def setVisible(self, visible): QDockWidget.setVisible(self, visible) if (visible): # set as current widget mainWindowDockWidget.setAsCurrent(self) # If dock widget is tabbed, then show on top. otherTabbedWidgets = self.parent().tabifiedDockWidgets(self) if (otherTabbedWidgets != []): self.raise_()
def lauchGUI(self, WorkSpace, aCase, sobjXML, Args):
"""
mw.dockWidgetBrowser is the Browser of the CFD MainView
"""
log.debug("lauchGUI")
from cs_gui import process_cmd_line
if CFD_Code() == CFD_Saturne:
from cs_package import package
from code_saturne.Base.MainView import MainView
elif CFD_Code() == CFD_Neptune:
from nc_package import package
from neptune_cfd.core.MainView import MainView
if sobjXML == None:
Title = "unnamed"
else:
Title = sobjXML.GetName()
self.Workspace = WorkSpace
pkg = package()
case, splash = process_cmd_line(Args)
mw = MainView(pkg, case, aCase)
# Put the standard panel of the MainView inside a QDockWidget
# in the SALOME Desktop
aTitle = self.setWindowTitle_CFD(mw, aCase, Title)
dsk = sgPyQt.getDesktop()
dock = QDockWidget(aTitle)
dock.setWidget(mw.frame)
dock.setMinimumWidth(520)
dsk.addDockWidget(Qt.RightDockWidgetArea, dock)
dock.setVisible(True)
dock.show()
# Put the QTreeView of the MainView which is already inside a QDockWidget
# in the SALOME Desktop
BrowserTitle = aTitle + " Browser"
mw.dockWidgetBrowser.setWindowTitle(BrowserTitle)
dsk.addDockWidget(Qt.LeftDockWidgetArea, mw.dockWidgetBrowser)
mw.dockWidgetBrowser.setVisible(True)
mw.dockWidgetBrowser.show()
mw.dockWidgetBrowser.raise_()
dock.raise_()
#Add Dock windows are managed by CFDGUI_Management class
studyId = sgPyQt.getStudyId()
aStudyCFD = aCase.GetFather()
aCaseCFD = aCase
xmlFileName = str(Title)
_c_CFDGUI.set_d_CfdCases(studyId, dock, mw.dockWidgetBrowser, mw, aStudyCFD, aCaseCFD, xmlFileName, sobjXML)
self.connect(dock, SIGNAL("visibilityChanged(bool)"), self.setdockWindowBrowserActivated)
self.connect(mw.dockWidgetBrowser, SIGNAL("visibilityChanged(bool)"),self.setdockWindowActivated)
self.connect(dock.toggleViewAction(), SIGNAL("toggled(bool)"), self.setdockWB)
self.connect(mw.dockWidgetBrowser.toggleViewAction(), SIGNAL("toggled(bool)"), self.setdock)
_c_CFDGUI.tabifyDockWindows(dsk, studyId)
self.showDockWindows(studyId, xmlFileName, aCaseCFD.GetName(), aStudyCFD.GetName())
updateObjectBrowser()
return mw
class MSMainWindow(QMainWindow):
"""Gui of the main window"""
# MAX_RECENT_FILES = 10
# start putting links spyder numpy scipy et tutti quanti
links = (
"http://numpy.scipy.org/",
"http://packages.python.org/spyder/",
"http://www.riverbankcomputing.co.uk/software/pyqt/intro",
)
pluginPath = path.normcase("pluginmanager/plugins/")
def __init__(self, availablePlugins):
"""
Constructor with all the models needed setup menus
"""
QMainWindow.__init__(self)
self.setDockOptions(QMainWindow.VerticalTabs | QMainWindow.AnimatedDocks)
self.plugins = availablePlugins
self.pluginsInst = []
settings = QSettings(
"INRA/INSA", "-".join([QApplication.instance().APPLICATION_NAME_STR, QApplication.instance().VERSION_STR])
)
self.recentFiles = list(settings.value("RecentFiles").toStringList())
self.setStyleSheet(stylesheet)
self.pipeline = MSPipelineToolBar("Pipeline toolbar", parent=self)
self.addToolBar(0x1, self.pipeline)
self._setupModels()
self._setupUi()
self._setupMenus()
def _setupModels(self):
"""
Warning:Causes segfault when horizontal labels set to True
on aura peu etre a la fin un model par sampleList c'est ce qui parait
le plus logique
"""
# drag and drop table sample
self.sampleModel = QStandardItemModel(self)
self.sampleModel.setHorizontalHeaderLabels(["Sample", "Class"])
# treeView1
self.spectraModel = QStandardItemModel(self)
# treeview2
self.peakModel = QStandardItemModel(self)
# treeview3
self.clusterModel = QStandardItemModel(self)
def _setupMenus(self):
# file
self.fileMenu = QMenu("&File")
self.fileMenu.setTearOffEnabled(True)
self.op = QMenu("&Open...", self.fileMenu)
self.op.setIcon(QIcon(path.normcase("gui/icons/fileopen.png")))
open_ = QAction("&Open rawfiles", self)
open_.setToolTip("Open an mzXML or netCDF file")
open_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_O))
open_icon = QIcon(path.normcase("gui/icons/fileopen.png"))
open_.setIcon(open_icon)
self.op.addAction(open_)
load_ = QAction("&Open projects...", self)
load_.setToolTip("load binary file containing saved objects")
load_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_S))
load_icon = QIcon(QPixmap(path.normcase("gui/icons/project_open.png")))
load_.setIcon(load_icon)
self.op.addAction(load_)
self.fileMenu.addMenu(self.op)
save_ = QAction("&Save...", self)
save_.setToolTip("save the actual application model")
save_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_S))
save_icon = QIcon(path.normcase("gui/icons/save_all.png"))
save_.setIcon(save_icon)
self.fileMenu.addAction(save_)
pkl = QAction("&load a peaklist", self) # TODO:load peaklist
pkl.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_P))
pkl.setToolTip("load a peaklist and process it")
pkl.setIcon(QIcon(path.normcase("gui/icons/featuredetect.png")))
self.fileMenu.addAction(pkl)
convert_ = QAction("&Convert...", self)
convert_.setEnabled(False)
convert_.setToolTip("Convert a .wiff file if Analyst(c) is installed")
convert_icon = QIcon(path.normcase("gui/icons/goto.png"))
convert_.setIcon(convert_icon)
self.fileMenu.addAction(convert_)
a = self.fileMenu.addAction(QIcon(path.normcase("gui/icons/process.png")), "&Launch a batch")
a.setEnabled(False)
b = self.fileMenu.addAction(QIcon(path.normcase("gui/icons/process.png")), "&Merge")
b.setToolTip("Merge MRM file")
# b.setEnabled(False)
self.fileMenu.addSeparator()
#
# for i in xrange(self.MAX_RECENT_FILES):
# a = QAction('', self)
# a.setVisible(False)
# self.fileMenu.addAction(a)
#
# for i in xrange(min(self.MAX_RECENT_FILES, len(self.recentFiles))):
# self.fileMenu.actions()[5+i].setVisible(True)
# self.fileMenu.actions()[5+i].setText(self.recentFiles[i].split('/')[-1])
exit_action = QAction("&Exit", self)
exit_action.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_Q))
exit_action.setIcon(QIcon(QPixmap(path.normcase("gui/icons/exit.png"))))
self.fileMenu.addAction(exit_action)
self.menuBar().addMenu(self.fileMenu)
self.editMenu = QMenu("&Edit")
self.editMenu.setTearOffEnabled(True)
self.editMenu.addAction(QIcon(path.normcase("gui/icons/edit_undo.png")), "&Undo...")
self.editMenu.addAction(QIcon(path.normcase("gui/icons/edit_redo.png")), "&Redo...")
self.editMenu.actions()[0].setEnabled(False)
self.editMenu.actions()[1].setEnabled(False)
self.editMenu.addSeparator()
self.editMenu.addAction(QIcon(path.normcase("gui/icons/run.png")), "&Preferences")
self.exportMenu = QMenu("&Export...")
self.exportMenu.setIcon(QIcon(path.normcase("gui/icons/file_export.png")))
self.exportMenu.addAction("&Peaklist")
self.exportMenu.addAction("&Clusters intensity matrix")
self.editMenu.addMenu(self.exportMenu)
self.menuBar().addMenu(self.editMenu)
# view
self.viewMenu = QMenu("&View")
self.viewMenu.setTearOffEnabled(True)
self.viewMenu.addAction(
QIcon(path.normcase("gui/icons/window_duplicate")),
"&Cascade View",
self.mdiArea.cascadeSubWindows,
QKeySequence(Qt.CTRL + Qt.Key_K),
)
self.viewMenu.addAction(
QIcon(path.normcase("gui/icons/view_icon")),
"&Title View",
self.mdiArea.tileSubWindows,
QKeySequence(Qt.CTRL + Qt.Key_N),
)
self.viewMenu.addAction(
QIcon(path.normcase("gui/icons/stop_process.png")),
"&Close all subWindows",
self.mdiArea.closeAllSubWindows,
QKeySequence(Qt.CTRL + Qt.Key_W),
)
self.plotting = QMenu("&Plotting...")
self.plotting.setIcon(QIcon(QPixmap(path.normcase("gui/icons/plot.png"))))
self.plotting.addAction("&3D Plot")
# self.plotting.addAction("&Cytoscape web")
self.plotting.addAction("&Spectrogram Plot")
# self.multiplePlot = QAction("&Visualize Raw/Treated Data", self)
# self.multiplePlot.setCheckable(True)
# self.multiplePlot.setEnabled(False)
# self.sub_plot_.addAction(self.multiplePlot)
self.viewMenu.addMenu(self.plotting)
self.viewMenu.addSeparator()
self.show_hide = QMenu("&Show/Hide")
m = self.createPopupMenu()
m.setTitle("&Show/Hide")
self.viewMenu.addMenu(m)
# self.pref = QMenu("&Preferences")
# self.pref.addAction(self.multiplePlot)
# self.viewMenu.addMenu(self.pref)
self.menuBar().addMenu(self.viewMenu)
# algorithm
self.algoMenu = QMenu("&Algorithm")
self.algoMenu.setTearOffEnabled(True)
self.preProcessing = QMenu("&PreProcessing(experimental)")
self.preProcessing.addAction("&Smoothing raw data...")
self.preProcessing.addAction("&Cut off raw data...")
self.preProcessing.addAction("&Calibration (mz dimension)")
self.preProcessing.addAction("&Resize sample...")
