size_t wxStreamBuffer::Write(const void *buffer, size_t size)
{
wxASSERT_MSG( buffer, wxT("Warning: Null pointer is about to be send") );
if (m_stream)
{
// lasterror is reset before all new IO calls
m_stream->Reset();
}
size_t ret;
if ( !HasBuffer() && m_fixed )
{
wxOutputStream *outStream = GetOutputStream();
wxCHECK_MSG( outStream, 0, wxT("should have a stream in wxStreamBuffer") );
// no buffer, just forward the call to the stream
ret = outStream->OnSysWrite(buffer, size);
}
else // we [may] have a buffer, use it
{
size_t orig_size = size;
while ( size > 0 )
{
size_t left = GetBytesLeft();
// if the buffer is too large to fit in the stream buffer, split
// it in smaller parts
//
// NB: If stream buffer isn't fixed (as for wxMemoryOutputStream),
// we always go to the second case.
//
// FIXME: fine, but if it fails we should (re)try writing it by
// chunks as this will (hopefully) always work (VZ)
if ( size > left && m_fixed )
{
PutToBuffer(buffer, left);
size -= left;
buffer = (char *)buffer + left;
if ( !FlushBuffer() )
{
SetError(wxSTREAM_WRITE_ERROR);
break;
}
m_buffer_pos = m_buffer_start;
}
else // we can do it in one gulp
{
PutToBuffer(buffer, size);
size = 0;
}
}
ret = orig_size - size;
}
if (m_stream)
{
// i am not entirely sure what we do this for
m_stream->m_lastcount = ret;
}
return ret;
}
CProcessAnalysis::CProcessAnalysis(
CDirEntry *pDirEntry,
const CVolume *pVolume,
wxEvtHandler *parent, int nID) :
CProcess(parent,nID),
m_psExe(NULL),
m_pDirEntry(pDirEntry)
{
#define END_LINE sStdin.Append(";\n")
#define APPEND_LINE(name,value) \
sStdin.Append(name); \
sStdin.Append(wxS("=")); \
sStdin.Append(value); \
END_LINE
#define FORMAT_INT(n) \
s.Printf("%d",n)
#define APPEND_INT(name,n) \
FORMAT_INT(n); \
APPEND_LINE(name,s)
wxString sStdin;
wxString s;
const CParmOsiris *pParm = pDirEntry->GetParmOsiris();
const ConfigDir *pDir = mainApp::GetConfig();
sStdin.Alloc(4096);
APPEND_LINE("InputDirectory",pParm->GetInputDirectory()); // 1
APPEND_LINE("LadderDirectory",pDir->GetExeConfigPath()); // 2
APPEND_LINE("ReportDirectory",pParm->GetOutputDirectory()); // 3
APPEND_LINE("MarkerSetName",pParm->GetKitName()); // 4
APPEND_LINE("LaneStandardName",pParm->GetLsName()); // 5
APPEND_LINE("CriticalOutputLevel","15"); // 6
APPEND_INT("MinSampleRFU",pParm->GetMinRFU_Sample()); // 7
APPEND_INT("MinLaneStandardRFU",pParm->GetMinRFU_ILS()); // 8
APPEND_INT("MinLadderRFU",pParm->GetMinRFU_Ladder()); // 9
APPEND_INT("MinInterlocusRFU",pParm->GetMinRFU_Interlocus()); // 10
// channel data
typedef struct
{
const vector<int> *pan;
const wxChar *ps;
} CHANNEL_OVERRIDE;
CHANNEL_OVERRIDE chanInfo[] =
{
{ &pParm->GetChannelRFU(), wxS("AnalysisThresholdOverride") },
{ &pParm->GetChannelDetection(), wxS("DetectionThresholdOverride") }
};
const size_t nOVR = sizeof(chanInfo) / sizeof(chanInfo[0]);
wxString sName;
for (size_t ndx = 0; ndx < nOVR; ndx++)
{
const vector<int> *pan = chanInfo[ndx].pan;
const wxChar *ps = chanInfo[ndx].ps;
vector<int>::const_iterator itr;
int nChannel;
for(itr = pan->begin(), nChannel = 1;
itr != pan->end();
++itr, ++nChannel)
{
if((*itr) > 0)
{
FORMAT_INT(nChannel);
sName = ps;
sName.Append(wxS(":"));
sName.Append(s);
APPEND_INT(sName,*itr);
}
}
}
// end channel data
if(pParm->GetTimeStampSubDir())
{
const wxString &s = pDirEntry->GetTimeStamp();
if(!s.IsEmpty())
{
APPEND_LINE("OutputSubdirectory",s);
}
else
{
wxASSERT_MSG(false,"Time stamp is empty");
}
}
// the following may eventually be moved to CParmOsiris and
// CLabSettings::GetMinRFU() if it is added to the user interface
int nMinLadderInterlocus = pParm->GetMinLadderInterlocusRFU();
// pVolume->GetLabSettings()->GetThresholds()->GetRFUladder()->GetMinRFUinterlocus();
int nMinDetection = pParm->GetSampleDetectionThreshold();
// pVolume->GetLabSettings()->GetThresholds()->GetRFUsample()->GetMinDetection();
if(nMinLadderInterlocus >= 0)
{
APPEND_INT("MinLadderInterlocusRFU",nMinLadderInterlocus); // 11
}
if(nMinDetection >= 0)
{
APPEND_INT("SampleDetectionThreshold",nMinDetection);
}
s = pParm->GetDataAnalyzed() ? "A" : "R";
APPEND_LINE("RawDataString",s); // 11 or 12
APPEND_LINE("LabSettings",pVolume->GetLabSettingsFileName());
APPEND_LINE("StandardSettings",pVolume->GetStdSettingsFileName());
APPEND_LINE("MessageBook",pDir->GetMessageBookFileName());
const wxString &sOverride(pParm->GetAnalysisOverride());
if(!sOverride.IsEmpty())
{
APPEND_LINE("override",sOverride);
}
END_LINE;
#undef APPEND_INT
#undef APPEND_LINE
#undef END_LINE
// finished building stdin for analysis program
wxASSERT_MSG(sizeof(char) == 1,
"sizeof(char) != 1, "
"therefore this code needs to be changed");
s = pDir->GetExePath();
nwxFileUtil::EndWithSeparator(&s);
#ifdef __WXMSW__
s += "TestAnalysisDirectoryLC.exe";
#else
s += "TestAnalysisDirectoryLC";
#endif
m_psExe = strdup(s.utf8_str());
char *argv[] = { m_psExe, NULL };
m_dProgress = 0.0;
Run(argv);
wxOutputStream *pOut = GetOutputStream();
wxASSERT_MSG(pOut != NULL,"Cannot get output stream for process");
mainApp::LogMessage(sStdin);
if(pOut != NULL)
{
const char *pChar = sStdin.ToUTF8();
size_t nLen = sStdin.Len();
size_t n;
while(nLen > 0)
{
n = pOut->Write((void *)pChar,nLen).LastWrite();
if(n)
{
pChar += n;
nLen -= n;
}
else
{
nLen = 0;
Cancel();
}
}
}
}
