adiosFunctions.cpp

/*
 * adiosFunctions.cpp
 *
 *  Created on: Oct 10, 2016
 *      Author: wfg
 */

/// \cond EXCLUDED_FROM_DOXYGEN
#include <algorithm> //std::count
#include <cmath>     // std::ceil, std::pow, std::log
#include <cstring>   //std::memcpy
#include <fstream>
#include <ios> //std::ios_base::failure
#include <sstream>
#include <stdexcept>
#include <thread> //std::thread

#include <sys/stat.h>  //stat
#include <sys/types.h> //CreateDirectory
#include <unistd.h>    //CreateDirectory
/// \endcond

#include "core/Support.h"
#include "functions/adiosFunctions.h"

#ifdef HAVE_BZIP2
#include "transform/BZIP2.h"
#endif

namespace adios
{

void DumpFileToString(const std::string fileName, std::string &fileContent)
{
  std::ifstream fileStream(fileName);

  if (fileStream.good() == false) // check file
    throw std::ios_base::failure(
        "ERROR: file " + fileName +
        " could not be opened. Check permissions or file existence\n");

  std::ostringstream fileSS;
  fileSS << fileStream.rdbuf();
  fileStream.close();
  fileContent = fileSS.str(); // convert to string and check

  if (fileContent.empty())
    throw std::invalid_argument("ERROR: file " + fileName + " is empty\n");
}

void GetSubString(const std::string initialTag, const std::string finalTag,
                  const std::string content, std::string &subString,
                  std::string::size_type &currentPosition)
{
  auto lf_Wipe = [](std::string &subString,
                    std::string::size_type &currentPosition) {
    subString.clear();
    currentPosition = std::string::npos;
  };

  auto lf_SetPositions =
      [](const char quote, const std::string::size_type quotePosition,
         const std::string &content, std::string::size_type &currentPosition,
         std::string::size_type &closingQuotePosition) {
        currentPosition = quotePosition;
        closingQuotePosition = content.find(quote, currentPosition + 1);
      };

  // BODY OF FUNCTION STARTS HERE
  std::string::size_type start(content.find(initialTag, currentPosition));
  if (start == content.npos)
  {
    lf_Wipe(subString, currentPosition);
    return;
  }
  currentPosition = start;

  std::string::size_type end(content.find(finalTag, currentPosition));
  if (end == content.npos)
  {
    lf_Wipe(subString, currentPosition);
    return;
  }

  // here make sure the finalTag is not a value surrounded by " " or ' ', if so
  // find next
  bool isValue = true;

  while (isValue == true)
  {
    std::string::size_type singleQuotePosition =
        content.find('\'', currentPosition);
    std::string::size_type doubleQuotePosition =
        content.find('\"', currentPosition);

    if ((singleQuotePosition == content.npos &&
         doubleQuotePosition == content.npos) ||
        (singleQuotePosition == content.npos && end < doubleQuotePosition) ||
        (doubleQuotePosition == content.npos && end < singleQuotePosition) ||
        (end < singleQuotePosition && end < doubleQuotePosition))
      break;

    // find the closing corresponding quote
    std::string::size_type closingQuotePosition;

    if (singleQuotePosition == content.npos) // no ' anywhere
      lf_SetPositions('\"', doubleQuotePosition, content, currentPosition,
                      closingQuotePosition);
    else if (doubleQuotePosition == content.npos) // no " anywhere
      lf_SetPositions('\'', singleQuotePosition, content, currentPosition,
                      closingQuotePosition);
    else
    {
      if (singleQuotePosition < doubleQuotePosition)
        lf_SetPositions('\'', singleQuotePosition, content, currentPosition,
                        closingQuotePosition);
      else // find the closing "
        lf_SetPositions('\"', doubleQuotePosition, content, currentPosition,
                        closingQuotePosition);
    }

    if (closingQuotePosition ==
        content.npos) // if can't find closing it's open until the end
    {
      lf_Wipe(subString, currentPosition);
      return;
    }

    currentPosition = closingQuotePosition + 1;

    if (closingQuotePosition < end)
      continue;

