From 296771b458f2c9c8d300d8497a8934b6a704f805 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Thu, 7 Sep 2017 21:29:41 +0200
Subject: [PATCH] new condor process class
---
src/CMakeLists.txt | 1 +
src/core/tandem_run/tandecondorprocess.cpp | 85 ++++++++++++++++++++++
src/core/tandem_run/tandecondorprocess.h | 44 +++++++++++
src/core/tandem_run/tandembatchprocess.cpp | 51 +++++++------
src/core/tandem_run/tandembatchprocess.h | 17 +++--
5 files changed, 167 insertions(+), 31 deletions(-)
create mode 100644 src/core/tandem_run/tandecondorprocess.cpp
create mode 100644 src/core/tandem_run/tandecondorprocess.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 3f2859b8..e2e6453e 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -58,6 +58,7 @@ SET(CPP_FILES
core/labeling/label.cpp
core/labeling/labelingmethod.cpp
core/tandem_run/tandembatchprocess.cpp
+ core/tandem_run/tandemcondorprocess.cpp
core/msrun.cpp
core/peptidematch.cpp
core/peptidextp.cpp
diff --git a/src/core/tandem_run/tandecondorprocess.cpp b/src/core/tandem_run/tandecondorprocess.cpp
new file mode 100644
index 00000000..2354a061
--- /dev/null
+++ b/src/core/tandem_run/tandecondorprocess.cpp
@@ -0,0 +1,85 @@
+/**
+ * \file /core/tandem_run/tandemcondorprocess.cpp
+ * \date 5/9/2017
+ * \author Olivier Langella
+ * \brief handles execution of a bunch of X!Tandem process throught condor job
+ */
+
+/*******************************************************************************
+* 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 "tandecondorprocess.h"
+
+TandeCondorProcess(WorkMonitorInterface * p_monitor, const TandemRunBatch & tandem_run_batch) : TandemBatchProcess(p_monitor, tandem_run_batch) {
+ /*
+ Universe = vanilla
+ notification = Error
+ Rank = Mips
+ request_memory= 50000
+ request_cpus = 1
+ Executable = /usr/bin/tandem
+ Log = /gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/submit_condor.log
+ Output = /gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/tandem.$(Process).out
+ Error = /gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/tandem.$(Process).error
+
+ Arguments = /gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/xtandem_param2054956555872858570.xml
+ Queue
+ */
+}
+
+void TandeCondorProcess::run() {
+ qDebug() << "TandeCondorProcess::run begin " << _tandem_run_batch._preset_file;
+ _preset_file = _tandem_run_batch._preset_file;
+
+ prepareXmlDatabaseFile();
+
+ std::vector<QTemporaryFile *> input_file_list;
+
+ int i=0;
+ _p_monitor->setProgressMaximumValue(_tandem_run_batch._mz_file_list.size());
+ for (QString mz_file : _tandem_run_batch._mz_file_list) {
+
+
+ QTemporaryFile * p_xml_input_file = new QTemporaryFile();
+
+ input_file_list.push_back(p_xml_input_file);
+ p_xml_input_file->setAutoRemove(false);
+ if (p_xml_input_file->open())
+ {
+ QXmlStreamWriter * p_out = new QXmlStreamWriter();
+ p_out->setDevice(p_xml_input_file);
+
+ writeXmlInputFile(p_out, mz_file);
+
+ p_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(p_xml_input_file->fileName()));
+ }
+ i++;
+ }
+ for (QTemporaryFile * p_xml_input_file: input_file_list) {
+ delete p_xml_input_file;
+ }
+ qDebug() << "TandeCondorProcess::run end" ;
+}
diff --git a/src/core/tandem_run/tandecondorprocess.h b/src/core/tandem_run/tandecondorprocess.h
new file mode 100644
index 00000000..57e85f6a
--- /dev/null
+++ b/src/core/tandem_run/tandecondorprocess.h
@@ -0,0 +1,44 @@
+/**
+ * \file /core/tandem_run/tandemcondorprocess.h
+ * \date 5/9/2017
+ * \author Olivier Langella
+ * \brief handles execution of a bunch of X!Tandem process throught condor job
+ */
+
+/*******************************************************************************
+* 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 TANDECONDORPROCESS_H
+#define TANDECONDORPROCESS_H
+
+#include "tandembatchprocess.h"
+
+class TandeCondorProcess: public TandemBatchProcess
+{
+public:
+ TandeCondorProcess(WorkMonitorInterface * p_monitor, const TandemRunBatch & tandem_run_batch);
+
+ virtual void run();
+
+};
+
+#endif // TANDECONDORPROCESS_H
diff --git a/src/core/tandem_run/tandembatchprocess.cpp b/src/core/tandem_run/tandembatchprocess.cpp
index b8532fce..b6ecc7ed 100644
--- a/src/core/tandem_run/tandembatchprocess.cpp
+++ b/src/core/tandem_run/tandembatchprocess.cpp
@@ -38,6 +38,32 @@ TandemBatchProcess::TandemBatchProcess(WorkMonitorInterface * p_monitor, const T
_p_monitor = p_monitor;
}
+void TandemBatchProcess::writeXmlDatabaseFile (QXmlStreamWriter * p_out) {
+ 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();
+}
+
void TandemBatchProcess::prepareXmlDatabaseFile() {
_xml_database_file.setAutoRemove(false);
@@ -45,30 +71,7 @@ void TandemBatchProcess::prepareXmlDatabaseFile() {
{
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();
+ writeXmlDatabaseFile(p_out);
_xml_database_file.close();
delete p_out;
} else
diff --git a/src/core/tandem_run/tandembatchprocess.h b/src/core/tandem_run/tandembatchprocess.h
index cdc6397e..cda9bdc9 100644
--- a/src/core/tandem_run/tandembatchprocess.h
+++ b/src/core/tandem_run/tandembatchprocess.h
@@ -39,19 +39,22 @@ class TandemBatchProcess
public:
TandemBatchProcess(WorkMonitorInterface * p_monitor, const TandemRunBatch & tandem_run_batch);
- void run();
+ virtual void run();
+protected:
+ void writeXmlDatabaseFile (QXmlStreamWriter * p_out);
+ void writeXmlInputFile (QXmlStreamWriter * p_out, const QString & mz_file);
+ void prepareXmlDatabaseFile();
private:
void runOne(const QString & mz_file);
- void prepareXmlDatabaseFile();
- void writeXmlInputFile (QXmlStreamWriter * p_out, const QString & mz_file);
-private:
+protected:
+ QString _preset_file;
TandemRunBatch _tandem_run_batch;
WorkMonitorInterface * _p_monitor;
- QString _preset_file;
- int _max_xt_time_ms = (60000 * 60 * 24); //1 day
-
QTemporaryFile _xml_database_file;
+
+private:
+ int _max_xt_time_ms = (60000 * 60 * 24); //1 day
};
#endif // TANDEMBATCHPROCESS_H
--
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