Commit 733c3450 authored by Langella Olivier's avatar Langella Olivier
Browse files

merge debian changelog

parents 54cebca9 7d7fb2ee
masschroq (2.2.19-4) buster; urgency=medium
* catch ods exception in main
-- Olivier Langella <olivier.langella@u-psud.fr> Fri, 20 Dec 2019 11:46:54 +0100
masschroq (2.2.19-3) buster; urgency=medium
* constraint on libodsstream version
-- Olivier Langella <olivier.langella@u-psud.fr> Fri, 20 Dec 2019 11:09:50 +0100
masschroq (2.2.19-2) buster; urgency=medium
* new pappsoms++ library
* new cmake system
-- Olivier Langella <olivier.langella@u-psud.fr> Wed, 08 Jan 2020 22:39:54 +0100
-- Olivier Langella <olivier.langella@u-psud.fr> Fri, 20 Dec 2019 10:49:15 +0100
masschroq (2.2.19-1) buster; urgency=medium
......
......@@ -19,7 +19,7 @@ Build-Depends: debhelper (>= 5),
libpappsomspp-dev (= @LIBPAPPSOMSPP_VERSION@),
libpappsomspp-widget-dev (= @LIBPAPPSOMSPP_VERSION@),
libpappsomspp-widget0 (= @LIBPAPPSOMSPP_VERSION@),
libodsstream-qt5-dev (>=0.4.4),
libodsstream-qt5-dev (>= 0.7.3),
qtbase5-dev,
libqcustomplot-dev,
libqt5xmlpatterns5-dev
......@@ -35,7 +35,7 @@ Depends: ${shlibs:Depends},
libqt5core5a,
libqt5concurrent5,
libpappsomspp0 (= @LIBPAPPSOMSPP_VERSION@),
libodsstream-qt5-0
libodsstream-qt5-0 (>= 0.7.3)
Replaces: masschroq (<< 1.5.0)
Conflicts: masschroq (<< 1.5.0)
Suggests: masschroq, masschroq-gui, masschroq-studio
......
......@@ -201,13 +201,19 @@ ENDIF (NOGUI)
ADD_LIBRARY(${MASSCHROQ_LIB_NAME} SHARED ${MASSCHROQ_LIB_SRCS} ${MASSCHROQ_LIB_MOC_SRCS}
${SAXLIB_SRCS} ${OBIWARP_SRCS} ${MASSCHROQ_RCC_SRCS_QT5})
TARGET_LINK_LIBRARIES(${MASSCHROQ_LIB_NAME}
Qt5::Core Qt5::Gui Qt5::Xml Qt5::XmlPatterns Qt5::Concurrent
${PAPPSOMSPP_QT5_LIBRARY} ${ODSSTREAM_QT5_LIBRARY}
TARGET_LINK_LIBRARIES(${MASSCHROQ_LIB_NAME}
Pappso::Core
Pappso::Widget
OdsStream::Core
Qt5::Core
Qt5::Gui
Qt5::Xml
Qt5::XmlPatterns
Qt5::Concurrent
)
target_include_directories (${MASSCHROQ_LIB_NAME} PUBLIC ${Qt5Core_INCLUDES} ${Qt5Concurrent_INCLUDES} ${Qt5Gui_INCLUDES}
${Qt5Xml_INCLUDES} ${Qt5XmlPatterns_INCLUDES} ${PAPPSOMSPP_INCLUDE_DIR} ${ODSSTREAM_INCLUDE_DIR}
${QCustomPlot_INCLUDES} ${QUAZIP_INCLUDE_DIR}
target_include_directories (${MASSCHROQ_LIB_NAME} PUBLIC
${QCustomPlot_INCLUDES}
${QUAZIP_INCLUDE_DIR}
)
SET_TARGET_PROPERTIES(${MASSCHROQ_LIB_NAME} PROPERTIES
VERSION ${MASSCHROQ_LIB_VERSION}
......@@ -215,9 +221,10 @@ SET_TARGET_PROPERTIES(${MASSCHROQ_LIB_NAME} PROPERTIES