    // if this point is reached it means it's a value inside " " or ' ', move to
    // the next end
    end = content.find(finalTag, currentPosition);
  }

  subString = content.substr(start, end - start + finalTag.size());
  currentPosition = end;
}

void GetQuotedValue(const char quote,
                    const std::string::size_type &quotePosition,
                    std::string &currentTag, std::string &value)
{
  currentTag = currentTag.substr(quotePosition + 1);
  auto nextQuotePosition = currentTag.find(quote);

  if (nextQuotePosition == currentTag.npos)
    throw std::invalid_argument("ERROR: Invalid attribute in..." + currentTag +
                                "...check XML file\n");

  value = currentTag.substr(0, nextQuotePosition);
  currentTag = currentTag.substr(nextQuotePosition + 1);
}

void GetPairs(const std::string tag,
              std::vector<std::pair<const std::string, const std::string>>
                  &pairs) noexcept
{
  std::string currentTag(
      tag.substr(tag.find_first_of(" \t\n"))); // initialize current tag

  while (currentTag.find('=') != currentTag.npos) // equalPosition
  {
    currentTag = currentTag.substr(currentTag.find_first_not_of(" \t\n"));
    auto equalPosition = currentTag.find('=');
    const std::string field(currentTag.substr(0, equalPosition)); // get field
    std::string value;

    const char quote = currentTag[equalPosition + 1];
    if (quote == '\'' || quote == '"') // single quotes
    {
      GetQuotedValue(quote, equalPosition + 1, currentTag, value);
    }

    pairs.push_back(
        std::pair<const std::string, const std::string>(field, value));
  }
}

void GetPairsFromTag(
    const std::string &fileContent, const std::string tag,
    std::vector<std::pair<const std::string, const std::string>> &pairs)
{
  if (tag.back() == '/') // last char is / --> "XML empty tag"
  {
    GetPairs(tag, pairs);
  }
  else if (tag[0] == '/') // first char is / ---> closing tag
  {
  }
  else // opening tag
  {
    const std::string tagName(tag.substr(0, tag.find_first_of(" \t\n\r")));
    const std::string closingTagName("</" + tagName +
                                     ">"); // check for closing tagName

    if (fileContent.find(closingTagName) == fileContent.npos)
      throw std::invalid_argument("ERROR: closing tag " + closingTagName +
                                  " missing, check XML file\n");

