/*=========================================================================

  Program:   Visualization Toolkit
  Module:    vtkBiomTableReader.cxx

  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
  All rights reserved.
  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notice for more information.

=========================================================================*/
#include "vtkBiomTableReader.h"

#include "vtkByteSwap.h"
#include "vtkCellArray.h"
#include "vtkFieldData.h"
#include "vtkFloatArray.h"
#include "vtkInformation.h"
#include "vtkInformationVector.h"
#include "vtkIntArray.h"
#include "vtkNew.h"
#include "vtkObjectFactory.h"
#include "vtkStreamingDemandDrivenPipeline.h"
#include "vtkStringArray.h"
#include "vtkTable.h"
#include "vtkVariantArray.h"

#include <algorithm>
#include <sstream>

vtkStandardNewMacro(vtkBiomTableReader);

#ifdef read
#undef read
#endif

//----------------------------------------------------------------------------
vtkBiomTableReader::vtkBiomTableReader()
{
  vtkTable *output = vtkTable::New();
  this->SetOutput(output);
  // Releasing data for pipeline parallism.
  // Filters will know it is empty.
  output->ReleaseData();
  output->Delete();
}

//----------------------------------------------------------------------------
vtkBiomTableReader::~vtkBiomTableReader()
{
}

//----------------------------------------------------------------------------
vtkTable* vtkBiomTableReader::GetOutput()
{
  return this->GetOutput(0);
}

//----------------------------------------------------------------------------
vtkTable* vtkBiomTableReader::GetOutput(int idx)
{
  return vtkTable::SafeDownCast(this->GetOutputDataObject(idx));
}

//----------------------------------------------------------------------------
void vtkBiomTableReader::SetOutput(vtkTable *output)
{
  this->GetExecutive()->SetOutputData(0, output);
}

//----------------------------------------------------------------------------
// I do not think this should be here, but I do not want to remove it now.
int vtkBiomTableReader::RequestUpdateExtent(
  vtkInformation *,
  vtkInformationVector **,
  vtkInformationVector *outputVector)
{
  vtkInformation *outInfo = outputVector->GetInformationObject(0);
  int piece, numPieces;

  piece = outInfo->Get(vtkStreamingDemandDrivenPipeline::UPDATE_PIECE_NUMBER());
  numPieces = outInfo->Get(vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_PIECES());

  // make sure piece is valid
  if (piece < 0 || piece >= numPieces)
  {
    return 1;
  }

  return 1;
}

//----------------------------------------------------------------------------
int vtkBiomTableReader::RequestData(
  vtkInformation *,
  vtkInformationVector **,
  vtkInformationVector *outputVector)
{
  vtkInformation *outInfo = outputVector->GetInformationObject(0);

  // Return all data in the first piece ...
  if(outInfo->Get(vtkStreamingDemandDrivenPipeline::UPDATE_PIECE_NUMBER()) > 0)
  {
    return 1;
  }

  vtkDebugMacro(<<"Reading biom table...");

  if(this->GetFileName() == NULL || strcmp(this->GetFileName(), "") == 0)
  {
    vtkErrorMacro(<<"Input filename not set");
    return 1;
  }

  std::ifstream ifs( this->GetFileName(), std::ifstream::in );
  if(!ifs.good())
  {
    vtkErrorMacro(<<"Unable to open " << this->GetFileName() << " for reading");
    return 1;
  }

  ifs.seekg(0, std::ios::end);
  this->FileContents.reserve(ifs.tellg());
  ifs.seekg(0, std::ios::beg);

  this->FileContents.assign((std::istreambuf_iterator<char>(ifs)),
                             std::istreambuf_iterator<char>());

  this->ParseShape();
  this->ParseDataType();

