diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 49be32736a59116c60bea9e0a4a712e63d967e97..3f2859b87a1bb24a6f1aedbe796f695306575a62 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -57,10 +57,11 @@ SET(CPP_FILES
core/identification_sources/identificationxtandemfile.cpp
core/labeling/label.cpp
core/labeling/labelingmethod.cpp
+ core/tandem_run/tandembatchprocess.cpp
core/msrun.cpp
core/peptidematch.cpp
core/peptidextp.cpp
- ./core/project.cpp
+ core/project.cpp
core/proteinmatch.cpp
core/proteinxtp.cpp
core/sequencedatabase.cpp
diff --git a/src/core/tandem_run/tandembatchprocess.cpp b/src/core/tandem_run/tandembatchprocess.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..20c2d4b331260b7ad70c43dec610830f492f6d43
--- /dev/null
+++ b/src/core/tandem_run/tandembatchprocess.cpp
@@ -0,0 +1,207 @@
+/**
+ * \file /core/tandem_run/tandembatchprocess.cpp
+ * \date 5/9/2017
+ * \author Olivier Langella
+ * \brief handles execution of a bunch of X!Tandem process
+ */
+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#include "tandembatchprocess.h"
+#include <QProcess>
+#include <pappsomspp/pappsoexception.h>
+#include <QXmlStreamWriter>
+#include <QFileInfo>
+
+TandemBatchProcess::TandemBatchProcess(WorkMonitorInterface * p_monitor, const TandemRunBatch & tandem_run_batch) {
+ _tandem_run_batch = tandem_run_batch;
+}
+
+void TandemBatchProcess::prepareXmlDatabaseFile() {
+ _xml_database_file.setAutoRemove(false);
+
+ if (_xml_database_file.open())
+ {
+ QXmlStreamWriter * p_out = new QXmlStreamWriter();
+ p_out->setDevice(&_xml_database_file);
+
+ p_out->setAutoFormatting(true);
+ p_out->writeStartDocument("1.0");
+
+ //<?xml version="1.0" encoding="UTF-8"?>
+ //<bioml label="x! taxon-to-file matching list">
+ p_out->writeStartElement("bioml");
+ p_out->writeAttribute("label","x! taxon-to-file matching list");
+ //<taxon label="usedefined">
+ p_out->writeStartElement("taxon");
+ p_out->writeAttribute("label","usedefined");
+ //<file format="peptide" URL="/gorgone/pappso/jouy/users/Didier/fasta/20170608_Delastours/contaminants_standards.fasta"></file>
+ //<file format="peptide" URL="/gorgone/pappso/jouy/users/Didier/fasta/20170608_Delastours/Escherichia coli 27J42_WGS_ECOLI_1.fasta"></file>
+ for (QString fasta_file:_tandem_run_batch._fasta_file_list) {
+ p_out->writeStartElement("file");
+ p_out->writeAttribute("format","peptide");
+ p_out->writeAttribute("URL",fasta_file);
+ p_out->writeEndElement();
+ }
+ //</taxon>
+ p_out->writeEndElement();
+ //</bioml>
+ p_out->writeEndElement();
+ p_out->writeEndDocument();
+ _xml_database_file.close();
+ delete p_out;
+ } else
+ {
+ throw pappso::PappsoException(QObject::tr("error : cannot open the XML database file : %1\n").arg(_xml_database_file.fileName()));
+ }
+
+}
+
+
+void TandemBatchProcess::run() {
+ _preset_file = _tandem_run_batch._preset_file;
+
+ prepareXmlDatabaseFile();
+
+ for (QString mz_file : _tandem_run_batch._mz_file_list) {
+ runOne(mz_file);
+ }
+}
+
+void TandemBatchProcess::writeXmlInputFile (QXmlStreamWriter * p_out, const QString & mz_file) {
+
+ QFileInfo mz_file_info(mz_file);
+ //<?xml version="1.0" encoding="UTF-8"?>
+
+ p_out->setAutoFormatting(true);
+ p_out->writeStartDocument("1.0");
+
+ //<bioml label="20170405_Delastour_11.xml">
+ p_out->writeStartElement("bioml");
+ p_out->writeAttribute("label",mz_file_info.getFilename());
+
+ //<note type="heading">Paths</note>
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type","heading");
+ p_out->writeCharacters("Paths");
+ p_out->writeEndElement();
+
+ //<note type="input" label="list path, default parameters">/gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/QExactive_IAM_4CPU_Classic_ClassicAvecReversed..xml</note>
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type","input");
+ p_out->writeAttribute("label","list path, default parameters");
+ p_out->writeCharacters(_preset_file);
+ p_out->writeEndElement();
+
+ //<note type="input" label="list path, taxonomy information">/gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/database.xml</note>
+ 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->writeEndElement();
+
+
+ //<note type="input" label="spectrum, path">/gorgone/pappso/jouy/raw/2017_Qex/20170405_Delastours/20170405_Delastour_11.mzXML</note>
+
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type","input");
+ p_out->writeAttribute("label","spectrum, path");
+ p_out->writeCharacters(mz_file);
+ p_out->writeEndElement();
+
+ //<note type="heading">Protein general</note>
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type","heading");
+ p_out->writeCharacters("Protein general");
+ p_out->writeEndElement();
+
+ //<note type="input" label="protein, taxon">usedefined</note>
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type","input");
+ p_out->writeAttribute("label","protein, taxon");
+ p_out->writeCharacters("usedefined");
+ p_out->writeEndElement();