    GetPairs(tag, pairs);
  }
}

// void SetMembers( const std::string& fileContent, const MPI_Comm mpiComm,
// const bool debugMode,
//                 std::string& hostLanguage, std::vector<
//                 std::shared_ptr<Transform> >& transforms,
//                 std::map< std::string, Group >& groups )
//{
//    //adios-config
//    std::string currentContent;
//    std::string::size_type currentPosition( 0 );
//    GetSubString( "<adios-config ", "</adios-config>", fileContent,
//    currentContent, currentPosition );
//
//    //remove comment sections
//    std::string::size_type startComment ( currentContent.find( "<!--" ) );
//
//    while( startComment != currentContent.npos )
//    {
//        std::string::size_type endComment( currentContent.find( "-->") );
//        currentContent.erase( startComment, endComment-startComment+3 );
//        startComment = currentContent.find( "<!--" );
//    }
//
//    //Tag <adios-config
//    currentPosition = 0;
//
//    std::string tag; //use for < > tags
//    GetSubString( "<adios-config", ">", currentContent, tag, currentPosition
//    );
//    tag = tag.substr( 1, tag.size() - 2 ); //eliminate < >
//
//    std::vector< std::pair<const std::string, const std::string> > pairs; //
//    pairs in tag
//    GetPairsFromTag( currentContent, tag, pairs );
//
//    for( auto& pair : pairs )
//        if( pair.first == "host-language" )
//            hostLanguage = pair.second;
//
//    if( debugMode == true )
//    {
//        if( Support::HostLanguages.count( hostLanguage ) == 0 )
//            throw std::invalid_argument("ERROR: host language " + hostLanguage
//            + " not supported.\n" );
//
//        if( hostLanguage.empty() == true )
//            throw std::invalid_argument("ERROR: host language is empty.\n" );
//    }
//
//    //adios-group
//    currentPosition = 0;
//
//    while( currentPosition != std::string::npos )
//    {
//        std::string xmlGroup;
//        GetSubString("<adios-group ", "</adios-group>", currentContent,
//        xmlGroup, currentPosition ); //Get all group contents
//
//        if( xmlGroup.empty() ) //no more groups to find
//            break;
//
//        //get group name
//        std::string::size_type groupPosition( 0 );
//        GetSubString( "<adios-group ", ">", xmlGroup, tag, groupPosition );
//        if( debugMode == true )
//        {
//            if( tag.size() < 2 )
//                throw std::invalid_argument( "ERROR: wrong tag " + tag + " in
//                adios-group\n" ); //check < or <=
//        }
//
//        tag = tag.substr( 1, tag.size() - 2 ); //eliminate < >
//        GetPairsFromTag( xmlGroup, tag, pairs );
//        std::string groupName;
//
//        for( auto& pair : pairs )
//        {
//            if( pair.first == "name")
//                groupName = pair.second;
//        }
//
//        if( debugMode == true )
//        {
//            if( groupName.empty() )
//                throw std::invalid_argument( "ERROR: group name not found. \n"
//                );
//
//            if( groups.count( groupName ) == 1 ) //group exists
//                throw std::invalid_argument( "ERROR: group " + groupName + "
//                defined twice.\n" );
//        }
//
//        groups.emplace( groupName, Group( groupName, xmlGroup, transforms,
//        debugMode ) );
//
//        currentContent.erase( currentContent.find( xmlGroup ), xmlGroup.size()
//        );
//        currentPosition = 0;
//    }
//
//    //transport
//    //lambda function to check priority and iteration casting to unsigned int
//    auto lf_UIntCheck = []( const std::string method, const std::string
//    fieldStr, const std::string fieldName,
//                            const bool debugMode, int& field )
//    {
//        field = 0;
//        if( fieldStr.empty() == false )
//        {
//            field = std::stoi( fieldStr ); //throws invalid_argument
//
//            if( debugMode == true )
//            {
//                if( field < 0 )
//                    throw std::invalid_argument("ERROR: " + fieldName + " in
//                    transport " + method + " can't be negative\n" );
//            }
//        }
//    };
//
//    //this section will have to change, doing nothing for now
//    currentPosition = 0;
//    while( currentPosition != std::string::npos )
//    {
//        GetSubString( "<transport ", ">", currentContent, tag, currentPosition
//        );
//        if( tag.empty() ) break;
//        tag = tag.substr( 1, tag.size() - 2 ); //eliminate < >
//        pairs.clear();
//        GetPairsFromTag( currentContent, tag, pairs );
//
//        std::string groupName, method, priorityStr, iterationStr;
//        for( auto& pair : pairs )
//        {
//            if( pair.first == "group" )  groupName = pair.second;
//            else if( pair.first == "method" ) method = pair.second;
//            else if( pair.first == "priority" ) priorityStr = pair.second;
//            else if( pair.first == "iteration" ) iterationStr = pair.second;
//        }
//
//        auto itGroup = groups.find( groupName );
//        if( debugMode == true )
//        {
//            if( itGroup == groups.end() ) //not found
//                throw std::invalid_argument( "ERROR: in transport " + method +
//                " group " + groupName + " not found.\n" );
//        }
//
//        int priority, iteration;
//        lf_UIntCheck( method, priorityStr, "priority", debugMode, priority );
//        lf_UIntCheck( method, iterationStr, "iteration", debugMode, iteration
//        );
//        //here do something with the capsule
//    }
//}

