diff --git a/src/core/tandem_run/tandemcondorprocess.cpp b/src/core/tandem_run/tandemcondorprocess.cpp
index 6bb30821a9e6a76d165e30b68069f00b34ccc205..adb6bebc101ef17ae9d01b106fc97f2a678d9989 100644
--- a/src/core/tandem_run/tandemcondorprocess.cpp
+++ b/src/core/tandem_run/tandemcondorprocess.cpp
@@ -73,6 +73,9 @@ TandemCondorProcess::TandemCondorProcess(MainWindow * p_main_window, WorkMonitor
TandemCondorProcess::~TandemCondorProcess () {
delete _p_tmp_dir;
}
+unsigned int TandemCondorProcess::getCondorJobSize() const {
+ return _condor_job_size;
+}
void TandemCondorProcess::prepareXmlDatabaseFile() {
@@ -386,3 +389,11 @@ void TandemCondorProcess::parseCondorJobNumber(QString condor_job) {
}
}
+
+void TandemCondorProcess::setCondorJobStatus(std::int8_t count_status[10]) {
+
+ QString status_message = QString("%1 unexpanded jobs\n%2 idle jobs\n%3 running jobs\n%4 removed jobs\n%5 completed jobs\n%6 held jobs\n%7 submission errors").arg(count_status[0]).arg(count_status[1]).arg(count_status[2]).arg(count_status[3]).arg(count_status[4]).arg(count_status[5]).arg(count_status[6]);
+
+ _p_monitor->setText(status_message);
+
+}
diff --git a/src/core/tandem_run/tandemcondorprocess.h b/src/core/tandem_run/tandemcondorprocess.h
index 499548c38fcb805ecf25728d3d2383f88c14608f..666282010f8b37c6ef5a290efca71a77a5ab91e0 100644
--- a/src/core/tandem_run/tandemcondorprocess.h
+++ b/src/core/tandem_run/tandemcondorprocess.h
@@ -41,6 +41,10 @@ public:
virtual void prepareXmlDatabaseFile();
virtual void run();
+
+ unsigned int getCondorJobSize() const;
+ void setCondorJobStatus(std::int8_t count_status[10]);
+
private :
void parseCondorJobNumber(QString condor_job);
void surveyCondorJob();
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 4ca131035d1fb5dd092fed968101be1d15f25e41..224713ac3ebd694468ae8df53a4def31c14a0885 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -138,6 +138,9 @@ void MainWindow::doDisplayLoadingMessagePercent(QString message, int value) {
ui->statusbar->showMessage(message);
}
+void MainWindow::doWorkerSetText(QString text) {
+ _p_waiting_message_dialog->setText(text);
+}
void MainWindow::doWorkerAppendText(char * text) {
_p_waiting_message_dialog->appendText(text);
}
diff --git a/src/gui/mainwindow.h b/src/gui/mainwindow.h
index 345901cea5b518f89d05f3b1092aac46c1018321..b1e56cefc345f039e579cd296945052393f00df6 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -76,6 +76,7 @@ public slots:
void doDisplayLoadingMessage(QString message);
void doDisplayLoadingMessagePercent(QString message, int value);
void doWorkerAppendText(char *);
+ void doWorkerSetText(QString);
void doProjectReady(ProjectSp project_sp);
void doProjectNotReady(QString error);
void doAcceptedLoadResultDialog();
diff --git a/src/gui/waiting_message_dialog/waitingmessagedialog.cpp b/src/gui/waiting_message_dialog/waitingmessagedialog.cpp
index 298f9e0bba20c6a2d55833f4d2943248758f77a7..881b8547fd8409421839cdc4a719bdcce398c569 100644
--- a/src/gui/waiting_message_dialog/waitingmessagedialog.cpp
+++ b/src/gui/waiting_message_dialog/waitingmessagedialog.cpp
@@ -100,6 +100,12 @@ void WaitingMessageDialog::appendText(char * text) {
ui->console_plaintextedit->insertPlainText (text);
}
+void WaitingMessageDialog::setText(const QString text) {
