[ref] Made changes after review 3

.travis.yml

@@ -87,7 +87,7 @@ script:
 
         # export encoded update repository URL
         export UPDATE_REPO_URL_BASE64=`echo $UPDATE_REPO_URL | base64`
-        
+
         qmake CONFIG+=release CONFIG+=force_debug_info CONFIG+=separate_debug_info NOTESTS=yes
         make -j4;
       fi

src/core/libmaven/PeakGroup.cpp

@@ -1071,18 +1071,7 @@ void PeakGroup::setUserLabel(char label)
         // ignore invalid labels
         return;
     }
-    _predictionProbability = 0.0f;
-    _predictionInference.clear();
     _userLabel = label;
-
-    if (parent != nullptr && parent->tagString == C12_PARENT_LABEL) {
-        parent->setUserLabel(label);
-        return;
-    }
-
-    for (auto& child : _childIsotopes) {
-            child->setUserLabel(label);
-    }
 }
 
 void PeakGroup::setPredictedLabel(const ClassifiedLabel label,
@@ -1099,16 +1088,6 @@ void PeakGroup::setPredictedLabel(const ClassifiedLabel label,
         this->_userLabel = 'g';
     }
     _predictionProbability = probability;
-
-    if (parent != nullptr && parent->tagString == C12_PARENT_LABEL) {
-        parent->setPredictedLabel(label, probability);
-        return;
-    }
-    for (auto& child : _childIsotopes) {
-        if (child->_predictedLabel != label
-            && child->_predictionProbability != probability)
-            child->setPredictedLabel(label, probability);
-    }
 }
 
 void PeakGroup::setPredictionInference(const multimap<float, string>& inference)

src/core/libmaven/mavenparameters.cpp

@@ -315,6 +315,7 @@ void MavenParameters::copyFrom(const MavenParameters& mp)
     // which will not be created by a copy operation like this.
     samples = mp.samples;
 
+    classifyUsingPeakMl = mp.classifyUsingPeakMl;
     peakMlModelType = mp.peakMlModelType;
     badGroupUpperLimit = mp.badGroupUpperLimit;
     goodGroupLowerLimit = mp.goodGroupLowerLimit;

src/gui/mzroll/backgroundopsthread.cpp

@@ -152,24 +152,6 @@ void BackgroundOpsThread::qtSignalSlot(const string& progressText,
                            total_slices);
 }
 
-void BackgroundOpsThread::writeCSVRep(string setName)
-{
-    // int lastUniqueId = 0;
-    // for (auto&group : mavenParameters->allgroups)
-    //     group.setUniqueId(++lastUniqueId);
-
-    // for(auto&group : mavenParameters->allgroups)
-    //     for (auto& child : group.childIsotopes())
-    //         child->setUniqueId(++lastUniqueId);
-
-    if (mainwindow->mavenParameters->classifyUsingPeakMl) 
-        classifyGroups(mavenParameters->allgroups);
-
-    emitGroups();
-
-    Q_EMIT(updateProgressBar("Done", 1, 1));
-}
-
 void BackgroundOpsThread::align()
 {
     // these if-else statements will take care of all corner cases of
@@ -298,7 +280,12 @@ void BackgroundOpsThread::computePeaks()
         peakDetector->mavenParameters()->searchAdducts = hadSearchAdducts;
     }
 
-    writeCSVRep("slices");
+    if (mainwindow->mavenParameters->classifyUsingPeakMl) 
+        classifyGroups(mavenParameters->allgroups);
+
+    emitGroups();
+
+    Q_EMIT(updateProgressBar("Done", 1, 1));
 
     emit updateProgressBar("Status", 0, 100);
 }
@@ -322,7 +309,12 @@ void BackgroundOpsThread::findFeatures()
         peakDetector->mavenParameters()->searchAdducts = hadSearchAdducts;
     }
 
-    writeCSVRep("allSlices");
+    if (mainwindow->mavenParameters->classifyUsingPeakMl) 
+        classifyGroups(mavenParameters->allgroups);
+
+    emitGroups();
+
+    Q_EMIT(updateProgressBar("Done", 1, 1));
 
     emit updateProgressBar("Status", 0, 100);
 }
@@ -405,11 +397,11 @@ void BackgroundOpsThread::classifyGroups(vector<PeakGroup>& groups)
 #ifdef Q_OS_WIN
     auto mlBinary = tempDir + QDir::separator() + "moi.exe";
 #endif
-    QString mlModel;
+    QString ml_model;
     // Following code is commented out because for now we have only one model in
     // aws bucket. Once, we have more comments would be removed.  
-    // if(mainwindow->mavenParameters->peakMlModelType == "Global Model Elucidata"){
-        mlModel = tempDir + QDir::separator() + "model.pickle.dat";
+    // if(mainwindow->mavenParameters->peakml_modelType == "Global Model Elucidata"){
+        ml_model = tempDir + QDir::separator() + "model.pickle.dat";
     // }
     // else{
     //     return;
@@ -424,30 +416,41 @@ void BackgroundOpsThread::classifyGroups(vector<PeakGroup>& groups)
             return;
         }
     }
-    if (!QFile::exists(mlModel)) {
+    if (!QFile::exists(ml_model)) {
         bool downloadSuccess = downloadPeakMlFilesFromURL("model.pickle.dat");
         if(!downloadSuccess) {
             cerr << "Error: ML model not found at path: "
-                << mlModel.toStdString()
+                << ml_model.toStdString()
                 << endl;
             return;
         }
     }
 
