def __init__(self, parent, id, dataSet):
super(DataBrowser, self).__init__(parent)
self.setupUi(self)
self._simWorkbench = None
self.dataService = None
self.id = id
self.data = dataSet
self.optionsService = OptionsService()
# create the custom selectable table header
self.selectableHeader = SelectableTableHeader(Qt.Horizontal,
self.tableView)
self.selectableHeader.setNonSelectableIndexes([0])
self.selectableHeader.sectionSelectionChanged.connect(
self.on_columnSelectionChanged)
self.tableView.setHorizontalHeader(self.selectableHeader)
# create the data model
self.dataModel = DataBrowserModel(self, self.id, self.data)
self.tableView.setModel(self.dataModel)
self._setUpSelectionCheckBox()
self._updateInfoPane()
if not self.optionsService.getDebug():
self.groupBoxPerturbation.setVisible(False)
def __init__(self, parent, id, dataSet):
super(DataBrowser, self).__init__(parent)
self.setupUi(self)
self._simWorkbench = None
self.dataService = None
self.id = id
self.data = dataSet
self.optionsService = OptionsService()
# create the custom selectable table header
self.selectableHeader = SelectableTableHeader(Qt.Horizontal, self.tableView)
self.selectableHeader.setNonSelectableIndexes([0])
self.selectableHeader.sectionSelectionChanged.connect(self.on_columnSelectionChanged)
self.tableView.setHorizontalHeader(self.selectableHeader)
# create the data model
self.dataModel = DataBrowserModel(self, self.id, self.data)
self.tableView.setModel(self.dataModel)
self._setUpSelectionCheckBox()
self._updateInfoPane()
if not self.optionsService.getDebug():
self.groupBoxPerturbation.setVisible(False)
def __init__(self, args, parent=None):
"""
This initialization does a lot of stuff. :)
* State variables are set up
* Views are created and tied to UI parts (e.g. Docks)
* Logging is set up
* Services (StatusBar, Data, ...) are started
* Necessary slots are connected
"""
super(BioParkinController, self).__init__(parent)
# for locale testing
# locale.setlocale(locale.LC_ALL, 'de_DE')
# locale.setlocale(locale.LC_ALL, 'deu_deu')
self.startTime = time.localtime()
# set file logger
self.rotatingFileHandler = logging.handlers.RotatingFileHandler(_LOG_FILENAME, maxBytes=1000000, backupCount=5)
self.rotatingFileHandler.setFormatter(logging.Formatter("%(asctime)s | %(levelname)s | %(message)s"))
self.logger = logging.getLogger() # gets root logger
self.logger.addHandler(self.rotatingFileHandler)
# Status bar logger
self.statusBarLoggingHandler = StatusBarLoggingHandler()
self.statusBarLoggingHandler.setLevel(logging.INFO) # only log on info level
self.logger.addHandler(self.statusBarLoggingHandler)
# parse command line arguments
parser = OptionParser()
parser.add_option(
"-d",
"--debug",
action="store_true",
dest=OPTION_DEBUG,
default=False,
help="Include debugging information in console and file log",
)
self.options, args = parser.parse_args()
self.optionsService = OptionsService()
self.optionsService.setDebug(self.options.debug)
# set logging options
if self.options.debug:
self.logger.setLevel(logging.DEBUG)
self.rotatingFileHandler.setLevel(logging.DEBUG)
logging.info("Debug logging active.")
else:
self.logger.setLevel(logging.INFO)
self.rotatingFileHandler.setLevel(logging.INFO)
logging.info("Debug logging not active.")
logging.info("Starting BioPARKIN... %s" % self.startTime)
##### LOGGING #####
logging.info("BioPARKIN started (version %s)" % BioParkinController.__version__)
logging.info("Command line arguments: %s" % args)
logging.info("Python version: %s" % sys.version)
logging.info("PySide version: %s" % PySide.__version__)
logging.info("PARKINcpp version: %s" % PARKINCPP_DOTTED_VERSION)
logging.info("libSBML version: %s" % LIBSBML_DOTTED_VERSION)
logging.info("Matplotlib version: %s" % matplotlib.__version__)
# logging.info("NetworkX version: %s" % networkx.__version__)
logging.info("Python Image Library version: %s" % Image.VERSION)
self.setupUi(self)
self._mdiArea.hide()
self.setWindowTitle("BioPARKIN v%s" % BioParkinController.__version__)
# restore previous settings
settings = QSettings()
try:
self.recentFiles = settings.value("RecentFiles", [])
# handles the case if only one file is in the "list" in Linux (it's retrieved as unicode string in this case)
if type(self.recentFiles) is str or type(self.recentFiles) is unicode:
self.recentFiles = [self.recentFiles]
logging.info("Recently opened files: %s" % self.recentFiles)
except:
logging.warning("Can't access list of recently opened files. Resetting the list.")
