ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
String target_run = getStringOption_("name");
String target_file = getStringOption_("run");
StringList qp_accs = getStringList_("qp_accessions");
//-------------------------------------------------------------
// reading input
//------------------------------------------------------------
if (target_file != "")
{
target_run = QFileInfo(QString::fromStdString(target_file)).baseName();
}
//~ !getFlag_("tables")
QcMLFile qcmlfile;
qcmlfile.load(in);
if (qp_accs.empty())
{
qp_accs.push_back("QC:0000044");
qp_accs.push_back("QC:0000047");
qp_accs.push_back("QC:0000022");
qp_accs.push_back("QC:0000038");
qp_accs.push_back("QC:0000049");
}
//TODO care for QualityParameter s
if (target_run == "")
{
for (Size i = 0; i < qp_accs.size(); ++i)
{
qcmlfile.removeAllAttachments(qp_accs[i]);
}
}
else
{
for (Size i = 0; i < qp_accs.size(); ++i)
{
qcmlfile.removeAttachment(target_run,qp_accs[i]);
}
}
qcmlfile.store(out);
return EXECUTION_OK;
}
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 **)
{
String plot_file = "";
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
StringList in_files = getStringList_("in");
String out = getStringOption_("out");
String setname = getStringOption_("setname");
//-------------------------------------------------------------
// reading input
//-------------------------------------------------------------
QcMLFile qcmlfile;
for (Size i = 0; i < in_files.size(); ++i)
{
QcMLFile tmpfile;
tmpfile.load(in_files[i]);
qcmlfile.merge(tmpfile,setname);
}
// make #ms2 set stats
std::vector<String> ms2nums_strings;
qcmlfile.collectSetParameter(setname,"QC:0000015", ms2nums_strings);
std::vector<Int> ms2nums;
for (std::vector<String>::iterator it = ms2nums_strings.begin(); it != ms2nums_strings.end(); ++it) //transform is too ugly and errorprone
{
ms2nums.push_back(it->toInt());
}
std::sort(ms2nums.begin(), ms2nums.end());
if (ms2nums.size()>0)
{
std::map<String,String> nums;
std::map<String,String> nams;
//~ min,q1,q2,q3,max
nums["QC:0000043"] = String(ms2nums.front());
nams["QC:0000043"] = "min ms2 number";
nums["QC:0000044"] = String(OpenMS::Math::quantile(ms2nums.begin(), ms2nums.end(),25));
nams["QC:0000044"] = "Q1 ms2 number";
nums["QC:0000045"] = String(OpenMS::Math::quantile(ms2nums.begin(), ms2nums.end(),50));
nams["QC:0000045"] = "Q2 ms2 number";
nums["QC:0000046"] = String(OpenMS::Math::quantile(ms2nums.begin(), ms2nums.end(),75));
nams["QC:0000046"] = "Q3 ms2 number";
nums["QC:0000047"] = String(ms2nums.back());
nams["QC:0000047"] = "max ms2 number";
addBoxPlotQPs(nums, nams, setname, qcmlfile);
}
// make #id set stats
std::vector<String> idnums_strings;
qcmlfile.collectSetParameter(setname,"QC:0000020", idnums_strings);
std::vector<Int> idnums;
for (std::vector<String>::iterator it = idnums_strings.begin(); it != idnums_strings.end(); ++it) //transform is too ugly and errorprone
{
idnums.push_back(it->toInt());
}
std::sort(idnums.begin(), idnums.end());
if (idnums.size()>0)
{
std::map<String,String> nums;
std::map<String,String> nams;
//~ min,q1,q2,q3,max
nums["QC:0000053"] = String(idnums.front());
nams["QC:0000053"] = "min id numbers";
nums["QC:0000054"] = String(OpenMS::Math::quantile(idnums.begin(), idnums.end(),25));
nams["QC:0000054"] = "Q1 id numbers";
nums["QC:0000055"] = String(OpenMS::Math::quantile(idnums.begin(), idnums.end(),50));
nams["QC:0000055"] = "Q2 id numbers";
nums["QC:0000056"] = String(OpenMS::Math::quantile(idnums.begin(), idnums.end(),75));
nams["QC:0000056"] = "Q3 id numbers";
nums["QC:0000057"] = String(idnums.back());
