new tandem batch process object

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

src/core/tandem_run/tandembatchprocess.cpp

+/**
+ * \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;
+}

src/core/tandem_run/tandembatchprocess.h

+/**
+ * \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

src/core/tandem_run/tandemrunbatch.cpp

 /**
- * \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

src/core/tandem_run/tandemrunbatch.h

 /**
- * \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

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);
     }
 }

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) {