self.recentFiles = []
self.updateFileMenu()
self.aboutDialog = None
geometry = settings.value("Geometry")
if geometry:
self.restoreGeometry(geometry)
state = settings.value("MainWindow/State")
if state:
self.restoreState(state)
self.ModelControllers = {}
# self.SubWindowToModelControllers = {}
# self.NetworkWindowCount = 0
# self.ActiveNetworkWindow = None
self.ActiveModelController = None
# self.networkSubWindows = {}
self.integrator = None
self.odeViewer = None
self.ModelView = ModelView(self.masterDetailSplitter, self)
self.ModelTreeView = SBMLEntityWidget(self.masterDetailSplitter)
self.EntityTableView = EntityTableView(self.masterDetailSplitter)
self.mainWindowViews = [self.ModelTreeView, self.EntityTableView] # used to iterate over Views
# set up Data Service and Data Viewer
datahandling.parkinController = self
self.dataService = DataService()
# debugging#############
BASE_PATH = reduce(
lambda l, r: l + os.path.sep + r, os.path.dirname(os.path.realpath(__file__)).split(os.path.sep)[:-1]
)
# add ../../templates (relative to the file (!) and not to the CWD)
dataPath = os.path.join(BASE_PATH, "data")
#######################
self.SimulationWorkbenchController = SimulationWorkbenchController(parent=None, parkinController=self)
self.mainTabWidget.addTab(self.SimulationWorkbenchController, "Workbench")
# hook up status bar with progress service (that threads can connect to)
self.statusBarService = StatusBarService(
self.statusBar()
) # first time, service is instantiated => give statusBar reference!
self.progressBarService = ProgressBarService(self, self.statusBarService)
self.statusBarLoggingHandler.setStatusBar(self.statusBarService)
self.warningsService = WarningService.getInstance()
self.warningsDialog = WarningsDialog(self, self.actionShow_Warnings, self.warningsService)
# register signals
self.activeModelChanged.connect(self.on_activeModelChanged)
self.modelClosed.connect(self.on_modelClosed)
self.menuFile.aboutToShow.connect(self.updateFileMenu)
# for debugging
self.dummyThread = None
try: # try to set correct taskbar icon in Windows 7
myappid = "ZIB.BioPARKIN" # arbitrary string
ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
except:
pass
class BioParkinController(QMainWindow, Ui_MainWindow):
"""
This is the heart of BioParkin. It sets up the general UI
(MainWindow, some Views, ...), handles creation and management of
individual network windows, and instantiates needed services
(for easy access to data, status bar, ...).
This class inherits from QMainWindow for its functionality and from
the (automatically generated) Ui_MainWindow for the design of the UI
(including the self.setupUi() method).
@param parent: The standard Qt parent.
@type parent: QWidget
@organization: Zuse Insitute Berlin
"""
__version__ = "1.2.27"
__author__ = "Moritz Wade & Thomas Dierkes"
__contact__ = "[email protected] or [email protected]"
__copyright__ = "Zuse Institute Berlin 2011"
newNetworkWindowCreated = Signal()
networkWindowRaised = Signal()
activeModelChanged = Signal(ModelController)
modelClosed = Signal(ModelController)
def __init__(self, args, parent=None):
"""
This initialization does a lot of stuff. :)
* State variables are set up
* Views are created and tied to UI parts (e.g. Docks)
* Logging is set up
* Services (StatusBar, Data, ...) are started
* Necessary slots are connected
"""
super(BioParkinController, self).__init__(parent)
# for locale testing
# locale.setlocale(locale.LC_ALL, 'de_DE')
# locale.setlocale(locale.LC_ALL, 'deu_deu')
self.startTime = time.localtime()
# set file logger
self.rotatingFileHandler = logging.handlers.RotatingFileHandler(_LOG_FILENAME, maxBytes=1000000, backupCount=5)
self.rotatingFileHandler.setFormatter(logging.Formatter("%(asctime)s | %(levelname)s | %(message)s"))
self.logger = logging.getLogger() # gets root logger
self.logger.addHandler(self.rotatingFileHandler)
# Status bar logger
self.statusBarLoggingHandler = StatusBarLoggingHandler()
self.statusBarLoggingHandler.setLevel(logging.INFO) # only log on info level
self.logger.addHandler(self.statusBarLoggingHandler)
# parse command line arguments
parser = OptionParser()
parser.add_option(
"-d",
"--debug",
action="store_true",
dest=OPTION_DEBUG,
default=False,
help="Include debugging information in console and file log",
)
self.options, args = parser.parse_args()
self.optionsService = OptionsService()
self.optionsService.setDebug(self.options.debug)
# set logging options
if self.options.debug:
self.logger.setLevel(logging.DEBUG)
self.rotatingFileHandler.setLevel(logging.DEBUG)
logging.info("Debug logging active.")
