pappso::cbor::mzcbor::ConvertToMzml Class Reference

#include <converttomzml.h>

Inheritance diagram for pappso::cbor::mzcbor::ConvertToMzml:

Public Member Functions
	ConvertToMzml (QXmlStreamWriter *p_writer)
virtual	~ConvertToMzml ()
virtual void	readCbor (QFile *cborp, pappso::UiMonitorInterface &monitor)
virtual void	readCbor (QIODevice *cborp, pappso::UiMonitorInterface &monitor)
virtual void	close ()
Public Member Functions inherited from pappso::cbor::CborStreamReaderInterface
	CborStreamReaderInterface ()
virtual	~CborStreamReaderInterface ()

Protected Member Functions
void	readRoot (pappso::UiMonitorInterface &monitor)
void	writeElementInMzml (const QString &name, pappso::UiMonitorInterface &monitor)
Protected Member Functions inherited from pappso::cbor::CborStreamReaderInterface
bool	getExpectedString ()
void	initCborReader (QFile *pcborfile)
void	initCborReader (QIODevice *pcborfile)

Private Attributes
QXmlStreamWriter *	mp_writer
bool	m_isMzcbor = false

Additional Inherited Members
Protected Attributes inherited from pappso::cbor::CborStreamReaderInterface
CborStreamReader *	mpa_cborReader = nullptr
QString	m_expectedString
QByteArray	m_data

Detailed Description

Todo:

write docs

Definition at line 47 of file converttomzml.h.

Constructor & Destructor Documentation

ConvertToMzml()

pappso::cbor::mzcbor::ConvertToMzml::ConvertToMzml

(

QXmlStreamWriter *

p_writer

)

Default constructor

Definition at line 38 of file converttomzml.cpp.

                                                       : mp_writer(p_writer)
{
}

~ConvertToMzml()

pappso::cbor::mzcbor::ConvertToMzml::~ConvertToMzml ( )

virtual

Destructor

Definition at line 42 of file converttomzml.cpp.

{
}

Member Function Documentation

close()

void pappso::cbor::mzcbor::ConvertToMzml::close ( )

virtual

Reimplemented from pappso::cbor::CborStreamReaderInterface.

Definition at line 47 of file converttomzml.cpp.

{
}

readCbor() [1/2]

void pappso::cbor::mzcbor::ConvertToMzml::readCbor ( QFile *  cborp, pappso::UiMonitorInterface &  monitor  )

virtual

Definition at line 52 of file converttomzml.cpp.

{
  qDebug();
  initCborReader(cborp);
 
  qDebug();
  if(mpa_cborReader->isMap())
    {
      readRoot(monitor);
    }
  qDebug();
}

readCbor() [2/2]

void pappso::cbor::mzcbor::ConvertToMzml::readCbor ( QIODevice *  cborp, pappso::UiMonitorInterface &  monitor  )

virtual

Definition at line 66 of file converttomzml.cpp.

{
  qDebug();
  initCborReader(cborp);
 
  qDebug();
  if(mpa_cborReader->isMap())
    {
      readRoot(monitor);
    }
  qDebug();
}

readRoot()

void pappso::cbor::mzcbor::ConvertToMzml::readRoot ( pappso::UiMonitorInterface &  monitor )

protected

Definition at line 81 of file converttomzml.cpp.

{
  qDebug();
  mpa_cborReader->enterContainer();
 
  while(getExpectedString())
    {
 
      if(m_expectedString == "mzCBOR")
        {
          m_isMzcbor = true;
          mpa_cborReader->next();
        }
      else if(m_expectedString == "mzML")
        {
 
          QCborMap mzml_cbor;
          mpa_cborReader->readCborMap(mzml_cbor);
          //<mzML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
          // xsi:schemaLocation="http://psi.hupo.org/ms/mzml
          // http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" version="1.1.0"
          // id="20120906_balliau_extract_1_A01_urnb-1" xmlns="http://psi.hupo.org/ms/mzml">
 
 
          mp_writer->setAutoFormatting(true);
          mp_writer->writeStartDocument("1.0");
          mp_writer->writeDefaultNamespace(mzml_cbor.value("xmlns").toString());
 
          mp_writer->writeNamespace("http://www.w3.org/2001/XMLSchema-instance", "xsi");
 
          mp_writer->writeStartElement("mzML");
 
          mp_writer->writeAttribute("http://www.w3.org/2001/XMLSchema-instance",
                                    "schemaLocation",
                                    mzml_cbor.value("schemaLocation").toString());
 