  vtkNew<vtkStringArray> rowNames;
  rowNames->SetName("name");
  this->GetOutput()->AddColumn(rowNames.GetPointer());
  for ( int i = 1; i < this->NumberOfColumns + 1; ++i )
  {
    switch(this->DataType)
    {
      case VTK_INT:
      {
        vtkNew<vtkIntArray> intCol;
        this->GetOutput()->AddColumn(intCol.GetPointer());
        break;
      }
      case VTK_FLOAT:
      {
        vtkNew<vtkFloatArray> floatCol;
        this->GetOutput()->AddColumn(floatCol.GetPointer());
        break;
      }
      case VTK_STRING:
      {
        vtkNew<vtkStringArray> stringCol;
        this->GetOutput()->AddColumn(stringCol.GetPointer());
        break;
      }
      default:
        break;
    }
  }
  this->GetOutput()->SetNumberOfRows(this->NumberOfRows);

  //row names are stored in another column.  add it before the rest of the data
  this->ParseRows();

  this->ParseSparseness();
  if(this->Sparse)
  {
    this->InitializeData();
    this->ParseSparseData();
  }
  else
  {
    this->ParseDenseData();
  }
  this->ParseId();
  this->ParseColumns();

  return 1;
}

void vtkBiomTableReader::ParseShape()
{
  this->NumberOfRows = this->NumberOfColumns = -1;

  // find "shape":
  size_t pos1 = this->FileContents.find("\"shape\":");
  if (pos1 == std::string::npos )
  {
    vtkErrorMacro(<<"shape not found in input file");
    return;
  }

  // find [
  size_t pos2 = this->FileContents.find("[", pos1+1);
  if (pos2 == std::string::npos )
  {
    vtkErrorMacro(<<"shape field not formatted properly");
    return;
  }

  // find ,
  size_t pos3 = this->FileContents.find(",", pos2+1);
  if (pos3 == std::string::npos )
  {
    vtkErrorMacro(<<"shape field not formatted properly");
    return;
  }

  // find ]
  size_t pos4 = this->FileContents.find("]", pos3+1);
  if (pos4 == std::string::npos )
  {
    vtkErrorMacro(<<"shape field not formatted properly");
    return;
  }

  // number of rows is between "[" and ","
  this->NumberOfRows =
    atoi(this->FileContents.substr(pos2+1,pos3-pos2).c_str());

  // number of columns is between "," and "]"
  this->NumberOfColumns =
    atoi(this->FileContents.substr(pos3+1,pos4-pos3-1).c_str());
}

//----------------------------------------------------------------------------
void vtkBiomTableReader::ParseDataType()
{
  // find "matrix_element_type":
  size_t pos1 = this->FileContents.find("\"matrix_element_type\":");
  if (pos1 == std::string::npos )
  {
    vtkErrorMacro(<<"matrix_element_type not found in input file");
    return;
  }

  // find :
  size_t pos2 = this->FileContents.find(":", pos1+1);
  if (pos2 == std::string::npos )
  {
    vtkErrorMacro(<<"matrix_element_type field not formatted properly");
    return;
  }

  // find first double quote
  size_t pos3 = this->FileContents.find("\"", pos2+1);
  if (pos3 == std::string::npos )
  {
    vtkErrorMacro(<<"matrix_element_type field not formatted properly");
    return;
  }

  // find second double quote
  size_t pos4 = this->FileContents.find("\"", pos3+1);
  if (pos4 == std::string::npos )
  {
    vtkErrorMacro(<<"matrix_element_type field not formatted properly");
    return;
  }

  // element type lies between these quotes
  std::string data_type = this->FileContents.substr(pos3+1,pos4-pos3-1);
  if (strcmp(data_type.c_str(), "int") == 0)
  {
    this->DataType = VTK_INT;
  }
  else if (strcmp(data_type.c_str(), "float") == 0)
  {
    this->DataType = VTK_FLOAT;
  }
  else if (strcmp(data_type.c_str(), "unicode") == 0)
  {
    this->DataType = VTK_STRING;
  }
  else
  {
    vtkErrorMacro(<<"unrecognized value found for matrix_element_type");
    this->DataType = VTK_VOID;
  }
}

