/**
 ** Copyright (c) 2007-2009 Illumina, Inc.
 **
 ** This software is covered by the "Illumina Genome Analyzer Software
 ** License Agreement" and the "Illumina Source Code License Agreement",
 ** and certain third party copyright/licenses, and any user of this
 ** source file is bound by the terms therein (see accompanying files
 ** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
 ** Illumina_Source_Code_License_Agreement.pdf and third party
 ** copyright/license notices).
 **
 ** This file is part of the Consensus Assessment of Sequence And VAriation
 ** (CASAVA) software package.
 **
 ** \file AlignStatsXmlWriter.hh
 **
 ** \brief Writes BCL files and other associated files (filter, position).
 **
 ** \author Roman Petrovski
 **/

#include <boost/foreach.hpp>
#include <boost/lexical_cast.hpp>
#include <boost/property_tree/xml_parser.hpp>

#include "common/Exceptions.hh"
#include "io/PtreeXml.hh"

#include "DemuxSummaryXmlWriter.hh"

namespace casava
{
namespace demultiplex
{


namespace cc=casava::common;

/**
 * \brief Records single tile summary in the tree.
 *
 * \param record Pair of Raw and Pf summary records
 */
void DemuxSummaryXmlWriter::addTileSummary(const std::pair<DemuxSummaryRecord, DemuxSummaryRecord> &p)
{
    const std::string tileValuePrefix("Summary"
                             ".<indexed>Lane.<index>" + boost::lexical_cast<std::string>(p.first.lane_)
                             +".<indexed>Sample.<index>" + p.first.sample_
                             +".<indexed>Barcode.<index>" + p.first.barcode_
                             +".<indexed>Tile.<index>" + boost::lexical_cast<std::string>(p.first.tile_)
                             +".<indexed>Read.<index>" + boost::lexical_cast<std::string>(p.first.readNumber_));

    const std::string tileValuePrefixRaw(tileValuePrefix + ".Raw.<value>.");
    const std::string tileValuePrefixPf(tileValuePrefix + ".Pf.<value>.");

    tree_.add(tileValuePrefixRaw + "Yield", p.first.yield_);
    tree_.add(tileValuePrefixRaw + "YieldQ30", p.first.yiedQ30_);
    tree_.add(tileValuePrefixRaw + "ClusterCount", p.first.clustersTotal_);
    tree_.add(tileValuePrefixRaw + "ClusterCount0MismatchBarcode", p.first.clusters0MismatchBarcode_);
    tree_.add(tileValuePrefixRaw + "ClusterCount1MismatchBarcode", p.first.clusters1MismatchBarcode_);
    tree_.add(tileValuePrefixRaw + "QualityScoreSum", p.first.qualityScoreSum_);

    tree_.add(tileValuePrefixPf + "Yield", p.second.yield_);
    tree_.add(tileValuePrefixPf + "YieldQ30", p.second.yiedQ30_);
    tree_.add(tileValuePrefixPf + "ClusterCount", p.second.clustersTotal_);
    tree_.add(tileValuePrefixPf + "ClusterCount0MismatchBarcode", p.second.clusters0MismatchBarcode_);
    tree_.add(tileValuePrefixPf + "ClusterCount1MismatchBarcode", p.second.clusters1MismatchBarcode_);
    tree_.add(tileValuePrefixPf + "QualityScoreSum", p.second.qualityScoreSum_);
}

void DemuxSummaryXmlWriter::close()
{
    std::ofstream os(summaryFilePath_.string().c_str());
    if (!os) {
        BOOST_THROW_EXCEPTION(cc::IoException(errno, "ERROR: Unable to open file for writing: " + summaryFilePath_.string()));
    }

    using namespace casava::io;
    os << tree_;

    if (!os) {
        BOOST_THROW_EXCEPTION(cc::IoException(errno, "ERROR: failed to store demultiplex summary: " + summaryFilePath_.string()));
    }
}


} //namespace statistics
} //namespace casava