// void InitXML( const std::string xmlConfigFile, const MPI_Comm mpiComm, const
// bool debugMode,
//              std::string& hostLanguage, std::vector<
//              std::shared_ptr<Transform> >& transforms,
//              std::map< std::string, Group >& groups )
//{
//    int xmlFileContentSize;
//    std::string xmlFileContent;
//
//    int rank;
//    MPI_Comm_rank( mpiComm, &rank );
//
//    if( rank == 0 ) //serial part
//    {
//        DumpFileToString( xmlConfigFile, xmlFileContent ); //in
//        ADIOSFunctions.h dumps all XML Config File to xmlFileContent
//        xmlFileContentSize = xmlFileContent.size( ) + 1; // add one for the
//        null character
//
//        MPI_Bcast( &xmlFileContentSize, 1, MPI_INT, 0, mpiComm ); //broadcast
//        size for allocation
//        MPI_Bcast( (char*)xmlFileContent.c_str(), xmlFileContentSize,
//        MPI_CHAR, 0, mpiComm ); //broadcast contents
//    }
//    else
//    {
//        MPI_Bcast( &xmlFileContentSize, 1, MPI_INT, 0, mpiComm  ); //receive
//        size
//
//        char* xmlFileContentMPI = new char[ xmlFileContentSize ]; //allocate
//        xml C-char
//        MPI_Bcast( xmlFileContentMPI, xmlFileContentSize, MPI_CHAR, 0, mpiComm
//        ); //receive xml C-char
//        xmlFileContent.assign( xmlFileContentMPI ); //copy to a string
//
//        delete []( xmlFileContentMPI ); //delete char* needed for MPI, might
//        add size is moving to C++14 for optimization, avoid memory leak
//    }
//
//    SetMembers( xmlFileContent,  mpiComm, debugMode, hostLanguage, transforms,
//    groups );
//}

std::size_t GetTotalSize(const std::vector<std::size_t> &dimensions)
{
  std::size_t product = 1;

  for (const auto dimension : dimensions)
    product *= dimension;

  return product;
}

void CreateDirectory(const std::string fullPath) noexcept
{
  auto lf_Mkdir = [](const std::string directory, struct stat &st) {
    if (stat(directory.c_str(), &st) == -1)
      mkdir(directory.c_str(), 0777);
  };

  auto directoryPosition = fullPath.find("/");

  if (fullPath[0] == '/' || fullPath[0] == '.') // find the second '/'
    directoryPosition = fullPath.find("/", directoryPosition + 1);

  struct stat st = {0};
  if (directoryPosition == fullPath.npos) // no subdirectories
  {
    lf_Mkdir(fullPath.c_str(), st);
    return;
  }

  std::string directory(fullPath.substr(0, directoryPosition));
  lf_Mkdir(directory.c_str(), st);

  while (directoryPosition != fullPath.npos)
  {
    directoryPosition = fullPath.find("/", directoryPosition + 1);
    directory = fullPath.substr(0, directoryPosition);
    lf_Mkdir(directory.c_str(), st);
  }
}

void SetTransformsHelper(const std::vector<std::string> &transformNames,
                         std::vector<std::shared_ptr<Transform>> &transforms,
                         const bool debugMode,
                         std::vector<short> &transformIndices,
                         std::vector<short> &parameters)
{
  // function to get a parameter from "method:parameter"
  auto lf_GetParameter = [](const std::string transformName,
                            std::string &transformMethod,
                            const bool debugMode) -> short {
    short parameter = -1;
    auto colonPosition = transformName.find(":");

    if (colonPosition != transformName.npos)
    {
      if (debugMode == true)
      {
        if (colonPosition == transformName.size() - 1)
          throw std::invalid_argument("ERROR: wrong format for transform " +
                                      transformName +
                                      ", in call to SetTransform\n");
      }

      transformMethod = transformName.substr(0, colonPosition);
      parameter =
          std::stoi(transformName.substr(colonPosition + 1)); // need to test
    }
    return parameter;
  };

  // Get transform index from transforms, if not found return -1
  auto lf_GetTransformIndex =
      [](const std::string transformMethod,
         const std::vector<std::shared_ptr<Transform>> &transforms) -> short {
    short transformIndex = -1;
    for (unsigned int i = 0; i < transforms.size(); ++i)
    {
      if (transforms[i]->m_Method == transformMethod)
      {
        transformIndex = i;
        break;
      }
    }
    return transformIndex;
  };