)
ADD_EXECUTABLE(masschroq_main main.cpp)
TARGET_LINK_LIBRARIES(masschroq_main ${MASSCHROQ_LIB_NAME}
${PAPPSOMSPP_QT5_LIBRARY}
${ODSSTREAM_QT5_LIBRARY}
TARGET_LINK_LIBRARIES(masschroq_main ${MASSCHROQ_LIB_NAME}
Pappso::Core
Pappso::Widget
OdsStream::Core
${Boost_chrono_LIBRARY}
${Boost_filesystem_LIBRARY}
${Boost_iostreams_LIBRARY}
......@@ -225,22 +232,24 @@ TARGET_LINK_LIBRARIES(masschroq_main ${MASSCHROQ_LIB_NAME}
${Boost_serialization_LIBRARY}
${Boost_system_LIBRARY}
${Boost_thread_LIBRARY}
Qt5::Core)
Qt5::Core
)
SET_TARGET_PROPERTIES(masschroq_main PROPERTIES OUTPUT_NAME masschroq)
target_include_directories (masschroq_main PUBLIC
${Qt5Core_INCLUDES} ${Qt5Concurrent_INCLUDES} ${Qt5Gui_INCLUDES} ${Qt5Xml_INCLUDES} ${Qt5XmlPatterns_INCLUDES} ${PAPPSOMSPP_INCLUDE_DIR} ${ODSSTREAM_INCLUDE_DIR} ${QUAZIP_INCLUDE_DIR}
${QUAZIP_INCLUDE_DIR}
)
IF (NOGUI)
ELSE (NOGUI)
ADD_EXECUTABLE(masschroq_gui gui/mcqgui/launcherGui.cpp ${GUI_SRCS} ${GUI_MOC_SRCS} ${GUI_UI_HDRS})
TARGET_LINK_LIBRARIES(masschroq_gui ${MASSCHROQ_LIB_NAME}
TARGET_LINK_LIBRARIES(masschroq_gui ${MASSCHROQ_LIB_NAME}
Pappso::Core
Pappso::Widget
OdsStream::Core
Qt5::Core
Qt5::Gui
Qt5::Widgets
${PAPPSOMSPP_QT5_LIBRARY}
${ODSSTREAM_QT5_LIBRARY}
Qt5::Widgets
${Boost_chrono_LIBRARY}
${Boost_filesystem_LIBRARY}
${Boost_iostreams_LIBRARY}
......@@ -249,21 +258,17 @@ ELSE (NOGUI)
${Boost_system_LIBRARY}
${Boost_thread_LIBRARY}
)
target_include_directories (masschroq_gui PUBLIC ${Qt5Core_INCLUDES} ${Qt5Concurrent_INCLUDES} ${Qt5Gui_INCLUDES}
${Qt5Xml_INCLUDES} ${Qt5XmlPatterns_INCLUDES} ${PAPPSOMSPP_INCLUDE_DIR}
)
ADD_EXECUTABLE(masschroq_studio gui/parameterGui.cpp ${STUDIO_SRCS} ${STUDIO_MOC_SRCS})
TARGET_LINK_LIBRARIES(masschroq_studio ${MASSCHROQ_LIB_NAME}
TARGET_LINK_LIBRARIES(masschroq_studio ${MASSCHROQ_LIB_NAME}
Pappso::Core
Pappso::Widget
OdsStream::Core
Qt5::Core
Qt5::Gui
Qt5::Widgets
Qt5::PrintSupport
${ODSSTREAM_QT5_LIBRARY}
${QCustomPlot_LIBRARIES}
${PAPPSOMSPP_QT5_LIBRARY}
${PAPPSOMSPP_WIDGET_QT5_LIBRARY}
${QCustomPlot_LIBRARIES}
${Boost_chrono_LIBRARY}
${Boost_filesystem_LIBRARY}
${Boost_iostreams_LIBRARY}
......@@ -272,9 +277,6 @@ ELSE (NOGUI)
${Boost_system_LIBRARY}
${Boost_thread_LIBRARY}
)
target_include_directories (masschroq_studio PUBLIC ${Qt5Core_INCLUDES} ${Qt5Concurrent_INCLUDES} ${Qt5Gui_INCLUDES}
${Qt5Xml_INCLUDES} ${Qt5XmlPatterns_INCLUDES} ${PAPPSOMSPP_INCLUDE_DIR}
)
ENDIF (NOGUI)
IF (MINGW)
......
