execute condor batch process

src/core/tandem_run/tandembatchprocess.cpp

@@ -38,6 +38,8 @@ TandemBatchProcess::TandemBatchProcess(WorkMonitorInterface * p_monitor, const T
     _p_monitor = p_monitor;
 }
 
+TandemBatchProcess::~TandemBatchProcess() {
+}
 void TandemBatchProcess::writeXmlDatabaseFile (QXmlStreamWriter * p_out) {
     p_out->setAutoFormatting(true);
     p_out->writeStartDocument("1.0");
@@ -65,18 +67,19 @@ void TandemBatchProcess::writeXmlDatabaseFile (QXmlStreamWriter * p_out) {
 }
 
 void TandemBatchProcess::prepareXmlDatabaseFile() {
-    _xml_database_file.setAutoRemove(false);
+    _tmp_database_file.setAutoRemove(true);
 
-    if (_xml_database_file.open())
+    if (_tmp_database_file.open())
     {
+        _xml_database_file = QFileInfo( _tmp_database_file.fileName()).absoluteFilePath();
         QXmlStreamWriter * p_out = new QXmlStreamWriter();
-        p_out->setDevice(&_xml_database_file);
+        p_out->setDevice(&_tmp_database_file);
         writeXmlDatabaseFile(p_out);
-        _xml_database_file.close();
+        _tmp_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()));
+        throw pappso::PappsoException(QObject::tr("error : cannot open the XML database file : %1\n").arg(_tmp_database_file.fileName()));
     }
 
 }
@@ -127,7 +130,7 @@ void TandemBatchProcess::writeXmlInputFile (QXmlStreamWriter * p_out, const QStr
     p_out->writeStartElement("note");
     p_out->writeAttribute("type","input");
     p_out->writeAttribute("label","list path, taxonomy information");
-    p_out->writeCharacters(_xml_database_file.fileName());
+    p_out->writeCharacters(_xml_database_file);
     p_out->writeEndElement();
 
 

src/core/tandem_run/tandembatchprocess.h

@@ -38,12 +38,13 @@ class TandemBatchProcess
 {
 public:
     TandemBatchProcess(WorkMonitorInterface * p_monitor, const TandemRunBatch & tandem_run_batch);
+     virtual ~TandemBatchProcess();
 
     virtual void run();
 protected:
     void writeXmlDatabaseFile (QXmlStreamWriter * p_out);
     void writeXmlInputFile (QXmlStreamWriter * p_out, const QString & mz_file);
-    void prepareXmlDatabaseFile();
+    virtual void prepareXmlDatabaseFile();
 private:
     void runOne(const QString & mz_file);
 
@@ -51,10 +52,13 @@ protected:
     QString _preset_file;
     TandemRunBatch _tandem_run_batch;
     WorkMonitorInterface * _p_monitor;
-    QTemporaryFile _xml_database_file;
+    QString _xml_database_file;
+    int _max_xt_time_ms = (60000 * 60 * 24); //1 day
     
 private:
-    int _max_xt_time_ms = (60000 * 60 * 24); //1 day
+    
+    
+    QTemporaryFile _tmp_database_file;
 };
 
 #endif // TANDEMBATCHPROCESS_H

src/core/tandem_run/tandemcondorprocess.cpp

@@ -30,6 +30,8 @@
 #include "tandemcondorprocess.h"
 #include <QDebug>
 #include <pappsomspp/pappsoexception.h>
+#include <QSettings>
+#include <QProcess>
 
 TandemCondorProcess::TandemCondorProcess(WorkMonitorInterface * p_monitor, const TandemRunBatch & tandem_run_batch) : TandemBatchProcess(p_monitor, tandem_run_batch) {
     /*
@@ -46,14 +48,87 @@ TandemCondorProcess::TandemCondorProcess(WorkMonitorInterface * p_monitor, const
     Arguments = /gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/xtandem_param2054956555872858570.xml
     Queue
     */
+
+    QSettings settings;
+    QString condor_tmp_dir = QString("%1/xtpcpp").arg(settings.value("condor/tmp_dir", "/gorgone/pappso/temp").toString());
+    _p_tmp_dir = new QTemporaryDir(condor_tmp_dir);
+    _condor_submit_command = settings.value("condor/submit", "/usr/bin/condor_submit").toString();
+
+
+    if (!_p_tmp_dir->isValid()) {
+        // dir.path() returns the unique directory path
+        throw pappso::PappsoException(QObject::tr("problem creating condor temporary directory in %1\n").arg(condor_tmp_dir));
+    }
+
+
+}
+
+TandemCondorProcess::~TandemCondorProcess () {
+    delete _p_tmp_dir;
+}
+
+void TandemCondorProcess::prepareXmlDatabaseFile() {
+
+    QFile xml_database_file(QString("%1/database.xml").arg(_p_tmp_dir->path()));
+
+    if (xml_database_file.open(QIODevice::WriteOnly))
+    {
+        _xml_database_file = QFileInfo( xml_database_file.fileName()).absoluteFilePath();
+        QXmlStreamWriter * p_out = new QXmlStreamWriter();
+        p_out->setDevice(&xml_database_file);
+        writeXmlDatabaseFile(p_out);
+        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 TandemCondorProcess::run() {
-    qDebug() << "TandeCondorProcess::run begin " << _tandem_run_batch._preset_file;
+    qDebug() << "TandeCondorProcess::run begin ";
+    QFileInfo preset_info(_tandem_run_batch._preset_file);
+    _preset_file = QString("%1/%2").arg(_p_tmp_dir->path()).arg(preset_info.fileName());
+    QFile::copy(_tandem_run_batch._preset_file, _preset_file);
     _preset_file = _tandem_run_batch._preset_file;
 
     prepareXmlDatabaseFile();
 
