seqan/system/file_sync.h

// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
//     * Redistributions of source code must retain the above copyright
//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above copyright
//       notice, this list of conditions and the following disclaimer in the
//       documentation and/or other materials provided with the distribution.
//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
//       its contributors may be used to endorse or promote products derived
//       from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================

//SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file

#ifndef SEQAN_HEADER_FILE_SIMPLE_H
#define SEQAN_HEADER_FILE_SIMPLE_H

#include <fcntl.h>          // O_CREAT ..
#include <sys/stat.h>       //
#include <cstdio>           // tmpnam(..)

#ifdef STDLIB_VS
# include <io.h>            // read(..) ..
#else
# include <cstdlib>
# include <cerrno>
# include <unistd.h>
#endif


/* IOREV
 *
 * _tested_
 * _nodoc_
 *
 * contains third way of file-io, low level platform specific, i.e. fd for
 * POSIX and handles for WINDOWS
 *
 * not clear in which places this is used exactly
 *
 * SEQAN_DIRECTIO used on UNIX, not sure exactly what it does
 * use of other macros unclear aswell
 *
 */


//////////////////////////////////////////////////////////////////////////////

namespace seqan
{


template <typename TSpec /* = void */>
struct Sync {};


#ifdef STDLIB_VS

//////////////////////////////////////////////////////////////////////////////
// Windows rtl file access
template <typename TSpec>
class File<Sync<TSpec> >
{
//IOREV _windows_ _nodoc_
public:

    typedef int64_t         FilePtr;
    typedef int64_t         SizeType;       // type of file size
    typedef unsigned int    SizeType_;      // type of transfer size (for read or write)
    typedef int             Handle;

    Handle handle;

    File(void * /*dummy*/ = NULL) :    // to be compatible with the FILE*(NULL) constructor
        handle(-1) {}

    virtual ~File()
    {
        close();
    }

    //File(int posixHandle) : handle(posixHandle) {}

    inline int _getOFlag(int openMode) const
    {
        int result;
        bool canWrite = false;

        switch (openMode & OPEN_MASK)
        {
        case OPEN_RDONLY:
            result = _O_RDONLY;
            break;

        case OPEN_WRONLY:
            canWrite = true;
            result = _O_WRONLY;
            break;

        case OPEN_RDWR:
        default:
            canWrite = true;
            result = _O_RDWR;
            break;
        }

        if (openMode & OPEN_CREATE)     result |= _O_CREAT;
        if (canWrite && !(openMode & OPEN_APPEND))    result |= _O_TRUNC;
        if (openMode & OPEN_TEMPORARY)  result |= _O_TEMPORARY;
        return result | _O_BINARY;
    }

    bool open(char const * fileName, int openMode = DefaultOpenMode<File>::VALUE)
    {
        handle = ::_open(fileName, _getOFlag(openMode), _S_IREAD | _S_IWRITE);
        if (handle == -1)
        {
            if (!(openMode & OPEN_QUIET))
                std::cerr << "Open failed on file " << fileName << ". (" << ::strerror(errno) << ")" << std::endl;
            return false;
        }
        SEQAN_PROADD(SEQAN_PROOPENFILES, 1);
        return true;
    }

    bool openTemp(int openMode = DefaultOpenTempMode<File>::VALUE)
    {
#ifdef SEQAN_DEFAULT_TMPDIR
        char * fileName = _tempnam(SEQAN_DEFAULT_TMPDIR, "SQN");
#else  // #ifdef SEQAN_DEFAULT_TMPDIR
        char * fileName = _tempnam(NULL, "SQN");
#endif  // #ifdef SEQAN_DEFAULT_TMPDIR
        if (!fileName)
        {
            if (!(openMode & OPEN_QUIET))
                std::cerr << "Cannot create a unique temporary filename" << std::endl;
            return false;
        }
        bool result = open(fileName, openMode | OPEN_TEMPORARY);
        ::free(fileName);
        return result;
    }

    inline bool close()
    {
        if (_close(handle) != 0)
            return false;

        handle = -1;
        SEQAN_PROSUB(SEQAN_PROOPENFILES, 1);
        return true;
    }

    inline int read(void * buffer, SizeType_ count) const
    {
        SEQAN_PROADD(SEQAN_PROIO, (count + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
        SEQAN_PROTIMESTART(tw);
        int result = ::_read(handle, buffer, count);
        SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
        return result;
    }

    inline int write(void const * buffer, SizeType_ count) const
    {
        SEQAN_PROADD(SEQAN_PROIO, (count + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
        SEQAN_PROTIMESTART(tw);
        int result = ::_write(handle, buffer, count);
        SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
        return result;
    }

