diff --git a/src/files/tandemparametersfile.cpp b/src/files/tandemparametersfile.cpp
index 481bafb64b44b66c59ee2a6dc93c86ac412cf9f5..bf0711d9ee148706248b837b91ef52d906a0df6f 100644
--- a/src/files/tandemparametersfile.cpp
+++ b/src/files/tandemparametersfile.cpp
@@ -67,6 +67,10 @@ bool TandemParametersFile::exists() const
{
return _param_source.exists();
}
+void TandemParametersFile::setDirectory(const QDir & directory) {
+ QFileInfo new_dir(QString("%1/%2").arg(directory.absolutePath()).arg(_param_source.fileName()));
+ _param_source = new_dir;
+}
void TandemParametersFile::setTandemParameters(const TandemParameters & parameters) {
@@ -110,20 +114,21 @@ TandemParameters TandemParametersFile::getTandemParameters() const {
QXmlInputSource xmlInputSource(&qfile);
if (simplereader.parse(xmlInputSource)) {
-
+ qDebug() << "TandemParametersFile::getTandemParameters parse ok";
qfile.close();
+ delete parser;
} else {
+ qDebug() << "TandemParametersFile::getTandemParameters parse error";
qfile.close();
- delete parser;
throw pappso::PappsoException(QObject::tr("Error reading %1 X!Tandem preset file :\n %2").arg(_param_source.absoluteFilePath()).arg(parser->errorString()));
+ delete parser;
}
- delete parser;
return parameters;
}
-bool TandemParametersFile::isTandemPresetFile() {
+bool TandemParametersFile::isTandemPresetFile() const {
if (this->exists()) {
diff --git a/src/files/tandemparametersfile.h b/src/files/tandemparametersfile.h
index fda4836871353960710569449b5a7686b7fc224f..73dcd62116dd079941b47bd123f6800500759d66 100644
--- a/src/files/tandemparametersfile.h
+++ b/src/files/tandemparametersfile.h
@@ -61,6 +61,10 @@ public:
*/
void setTandemParameters(const TandemParameters & parameters);
+ /** @brief set param file directory
+ */
+ void setDirectory(const QDir & directory);
+
private :
void writeXmlParametersFile (QXmlStreamWriter * p_out, const TandemParameters & parameters) const;
diff --git a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
index 88f67be1eddbf978c411ffd70873e96e7571ffd5..cc7b41badd0cd3c25e50defdcea226eed7b75cc3 100644
--- a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
+++ b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
@@ -70,13 +70,15 @@ void EditTandemPresetDialog::setTandemParametersFile(const TandemParametersFile
if (tandem_preset_file.exists()) {
_p_tandem_preset_file = new TandemParametersFile( tandem_preset_file);
_preset_directory = _p_tandem_preset_file->getAbsoluteDir().absolutePath();
+ _tandem_params = _p_tandem_preset_file->getTandemParameters();
} else {
- _p_tandem_preset_file = new TandemParametersFile(":/tandem/ressources/model/QExactive_analysis_FDR_nosemi.xml");
-
+ _p_tandem_preset_file = new TandemParametersFile(":/tandem/resources/model/QExactive_analysis_FDR_nosemi.xml");
+ _tandem_params = _p_tandem_preset_file->getTandemParameters();
QSettings settings;
_preset_directory = settings.value("path/tandemrun_preset_directory", "").toString();
+ _p_tandem_preset_file->setDirectory(QDir(_preset_directory));
}
- _tandem_params = _p_tandem_preset_file->getTandemParameters();
+
fillPresetComboBox();
populate();
@@ -118,6 +120,7 @@ void EditTandemPresetDialog::doSave() {
if (_p_tandem_preset_file == nullptr) {
throw pappso::PappsoException(QObject::tr("_p_tandem_preset_file == nullptr"));
}
+ _p_tandem_preset_file->setDirectory(QDir(_preset_directory));
_p_tandem_preset_file->setTandemParameters(_tandem_params);
fillPresetComboBox();
populate();
@@ -126,17 +129,23 @@ void EditTandemPresetDialog::doSave() {
void EditTandemPresetDialog::doLoad() {
int index = ui->preset_combo_box->currentIndex();
if ( index != -1 ) { // -1 for not found
- if (_p_tandem_preset_file == nullptr) {
- throw pappso::PappsoException(QObject::tr("_p_tandem_preset_file == nullptr"));
