file_input_source.hpp

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#ifndef GENESIS_UTILS_IO_FILE_INPUT_SOURCE_H_
#define GENESIS_UTILS_IO_FILE_INPUT_SOURCE_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2020 Lucas Czech and HITS gGmbH
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lucas.czech@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/
 
#include "genesis/utils/core/fs.hpp"
#include "genesis/utils/io/base_input_source.hpp"
 
#include <cstdio>
#include <cerrno>
#include <cstring>
#include <istream>
#include <stdexcept>
#include <string>
 
namespace genesis {
namespace utils {
 
// =================================================================================================
//     File Input Source
// =================================================================================================
 
class FileInputSource final : public BaseInputSource
{
public:
 
    // -------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------
 
    explicit FileInputSource( std::string const& file_name )
        : file_name_( file_name )
    {
        if( ! file_exists( file_name ) ) {
            throw std::runtime_error( "File does not exist or is not readable: " + file_name );
        }
    }
 
    explicit FileInputSource( std::string const& file_name, FILE* file )
        : file_( file )
        , file_name_( file_name )
    {
        // We do our own buffering.
        std::setvbuf( file_, nullptr, _IONBF, 0 );
    }
 
    FileInputSource( FileInputSource const& ) = default;
    FileInputSource( FileInputSource&& )      = default;
 
    FileInputSource& operator= ( FileInputSource const& ) = default;
    FileInputSource& operator= ( FileInputSource&& )      = default;
 
    ~FileInputSource() override = default;
 
    // -------------------------------------------------------------
    //     Overloaded Internal Members
    // -------------------------------------------------------------
 
private:
 
    size_t read_( char* buffer, size_t size ) override
    {
        // Special case: we already finished reading the file.
        // We need this check as otherwise the file would be reopened again and
        // read again from the start.
        if( finished_ ) {
            return 0;
        }
 
        // We need to do lazy loading, otherwise, we might end up having too many open files
        // if we are using the from_files() function, which opens all files at once...
        if( file_ == nullptr ) {
            errno = 0;
            file_ = std::fopen( file_name_.c_str(), "rb" );
 
            if( file_ == nullptr ) {
                throw std::runtime_error(
                    "Cannot open file " + file_name_ + ": " + std::string( strerror( errno ))
                );
            }
 
            // We do our own buffering.
            std::setvbuf( file_, nullptr, _IONBF, 0 );
        }
 
        // Do the reading.
        size_t const ret = std::fread( buffer, 1, size, file_ );
        if( std::ferror( file_ ) ) {
            throw std::runtime_error( "Cannot read from file: " + file_name_ );
        }
 
        // Similarly, we need to close again once we are done, so that the file is not kept
        // open unnecessarily long after reading.
        if( ret < size ) {
            std::fclose( file_ );
            file_ = nullptr;
            finished_ = true;
        }
 
        return ret;
    }
 
    std::string source_name_() const override
    {
        return "input file (" + file_name_ + ")";
    }
 
    std::string source_string_() const override
    {
        return file_name_;
    }
 
    // -------------------------------------------------------------
    //     Member Variables
    // -------------------------------------------------------------
 
    FILE*       file_ = nullptr;
    std::string file_name_;
    bool        finished_ = false;
};
 
} // namespace utils
} // namespace genesis
 
#endif // include guard