File.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// This software is released under a three-clause BSD license:
//  * 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 any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// 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 ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS 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.
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Andreas Bertsch, Chris Bielow, Marc Sturm $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/StringListUtils.h>
#include <OpenMS/config.h>
#include <cstdlib>
#include <mutex>


namespace OpenMS
{
  class Param;
  class TOPPBase;

  class OPENMS_DLLAPI File
  {
public:

    friend class TOPPBase;

    class OPENMS_DLLAPI TempDir
    {
    public:
      
      TempDir(bool keep_dir = false);

      ~TempDir();

      TempDir(const TempDir&) = delete;
      TempDir& operator=(const TempDir&) = delete;
      TempDir(TempDir&&) = delete;
      TempDir& operator=(TempDir&&) = delete;

      const String& getPath() const;

    private:
      String temp_dir_;
      bool keep_dir_;
    };

    static String getExecutablePath();

    static bool exists(const String& file);

    static bool empty(const String& file);

    static bool executable(const String& file);

    static bool rename(const String& from, const String& to, bool overwrite_existing = true, bool verbose = true);

    enum class CopyOptions {OVERWRITE,SKIP,CANCEL};
    static bool copyDirRecursively(const QString &from_dir, const QString &to_dir, File::CopyOptions option = CopyOptions::OVERWRITE);

    static bool remove(const String& file);

    static bool removeDirRecursively(const String& dir_name);

    static bool removeDir(const QString& dir_name);

    static String absolutePath(const String& file);

    static String basename(const String& file);

    static String path(const String& file);

    static bool readable(const String& file);

    static bool writable(const String& file);

    static bool isDirectory(const String& path);

    static String find(const String& filename, StringList directories = StringList());

    static bool fileList(const String& dir, const String& file_pattern, StringList& output, bool full_path = false);

    static String findDoc(const String& filename);
    
    static String getUniqueName(bool include_hostname = true);

    static String getOpenMSDataPath();

    static String getOpenMSHomePath();

    static String getTempDirectory();

    static String getUserDirectory();

    static Param getSystemParameters();

    static String findDatabase(const String& db_name);

    static StringList getPathLocations(const String& path = std::getenv("PATH"));

    static bool findExecutable(OpenMS::String& exe_filename);

    static String findSiblingTOPPExecutable(const String& toolName);

    static String getTemporaryFile(const String& alternative_file = "");

    static bool validateMatchingFileNames(const StringList& sl1, const StringList& sl2, bool basename = true, bool ignore_extension = true, bool strict = false);

    static void download(const std::string& url, const std::string& download_folder);

private:

    static Param getSystemParameterDefaults_();

    static bool isOpenMSDataPath_(const String& path);

#ifdef OPENMS_WINDOWSPLATFORM

    static StringList executableExtensions_(const String& ext = std::getenv("PATHEXT"));
#endif

    class TemporaryFiles_
    {
      public:
        TemporaryFiles_(const TemporaryFiles_&) = delete; // copy is forbidden
        TemporaryFiles_& operator=(const TemporaryFiles_&) = delete;
        TemporaryFiles_();
        String newFile();

        ~TemporaryFiles_();
      private:
        StringList filenames_;
        std::mutex mtx_;
    };


    static TemporaryFiles_ temporary_files_;
  };
}