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Commit fdc69f0e authored by Langella Olivier's avatar Langella Olivier
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better error messages, MS run file check is made by workerthread

parent 44133390
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src/core/msrun.cpp
+ 48
− 9
View file @ fdc69f0e
......@@ -66,20 +66,46 @@ MsRun::getMsRunReaderSPtr()
<< " filename=" << getFileName();
if(_msrun_reader_sp == nullptr)
{
qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
<< " runid=" << getRunId() << " xmlid=" << getXmlId();
pappso::MsFileAccessor *p_accessor = nullptr;
try
{
pappso::MsFileAccessor accessor(getFileName(), "");
qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
<< " runid=" << getRunId() << " xmlid=" << getXmlId();
_msrun_reader_sp =
accessor.getMsRunReaderSPtrByRunId(getRunId(), getXmlId());
// pappso::MsFileAccessor accessor(getFileName(), "");
p_accessor = new pappso::MsFileAccessor(getFileName(), "");
}
catch(pappso::PappsoException &error)
catch(pappso::ExceptionNotFound &error)
{
_msrun_reader_sp = nullptr;
// throw error;
// file not found, don't throw exception, we'll try another location
}
if(p_accessor != nullptr)
{
try
{
_msrun_reader_sp =
p_accessor->getMsRunReaderSPtrByRunId(getRunId(), getXmlId());
delete p_accessor;
p_accessor = nullptr;
}
catch(pappso::PappsoException &error2)
{
_msrun_reader_sp = nullptr;
if(p_accessor != nullptr)
{
delete p_accessor;
p_accessor = nullptr;
}
throw error2;
}
}
}
return _msrun_reader_sp;
}
......@@ -274,13 +300,26 @@ void
MsRun::buildMsRunRetentionTime(
const PeptideEvidenceStore &peptide_evidence_store)
{
pappso::MsRunReaderSPtr reader = getMsRunReaderSPtr();
pappso::MsRunReaderSPtr reader;
try
{
reader = getMsRunReaderSPtr();
}
catch(pappso::PappsoException &error)
{
throw pappso::ExceptionNotFound(
QObject::tr(
"Error while processing MSrun \"%1\" for sample named \"%2\" :\n%3")
.arg(getXmlId())
.arg(getSampleName())
.arg(error.qwhat()));
}
if(reader == nullptr)
{
throw pappso::ExceptionNotFound(
QObject::tr("MSrun \"%1\" for sample named \"%2\" not found")
QObject::tr("MSrun \"%1\" for sample named \"%2\" file \"%3\" not found")
.arg(getXmlId())
.arg(getSampleName()));
.arg(getSampleName()).arg(getFileName()));
}
if(mpa_msrunRetentionTime == nullptr)
{
......
src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
+ 35
− 116
View file @ fdc69f0e
......@@ -62,12 +62,22 @@ ExportMasschroqDialog::ExportMasschroqDialog(MainWindow *parent,
&ExportMasschroqDialog::operateFindBestMsrunForAlignment,
p_worker,
&WorkerThread::doFindBestMsrunForAlignment);
connect(p_worker,
&WorkerThread::findingBestMsrunForAlignmentFinished,
this,
&ExportMasschroqDialog::setBestMsrunForAlignment);
connect(this,
&ExportMasschroqDialog::operateCheckingMsrunFilePath,
p_worker,
&WorkerThread::doCheckMsrunFilePath);
connect(p_worker,
&WorkerThread::checkingMsrunFilePathFinished,
this,
&ExportMasschroqDialog::setCheckMsrunFilePathOk);
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
......@@ -237,39 +247,9 @@ void
ExportMasschroqDialog::doCheckMsrunFilepath()
{
ui->msrunFilepathOkLabel->setHidden(true);
bool is_ok = true;
for(IdentificationDataSourceSp p_ident_data_source :
msp_project->getIdentificationDataSourceStore()
.getIdentificationDataSourceList())
{
MsRunSp msrun_sp = p_ident_data_source->getMsRunSp();
if(msrun_sp->findMsRunFile())
{
// msrun_sp->checkMsRunStatistics();
}
else
{
is_ok = false;
}
if(!is_ok)
{
ui->warningDirectoryLabel->setText(
tr("%1 not found : Please choose the directory to look for this MS "
"run file.")
.arg(msrun_sp.get()->getFileName()));
ui->directorySelectWidget->setHidden(false);
break;
}
}
if(is_ok)
{
ui->directorySelectWidget->setHidden(true);
mp_main->showWaitingMessage(tr("Checking MSrun files path"));
emit operateCheckingMsrunFilePath(msp_project);
ui->msrunFilepathOkLabel->setText(tr("All MS run files found"));
ui->msrunFilepathOkLabel->setHidden(false);
}
}
void
......@@ -298,89 +278,6 @@ ExportMasschroqDialog::doFindBestMsrunForAlignment()
{
mp_main->showWaitingMessage(tr("Looking for MSrun reference"));
emit operateFindBestMsrunForAlignment(msp_project);
/*
bool is_ok = true;
for(auto &msrun_sp : msp_project->getMsRunStore().getMsRunList())
{
if(msrun_sp->findMsRunFile())
{
}
else
{
is_ok = false;
ui->warningDirectoryLabel->setText(
tr("%1 not found : Please choose the directory to look for this MS "
"run file.")