 
          for(auto &str_key : mzml_cbor.keys())
            {
              if((str_key != "xmlns") && (str_key != "schemaLocation"))
                {
                  mp_writer->writeAttribute(str_key.toString(),
                                            mzml_cbor.value(str_key).toString());
                }
            }
 
          m_isMzcbor = true;
          // getExpectedString();
          // qDebug() << m_expectedString;
          // mpa_cborReader->next();
 
          while(getExpectedString())
            {
              qDebug() << m_expectedString;
              writeElementInMzml(m_expectedString, monitor);
            }
          mp_writer->writeEndElement();
        }
    }
  mpa_cborReader->leaveContainer();
  mp_writer->writeEndDocument();
}

writeElementInMzml()

void pappso::cbor::mzcbor::ConvertToMzml::writeElementInMzml ( const QString &  name, pappso::UiMonitorInterface &  monitor  )

protected

Definition at line 146 of file converttomzml.cpp.

{
  bool is_array = false;
  if(name == "cvParam")
    { // this is an array
      qDebug();
      std::map<QString, pappso::cbor::mzcbor::CvParam> cvparam_map =
        CvParam::getCvParamsMapFromCbor(*mpa_cborReader);
      for(auto &cvparam_pair : cvparam_map)
        {
          cvparam_pair.second.toMzml(*mp_writer);
        }
    }
  else if(name == "binaryDataArray")
    {
 
      mp_writer->writeStartElement("binaryDataArrayList");
 
      mp_writer->writeAttribute("count", QString("%1").arg(mpa_cborReader->length()));
      mpa_cborReader->enterContainer();
      while(mpa_cborReader->hasNext())
        {
          BinaryDataArray binary_data_array;
          binary_data_array.fromCbor(*mpa_cborReader);
          binary_data_array.toMzml(*mp_writer);
        }
 
      mpa_cborReader->leaveContainer();
 
      mp_writer->writeEndElement();
    }
  else
    {
      if(mpa_cborReader->isArray())
        {
          is_array = true;
        }
      else if(mpa_cborReader->isMap())
        {
        }
      else
        {
          // error
          qWarning() << "not a map, not an array";
        }
      if(is_array)
        {
          mpa_cborReader->enterContainer();
          while(mpa_cborReader->hasNext())
            {
              writeElementInMzml(name, monitor);
            }
 
          mpa_cborReader->leaveContainer();
        }
      else
        {
          mp_writer->writeStartElement(name);
          mpa_cborReader->enterContainer();
 
          while(getExpectedString())
            {
              qDebug() << m_expectedString;
              QString current_attribute = m_expectedString;
              if(mpa_cborReader->isContainer())
                {
                  qDebug() << current_attribute;
                  writeElementInMzml(current_attribute, monitor);
                }
              else if(mpa_cborReader->isInteger())
                {
                  qDebug() << current_attribute;
                  mp_writer->writeAttribute(current_attribute,
                                            QString("%1").arg(mpa_cborReader->toInteger()));
                  mpa_cborReader->next();
                }
              else if(mpa_cborReader->isUnsignedInteger())
                {
                  qDebug() << current_attribute;
                  mp_writer->writeAttribute(current_attribute,
                                            QString("%1").arg(mpa_cborReader->toUnsignedInteger()));
                }
              else if(mpa_cborReader->isString())
                {
                  getExpectedString();
                  qDebug() << current_attribute;
                  mp_writer->writeAttribute(current_attribute, m_expectedString);
                }
              else
                {
                  qDebug() << current_attribute;
                  mpa_cborReader->next();
                }
            }
 
          mpa_cborReader->leaveContainer();
 
          mp_writer->writeEndElement();
        }
    }
}

References pappso::cbor::mzcbor::BinaryDataArray::fromCbor(), pappso::cbor::mzcbor::CvParam::getCvParamsMapFromCbor(), and pappso::cbor::mzcbor::BinaryDataArray::toMzml().

Member Data Documentation

m_isMzcbor

bool pappso::cbor::mzcbor::ConvertToMzml::m_isMzcbor = false

private

Definition at line 73 of file converttomzml.h.

mp_writer

QXmlStreamWriter* pappso::cbor::mzcbor::ConvertToMzml::mp_writer

private

Definition at line 72 of file converttomzml.h.

---

The documentation for this class was generated from the following files:

• pappsomspp/core/processing/cbor/mzcbor/converttomzml.h
• pappsomspp/core/processing/cbor/mzcbor/converttomzml.cpp