self.algoMenu.addMenu(self.preProcessing)
self.peakPickingMenu = QMenu("&Peack Picking & Alignement(XCMS)", self)
self.peakPickingMenu.setIcon(QIcon(path.normcase("gui/icons/pickedpeakicon.png")))
matched = QAction("&MatchedFiltered", self)
matched.setIcon(QIcon(path.normcase("gui/icons/RLogo")))
matched.setToolTip("Peak Detection and Integration using MatchedFiltered algorithm")
self.peakPickingMenu.addAction(matched)
centwave = QAction("&CentWave", self)
centwave.setIcon(QIcon(path.normcase("gui/icons/RLogo")))
centwave.setToolTip("Peak Detection and Integration using CentWave algorithm")
self.peakPickingMenu.addAction(centwave)
# peak_.setShortcut(.QKeySequence(CTRL + Key_P))
# peak_icon=.QIcon(.QPixmap(path.normcase("gui/icons/pickedpeakicon.png")))
# peak_.setIcon(peak_icon)
self.algoMenu.addMenu(self.peakPickingMenu)
self.alignment = QMenu("&Alignment")
self.alignment.setIcon(QIcon(path.normcase("gui/icons/format_indent_more.png")))
self.alignment.addAction("&Polynomial fitting(exp)")
self.alignment.addAction("&DynamicTimeWarping")
self.alignment.addAction("&ObiWarp")
self.alignment.actions()[2].setEnabled(False)
self.algoMenu.addMenu(self.alignment)
self.algoMenu.addAction("Normalization")
clust_ = QAction("&Clustering", self)
clust_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_L))
clust_icon = QIcon(QPixmap(path.normcase("gui/icons/cluster.png")))
clust_.setIcon(clust_icon)
self.algoMenu.addAction(clust_)
id_ = QAction("&Identification", self)
id_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_I))
id_.setToolTip("Try to identify peaks with several methods")
id_.setIcon(QIcon(QPixmap(path.normcase("gui/icons/findcompound.png"))))
self.algoMenu.addAction(id_)
self.menuBar().addMenu(self.algoMenu)
# tools
self.toolsMenu = QMenu("&Tools")
self.toolsMenu.setTearOffEnabled(True)
web = QAction("&Web Browser", self)
web.setIcon(QIcon(QPixmap(path.normcase("gui/icons/applications_internet.png"))))
self.toolsMenu.addAction(web)
# cyto = QAction("&cytoscape", self)
# cyto_icon =QIcon(QPixmap(path.normcase("gui/icons/cytoscape.jpeg")))
# cyto.setIcon(cyto_icon)
# self.toolsMenu.addAction(cyto)
editor = QAction("&Editor", self)
editor.setIcon(QIcon(QPixmap(path.normcase("gui/icons/document_sign.png"))))
self.toolsMenu.addAction(editor)
pet = QAction("&Short Periodic Table", self)
pet.setIcon(QIcon(QPixmap(path.normcase("gui/icons/pet.jpg"))))
self.toolsMenu.addAction(pet)
self.menuBar().addMenu(self.toolsMenu)
# plugins
self.pluginMenu = QMenu("&Plugins")
self.pluginMenu.setTearOffEnabled(True)
instPl = QAction("&Install a plugin", self)
instPl.setIcon(QIcon(path.normcase("gui/icons/pluginInstall.png")))
self.pluginMenu.addAction(instPl)
self.launchingMenu = QMenu("&Launch PLugins", self)
self.launchingMenu.setIcon(QIcon(path.normcase("gui/icons/plugin")))
for plug in self.plugins:
# fullname="".join([self.pluginPath, str(plug)])
mod = imp.load_source(self.__module__, plug)
if mod.autoActivation:
qApp = QApplication.instance()
name = getattr(mod, "className")
cls = getattr(mod, name)
p = cls(qApp.model, self, parent=self)
# p=qApp.pluginManager.loadPlugin(qApp.model, self, plug.split('/')[-1])
self.pluginsInst.append(p)
else:
self.launchingMenu.addAction(plug.split("/")[-1])
self.pluginMenu.addMenu(self.launchingMenu)
self.pluginMenu.addAction(QIcon(path.normcase("gui/icons/process_stop.png")), "&Remove loaded Plugin")
self.menuBar().addMenu(self.pluginMenu)
# about
self.aboutMenu = QMenu("&About")
self.aboutMenu.setTearOffEnabled(True)
metms = QAction(QIcon(path.normcase("gui/icons/deluge.png")), "&about metMS...", self)
self.aboutMenu.addAction(metms)
pyqt = QAction("&about PyQt4...", self)
pyqt_icon = QIcon(QPixmap(path.normcase("gui/icons/logo_QT4.png")))
pyqt.setIcon(pyqt_icon)
self.aboutMenu.addAction(pyqt)
metms = QAction("&metMS Documentation", self)
metms_icon = QIcon(QPixmap(path.normcase("gui/icons/deluge.png")))
metms.setIcon(metms_icon)
self.aboutMenu.addAction(metms)
self.menuBar().addMenu(self.aboutMenu)
def _setupUi(self, background=None):
"""
Make the GUI
"""
# mdi
self.mdiArea = MSMdiArea(self)
self.mdiArea.setBackground(QBrush(QPixmap(path.normcase("gui/icons/blac2.png")))) # QColor(Qt.blue).darker()))
self.setCentralWidget(self.mdiArea)
# sample dock widget
self.sampleDockWidget = QDockWidget("Samples", self)
# sampleWidget = QWidget()
self.sampleTableView = MSDragFromTableView()
self.sampleTableView.setModel(self.sampleModel)
self.sampleTableView.setSelectionBehavior(1)
self.sampleTableView.verticalHeader().hide()
self.sampleTableView.verticalHeader().setDefaultSectionSize(15)
self.sampleTableView.horizontalHeader().setDefaultSectionSize(150)
self.sampleDockWidget.setWidget(self.sampleTableView) # sampleWidget)
self.sampleDockWidget.visible = True
# workflow dock
self.workflowDockWidget = QDockWidget("Visualizer", self)
self.workflowDockWidget.visible = True
a = QWidget(self)
v = QVBoxLayout(a)
q = QToolBar()
# self.workingSample = QLabel("Working Sample:None")
# q.addWidget(self.workingSample)
q.addWidget(QLabel("ppm :"))
self.ppmEditer = QDoubleSpinBox()
self.usePpm = QCheckBox("use ?")
q.addWidget(self.ppmEditer)
q.addWidget(self.usePpm)
q.addSeparator()
self.removeButton = QToolButton(self)
self.removeButton.setIcon(QIcon(path.normcase("gui/icons/delete.png")))
q.addWidget(self.removeButton)
self.markAsGood = QAction(QIcon(path.normcase("gui/icons/button_ok.png")), "mark peak as good", self)
self.markAsBad = QAction(QIcon(path.normcase("gui/icons/stop.png")), "mark peak as bad", self)
self.hideItem = QAction(QIcon(path.normcase("gui/icons/list_remove.png")), "Hide Item", self)
q.addAction(self.markAsGood)
q.addAction(self.markAsBad)
q.addAction(self.hideItem)
v.addWidget(q)
self.tabWidget = QTabWidget()
self.tab = QWidget()
verticalLayout = QVBoxLayout(self.tab)
self.treeView = MSToDropTableView()
self.treeView.verticalHeader().setDefaultSectionSize(20)
self.treeView.setModel(self.spectraModel)
self.spectraLabel = QLabel("Sample: None")
verticalLayout.addWidget(self.treeView)
verticalLayout.addWidget(self.spectraLabel)
self.tabWidget.addTab(self.tab, QIcon(path.normcase("gui/icons/spectrumicon.png")), "Spectra")
self.tab_2 = QWidget()
verticalLayout_4 = QVBoxLayout(self.tab_2)
self.treeView_2 = MSToDropTableView() # MSTreeView(self.tab_2)# QTableView(self)#
self.treeView_2.verticalHeader().setDefaultSectionSize(20)
self.treeView_2.setModel(self.peakModel)
self.peakLabel = QLabel("Sample: None")
verticalLayout_4.addWidget(self.treeView_2)
verticalLayout_4.addWidget(self.peakLabel)
self.tabWidget.addTab(self.tab_2, QIcon(path.normcase("gui/icons/peakicon.png")), "Peaks List")
self.tab_3 = QWidget()
verticalLayout_5 = QVBoxLayout(self.tab_3)
self.treeView_3 = MSToDropTreeView()
self.treeView_3.setAnimated(True)
self.treeView_3.setModel(self.clusterModel)
self.clusterLabel = QLabel("Sample: None")
verticalLayout_5.addWidget(self.treeView_3)
verticalLayout_5.addWidget(self.clusterLabel)
self.tabWidget.addTab(self.tab_3, QIcon(path.normcase("gui/icons/clustering.png")), "Clusters")
self.tabWidget.setCurrentIndex(0)
for l in (self.spectraLabel, self.peakLabel, self.clusterLabel):
l.setAutoFillBackground(True)
v.addWidget(self.tabWidget)
self.workflowDockWidget.setWidget(a)
self.addDockWidget(Qt.DockWidgetArea(0x2), self.workflowDockWidget)
from gui.MetBaseGui import MSIsoCalculator
self.isoCalc = MSIsoCalculator(self)
self.isoCalcDockWidget = QDockWidget("isotopes calculation", self)
self.isoCalcDockWidget.setWidget(self.isoCalc)
self.addDockWidget(Qt.DockWidgetArea(0x2), self.isoCalcDockWidget)
self.isoCalcDockWidget.setVisible(False)
self.isoCalcDockWidget.visible = False
from gui.MetBaseGui import FormulaGenerator
self.generator = FormulaGenerator(self)
self.generatorDockWidget = QDockWidget("formula generator", self)
self.generatorDockWidget.setWidget(self.generator)
self.addDockWidget(Qt.DockWidgetArea(0x2), self.generatorDockWidget)
self.generatorDockWidget.setVisible(False)
self.generatorDockWidget.visible = False
self.compoundTreeView = MSCompoundTreeView(self)
self.compoundDockWidget = QDockWidget("Compounds", self)
self.compoundDockWidget.setWidget(self.compoundTreeView)
self.addDockWidget(Qt.DockWidgetArea(0x2), self.compoundDockWidget)
self.compoundDockWidget.setVisible(False)
self.compoundDockWidget.visible = False
self.comparativeTableView = QTableView(self)
self.comparativeTableView.horizontalHeader().setStretchLastSection(True)
self.comparativeTableView.verticalHeader().setDefaultSectionSize(20)
self.comparativeDock = QDockWidget("Comparative View", self)
self.comparativeDock.setWidget(self.comparativeTableView)
self.addDockWidget(Qt.DockWidgetArea(0x8), self.comparativeDock)
self.comparativeDock.setVisible(False)
self.comparativeDock.visible = False
self.tabifyDockWidget(self.compoundDockWidget, self.isoCalcDockWidget)
self.tabifyDockWidget(self.isoCalcDockWidget, self.workflowDockWidget)
self.tabifyDockWidget(self.workflowDockWidget, self.generatorDockWidget)
