OutputFileHandler.cpp

/*
 
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*/
 
#include "OutputFileHandler.hpp"
 
#include <cstdlib>
#include <fstream>
#include <sstream>
#include <cassert>
 
#include "ArchiveLocationInfo.hpp"
#include "Exception.hpp"
#include "FileFinder.hpp"
#include "GetCurrentWorkingDirectory.hpp"
#include "PetscTools.hpp"
 
 
const std::string OutputFileHandler::SIG_FILE_NAME(".chaste_deletable_folder");
 
void CleanFolder(const fs::path& rPath, bool isTop=true);
 
void CleanFolder(const fs::path& rPath, bool isTop)
{
    assert(fs::is_directory(rPath));
    fs::directory_iterator end_iter;
    // First recursively remove the children
    for (fs::directory_iterator dir_iter(rPath); dir_iter != end_iter; ++dir_iter)
    {
        if (fs::is_directory(dir_iter->status()))
        {
            CleanFolder(dir_iter->path(), false);
        }
        else
        {
            const fs::path& r_item_path(dir_iter->path());
            if (!isTop || (r_item_path.filename().string())[0] != '.')
            {
                fs::remove(r_item_path);
            }
        }
    }
    // Now remove the folder itself, if not top
    if (!isTop)
    {
        fs::remove(rPath);
    }
}
 
 
OutputFileHandler::OutputFileHandler(const std::string& rDirectory,
                                     bool cleanOutputDirectory)
{
    CommonConstructor(rDirectory, cleanOutputDirectory);
}
 
 
OutputFileHandler::OutputFileHandler(const FileFinder& rDirectory,
                                     bool cleanOutputDirectory)
{
    FileFinder output_root("", RelativeTo::ChasteTestOutput);
    std::string relative_path;
    try
    {
        relative_path = rDirectory.GetRelativePath(output_root);
    }
    catch (const Exception&)
    {
        EXCEPTION("The location provided to OutputFileHandler must be inside CHASTE_TEST_OUTPUT; '"
                  << rDirectory.GetAbsolutePath() << "' is not under '"
                  << output_root.GetAbsolutePath() << "'.");
    }
    if (*output_root.GetAbsolutePath().rbegin() != '/' && !relative_path.empty())
    {
        assert(*relative_path.begin() == '/');
        relative_path.erase(0, 1); // Remove leading slash
    }
    CommonConstructor(relative_path, cleanOutputDirectory);
}
 
 
void OutputFileHandler::CommonConstructor(const std::string& rDirectory,
                                          bool cleanOutputDirectory)
{
    // Is it a valid request for a directory?
    if (rDirectory.find("..") != std::string::npos)
    {
        EXCEPTION("Will not create directory: " + rDirectory +
                  " due to it potentially being above, and cleaning, CHASTE_TEST_OUTPUT.");
        // Note: in Boost 1.48 and above we could use 'canonical' to check this better
    }
    //The notion of absolute path on Windows is rather different.
    //For example, / and /foo are not absolute paths.
    //However, fs::path.has_root_path() captures the intended semantics here as follows
 
    if (fs::path(rDirectory).has_root_path())
    {
        EXCEPTION("The constructor argument to OutputFileHandler must be a relative path; '"
                  << rDirectory << "' is absolute.");
    }
 
    mDirectory = MakeFoldersAndReturnFullPath(rDirectory);
 
    // Clean the directory (default)
    if (rDirectory != "" && cleanOutputDirectory) // Clean directory but don't ever clean CHASTE_TEST_OUTPUT at the top level
    {
        FileFinder signature_file(mDirectory + SIG_FILE_NAME, RelativeTo::Absolute);
        if (!signature_file.Exists())
        {
            EXCEPTION("Cannot delete " + mDirectory + " because signature file \"" + SIG_FILE_NAME + "\" is not present.");
        }
 
        // Are we the master process? Only the master should delete files
        if (PetscTools::AmMaster())
        {
            CleanFolder(mDirectory);
        }
        // Wait for master to finish before going on to use the directory.
        PetscTools::Barrier("OutputFileHandler");
    }
}
 
std::string OutputFileHandler::GetChasteTestOutputDirectory()
{
    char* chaste_test_output = getenv("CHASTE_TEST_OUTPUT");
    FileFinder directory_root;
    if (chaste_test_output == nullptr || *chaste_test_output == 0)
    {
        // Mimic the old behaviour of setting CHASTE_TEST_OUTPUT: /tmp/'+os.environ['USER']+'/testoutput/
        std::stringstream  tmp_directory;
        if (getenv("USER")!=NULL)
        {
            tmp_directory << "/tmp/" << getenv("USER") << "/testoutput/"; // LCOV_EXCL_LINE
        }
        else
        {
            // No $USER in environment (which may be the case in Docker)
            tmp_directory << "/tmp/chaste/testoutput/";
        }
        directory_root.SetPath(tmp_directory.str(), RelativeTo::AbsoluteOrCwd);
        /* // Former behaviour: default to 'testoutput' folder within the current directory
         * directory_root.SetPath("testoutput", RelativeTo::CWD); */
    }
    else
    {
        directory_root.SetPath(chaste_test_output, RelativeTo::AbsoluteOrCwd);
    }
    // Note that FileFinder::GetAbsolutePath adds a trailing slash, but only
    // if the directory exists at the time of the call
    std::string chaste_test_output_directory = directory_root.GetAbsolutePath();
    AddTrailingSlash(chaste_test_output_directory);
    return chaste_test_output_directory;
}
 
std::string OutputFileHandler::MakeFoldersAndReturnFullPath(const std::string& rDirectory) const
{
    fs::path output_root(GetChasteTestOutputDirectory());
    fs::path rel_path(rDirectory);
 
