From 3243071d5cd374ee9c7a7f73e583a48c5d552568 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Tue, 5 Sep 2017 21:05:53 +0200
Subject: [PATCH] first X\!Tandem run ok
---
src/core/tandem_run/tandembatchprocess.cpp | 14 +++++++++-----
src/core/tandem_run/tandembatchprocess.h | 1 +
src/gui/tandem_run_dialog/tandemrundialog.cpp | 2 +-
src/gui/workerthread.cpp | 5 +++--
4 files changed, 14 insertions(+), 8 deletions(-)
diff --git a/src/core/tandem_run/tandembatchprocess.cpp b/src/core/tandem_run/tandembatchprocess.cpp
index 20c2d4b3..50005afa 100644
--- a/src/core/tandem_run/tandembatchprocess.cpp
+++ b/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;
diff --git a/src/core/tandem_run/tandembatchprocess.h b/src/core/tandem_run/tandembatchprocess.h
index 9e1dbdbc..cdc6397e 100644
--- a/src/core/tandem_run/tandembatchprocess.h
+++ b/src/core/tandem_run/tandembatchprocess.h
@@ -32,6 +32,7 @@
#include "tandemrunbatch.h"
#include "../../utils/workmonitor.h"
#include <QTemporaryFile>
+#include <QXmlStreamWriter>
class TandemBatchProcess
{
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.cpp b/src/gui/tandem_run_dialog/tandemrundialog.cpp
index 9d40f8e8..e3a2ebf8 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.cpp
+++ b/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;
}
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index 39889c4c..4958d4c2 100644
--- a/src/gui/workerthread.cpp
+++ b/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) {
--
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