TOPPBase.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// 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: Timo Sachsenberg $
// $Authors:  Marc Sturm, Clemens Groepl $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/GlobalExceptionHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/CONCEPT/VersionInfo.h>

#include <OpenMS/DATASTRUCTURES/Param.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/StringListUtils.h>

#include <OpenMS/METADATA/DataProcessing.h>

#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/StandardTypes.h>

#include <OpenMS/APPLICATIONS/ParameterInformation.h>
#include <OpenMS/APPLICATIONS/ToolHandler.h>

#include <fstream>

#include <QStringList>


namespace OpenMS
{

  class ConsensusMap;
  struct Citation
  {
    std::string authors;    
    std::string title;      
    std::string when_where; 
    std::string doi;        

    std::string toString() const
    {
      return authors + ". " + title + ". " + when_where + ". doi:" + doi + ".";
    }
  };

  namespace Exception
  {
    class OPENMS_DLLAPI UnregisteredParameter :
      public Exception::BaseException
    {
public:
      UnregisteredParameter(const char* file, int line, const char* function, const String& parameter) :
        BaseException(file, line, function, "UnregisteredParameter", parameter)
      {
        GlobalExceptionHandler::getInstance().setMessage(what_);
      }

    };
    class OPENMS_DLLAPI WrongParameterType :
      public Exception::BaseException
    {
public:
      WrongParameterType(const char* file, int line, const char* function, const String& parameter) :
        BaseException(file, line, function, "WrongParameterType", parameter)
      {
        GlobalExceptionHandler::getInstance().setMessage(what_);
      }

    };
    class OPENMS_DLLAPI RequiredParameterNotGiven :
      public Exception::BaseException
    {
public:
      RequiredParameterNotGiven(const char* file, int line, const char* function, const String& parameter) :
        BaseException(file, line, function, "RequiredParameterNotGiven", parameter)
      {
        GlobalExceptionHandler::getInstance().setMessage(what_);
      }

    };
  }

  class OPENMS_DLLAPI TOPPBase
  {
public:

    enum ExitCodes
    {
      EXECUTION_OK,
      INPUT_FILE_NOT_FOUND,
      INPUT_FILE_NOT_READABLE,
      INPUT_FILE_CORRUPT,
      INPUT_FILE_EMPTY,
      CANNOT_WRITE_OUTPUT_FILE,
      ILLEGAL_PARAMETERS,
      MISSING_PARAMETERS,
      UNKNOWN_ERROR,
      EXTERNAL_PROGRAM_ERROR,
      PARSE_ERROR,
      INCOMPATIBLE_INPUT_DATA,
      INTERNAL_ERROR,
      UNEXPECTED_RESULT
    };

    TOPPBase(const String& name, const String& description, bool official = true, const std::vector<Citation>& citations = {});

    virtual ~TOPPBase();

    ExitCodes main(int argc, const char** argv);

    static void setMaxNumberOfThreads(int num_threads);

private:
    String const tool_name_;

    String const tool_description_;

    Int const instance_number_;

    String const ini_location_;

    String working_dir_;

    Int working_dir_keep_debug_lvl_;

    TOPPBase();

    TOPPBase(const TOPPBase&);

    Param param_;

    Param param_inifile_;

    Param param_cmdline_;

    Param param_instance_;

    Param param_common_tool_;

    Param param_common_;

    mutable std::ofstream log_;

    void enableLogging_() const;

    std::vector<ParameterInformation> parameters_;

    virtual Param getSubsectionDefaults_(const String& section) const;

    Param getSubsectionDefaults_() const;

    std::map<String, String> subsections_;

    std::map<String, String> subsections_TOPP_;


    Param parseCommandLine_(const int argc, const char** argv, const String& misc = "misc", const String& unknown = "unknown");

    String getParamAsString_(const String& key, const String& default_value = "") const;

    Int getParamAsInt_(const String& key, Int default_value = 0) const;

    double getParamAsDouble_(const String& key, double default_value = 0) const;

    StringList getParamAsStringList_(const String& key, const StringList& default_value) const;

    IntList getParamAsIntList_(const String& key, const IntList& default_value) const;

    DoubleList getParamAsDoubleList_(const String& key, const DoubleList& default_value) const;

    bool getParamAsBool_(const String& key) const;

    const DataValue& getParam_(const String& key) const;

    String getSubsection_(const String& name) const;

    Param getDefaultParameters_() const;

    Param getToolUserDefaults_(const String& tool_name) const;

protected:
    String version_;

    String verboseVersion_;

    bool official_;

    std::vector<Citation> citations_;
    
    const String& getIniLocation_() const
    {
      return ini_location_;
    }

    const String& toolName_() const;

    virtual void registerOptionsAndFlags_() = 0;

    String getParamArgument_(const Param::ParamEntry& entry) const;

    std::vector<ParameterInformation> paramToParameterInformation_(const Param& param) const;