    inline FilePtr seek(FilePtr pos, int origin = SEEK_SET) const
    {
        return _lseeki64(handle, pos, origin);
    }

    inline FilePtr tell() const
    {
        return _telli64(handle);
    }

    static int error()
    {
        return errno;
    }

    operator bool() const
    {
        return handle != -1;
    }
};

inline bool fileExists(const char * fileName)
{
//IOREV _windows_ _nodoc_
    struct _stat buf;
    return _stat(fileName, &buf) == 0;
}

inline bool fileUnlink(const char * fileName)
{
//IOREV _windows_ _nodoc_
    return _unlink(fileName) == 0;
}

#else

//////////////////////////////////////////////////////////////////////////////
// Unix file access
template <typename TSpec>
class File<Sync<TSpec> >
{
//IOREV __nodoc_
public:

    typedef off_t           FilePtr;
    typedef off_t           SizeType;       // type of file size
    typedef size_t          SizeType_;      // type of transfer size (for read or write)
    typedef int             Handle;

    Handle handle;

    File(void * /*dummy*/ = NULL) :    // to be compatible with the FILE*(NULL) constructor
        handle(-1) {}

    ///File(int posixHandle) : handle(posixHandle) {}

    virtual ~File()
    {
        this->close();
    }

    inline int _getOFlag(int openMode) const
    {
        int result = O_LARGEFILE;

        switch (openMode & OPEN_MASK)
        {
        case OPEN_RDONLY:
            result |= O_RDONLY;
            break;

        case OPEN_WRONLY:
            result |= O_WRONLY;
            if (!(openMode & OPEN_APPEND))    result |= O_TRUNC;
            break;

        case OPEN_RDWR:
            result |= O_RDWR;
            if (!(openMode & OPEN_APPEND))    result |= O_TRUNC;
            break;
        }

        if (openMode & OPEN_CREATE)     result |= O_CREAT;
//            if (openMode & OPEN_TEMPORARY)  result |= O_TEMPORARY;
        #ifdef SEQAN_DIRECTIO
        if (openMode & OPEN_ASYNC)        result |= O_DIRECT;
        #endif
        return result;
    }

    virtual bool open(char const * fileName, int openMode = DefaultOpenMode<File>::VALUE)
    {
        handle = ::open(fileName, _getOFlag(openMode), S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH);
        if (handle == -1 && errno == EINVAL)          // fall back to cached access
        {
                #ifdef SEQAN_DEBUG_OR_TEST_
            if (!(openMode & OPEN_QUIET))
                std::cerr << "Warning: Direct access openening failed: " << fileName << "." << std::endl;
                #endif
            handle = ::open(fileName, _getOFlag(openMode & ~OPEN_ASYNC), S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH);
        }

        if (handle == -1)
        {
            if (!(openMode & OPEN_QUIET))
                std::cerr << "Open failed on file " << fileName << ". (" << ::strerror(errno) << ")" << std::endl;
            return false;
        }

        if (sizeof(FilePtr) < 8 && !(openMode & OPEN_QUIET))
            // To remove this warning, you have to options:
            // 1. include the following line before including anything in your application
            //    #define _FILE_OFFSET_BITS 64
            // 2. include <seqan/platform.h> or <seqan/sequence.h> before any other include
            std::cerr << "WARNING: FilePtr is not 64bit wide" << std::endl;

        SEQAN_PROADD(SEQAN_PROOPENFILES, 1);
        return true;
    }

    bool openTemp(int openMode = DefaultOpenTempMode<File>::VALUE)
    {
        // Construct the pattern for the temporary file.
        //
        // First, try to get the temporary directory from the environment
        // variables TMPDIR, TMP.
        std::string tmpDir;
        if ((getuid() == geteuid()) && (getgid() == getegid()))
        {
            char * res;
            if ((res = getenv("TMPDIR")) != NULL)
                tmpDir = res;
            else if ((res = getenv("TMP")) != NULL)
                tmpDir = res;
        }
        // If this does not work, try to use the constant
        // SEQAN_DEFAULT_TMPDIR, fall back to "/tmp", if this does not
        // work.
#ifdef SEQAN_DEFAULT_TMPDIR
        if (empty(tmpDir))
            tmpDir = SEQAN_DEFAULT_TMPDIR;
#else  // #ifdef SEQAN_DEFAULT_TMPDIR
        if (empty(tmpDir))
            tmpDir = "/tmp";
#endif  // #ifdef SEQAN_DEFAULT_TMPDIR