+ ui->console_plaintextedit->setHidden(false);
+ //ui->console_plaintextedit->appendText(text);
+ ui->console_plaintextedit->setPlainText(text);
+}
+
void WaitingMessageDialog::hideEvent( QHideEvent* event ) {
QWidget::hideEvent( event );
qDebug() << "WaitingMessageDialog::hideEvent";
diff --git a/src/gui/waiting_message_dialog/waitingmessagedialog.h b/src/gui/waiting_message_dialog/waitingmessagedialog.h
index 4713f06015d6860205e5b5c82387b7ffb1370f02..9c9fc3e56bfcba2b262fac3cd5031af17ebb322a 100644
--- a/src/gui/waiting_message_dialog/waitingmessagedialog.h
+++ b/src/gui/waiting_message_dialog/waitingmessagedialog.h
@@ -47,6 +47,7 @@ public:
void message(const QString & message);
void message(const QString & message, int progress_value);
void appendText(char * text);
+ void setText(const QString text);
void showEvent( QShowEvent* event );
void hideEvent( QHideEvent* event );
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index f1a5e822996979ad31b82f6266984bc315830124..4588035be4ba0ef7979ee404de57d1dc9aac73d8 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -54,6 +54,7 @@ WorkerThread::WorkerThread(MainWindow * p_main_window)
connect(_p_work_monitor, &WorkMonitor::workerMessage, p_main_window,&MainWindow::doDisplayLoadingMessage);
connect(_p_work_monitor, &WorkMonitor::workerMessagePercent, p_main_window,&MainWindow::doDisplayLoadingMessagePercent);
connect(_p_work_monitor, &WorkMonitor::workerAppendText, p_main_window,&MainWindow::doWorkerAppendText);
+ connect(_p_work_monitor, &WorkMonitor::workerSetText, p_main_window,&MainWindow::doWorkerSetText);
connect(p_main_window, &MainWindow::operateXpipFile, this,&WorkerThread::doXpipFileLoad);
connect(this, &WorkerThread::projectReady, p_main_window,&MainWindow::doProjectReady);
diff --git a/src/input/condorqxmlsaxhandler.cpp b/src/input/condorqxmlsaxhandler.cpp
index 7b8a557b4065b8dcb432399500101987c4b1b174..645239f85792a7a819304d573139200e4a49303a 100644
--- a/src/input/condorqxmlsaxhandler.cpp
+++ b/src/input/condorqxmlsaxhandler.cpp
@@ -33,6 +33,8 @@
#include <pappsomspp/pappsoexception.h>
CondorQxmlSaxHandler::CondorQxmlSaxHandler(TandemCondorProcess * tandem_condor_process) {
+ _is_empty = true;
+ _tandem_condor_process = tandem_condor_process;
}
CondorQxmlSaxHandler::~CondorQxmlSaxHandler() {
}
@@ -40,20 +42,20 @@ CondorQxmlSaxHandler::~CondorQxmlSaxHandler() {
bool CondorQxmlSaxHandler::startElement(const QString & namespaceURI, const QString & localName,
- const QString & qName, const QXmlAttributes & attributes) {
+ const QString & qName, const QXmlAttributes & attributes) {
qDebug()<< "CondorQxmlSaxHandler::startElement begin" << namespaceURI << " " << localName << " " << qName ;
_tag_stack.push_back(qName);
bool is_ok = true;
try {
//startElement_group
- /*
- if (qName == "match") {
- is_ok = startElement_match(attributes);
- } else if (qName == "protein") {
- is_ok = startElement_protein(attributes);
+
+ if (qName == "c") {
+ is_ok = startElement_c(attributes);
+ } else if (qName == "a") {
+ is_ok = startElement_a(attributes);
}
-*/
+
_current_text.clear();
}
catch (pappso::PappsoException exception_pappso) {
@@ -68,20 +70,26 @@ bool CondorQxmlSaxHandler::startElement(const QString & namespaceURI, const QStr
}