    ParameterInformation paramEntryToParameterInformation_(const Param::ParamEntry& entry, const String& argument = "", const String& full_name = "") const;

    void registerParamSubsectionsAsTOPPSubsections_(const Param& param);

    void registerFullParam_(const Param& param);

    void registerStringOption_(const String& name, const String& argument, const String& default_value, const String& description, bool required = true, bool advanced = false);

    void setValidStrings_(const String& name, const std::vector<String>& strings);

    void setValidStrings_(const String& name, const std::string vstrings[], int count);

    void registerInputFile_(const String& name, const String& argument, const String& default_value, const String& description, bool required = true, bool advanced = false, const StringList& tags = StringList());

    void registerOutputFile_(const String& name, const String& argument, const String& default_value, const String& description, bool required = true, bool advanced = false);

    void setValidFormats_(const String& name, const std::vector<String>& formats, const bool force_OpenMS_format = true);


    void registerDoubleOption_(const String& name, const String& argument, double default_value, const String& description, bool required = true, bool advanced = false);

    void setMinInt_(const String& name, Int min);
    void setMaxInt_(const String& name, Int max);
    void setMinFloat_(const String& name, double min);
    void setMaxFloat_(const String& name, double max);

    void registerIntOption_(const String& name, const String& argument,
                            Int default_value, const String& description,
                            bool required = true, bool advanced = false);

    void registerIntList_(const String& name, const String& argument, IntList default_value, const String& description, bool required = true, bool advanced = false);

    void registerDoubleList_(const String& name, const String& argument, DoubleList default_value, const String& description, bool required = true, bool advanced = false);

    void registerStringList_(const String& name, const String& argument, StringList default_value, const String& description, bool required = true, bool advanced = false);

    void registerInputFileList_(const String& name, const String& argument, StringList default_value, const String& description, bool required = true, bool advanced = false, const StringList& tags = StringList());

    void registerOutputFileList_(const String& name, const String& argument, StringList default_value, const String& description, bool required = true, bool advanced = false);

    void registerFlag_(const String& name, const String& description, bool advanced = false);

    void registerSubsection_(const String& name, const String& description);

    void registerTOPPSubsection_(const String& name, const String& description);


    void addEmptyLine_();


    String getStringOption_(const String& name) const;

    double getDoubleOption_(const String& name) const;

    Int getIntOption_(const String& name) const;

    StringList getStringList_(const String& name) const;

    IntList getIntList_(const String& name) const;

    DoubleList getDoubleList_(const String& name) const;

    bool getFlag_(const String& name) const;

    const ParameterInformation& findEntry_(const String& name) const;

    Param const& getParam_() const;

    void checkParam_(const Param& param, const String& filename, const String& location) const;


    void checkIfIniParametersAreApplicable_(const Param& ini_params);

    void printUsage_();

    virtual ExitCodes main_(int argc, const char** argv) = 0;


    void writeLog_(const String& text) const;

    void writeDebug_(const String& text, UInt min_level) const;

    void writeDebug_(const String& text, const Param& param, UInt min_level) const;


    String makeTempDirectory_() const;

    String makeAutoRemoveTempDirectory_(Int keep_debug = 2);

    void removeTempDirectory_(const String& dirname, Int keep_debug = 2) const;


    ExitCodes runExternalProcess_(const QString& executable, const QStringList& arguments, const QString& workdir = "") const;

    void inputFileReadable_(const String& filename, const String& param_name) const;

    void outputFileWritable_(const String& filename, const String& param_name) const;

    bool parseRange_(const String& text, double& low, double& high) const;

    bool parseRange_(const String& text, Int& low, Int& high) const;

    ProgressLogger::LogType log_type_;



    void addDataProcessing_(ConsensusMap& map, const DataProcessing& dp) const;

    void addDataProcessing_(FeatureMap& map, const DataProcessing& dp) const;

    void addDataProcessing_(PeakMap& map, const DataProcessing& dp) const
    {
      boost::shared_ptr< DataProcessing > dp_(new DataProcessing(dp));
      for (Size i = 0; i < map.size(); ++i)
      {
        map[i].getDataProcessing().push_back(dp_);
      }
      for (Size i = 0; i < map.getNrChromatograms(); ++i)
      {
        map.getChromatogram(i).getDataProcessing().push_back(dp_);
      }
    }

    DataProcessing getProcessingInfo_(DataProcessing::ProcessingAction action) const;

    DataProcessing getProcessingInfo_(const std::set<DataProcessing::ProcessingAction>& actions) const;


    bool writeCTD_();

    ExitCodes writeWSDL_(const String& filename);

    bool test_mode_;

    static String topp_ini_file_;

    static const Citation cite_openms_;

    Int debug_level_;
private:

    void addText_(const String& text);

    ParameterInformation& getParameterByName_(const String& name);

  };

} // namespace OpenMS