.arg(msrun_sp.get()->getFileName()));
ui->directorySelectWidget->setHidden(false);
break;
}
}
try
{
msp_project->prepareMsrunRetentionTimesForAlignment();
MsRunSp ms_run_best_reference;
std::size_t best_number = 0;
for(auto &msrun_ref_sp : msp_project->getMsRunStore().getMsRunList())
{
if(ms_run_best_reference == nullptr)
{
ms_run_best_reference = msrun_ref_sp;
}
std::size_t min_number = std::numeric_limits<std::size_t>::max();
for(auto &msrun_sp : msp_project->getMsRunStore().getMsRunList())
{
if(msrun_sp.get() != msrun_ref_sp.get())
{
pappso::Trace trace;
trace = msrun_sp.get()
->getMsRunRetentionTimePtr()
->getCommonDeltaRt(msrun_ref_sp.get()
->getMsRunRetentionTimePtr()
->getSeamarks());
if(trace.size() < min_number)
{
min_number = trace.size();
}
}
}
if(min_number > best_number)
{
best_number = min_number;
ms_run_best_reference = msrun_ref_sp;
}
}
if(ms_run_best_reference != nullptr)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< ms_run_best_reference.get()->getXmlId()
<< " best_number=" << best_number;
for(int index = 0; index < ui->msrun_list_combo_box->count(); index++)
{
MsRunSp msrun_sp = qvariant_cast<MsRunSp>(
ui->msrun_list_combo_box->itemData(index));
if(msrun_sp.get() == ms_run_best_reference.get())
{
ui->msrun_list_combo_box->setCurrentIndex(index);
}
}
}
}
catch(pappso::PappsoException &error)
{
QMessageBox msgBox;
msgBox.setWindowTitle("Error");
msgBox.setText(
tr("Error preparing MS run retention times: %1").arg(error.qwhat()));
msgBox.setIcon(QMessageBox::Critical);
msgBox.exec();
}
*/
}
void
......@@ -405,6 +302,28 @@ ExportMasschroqDialog::setBestMsrunForAlignment(MsRunSp best_msrun_sp)
}
}
void
ExportMasschroqDialog::setCheckMsrunFilePathOk(MsRunSp msrun_sp)
{
mp_main->hideWaitingMessage();
if(msrun_sp == nullptr)
{
ui->directorySelectWidget->setHidden(true);
ui->msrunFilepathOkLabel->setText(tr("All MS run files found"));
ui->msrunFilepathOkLabel->setHidden(false);
}
else
{
ui->warningDirectoryLabel->setText(
tr("\"%1\" not found : Please choose the directory to look for this MS "
"run file.")
.arg(msrun_sp.get()->getFileName()));
ui->directorySelectWidget->setHidden(false);
}
}
void
ExportMasschroqDialog::fillMsrunListComboBox()
{
......
src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
+ 2
− 2
View file @ fdc69f0e
......@@ -61,10 +61,12 @@ class ExportMasschroqDialog : public QDialog
signals:
// void peptideChanged(pappso::PeptideSp peptide);
void operateFindBestMsrunForAlignment(ProjectSp project_sp);
void operateCheckingMsrunFilePath(ProjectSp project_sp);
public slots:
void setBestMsrunForAlignment(MsRunSp msrun_sp);
void setCheckMsrunFilePathOk(MsRunSp msrun_sp);
private:
Ui::ExportMasschroqDialog *ui;
......@@ -79,6 +81,4 @@ class ExportMasschroqDialog : public QDialog
private:
void fillMsrunListComboBox();
signals:
};
src/gui/workerthread.cpp
+ 104
− 32
View file @ fdc69f0e
......@@ -807,57 +807,80 @@ WorkerThread::doFindBestMsrunForAlignment(ProjectSp project_sp)
}
else
{
throw pappso::PappsoException(
tr("Error while checking MS run file path :\nMSrun \"%1\" for "
"sample named \"%2\" not found")
.arg(msrun_sp->getXmlId())
.arg(msrun_sp->getSampleName()));
}
i++;
}
_p_work_monitor->message("preparing MS run retention times");
project_sp->prepareMsrunRetentionTimesForAlignment();
try
{
project_sp->prepareMsrunRetentionTimesForAlignment();
}
catch(pappso::PappsoException &error)
{
throw pappso::PappsoException(
tr("Error while preparing MS run retention times :\n%1")
.arg(error.qwhat()));
}
_p_work_monitor->message("choosing MS run");
MsRunSp ms_run_best_reference;
std::size_t best_number = 0;
for(auto &msrun_ref_sp : project_sp->getMsRunStore().getMsRunList())
try
{
if(ms_run_best_reference == nullptr)