//----------------------------------------------------------------------------
void vtkBiomTableReader::InitializeData()
{
  switch(this->DataType)
  {
    case VTK_INT:
    {
      int i = 0;
      vtkVariant v(i);
      this->FillData(v);
      break;
    }
    case VTK_FLOAT:
    {
      float f = 0.0;
      vtkVariant v(f);
      this->FillData(v);
      break;
    }
    case VTK_STRING:
    default:
    {
      std::string s = "";
      vtkVariant v(s);
      this->FillData(v);
      break;
    }
  }
}

//----------------------------------------------------------------------------
void vtkBiomTableReader::FillData(vtkVariant v)
{
  for(int row = 0; row < this->NumberOfRows; ++row)
  {
    for(int col = 1; col < this->NumberOfColumns + 1; ++col)
    {
      this->GetOutput()->SetValue(row, col, v);
    }
  }
}

//----------------------------------------------------------------------------
void vtkBiomTableReader::ParseSparseness()
{
  // find "matrix_type":
  size_t pos1 = this->FileContents.find("\"matrix_type\":");
  if (pos1 == std::string::npos )
  {
    vtkErrorMacro(<<"matrix_type not found in input file");
    return;
  }

  // find first double quote
  size_t pos2 = this->FileContents.find("\"", pos1+13);
  if (pos2 == std::string::npos )
  {
    vtkErrorMacro(<<"matrix_type field not formatted properly");
    return;
  }

  // find second double quote
  size_t pos3 = this->FileContents.find("\"", pos2+1);
  if (pos2 == std::string::npos )
  {
    vtkErrorMacro(<<"matrix_type field not formatted properly");
    return;
  }

  // We should find either 'sparse' or 'dense' between these quotes
  std::string matrix_type = this->FileContents.substr(pos2+1,pos3-pos2-1);
  if (matrix_type.compare("sparse") == 0)
  {
    this->Sparse = true;
  }
  else if (matrix_type.compare("dense") == 0)
  {
    this->Sparse = false;
  }
  else
  {
    vtkErrorMacro(<<"matrix_type field not formatted properly");
    return;
  }
}

//----------------------------------------------------------------------------
void vtkBiomTableReader::ParseSparseData()
{
  // find "data":
  size_t pos1 = this->FileContents.find("\"data\":");
  if (pos1 == std::string::npos)
  {
    vtkErrorMacro(<<"data not found in input file");
    return;
  }

  // find first [ (beginning of matrix)
  size_t pos_start = this->FileContents.find("[", pos1) + 1;
  if (pos_start == std::string::npos)
  {
    vtkErrorMacro(<<"data field not formatted properly");
    return;
  }

  while(1)
  {
    // find [ (beginning of triplet)
    pos1 = this->FileContents.find("[", pos_start);
    if (pos1 == std::string::npos)
    {
      vtkErrorMacro(<<"data field not formatted properly");
      return;
    }
    // find first comma
    size_t pos2 = this->FileContents.find(",", pos1 + 1);
    if (pos2 == std::string::npos)
    {
      vtkErrorMacro(<<"data field not formatted properly");
      return;
    }
    // find second comma
    size_t pos3 = this->FileContents.find(",", pos2 + 1);
    if (pos3 == std::string::npos)
    {
      vtkErrorMacro(<<"data field not formatted properly");
      return;
    }
    // find ] (end of triplet)
    size_t pos4 = this->FileContents.find("]", pos3 + 1);
    if (pos4 == std::string::npos)
    {
      vtkErrorMacro(<<"data field not formatted properly");
      return;
    }
    // row is between "[" and ","
    int row =
      atoi(this->FileContents.substr(pos1+1,pos2-pos1).c_str());

    // column is between first and second comma
    int column = 1 +
      atoi(this->FileContents.substr(pos2+1,pos3-pos2-1).c_str());

    std::string value = this->FileContents.substr(pos3+1,pos4-pos3-1);
    this->InsertValue(row, column, value);

    pos_start = pos4 + 1;
    if (strcmp(this->FileContents.substr(pos_start, 1).c_str(), ",") != 0)
    {
      return;
    }
  }
}