# set the end
# WARNING: possible that the internal shell widget cause random segfault
# with the error of QObject::killTimers...? not sure !
self.shell = QWidget() # InternalShell(namespace={'metms': QApplication.instance()},
# parent=self,
# multithreaded=False)
self.shellDock = QDockWidget("Python Shell", self)
self.shellDock.setWindowIcon(QIcon(path.normcase("gui/icons/stop.png")))
self.shellDock.setWidget(self.shell)
self.shellDock.setMinimumWidth(255)
self.shellDock.visible = True
self.addDockWidget(0x2, self.shellDock)
self.addDockWidget(0x2, self.sampleDockWidget)
self.tabifyDockWidget(self.shellDock, self.sampleDockWidget)
self.pb = QProgressBar(self)
self.pb.setMaximumWidth(245)
self.stopProcess = QToolButton(self)
self.stopProcess.setIcon(QIcon(path.normcase("gui/icons/process_stop.png")))
m = QMenu()
# self.connect(m, SIGNAL('triggered(QAction*'), QApplication.instance().taskManager.abortByName)
self.stopProcess.setMenu(m)
self.stopProcess.setPopupMode(1) # Menu Button
# self.connect(self.stopProcess, SIGNAL("clicked()"), self.stopThread)
self.statusBar().addPermanentWidget(self.stopProcess)
self.statusBar().addPermanentWidget(self.pb)
def updateStopProcessMenu(self):
"""
update the menu of the stop process
button, based directly on the processes
stored by the task manager
"""
self.stopProcess.menu().clear()
for c in QApplication.instance().taskManager:
self.stopProcess.menu().addAction(c.title)
# QApplication.instance().taskManager.abort(QApplication.instance().taskManager[-1])
def addMdiSubWindow(self, plot, title="", showMaximized=False):
"""
Allow addition of new window in the mdiarea
"""
win = self.mdiArea.addSubWindow(plot)
# print "widget parent", plot.parent()
win.setAttribute(Qt.WA_DeleteOnClose)
# win.connect(win, SIGNAL('destroyed(QObject *)'), self.testdestroy)
# plot.setParent(win)
win.setWindowTitle(title)
if showMaximized:
win.showMaximized()
else:
win.resize(400, 300)
win.show()
return win
def updateTreeView(self):
"""
Tree View update switch spectre/chromato
"""
if self.treeView.model() == self.spectraModel:
self.treeView.setModel(self.chromaModel)
self.tabWidget.setTabText(0, "Chroma")
else:
self.treeView.setModel(self.spectraModel)
# self.treeView.setSelectionMode(1)
self.tabWidget.setTabText(0, "Spectra")
def addTreeViewModel(self, model1, model2):
"""Add a model """
self.chromaModel.appendRow(model1)
self.spectraModel.appendRow(model2)
def _actionHovered(self, action):
"""emulate tooltip cause they do not work that much"""
tip = action.toolTip()
QToolTip.showText(QCursor.pos(), tip)
def showErrorMessage(self, title, string):
QMessageBox.critical(self, title, string, 0, 0)
def showWarningMessage(self, title, string):
return QMessageBox.warning(self, title, string, QMessageBox.Ok | QMessageBox.Cancel)
def showInformationMessage(self, title, string):
QMessageBox.information(self, title, string, 0)
def updateProgressBar(self, i):
"""update the value of the progress bar for all the treatment"""
self.pb.setValue(min(i, 100))
def to_indetermined_mode(self):
self.pb.setMaximum(0)
def to_determined_mode(self):
self.pb.setMaximum(100)
def showInStatusBar(self, string, time=5000):
self.statusBar().showMessage(string, time)
def addInterpreterDock(self, shell):
self.shellDock = QDockWidget(self)
self.shellDock.setWidget(shell)
self.shellDock.setWindowTitle("shell")
self.addDockWidget(0x2, self.shellDock)
def showMetMSInformation(self):
QMessageBox.about(
self,
self.tr("About %1").arg("metMS"),
self.tr(
"""<b>%1 %2</b>
<br>metabolite Mass Spectrometry
<p>Copyright © 2010 Marco INSA, INRA
<br>Licensed under the terms of the CeciLL License
<p>Developed and maintained by Marco
<br>Bug reports and feature requests:
<a href="http://github.com/jerkos/metms">metMS site</a><br>
Discussions around the project:
<a href="http://groups.google.com/group/spyderlib">Google Group</a>
<p>This project is part of the BRIDGE project
<p>Python %3, Qt %4, PyQt %5"""
)
.arg("metMS")
.arg(__version__)
.arg(platform.python_version())
.arg(QT_VERSION_STR)
.arg(PYQT_VERSION_STR),
)
class MenuBuilderDialog(QDialog, Ui_Dialog):
def __init__(self, uiparent):
super(MenuBuilderDialog, self).__init__()
self.setupUi(self)
# reference to caller
self.uiparent = uiparent
self.combo_profile.lineEdit().setPlaceholderText(
self.tr("Profile name"))
# add icons
self.button_add_menu.setIcon(
QIcon(":/plugins/MenuBuilder/resources/plus.svg"))
self.button_delete_profile.setIcon(
QIcon(":/plugins/MenuBuilder/resources/delete.svg"))
# custom qtreeview
self.target = CustomQtTreeView(self)
self.target.setGeometry(QRect(440, 150, 371, 451))
self.target.setAcceptDrops(True)
self.target.setDragEnabled(True)
self.target.setDragDropMode(QAbstractItemView.DragDrop)
self.target.setObjectName("target")
self.target.setDropIndicatorShown(True)
self.target.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.target.setHeaderHidden(True)
sizePolicy = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(
self.target.sizePolicy().hasHeightForWidth())
self.target.setSizePolicy(sizePolicy)
self.target.setAutoFillBackground(True)
self.verticalLayout_2.addWidget(self.target)
self.browser = QgsBrowserModel()
self.source.setModel(self.browser)
self.source.setHeaderHidden(True)
self.source.setDragEnabled(True)
self.source.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.menumodel = MenuTreeModel(self)
self.target.setModel(self.menumodel)
self.target.setAnimated(True)
# add a dock widget
self.dock_widget = QDockWidget("Menus")
self.dock_widget.resize(400, 300)
self.dock_widget.setFloating(True)
self.dock_widget.setObjectName(self.tr("Menu Tree"))
self.dock_widget_content = QWidget()
self.dock_widget.setWidget(self.dock_widget_content)
dock_layout = QVBoxLayout()
self.dock_widget_content.setLayout(dock_layout)
self.dock_view = DockQtTreeView(self.dock_widget_content)
self.dock_view.setDragDropMode(QAbstractItemView.DragOnly)
self.dock_menu_filter = QLineEdit()
self.dock_menu_filter.setPlaceholderText(
self.tr("Filter by table description (postgis only)"))
dock_layout.addWidget(self.dock_menu_filter)
dock_layout.addWidget(self.dock_view)
self.dock_view.setHeaderHidden(True)
self.dock_view.setDragEnabled(True)
self.dock_view.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.dock_view.setAnimated(True)
self.dock_view.setObjectName("treeView")
self.proxy_model = LeafFilterProxyModel(self)
self.proxy_model.setFilterRole(Qt.ToolTipRole)
self.proxy_model.setFilterCaseSensitivity(Qt.CaseInsensitive)
self.profile_list = []
self.table = 'qgis_menubuilder_metadata'
self.layer_handler = {
'vector': self.load_vector,
'raster': self.load_raster
}
# connect signals and handlers
self.combo_database.activated.connect(
partial(self.set_connection, dbname=None))
self.combo_schema.activated.connect(self.update_profile_list)
self.combo_profile.activated.connect(
partial(self.update_model_idx, self.menumodel))
self.button_add_menu.released.connect(self.add_menu)
self.button_delete_profile.released.connect(self.delete_profile)
self.dock_menu_filter.textEdited.connect(self.filter_update)
self.dock_view.doubleClicked.connect(self.load_from_index)
self.buttonBox.rejected.connect(self.reject)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.button(QDialogButtonBox.Apply).clicked.connect(
self.apply)
def filter_update(self):
text = self.dock_menu_filter.displayText()
self.proxy_model.setFilterRegExp(text)
def show_dock(self, state, profile=None, schema=None):
if not state:
# just hide widget
self.dock_widget.setVisible(state)
return
# dock must be read only and deepcopy of model is not supported (c++ inside!)
self.dock_model = MenuTreeModel(self)
if profile:
# bypass combobox
self.update_model(self.dock_model, schema, profile)
else:
self.update_model_idx(self.dock_model,
self.combo_profile.currentIndex())
self.dock_model.setHorizontalHeaderLabels(["Menus"])
self.dock_view.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.proxy_model.setSourceModel(self.dock_model)
self.dock_view.setModel(self.proxy_model)
self.dock_widget.setVisible(state)
def show_menus(self, state, profile=None, schema=None):
if state:
self.load_menus(profile=profile, schema=schema)
return
# remove menus
for menu in self.uiparent.menus:
self.uiparent.iface.mainWindow().menuBar().removeAction(
menu.menuAction())
def add_menu(self):
"""
Add a menu inside qtreeview
"""
item = QStandardItem('NewMenu')
item.setIcon(QIcon(':/plugins/MenuBuilder/resources/menu.svg'))
# select current index selected and insert as a sibling
brother = self.target.selectedIndexes()
if not brother or not brother[0].parent():
# no selection, add menu at the top level
self.menumodel.insertRow(self.menumodel.rowCount(), item)
return
parent = self.menumodel.itemFromIndex(brother[0].parent())
if not parent:
self.menumodel.insertRow(self.menumodel.rowCount(), item)
return
parent.appendRow(item)
def update_database_list(self):
"""update list of defined postgres connections"""
settings = QSettings()
settings.beginGroup("/PostgreSQL/connections")
keys = settings.childGroups()
self.combo_database.clear()
self.combo_schema.clear()
self.menumodel.clear()
self.combo_database.addItems(keys)
self.combo_database.setCurrentIndex(-1)
settings.endGroup()
# clear profile list
self.combo_profile.clear()
self.combo_profile.setCurrentIndex(-1)
def set_connection(self, databaseidx, dbname=None):
"""
Connect to selected postgresql database
"""
selected = self.combo_database.itemText(databaseidx) or dbname
if not selected:
return
settings = QSettings()
settings.beginGroup("/PostgreSQL/connections/{}".format(selected))
if not settings.contains("database"):
