ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
String target_qp = getStringOption_("qp_att_acc");
String target_acc = getStringOption_("cv_acc");
String target_run = getStringOption_("name");
String target_file = getStringOption_("run");
String plot_file = getStringOption_("plot");
String tab = getStringOption_("table");
//-------------------------------------------------------------
// fetch vocabularies
//------------------------------------------------------------
ControlledVocabulary cv;
cv.loadFromOBO("PSI-MS", File::find("/CV/psi-ms.obo"));
cv.loadFromOBO("QC", File::find("/CV/qc-cv.obo"));
//-------------------------------------------------------------
// reading input
//------------------------------------------------------------
if (target_file != "")
{
target_run = QFileInfo(QString::fromStdString(target_file)).baseName();
}
QcMLFile qcmlfile;
if (in != "")
{
qcmlfile.load(in);
}
if (target_run == "")
{
//~ check if only one run in file
std::vector<String> nas;
qcmlfile.getRunNames(nas);
if (nas.size() == 1)
{
target_run = nas.front();
}
else
{
cerr << "Error: You have to give at least one of the following parameter (in ascending precedence): name, run. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
}
QFile f(plot_file.c_str());
String plot_b64;
if (f.open(QIODevice::ReadOnly))
{
QByteArray ba = f.readAll();
f.close();
plot_b64 = String(QString(ba.toBase64()));
}
QcMLFile::Attachment at;
at.cvAcc = target_acc;
at.id = String(UniqueIdGenerator::getUniqueId());
at.cvRef = "QC"; //TODO assign right cv reference
if (plot_b64 != "" || tab != "")
{
if (plot_b64 != "")
{
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(target_acc);
at.name = term.name; ///< Name
//~ at.unitRef; //TODO MIME type
//~ at.unitAcc;
}
catch (...)
{
cerr << "Error: You have to give the accession of a existing cv term. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
at.binary = plot_b64;
}
else if (tab != "")
{
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(target_acc);
at.name = term.name; ///< Name
//~ at.unitRef; //TODO MIME type
//~ at.unitAcc;
}
catch (...)
{
cerr << "Error: You have to give the accession of a existing cv term. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
CsvFile csv_file(tab);
if (csv_file.size()>1)
{
StringList li;
csv_file.getRow(0, li);
for (Size i = 0; i < li.size(); ++i)
{
at.colTypes.push_back(li[i]);
}
for (UInt i = 1; i < csv_file.size(); ++i)
{
StringList li;
std::vector<String> v;
csv_file.getRow(i, li);
//TODO throw error if li.size() != at.colTypes.size()
for (Size i = 0; i < li.size(); ++i)
{
v.push_back(li[i]);
}
at.tableRows.push_back(v);
}
}
}
else
{
cerr << "Error: Nothing valid to attach. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
std::vector<String> ids;
qcmlfile.existsRunQualityParameter(target_run, target_qp, ids);
if (!ids.empty())
{
at.qualityRef = ids.front();
qcmlfile.addRunAttachment(target_run, at);
}
else
{
qcmlfile.existsSetQualityParameter(target_run, target_qp, ids);
if (!ids.empty())
{
at.qualityRef = ids.front();
qcmlfile.addSetAttachment(target_run, at);
}
else
{
cerr << "Error: You have to give the accession of a existing cv term to attacht to. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
}
}
qcmlfile.store(out);
return EXECUTION_OK;
}
ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
String in = getStringOption_("in");
String csv = getStringOption_("out_csv");
String target_qp = getStringOption_("qp");
String target_run = getStringOption_("name");
String target_file = getStringOption_("run");
//-------------------------------------------------------------
// reading input
//------------------------------------------------------------
if (target_file != "")
{
target_run = QFileInfo(QString::fromStdString(target_file)).baseName();
}
QcMLFile qcmlfile;
qcmlfile.load(in);
if (target_run == "")
{
//~ check if only one run in file
std::vector<String> nas;
qcmlfile.getRunNames(nas);
if (nas.size() == 1)
{
target_run = nas.front();
}
else
{
cerr << "Error: You have to give at least one of the following parameter (in ascending precedence): name, run. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
}
String csv_str = "";
if (target_qp == "set id")
{
if (qcmlfile.existsSet(target_run,true))
{
csv_str = qcmlfile.exportIDstats(target_run);
}
else
{
cerr << "Error: You have to specify a existing set for this qp. " << target_run << " seems not to exist. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
}
else
{
//TODO warn when target_run is empty or not present in qcml
csv_str = qcmlfile.exportAttachment(target_run, target_qp);
}
ofstream fout(csv.c_str());
fout << csv_str << endl;
fout.close();
//~ qcmlfile.store(out);
return EXECUTION_OK;
//~ TODO export table containing all given qp
}