......@@ -52,12 +52,6 @@ lmatReader::set_from_xml(const Msrun &msrun,
return (false);
}
catch(mcqError &errorException)
{
throw mcqError(QObject::tr("error converting file '%1' to lmat :\n%2")
.arg(file)
.arg(errorException.what()));
}
mcqout() << QObject::tr(
"MS run '%1' : xml file '%2' : obiwarp parsing for lmat: OK")
......
......@@ -668,13 +668,6 @@ MassChroq::executeQuantification(const QString &quantify_id)
.arg(quantify_id)
.arg(error.qwhat()));
}
catch(mcqError &error)
{
throw mcqError(QObject::tr("error in MassChroQ::executeQuantification %1 "
"mcqError :\n%2")
.arg(quantify_id)
.arg(error.qwhat()));
}
catch(std::exception &std_error)
{
throw mcqError(
......
......@@ -51,7 +51,6 @@ MonitorComparOdsOutput::MonitorComparOdsOutput(const QString &ods_file)
MonitorComparOdsOutput::~MonitorComparOdsOutput()
{
qDebug() << "MonitorComparOdsOutput::~MonitorComparOdsOutput begin";
_p_writer->close();
}
......@@ -208,57 +207,70 @@ MonitorComparInterfaceOutput::privWriteMatchedPeak(
const QuantiItemBase *p_quanti_item,
const AlignedXicPeak *peak)
{
if(peak != nullptr)
try
{
// store aligned peak in a table
// rows are quanti items
// columns are MSruns
//_compar_table[p_quanti_item][p_msrun] = peak->getArea();
std::map<const Msrun *, pappso::pappso_double> *p_msrun_value = nullptr;
std::pair<
std::map<const QuantiItemBase *,
std::map<const Msrun *, pappso::pappso_double>>::iterator,
bool>
pair_insert_qitem = _compar_table.insert(
std::pair<const QuantiItemBase *,
std::map<const Msrun *, pappso::pappso_double>>(
p_quanti_item, std::map<const Msrun *, pappso::pappso_double>()));
if(pair_insert_qitem.second == true)
{
// new qitem
_qitem_list.push_back(p_quanti_item);
}
else
if(peak != nullptr)
{
// existing qitem
}
// store aligned peak in a table
// rows are quanti items
// columns are MSruns
//_compar_table[p_quanti_item][p_msrun] = peak->getArea();
std::map<const Msrun *, pappso::pappso_double> *p_msrun_value =
nullptr;
std::pair<
std::map<const QuantiItemBase *,
std::map<const Msrun *, pappso::pappso_double>>::iterator,
bool>
pair_insert_qitem = _compar_table.insert(
std::pair<const QuantiItemBase *,
std::map<const Msrun *, pappso::pappso_double>>(
p_quanti_item,
std::map<const Msrun *, pappso::pappso_double>()));
if(pair_insert_qitem.second == true)
{
// new qitem
_qitem_list.push_back(p_quanti_item);
}
else
{
// existing qitem
}
p_msrun_value = &pair_insert_qitem.first->second;
std::pair<std::map<const Msrun *, pappso::pappso_double>::iterator, bool>
pair_insert_msrun =
p_msrun_value->insert(std::pair<const Msrun *, pappso::pappso_double>(
p_msrun, peak->getArea()));
if(pair_insert_msrun.second == true)
{
// new msrun
if(std::find(_msrun_list.begin(), _msrun_list.end(), p_msrun) ==
_msrun_list.end())
p_msrun_value = &pair_insert_qitem.first->second;
std::pair<std::map<const Msrun *, pappso::pappso_double>::iterator,
bool>
pair_insert_msrun = p_msrun_value->insert(
std::pair<const Msrun *, pappso::pappso_double>(p_msrun,
peak->getArea()));
if(pair_insert_msrun.second == true)
{
_msrun_list.push_back(p_msrun);
// new msrun
if(std::find(_msrun_list.begin(), _msrun_list.end(), p_msrun) ==
_msrun_list.end())
{
_msrun_list.push_back(p_msrun);
}
}
else
{
// existing msrun
// this means that we have more than one area value for a single
// mcq item : potential problem we decide to store only the last