    // Boost filesystem needed this, but std::filesystem is okay
    //if (!rel_path.empty() && (*(--rel_path.end())) == ".")
    //{
    //    // rDirectory has a trailing slash, which gives an unhelpful last component
    //    rel_path.remove_filename();
    //}
    if (!rel_path.empty())
    {
        assert( (*(--rel_path.end())) != ".");
    }
 
    // Make master wait (because other processes may be checking whether a directory exists)
    PetscTools::Barrier("OutputFileHandler::MakeFoldersAndReturnFullPathBeforeCreation");
    // Are we the master process? Only the master should make any new directories
    if (PetscTools::AmMaster())
    {
        try
        {
            // If necessary make the ChasteTestOutputDirectory - don't make it deleteable by Chaste
            fs::create_directories(output_root); // Note that this is a no-op if the folder exists already
 
            // Now make all the sub-folders requested one-by-one and add the .chaste_deletable_folder file to them
            fs::path next_folder(output_root);
            for (fs::path::iterator path_iter = rel_path.begin(); path_iter != rel_path.end(); ++path_iter)
            {
                next_folder /= *path_iter;
                bool created_dir = fs::create_directory(next_folder);
                if (created_dir)
                {
                    // Add the Chaste signature file
                    std::ofstream sig_file(next_folder / SIG_FILE_NAME);
                    sig_file.close();
                }
            }
        }
        // LCOV_EXCL_START
        catch (const fs::filesystem_error& e)
        {
            TERMINATE("Error making test output folder: " << e.what());
        }
        // LCOV_EXCL_STOP
    }
 
    // Wait for master to finish before going on to use the directory.
    PetscTools::Barrier("OutputFileHandler::MakeFoldersAndReturnFullPath");
 
    std::string path_with_slash = (output_root / rel_path).string();
    AddTrailingSlash(path_with_slash);
    return path_with_slash;
}
 
std::string OutputFileHandler::GetOutputDirectoryFullPath() const
{
    return mDirectory;
}
 
std::string OutputFileHandler::GetRelativePath() const
{
    FileFinder output_root("", RelativeTo::ChasteTestOutput);
    std::string relative_path = FindFile("").GetRelativePath(output_root);
    if (!relative_path.empty() && *relative_path.rbegin() == '/')
    {
        relative_path.erase(--relative_path.end()); // Remove trailing slash
    }
    return relative_path;
}
 
out_stream OutputFileHandler::OpenOutputFile(const std::string& rFileName,
                                             std::ios_base::openmode mode) const
{
    out_stream p_output_file(new std::ofstream((mDirectory+rFileName).c_str(), mode));
    if (!p_output_file->is_open())
    {
        EXCEPTION("Could not open file \"" + rFileName + "\" in " + mDirectory);
    }
    return p_output_file;
}
 
out_stream OutputFileHandler::OpenOutputFile(const std::string& rFileName,
                                             unsigned number,
                                             const std::string& rFileFormat,
                                             std::ios_base::openmode mode) const
{
    std::stringstream string_stream;
    string_stream << rFileName << number << rFileFormat;
    return OpenOutputFile(string_stream.str(), mode);
}
 
void OutputFileHandler::SetArchiveDirectory() const
{
    FileFinder dir(GetOutputDirectoryFullPath(), RelativeTo::Absolute);
    ArchiveLocationInfo::SetArchiveDirectory(dir);
}
 
void OutputFileHandler::AddTrailingSlash(std::string& rDirectory)
{
    // Add a trailing slash if not already there
    if (rDirectory!="" && !( *(rDirectory.end()-1) == '/'))
    {
        rDirectory = rDirectory + "/";
    }
}
 
FileFinder OutputFileHandler::CopyFileTo(const FileFinder& rSourceFile) const
{
    if (!rSourceFile.IsFile())
    {
        EXCEPTION("Can only copy single files:\n" << rSourceFile.GetAbsolutePath() << " is not a file.");
    }
    fs::path from_path(rSourceFile.GetAbsolutePath());
    fs::path to_path(GetOutputDirectoryFullPath());
    to_path /= from_path.filename();
    if (PetscTools::AmMaster())
    {
        try
        {
            fs::copy_file(from_path, to_path);
        }
        // LCOV_EXCL_START
        catch (const fs::filesystem_error& e)
        {
            TERMINATE("Error copying file '" << rSourceFile.GetAbsolutePath() << "': " << e.what());
        }
        // LCOV_EXCL_STOP
    }
    PetscTools::Barrier("OutputFileHandler::CopyFileTo");
    return FileFinder(to_path.string(), RelativeTo::Absolute);
}
 
FileFinder OutputFileHandler::FindFile(std::string leafName) const
{
    return FileFinder(GetOutputDirectoryFullPath() + leafName, RelativeTo::Absolute);
}