# no entry?
QMessageBox.critical(self, "Error",
"There is no defined database connection")
return
uri = QgsDataSourceURI()
settingsList = [
"service", "host", "port", "database", "username", "password"
]
service, host, port, database, username, password = map(
lambda x: settings.value(x, "", type=str), settingsList)
useEstimatedMetadata = settings.value("estimatedMetadata",
False,
type=bool)
sslmode = settings.value("sslmode",
QgsDataSourceURI.SSLprefer,
type=int)
settings.endGroup()
if service:
uri.setConnection(service, database, username, password, sslmode)
else:
uri.setConnection(host, port, database, username, password,
sslmode)
uri.setUseEstimatedMetadata(useEstimatedMetadata)
# connect to db
self.connect_to_uri(uri)
# update schema list
self.update_schema_list()
@contextmanager
def transaction(self):
try:
yield
self.connection.commit()
except self.pg_error_types() as e:
self.connection.rollback()
raise e
def check_connected(func):
"""
Decorator that checks if a database connection is active before executing function
"""
@wraps(func)
def wrapped(inst, *args, **kwargs):
if not getattr(inst, 'connection', False):
QMessageBox(
QMessageBox.Warning, "Menu Builder",
inst.tr(
"Not connected to any database, please select one"),
QMessageBox.Ok, inst).exec_()
return
if inst.connection.closed:
QMessageBox(
QMessageBox.Warning, "Menu Builder",
inst.tr(
"Not connected to any database, please select one"),
QMessageBox.Ok, inst).exec_()
return
return func(inst, *args, **kwargs)
return wrapped
def connect_to_uri(self, uri):
self.close_connection()
self.host = uri.host() or os.environ.get('PGHOST')
self.port = uri.port() or os.environ.get('PGPORT')
username = uri.username() or os.environ.get(
'PGUSER') or os.environ.get('USER')
password = uri.password() or os.environ.get('PGPASSWORD')
try:
self.connection = psycopg2.connect(uri.connectionInfo())
except self.pg_error_types() as e:
err = str(e)
conninfo = uri.connectionInfo()
ok, username, password = QgsCredentials.instance().get(
conninfo, username, password, err)
if not ok:
raise Exception(e)
if username:
uri.setUsername(username)
if password:
uri.setPassword(password)
self.connection = psycopg2.connect(uri.connectionInfo())
self.pgencoding = self.connection.encoding
return True
def pg_error_types(self):
return (psycopg2.InterfaceError, psycopg2.OperationalError,
psycopg2.ProgrammingError)
@check_connected
def update_schema_list(self):
self.combo_schema.clear()
with self.transaction():
cur = self.connection.cursor()
cur.execute("""
select nspname
from pg_namespace
where nspname not ilike 'pg_%'
and nspname not in ('pg_catalog', 'information_schema')
""")
schemas = [row[0] for row in cur.fetchall()]
self.combo_schema.addItems(schemas)
@check_connected
def update_profile_list(self, schemaidx):
"""
update profile list from database
"""
schema = self.combo_schema.itemText(schemaidx)
with self.transaction():
cur = self.connection.cursor()
cur.execute("""
select 1
from pg_tables
where schemaname = '{0}'
and tablename = '{1}'
union
select 1
from pg_matviews
where schemaname = '{0}'
and matviewname = '{1}'
""".format(schema, self.table))
tables = cur.fetchone()
if not tables:
box = QMessageBox(
QMessageBox.Warning, "Menu Builder",
self.tr("Table '{}.{}' not found in this database, "
"would you like to create it now ?").format(
schema, self.table),
QMessageBox.Cancel | QMessageBox.Yes, self)
ret = box.exec_()
if ret == QMessageBox.Cancel:
return False
elif ret == QMessageBox.Yes:
cur.execute("""
create table {}.{} (
id serial,
name varchar,
profile varchar,
model_index varchar,
datasource_uri text
)
""".format(schema, self.table))
self.connection.commit()
return False
cur.execute("""
select distinct(profile) from {}.{}
""".format(schema, self.table))
profiles = [row[0] for row in cur.fetchall()]
saved_profile = self.combo_profile.currentText()
self.combo_profile.clear()
self.combo_profile.addItems(profiles)
self.combo_profile.setCurrentIndex(
self.combo_profile.findText(saved_profile))
@check_connected
def delete_profile(self):
"""
Delete profile currently selected
"""
idx = self.combo_profile.currentIndex()
schema = self.combo_schema.currentText()
profile = self.combo_profile.itemText(idx)
box = QMessageBox(QMessageBox.Warning, "Menu Builder",
self.tr("Delete '{}' profile ?").format(profile),
QMessageBox.Cancel | QMessageBox.Yes, self)
ret = box.exec_()
if ret == QMessageBox.Cancel:
return False
elif ret == QMessageBox.Yes:
self.combo_profile.removeItem(idx)
with self.transaction():
cur = self.connection.cursor()
cur.execute("""
delete from {}.{}
where profile = '{}'
""".format(schema, self.table, profile))
self.menumodel.clear()
self.combo_profile.setCurrentIndex(-1)
def update_model_idx(self, model, profile_index):
"""
wrapper that checks combobox
"""
profile = self.combo_profile.itemText(profile_index)
schema = self.combo_schema.currentText()
self.update_model(model, schema, profile)
def sortby_modelindex(self, rows):
return sorted(
rows,
key=lambda line: '/'.join(
['{:04}'.format(elem[0]) for elem in json.loads(line[2])]))
@check_connected
def update_model(self, model, schema, profile):
"""
Update the model by retrieving the profile given in database
"""
menudict = {}
with self.transaction():
cur = self.connection.cursor()
select = """
select name, profile, model_index, datasource_uri
from {}.{}
where profile = '{}'
""".format(schema, self.table, profile)
cur.execute(select)
rows = cur.fetchall()
model.clear()
for name, profile, model_index, datasource_uri in self.sortby_modelindex(
rows):
menu = model.invisibleRootItem()
indexes = json.loads(model_index)
parent = ''
for idx, subname in indexes[:-1]:
parent += '{}-{}/'.format(idx, subname)
if parent in menudict:
# already created entry
menu = menudict[parent]
continue
# create menu
item = QStandardItem(subname)
uri_struct = QgsMimeDataUtils.Uri(datasource_uri)
item.setData(uri_struct)
item.setIcon(
QIcon(':/plugins/MenuBuilder/resources/menu.svg'))
item.setFlags(Qt.ItemIsSelectable | Qt.ItemIsUserCheckable
| Qt.ItemIsEnabled | Qt.ItemIsDropEnabled
| Qt.ItemIsEditable)
item.setWhatsThis("menu")
menu.appendRow(item)
menudict[parent] = item
# set current menu to the new created item
menu = item
# add leaf (layer item)
item = QStandardItem(name)
uri_struct = QgsMimeDataUtils.Uri(datasource_uri)
# fix layer name instead of table name
# usefull when the layer has been renamed in menu
uri_struct.name = name
if uri_struct.providerKey in ICON_MAPPER:
item.setIcon(QIcon(ICON_MAPPER[uri_struct.providerKey]))
item.setData(uri_struct)
# avoid placing dragged layers on it
item.setDropEnabled(False)
if uri_struct.providerKey == 'postgres':
# set tooltip to postgres comment
comment = self.get_table_comment(uri_struct.uri)
item.setToolTip(comment)
menudict[parent].appendRow(item)
@check_connected
def save_changes(self, save_to_db=True):
"""
Save changes in the postgres table
"""
schema = self.combo_schema.currentText()
profile = self.combo_profile.currentText()
if not profile:
QMessageBox(QMessageBox.Warning, "Menu Builder",
self.tr("Profile cannot be empty"), QMessageBox.Ok,
self).exec_()
return False
if save_to_db:
try:
with self.transaction():
cur = self.connection.cursor()
cur.execute(
"delete from {}.{} where profile = '{}'".format(
schema, self.table, profile))
for item, data in self.target.iteritems():
if not data:
continue
cur.execute(
"""
insert into {}.{} (name,profile,model_index,datasource_uri)
values (%s, %s, %s, %s)
""".format(schema, self.table),
(item[-1][1], profile, json.dumps(item),
data.data()))
except Exception as exc:
QMessageBox(QMessageBox.Warning, "Menu Builder",
exc.message.decode(self.pgencoding),
QMessageBox.Ok, self).exec_()
return False
self.save_session(self.combo_database.currentText(), schema, profile,
self.activate_dock.isChecked(),
self.activate_menubar.isChecked())
self.update_profile_list(self.combo_schema.currentIndex())
self.show_dock(self.activate_dock.isChecked())
self.show_menus(self.activate_menubar.isChecked())
return True
@check_connected
def load_menus(self, profile=None, schema=None):
"""
Load menus in the main windows qgis bar
"""
if not schema:
schema = self.combo_schema.currentText()
if not profile:
profile = self.combo_profile.currentText()
# remove previous menus
for menu in self.uiparent.menus:
self.uiparent.iface.mainWindow().menuBar().removeAction(
menu.menuAction())
with self.transaction():
cur = self.connection.cursor()
select = """
select name, profile, model_index, datasource_uri
from {}.{}
where profile = '{}'
""".format(schema, self.table, profile)
cur.execute(select)
rows = cur.fetchall()
# item accessor ex: '0-menu/0-submenu/1-item/'
menudict = {}
# reference to parent item
parent = ''
# reference to qgis main menu bar
menubar = self.uiparent.iface.mainWindow().menuBar()
for name, profile, model_index, datasource_uri in self.sortby_modelindex(
rows):
uri_struct = QgsMimeDataUtils.Uri(datasource_uri)
indexes = json.loads(model_index)
# root menu
parent = '{}-{}/'.format(indexes[0][0], indexes[0][1])
if parent not in menudict:
menu = QMenu(self.uiparent.iface.mainWindow())
self.uiparent.menus.append(menu)
menu.setObjectName(indexes[0][1])
menu.setTitle(indexes[0][1])
menubar.insertMenu(
self.uiparent.iface.firstRightStandardMenu().menuAction(),
menu)
menudict[parent] = menu
else:
# menu already there
menu = menudict[parent]
for idx, subname in indexes[1:-1]:
# intermediate submenus
parent += '{}-{}/'.format(idx, subname)
if parent not in menudict:
submenu = menu.addMenu(subname)
submenu.setObjectName(subname)
submenu.setTitle(subname)
menu = submenu
# store it for later use
menudict[parent] = menu
continue
# already treated
menu = menudict[parent]
# last item = layer
layer = QAction(name, self.uiparent.iface.mainWindow())
if uri_struct.providerKey in ICON_MAPPER:
layer.setIcon(QIcon(ICON_MAPPER[uri_struct.providerKey]))
if uri_struct.providerKey == 'postgres':
# set tooltip to postgres comment
comment = self.get_table_comment(uri_struct.uri)
layer.setStatusTip(comment)
layer.setToolTip(comment)
layer.setData(uri_struct.uri)
layer.setWhatsThis(uri_struct.providerKey)
layer.triggered.connect(self.layer_handler[uri_struct.layerType])
menu.addAction(layer)
def get_table_comment(self, uri):
schema, table = re.match('.*table=(.*)\(.*',
uri).group(1).strip().replace('"',
'').split('.')