// value
qDebug() << "MonitorComparInterfaceOutput::privWriteMatchedPeak "
"multiple "
"value for qitem:"
<< p_quanti_item->getQuantiItemId()
<< " msrun:" << p_msrun->getMsRunIdCstSPtr()->getXmlId();
pair_insert_msrun.first->second = peak->getArea();
}
}
else
{
// existing msrun
// this means that we have more than one area value for a single mcq
// item : potential problem we decide to store only the last value
qDebug()
<< "MonitorComparInterfaceOutput::privWriteMatchedPeak multiple "
"value for qitem:"
<< p_quanti_item->getQuantiItemId()
<< " msrun:" << p_msrun->getMsRunIdCstSPtr()->getXmlId();
pair_insert_msrun.first->second = peak->getArea();
}
}
catch(OdsException &error)
{
throw mcqError(
QObject::tr(
"Error in MonitorComparInterfaceOutput::privWriteMatchedPeak :\n%1")
.arg(error.qwhat()));
}
}
......@@ -244,23 +244,32 @@ MonitorOdsInterfaceOutput::privWriteMatchedPeak(
const QuantiItemBase *p_quanti_item,
const AlignedXicPeak *peak)
{
if(peak != nullptr)
try
{
_p_writer->writeLine();
_p_writer->writeCell(_current_quantification_id);
_p_writer->writeCell(_current_group_id);
_p_writer->writeCell(p_msrun->getMsRunIdCstSPtr()->getXmlId());
_p_writer->writeCell(
QFileInfo(p_msrun->getMsRunIdCstSPtr()->getFileName()).baseName());
_p_writer->writeCell(p_quanti_item->getMz());
_p_writer->writeCell(peak->getMaxXicElement().x);
_p_writer->writeCell(peak->getMaxXicElement().y);
if(peak != nullptr)
{
_p_writer->writeLine();
_p_writer->writeCell(_current_quantification_id);
_p_writer->writeCell(_current_group_id);
_p_writer->writeCell(p_msrun->getMsRunIdCstSPtr()->getXmlId());
_p_writer->writeCell(
QFileInfo(p_msrun->getMsRunIdCstSPtr()->getFileName()).baseName());
_p_writer->writeCell(p_quanti_item->getMz());
_p_writer->writeCell(peak->getMaxXicElement().x);
_p_writer->writeCell(peak->getMaxXicElement().y);
_p_writer->writeCell(peak->getArea());
_p_writer->writeCell(peak->getLeftBoundary().x);
_p_writer->writeCell(peak->getRightBoundary().x);
_p_writer->writeCell(peak->getArea());
_p_writer->writeCell(peak->getLeftBoundary().x);
_p_writer->writeCell(peak->getRightBoundary().x);
p_quanti_item->writeOdsPeptideLine(*_p_writer);
p_quanti_item->writeOdsPeptideLine(*_p_writer);
}
}
catch(OdsException &error)
{
throw mcqError(
QObject::tr(
"Error in MonitorOdsInterfaceOutput::privWriteMatchedPeak :\n%1")
.arg(error.qwhat()));
}
}
......@@ -21,6 +21,7 @@
#include <QCommandLineParser>
#include <QDebug>
#include <odsstream/odsexception.h>
masschroqCli::masschroqCli(QObject *parent) : QObject(parent)
{
......@@ -252,7 +253,16 @@ masschroqCli::run()
quit();
// delete logger;
}
catch(mcqError &error)
catch(OdsException &error)
{
mcqerr() << "Oops! an error occurred in MassChroQ. Dont Panic :" << endl;
mcqerr() << error.qwhat() << endl;
windaube_exit();
exit(1);
app->exit(1);
}
catch(pappso::PappsoException &error)
{
mcqerr() << "Oops! an error occurred in MassChroQ. Dont Panic :" << endl;
mcqerr() << error.qwhat() << endl;
......
......@@ -533,12 +533,6 @@ MasschroqmlParser::startElement_data_file(const QXmlAttributes &attributes)
.arg(idname, pappso_error.qwhat());
return false;
}
catch(mcqError &error)
{
_errorStr =
QObject::tr("problem creating msrun %1:\n%2").arg(idname, error.what());
return false;
}
return (true);
}
......
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