mzcborcopyreplacebase.cpp

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/**
 * \file pappsomspp/core/processing/cbor/mzcbor/mzcborreaderbase.cpp
 * \date 2/10/2026
 * \author Olivier Langella
 * \brief read mzcbor stream or file, process it and write processed mzcbor output
 */
 
/*******************************************************************************
 * Copyright (c) 2026 Olivier Langella <Olivier.Langella@cnrs.fr>.
 *
 * This file is part of PAPPSOms-tools.
 *
 *     PAPPSOms-tools is free software: you can redistribute it and/or modify
 *     it under the terms of the GNU General Public License as published by
 *     the Free Software Foundation, either version 3 of the License, or
 *     (at your option) any later version.
 *
 *     PAPPSOms-tools is distributed in the hope that it will be useful,
 *     but WITHOUT ANY WARRANTY; without even the implied warranty of
 *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *     GNU General Public License for more details.
 *
 *     You should have received a copy of the GNU General Public License
 *     along with PAPPSOms-tools.  If not, see <http://www.gnu.org/licenses/>.
 *
 ******************************************************************************/
 
 
#include "mzcborcopyreplacebase.h"
#include "pappsomspp/core/pappsoexception.h"
#include "pappsomspp/core/utils.h"
#include <qcbormap.h>
#include <qcontainerfwd.h>
#include <qlogging.h>
#include <qobject.h>
#include <qtypes.h>
namespace pappso
{
namespace cbor
{
namespace mzcbor
{
MzcborCopyReplaceBase::MzcborCopyReplaceBase(CborStreamWriter *cbor_output_p,
                                             const QString &operation)
{
 
  mp_cborOutput = cbor_output_p;
  m_operation   = operation;
}
MzcborCopyReplaceBase::~MzcborCopyReplaceBase()
{
}
 
void
MzcborCopyReplaceBase::close()
{
}
 
void
MzcborCopyReplaceBase::readCbor(QFile *cborp, pappso::UiMonitorInterface &monitor)
{
  qDebug();
  initCborReader(cborp);
 
  qDebug();
  if(mpa_cborReader->isMap())
    {
      readRoot(monitor);
    }
  qDebug();
}
 
void
MzcborCopyReplaceBase::readCbor(QIODevice *cborp, pappso::UiMonitorInterface &monitor)
{
  qDebug();
  initCborReader(cborp);
 
  qDebug();
  if(mpa_cborReader->isMap())
    {
      readRoot(monitor);
    }
  qDebug();
}
 
void
MzcborCopyReplaceBase::readRoot(pappso::UiMonitorInterface &monitor)
{
  mp_cborOutput->startMap();
  mpa_cborReader->enterContainer();
 
 
  getExpectedString();
  if(m_expectedString == "mzCBOR")
    {
      mp_cborOutput->append("mzCBOR");
      qDebug() << m_expectedString;
      readCbor(monitor);
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting mzCBOR element");
    }
 
 
  QCborMap tmp_map;
  getExpectedString();
  if(m_expectedString == "mzML")
    {
      mp_cborOutput->append("mzML");
 
      mpa_cborReader->readCborMap(tmp_map);
      mp_cborOutput->writeCborMap(tmp_map);
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting mzML element");
    }
 
 
  QStringList copy_tags;
  copy_tags << "cvList"
            << "fileDescription" << "referenceableParamGroupList" << "softwareList"
            << "instrumentConfigurationList" << "dataProcessingList";
  while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
    {
      getExpectedString();
      qDebug() << m_expectedString;
 
 
      if(copy_tags.contains(m_expectedString))
        {
          mp_cborOutput->append(m_expectedString);
          mpa_cborReader->readCborMap(tmp_map);
          mp_cborOutput->writeCborMap(tmp_map);
        }
      else if(m_expectedString == "run")
        {
 
          mp_cborOutput->append("run");
          qDebug() << m_expectedString;
          readRun(monitor);
        }
 
      else
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR: %1 not expected in mzCBOR root").arg(m_expectedString));
        }
    }
 
  mp_cborOutput->endMap();
  mpa_cborReader->leaveContainer();
}
 
void
MzcborCopyReplaceBase::readCbor(pappso::UiMonitorInterface &monitor)
{
  mp_cborOutput->startMap();
  mpa_cborReader->enterContainer();
  QCborMap old_informations;
 
  while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
    {
      // mode
      //  informations
      //  log
      //  parameter_map
      getExpectedString();
      qDebug() << m_expectedString;
      if(m_expectedString == "mode")
        {
          mp_cborOutput->append("mode");
          mp_cborOutput->append(mpa_cborReader->toInteger());
          mpa_cborReader->next();
        }
      else if(m_expectedString == "informations")
        {
 
