diff --git a/src/gui/mcqr_run_view/mcqr_sds_widget/mcqrsdswidget.cpp b/src/gui/mcqr_run_view/mcqr_sds_widget/mcqrsdswidget.cpp
index efdd977449deb3e5bb412bc1e10bb3ccbc93f082..945f31fcfb45778486d5ad8212b306e9eca72b8e 100644
--- a/src/gui/mcqr_run_view/mcqr_sds_widget/mcqrsdswidget.cpp
+++ b/src/gui/mcqr_run_view/mcqr_sds_widget/mcqrsdswidget.cpp
@@ -243,8 +243,8 @@ McqrSdsWidget::analyseQualityData()
grantlee_context.insert("factors_list", factors_list.join("\", \""));
- getMcqrRunParentView()->getRProcessRunning()->write(
- msp_rscriptTemplate->render(&grantlee_context).toUtf8());
+ getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
+ "analyzing_sc", msp_rscriptTemplate->render(&grantlee_context));
}
}
@@ -291,8 +291,8 @@ McqrSdsWidget::filteringData()
ui->fc_cutoff_spinbox->value());
grantlee_context.insert("factors_list", factors.join("\", \""));
- getMcqrRunParentView()->getRProcessRunning()->write(
- msp_rscriptTemplate->render(&grantlee_context).toUtf8());
+ getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
+ "filtering_sc", msp_rscriptTemplate->render(&grantlee_context));
}
}
@@ -348,8 +348,9 @@ McqrSdsWidget::plotProteinHeatmapAbundance()
grantlee_context.insert("agg_method",
ui->agg_method_combobox->currentText());
- getMcqrRunParentView()->getRProcessRunning()->write(
- msp_rscriptTemplate->render(&grantlee_context).toUtf8());
+ getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
+ "heatmap_abundance",
+ msp_rscriptTemplate->render(&grantlee_context));
}
else
{
@@ -392,8 +393,8 @@ McqrSdsWidget::runProteinClustering()
grantlee_context.insert("factor_list", factors_list.join("\", \""));
grantlee_context.insert("nb_cluster", ui->cluster_spin->value());
- getMcqrRunParentView()->getRProcessRunning()->write(
- msp_rscriptTemplate->render(&grantlee_context).toUtf8());
+ getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
+ "protein_clustering", msp_rscriptTemplate->render(&grantlee_context));
}
}
@@ -434,8 +435,8 @@ McqrSdsWidget::runProteinAnova()
grantlee_context.insert("interaction", "FALSE");
}
- getMcqrRunParentView()->getRProcessRunning()->write(
- msp_rscriptTemplate->render(&grantlee_context).toUtf8());
+ getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
+ "protein_anova", msp_rscriptTemplate->render(&grantlee_context));
}
}
@@ -485,8 +486,8 @@ McqrSdsWidget::runProteinAbundance()
}
grantlee_context.insert("alpha", ui->alpha_spin->value());
- getMcqrRunParentView()->getRProcessRunning()->write(
- msp_rscriptTemplate->render(&grantlee_context).toUtf8());
+ getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
+ "protein_abundance", msp_rscriptTemplate->render(&grantlee_context));
}
}
@@ -502,8 +503,8 @@ McqrSdsWidget::runProteinFcAbundance()
grantlee_context.insert("num", ui->numerator_combobox->currentText());
grantlee_context.insert("denom", ui->denominator_combobox->currentText());
- getMcqrRunParentView()->getRProcessRunning()->write(
- msp_rscriptTemplate->render(&grantlee_context).toUtf8());
+ getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
+ "protein_fc_abundance", msp_rscriptTemplate->render(&grantlee_context));
}
void
@@ -525,8 +526,8 @@ McqrSdsWidget::saveFinalRData()
grantlee_context.insert("mcqr_step", (std::int8_t)m_ongoingMcqrStep);
grantlee_context.insert("rdata_file", file_name);
- getMcqrRunParentView()->getRProcessRunning()->write(
- msp_rscriptTemplate->render(&grantlee_context).toUtf8());
+ getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