else:
self.logger.setLevel(logging.INFO)
self.rotatingFileHandler.setLevel(logging.INFO)
logging.info("Debug logging not active.")
logging.info("Starting BioPARKIN... %s" % self.startTime)
##### LOGGING #####
logging.info("BioPARKIN started (version %s)" % BioParkinController.__version__)
logging.info("Command line arguments: %s" % args)
logging.info("Python version: %s" % sys.version)
logging.info("PySide version: %s" % PySide.__version__)
logging.info("PARKINcpp version: %s" % PARKINCPP_DOTTED_VERSION)
logging.info("libSBML version: %s" % LIBSBML_DOTTED_VERSION)
logging.info("Matplotlib version: %s" % matplotlib.__version__)
# logging.info("NetworkX version: %s" % networkx.__version__)
logging.info("Python Image Library version: %s" % Image.VERSION)
self.setupUi(self)
self._mdiArea.hide()
self.setWindowTitle("BioPARKIN v%s" % BioParkinController.__version__)
# restore previous settings
settings = QSettings()
try:
self.recentFiles = settings.value("RecentFiles", [])
# handles the case if only one file is in the "list" in Linux (it's retrieved as unicode string in this case)
if type(self.recentFiles) is str or type(self.recentFiles) is unicode:
self.recentFiles = [self.recentFiles]
logging.info("Recently opened files: %s" % self.recentFiles)
except:
logging.warning("Can't access list of recently opened files. Resetting the list.")
self.recentFiles = []
self.updateFileMenu()
self.aboutDialog = None
geometry = settings.value("Geometry")
if geometry:
self.restoreGeometry(geometry)
state = settings.value("MainWindow/State")
if state:
self.restoreState(state)
self.ModelControllers = {}
# self.SubWindowToModelControllers = {}
# self.NetworkWindowCount = 0
# self.ActiveNetworkWindow = None
self.ActiveModelController = None
# self.networkSubWindows = {}
self.integrator = None
self.odeViewer = None
self.ModelView = ModelView(self.masterDetailSplitter, self)
self.ModelTreeView = SBMLEntityWidget(self.masterDetailSplitter)
self.EntityTableView = EntityTableView(self.masterDetailSplitter)
self.mainWindowViews = [self.ModelTreeView, self.EntityTableView] # used to iterate over Views
# set up Data Service and Data Viewer
datahandling.parkinController = self
self.dataService = DataService()
# debugging#############
BASE_PATH = reduce(
lambda l, r: l + os.path.sep + r, os.path.dirname(os.path.realpath(__file__)).split(os.path.sep)[:-1]
)
# add ../../templates (relative to the file (!) and not to the CWD)
dataPath = os.path.join(BASE_PATH, "data")
#######################
self.SimulationWorkbenchController = SimulationWorkbenchController(parent=None, parkinController=self)
self.mainTabWidget.addTab(self.SimulationWorkbenchController, "Workbench")
# hook up status bar with progress service (that threads can connect to)
self.statusBarService = StatusBarService(
self.statusBar()
) # first time, service is instantiated => give statusBar reference!
self.progressBarService = ProgressBarService(self, self.statusBarService)
self.statusBarLoggingHandler.setStatusBar(self.statusBarService)
self.warningsService = WarningService.getInstance()
self.warningsDialog = WarningsDialog(self, self.actionShow_Warnings, self.warningsService)
# register signals
self.activeModelChanged.connect(self.on_activeModelChanged)
self.modelClosed.connect(self.on_modelClosed)
self.menuFile.aboutToShow.connect(self.updateFileMenu)
# for debugging
self.dummyThread = None
try: # try to set correct taskbar icon in Windows 7
myappid = "ZIB.BioPARKIN" # arbitrary string
ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
except:
pass
def updateFileMenu(self):
"""
Updates the file menu dynamically, so that recent files can be shown.