bool CondorQxmlSaxHandler::endElement(const QString & namespaceURI, const QString & localName,
- const QString & qName) {
+ const QString & qName) {
bool is_ok = true;
// endElement_peptide_list
try {
- /*
- if (qName == "protein")
+
+ if (qName == "a")
{
- is_ok = endElement_protein();
+ is_ok = endElement_a();
+ }
+ else if (qName == "c") {
+ is_ok = endElement_c();
}
- else if (qName == "identification") {
- is_ok = endElement_identification();
+ else if (qName == "i") {
+ is_ok = endElement_i();
}
- */
+ else if (qName == "s") {
+ is_ok = endElement_s();
+ }
+
}
catch (pappso::PappsoException exception_pappso) {
_errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::endElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
@@ -121,11 +129,37 @@ QString CondorQxmlSaxHandler::errorString() const {
bool CondorQxmlSaxHandler::endDocument() {
- //_p_project->getProteinStore().setRegexpDecoyPattern(_p_project->getProteinStore().getRegexpDecoy().pattern());
+
+ unsigned int really_completed_jobs = 0;
+ if (_is_empty) {
+ really_completed_jobs = _tandem_condor_process->getCondorJobSize();
+ } else {
+ int total_jobs = 0;
+ for (std::int8_t i=0; i < 10; i++) {
+ total_jobs += _count_status[i];
+ }
+
+ int diff_jobs = _tandem_condor_process->getCondorJobSize()
+ - total_jobs;
+ really_completed_jobs = _count_status[(std::int8_t) CondorJobStatus::Completed] + diff_jobs;
+ }
+ _count_status[(std::int8_t) CondorJobStatus::Completed] = really_completed_jobs;
+
+ _tandem_condor_process->setCondorJobStatus(_count_status);
+ /*
+ xtandemCondorAnalysis.setJobCompleted(junexpanded, jidle, jrunning,
+ jremoved, reallyCompletedJobs, jheld, jsubmission_error);
+
+ */
+
return true;
}
bool CondorQxmlSaxHandler::startDocument() {
+ for (std::int8_t i=0; i < 10; i++) {
+ _count_status[i] = 0;
+ }
+ _is_empty = true;
return true;
}
@@ -134,6 +168,67 @@ bool CondorQxmlSaxHandler::characters(const QString &str) {
return true;
}
+bool CondorQxmlSaxHandler::startElement_c(QXmlAttributes attributes) {
+
+// <c>
+// <a n="ProcId"><i>0</i></a>
+ _condor_job_status = CondorJobStatus::Unexpanded;
+ _current_proc_id = 0;
+ _is_empty = false;
+ _current_remote_host = "";
+ _current_last_remote_host = "";
+ return true;
+
+}
+
+bool CondorQxmlSaxHandler::startElement_a(QXmlAttributes attributes) {
+ // logger.debug("startElementgroup begin");
+ // <group label="performance parameters" type="parameters">
+ _in_name = attributes.value("n");
+ return true;
+
+}
+
+bool CondorQxmlSaxHandler::endElement_a() {
+ _in_name = "";
+ return true;
+}
+
+bool CondorQxmlSaxHandler::endElement_i() {
+ if (_in_name == "ProcId") {
+ _current_proc_id = _current_text.toInt();
+ } else if (_in_name == "JobStatus") {
+ // <a n="JobStatus"><i>2</i></a>
+ _condor_job_status = static_cast<CondorJobStatus>(_current_text.toInt());
+ // logger.debug(currentProcId);
+ }
+ return true;
+}
+
+bool CondorQxmlSaxHandler::endElement_s() {
+ if (_in_name == "RemoteHost") {
+ // <a n="RemoteHost"><s>slot1@proteus3</s></a>
+ _current_remote_host = _current_text;
+ } else if ( _in_name == "LastRemoteHost") {
+ // <a n="LastRemoteHost"><s>slot1@proteus4</s></a>
+ _current_last_remote_host = _current_text;
+ }
+ return true;
+
+}
+
+bool CondorQxmlSaxHandler::endElement_c() {
+ /*
+ * 0 Unexpanded U 1 Idle I 2 Running R 3 Removed X 4 Completed C 5 Held
