write tandem parameter file should be ok, overwriting number of threads

src/core/tandem_run/tandembatchprocess.cpp

@@ -32,6 +32,8 @@
 #include <pappsomspp/pappsoexception.h>
 #include <QFileInfo>
 #include <QDebug>
+#include <QTemporaryDir>
+#include "../../files/tandemparametersfile.h"
 
 TandemBatchProcess::TandemBatchProcess(MainWindow * p_main_window, WorkMonitorInterface * p_monitor, const TandemRunBatch & tandem_run_batch) {
     _p_main_window = p_main_window;
@@ -95,7 +97,20 @@ void TandemBatchProcess::prepareXmlDatabaseFile() {
 
 void TandemBatchProcess::run() {
     qDebug() << "TandemBatchProcess::run begin " << _tandem_run_batch._preset_file;
-    _preset_file = _tandem_run_batch._preset_file;
+    QTemporaryDir tmp_dir;
+    if (!tmp_dir.isValid()) {
+        // dir.path() returns the unique directory path
+        throw pappso::PappsoException(QObject::tr("problem creating temporary directory in %1\n").arg(tmp_dir.path()));
+    }
+    
+    TandemParametersFile orig_parameter_file(_tandem_run_batch._preset_file);
+    _preset_file = QString("%1/%2").arg(tmp_dir.path()).arg(orig_parameter_file.getFilename());
+    
+    TandemParametersFile new_parameter_file(_preset_file);
+    TandemParameters new_param = orig_parameter_file.getTandemParameters();
+    //  <note type="input" label="spectrum, threads">1</note>
+    new_param.setParamLabelValue("spectrum, threads",QString("%1").arg(_tandem_run_batch._number_of_threads));
+    new_parameter_file.setTandemParameters(new_param);
 
     prepareXmlDatabaseFile();
 

src/core/tandem_run/tandemcondorprocess.cpp

@@ -105,7 +105,7 @@ void TandemCondorProcess::run() {
     TandemParametersFile new_parameter_file(_preset_file);
     TandemParameters new_param = orig_parameter_file.getTandemParameters();
     //  <note type="input" label="spectrum, threads">1</note>
-    new_param.setParamLabel("spectrum, threads",QString("%1").arg(_tandem_run_batch._number_of_threads));
+    new_param.setParamLabelValue("spectrum, threads",QString("%1").arg(_tandem_run_batch._number_of_threads));
     new_parameter_file.setTandemParameters(new_param);
 
     prepareXmlDatabaseFile();

src/core/tandem_run/tandemparameters.cpp

@@ -28,6 +28,7 @@
 ******************************************************************************/
 
 #include "tandemparameters.h"
+#include <QDebug>
 
 TandemParameters::TandemParameters() {
 }
@@ -35,17 +36,33 @@ TandemParameters::~TandemParameters() {
 }
 
 TandemParameters::TandemParameters(const TandemParameters & other) {
+    qDebug() << "TandemParameters::TandemParameters copy begin";
     //_map_label_value = other._map_label_value;
     _method_name = other._method_name;
 
     QMap<QString, QString>::const_iterator i = other._map_label_value.constBegin();
     while (i != other._map_label_value.constEnd()) {
+        qDebug() << "TandemParameters::TandemParameters copy " << i.key() << " " << i.value();
         _map_label_value.insert(i.key(), i.value());
         i++; // added
     }
+    qDebug() << "TandemParameters::TandemParameters copy end";
 }
+const QString TandemParameters::getLabelCategory(const QString & value) const {
+    return value.split(", ").at(0);
+}
+
+void TandemParameters::setParamLabelValue(const QString & label, const QString & value) {
+    //list path
+    //<note type="input" label="list path, default parameters">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/QExactive_analysis_FDR_nosemi.xml</note>
+    //<note type="input" label="list path, taxonomy information">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/database.xml</note>
+    if (getLabelCategory(label) == "list path") {
+        return;
+    }
+    if (label == "spectrum, path") {
+        return;
+    }
 
-void TandemParameters::setParamLabel(const QString & label, const QString & value) {
     _map_label_value.insert(label, value);
 }
 void TandemParameters::setMethodName(const QString & method) {

src/core/tandem_run/tandemparameters.h

@@ -41,8 +41,10 @@ public:
     virtual ~TandemParameters();
 
     void setMethodName(const QString & method);
-    void setParamLabel(const QString & label, const QString & value);
+    void setParamLabelValue(const QString & label, const QString & value);
     const QMap<QString, QString> & getMapLabelValue() const;
+private:
+    const QString getLabelCategory(const QString & value) const;
 private:
     QString _method_name;
     QMap<QString, QString> _map_label_value;

src/gui/waiting_message_dialog/waitingmessagedialog.cpp

@@ -115,4 +115,7 @@ void WaitingMessageDialog::hideEvent( QHideEvent* event ) {
 void WaitingMessageDialog::showEvent( QShowEvent* event ) {
     QWidget::showEvent( event );
     _p_movie->start();
+    ui->stop_push_button->setChecked(false);
+    ui->stop_push_button->setVisible(false);
+    _asked_to_stop = false;
 }

src/input/xtandemparamsaxhandler.cpp

@@ -48,7 +48,7 @@ bool XtandemParamSaxHandler::startElement(const QString & namespaceURI, const QS
     try {
         //startElement_group
 
-        if (qName == "c") {
+        if (qName == "note") {
             is_ok = startElement_note(attributes);
         }
         _current_text.clear();
@@ -134,19 +134,22 @@ bool XtandemParamSaxHandler::characters(const QString &str) {
 }
 
 bool XtandemParamSaxHandler::startElement_note(QXmlAttributes attributes) {
-    // logger.debug("startElementgroup begin");
+    qDebug() << "XtandemParamSaxHandler::startElement_note begin " << attributes.value("type");
     _current_label = "";
 
     if (attributes.value("type") == "input") {
         _current_label = attributes.value("label");
     }
+    
+    qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " << _current_label;
     return true;
 
 }
 
 bool XtandemParamSaxHandler::endElement_note() {
+    qDebug() << "XtandemParamSaxHandler::endElement_note begin " << _current_label << " " << _current_text.simplified();
     if (!_current_label.isEmpty()) {
-        _p_tandem_parameters->setParamLabel( _current_label, _current_text.simplified());
+        _p_tandem_parameters->setParamLabelValue( _current_label, _current_text.simplified());
     }
     return true;
 }