/*
* Update the file with new FileHeader information
*/
bool FileHeaderUpdater::Update(std::ofstream& os, FileHeader& updateHdr, FileHeader& currentHdr)
{
// There is nothing at this time to update in the FileHeader
// Move on to the GenericDataHeader
GenericDataHeaderUpdater genUpdater;
return genUpdater.Update(os, *updateHdr.GetGenericDataHdr(), *currentHdr.GetGenericDataHdr());
}
/**
* No more probesets will be processed, this is a chance to finish outputting
* results and clean up.
* @param qMethod - Quantification method that was used.
* @return true if success, false otherwise.
*/
bool QuantMethodExprCCCHPReport::finish(QuantMethod &qMethod)
{
// Sanity to check we saw all the probe sets we were expecting.
if (m_CurrentProbeSetCount != m_Info.m_NumProbeSets) {
Err::errAbort("QuantMethodExprCCCHPReport::finish() - Expecting: " + ToStr(m_Info.m_NumProbeSets) +
" but got: " + ToStr(m_CurrentProbeSetCount) + ". Command Console CHP file will be corrupt.");
}
// Flush remaining signal entries in the buffer.
m_ExpressionQuantificationBufferWriter.FlushBuffer();
// Rewrite CHP files to get chip summary entires
Verbose::out(1,"Creating final files for CHP output");
Verbose::progressBegin(1, ToStr("Finalizing Expression CHP Files"),
m_CHPFileNames.size(), 1, m_CHPFileNames.size());
try {
for (unsigned int chip = 0; chip < m_CHPFileNames.size(); chip++) {
// open up tmp chp file to pull results from
GenericData data;
GenericFileReader reader;
std::string filename = m_CHPFileNames[chip]+".tmp";
reader.SetFilename(filename);
reader.ReadHeader(data);
GenericDataHeader* hdr = data.Header().GetGenericDataHdr();
GenericDataHeader updateHdr;
for (int source = 0; source < m_ChipSummaries.size(); source++) {
ChipSummary::metricDefVec_t metricDefs = m_ChipSummaries[source]->getMetricDefs();
for (int i = 0; i < metricDefs.size(); i++) {
ChipSummary::Metric metric;
if (!m_ChipSummaries[source]->getMetric(chip, metricDefs[i].m_name, metric)) {
Err::errAbort("QuantMethodExprCCCHPReport: metric '" + metricDefs[i].m_name +
"' was not found");
}
std::wstring mName(CHIP_SUMMARY_PARAMETER_NAME_PREFIX);
mName += StringUtils::ConvertMBSToWCS(metric.m_Name);
ParameterNameValueType param;
if (hdr->FindNameValParam(mName, param) == false) {
Err::errAbort("QuantMethodExprCCCHPReport: metric name '" + StringUtils::ConvertWCSToMBS(mName) +
"' could not be found in the header of " + filename);
}
switch (param.GetParameterType()) {
case ParameterNameValueType::Int8Type:
param.SetValueInt8((int8_t)metric.m_Integer);
break;
case ParameterNameValueType::UInt8Type:
param.SetValueUInt8((u_int8_t)metric.m_Integer);
break;
case ParameterNameValueType::Int16Type:
param.SetValueInt16((int16_t)metric.m_Integer);
break;
case ParameterNameValueType::UInt16Type:
param.SetValueUInt16((u_int16_t)metric.m_Integer);
break;
case ParameterNameValueType::Int32Type:
param.SetValueInt32((int32_t)metric.m_Integer);
break;
case ParameterNameValueType::UInt32Type:
param.SetValueUInt32((u_int32_t)metric.m_Integer);
break;
case ParameterNameValueType::FloatType:
param.SetValueFloat((float)metric.m_Double);
break;
case ParameterNameValueType::TextType:
param.SetValueText(StringUtils::ConvertMBSToWCS(metric.m_String), (int) metric.m_String.length());
break;
case ParameterNameValueType::AsciiType:
if (metric.m_String.size() > 256) {
Err::errAbort("QuantMethodExprCCCHPReport: string header parameter too long, name = '" +
metric.m_Name + "', value = '" + metric.m_String + "'");
}
param.SetValueAscii(metric.m_String, (int) metric.m_String.length());
break;
default:
Err::errAbort("QuantMethodExprCCCHPReport: unknown header parameter type found in file " +
filename);
}
updateHdr.AddNameValParam(param);
}
}
std::ofstream os;
Fs::aptOpen(os, filename, std::ios::out|std::ios::binary|std::ios::in);
if (!os) {
Err::errAbort("QuantMethodExprCCCHPReport: file " + filename +
" could not be opened for writing");
}
GenericDataHeaderUpdater updater;
updater.Update(os, updateHdr, *hdr);
os.close();
Verbose::progressStep(1);
}
} catch (...) {
removeAllChps();
Err::errAbort("Error in creating final CHP output.");
}
Verbose::progressEnd(1, ToStr("Done."));
// Remove .tmp extension
for (unsigned int i = 0; i < m_CHPFileNames.size(); i++) {
std::string from = m_CHPFileNames[i] + ".tmp";
std::string to = m_CHPFileNames[i];
if (!Fs::fileRename(from.c_str(),to.c_str())) {
removeAllChps();
Err::errAbort("Unable to rename '" + from + "' to '" + to + "'");
}
}
removeTmpChps();
return true;
}