          mpa_cborReader->readCborMap(old_informations);
          mp_cborOutput->writeInformations(
            "libpappsomspp", Utils::getVersion(), "mzCBOR", m_operation);
        }
      else
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR: %1 not expected in mzCBOR").arg(m_expectedString));
        }
    }
 
 
  mp_cborOutput->endMap();
  mpa_cborReader->leaveContainer();
}
 
void
MzcborCopyReplaceBase::readRun(pappso::UiMonitorInterface &monitor)
{
 
  // <run
  //       id="20120906_balliau_extract_1_A01_urnb-1"
  //       defaultInstrumentConfigurationRef="IC1"
  //       startTimeStamp="2012-09-06T16:17:42.762Z"
  //       defaultSourceFileRef="RAW1"
  //   >
  //   <spectrumList
  //           count="3"
  //           defaultDataProcessingRef="ThermoRawFileParserProcessing"
  //       >
  //
  mp_cborOutput->startMap();
  mpa_cborReader->enterContainer();
  QCborMap tmp_map;
 
  QStringList copy_tags;
  copy_tags << "id" << "defaultInstrumentConfigurationRef" << "startTimeStamp"
            << "defaultSourceFileRef";
  while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
    {
      getExpectedString();
      qDebug() << m_expectedString;
 
 
      if(copy_tags.contains(m_expectedString))
        {
          mp_cborOutput->append(m_expectedString);
          getExpectedString();
          qDebug() << m_expectedString;
          mp_cborOutput->append(m_expectedString);
        }
 
      else if(m_expectedString == "spectrumList")
        {
          mp_cborOutput->append(m_expectedString);
          readSpectrumList(monitor);
        }
      else if(m_expectedString == "chromatogramList")
        {
          mp_cborOutput->append(m_expectedString);
          mpa_cborReader->readCborMap(tmp_map);
          mp_cborOutput->writeCborMap(tmp_map);
        }
      else
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR: %1 not expected in mzCBOR run").arg(m_expectedString));
        }
    }
 
  mp_cborOutput->endMap();
  mpa_cborReader->leaveContainer();
}
 
 
void
MzcborCopyReplaceBase::readSpectrumList(pappso::UiMonitorInterface &monitor)
{
 
  //   <spectrumList
  //           count="3"
  //           defaultDataProcessingRef="ThermoRawFileParserProcessing"
  //       >
  //
  mp_cborOutput->startMap();
  mpa_cborReader->enterContainer();
  QCborMap tmp_map;
  QCborValue tmp_value;
  QcborSpectrum cbor_spectrum;
 
  SpectrumTube spectrum_tube;
 
  QStringList copy_tags;
  copy_tags << "defaultDataProcessingRef";
  while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
    {
      getExpectedString();
      qDebug() << m_expectedString;
 
 
      if(copy_tags.contains(m_expectedString))
        {
          mp_cborOutput->append(m_expectedString);
          mpa_cborReader->readCborValue(tmp_value);
          mp_cborOutput->writeCborValue(tmp_value);
        }
      else if(m_expectedString == "count")
        {
          if(mpa_cborReader->isInteger())
            {
              monitor.setStatus(
                QObject::tr("original spectrumList count=%1").arg(mpa_cborReader->toInteger()));
              monitor.setTotalSteps(mpa_cborReader->toInteger());
            }
          mpa_cborReader->next();
        }
      else if(m_expectedString == "spectrum")
        {
          qDebug() << m_expectedString;
 
          // this is an array
          mpa_cborReader->enterContainer();
          while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
            {
              mpa_cborReader->readCborMap(cbor_spectrum);
              monitor.count();
              processQcborSpectrum(spectrum_tube, cbor_spectrum);
            }
 
 
          mpa_cborReader->leaveContainer();
 
 
          monitor.setStatus(QObject::tr("new spectrumList count=%1").arg(spectrum_tube.size()));
          mp_cborOutput->append("count");
          mp_cborOutput->append((quint64)spectrum_tube.size());
          mp_cborOutput->append(m_expectedString);
          mp_cborOutput->startArray();
 
          spectrum_tube.flush(mp_cborOutput);
 
          mp_cborOutput->endArray();
        }
      else
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR: %1 not expected in mzCBOR spectrumList").arg(m_expectedString));
        }
    }
 
 
  mp_cborOutput->endMap();
  mpa_cborReader->leaveContainer();
}
 
void
MzcborCopyReplaceBase::processQcborSpectrum(SpectrumTube &spectrum_tube,
                                            QcborSpectrum &cbor_spectrum)
{
  qDebug() << cbor_spectrum.getId() << " mslevel=" << cbor_spectrum.getMsLevel();
  cbor_spectrum.setId(QString("%1 oliv=%2").arg(cbor_spectrum.getId()).arg("cc"));
  if(cbor_spectrum.getMsLevel() == 2)
    {
      spectrum_tube.push_back(cbor_spectrum);
    }
}
} // namespace mzcbor
} // namespace cbor
} // namespace pappso