  // BODY of FUNCTION STARTS HERE
  for (const std::string transformName : transformNames)
  {
    std::string transformMethod(transformName);
    short parameter =
        lf_GetParameter(transformName, transformMethod,
                        debugMode); // from transform = "method:parameter"
    short transformIndex = lf_GetTransformIndex(transformMethod, transforms);

    if (transformIndex == -1) // not found, then create a new transform
    {
      if (transformMethod == "bzip2")
      {
#ifdef HAVE_BZIP2
        transforms.push_back(std::make_shared<CBZIP2>());
#endif
      }

      transformIndex = static_cast<short>(transforms.size() - 1);
    }
    transformIndices.push_back(transformIndex);
    parameters.push_back(parameter);
  }
}

std::map<std::string, std::string>
BuildParametersMap(const std::vector<std::string> &parameters,
                   const bool debugMode)
{
  auto lf_GetFieldValue = [](const std::string parameter, std::string &field,
                             std::string &value, const bool debugMode) {
    auto equalPosition = parameter.find("=");

    if (debugMode == true)
    {
      if (equalPosition == parameter.npos)
        throw std::invalid_argument("ERROR: wrong format for parameter " +
                                    parameter +
                                    ", format must be field=value \n");

      if (equalPosition == parameter.size() - 1)
        throw std::invalid_argument("ERROR: empty value in parameter " +
                                    parameter +
                                    ", format must be field=value \n");
    }

    field = parameter.substr(0, equalPosition);
    value = parameter.substr(equalPosition + 1); // need to test
  };

  // BODY OF FUNCTION STARTS HERE
  std::map<std::string, std::string> parametersOutput;

  for (const auto parameter : parameters)
  {
    std::string field, value;
    lf_GetFieldValue(parameter, field, value, debugMode);

    if (debugMode == true)
    {
      if (parametersOutput.count(field) == 1)
        throw std::invalid_argument("ERROR: parameter " + field +
                                    " already exists, must be unique\n");
    }

    parametersOutput[field] = value;
  }

  return parametersOutput;
}

std::vector<int> CSVToVectorInt(const std::string csv)
{
  std::vector<int> numbers;
  if (csv.empty())
    return numbers;

  if (csv.find(",") == csv.npos) // check if no commas, one int
  {
    numbers.push_back(std::stoi(csv)); // might need to be checked
  }
  else
  {
    int count = std::count(csv.begin(), csv.end(), ',');
    numbers.reserve(count);

    std::istringstream csvSS(csv);
    std::string value;
    while (std::getline(csvSS, value, ',')) // need to test
    {
      numbers.push_back(std::stoi(csv));
    }
  }

  return numbers;
}

bool CheckBufferAllocation(const std::size_t newSize, const float growthFactor,
                           const std::size_t maxBufferSize,
                           std::vector<char> &buffer)
{
  // Check if data in buffer needs to be reallocated
  const std::size_t requiredDataSize =
      buffer.size() + newSize + 100; // adding some bytes for tolerance
  // might need to write payload in batches
  bool doTransportsFlush = (requiredDataSize > maxBufferSize) ? true : false;

  if (GrowBuffer(requiredDataSize, growthFactor, buffer) == -1)
    doTransportsFlush = true;

  return doTransportsFlush;
}

int GrowBuffer(const std::size_t incomingDataSize, const float growthFactor,
               std::vector<char> &buffer)
{
  const std::size_t currentCapacity = buffer.capacity();
  const std::size_t availableSpace = currentCapacity - buffer.size();
  const double gf = static_cast<double>(growthFactor);

  if (incomingDataSize > availableSpace)
  {
    const std::size_t neededCapacity = incomingDataSize + buffer.size();
    const double numerator = std::log(static_cast<double>(neededCapacity) /
                                      static_cast<double>(currentCapacity));
    const double denominator = std::log(gf);

    double n = std::ceil(numerator / denominator);
    const std::size_t newSize =
        static_cast<std::size_t>(std::ceil(std::pow(gf, n) * currentCapacity));

    try
    {
      buffer.reserve(newSize);
    }
    catch (std::bad_alloc &e)
    {
      return -1;
    }

    return 1;
  }
  return 0;
}

bool IsLittleEndian() noexcept
{
  std::uint16_t hexa = 0x1234;
  return *reinterpret_cast<std::uint8_t *>(&hexa) != 0x12;
}

} // end namespace