"""
self.menuFile.clear()
# self.menuFile.addAction(self.actionNew) # disable for now
self.menuFile.addAction(self.actionOpen)
self.menuFile.addAction(self.actionSave)
self.menuFile.addAction(self.actionSave_as)
self.menuFile.addAction(self.actionClose_Model)
recentFiles = []
for filename in self.recentFiles:
if QFile.exists(filename):
recentFiles.append(filename)
if len(self.recentFiles) > 0:
self.menuFile.addSeparator()
for i, filename in enumerate(recentFiles):
action = QAction("&%d %s" % (i + 1, QFileInfo(filename).fileName()), self)
action.setData(filename)
action.setStatusTip("Opens recent file %s" % QFileInfo(filename).fileName())
action.setShortcut(QKeySequence(Qt.CTRL | (Qt.Key_1 + i)))
action.triggered.connect(self.load_model)
self.menuFile.addAction(action)
self.menuFile.addSeparator()
self.menuFile.addAction(self.actionQuit)
def new_model(self):
"""
Not yet supported.
"""
pass
def load_model(self, filename=None):
"""
Loads a given SBML file, thereby creating a new subwindow
on the main MDI Area.
If filename is None, it creates a new model.
There are a lot of reference variables, so that the system knows the
currently active subwindow, etc.
@param filename: The filename of the model. If None, a new model is created.
@type filename: str
"""
if not filename:
action = self.sender()
if type(action) == QAction:
filename = action.data()
else:
return
# note: this has been (temporarily added) to allow only one file to be open at the same time
# We will probably change this behaviour again later, once we have decided how to handle
# multiple-model results, etc. intelligently
if len(self.ModelControllers) > 0:
# show warning dialog
msgBox = QMessageBox()
infoText = """<b>Another model is currently loaded.</b><br>
"""
msgBox.setText(infoText)
infoTextShort = "Do you want to save the current model (you will be prompted to enter a new filename)?"
msgBox.setInformativeText(infoTextShort)
msgBox.setWindowTitle(infoTextShort)
msgBox.setStandardButtons(QMessageBox.Save | QMessageBox.Discard)
msgBox.setDefaultButton(QMessageBox.Save)
msgBox.setIcon(QMessageBox.Warning)
clickedButton = msgBox.exec_()
if clickedButton == QMessageBox.Save:
self.actionSave_as.trigger()
for (
modelController
) in self.ModelControllers.values(): # close all models (in theory, there should be only one :)
self.modelClosed.emit(modelController)
# self.NetworkWindowCount += 1
# self.setStatusTip("Opening file %s..." % filename)
self.statusBar().showMessage("Opening file %s..." % filename, 2000)
modelController = ModelController(filename=filename, views=self.mainWindowViews)
# # create NetworkViewController
# networkViewController = NetworkViewController(modelController=modelController)
# networkView = networkViewController.createNetworkView(self) # sets networkController.networkView internally
# networkView.setMinimumSize(400, 300)
# modelController.setViews(networkViewController=networkViewController)
# # Create Subwindow to hold the NetworkView
# subWindow = QMdiSubWindow(parent=self._mdiArea)
# networkViewController.subWindow = subWindow
# subWindow.setAttribute(Qt.WA_DeleteOnClose)
# subWindow.setWidget(networkView)
# subWindow.setOption(QMdiSubWindow.RubberBandResize, True)
# self._mdiArea.addSubWindow(subWindow)
# subWindow.activateWindow()
# subWindow.show() # important!
# networkView.show()
# handle references
filename = modelController.filename
# self.SubWindowToModelControllers[subWindow] = modelController
# self.networkSubWindows[modelController] = subWindow #networkView
self.ModelControllers[filename] = modelController
# self.ActiveNetworkWindow = networkWindow
self.ActiveModelController = modelController
# self.connectNetworkWindowSignals(networkView, subWindow)
# emit custom Signal so that e.g. Simulationworkbench are notified of the new subwindow
# self.newNetworkWindowCreated.emit()
self.activeModelChanged.emit(modelController)
# handle recent files list
if filename in self.recentFiles:
self.recentFiles.remove(filename)
self.recentFiles.insert(0, filename)
if len(self.recentFiles) > NUM_RECENT_FILES: # cap list at length of NUM_RECENT_FILES
self.recentFiles = self.recentFiles[:NUM_RECENT_FILES]