+ * H 6 Submission_err E
+ */
+ _count_status[(std::int8_t) _condor_job_status] += 1;
+
+ qDebug() << "currentRemoteHost:" << _current_remote_host <<
+ " currentLastRemoteHost" << _current_last_remote_host << " "
+ << (std::int8_t)_condor_job_status;
+}
+
/*
package fr.inra.pappso.xtandempipeline.sax_parse;
@@ -174,110 +269,6 @@ public void startDocument() throws SAXException {
this.empty = true;
}
-@Override
-public void endDocument() throws SAXException {
- int reallyCompletedJobs = 0;
- if (this.empty) {
- reallyCompletedJobs = xtandemCondorAnalysis.getCondorJobNumber();
- } else {
- int totalJobs = junexpanded + jidle + jrunning + jremoved
- + jcompleted + jheld + jsubmission_error;
- int diffJobs = xtandemCondorAnalysis.getCondorJobNumber()
- - totalJobs;
- reallyCompletedJobs = jcompleted + diffJobs;
- }
-
- xtandemCondorAnalysis.setJobCompleted(junexpanded, jidle, jrunning,
- jremoved, reallyCompletedJobs, jheld, jsubmission_error);
-
- String statusMessage = "" + junexpanded + " unexpanded jobs\n";
- statusMessage += jidle + " idle jobs\n";
- statusMessage += jrunning + " running jobs\n";
- statusMessage += jremoved + " removed jobs\n";
- statusMessage += reallyCompletedJobs + " completed jobs\n";
- statusMessage += jheld + " held jobs\n";
- statusMessage += jsubmission_error + " submission_errors\n";
-
- logger.debug(statusMessage);
- xtandemCondorAnalysis.setStatusMessage(statusMessage);
-
-}
-
-// <c>
-// <a n="ProcId"><i>0</i></a>
-public void startElementc(String nameSpaceUri, Attributes attrs) {
- this.empty = false;
- currentProcId = null;
- currentJobStatus = null;
- currentRemoteHost = null;
- currentLastRemoteHost = null;
-
-}
-
-public void startElementa(String nameSpaceUri, Attributes attrs) {
- // logger.debug("startElementgroup begin");
- // <group label="performance parameters" type="parameters">
- this.inName = attrs.getValue("n");
-
-}
-
-public void endElementi(String nameSpaceUri, String data)
- throws MSMSException {
- if (inName.equals("ProcId")) {
- this.currentProcId = new Integer(data);
- // logger.debug(currentProcId);
- } else if (inName.equals("JobStatus")) {
- // <a n="JobStatus"><i>2</i></a>
- this.currentJobStatus = new Integer(data);
- // logger.debug(currentProcId);
- }
-
-}
-
-public void endElements(String nameSpaceUri, String data)
- throws MSMSException {
- if (inName.equals("RemoteHost")) {
- // <a n="RemoteHost"><s>slot1@proteus3</s></a>
- this.currentRemoteHost = data;
- // logger.debug(currentProcId);
- } else if (inName.equals("LastRemoteHost")) {
- // <a n="LastRemoteHost"><s>slot1@proteus4</s></a>
- this.currentLastRemoteHost = data;
- // logger.debug(currentProcId);
- }
-
-}
-
-public void endElementa(String nameSpaceUri, String data) {
- this.inName = "";
-}
-
-public void endElementc(String nameSpaceUri, String data)
- throws MSMSException {
- /*
- * 0 Unexpanded U 1 Idle I 2 Running R 3 Removed X 4 Completed C 5 Held
- * H 6 Submission_err E
- *
- if (currentJobStatus == 0) {
- this.junexpanded += 1;
- } else if (currentJobStatus == 1) {
- this.jidle += 1;
- } else if (currentJobStatus == 2) {
- this.jrunning += 1;
- } else if (currentJobStatus == 3) {
- this.jremoved += 1;
- } else if (currentJobStatus == 4) {
- this.jcompleted += 1;