     Q_EMIT(updateProgressBar("Preparing inputs for classification…", 0, 0));
 
-    QString peakAttributesFile = tempDir
+    QString peak_attributes_file = tempDir
                                  + QDir::separator()
                                  + "peak_ml_input.csv";
-    QString classificationOutputFile = tempDir
+    QString classification_output_file = tempDir
                                        + QDir::separator()
                                        + "peak_ml_output.csv";
 
-    CSVReports::writeDataForPeakMl(peakAttributesFile.toStdString(),
+    int startId = 1;
+    for (auto& group : groups) {
+        group.setGroupId(startId++);
+        for (auto& child : group.childIsotopes()) {
+            child->setGroupId(startId++);
+        }
+        for (auto& child : group.childAdducts()) {
+            child->setGroupId(startId++);
+        }
+    }
+
+    CSVReports::writeDataForPeakMl(peak_attributes_file.toStdString(),
                                    groups);
-    if (!QFile::exists(peakAttributesFile)) {
+    if (!QFile::exists(peak_attributes_file)) {
         cerr << "Error: peak attributes input file not found at path: "
-             << peakAttributesFile.toStdString()
+             << peak_attributes_file.toStdString()
              << endl;
         return;
     }
@@ -456,25 +459,25 @@ void BackgroundOpsThread::classifyGroups(vector<PeakGroup>& groups)
     QString maybeGood_group_limit = QString::fromStdString(
                                     mzUtils::float2string(mavenParameters->goodGroupLowerLimit, 1));
     QStringList mlArguments;
-    mlArguments << "--input_attributes_file" << peakAttributesFile
-                << "--output_moi_file" << classificationOutputFile
-                << "--model_path" << mlModel
+    mlArguments << "--input_attributes_file" << peak_attributes_file
+                << "--output_moi_file" << classification_output_file
+                << "--model_path" << ml_model
                 << "--bad_group_limit" << bad_group_limit
                 << "--maybeGood_group_limit" << maybeGood_group_limit;
     QProcess subProcess;
     subProcess.setWorkingDirectory(QFileInfo(mlBinary).path());
     subProcess.start(mlBinary, mlArguments);
     subProcess.waitForFinished(-1);
-    if (!QFile::exists(classificationOutputFile)) {
+    if (!QFile::exists(classification_output_file)) {
         qDebug() << "MOI stdout:" << subProcess.readAllStandardOutput();
         qDebug() << "MOI stderr:" << subProcess.readAllStandardError();
         cerr << "Error: peak classification output file not found at path: "
-             << peakAttributesFile.toStdString()
+             << peak_attributes_file.toStdString()
              << endl;
         return;
     }
 
-    QFile file(classificationOutputFile);
+    QFile file(classification_output_file);
     if (!file.open(QIODevice::ReadOnly | QIODevice::Text)) {
         cerr << "Error: failed to open classification output file" << endl;
         return;

src/gui/mzroll/backgroundopsthread.h

@@ -140,12 +140,6 @@ class BackgroundOpsThread : public QThread
     // perform PolyFit alignment just after peak detection (if true)
     bool _performPolyFitAlignment;
 
-    /**
-	 * [write CSV Report]
-	 * @param setName [name of the set]
-	 */
-	void writeCSVRep(string setName);
-
     /**
 	 * @brief Downloads binary and model from S3 bucket 
 	 * if the two files does not exist on user's pc. 

src/gui/mzroll/loginform.cpp

@@ -7,6 +7,7 @@
 #include "mainwindow.h"
 #include "pollyelmaveninterface.h"
 #include "pollyintegration.h"
+#include "peakdetectiondialog.h"
 #include "ui_loginform.h"
 
 
@@ -45,8 +46,14 @@ LoginForm::LoginForm(PollyElmavenInterfaceDialog* pollyelmaveninterfacedialog, b
                 ui->login_label->clear();
                 ui->pushButton->setEnabled(true);
             });
-    connect(this, SIGNAL(loginSuccessful()), _pollyelmaveninterfacedialog, SLOT(emitLoginReady()));
-    connect(this, SIGNAL(widgetClosed()), _pollyelmaveninterfacedialog, SLOT(loginFormClosed()));
+    connect(this, 
+            &LoginForm::loginSuccessful, 
+            _pollyelmaveninterfacedialog->getMainWindow()->peakDetectionDialog, 
+            &PeakDetectionDialog::loginSuccessful);
+    connect(this, 
+            &LoginForm::widgetClosed, 
+            _pollyelmaveninterfacedialog->getMainWindow()->peakDetectionDialog, 
+            &PeakDetectionDialog::unsuccessfulLogin);
 }
 
