File.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $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:
    class OPENMS_DLLAPI TempDir
    {
    public:
      
      TempDir(bool keep_dir = false);
 
      TempDir(const std::string& base_dir, bool keep_dir = false);
 
      ~TempDir();
 
      TempDir(const TempDir&) = delete;
      TempDir& operator=(const TempDir&) = delete;
      TempDir(TempDir&&) = delete;
      TempDir& operator=(TempDir&&) = delete;
 
      const std::string& getPath() const;
 
    private:
      std::string temp_dir_;
      bool keep_dir_;
    };
 
    static std::string getExecutablePath();
 
    static bool exists(const std::string& file);
 
    static bool empty(const std::string& file);
 
    static bool executable(const std::string& file);
 
    static UInt64 fileSize(const std::string& file);
 
    static bool rename(const std::string& from, const std::string& to, bool overwrite_existing = true, bool verbose = true);
 
    enum class CopyOptions {OVERWRITE,SKIP,CANCEL};
    static bool copyDirRecursively(const std::string& from_dir, const std::string& to_dir, File::CopyOptions option = CopyOptions::OVERWRITE);
 
    static bool copy(const std::string& from, const std::string& to);
 
    static bool remove(const std::string& file);
 
    static bool removeDirRecursively(const std::string& dir_name);
 
    static bool removeDir(const std::string& dir_name);
 
    static bool makeDir(const std::string& dir_name);
 
    static std::string absolutePath(const std::string& file);
 
    static std::string basename(const std::string& file);
 
    static std::string stemName(const std::string& file);
 
    static std::string extension(const std::string& file);
 
    static StringList listDirectories(const std::string& dir);
 
    static std::string path(const std::string& file);
 
    static bool readable(const std::string& file);
 
    static bool writable(const std::string& file);
 
    static bool isDirectory(const std::string& path);
 
    static std::string find(const std::string& filename, StringList directories = StringList());
 
    static bool fileList(const std::string& dir, const std::string& file_pattern, StringList& output, bool full_path = false);
 
    static std::string findDoc(const std::string& filename);
    
    static std::string getUniqueName(bool include_hostname = true);
 
    static std::string getOpenMSDataPath();
 
    static const std::string& getOpenMSDataPathSource();
 
    static std::string getOpenMSHomePath();
 
    static std::string getOpenMSConfigDir();
 
    static std::string getTempDirectory();
 
    static std::string getUserDirectory();
 
    static Param getSystemParameters();
 
    static std::string findDatabase(const std::string& db_name);
 
    static StringList getPathLocations();
 
    static StringList getPathLocations(const std::string& path);
 
    static bool findExecutable(std::string& exe_filename);
 
    static std::string findSiblingTOPPExecutable(const std::string& toolName);
 
    static std::string getTemporaryFile(const std::string& alternative_file = "");
 
 
    enum class MatchingFileListsStatus 
    {
        MATCH = 0,           // Everything matches perfectly
        ORDER_MISMATCH = 1,  // Same set of files but in wrong order
        SET_MISMATCH = 2     // Different sets of files (including size mismatch)
    };
 
    static MatchingFileListsStatus validateMatchingFileNames(const StringList& sl1, 
                                                       const StringList& sl2, 
                                                       bool basename = true, 
                                                       bool ignore_extension = true);
 
private:
 
    static Param getSystemParameterDefaults_();
 
    static bool isOpenMSDataPath_(const std::string& path);
 
    struct OpenMSDataPath_
    {
      std::string path;    
      std::string source;  
    };
 
    static const OpenMSDataPath_& resolveOpenMSDataPath_();
 
#ifdef OPENMS_WINDOWSPLATFORM
    static StringList executableExtensions_();
 
    static StringList executableExtensions_(const std::string& ext);
#endif
 
    class TemporaryFiles_
    {
      public:
        TemporaryFiles_(const TemporaryFiles_&) = delete; // copy is forbidden
        TemporaryFiles_& operator=(const TemporaryFiles_&) = delete;
        TemporaryFiles_();
        std::string newFile();
 
        ~TemporaryFiles_();
      private:
        StringList filenames_;
        std::mutex mtx_;
    };
 
 
    static TemporaryFiles_ temporary_files_;
  };
}