From 057f78d86a9bc18934398dfe5aaf8a96a49e0db4 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Wed, 31 Oct 2018 17:16:33 +0100
Subject: [PATCH] WIP: check tandem.exe binary and version
---
.../tandem_run_dialog/tandem_run_dialog.ui | 71 ++++++++++---------
src/gui/tandem_run_dialog/tandemrundialog.cpp | 6 ++
src/utils/utils.cpp | 60 ++++++++++++++++
src/utils/utils.h | 1 +
4 files changed, 106 insertions(+), 32 deletions(-)
diff --git a/src/gui/tandem_run_dialog/tandem_run_dialog.ui b/src/gui/tandem_run_dialog/tandem_run_dialog.ui
index 336fae989..1f1639d9a 100644
--- a/src/gui/tandem_run_dialog/tandem_run_dialog.ui
+++ b/src/gui/tandem_run_dialog/tandem_run_dialog.ui
@@ -28,7 +28,45 @@
<property name="checked">
<bool>false</bool>
</property>
- <layout class="QHBoxLayout" name="horizontalLayout_6">
+ <layout class="QVBoxLayout" name="verticalLayout">
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_3">
+ <item>
+ <widget class="QLabel" name="tandem_bin_label">
+ <property name="text">
+ <string>TextLabel</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_4">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>528</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_4">
+ <property name="text">
+ <string>change</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <widget class="QLabel" name="tandem_version_label">
+ <property name="text">
+ <string>X!Tandem not found</string>
+ </property>
+ </widget>
+ </item>
<item>
<widget class="QWidget" name="exe_group_widget" native="true">
<layout class="QVBoxLayout" name="verticalLayout_3">
@@ -47,37 +85,6 @@
<property name="bottomMargin">
<number>0</number>
</property>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <item>
- <widget class="QLabel" name="tandem_bin_label">
- <property name="text">
- <string>TextLabel</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_4">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>528</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_4">
- <property name="text">
- <string>change</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
<item>
<widget class="QGroupBox" name="use_htcondor_groupbox">
<property name="title">
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.cpp b/src/gui/tandem_run_dialog/tandemrundialog.cpp
index fd78ee5f5..def39f97e 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.cpp
+++ b/src/gui/tandem_run_dialog/tandemrundialog.cpp
@@ -37,6 +37,7 @@
#include <QStandardPaths>
#include <pappsomspp/pappsoexception.h>
#include "../../files/tandemparametersfile.h"
+#include "../../utils/utils.h"
// Q_DECLARE_METATYPE(QFileInfo)
@@ -182,6 +183,11 @@ TandemRunDialog::reset()
QString tandem_bin_path =
settings.value("path/tandem_bin", "/usr/bin/tandem").toString();
+
+ ui->tandem_version_label->setText(
+ Utils::checkXtandemVersion(tandem_bin_path));
+
+
ui->output_directory_label->setText(default_output_location);
ui->tandem_bin_label->setText(tandem_bin_path);
diff --git a/src/utils/utils.cpp b/src/utils/utils.cpp
index 737282c2c..c236c399d 100644
--- a/src/utils/utils.cpp
+++ b/src/utils/utils.cpp
@@ -2,6 +2,8 @@
#include <pappsomspp/exception/exceptionnotfound.h>
#include <pappsomspp/mass_range.h>
#include <cmath>
+#include <QProcess>
+#include <QDebug>
const QUrl
Utils::getOlsUrl(QString psimod_accession)
@@ -239,3 +241,61 @@ Utils::translateAaModificationFromUnimod(const QString &unimod_accession)
<< unimod_accession << " not found";
return nullptr;
}
+
+
+const QString
+Utils::checkXtandemVersion(const QString &tandem_bin_path)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ QString version_return;
+ QStringList arguments;
+
+ arguments << "-v";
+
+ QProcess *xt_process = new QProcess();
+ // hk_process->setWorkingDirectory(QFileInfo(_hardklor_exe).absolutePath());
+
+ xt_process->start(tandem_bin_path, arguments);
+
+ if(!xt_process->waitForStarted())
+ {
+ throw pappso::PappsoException(
+ QObject::tr("X!Tandem process failed to start"));
+ }
+
+ while(xt_process->waitForReadyRead(1000))
+ {
+ }
+ /*
+ if (!xt_process->waitForFinished(_max_xt_time_ms)) {
+ throw pappso::PappsoException(QObject::tr("can't wait for X!Tandem process
+ to finish : timeout at %1").arg(_max_xt_time_ms));
+ }
+ */
+ QByteArray result = xt_process->readAll();
+
+
+ qDebug() << result.constData();
+
+ QRegExp parse_version("X! TANDEM ([A-Z]+) \\((.*)\\)");
+ // Pattern patt = Pattern.compile("X! TANDEM [A-Z]+ \\((.*)\\)",
+ // Pattern.CASE_INSENSITIVE);
+
+ if(parse_version.exactMatch(result.constData()))
+ {
+ version_return = parse_version.capturedTexts().join(" ");
+ }
+
+ QProcess::ExitStatus Status = xt_process->exitStatus();
+ delete xt_process;
+ if(Status != 0)
+ {
+ // != QProcess::NormalExit
+ throw pappso::PappsoException(
+ QObject::tr("error executing X!Tandem Status != 0 : %1 %2\n%3")
+ .arg(tandem_bin_path)
+ .arg(arguments.join(" ").arg(result.data())));
+ }
+ return version_return;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+}
diff --git a/src/utils/utils.h b/src/utils/utils.h
index 13de1f616..52ecc77f5 100644
--- a/src/utils/utils.h
+++ b/src/utils/utils.h
@@ -36,6 +36,7 @@ class Utils
static const QString getIdentificationEngineName(IdentificationEngine engine);
static const QString getDatabaseName(ExternalDatabase database);
static const QString getXmlDouble(pappso::pappso_double number);
+ static const QString checkXtandemVersion(const QString &tandem_bin_path);
static pappso::AaModificationP
guessAaModificationPbyMonoisotopicMassDelta(pappso::mz mass);
static pappso::AaModificationP
--
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