+ //<note type="heading">Output</note>
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type","heading");
+ p_out->writeCharacters("Output");
+ 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->writeEndElement();
+
+ //</bioml>
+ p_out->writeEndElement();
+
+
+ p_out->writeEndDocument();
+}
+
+void TandemBatchProcess::runOne(const QString & mz_file) {
+ QTemporaryFile xml_input_file;
+ if (xml_input_file.open())
+ {
+ QXmlStreamWriter * p_out = new QXmlStreamWriter();
+ p_out->setDevice(&xml_input_file);
+
+ writeXmlInputFile(p_out, mz_file);
+
+ xml_input_file.close();
+ delete p_out;
+ } else
+ {
+ throw pappso::PappsoException(QObject::tr("error : cannot open the XML X!Tandem input file : %1\n").arg(xml_input_file.fileName()));
+ }
+
+
+ QStringList arguments;
+
+ arguments << xml_input_file.fileName();
+
+ QProcess * xt_process = new QProcess();
+ //hk_process->setWorkingDirectory(QFileInfo(_hardklor_exe).absolutePath());
+ xt_process->start(_tandem_run_batch._tandem_bin_path, arguments);
+
+
+ if (!xt_process->waitForStarted()) {
+ throw pappso::PappsoException(QObject::tr("X!Tandem process failed to start"));
+ }
+ 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();
+
+ QProcess::ExitStatus Status = xt_process->exitStatus();
+
+ 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())));
+ }
+
+ delete xt_process;
+}
diff --git a/src/core/tandem_run/tandembatchprocess.h b/src/core/tandem_run/tandembatchprocess.h
new file mode 100644
index 0000000000000000000000000000000000000000..9e1dbdbc324c622a955df15758814923abaa9e52
--- /dev/null
+++ b/src/core/tandem_run/tandembatchprocess.h
@@ -0,0 +1,56 @@
+/**
+ * \file /core/tandem_run/tandembatchprocess.h
+ * \date 5/9/2017
+ * \author Olivier Langella
+ * \brief handles execution of a bunch of X!Tandem process
+ */
+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#ifndef TANDEMBATCHPROCESS_H
+#define TANDEMBATCHPROCESS_H
+#include "tandemrunbatch.h"
+#include "../../utils/workmonitor.h"
+#include <QTemporaryFile>
+
+class TandemBatchProcess
+{
+public:
+ TandemBatchProcess(WorkMonitorInterface * p_monitor, const TandemRunBatch & tandem_run_batch);
+
+ void run();
+private:
+ void runOne(const QString & mz_file);
+ void prepareXmlDatabaseFile();
+ void writeXmlInputFile (QXmlStreamWriter * p_out, const QString & mz_file);
+
+private:
+ TandemRunBatch _tandem_run_batch;
+ WorkMonitorInterface * _p_monitor;
+ QString _preset_file;
+ int _max_xt_time_ms = (60000 * 60 * 24); //1 day
+
+ QTemporaryFile _xml_database_file;
+};
+
+#endif // TANDEMBATCHPROCESS_H
diff --git a/src/core/tandem_run/tandemrunbatch.cpp b/src/core/tandem_run/tandemrunbatch.cpp
index c617687bf1477ee85538318883736de981da6fbc..64a06a41a6e405fa8e5d0bd131ccf551f26181f7 100644
--- a/src/core/tandem_run/tandemrunbatch.cpp
+++ b/src/core/tandem_run/tandemrunbatch.cpp
@@ -1,5 +1,5 @@
/**
- * \file /core/tandem_run/tandem_run_batch.cpp
+ * \file /core/tandem_run/tandemrunbatch.cpp
* \date 2/9/2017
* \author Olivier Langella
* \brief all data needed to run a Tandem batch
diff --git a/src/core/tandem_run/tandemrunbatch.h b/src/core/tandem_run/tandemrunbatch.h
index 5e254a3a8a2fd325fdd95706fd3cb29780cc52c5..85ca526ac0b452deb04b256a67c658d46d6d5ce6 100644
--- a/src/core/tandem_run/tandemrunbatch.h
+++ b/src/core/tandem_run/tandemrunbatch.h
@@ -1,5 +1,5 @@
/**
- * \file /core/tandem_run/tandem_run_batch.h
+ * \file /core/tandem_run/tandemrunbatch.h
* \date 2/9/2017
* \author Olivier Langella
* \brief all data needed to run a Tandem batch
diff --git a/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp b/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
index ab9113d22f52bb8c70013b2e6e0022e94f7383b4..423e2a1cb31fe3f3a1079b7ace3f5bd16d48fa96 100644
--- a/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
+++ b/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
@@ -77,5 +77,6 @@ void IdentificationGroupWidget::doIdentificationGroupGrouped(IdentificationGroup
ui->group_number_display->setText(QString("%1").arg(_p_identification_group->countGroup()));
ui->subgroup_number_display->setText(QString("%1").arg(_p_identification_group->countSubGroup()));
ui->protein_number_display->setText(QString("%1").arg(_p_identification_group->countProteinMatch(ValidationState::grouped)));
+ _p_identification_group->countPeptideMatch(ValidationState::grouped);
}
}
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index ed1fea68307e391742fe4dccf7f4292a42b7f6db..39889c4c0170209c050acb1d29b6ddb5a92773c4 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -37,6 +37,7 @@
#include "files/xpipfile.h"
#include "mainwindow.h"
#include "project_view/projectwindow.h"
+#include "../core/tandem_run/tandembatchprocess.h"
WorkerThread::WorkerThread(MainWindow * p_main_window)
{
@@ -294,6 +295,9 @@ 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);
+
emit operationFinished();
}
catch (pappso::PappsoException & error) {