- } else if (currentJobStatus == 5) {
- this.jheld += 1;
- } else if (currentJobStatus == 6) {
- this.jsubmission_error += 1;
- }
-
- logger.debug("currentRemoteHost:" + this.currentRemoteHost
- + " currentLastRemoteHost" + this.currentLastRemoteHost + " "
- + currentJobStatus);
-}
}
*/
diff --git a/src/input/condorqxmlsaxhandler.h b/src/input/condorqxmlsaxhandler.h
index a0c7fcab6cd044f7e151c7cc76db0340f19b6676..dd946473b291d18a697f382681ff8dea937ca294 100644
--- a/src/input/condorqxmlsaxhandler.h
+++ b/src/input/condorqxmlsaxhandler.h
@@ -35,13 +35,24 @@
class TandemCondorProcess;
+/** \def CondorJobStatus
+ * */
+enum class CondorJobStatus: std::int8_t {
+ Unexpanded =0, ///< 0 Unexpanded U
+ Idle =1, ///< 1 Idle I
+ Running=2, ///< 2 Running R
+ Removed=3, ///< 3 Removed X
+ Completed=4, ///< 4 Completed C
+ Held=5, ///< 5 Held H
+ Submission_err=6 ///< 6 Submission_err E
+};
+
class CondorQxmlSaxHandler: public QXmlDefaultHandler
{
public:
CondorQxmlSaxHandler(TandemCondorProcess * tandem_condor_process);
~CondorQxmlSaxHandler();
-
bool startElement(const QString & namespaceURI, const QString & localName,
const QString & qName, const QXmlAttributes & attributes);
@@ -58,6 +69,14 @@ public:
bool error(const QXmlParseException &exception);
QString errorString() const;
+
+private:
+ bool startElement_c(QXmlAttributes attributes);
+ bool startElement_a(QXmlAttributes attributes);
+ bool endElement_c();
+ bool endElement_a();
+ bool endElement_i();
+ bool endElement_s();
private:
TandemCondorProcess * _tandem_condor_process;
@@ -65,6 +84,15 @@ private:
std::vector<QString> _tag_stack;
QString _errorStr;
QString _current_text;
+
+ QString _in_name;
+ CondorJobStatus _condor_job_status;
+ unsigned int _current_proc_id;
+ QString _current_remote_host;
+ QString _current_last_remote_host;
+
+ std::int8_t _count_status[10];
+ bool _is_empty;
};
diff --git a/src/utils/workmonitor.cpp b/src/utils/workmonitor.cpp
index a67d70c484c9a7175b70d01ada8449585e67037a..76ac1899141c34e0f64927e6cacef8e3ccada73d 100644
--- a/src/utils/workmonitor.cpp
+++ b/src/utils/workmonitor.cpp
@@ -60,3 +60,7 @@ void WorkMonitor::appendText(char * p_char) {
//qDebug() << "WorkMonitor::setProgressMaximumValue " << max_value;
emit workerAppendText(p_char);
}
+
+void WorkMonitor::setText(const QString text) {
+ emit workerSetText(text);
+}
diff --git a/src/utils/workmonitor.h b/src/utils/workmonitor.h
index d347155190aedb1767ef6e63d449d52091bc458a..bf53e37f4eb3bfccda6d1eddace1937be660e050 100644
--- a/src/utils/workmonitor.h
+++ b/src/utils/workmonitor.h
@@ -41,6 +41,7 @@ public:
virtual void message(const QString & message, int value) = 0;
virtual void setProgressMaximumValue(int max_value) = 0;
virtual void appendText(char * p_char) =0;
+ virtual void setText(const QString text)=0;
};
class WorkMonitor: public QObject, public WorkMonitorInterface
@@ -52,11 +53,13 @@ public:
void message(const QString & message, int value) override;
void setProgressMaximumValue(int max_value) override;
void appendText(char * p_char) override;
+ void setText(const QString text) override;
signals:
void workerMessage(QString message);
void workerMessagePercent(QString message, int value);
void workerAppendText(char * p_char);
+ void workerSetText(QString text);
private :
QTime _time;