nams["QC:0000057"] = "max id number";
addBoxPlotQPs(nums, nams, setname, qcmlfile);
}
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
}
ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
String mappi = getStringOption_("mapping");
String tab = getStringOption_("table");
ControlledVocabulary cv;
cv.loadFromOBO("PSI-MS", File::find("/CV/psi-ms.obo"));
cv.loadFromOBO("QC", File::find("/CV/qc-cv.obo"));
//-------------------------------------------------------------
// reading input
//------------------------------------------------------------
QcMLFile qcmlfile;
if (in != "")
{
qcmlfile.load(in);
}
if (mappi != "" && tab != "")
{
CsvFile csv_file(tab);
CsvFile map_file(mappi);
if (map_file.size()<2) //assumed that first row is the header of table and second row is the according qc
{
cerr << "Error: You have to give a mapping of your table (first row is the header of table and second row is the according qc). Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
StringList header,according;
map_file.getRow(0, header);
map_file.getRow(1, according);
if (header.size() != according.size())
{
cerr << "Error: You have to give a mapping of your table (first row is the header of table and second row is the according qc). Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
//~ std::map<String,String> mapping;
//~ std::transform( header.begin(), header.end(), according.begin(), std::inserter(mapping, mapping.end() ), std::make_pair<String,String> );
int runset_col = -1;
for (Size i = 0; i < according.size(); ++i)
{
if (!cv.exists(according[i]))
{
try
{
const ControlledVocabulary::CVTerm& term = cv.getTermByName(according[i]);
header[i] = term.name;
according[i] = term.id;
}
catch (...)
{
cerr << "Error: You have to specify a correct cv with accession or name in col "<< String(i) <<". Aborting!" << endl;
//~ cerr << "Header was: "<< header[i] << " , according value was: " << according[i] << endl;
return ILLEGAL_PARAMETERS;
}
}
else
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(according[i]);
header[i] = term.name;
}
if (header[i] == "raw data file") //TODO add set name as possibility!
{
runset_col = i;
}
}
if (runset_col < 0)
{
cerr << "Error: You have to give a mapping of your table - rows to runs/sets. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
if (csv_file.size()>1)
{
StringList li;
for (Size i = 1; i < csv_file.size(); ++i)
{
StringList li;
csv_file.getRow(i, li);
if (li.size() < according.size())
{
cerr << "Error: You have to give a correct mapping of your table - row " << String(i+1) <<" is too short. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
std::vector< QcMLFile::QualityParameter > qps;
String id;
bool set = false;
for (Size j = 0; j < li.size(); ++j)
{
if (j==runset_col)
{
if (qcmlfile.existsRun(li[j])) //TODO this only works for real run IDs
{
id = li[j];
}
else if (qcmlfile.existsSet(li[j])) //TODO this only works for real set IDs
{
id = li[j];
set = true;
}
else
{
id = li[j];
qcmlfile.registerRun(id,id);
//TODO warn that if this was supposed to be a set - now it is not!
}
}
QcMLFile::QualityParameter def;
def.name = header[j]; ///< Name
def.id = String(UniqueIdGenerator::getUniqueId());
def.cvRef = "QC"; ///< cv reference ('full name')
def.cvAcc = according[j];
def.value = li[j];
qps.push_back(def);
}
if (id!="")
{
for (std::vector<QcMLFile::QualityParameter>::const_iterator qit = qps.begin(); qit != qps.end(); ++qit)
{
if (!set)
{
qcmlfile.addRunQualityParameter(id, *qit);
}
else
{
qcmlfile.addSetQualityParameter(id, *qit);
}
}
}
}
}
}
qcmlfile.store(out);
return EXECUTION_OK;
}