+ "last", msp_rscriptTemplate->render(&grantlee_context));
}
void
diff --git a/src/gui/mcqr_run_view/mcqr_sds_xic_widget/mcqrsdsxicwidget.cpp b/src/gui/mcqr_run_view/mcqr_sds_xic_widget/mcqrsdsxicwidget.cpp
index 1573fd08f6d1069f8f6dc057047bfc2326dc2eca..98900e553243e4f9a7f870e5b14ea0a21d18b42d 100644
--- a/src/gui/mcqr_run_view/mcqr_sds_xic_widget/mcqrsdsxicwidget.cpp
+++ b/src/gui/mcqr_run_view/mcqr_sds_xic_widget/mcqrsdsxicwidget.cpp
@@ -467,8 +467,6 @@ McqrSdsXicWidget::runReconstitutingTracks()
grantlee_context.insert("track_level",
ui->track_ref_combobox->currentText());
- getMcqrRunParentView()->getRProcessRunning()->write(
- msp_rscriptTemplate->render(&grantlee_context).toUtf8());
getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
"reconstituting_tracks",
@@ -532,8 +530,7 @@ McqrSdsXicWidget::runNormaliseIntensities()
ui->norm_method_combo->currentText());
getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
- "normalise",
- msp_rscriptTemplate->render(&grantlee_context));
+ "normalise", msp_rscriptTemplate->render(&grantlee_context));
}
qDebug();
}
@@ -573,10 +570,9 @@ McqrSdsXicWidget::runFilteringSharedPeptides()
grantlee_context.insert("corr_cutoff", ui->corr_cutoff_spin->value());
grantlee_context.insert("n_prot_corr", ui->nb_prot_corr_spin->value());
-
+
getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
- "filtering_shared",
- msp_rscriptTemplate->render(&grantlee_context));
+ "filtering_shared", msp_rscriptTemplate->render(&grantlee_context));
}
qDebug();
}
@@ -613,7 +609,7 @@ McqrSdsXicWidget::runFilteringUncorrelatedPeptides()
grantlee_context.insert("corr_cutoff", ui->corr_cutoff_spin->value());
grantlee_context.insert("nb_pep", ui->nb_peptides_cutoff_spin->value());
-
+
getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
"filtering_uncorrelated",
msp_rscriptTemplate->render(&grantlee_context));
@@ -646,10 +642,9 @@ McqrSdsXicWidget::runImputingPeptidesProteins()
grantlee_context.insert("abundance_method",
ui->abundance_method_combo->currentText());
-
- getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
- "imputing",
- msp_rscriptTemplate->render(&grantlee_context));
+
+ getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
+ "imputing", msp_rscriptTemplate->render(&grantlee_context));
qDebug();
}
@@ -685,9 +680,8 @@ McqrSdsXicWidget::runHeatMapProteinAbundance()
grantlee_context.insert("distance_fun", ui->distfun_combobox->currentText());
grantlee_context.insert("agg_method", ui->agg_method_combobox->currentText());
- getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
- "heatmap",
- msp_rscriptTemplate->render(&grantlee_context));
+ getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
+ "heatmap", msp_rscriptTemplate->render(&grantlee_context));
qDebug();
}
@@ -716,7 +710,7 @@ McqrSdsXicWidget::runProteinClustering()
getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
"protein_clustering", msp_rscriptTemplate->render(&grantlee_context));
-
+
qDebug();
}
@@ -786,10 +780,9 @@ McqrSdsXicWidget::runProteinAbundance()
pappso::Utils::booleanToString(ui->padjust_switch->getSwitchValue()));
grantlee_context.insert("alpha", ui->alpha_spin->value());
-
- getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
- "protein_abundance",
- msp_rscriptTemplate->render(&grantlee_context));
+
+ getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
+ "protein_abundance", msp_rscriptTemplate->render(&grantlee_context));
qDebug();
}
diff --git a/src/gui/mcqr_run_view/mcqrparamwidget.cpp b/src/gui/mcqr_run_view/mcqrparamwidget.cpp
