ExitCodes main_(int, const char **)
{
// parameter handling
String in = getStringOption_("in");
String out = getStringOption_("out");
// input file type
FileTypes::Type in_type = FileHandler::getType(in);
writeDebug_(String("Input file type: ") + FileTypes::typeToName(in_type), 2);
if (in_type == FileTypes::UNKNOWN)
{
writeLog_("Error: Could not determine input file type!");
return PARSE_ERROR;
}
String document_id;
vector<ProteinIdentification> prot_ids;
vector<PeptideIdentification> pep_ids;
IdXMLFile().load(in, prot_ids, pep_ids, document_id);
MzTabFile mztab;
mztab.store(out, prot_ids, pep_ids, in, document_id);
return EXECUTION_OK;
}
ExitCodes main_(int, const char **) override
{
//-------------------------------------------------------------
// Parsing parameters
//-------------------------------------------------------------
String in = getStringOption_("in");
String out_sirius = getStringOption_("out_sirius");
String out_csifingerid = getStringOption_("out_fingerid");
// needed for counting
int number_compounds = getIntOption_("number");
// Parameter for Sirius3
QString executable = getStringOption_("executable").toQString();
const QString profile = getStringOption_("profile").toQString();
const QString elements = getStringOption_("elements").toQString();
const QString database = getStringOption_("database").toQString();
const QString isotope = getStringOption_("isotope").toQString();
const QString noise = QString::number(getIntOption_("noise"));
const QString ppm_max = QString::number(getIntOption_("ppm_max"));
const QString candidates = QString::number(getIntOption_("candidates"));
bool auto_charge = getFlag_("auto_charge");
bool no_recalibration = getFlag_("no_recalibration");
bool iontree = getFlag_("iontree");
//-------------------------------------------------------------
// Determination of the Executable
//-------------------------------------------------------------
// Parameter executable not provided
if (executable.isEmpty())
{
const QProcessEnvironment env;
const QString & qsiriuspathenv = env.systemEnvironment().value("SIRIUS_PATH");
if (qsiriuspathenv.isEmpty())
{
writeLog_( "FATAL: Executable of Sirius could not be found. Please either use SIRIUS_PATH env variable or provide with -executable");
return MISSING_PARAMETERS;
}
executable = qsiriuspathenv;
}
// Normalize file path
QFileInfo file_info(executable);
executable = file_info.canonicalFilePath();
writeLog_("Executable is: " + executable);
const QString & path_to_executable = File::path(executable).toQString();
//-------------------------------------------------------------
// Calculations
//-------------------------------------------------------------
PeakMap spectra;
MzMLFile f;
f.setLogType(log_type_);
f.load(in, spectra);
std::vector<String> subdirs;
QString tmp_base_dir = File::getTempDirectory().toQString();
QString tmp_dir = QDir(tmp_base_dir).filePath(File::getUniqueName().toQString());
String tmp_ms_file = QDir(tmp_base_dir).filePath((File::getUniqueName() + ".ms").toQString());
String out_dir = QDir(tmp_dir).filePath("sirius_out");
//Write msfile
SiriusMSFile::store(spectra, tmp_ms_file);
// Assemble SIRIUS parameters
QStringList process_params;
process_params << "-p" << profile
<< "-e" << elements
<< "-d" << database
<< "-s" << isotope
<< "--noise" << noise
<< "--candidates" << candidates
<< "--ppm-max" << ppm_max
<< "--quiet"
<< "--output" << out_dir.toQString(); //internal output folder for temporary SIRIUS output file storage
// Add flags
if (no_recalibration)
{
process_params << "--no-recalibration";
}
if (!out_csifingerid.empty())
{
process_params << "--fingerid";
}
if (iontree)
{
process_params << "--iontree";
}
if (auto_charge)
{
process_params << "--auto-charge";
}
process_params << tmp_ms_file.toQString();
// The actual process
QProcess qp;
qp.setWorkingDirectory(path_to_executable); //since library paths are relative to sirius executable path
qp.start(executable, process_params); // does automatic escaping etc... start
std::stringstream ss;
ss << "COMMAND: " << executable.toStdString();
for (QStringList::const_iterator it = process_params.begin(); it != process_params.end(); ++it)
{
ss << " " << it->toStdString();
}
LOG_DEBUG << ss.str() << endl;
writeLog_("Executing: " + String(executable));
writeLog_("Working Dir is: " + path_to_executable);
const bool success = qp.waitForFinished(-1); // wait till job is finished
qp.close();
if (success == false || qp.exitStatus() != 0 || qp.exitCode() != 0)
{
writeLog_( "FATAL: External invocation of Sirius failed. Standard output and error were:");
const QString sirius_stdout(qp.readAllStandardOutput());
const QString sirius_stderr(qp.readAllStandardOutput());
writeLog_(sirius_stdout);
writeLog_(sirius_stderr);
writeLog_(String(qp.exitCode()));
return EXTERNAL_PROGRAM_ERROR;
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//Extract path to subfolders (sirius internal folder structure)
QDirIterator it(out_dir.toQString(), QDir::Dirs | QDir::NoDotAndDotDot, QDirIterator::NoIteratorFlags);
while (it.hasNext())
{
subdirs.push_back(it.next());
}
//sort vector path list
std::sort(subdirs.begin(), subdirs.end(), sortByScanIndex);
//Convert sirius_output to mztab and store file
MzTab sirius_result;
MzTabFile siriusfile;
SiriusMzTabWriter::read(subdirs, number_compounds, sirius_result);
siriusfile.store(out_sirius, sirius_result);
//Convert sirius_output to mztab and store file
if (out_csifingerid.empty() == false)
{
MzTab csi_result;
MzTabFile csifile;
CsiFingerIdMzTabWriter::read(subdirs, number_compounds, csi_result);
csifile.store(out_csifingerid, csi_result);
}
//clean tmp directory if debug level < 2
if (debug_level_ >= 2)
{
writeDebug_("Keeping temporary files in directory '" + String(tmp_dir) + " and msfile at this location "+ tmp_ms_file + ". Set debug level to 1 or lower to remove them.", 2);
}
else
{
if (tmp_dir.isEmpty() == false)
{
writeDebug_("Deleting temporary directory '" + String(tmp_dir) + "'. Set debug level to 2 or higher to keep it.", 0);
File::removeDir(tmp_dir);
}
if (tmp_ms_file.empty() == false)
{
writeDebug_("Deleting temporary msfile '" + tmp_ms_file + "'. Set debug level to 2 or higher to keep it.", 0);
File::remove(tmp_ms_file); // remove msfile
}
}
return EXECUTION_OK;
}