with self.transaction():
cur = self.connection.cursor()
select = """
select description from pg_description
join pg_class on pg_description.objoid = pg_class.oid
join pg_namespace on pg_class.relnamespace = pg_namespace.oid
where relname = '{}' and nspname='{}'
""".format(table, schema)
cur.execute(select)
row = cur.fetchone()
if row:
return row[0]
return ''
def load_from_index(self, index):
"""Load layers from selected item index"""
item = self.dock_model.itemFromIndex(
self.proxy_model.mapToSource(index))
if item.whatsThis() == 'menu':
return
if item.data().layerType == 'vector':
layer = QgsVectorLayer(
item.data().uri, # uri
item.text(), # layer name
item.data().providerKey # provider name
)
elif item.data().layerType == 'raster':
layer = QgsRasterLayer(
item.data().uri, # uri
item.text(), # layer name
item.data().providerKey # provider name
)
if not layer:
return
QgsMapLayerRegistry.instance().addMapLayer(layer)
def load_vector(self):
action = self.sender()
layer = QgsVectorLayer(
action.data(), # uri
action.text(), # layer name
action.whatsThis() # provider name
)
QgsMapLayerRegistry.instance().addMapLayer(layer)
def load_raster(self):
action = self.sender()
layer = QgsRasterLayer(
action.data(), # uri
action.text(), # layer name
action.whatsThis() # provider name
)
QgsMapLayerRegistry.instance().addMapLayer(layer)
def accept(self):
if self.save_changes():
QDialog.reject(self)
self.close_connection()
def apply(self):
if self.save_changes(save_to_db=False):
QDialog.reject(self)
def reject(self):
self.close_connection()
QDialog.reject(self)
def close_connection(self):
"""close current pg connection if exists"""
if getattr(self, 'connection', False):
if self.connection.closed:
return
self.connection.close()
def save_session(self, database, schema, profile, dock, menubar):
"""save current profile for next session"""
settings = QSettings()
settings.setValue("MenuBuilder/database", database)
settings.setValue("MenuBuilder/schema", schema)
settings.setValue("MenuBuilder/profile", profile)
settings.setValue("MenuBuilder/dock", dock)
settings.setValue("MenuBuilder/menubar", menubar)
def restore_session(self):
settings = QSettings()
database = settings.value("MenuBuilder/database", False)
schema = settings.value("MenuBuilder/schema", 'public')
profile = settings.value("MenuBuilder/profile", False)
dock = settings.value("MenuBuilder/dock", False)
menubar = settings.value("MenuBuilder/menubar", False)
if not any([database, profile]):
return
self.set_connection(0, dbname=database)
self.show_dock(bool(dock), profile=profile, schema=schema)
if bool(dock):
self.uiparent.iface.addDockWidget(Qt.LeftDockWidgetArea,
self.dock_widget)
self.show_menus(bool(menubar), profile=profile, schema=schema)
class MenuBuilderDialog(QDialog, FORM_CLASS):
def __init__(self, uiparent):
super(MenuBuilderDialog, self).__init__()
self.setupUi(self)
# reference to caller
self.uiparent = uiparent
self.combo_profile.lineEdit().setPlaceholderText(self.tr("Profile name"))
# add icons
self.button_add_menu.setIcon(QIcon(":/plugins/MenuBuilder/resources/plus.svg"))
self.button_delete_profile.setIcon(QIcon(":/plugins/MenuBuilder/resources/delete.svg"))
# custom qtreeview
self.target = CustomQtTreeView(self)
self.target.setGeometry(QRect(440, 150, 371, 451))
self.target.setAcceptDrops(True)
self.target.setDragEnabled(True)
self.target.setDragDropMode(QAbstractItemView.DragDrop)
self.target.setObjectName("target")
self.target.setDropIndicatorShown(True)
self.target.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.target.setHeaderHidden(True)
sizePolicy = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.target.sizePolicy().hasHeightForWidth())
self.target.setSizePolicy(sizePolicy)
self.target.setAutoFillBackground(True)
self.verticalLayout_2.addWidget(self.target)
self.browser = QgsBrowserModel()
self.source.setModel(self.browser)
self.source.setHeaderHidden(True)
self.source.setDragEnabled(True)
self.source.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.menumodel = MenuTreeModel(self)
self.target.setModel(self.menumodel)
self.target.setAnimated(True)
# add a dock widget
self.dock_widget = QDockWidget("Menus", self.uiparent.iface.mainWindow())
self.dock_widget.resize(400, 300)
self.dock_widget.setFloating(True)
self.dock_widget.setObjectName(self.tr("Menu Tree"))
self.dock_widget_content = QWidget()
self.dock_widget.setWidget(self.dock_widget_content)
dock_layout = QVBoxLayout()
self.dock_widget_content.setLayout(dock_layout)
self.dock_view = DockQtTreeView(self.dock_widget_content)
self.dock_view.setDragDropMode(QAbstractItemView.DragOnly)
self.dock_menu_filter = QLineEdit()
self.dock_menu_filter.setPlaceholderText(self.tr("Filter by table description (postgis only)"))
dock_layout.addWidget(self.dock_menu_filter)
dock_layout.addWidget(self.dock_view)
self.dock_view.setHeaderHidden(True)
self.dock_view.setDragEnabled(True)
self.dock_view.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.dock_view.setAnimated(True)
self.dock_view.setObjectName("treeView")
self.proxy_model = LeafFilterProxyModel(self)
self.proxy_model.setFilterRole(Qt.ToolTipRole)
self.proxy_model.setFilterCaseSensitivity(Qt.CaseInsensitive)
self.profile_list = []
self.table = 'qgis_menubuilder_metadata'
self.layer_handler = {
'vector': self.load_vector,
'raster': self.load_raster
}
# connect signals and handlers
self.combo_database.activated.connect(partial(self.set_connection, dbname=None))
self.combo_schema.activated.connect(self.update_profile_list)
self.combo_profile.activated.connect(partial(self.update_model_idx, self.menumodel))
self.button_add_menu.released.connect(self.add_menu)
self.button_delete_profile.released.connect(self.delete_profile)
self.dock_menu_filter.textEdited.connect(self.filter_update)
self.dock_view.doubleClicked.connect(self.load_from_index)
def filter_update(self):
text = self.dock_menu_filter.displayText()
self.proxy_model.setFilterRegExp(text)
def show_dock(self, state, profile=None, schema=None):
if not state:
# just hide widget
self.dock_widget.setVisible(state)
return
# dock must be read only and deepcopy of model is not supported (c++ inside!)
self.dock_model = MenuTreeModel(self)
if profile:
# bypass combobox
self.update_model(self.dock_model, schema, profile)
else:
self.update_model_idx(self.dock_model, self.combo_profile.currentIndex())
self.dock_model.setHorizontalHeaderLabels(["Menus"])
self.dock_view.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.proxy_model.setSourceModel(self.dock_model)
self.dock_view.setModel(self.proxy_model)
self.dock_widget.setVisible(state)
def show_menus(self, state, profile=None, schema=None):
if state:
self.load_menus(profile=profile, schema=schema)
return
# remove menus
for menu in self.uiparent.menus:
self.uiparent.iface.mainWindow().menuBar().removeAction(menu.menuAction())
def add_menu(self):
"""
Add a menu inside qtreeview
"""
item = QStandardItem('NewMenu')
item.setIcon(QIcon(':/plugins/MenuBuilder/resources/menu.svg'))
# select current index selected and insert as a sibling
brother = self.target.selectedIndexes()
if not brother or not brother[0].parent():
# no selection, add menu at the top level
self.menumodel.insertRow(self.menumodel.rowCount(), item)
return
parent = self.menumodel.itemFromIndex(brother[0].parent())
if not parent:
self.menumodel.insertRow(self.menumodel.rowCount(), item)
return
parent.appendRow(item)
def update_database_list(self):
"""update list of defined postgres connections"""
settings = QSettings()
settings.beginGroup("/PostgreSQL/connections")
keys = settings.childGroups()
self.combo_database.clear()
self.combo_schema.clear()
self.menumodel.clear()
self.combo_database.addItems(keys)
self.combo_database.setCurrentIndex(-1)
settings.endGroup()
# clear profile list
self.combo_profile.clear()
self.combo_profile.setCurrentIndex(-1)
def set_connection(self, databaseidx, dbname=None):
"""
Connect to selected postgresql database
"""
selected = self.combo_database.itemText(databaseidx) or dbname
if not selected:
return
settings = QSettings()
settings.beginGroup("/PostgreSQL/connections/{}".format(selected))
if not settings.contains("database"):
# no entry?
QMessageBox.critical(self, "Error", "There is no defined database connection")
return
uri = QgsDataSourceURI()
settingsList = ["service", "host", "port", "database", "username", "password"]
service, host, port, database, username, password = map(
lambda x: settings.value(x, "", type=str), settingsList)
useEstimatedMetadata = settings.value("estimatedMetadata", False, type=bool)
sslmode = settings.value("sslmode", QgsDataSourceURI.SSLprefer, type=int)
settings.endGroup()
if service:
uri.setConnection(service, database, username, password, sslmode)
else:
uri.setConnection(host, port, database, username, password, sslmode)
uri.setUseEstimatedMetadata(useEstimatedMetadata)
# connect to db
self.connect_to_uri(uri)
# update schema list
self.update_schema_list()
@contextmanager
def transaction(self):
try:
yield
self.connection.commit()
except self.pg_error_types() as e:
self.connection.rollback()
raise e
def check_connected(func):
"""
Decorator that checks if a database connection is active before executing function
"""
@wraps(func)
def wrapped(inst, *args, **kwargs):
if not getattr(inst, 'connection', False):
QMessageBox(
QMessageBox.Warning,
"Menu Builder",
inst.tr("Not connected to any database, please select one"),
QMessageBox.Ok,
inst
).exec_()
return
if inst.connection.closed:
QMessageBox(
QMessageBox.Warning,
"Menu Builder",
inst.tr("Not connected to any database, please select one"),
QMessageBox.Ok,
inst
).exec_()
return
return func(inst, *args, **kwargs)
return wrapped
def connect_to_uri(self, uri):
self.close_connection()
self.host = uri.host() or os.environ.get('PGHOST')
self.port = uri.port() or os.environ.get('PGPORT')
username = uri.username() or os.environ.get('PGUSER') or os.environ.get('USER')
password = uri.password() or os.environ.get('PGPASSWORD')
try:
self.connection = psycopg2.connect(uri.connectionInfo())
except self.pg_error_types() as e:
err = str(e)
conninfo = uri.connectionInfo()
ok, username, password = QgsCredentials.instance().get(
conninfo, username, password, err)
if not ok:
raise Exception(e)
if username:
uri.setUsername(username)
if password:
uri.setPassword(password)
self.connection = psycopg2.connect(uri.connectionInfo())
self.pgencoding = self.connection.encoding
return True
def pg_error_types(self):
return psycopg2.InterfaceError,\
psycopg2.OperationalError,\
psycopg2.ProgrammingError
@check_connected
def update_schema_list(self):
self.combo_schema.clear()
with self.transaction():
cur = self.connection.cursor()
cur.execute("""
select nspname
from pg_namespace
where nspname not ilike 'pg_%'
and nspname not in ('pg_catalog', 'information_schema')
""")
schemas = [row[0] for row in cur.fetchall()]
self.combo_schema.addItems(schemas)
@check_connected
def update_profile_list(self, schemaidx):
"""
update profile list from database
"""
schema = self.combo_schema.itemText(schemaidx)
with self.transaction():
cur = self.connection.cursor()
cur.execute("""
select 1
from pg_tables
where schemaname = '{0}'
and tablename = '{1}'
union
select 1
from pg_matviews
where schemaname = '{0}'
and matviewname = '{1}'
""".format(schema, self.table))
tables = cur.fetchone()
if not tables:
box = QMessageBox(
QMessageBox.Warning,
"Menu Builder",
self.tr("Table '{}.{}' not found in this database, "
"would you like to create it now ?")