index 1caf0b334f051512d0f2f7ee803842d75bd5a292..517c046ed3476310a81add168c1bda3a510d3f76 100644
--- a/src/gui/mcqr_run_view/mcqrparamwidget.cpp
+++ b/src/gui/mcqr_run_view/mcqrparamwidget.cpp
@@ -96,5 +96,5 @@ McqrParamWidget::saveModifiedRData(QString new_rdata_path)
{
QString save_script;
save_script = " save.image(file=\"" + new_rdata_path + "\")";
- mp_mcqrRunWindow->getRProcessRunning()->write(save_script.toUtf8());
+ mp_mcqrRunWindow->getRProcessRunning()->executeOffTheRecord(save_script);
}
diff --git a/src/gui/mcqr_run_view/mcqrqprocess.cpp b/src/gui/mcqr_run_view/mcqrqprocess.cpp
index b16271a388e66529c67c7ad1d491a56a87f3064f..0aac5233b7e869a53c31d7f63cc96ce3bc6ba32f 100644
--- a/src/gui/mcqr_run_view/mcqrqprocess.cpp
+++ b/src/gui/mcqr_run_view/mcqrqprocess.cpp
@@ -40,7 +40,7 @@ McqrQProcess::~McqrQProcess()
}
qint64
-McqrQProcess::write(const QString &mcqr_code)
+McqrQProcess::executeOnTheRecord(const QString &mcqr_code)
{
m_RscriptRun << mcqr_code;
return QProcess::write(mcqr_code.toUtf8());
@@ -52,10 +52,10 @@ McqrQProcess::getRScriptRun() const
return m_RscriptRun;
}
-void
+qint64
McqrQProcess::executeOffTheRecord(const QString &mcqr_otr)
{
- QProcess::write(mcqr_otr.toUtf8());
+ return QProcess::write(mcqr_otr.toUtf8());
}
@@ -64,12 +64,13 @@ McqrQProcess::executeMcqrStep(const QString &mcqr_step_name,
const QString &mcqr_step)
{
- write(QString("message(\"MCQRBegin: %1\")\n").arg(mcqr_step_name).toUtf8());
+ executeOnTheRecord(
+ QString("message(\"MCQRBegin: %1\")\n").arg(mcqr_step_name));
executeOffTheRecord("vl <- tryCatch({\n");
- write(mcqr_step.toUtf8());
+ executeOnTheRecord(mcqr_step);
- write(QString("message(\"MCQREnd: %1\")\n").arg(mcqr_step_name).toUtf8());
+ executeOnTheRecord(QString("message(\"MCQREnd: %1\")\n").arg(mcqr_step_name));
// write(mcqr_step.toUtf8());
executeOffTheRecord(
QString(
diff --git a/src/gui/mcqr_run_view/mcqrqprocess.h b/src/gui/mcqr_run_view/mcqrqprocess.h
index 9f3220716bce484b0f9aefeb5bad817058581b18..d4529722344ed10d7cd91638339a39604f810e8d 100644
--- a/src/gui/mcqr_run_view/mcqrqprocess.h
+++ b/src/gui/mcqr_run_view/mcqrqprocess.h
@@ -39,9 +39,8 @@ class McqrQProcess : public QProcess
McqrQProcess(QObject *parent = nullptr);
~McqrQProcess();
-
- qint64 write(const QString &mcqr_code);
- void executeOffTheRecord(const QString &mcqr_otr);
+ qint64 executeOnTheRecord(const QString &mcqr_code);
+ qint64 executeOffTheRecord(const QString &mcqr_otr);
void executeMcqrStep(const QString &mcqr_step_name, const QString &mcqr_step);
const QTextStream &getRScriptRun() const;
diff --git a/src/gui/mcqr_run_view/mcqrrunview.cpp b/src/gui/mcqr_run_view/mcqrrunview.cpp
index 823f099fc9b1759a7694fb83d69e0344ea530e2d..7bc47c86174aa36724b5cf36a4d274f343f1b8b2 100644
--- a/src/gui/mcqr_run_view/mcqrrunview.cpp
+++ b/src/gui/mcqr_run_view/mcqrrunview.cpp
@@ -140,7 +140,7 @@ McqrRunView::checkLibrariesInstalled()
Grantlee::Template rscript_template_sp =
engine_p->loadByName("mcqr_packages_handler.R");
Grantlee::Context empty_context;
- mp_rProcess->write(rscript_template_sp->render(&empty_context).toUtf8());
+ mp_rProcess->executeOnTheRecord(rscript_template_sp->render(&empty_context));
}
void
@@ -153,7 +153,7 @@ McqrRunView::endRProcess()
}
else
{
- mp_rProcess->write(QString("quit( save = \"no\")").toUtf8());
+ mp_rProcess->executeOffTheRecord(QString("quit( save = \"no\")"));
mp_rProcess->waitForFinished();
QProcess::ExitStatus Status = mp_rProcess->exitStatus();
qDebug() << Status;