cwd);
            // Copy the .so to the same folder as the original .cellml file
            EXPECT0(system, "cp " + tmp_folder + "/lib" + rModelLeafName + "so " + rCellmlFolder);
            if (mPreserveGeneratedSources)
            {
                // Copy generated source code as well
                EXPECT0(system, "cp " + build_folder + "/*.?pp " + rCellmlFolder);
            }
            // Delete the temporary folders
            EXPECT0(system, "rm -r " + build_folder);
            EXPECT0(system, "rm -r " + tmp_folder);
        }
    }
    catch (Exception& e)
    {
        PetscTools::ReplicateException(true);
        if (FileFinder(tmp_folder, RelativeTo::Absolute).Exists())
        {
            if (mPreserveGeneratedSources)
            {
                // Copy any temporary files
                IGNORE_RET(system, "cp -r " + build_folder + " " + rCellmlFolder + "/build/");
                IGNORE_RET(system, "cp -r " + tmp_folder + " " + rCellmlFolder + "/tmp/");
            }
            // Delete the temporary folders
            IGNORE_RET(system, "rm -rf " + build_folder); // -f because folder might not exist
            IGNORE_RET(system, "rm -r " + tmp_folder);
        }
        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");
}