+
+    //condor submit file :
+    QFile submit_file(QString("%1/submit.txt").arg(_p_tmp_dir->path()));
+    QTextStream * p_out = nullptr;
+
+    if (submit_file.open(QIODevice::WriteOnly))
+    {
+        p_out = new QTextStream();
+        p_out->setDevice(&submit_file);
+
+        *p_out <<     "Universe   = vanilla" << endl;
+        *p_out <<     "notification   = Error" << endl;
+        *p_out <<     "Rank       = Mips" << endl;
+        *p_out <<     "request_memory= 50000" << endl;
+        *p_out <<     "request_cpus = 1" << endl;
+        *p_out <<     "Executable = " << _tandem_run_batch._tandem_bin_path << endl;
+        *p_out <<     "Log        = \"" << _p_tmp_dir->path() << "/condor.log\"" << endl;
+        *p_out <<     "Output        = \"" << _p_tmp_dir->path() << "/tandem.$(Process).out\"" << endl;
+        *p_out <<     "Error        = \"" << _p_tmp_dir->path() << "/tandem.$(Process).error\"" << endl;
+        /*
+        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
+        */
+    } else
+    {
+        throw pappso::PappsoException(QObject::tr("error : cannot open condor submit file : %1\n").arg(submit_file.fileName()));
+    }
+
+
+
     std::vector<QTemporaryFile *> input_file_list;
 
     int i=0;
@@ -61,19 +136,23 @@ void TandemCondorProcess::run() {
     for (QString mz_file : _tandem_run_batch._mz_file_list) {
 
 
-        QTemporaryFile *  p_xml_input_file = new QTemporaryFile();
+        QTemporaryFile *  p_xml_input_file = new QTemporaryFile(_p_tmp_dir->path());
 
         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);
+            QXmlStreamWriter * p_xml_out = new QXmlStreamWriter();
+            p_xml_out->setDevice(p_xml_input_file);
 
-            writeXmlInputFile(p_out, mz_file);
+            writeXmlInputFile(p_xml_out, mz_file);
 
             p_xml_input_file->close();
-            delete p_out;
+            delete p_xml_out;
+
+
+            *p_out <<     "Arguments        = \"" << QFileInfo( p_xml_input_file->fileName()).absolutePath() << "\"" << endl;
+            *p_out <<     "Queue" << endl;
         } else
         {
             throw pappso::PappsoException(QObject::tr("error : cannot open the XML X!Tandem input file : %1\n").arg(p_xml_input_file->fileName()));
@@ -83,5 +162,50 @@ void TandemCondorProcess::run() {
     for (QTemporaryFile *  p_xml_input_file: input_file_list) {
         delete p_xml_input_file;
     }
+
+
+    if (p_out != nullptr) {
+        submit_file.close();
+        delete p_out;
+    }
+
+    
+    //now run condor job on submit_file
+    
+
+    QStringList arguments;
+
+    arguments << QFileInfo( submit_file.fileName()).absoluteFilePath();
+
+    QProcess * condor_process = new QProcess();
+    //hk_process->setWorkingDirectory(QFileInfo(_hardklor_exe).absolutePath());
+    condor_process->start(_condor_submit_command, arguments);
+
+
+    if (!condor_process->waitForStarted()) {
+        throw pappso::PappsoException(QObject::tr("HTCondor X!Tandem process failed to start"));
+    }
+
+    while(condor_process->waitForReadyRead(_max_xt_time_ms)) {
+        _p_monitor->appendText( condor_process->readAll().data());
+        //data.append(xt_process->readAll());
+    }
+    /*
+    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 = condor_process->readAll();
+
+    QProcess::ExitStatus Status = condor_process->exitStatus();
+
+    if (Status != 0)
+    {
+        // != QProcess::NormalExit
+        throw pappso::PappsoException(QObject::tr("error executing HTCondor Status != 0 : %1 %2\n%3").arg(_tandem_run_batch._tandem_bin_path).arg(arguments.join(" ").arg(result.data())));
+    }
+
+    delete condor_process;
+    
     qDebug() << "TandeCondorProcess::run end" ;
 }

src/core/tandem_run/tandemcondorprocess.h

@@ -31,13 +31,19 @@
 #define TANDEMCONDORPROCESS_H
 
 #include "tandembatchprocess.h"
+#include <QTemporaryDir>
 
 class TandemCondorProcess: public TandemBatchProcess
 {
 public:
     TandemCondorProcess(WorkMonitorInterface * p_monitor, const TandemRunBatch & tandem_run_batch);
+    virtual ~TandemCondorProcess();
 
+    virtual void prepareXmlDatabaseFile();
     virtual void run();
+private:
+    QTemporaryDir * _p_tmp_dir;
+    QString _condor_submit_command;
 
 };