MsRunSp ms_run_best_reference;
std::size_t best_number = 0;
for(auto &msrun_ref_sp : project_sp->getMsRunStore().getMsRunList())
{
ms_run_best_reference = msrun_ref_sp;
}
if(ms_run_best_reference == nullptr)
{
ms_run_best_reference = msrun_ref_sp;
}
std::size_t min_number = std::numeric_limits<std::size_t>::max();
for(auto &msrun_sp : project_sp->getMsRunStore().getMsRunList())
{
if(msrun_sp.get() != msrun_ref_sp.get())
std::size_t min_number = std::numeric_limits<std::size_t>::max();
for(auto &msrun_sp : project_sp->getMsRunStore().getMsRunList())
{
pappso::Trace trace;
trace = msrun_sp.get()
->getMsRunRetentionTimePtr()
->getCommonDeltaRt(msrun_ref_sp.get()
->getMsRunRetentionTimePtr()
->getSeamarks());
if(trace.size() < min_number)
if(msrun_sp.get() != msrun_ref_sp.get())
{
min_number = trace.size();
pappso::Trace trace;
trace =
msrun_sp.get()
->getMsRunRetentionTimePtr()
->getCommonDeltaRt(msrun_ref_sp.get()
->getMsRunRetentionTimePtr()
->getSeamarks());
if(trace.size() < min_number)
{
min_number = trace.size();
}
}
}
}
if(min_number > best_number)
{
best_number = min_number;
if(min_number > best_number)
{
best_number = min_number;
ms_run_best_reference = msrun_ref_sp;
ms_run_best_reference = msrun_ref_sp;
}
}
if(ms_run_best_reference != nullptr)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
<< " " << ms_run_best_reference.get()->getXmlId()
<< " best_number=" << best_number;
}
_p_work_monitor->message("done");
// emit operateXpipFile(filename);
emit findingBestMsrunForAlignmentFinished(ms_run_best_reference);
}
if(ms_run_best_reference != nullptr)
catch(pappso::PappsoException &error)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< ms_run_best_reference.get()->getXmlId()
<< " best_number=" << best_number;
throw pappso::PappsoException(
tr("Error while choosing best MS run :\n%1").arg(error.qwhat()));
}
_p_work_monitor->message("done");
// emit operateXpipFile(filename);
emit findingBestMsrunForAlignmentFinished(ms_run_best_reference);
}
catch(pappso::PappsoException &error)
{
......@@ -866,3 +889,52 @@ WorkerThread::doFindBestMsrunForAlignment(ProjectSp project_sp)
.arg(error.qwhat()));
}
}
void
WorkerThread::doCheckMsrunFilePath(ProjectSp msp_project)
{
MsRunSp msrun_sp = nullptr;
try
{
_p_work_monitor->setProgressMaximumValue(
msp_project->getIdentificationDataSourceStore()
.getIdentificationDataSourceList()
.size());
std::size_t i = 0;
for(IdentificationDataSourceSp p_ident_data_source :
msp_project->getIdentificationDataSourceStore()
.getIdentificationDataSourceList())
{
msrun_sp = p_ident_data_source->getMsRunSp();
_p_work_monitor->message(
tr("checking MS run file path for \"%1\", named \"%2\"")
.arg(msrun_sp.get()->getXmlId())
.arg(msrun_sp.get()->getSampleName()),
i);
if(msrun_sp->findMsRunFile())
{
// msrun_sp->checkMsRunStatistics();
msrun_sp = nullptr;
}
else
{
// is_ok = false;
break;
}
i++;
}
}
catch(pappso::PappsoException &error)
{
emit operationFailed(
tr("Error checking MSrun files path :\n%1").arg(error.qwhat()));
}
emit checkingMsrunFilePathFinished(msrun_sp);
}
src/gui/workerthread.h
+ 2
− 0
View file @ fdc69f0e
......@@ -79,6 +79,7 @@ class WorkerThread : public QObject
doPtmGroupingOnIdentification(IdentificationGroup *p_identification_group);
void doRunningXtandem(TandemRunBatch tandem_run_batch);
void doFindBestMsrunForAlignment(ProjectSp project_sp);
void doCheckMsrunFilePath(ProjectSp project_sp);
signals:
......@@ -94,6 +95,7 @@ class WorkerThread : public QObject
void operationFinished();
void operationFailed(QString error);
void findingBestMsrunForAlignmentFinished(MsRunSp msrun_sp);
void checkingMsrunFilePathFinished(MsRunSp msrun_sp);
private:
WorkMonitor *_p_work_monitor;
......
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