Renne

src/gui/mcqr_run_view/mcqr_sds_widget/mcqrsdswidget.cpp

@@ -37,16 +37,6 @@
 
 #include "../mcqrrunview.h"
 
-McqrSdsWidget::McqrSdsWidget(QWidget* parent): McqrParamWidget(parent)
-{
-  qDebug() << "SDS";
-    qDebug() << parent->accessibleName() << "unused";
-  QLayout *layouty = new QVBoxLayout();
-  layouty->addWidget(new QLabel("Test"));
-  setLayout(layouty);
-}
-
-
 McqrSdsWidget::McqrSdsWidget(McqrRunView *mcqr_window,
                              QString rdata_path,
                              McqrExperiment *p_mcqr_experiment)
@@ -54,17 +44,14 @@ McqrSdsWidget::McqrSdsWidget(McqrRunView *mcqr_window,
     ui(new Ui::McqrSdsWidget)
 {
   qDebug() << "Open SDS parameters widget";
-  //   mp_mcqrView             = parent;
-  //   m_rdataPath             = rdata_path;
-  //   mp_mcqrExperimentLoaded = p_mcqr_experiment;
-
   ui->setupUi(this);
 
   mp_factorsModel     = new QStandardItemModel(ui->factors_list_view);
   mp_msrunRemoveModel = new QStandardItemModel(ui->msrun_listView);
 
-  //   disableFutureStepsInToolBox();
-  //   addFactorsToQMenu();
+  disableFutureStepsInToolBox();
+  addFactorsToQMenu();
+  initGrantleeEngine();
 }
 
 
@@ -86,7 +73,7 @@ void
 McqrSdsWidget::addFactorsToQMenu()
 {
   int i = 0;
-  for(QString factor : mp_mcqrExperimentLoaded->getmetadataColumns())
+  for(QString factor : getMcqrExperimentLoaded()->getmetadataColumns())
     {
       if(factor != "msrun" && factor != "msrunfile")
         {
@@ -108,7 +95,7 @@ McqrSdsWidget::initGrantleeEngine()
   loader->setTemplateDirs({":/templates/resources/templates/mcqr_scripts"});
   mp_grantleeEngine->addTemplateLoader(loader);
 
-  msp_rscriptTemplate = mp_grantleeEngine->loadByName("mcqr_sds_analysis_1.R");
+  msp_rscriptTemplate = mp_grantleeEngine->loadByName("mcqr_sds_analysis.R");
   if(!msp_rscriptTemplate->errorString().isEmpty())
     {
       throw pappso::PappsoException(
@@ -131,25 +118,27 @@ McqrSdsWidget::analyseQualityData()
         }
     }
 
-  Grantlee::Context context_p;
-  context_p.insert("mcqr_step", m_mcqrStep);
-  context_p.insert("rdata_path", m_rdataPath);
-  context_p.insert("rdata_folder", QFileInfo(m_rdataPath).dir().path());
-  context_p.insert("tmp_path", "/data/test_mcqr/output_svg/");
-  //   context_p.insert("factor_list", factors);
   QString factors_join;
   if(factors.size() != 0)
     {
       factors_join = "\"" + factors.join("\", \"") + "\"";
     }
+
+  Grantlee::Context context_p;
+  context_p.insert("mcqr_step", m_mcqrStep);
+  context_p.insert("rdata_path", getRDataPath());
+  context_p.insert("rdata_folder", QFileInfo(getRDataPath()).dir().path());
+  context_p.insert("tmp_path", "/data/test_mcqr/output_svg/");
+  //   context_p.insert("factor_list", factors);
   context_p.insert("factors_join", factors_join);
-  qDebug() << factors_join;
-  context_p.insert(
-    "msrun_reference",
-    mp_mcqrExperimentLoaded->getAlignmentGroupLinkedToExperiment()
-      ->getMsRunReference()
-      ->getXmlId());
-  mp_mcqrView->getRProcessRunning()->write(
+
+  context_p.insert("msrun_reference",
+                   getMcqrExperimentLoaded()
+                     ->getAlignmentGroupLinkedToExperiment()
+                     ->getMsRunReference()
+                     ->getXmlId());
+
+  getMcqrRunParentView()->getRProcessRunning()->write(
     msp_rscriptTemplate->render(&context_p).toUtf8());
 }
 
@@ -169,7 +158,7 @@ McqrSdsWidget::removeMsRunOutliers()
   Grantlee::Context context_p;
   context_p.insert("mcqr_step", m_mcqrStep);
   context_p.insert("msrun_to_remove", msrun_outliers.join("\", \""));
-  mp_mcqrView->getRProcessRunning()->write(
+  getMcqrRunParentView()->getRProcessRunning()->write(
     msp_rscriptTemplate->render(&context_p).toUtf8());
 }
 
@@ -192,7 +181,8 @@ void
 McqrSdsWidget::openMsrunOutliersTab()
 {
   int i = 0;
-  for(McqrMetadata *metadata : mp_mcqrExperimentLoaded->getmetadataInfoVector())
+  for(McqrMetadata *metadata :
+      getMcqrExperimentLoaded()->getmetadataInfoVector())
     {
       QStandardItem *new_item = new QStandardItem(metadata->m_msrunId);
       new_item->setCheckable(true);