+ TandemParametersFile * p_tandem_preset_file = new TandemParametersFile(
+ ui->preset_combo_box->itemData(index).value<QString>());
+ if (p_tandem_preset_file->isTandemPresetFile()) {
+ if (_p_tandem_preset_file == nullptr) {
+ throw pappso::PappsoException(QObject::tr("_p_tandem_preset_file == nullptr"));
+ }
+ else {
+ delete _p_tandem_preset_file;
+ }
+
+ _p_tandem_preset_file = p_tandem_preset_file;
+ _tandem_params = _p_tandem_preset_file->getTandemParameters();
+ populate();
}
else {
- delete _p_tandem_preset_file;
+ QMessageBox::warning(this,tr("Error :"), tr("%1 is not an X!Tandem parameter file").arg(p_tandem_preset_file->getAbsoluteFilePath()));
}
-
- _p_tandem_preset_file = new TandemParametersFile(
- ui->preset_combo_box->itemData(index).value<QString>());
- _tandem_params = _p_tandem_preset_file->getTandemParameters();
- populate();
}
}
const TandemParametersFile & EditTandemPresetDialog::getTandemParametersFile() const {
@@ -972,6 +981,11 @@ void EditTandemPresetDialog::done(int r)
if(QDialog::Accepted == r) // ok was pressed
{
readUi();
+ if (!_p_tandem_preset_file->exists()) {
+ QMessageBox::warning(this,
+ tr("Save parameters"), tr("Parameters file does not exists.\nPlease save it before pressing ok or cancel edition"));
+ return;
+ }
TandemParameters ref_params = _p_tandem_preset_file->getTandemParameters();
if(ref_params.equals(_tandem_params)) // validate the data somehow
{
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.cpp b/src/gui/tandem_run_dialog/tandemrundialog.cpp
index 7be7e716d14164a7fd0def04b09b6736a9451043..3b4bb303e97448ae1d7c93918f2ef5e97cc20dd0 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.cpp
+++ b/src/gui/tandem_run_dialog/tandemrundialog.cpp
@@ -104,7 +104,10 @@ void TandemRunDialog::fillPresetComboBox() {
filters << "*.xml";
preset_dir.setNameFilters(filters);
for (QFileInfo file_info: preset_dir.entryInfoList() ) {
- ui->preset_combobox->addItem(file_info.baseName(), QVariant(file_info.absoluteFilePath()));
+ TandemParametersFile param_file(file_info.absoluteFilePath());
+ if (param_file.isTandemPresetFile()) {
+ ui->preset_combobox->addItem(file_info.baseName(), QVariant(file_info.absoluteFilePath()));
+ }
}
int index = ui->preset_combobox->findText(default_preset_name);
if ( index != -1 ) { // -1 for not found
diff --git a/src/input/xtandemparamsaxhandler.cpp b/src/input/xtandemparamsaxhandler.cpp
index f68fbabce17faca23748727c04b91ac806336f58..06e44a24258b5f4e20dc39f545f6214bde652c53 100644
--- a/src/input/xtandemparamsaxhandler.cpp
+++ b/src/input/xtandemparamsaxhandler.cpp
@@ -29,6 +29,7 @@
#include "xtandemparamsaxhandler.h"
#include <pappsomspp/pappsoexception.h>
+#include <QDebug>
XtandemParamSaxHandler::XtandemParamSaxHandler(TandemParameters * p_tandem_parameters) {
@@ -51,6 +52,13 @@ bool XtandemParamSaxHandler::startElement(const QString & namespaceURI, const QS
bool is_ok = true;
try {
+ //<bioml label="example api document">
+ if (_tag_stack.size() == 1) {
+ if (qName != "bioml") {
+ _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::startElement root tag %1 is not <bioml>").arg(qName);
+ return false;
+ }
+ }
//startElement_group
if (qName == "note") {
@@ -102,7 +110,7 @@ bool XtandemParamSaxHandler::error(const QXmlParseException &exception) {
_errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
"%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
exception.message());
-
+ qDebug() << "XtandemParamSaxHandler::error " << _errorStr;
return false;
}
@@ -111,6 +119,7 @@ bool XtandemParamSaxHandler::fatalError(const QXmlParseException &exception) {
_errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
"%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
exception.message());
+ qDebug() << "XtandemParamSaxHandler::fatalError " << _errorStr;
return false;
}