//----------------------------------------------------------------------------
void vtkBiomTableReader::ParseDenseData()
{
  // find "data":
  size_t pos1 = this->FileContents.find("\"data\":");
  if (pos1 == std::string::npos)
  {
    vtkErrorMacro(<<"data not found in input file");
    return;
  }

  // find first [ (beginning of matrix)
  size_t pos_start = this->FileContents.find("[", pos1) + 1;
  if (pos_start == std::string::npos)
  {
    vtkErrorMacro(<<"data field not formatted properly");
    return;
  }

  for (int currentRow = 0; currentRow < this->NumberOfRows; ++currentRow)
  {
    // find [ (beginning of row)
    size_t pos_row_1 = this->FileContents.find("[", pos_start);
    if (pos_row_1 == std::string::npos)
    {
      vtkErrorMacro(<<"data field not formatted properly");
      return;
    }
    int currentCol;
    for (currentCol = 1; currentCol < this->NumberOfColumns; ++currentCol)
    {
      // find next comma
      size_t pos_row_2 = this->FileContents.find(",", pos_row_1 + 1);
      if (pos_row_2 == std::string::npos)
      {
        vtkErrorMacro(<<"data field not formatted properly");
        return;
      }

      // parse data value and insert it into the table
      std::string value =
        this->FileContents.substr(pos_row_1 + 1, pos_row_2 - pos_row_1 - 1);
      this->InsertValue(currentRow, currentCol, value);

      pos_row_1 = pos_row_2;
    }

    //the last value of the row ends with a ] instead of a comma
    size_t pos_row_2 = this->FileContents.find("]", pos_row_1 + 1);
    if (pos_row_2 == std::string::npos)
    {
      vtkErrorMacro(<<"data field not formatted properly");
      return;
    }
    std::string value =
      this->FileContents.substr(pos_row_1 + 1, pos_row_2 - pos_row_1 - 1);
    this->InsertValue(currentRow, currentCol, value);
    pos_start = pos_row_2;
  }
}

//----------------------------------------------------------------------------
void vtkBiomTableReader::InsertValue(int row, int col, std::string value)
{
  std::stringstream stream;
  stream << value;

  switch(this->DataType)
  {
    case VTK_INT:
      int i;
      if (!(stream >> i))
      {
        vtkErrorMacro(<<"error converting '" << value << " to integer");
      }
      else
      {
        vtkVariant v(i);
        this->GetOutput()->SetValue(row, col, v);
      }
      break;
    case VTK_FLOAT:
      float f;
      if (!(stream >> f))
      {
        vtkErrorMacro(<<"error converting '" << value << " to float");
      }
      else
      {
        vtkVariant v(f);
        this->GetOutput()->SetValue(row, col, v);
      }
      break;
    case VTK_STRING:
    default:
      vtkVariant v(value);
      this->GetOutput()->SetValue(row, col, v);
  }
}

//----------------------------------------------------------------------------
void vtkBiomTableReader::ParseColumns()
{
  // find "columns":
  size_t pos_start = this->FileContents.find("\"columns\":");
  if (pos_start == std::string::npos)
  {
    vtkErrorMacro(<<"columns not found in input file");
    return;
  }

  for (int currentCol = 1; currentCol < this->NumberOfColumns + 1; ++currentCol)
  {
    // find id for this column
    size_t pos_column_1 = this->FileContents.find("\"id\":", pos_start);
    if (pos_column_1 == std::string::npos)
    {
      vtkErrorMacro(<<"columns field not formatted properly");
      return;
    }
    size_t pos_column_2 = this->FileContents.find("\", \"metadata\":", pos_column_1);
    if (pos_column_2 == std::string::npos)
    {
      vtkErrorMacro(<<"columns field not formatted properly");
      return;
    }
    std::string name =
      this->FileContents.substr(pos_column_1 + 5, pos_column_2 - pos_column_1 - 5);
    // remove quotes
    name.erase( remove( name.begin(), name.end(), '\"' ), name.end());
    // trim whitespace
    const size_t beginStr = name.find_first_not_of(" \t");
    const size_t endStr = name.find_last_not_of(" \t");
    const size_t range = endStr - beginStr + 1;
    name = name.substr(beginStr, range);
    this->GetOutput()->GetColumn(currentCol)->SetName(name.c_str());
    pos_start = pos_column_2;

