From c5fb4c493b81d5b5fcf5ca65269e3c6b7dbaac74 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 24 Sep 2020 15:19:10 +0200
Subject: [PATCH] findMsRunFile interface has changed to fix issue #31
---
.../identificationdatasource.cpp | 4 +-
src/core/msrun.cpp | 50 +++++++++++++------
src/core/msrun.h | 5 +-
src/gui/workerthread.cpp | 1 +
src/gui/xic_view/xicwindow.cpp | 5 +-
5 files changed, 45 insertions(+), 20 deletions(-)
diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index 188c58c9..49df2dfb 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -222,13 +222,15 @@ IdentificationDataSource::getMassSpectrumCstSPtr(unsigned int scan_number) const
if(msrun_reader_sp == nullptr)
{
- if(_ms_run_sp.get()->findMsRunFile() == false)
+ msrun_reader_sp = _ms_run_sp.get()->findMsRunFile();
+ if(msrun_reader_sp == nullptr)
{
throw pappso::ExceptionNotFound(
QObject::tr("mz data \"%1\" file not found")
.arg(_ms_run_sp.get()->getFileName()));
}
}
+ qDebug();
msrun_reader_sp = _ms_run_sp.get()->getMsRunReaderSPtr();
if(msrun_reader_sp == nullptr)
{
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index c7bb96ac..6bb3f262 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -132,6 +132,10 @@ MsRun::getMsRunReaderSPtr()
}
}
}
+ else
+ {
+ qDebug();
+ }
return _msrun_reader_sp;
}
@@ -167,23 +171,29 @@ MsRun::getMsRunStatistics(MsRunStatistics param) const
}
}
-bool
+pappso::MsRunReaderSPtr
MsRun::findMsRunFile()
{
// first look at the file path :)
- _msrun_reader_sp = getMsRunReaderSPtr();
- if(_msrun_reader_sp != nullptr)
+ qDebug();
+ pappso::MsRunReaderSPtr msrun_reader_sp = getMsRunReaderSPtr();
+ if(msrun_reader_sp != nullptr)
{
QFileInfo real_file(this->getFileName());
if(real_file.exists())
{
- return true;
+
+ qDebug();
+ freeMsRunReaderSp();
+ qDebug();
+ return msrun_reader_sp;
}
else
{
- _msrun_reader_sp = nullptr;
+ msrun_reader_sp = nullptr;
}
}
+ qDebug();
QFileInfo file_original(this->getFileName());
QString basename = file_original.baseName();
QString onlyfilename = file_original.fileName();
@@ -207,7 +217,7 @@ MsRun::findMsRunFile()
this->setFileName(file.absoluteFilePath());
try
{
- if(_msrun_reader_sp == nullptr)
+ if(msrun_reader_sp == nullptr)
{
pappso::MsFileAccessor accessor(getFileName(), "");
@@ -217,14 +227,15 @@ MsRun::findMsRunFile()
qDebug()
<< " runid=" << getRunId() << " xmlid=" << getXmlId();
- _msrun_reader_sp = accessor.getMsRunReaderSPtrByRunId(
+ msrun_reader_sp = accessor.getMsRunReaderSPtrByRunId(
getRunId(), getXmlId());
- return true;
+
+ freeMsRunReaderSp();
+ return msrun_reader_sp;
}
}
catch(pappso::PappsoException &error)
{
- _msrun_reader_sp = nullptr;
}
}
if((file.fileName().contains(onlyfilename)) ||
@@ -235,7 +246,7 @@ MsRun::findMsRunFile()
{
this->setFileName(file.absoluteFilePath());
- if(_msrun_reader_sp == nullptr)
+ if(msrun_reader_sp == nullptr)
{
pappso::MsFileAccessor accessor(getFileName(), "");
@@ -245,21 +256,24 @@ MsRun::findMsRunFile()
pappso::FileReaderType::tims_ms2);
qDebug()
<< " runid=" << getRunId() << " xmlid=" << getXmlId();
- _msrun_reader_sp = accessor.getMsRunReaderSPtrByRunId(
+ msrun_reader_sp = accessor.getMsRunReaderSPtrByRunId(
getRunId(), getXmlId());
- return true;
+
+ freeMsRunReaderSp();
+ return msrun_reader_sp;
}
}
catch(pappso::PappsoException &error)
{
- _msrun_reader_sp = nullptr;
+ msrun_reader_sp = nullptr;
}
}
}
}
this->setFileName(file_original.absoluteFilePath());
freeMsRunReaderSp();
- return false;
+ qDebug();
+ return msrun_reader_sp;
}
void
@@ -388,9 +402,12 @@ MsRun::getMsRunXicExtractorInterfaceSp()
{
return _xic_extractor_sp;
}
- if(this->findMsRunFile())
+ qDebug();
+ _msrun_reader_sp = this->findMsRunFile();
+ if(_msrun_reader_sp != nullptr)
{
+ qDebug();
pappso::MsRunXicExtractorFactory::getInstance().setTmpDir(
QDir::tempPath());
@@ -410,7 +427,10 @@ MsRun::getMsRunXicExtractorInterfaceSp()
}
//_xic_extractor_sp = pappso::MsRunXicExtractorFactory::getInstance()
// .buildMsRunXicExtractorDiskBufferSp(*this);
+
+ qDebug();
}
+ freeMsRunReaderSp();
return _xic_extractor_sp;
}
diff --git a/src/core/msrun.h b/src/core/msrun.h
index 031c1e28..b42820b4 100644
--- a/src/core/msrun.h
+++ b/src/core/msrun.h
@@ -73,7 +73,9 @@ class MsRun : public pappso::MsRunId
virtual const std::map<MsRunStatistics, QVariant> &
getMsRunStatisticsMap() const;
- bool findMsRunFile();
+ /** \brief find the msRun file and return an msrunreader shared pointer on it
+ */
+ pappso::MsRunReaderSPtr findMsRunFile();
pappso::MsRunReaderSPtr &getMsRunReaderSPtr();
@@ -113,3 +115,4 @@ class MsRun : public pappso::MsRunId
Q_DECLARE_METATYPE(MsRunSp)
+
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index 18174637..35c9638f 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -909,6 +909,7 @@ WorkerThread::doCheckMsrunFilePath(ProjectSp msp_project)
// is_ok = false;
break;
}
+ msrun_sp->freeMsRunReaderSp();
i++;
}
}
diff --git a/src/gui/xic_view/xicwindow.cpp b/src/gui/xic_view/xicwindow.cpp
index 6db88772..06373f04 100644
--- a/src/gui/xic_view/xicwindow.cpp
+++ b/src/gui/xic_view/xicwindow.cpp
@@ -140,10 +140,9 @@ XicWindow::getXicExtractionMethod() const
void
XicWindow::xicPrecisionChanged(pappso::PrecisionPtr precision [[maybe_unused]])
{
- qDebug() << "XicWindow::xicPrecisionChanged begin";
- qDebug() << "XicWindow::xicPrecisionChanged emit";
+ qDebug();
emit reExtractXicNeeded();
- qDebug() << "XicWindow::xicPrecisionChanged end";
+ qDebug();
}
void
--
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