 LoginForm::~LoginForm()

src/gui/mzroll/pollyelmaveninterface.cpp

@@ -24,8 +24,6 @@ PollyElmavenInterfaceDialog::PollyElmavenInterfaceDialog(MainWindow* mw)
     qRegisterMetaType<PollyApp>("PollyApp");
     qRegisterMetaType<QMap<PollyApp, bool>>();
 
-    showPollyApps = true;
-
     auto configLocation = QStandardPaths::QStandardPaths::GenericConfigLocation;
     _writeableTempDir = QStandardPaths::writableLocation(configLocation)
                         + QDir::separator()
@@ -198,8 +196,6 @@ PollyElmavenInterfaceDialog::PollyElmavenInterfaceDialog(MainWindow* mw)
             &QTabWidget::currentChanged,
             this,
             &PollyElmavenInterfaceDialog::_changeMode);
-    connect(this, SIGNAL(loginResponse()), _mainwindow->peakDetectionDialog, SLOT(loginSuccessful()));
-    connect(this, SIGNAL(loginUnsuccessful()), _mainwindow->peakDetectionDialog, SLOT(unsuccessfulLogin()));
 }
 PollyElmavenInterfaceDialog::~PollyElmavenInterfaceDialog()
 {
@@ -435,15 +431,6 @@ void PollyElmavenInterfaceDialog::loginForPeakMl()
     } 
 }
 
-void PollyElmavenInterfaceDialog::emitLoginReady()
-{
-    emit loginResponse();
-}
-void PollyElmavenInterfaceDialog::loginFormClosed()
-{
-    emit loginUnsuccessful();
-}
-
 void PollyElmavenInterfaceDialog::initialSetup()
 {
     int nodeStatus = _pollyIntegration->checkNodeExecutable();
@@ -457,7 +444,7 @@ void PollyElmavenInterfaceDialog::initialSetup()
     int askForLogin = _pollyIntegration->askForLogin();
     if (askForLogin == 1) {
         try {
-            _callLoginForm(showPollyApps);
+            _callLoginForm();
         } catch (...) {
             QMessageBox msgBox(this);
             msgBox.setWindowModality(Qt::NonModal);
@@ -489,9 +476,9 @@ void PollyElmavenInterfaceDialog::showEPIError(QString errorMessage)
     QCoreApplication::processEvents();
 }
 
-void PollyElmavenInterfaceDialog::_callLoginForm(bool showPollyApp)
+void PollyElmavenInterfaceDialog::_callLoginForm(bool showPollyApps)
 {
-    _loginform = new LoginForm(this, showPollyApp);
+    _loginform = new LoginForm(this, showPollyApps);
     _loginform->setModal(true);
     _loginform->show();
 }
@@ -787,7 +774,7 @@ void PollyElmavenInterfaceDialog::_uploadDataToPolly()
     // redirect to login form if user credentials have not been saved
     int askForLogin = _pollyIntegration->askForLogin();
     if (askForLogin == 1) {
-        _callLoginForm(showPollyApps);
+        _callLoginForm();
         emit uploadFinished(false);
         return;
     }
@@ -1113,9 +1100,9 @@ QStringList PollyElmavenInterfaceDialog::_prepareFilesToUpload(QDir qdir,
                             + QDir::separator()
                             + datetimestamp
                             + "_Peaks_information_json_Elmaven_Polly.json";
-    peakTable->exportJsonToPolly(_writeableTempDir, jsonFilename, true);
 
     if (_selectedApp == PollyApp::PollyPhi) {
+        peakTable->exportJsonToPolly(_writeableTempDir, jsonFilename, true);
         QCoreApplication::processEvents();
         //Preparing the sample cohort file
         QString sampleCohortFileName = _writeableTempDir + QDir::separator() + datetimestamp +

src/gui/mzroll/pollyelmaveninterface.h

@@ -196,11 +196,6 @@ public Q_SLOTS:
 
     void showEPIError(QString errorMessage);
 
-    void emitLoginReady();
-
-    void loginFormClosed();
-
-
 Q_SIGNALS:
 
     /**
@@ -318,7 +313,7 @@ public Q_SLOTS:
     /**
      * @brief This function calls login form UI to take credentials from user.
      */
-    void _callLoginForm(bool showPollyApps);
+    void _callLoginForm(bool showPollyApps = true);
 
     /**
      * @brief This function calls initial login UI to connect to Polly and fetch

src/gui/mzroll/rangeSlider.h

@@ -1,6 +1,5 @@
 #ifndef RANGESLIDER_H
 #define RANGESLIDER_H
-#pragma once
 
 #include <QWidget>
 #include <QPainter>