first X\!Tandem run ok

src/core/tandem_run/tandembatchprocess.cpp

@@ -30,8 +30,8 @@
 #include "tandembatchprocess.h"
 #include <QProcess>
 #include <pappsomspp/pappsoexception.h>
-#include <QXmlStreamWriter>
 #include <QFileInfo>
+#include <QDebug>
 
 TandemBatchProcess::TandemBatchProcess(WorkMonitorInterface * p_monitor, const TandemRunBatch & tandem_run_batch) {
     _tandem_run_batch = tandem_run_batch;
@@ -79,6 +79,7 @@ void TandemBatchProcess::prepareXmlDatabaseFile() {
 
 
 void TandemBatchProcess::run() {
+    qDebug() << "TandemBatchProcess::run begin " << _tandem_run_batch._preset_file;
     _preset_file = _tandem_run_batch._preset_file;
 
     prepareXmlDatabaseFile();
@@ -86,6 +87,7 @@ void TandemBatchProcess::run() {
     for (QString mz_file : _tandem_run_batch._mz_file_list) {
         runOne(mz_file);
     }
+    qDebug() << "TandemBatchProcess::run end" ;
 }
 
 void TandemBatchProcess::writeXmlInputFile (QXmlStreamWriter * p_out, const QString & mz_file) {
@@ -98,7 +100,7 @@ void TandemBatchProcess::writeXmlInputFile (QXmlStreamWriter * p_out, const QStr
 
     //<bioml label="20170405_Delastour_11.xml">
     p_out->writeStartElement("bioml");
-    p_out->writeAttribute("label",mz_file_info.getFilename());
+    p_out->writeAttribute("label",mz_file_info.fileName());
 
     //<note type="heading">Paths</note>
     p_out->writeStartElement("note");
@@ -117,7 +119,7 @@ void TandemBatchProcess::writeXmlInputFile (QXmlStreamWriter * p_out, const QStr
     p_out->writeStartElement("note");
     p_out->writeAttribute("type","input");
     p_out->writeAttribute("label","list path, taxonomy information");
-    p_out->writeCharacters(_xml_database_file.getFilename());
+    p_out->writeCharacters(_xml_database_file.fileName());
     p_out->writeEndElement();
 
 
@@ -148,10 +150,11 @@ void TandemBatchProcess::writeXmlInputFile (QXmlStreamWriter * p_out, const QStr
     p_out->writeEndElement();
 
     //<note type="input" label="output, path">/gorgone/pappso/jouy/users/Didier/Xcal2017/2017_05_04_Delastours/Interrogation_souches_sequencees/Patient27/J42/20170405_Delastour_11.xml</note>
+    
     p_out->writeStartElement("note");
     p_out->writeAttribute("type","input");
     p_out->writeAttribute("label","output, path");
-    p_out->writeCharacters("usedefined");
+    p_out->writeCharacters(QString("%1/%2.xml").arg(_tandem_run_batch._output_directory).arg(mz_file_info.baseName()));
     p_out->writeEndElement();
 
     //</bioml>
@@ -163,6 +166,7 @@ void TandemBatchProcess::writeXmlInputFile (QXmlStreamWriter * p_out, const QStr
 
 void TandemBatchProcess::runOne(const QString & mz_file) {
     QTemporaryFile xml_input_file;
+    xml_input_file.setAutoRemove(false);
     if (xml_input_file.open())
     {
         QXmlStreamWriter * p_out = new QXmlStreamWriter();
@@ -200,7 +204,7 @@ void TandemBatchProcess::runOne(const QString & mz_file) {
     if (Status != 0)
     {
         // != QProcess::NormalExit
-        throw pappso::PappsoException(QObject::tr("error executing X!Tandem Status != 0 : %1 %2\n%3").arg(_tandem_run_batch._tandem_bin_path).arg(arguments.join(" ").arg(result.toStdString().c_str())));
+        throw pappso::PappsoException(QObject::tr("error executing X!Tandem Status != 0 : %1 %2\n%3").arg(_tandem_run_batch._tandem_bin_path).arg(arguments.join(" ").arg(result.data())));
     }
 
     delete xt_process;

src/core/tandem_run/tandembatchprocess.h

@@ -32,6 +32,7 @@
 #include "tandemrunbatch.h"
 #include "../../utils/workmonitor.h"
 #include <QTemporaryFile>
+#include <QXmlStreamWriter>
 
 class TandemBatchProcess
 {

src/gui/tandem_run_dialog/tandemrundialog.cpp

@@ -198,7 +198,7 @@ TandemRunBatch TandemRunDialog::getTandemRunBatch() const {
     tandem_run_batch._mz_file_list = _p_mz_file_list->stringList();
     tandem_run_batch._fasta_file_list = _p_fasta_file_list->stringList();
     //tandem_run_batch._preset_file = ui->preset_combobox->itemData(ui->preset_combobox->currentIndex()).value<QFileInfo>().absoluteFilePath();
-    tandem_run_batch._preset_file = ui->preset_combobox->itemData(ui->preset_combobox->currentIndex()).value<QFileInfo>().absoluteFilePath();
+    tandem_run_batch._preset_file = ui->preset_combobox->itemData(ui->preset_combobox->currentIndex()).value<QString>();
     tandem_run_batch._output_directory = ui->output_directory_label->text();
     return tandem_run_batch;
 }

src/gui/workerthread.cpp

@@ -295,9 +295,10 @@ void WorkerThread::doRunningXtandem(TandemRunBatch tandem_run_batch) {
     try {
         emit loadingMessage(tr("Running X!Tandem, please wait"));
         qDebug() <<  "WorkerThread::doRunningXtandem tandem_run_batch " << tandem_run_batch._tandem_bin_path;
-        
+
         TandemBatchProcess xt_process (_p_work_monitor, tandem_run_batch);
-        
+        xt_process.run();
+
         emit operationFinished();
     }
     catch (pappso::PappsoException & error) {