.format(schema, self.table),
QMessageBox.Cancel | QMessageBox.Yes,
self
)
ret = box.exec_()
if ret == QMessageBox.Cancel:
return False
elif ret == QMessageBox.Yes:
cur.execute("""
create table {}.{} (
id serial,
name varchar,
profile varchar,
model_index varchar,
datasource_uri text
)
""".format(schema, self.table))
self.connection.commit()
return False
cur.execute("""
select distinct(profile) from {}.{}
""".format(schema, self.table))
profiles = [row[0] for row in cur.fetchall()]
saved_profile = self.combo_profile.currentText()
self.combo_profile.clear()
self.combo_profile.addItems(profiles)
self.combo_profile.setCurrentIndex(self.combo_profile.findText(saved_profile))
@check_connected
def delete_profile(self):
"""
Delete profile currently selected
"""
idx = self.combo_profile.currentIndex()
schema = self.combo_schema.currentText()
profile = self.combo_profile.itemText(idx)
box = QMessageBox(
QMessageBox.Warning,
"Menu Builder",
self.tr("Delete '{}' profile ?").format(profile),
QMessageBox.Cancel | QMessageBox.Yes,
self
)
ret = box.exec_()
if ret == QMessageBox.Cancel:
return False
elif ret == QMessageBox.Yes:
self.combo_profile.removeItem(idx)
with self.transaction():
cur = self.connection.cursor()
cur.execute("""
delete from {}.{}
where profile = '{}'
""".format(schema, self.table, profile))
self.menumodel.clear()
self.combo_profile.setCurrentIndex(-1)
def update_model_idx(self, model, profile_index):
"""
wrapper that checks combobox
"""
profile = self.combo_profile.itemText(profile_index)
schema = self.combo_schema.currentText()
self.update_model(model, schema, profile)
def sortby_modelindex(self, rows):
return sorted(
rows,
key=lambda line: '/'.join(
['{:04}'.format(elem[0]) for elem in json.loads(line[2])]
))
@check_connected
def update_model(self, model, schema, profile):
"""
Update the model by retrieving the profile given in database
"""
menudict = {}
with self.transaction():
cur = self.connection.cursor()
select = """
select name, profile, model_index, datasource_uri
from {}.{}
where profile = '{}'
""".format(schema, self.table, profile)
cur.execute(select)
rows = cur.fetchall()
model.clear()
for name, profile, model_index, datasource_uri in self.sortby_modelindex(rows):
menu = model.invisibleRootItem()
indexes = json.loads(model_index)
parent = ''
for idx, subname in indexes[:-1]:
parent += '{}-{}/'.format(idx, subname)
if parent in menudict:
# already created entry
menu = menudict[parent]
continue
# create menu
item = QStandardItem(subname)
uri_struct = QgsMimeDataUtils.Uri(datasource_uri)
item.setData(uri_struct)
item.setIcon(QIcon(':/plugins/MenuBuilder/resources/menu.svg'))
item.setFlags(Qt.ItemIsSelectable | Qt.ItemIsUserCheckable |
Qt.ItemIsEnabled | Qt.ItemIsDropEnabled |
Qt.ItemIsEditable)
item.setWhatsThis("menu")
menu.appendRow(item)
menudict[parent] = item
# set current menu to the new created item
menu = item
# add leaf (layer item)
item = QStandardItem(name)
uri_struct = QgsMimeDataUtils.Uri(datasource_uri)
# fix layer name instead of table name
# usefull when the layer has been renamed in menu
uri_struct.name = name
if uri_struct.providerKey in ICON_MAPPER:
item.setIcon(QIcon(ICON_MAPPER[uri_struct.providerKey]))
item.setData(uri_struct)
# avoid placing dragged layers on it
item.setDropEnabled(False)
if uri_struct.providerKey == 'postgres':
# set tooltip to postgres comment
comment = self.get_table_comment(uri_struct.uri)
item.setToolTip(comment)
menudict[parent].appendRow(item)
@check_connected
def save_changes(self):
"""
Save changes in the postgres table
"""
schema = self.combo_schema.currentText()
profile = self.combo_profile.currentText()
if not profile:
QMessageBox(
QMessageBox.Warning,
"Menu Builder",
self.tr("Profile cannot be empty"),
QMessageBox.Ok,
self
).exec_()
return False
try:
with self.transaction():
cur = self.connection.cursor()
cur.execute("delete from {}.{} where profile = '{}'".format(
schema, self.table, profile))
for item, data in self.target.iteritems():
if not data:
continue
cur.execute("""
insert into {}.{} (name,profile,model_index,datasource_uri)
values (%s, %s, %s, %s)
""".format(schema, self.table), (
item[-1][1],
profile,
json.dumps(item),
data.data())
)
except psycopg2.ProgrammingError as exc:
QMessageBox(
QMessageBox.Warning,
"Menu Builder",
exc.message.decode(self.pgencoding),
QMessageBox.Ok,
self
).exec_()
self.save_session(
self.combo_database.currentText(),
schema,
profile,
self.activate_dock.isChecked(),
self.activate_menubar.isChecked()
)
self.update_profile_list(self.combo_schema.currentIndex())
self.show_dock(self.activate_dock.isChecked())
self.show_menus(self.activate_menubar.isChecked())
return True
@check_connected
def load_menus(self, profile=None, schema=None):
"""
Load menus in the main windows qgis bar
"""
if not schema:
schema = self.combo_schema.currentText()
if not profile:
profile = self.combo_profile.currentText()
# remove previous menus
for menu in self.uiparent.menus:
self.uiparent.iface.mainWindow().menuBar().removeAction(menu.menuAction())
with self.transaction():
cur = self.connection.cursor()
select = """
select name, profile, model_index, datasource_uri
from {}.{}
where profile = '{}'
""".format(schema, self.table, profile)
cur.execute(select)
rows = cur.fetchall()
# item accessor ex: '0-menu/0-submenu/1-item/'
menudict = {}
# reference to parent item
parent = ''
# reference to qgis main menu bar
menubar = self.uiparent.iface.mainWindow().menuBar()
for name, profile, model_index, datasource_uri in self.sortby_modelindex(rows):
uri_struct = QgsMimeDataUtils.Uri(datasource_uri)
indexes = json.loads(model_index)
# root menu
parent = '{}-{}/'.format(indexes[0][0], indexes[0][1])
if parent not in menudict:
menu = QMenu(self.uiparent.iface.mainWindow())
self.uiparent.menus.append(menu)
menu.setObjectName(indexes[0][1])
menu.setTitle(indexes[0][1])
menubar.insertMenu(
self.uiparent.iface.firstRightStandardMenu().menuAction(),
menu)
menudict[parent] = menu
else:
# menu already there
menu = menudict[parent]
for idx, subname in indexes[1:-1]:
# intermediate submenus
parent += '{}-{}/'.format(idx, subname)
if parent not in menudict:
submenu = menu.addMenu(subname)
submenu.setObjectName(subname)
submenu.setTitle(subname)
menu = submenu
# store it for later use
menudict[parent] = menu
continue
# already treated
menu = menudict[parent]
# last item = layer
layer = QAction(name, self.uiparent.iface.mainWindow())
if uri_struct.providerKey in ICON_MAPPER:
layer.setIcon(QIcon(ICON_MAPPER[uri_struct.providerKey]))
if uri_struct.providerKey == 'postgres':
# set tooltip to postgres comment
comment = self.get_table_comment(uri_struct.uri)
layer.setStatusTip(comment)
layer.setToolTip(comment)
layer.setData(uri_struct.uri)
layer.setWhatsThis(uri_struct.providerKey)
layer.triggered.connect(self.layer_handler[uri_struct.layerType])
menu.addAction(layer)
def get_table_comment(self, uri):
schema, table = re.match(
'.*table=(.*)\(.*',
uri
).group(1).strip().replace('"', '').split('.')
with self.transaction():
cur = self.connection.cursor()
select = """
select description from pg_description
join pg_class on pg_description.objoid = pg_class.oid
join pg_namespace on pg_class.relnamespace = pg_namespace.oid
where relname = '{}' and nspname='{}'
""".format(table, schema)
cur.execute(select)
row = cur.fetchone()
if row:
return row[0]
return ''
def load_from_index(self, index):
"""Load layers from selected item index"""
item = self.dock_model.itemFromIndex(self.proxy_model.mapToSource(index))
if item.whatsThis() == 'menu':
return
if item.data().layerType == 'vector':
layer = QgsVectorLayer(
item.data().uri, # uri
item.text(), # layer name
item.data().providerKey # provider name
)
elif item.data().layerType == 'raster':
layer = QgsRasterLayer(
item.data().uri, # uri
item.text(), # layer name
item.data().providerKey # provider name
)
if not layer:
return
QgsMapLayerRegistry.instance().addMapLayer(layer)
def load_vector(self):
action = self.sender()
layer = QgsVectorLayer(
action.data(), # uri
action.text(), # layer name
action.whatsThis() # provider name
)
QgsMapLayerRegistry.instance().addMapLayer(layer)
def load_raster(self):
action = self.sender()
layer = QgsRasterLayer(
action.data(), # uri
action.text(), # layer name
action.whatsThis() # provider name
)
QgsMapLayerRegistry.instance().addMapLayer(layer)
def accept(self):
if self.save_changes():
QDialog.reject(self)
self.close_connection()
def reject(self):
self.close_connection()
QDialog.reject(self)
def close_connection(self):
"""close current pg connection if exists"""
if getattr(self, 'connection', False):
if self.connection.closed:
return
self.connection.close()
def save_session(self, database, schema, profile, dock, menubar):
"""save current profile for next session"""
settings = QSettings()
settings.setValue("MenuBuilder/database", database)
settings.setValue("MenuBuilder/schema", schema)
settings.setValue("MenuBuilder/profile", profile)
settings.setValue("MenuBuilder/dock", dock)
settings.setValue("MenuBuilder/menubar", menubar)
def restore_session(self):
settings = QSettings()
database = settings.value("MenuBuilder/database", False)
schema = settings.value("MenuBuilder/schema", 'public')
profile = settings.value("MenuBuilder/profile", False)
dock = settings.value("MenuBuilder/dock", False)
menubar = settings.value("MenuBuilder/menubar", False)
if not any([database, profile]):
return
self.set_connection(0, dbname=database)
self.show_dock(bool(dock), profile=profile, schema=schema)
self.show_menus(bool(menubar), profile=profile, schema=schema)
class MSMainWindow(QMainWindow):
"""Gui of the main window"""
#MAX_RECENT_FILES = 10
#start putting links spyder numpy scipy et tutti quanti
links=('http://numpy.scipy.org/',
'http://packages.python.org/spyder/',
'http://www.riverbankcomputing.co.uk/software/pyqt/intro')
pluginPath=path.normcase('pluginmanager/plugins/')
def __init__(self, availablePlugins):
"""
Constructor with all the models needed setup menus
"""
QMainWindow.__init__(self)
self.setDockOptions(QMainWindow.VerticalTabs | QMainWindow.AnimatedDocks)
self.plugins = availablePlugins
self.pluginsInst=[]
settings=QSettings('INRA/INSA', '-'.join([QApplication.instance().APPLICATION_NAME_STR,
QApplication.instance().VERSION_STR]))
self.recentFiles = list(settings.value("RecentFiles").toStringList())
self.setStyleSheet(stylesheet)
self.pipeline = MSPipelineToolBar("Pipeline toolbar", parent=self)
self.addToolBar(0x1,self.pipeline)
self._setupModels()
self._setupUi()
self._setupMenus()
def _setupModels(self):
"""
Warning:Causes segfault when horizontal labels set to True
on aura peu etre a la fin un model par sampleList c'est ce qui parait
le plus logique
"""
#drag and drop table sample
self.sampleModel = QStandardItemModel(self)
self.sampleModel.setHorizontalHeaderLabels(["Sample", "Class"])
#treeView1
self.spectraModel = QStandardItemModel(self)
#treeview2
self.peakModel = QStandardItemModel(self)
#treeview3
self.clusterModel = QStandardItemModel(self)
def _setupMenus(self):
#file
self.fileMenu = QMenu('&File')
self.fileMenu.setTearOffEnabled(True)
self.op=QMenu("&Open...",self.fileMenu)
self.op.setIcon(QIcon(path.normcase("gui/icons/fileopen.png")))
open_=QAction("&Open rawfiles", self)
open_.setToolTip("Open an mzXML or netCDF file")
open_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_O))
open_icon=QIcon(path.normcase("gui/icons/fileopen.png"))
open_.setIcon(open_icon)
self.op.addAction(open_)
load_=QAction("&Open projects...", self)
load_.setToolTip("load binary file containing saved objects")
load_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_S))
load_icon=QIcon(QPixmap(path.normcase("gui/icons/project_open.png")))
load_.setIcon(load_icon)
self.op.addAction(load_)
self.fileMenu.addMenu(self.op)
save_=QAction("&Save...", self)
save_.setToolTip("save the actual application model")
save_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_S))
save_icon=QIcon(path.normcase("gui/icons/save_all.png"))
save_.setIcon(save_icon)
self.fileMenu.addAction(save_)
pkl = QAction("&load a peaklist", self) #TODO:load peaklist
pkl.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_P))
pkl.setToolTip("load a peaklist and process it")
pkl.setIcon(QIcon(path.normcase("gui/icons/featuredetect.png")))
self.fileMenu.addAction(pkl)
convert_=QAction("&Convert...", self)
convert_.setEnabled(False)
convert_.setToolTip("Convert a .wiff file if Analyst(c) is installed")
convert_icon=QIcon(path.normcase("gui/icons/goto.png"))
convert_.setIcon(convert_icon)
self.fileMenu.addAction(convert_)
a = self.fileMenu.addAction(QIcon(path.normcase("gui/icons/process.png")), "&Launch a batch")
a.setEnabled(False)
b = self.fileMenu.addAction(QIcon(path.normcase("gui/icons/process.png")), "&Merge")
b.setToolTip("Merge MRM file")
#b.setEnabled(False)
self.fileMenu.addSeparator()
#
# for i in xrange(self.MAX_RECENT_FILES):
# a = QAction('', self)
# a.setVisible(False)
# self.fileMenu.addAction(a)
#
# for i in xrange(min(self.MAX_RECENT_FILES, len(self.recentFiles))):
# self.fileMenu.actions()[5+i].setVisible(True)
# self.fileMenu.actions()[5+i].setText(self.recentFiles[i].split('/')[-1])
exit_action =QAction("&Exit", self)
exit_action.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_Q))
exit_action.setIcon(QIcon(QPixmap(path.normcase('gui/icons/exit.png'))))
self.fileMenu.addAction(exit_action)
self.menuBar().addMenu(self.fileMenu)
self.editMenu=QMenu("&Edit")
self.editMenu.setTearOffEnabled(True)
self.editMenu.addAction(QIcon(path.normcase('gui/icons/edit_undo.png')), '&Undo...')