    //this is where we would capture the metadata for this column
  }
}

//----------------------------------------------------------------------------
void vtkBiomTableReader::ParseRows()
{
  // find "rows":
  size_t pos_start = this->FileContents.find("\"rows\":");
  if (pos_start == std::string::npos)
  {
    vtkErrorMacro(<<"rows not found in input file");
    return;
  }

  for (int currentRow = 0; currentRow < this->NumberOfRows; ++currentRow)
  {
    // find id for this row
    size_t pos_row_1 = this->FileContents.find("\"id\":", pos_start);
    if (pos_row_1 == std::string::npos)
    {
      vtkErrorMacro(<<"rows field not formatted properly");
      return;
    }
    size_t pos_row_2 = this->FileContents.find("\", \"metadata\":", pos_row_1);
    if (pos_row_2 == std::string::npos)
    {
      vtkErrorMacro(<<"rows field not formatted properly");
      return;
    }
    std::string name =
      this->FileContents.substr(pos_row_1 + 5, pos_row_2 - pos_row_1 - 5);
    // remove quotes
    name.erase( remove( name.begin(), name.end(), '\"' ), name.end());
    // trim whitespace
    const size_t beginStr = name.find_first_not_of(" \t");
    const size_t endStr = name.find_last_not_of(" \t");
    const size_t range = endStr - beginStr + 1;
    name = name.substr(beginStr, range);

    this->GetOutput()->SetValue(currentRow, 0, vtkVariant(name));
    pos_start = pos_row_2;

    //this is where we would capture the metadata for this row
  }
}

//----------------------------------------------------------------------------
void vtkBiomTableReader::ParseId()
{
  bool done = false;
  size_t pos_start = 0;
  while( !done )
  {
    size_t pos_id = this->FileContents.find("\"id\":", pos_start);
    if (pos_id == std::string::npos)
    {
      vtkErrorMacro(<<"top-level id not found in input file");
      return;
    }

    //check that this is the toplevel id by matching preceding brackets
    std::string substring = this->FileContents.substr(0, pos_id);
    int numOpenBrackets = std::count(substring.begin(), substring.end(), '[');
    int numClosedBrackets = std::count(substring.begin(), substring.end(), ']');

    if (numOpenBrackets == numClosedBrackets)
    {
      size_t pos_comma = this->FileContents.find(",", pos_id + 1);
      if (pos_comma == std::string::npos )
      {
        vtkErrorMacro(<<"top-level id field not formatted properly");
        return;
      }
      std::string name =
        this->FileContents.substr(pos_id + 5, pos_comma - pos_id - 5);
      //remove trailing whitespace in our captured name
      size_t pos_id_begin = name.find_first_not_of(" \t");
      name = name.substr(pos_id_begin);
      //remove double quotes in the name
      name.erase( remove( name.begin(), name.end(), '\"' ), name.end());
      done = true;
    }
    else
    {
      pos_start = pos_id + 5;
    }
  }
}

//----------------------------------------------------------------------------
int vtkBiomTableReader::FillOutputPortInformation(int, vtkInformation* info)
{
  info->Set(vtkDataObject::DATA_TYPE_NAME(), "vtkTable");
  return 1;
}

//----------------------------------------------------------------------------
void vtkBiomTableReader::PrintSelf(ostream& os, vtkIndent indent)
{
  this->Superclass::PrintSelf(os,indent);
}