        // At this point, we have a temporary directory.  Now, we add the
        // file name template to get the full path template.
        tmpDir += "/SQNXXXXXX";
        // Open temporary file and unlink it immediately afterwards so the
        // memory is released when the program exits.
        int oldMode = umask(077);      // Create with restrictive permissions.
        if ((handle = ::mkstemp((char *)tmpDir.c_str())) == -1)
        {
            umask(oldMode);      // Reset umask mode.
            if (!(openMode & OPEN_QUIET))
                std::cerr << "Couldn't create temporary file " << tmpDir << ". (" << ::strerror(errno) << ")" << std::endl;
            return false;
        }
        if (!(close() && open(toCString(tmpDir), openMode)))
        {
            umask(oldMode);      // Reset umask mode.
            return false;
        }
        umask(oldMode);      // Reset umask mode.
            #ifdef SEQAN_DEBUG
        if (::unlink(toCString(tmpDir)) == -1 && !(openMode & OPEN_QUIET))
            std::cerr << "Couldn't unlink temporary file " << tmpDir << ". (" << ::strerror(errno) << ")" << std::endl;
            #else
        ::unlink(toCString(tmpDir));
            #endif
        return true;
    }

    virtual bool close()
    {
        if (::close(this->handle) == -1) return false;

        handle = -1;
        SEQAN_PROSUB(SEQAN_PROOPENFILES, 1);
        return true;
    }

    inline ssize_t read(void * buffer, SizeType_ count) const
    {
        SEQAN_PROADD(SEQAN_PROIO, (count + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
        SEQAN_PROTIMESTART(tw);
        ssize_t result = ::read(handle, buffer, count);
        SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
        return result;
    }

    inline ssize_t write(void const * buffer, SizeType_ count) const
    {
        SEQAN_PROADD(SEQAN_PROIO, (count + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
        SEQAN_PROTIMESTART(tw);
        ssize_t result = ::write(handle, buffer, count);
        SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
        return result;
    }

    inline FilePtr seek(FilePtr pos, int origin = SEEK_SET) const
    {
        FilePtr result = ::lseek(handle, pos, origin);
//            #ifdef SEQAN_DEBUG
        if (result < 0)
            std::cerr << "lseek returned " << result << ". (" << ::strerror(errno) << ")" << std::endl;
//            #endif
        return result;
    }

    inline FilePtr tell() const
    {
        return seek(0, SEEK_CUR);
    }

    inline bool resize(SizeType new_length) const
    {
        return ftruncate(handle, new_length) == 0;
    }

    static int error()
    {
        return errno;
    }

    operator bool() const {
        return handle != -1;
    }
};

inline bool fileExists(const char * fileName)
{
//IOREV _nodoc_
    struct stat buf;
    return stat(fileName, &buf) != -1;
}

inline bool fileUnlink(const char * fileName)
{
//IOREV _noddoc_
    return unlink(fileName) == 0;
}

template <typename TSpec, typename TSize>
inline void resize(File<Sync<TSpec> > & me, TSize new_length)
{
//IOREV _doc_
    if (!me.resize(new_length))
        SEQAN_FAIL(
            "resize(%d, %d) failed: \"%s\"",
            me.handle, new_length, strerror(errno));
}

#endif

//////////////////////////////////////////////////////////////////////////////
// global functions

template <typename TSpec>
struct Size<File<Sync<TSpec> > >
{
//IOREV
    typedef typename File<Sync<TSpec> >::SizeType Type;
};

template <typename TSpec>
struct Position<File<Sync<TSpec> > >
{
//IOREV
    typedef typename File<Sync<TSpec> >::FilePtr Type;
};

template <typename TSpec>
struct Difference<File<Sync<TSpec> > >
{
//IOREV
    typedef typename File<Sync<TSpec> >::FilePtr Type;
};

template <typename TSpec, typename TValue, typename TSize>
inline bool read(File<Sync<TSpec> > & me, TValue * memPtr, TSize const count)
{
    return (size_t)me.read(memPtr, count * sizeof(TValue)) == (size_t)(count * sizeof(TValue));
}

template <typename TSpec, typename TValue, typename TSize>
inline bool write(File<Sync<TSpec> > & me, TValue * memPtr, TSize const count)
{
    return (size_t)me.write(memPtr, count * sizeof(TValue)) == (size_t)(count * sizeof(TValue));
}

template <typename TSpec, typename TValue, typename TSize>
inline bool write(File<Sync<TSpec> > & me, TValue const * memPtr, TSize const count)
{
    return (size_t)me.write(memPtr, count * sizeof(TValue)) == (size_t)(count * sizeof(TValue));
}

}

#endif