self.editMenu.addAction(QIcon(path.normcase('gui/icons/edit_redo.png')), '&Redo...')
self.editMenu.actions()[0].setEnabled(False)
self.editMenu.actions()[1].setEnabled(False)
self.editMenu.addSeparator()
self.editMenu.addAction(QIcon(path.normcase('gui/icons/run.png')), '&Preferences')
self.exportMenu = QMenu("&Export...")
self.exportMenu.setIcon(QIcon(path.normcase('gui/icons/file_export.png')))
self.exportMenu.addAction("&Peaklist")
self.exportMenu.addAction("&Clusters intensity matrix")
self.editMenu.addMenu(self.exportMenu)
self.menuBar().addMenu(self.editMenu)
#view
self.viewMenu =QMenu("&View")
self.viewMenu.setTearOffEnabled(True)
self.viewMenu.addAction(QIcon(path.normcase('gui/icons/window_duplicate')),
"&Cascade View",
self.mdiArea.cascadeSubWindows,
QKeySequence(Qt.CTRL + Qt.Key_K))
self.viewMenu.addAction(QIcon(path.normcase('gui/icons/view_icon')),
"&Title View",
self.mdiArea.tileSubWindows,
QKeySequence(Qt.CTRL + Qt.Key_N))
self.viewMenu.addAction(QIcon(path.normcase("gui/icons/stop_process.png")),
"&Close all subWindows",
self.mdiArea.closeAllSubWindows,
QKeySequence(Qt.CTRL+Qt.Key_W))
self.plotting =QMenu("&Plotting...")
self.plotting.setIcon(QIcon(QPixmap(path.normcase("gui/icons/plot.png"))))
self.plotting.addAction("&3D Plot")
#self.plotting.addAction("&Cytoscape web")
self.plotting.addAction("&Spectrogram Plot")
#self.multiplePlot = QAction("&Visualize Raw/Treated Data", self)
#self.multiplePlot.setCheckable(True)
#self.multiplePlot.setEnabled(False)
#self.sub_plot_.addAction(self.multiplePlot)
self.viewMenu.addMenu(self.plotting)
self.viewMenu.addSeparator()
self.show_hide=QMenu("&Show/Hide")
m=self.createPopupMenu()
m.setTitle("&Show/Hide")
self.viewMenu.addMenu(m)
#self.pref = QMenu("&Preferences")
#self.pref.addAction(self.multiplePlot)
#self.viewMenu.addMenu(self.pref)
self.menuBar().addMenu(self.viewMenu)
#algorithm
self.algoMenu= QMenu("&Algorithm")
self.algoMenu.setTearOffEnabled(True)
self.preProcessing=QMenu("&PreProcessing(experimental)")
self.preProcessing.addAction("&Smoothing raw data...")
self.preProcessing.addAction("&Cut off raw data...")
self.preProcessing.addAction('&Calibration (mz dimension)')
self.preProcessing.addAction("&Resize sample...")
self.algoMenu.addMenu(self.preProcessing)
self.peakPickingMenu = QMenu("&Peack Picking & Alignement(XCMS)", self)
self.peakPickingMenu.setIcon(QIcon(path.normcase("gui/icons/pickedpeakicon.png")))
matched = QAction("&MatchedFiltered", self)
matched.setIcon(QIcon(path.normcase('gui/icons/RLogo')))
matched.setToolTip("Peak Detection and Integration using MatchedFiltered algorithm")
self.peakPickingMenu.addAction(matched)
centwave=QAction("&CentWave", self)
centwave.setIcon(QIcon(path.normcase('gui/icons/RLogo')))
centwave.setToolTip("Peak Detection and Integration using CentWave algorithm")
self.peakPickingMenu.addAction(centwave)
#peak_.setShortcut(.QKeySequence(CTRL + Key_P))
# peak_icon=.QIcon(.QPixmap(path.normcase("gui/icons/pickedpeakicon.png")))
#peak_.setIcon(peak_icon)
self.algoMenu.addMenu(self.peakPickingMenu)
self.alignment = QMenu("&Alignment")
self.alignment.setIcon(QIcon(path.normcase('gui/icons/format_indent_more.png')))
self.alignment.addAction("&Polynomial fitting(exp)")
self.alignment.addAction("&DynamicTimeWarping")
self.alignment.addAction("&ObiWarp")
self.alignment.actions()[2].setEnabled(False)
self.algoMenu.addMenu(self.alignment)
self.algoMenu.addAction("Normalization")
clust_ = QAction("&Clustering", self)
clust_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_L))
clust_icon=QIcon(QPixmap(path.normcase("gui/icons/cluster.png")))
clust_.setIcon(clust_icon)
self.algoMenu.addAction(clust_)
id_ = QAction("&Identification", self)
id_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_I))
id_.setToolTip("Try to identify peaks with several methods")
id_.setIcon(QIcon(QPixmap(path.normcase("gui/icons/findcompound.png"))))
self.algoMenu.addAction(id_)
self.menuBar().addMenu(self.algoMenu)
#tools
self.toolsMenu =QMenu("&Tools")
self.toolsMenu.setTearOffEnabled(True)
web = QAction("&Web Browser", self)
web.setIcon(QIcon(QPixmap(path.normcase("gui/icons/applications_internet.png"))))
self.toolsMenu.addAction(web)
#cyto = QAction("&cytoscape", self)
#cyto_icon =QIcon(QPixmap(path.normcase("gui/icons/cytoscape.jpeg")))
#cyto.setIcon(cyto_icon)
#self.toolsMenu.addAction(cyto)
editor = QAction("&Editor", self)
editor.setIcon(QIcon(QPixmap(path.normcase("gui/icons/document_sign.png"))))
self.toolsMenu.addAction(editor)
pet=QAction("&Short Periodic Table", self)
pet.setIcon(QIcon(QPixmap(path.normcase("gui/icons/pet.jpg"))))
self.toolsMenu.addAction(pet)
self.menuBar().addMenu(self.toolsMenu)
#plugins
self.pluginMenu = QMenu('&Plugins')
self.pluginMenu.setTearOffEnabled(True)
instPl= QAction("&Install a plugin", self)
instPl.setIcon(QIcon(path.normcase('gui/icons/pluginInstall.png')))
self.pluginMenu.addAction(instPl)
self.launchingMenu = QMenu("&Launch PLugins", self)
self.launchingMenu.setIcon(QIcon(path.normcase('gui/icons/plugin')))
for plug in self.plugins:
#fullname="".join([self.pluginPath, str(plug)])
mod=imp.load_source(self.__module__, plug)
if mod.autoActivation:
qApp=QApplication.instance()
name=getattr(mod, 'className')
cls=getattr(mod, name)
p=cls(qApp.model, self, parent=self)
#p=qApp.pluginManager.loadPlugin(qApp.model, self, plug.split('/')[-1])
self.pluginsInst.append(p)
else:
self.launchingMenu.addAction(plug.split('/')[-1])
self.pluginMenu.addMenu(self.launchingMenu)
self.pluginMenu.addAction(QIcon(path.normcase("gui/icons/process_stop.png")),
"&Remove loaded Plugin")
self.menuBar().addMenu(self.pluginMenu)
#about
self.aboutMenu= QMenu("&About")
self.aboutMenu.setTearOffEnabled(True)
metms = QAction(QIcon(path.normcase('gui/icons/deluge.png')), "&about metMS...", self)
self.aboutMenu.addAction(metms)
pyqt = QAction("&about PyQt4...", self)
pyqt_icon =QIcon(QPixmap(path.normcase("gui/icons/logo_QT4.png")))
pyqt.setIcon(pyqt_icon)
self.aboutMenu.addAction(pyqt)
metms = QAction("&metMS Documentation", self)
metms_icon =QIcon(QPixmap(path.normcase("gui/icons/deluge.png")))
metms.setIcon(metms_icon)
self.aboutMenu.addAction(metms)
self.menuBar().addMenu(self.aboutMenu)
def _setupUi(self, background=None):
"""
Make the GUI
"""
#mdi
self.mdiArea = MSMdiArea(self)
self.mdiArea.setBackground(QBrush(QPixmap(path.normcase('gui/icons/blac2.png'))))#QColor(Qt.blue).darker()))
self.setCentralWidget(self.mdiArea)
#sample dock widget
self.sampleDockWidget = QDockWidget("Samples", self)
#sampleWidget = QWidget()
self.sampleTableView = MSDragFromTableView()
self.sampleTableView.setModel(self.sampleModel)
self.sampleTableView.setSelectionBehavior(1)
self.sampleTableView.verticalHeader().hide()
self.sampleTableView.verticalHeader().setDefaultSectionSize(15)
self.sampleTableView.horizontalHeader().setDefaultSectionSize(150)
self.sampleDockWidget.setWidget(self.sampleTableView)#sampleWidget)
self.sampleDockWidget.visible=True
#workflow dock
self.workflowDockWidget = QDockWidget("Visualizer", self)
self.workflowDockWidget.visible = True
a=QWidget(self)
v=QVBoxLayout(a)
q=QToolBar()
#self.workingSample = QLabel("Working Sample:None")
#q.addWidget(self.workingSample)
q.addWidget(QLabel("ppm :"))
self.ppmEditer=QDoubleSpinBox()
self.usePpm=QCheckBox("use ?")
