int CTAbleValApp::Run(void)
{
const CArgs& args = GetArgs();
Setup(args);
m_LogStream = args["logfile"] ? &(args["logfile"].AsOutputFile()) : &NcbiCout;
m_logger.Reset(new CMessageListenerLenient());
m_logger->SetProgressOstream(m_LogStream);
// note - the C Toolkit uses 0 for SEV_NONE, but the C++ Toolkit uses 0 for SEV_INFO
// adjust here to make the inputs to table2asn match tbl2asn expectations
//m_ReportLevel = args["R"].AsInteger() - 1;
//m_LowCutoff = static_cast<EDiagSev>(args["Q"].AsInteger() - 1);
//m_HighCutoff = static_cast<EDiagSev>(args["P"].AsInteger() - 1);
CTabDelimitedValidator::RegisterAliases(args["aliases"]?&args["aliases"].AsInputFile():0);
if (args["print-supported"])
{
CColumnValidatorRegistry::GetInstance().PrintSupported(ncbi::cout);
return 0;
}
m_comma_separated = args["comma"];
if (args["columns"])
{
m_columns_def = args["columns"].AsString();
NStr::ToLower(m_columns_def);
}
if (args["required"])
{
m_required_cols = args["required"].AsString();
NStr::ToLower(m_required_cols);
}
if (args["ignore"])
{
m_ignored_cols = args["ignore"].AsString();
NStr::ToLower(m_ignored_cols);
}
if (args["unique"])
{
m_unique_cols = args["unique"].AsString();
NStr::ToLower(m_unique_cols);
}
m_no_header = args["no-header"];
m_skip_empty = args["skip-empty"];
m_format = args["format"].AsString();
m_ignore_unknown_types = args["ignore-unknown"];
if (args["discouraged"])
{
m_discouraged = args["discouraged"].AsString();
NStr::ToLower(m_discouraged);
}
if (args["require-one"])
{
m_require_one = args["require-one"].GetStringList();
}
// Designate where do we output files: local folder, specified folder or a specific single output file
if (args["o"])
{
m_output = &args["o"].AsOutputFile();
}
else
{
if (args["r"])
{
m_ResultsDirectory = args["r"].AsString();
}
else
{
m_ResultsDirectory = ".";
}
m_ResultsDirectory = CDir::AddTrailingPathSeparator(m_ResultsDirectory);
CDir outputdir(m_ResultsDirectory);
if (!IsDryRun())
if (!outputdir.Exists())
outputdir.Create();
}
try
{
// Designate where do we get input: single file or a folder or folder structure
if ( args["p"] )
{
CDir directory(args["p"].AsString());
if (directory.Exists())
{
CMaskFileName masks;
masks.Add("*" +args["x"].AsString());
ProcessOneDirectory (directory, masks, args["E"].AsBoolean());
}
} else {
if (args["i"])
{
ProcessOneFile (args["i"].AsString());
}
}
}
catch (CException& e)
{
m_logger->PutError(*CLineError::Create(CLineError::eProblem_GeneralParsingError, eDiag_Error,
"", 0, "", "", "",
e.GetMsg()));
}
if (m_logger->Count() == 0)
return 0;
else
{
m_logger->Dump(*m_LogStream);
int errors = m_logger->LevelCount(eDiag_Critical) +
m_logger->LevelCount(eDiag_Error) +
m_logger->LevelCount(eDiag_Fatal);
// all errors reported as failure
if (errors > 0)
return 1;
// only warnings reported as 2
if (m_logger->LevelCount(eDiag_Warning)>0)
return 2;
// otherwise it's ok
return 0;
}
}