q.addWidget(self.ppmEditer)
q.addWidget(self.usePpm)
q.addSeparator()
self.removeButton=QToolButton(self)
self.removeButton.setIcon(QIcon(path.normcase("gui/icons/delete.png")))
q.addWidget(self.removeButton)
self.markAsGood=QAction(QIcon(path.normcase("gui/icons/button_ok.png")),"mark peak as good", self)
self.markAsBad=QAction(QIcon(path.normcase("gui/icons/stop.png")), "mark peak as bad", self)
self.hideItem = QAction(QIcon(path.normcase("gui/icons/list_remove.png")), "Hide Item", self)
q.addAction(self.markAsGood)
q.addAction(self.markAsBad)
q.addAction(self.hideItem)
v.addWidget(q)
self.tabWidget = QTabWidget()
self.tab = QWidget()
verticalLayout = QVBoxLayout(self.tab)
self.treeView = MSToDropTableView()
self.treeView.verticalHeader().setDefaultSectionSize(20)
self.treeView.setModel(self.spectraModel)
self.spectraLabel = QLabel("Sample: None")
verticalLayout.addWidget(self.treeView)
verticalLayout.addWidget(self.spectraLabel)
self.tabWidget.addTab(self.tab, QIcon(path.normcase("gui/icons/spectrumicon.png")),"Spectra")
self.tab_2 = QWidget()
verticalLayout_4 = QVBoxLayout(self.tab_2)
self.treeView_2 = MSToDropTableView()#MSTreeView(self.tab_2)# QTableView(self)#
self.treeView_2.verticalHeader().setDefaultSectionSize(20)
self.treeView_2.setModel(self.peakModel)
self.peakLabel = QLabel("Sample: None")
verticalLayout_4.addWidget(self.treeView_2)
verticalLayout_4.addWidget(self.peakLabel)
self.tabWidget.addTab(self.tab_2,QIcon(path.normcase("gui/icons/peakicon.png")), "Peaks List")
self.tab_3 = QWidget()
verticalLayout_5 = QVBoxLayout(self.tab_3)
self.treeView_3 = MSToDropTreeView()
self.treeView_3.setAnimated(True)
self.treeView_3.setModel(self.clusterModel)
self.clusterLabel = QLabel("Sample: None")
verticalLayout_5.addWidget(self.treeView_3)
verticalLayout_5.addWidget(self.clusterLabel)
self.tabWidget.addTab(self.tab_3, QIcon(path.normcase("gui/icons/clustering.png")), "Clusters")
self.tabWidget.setCurrentIndex(0)
for l in (self.spectraLabel, self.peakLabel, self.clusterLabel):
l.setAutoFillBackground(True)
v.addWidget(self.tabWidget)
self.workflowDockWidget.setWidget(a)
self.addDockWidget(Qt.DockWidgetArea(0x2),self.workflowDockWidget)
from gui.MetBaseGui import MSIsoCalculator
self.isoCalc = MSIsoCalculator(self)
self.isoCalcDockWidget=QDockWidget('isotopes calculation', self)
self.isoCalcDockWidget.setWidget(self.isoCalc)
self.addDockWidget(Qt.DockWidgetArea(0x2), self.isoCalcDockWidget)
self.isoCalcDockWidget.setVisible(False)
self.isoCalcDockWidget.visible=False
from gui.MetBaseGui import FormulaGenerator
self.generator=FormulaGenerator(self)
self.generatorDockWidget=QDockWidget('formula generator', self)
self.generatorDockWidget.setWidget(self.generator)
self.addDockWidget(Qt.DockWidgetArea(0x2), self.generatorDockWidget)
self.generatorDockWidget.setVisible(False)
self.generatorDockWidget.visible=False
self.compoundTreeView = MSCompoundTreeView(self)
self.compoundDockWidget = QDockWidget("Compounds", self)
self.compoundDockWidget.setWidget(self.compoundTreeView)
self.addDockWidget(Qt.DockWidgetArea(0x2),self.compoundDockWidget)
self.compoundDockWidget.setVisible(False)
self.compoundDockWidget.visible=False
self.comparativeTableView = QTableView(self)
self.comparativeTableView.horizontalHeader().setStretchLastSection(True)
self.comparativeTableView.verticalHeader().setDefaultSectionSize(20)
self.comparativeDock = QDockWidget("Comparative View", self)
self.comparativeDock.setWidget(self.comparativeTableView)
self.addDockWidget(Qt.DockWidgetArea(0x8), self.comparativeDock)
self.comparativeDock.setVisible(False)
self.comparativeDock.visible = False
self.tabifyDockWidget(self.compoundDockWidget, self.isoCalcDockWidget)
self.tabifyDockWidget(self.isoCalcDockWidget, self.workflowDockWidget )
self.tabifyDockWidget(self.workflowDockWidget, self.generatorDockWidget)
#set the end
#WARNING: possible that the internal shell widget cause random segfault
#with the error of QObject::killTimers...? not sure !
self.shell = QWidget()#InternalShell(namespace={'metms': QApplication.instance()},
# parent=self,
# multithreaded=False)
self.shellDock = QDockWidget("Python Shell", self)
self.shellDock.setWindowIcon(QIcon(path.normcase('gui/icons/stop.png')))
self.shellDock.setWidget(self.shell)
self.shellDock.setMinimumWidth(255)
self.shellDock.visible=True
self.addDockWidget(0x2, self.shellDock)
self.addDockWidget(0x2, self.sampleDockWidget)
self.tabifyDockWidget(self.shellDock, self.sampleDockWidget)
self.pb = QProgressBar(self)
self.pb.setMaximumWidth(245)
self.stopProcess = QToolButton(self)
self.stopProcess.setIcon(QIcon(path.normcase("gui/icons/process_stop.png")))
m = QMenu()
#self.connect(m, SIGNAL('triggered(QAction*'), QApplication.instance().taskManager.abortByName)
self.stopProcess.setMenu(m)
self.stopProcess.setPopupMode(1) #Menu Button
#self.connect(self.stopProcess, SIGNAL("clicked()"), self.stopThread)
self.statusBar().addPermanentWidget(self.stopProcess)
self.statusBar().addPermanentWidget(self.pb)
def updateStopProcessMenu(self):
"""
update the menu of the stop process
button, based directly on the processes
stored by the task manager
"""
self.stopProcess.menu().clear()
for c in QApplication.instance().taskManager:
self.stopProcess.menu().addAction(c.title)
#QApplication.instance().taskManager.abort(QApplication.instance().taskManager[-1])
def addMdiSubWindow(self, plot, title="", showMaximized=False):
"""
Allow addition of new window in the mdiarea
"""
win=self.mdiArea.addSubWindow(plot)
#print "widget parent", plot.parent()
win.setAttribute(Qt.WA_DeleteOnClose)
#win.connect(win, SIGNAL('destroyed(QObject *)'), self.testdestroy)
#plot.setParent(win)
win.setWindowTitle(title)
if showMaximized:
win.showMaximized()
else:
win.resize(400, 300)
win.show()
return win
def updateTreeView(self):
"""
Tree View update switch spectre/chromato
"""
if self.treeView.model() == self.spectraModel:
self.treeView.setModel(self.chromaModel)
self.tabWidget.setTabText(0, "Chroma")
else:
self.treeView.setModel(self.spectraModel)
#self.treeView.setSelectionMode(1)
self.tabWidget.setTabText(0, "Spectra")
def addTreeViewModel (self,model1, model2):
"""Add a model """
self.chromaModel.appendRow(model1)
self.spectraModel.appendRow(model2)
def _actionHovered(self, action):
"""emulate tooltip cause they do not work that much"""
tip = action.toolTip()
QToolTip.showText(QCursor.pos(), tip)
def showErrorMessage(self, title, string):
QMessageBox.critical(self, title, string, 0, 0)
def showWarningMessage(self, title, string):
return QMessageBox.warning(self, title, string, QMessageBox.Ok|QMessageBox.Cancel)
def showInformationMessage(self, title, string):
QMessageBox.information(self, title, string, 0)
def updateProgressBar(self, i):
"""update the value of the progress bar for all the treatment"""
self.pb.setValue(min(i, 100))
def to_indetermined_mode(self):
self.pb.setMaximum(0)
def to_determined_mode(self):
self.pb.setMaximum(100)
def showInStatusBar(self, string, time=5000):
self.statusBar().showMessage(string, time)
def addInterpreterDock(self, shell):
self.shellDock = QDockWidget(self)
self.shellDock.setWidget(shell)
self.shellDock.setWindowTitle("shell")
self.addDockWidget(0x2, self.shellDock)
def showMetMSInformation(self):
QMessageBox.about(self,
self.tr("About %1").arg("metMS"),
self.tr("""<b>%1 %2</b>
<br>metabolite Mass Spectrometry
<p>Copyright © 2010 Marco INSA, INRA
<br>Licensed under the terms of the CeciLL License
<p>Developed and maintained by Marco
<br>Bug reports and feature requests:
<a href="http://github.com/jerkos/metms">metMS site</a><br>
Discussions around the project:
<a href="http://groups.google.com/group/spyderlib">Google Group</a>
<p>This project is part of the BRIDGE project
<p>Python %3, Qt %4, PyQt %5""") \
.arg("metMS").arg(__version__) \
.arg(platform.python_version()).arg(QT_VERSION_STR) \
.arg(PYQT_VERSION_STR))
def lauchGUI(self, WorkSpace, aCase, sobjXML, Args):
"""
mw.dockWidgetBrowser is the Browser of the CFD MainView
"""
log.debug("lauchGUI")
from cs_gui import process_cmd_line
if CFD_Code() == CFD_Saturne:
from cs_package import package
from code_saturne.Base.MainView import MainView
elif CFD_Code() == CFD_Neptune:
from nc_package import package
from neptune_cfd.core.MainView import MainView
if sobjXML == None:
Title = "unnamed"
else:
Title = sobjXML.GetName()
self.Workspace = WorkSpace
pkg = package()
case, splash = process_cmd_line(Args)
mw = MainView(pkg, case, aCase)
# Put the standard panel of the MainView inside a QDockWidget
# in the SALOME Desktop
aTitle = self.setWindowTitle_CFD(mw, aCase, Title)
dsk = sgPyQt.getDesktop()
dock = QDockWidget(aTitle)
dock.setWidget(mw.frame)
dock.setMinimumWidth(520)
dsk.addDockWidget(Qt.RightDockWidgetArea, dock)
dock.setVisible(True)
dock.show()
# Put the QTreeView of the MainView which is already inside a QDockWidget
# in the SALOME Desktop
BrowserTitle = aTitle + " Browser"
mw.dockWidgetBrowser.setWindowTitle(BrowserTitle)
dsk.addDockWidget(Qt.LeftDockWidgetArea, mw.dockWidgetBrowser)
mw.dockWidgetBrowser.setVisible(True)
mw.dockWidgetBrowser.show()
mw.dockWidgetBrowser.raise_()
dock.raise_()
#Add Dock windows are managed by CFDGUI_Management class
studyId = sgPyQt.getStudyId()
aStudyCFD = aCase.GetFather()
aCaseCFD = aCase
xmlFileName = str(Title)
_c_CFDGUI.set_d_CfdCases(studyId, dock, mw.dockWidgetBrowser, mw,
aStudyCFD, aCaseCFD, xmlFileName, sobjXML)
self.connect(dock, SIGNAL("visibilityChanged(bool)"),
self.setdockWindowBrowserActivated)
self.connect(mw.dockWidgetBrowser, SIGNAL("visibilityChanged(bool)"),
self.setdockWindowActivated)
self.connect(dock.toggleViewAction(), SIGNAL("toggled(bool)"),
self.setdockWB)
self.connect(mw.dockWidgetBrowser.toggleViewAction(),
SIGNAL("toggled(bool)"), self.setdock)
_c_CFDGUI.tabifyDockWindows(dsk, studyId)
self.showDockWindows(studyId, xmlFileName, aCaseCFD.GetName(),
aStudyCFD.GetName())
updateObjectBrowser()
return mw