# def getMdiArea(self):
# return self._mdiArea
# @Slot("QWidget")
# def connectNetworkWindowSignals(self, networkWindow, subWindow):
# """
# Connect the signals of network windows (e.g. network is about to be destroyed, etc.)
#
# @param networkWindow: A network view
# @type networkWindow: NetworkView
#
# @param subWindow: A Qt QMdiArea sub window
# @type subWindow: QMdiSubWindow
# """
# #self.connect(button3, SIGNAL("clicked()"), lambda who="Three": self.anyButton(who))
#
# self.connect(networkWindow, SIGNAL("destroyed()"),
# lambda who=networkWindow: self.on_networkwindow_destroyed(who))
def dragEnterEvent(self, event):
if event.mimeData().hasFormat("Filename"):
event.accept()
else:
event.ignore()
def dropEvent(self, event):
"""
Handles the drop event if the user "drops" a file somewhere within BioPARKIN's window.
"""
# get filename
uris = event.mimeData().urls() # support opening several models at once
# note: uncomment this, to enable drag'n'dropping of multiple models again
# for uri in uris:
# filename = uri.toLocalFile()
# #open file
# self.load_model(filename)
filename = uris[0].toLocalFile()
self.load_model(filename)
if len(uris) > 1:
logging.info(
"You dragged more than one model to BioPARKIN. Currently, only one model is supported to be opened at the same time. Only the first dragged model was loaded."
)
def on_modelClosed(self, modelController):
"""
Whenever the Signal self.modelClosed is emitted, this
method is called.
It removes the modelController of the closed model from
the management dictionary and updates all local Views.
"""
if not modelController:
logging.info("Can't close the model. No model selected.")
#### abusing this place for testing ####
# self.dummyThread = DummyProgressThread()
# self.progressBarService.connect_to_thread(self.dummyThread)
# self.dummyThread.start()
# self.dummyThread = DummyThrobberThread()
# self.progressBarService.connect_to_thread(self.dummyThread)
# self.dummyThread.start()
########################################
return
if self.ModelControllers.has_key(
modelController.filename
): # we do this to remove the model controller from the management dict
self.ModelControllers.pop(modelController.filename)
if len(self.ModelControllers) == 0:
# 26.07.12 td: the next line has been commented out
self.dataService.remove_all_simulated_data()
self.ActiveModelController = None
for view in self.mainWindowViews:
view.setModel(None)
# def on_networkwindow_destroyed(self, networkWindow):
# """
# This is a slot. It's called to clean things up when a network
# window is destroyed. Basically, it just gets the correct ModelController
# and passes it on using the modelClosed signal of the BioPARKIN controller.
#
# @param networkWindow: A network view
# @type networkWindow: NetworkView
# """
# logging.debug("Destroying a NetworkWindow: %s" % networkWindow)
# modelController = networkWindow.controller.modelController
# self.modelClosed.emit(modelController)
#
# def closeNetworkWindow(self, modelController):
# if self.networkSubWindows.has_key(modelController): # might have been removed already
# self.networkSubWindows.pop(modelController).close() #removes window from dict and closes it
def on_activeModelChanged(self, activeModelController):
"""
Whenever the active model changes, the appropriate Signal
self.activeModelChanged should be emitted. When that is done, this method
is called.
"""
logging.info("Active Model: %s" % activeModelController.filename)
if activeModelController is not None:
self.ActiveModelController = activeModelController
for view in self.mainWindowViews:
view.setModel(self.ActiveModelController.proxyModel, mainModel=self.ActiveModelController.sbmlModel)
view.setSelectionModel(self.ActiveModelController.selectionModel)
# def selectNetworkView(self, modelController):
# subwindow = self.networkSubWindows[modelController]
## subwindow.show()
# subwindow.raise_()
# subwindow.activateWindow()
## subwindow.setFocus()
# def on_networkwindow_raised(self, subWindow):
# """
# This is a slot. It's called when a network window gets focus.
# Some references have to be set, and most importantly, all the Views
# have to be switched so that they use the data model behind the
# newly focused network window.
#
# @param subWindow: A sub window
# @type subWindow: QMdiSubWindow
# """
# if subWindow is None:
# return
# if not self.SubWindowToModelControllers.has_key(subWindow):
# return
#
# activeModelController = self.SubWindowToModelControllers[subWindow]
## self.ActiveNetworkWindow = self.ActiveModelController.getNetworkView()
#
## self.on_activeModelChanged()
# self.activeModelChanged.emit(activeModelController)
## self.networkWindowRaised.emit()
#
## logging.debug("Leaving on_networkwindow_raised()")
@Slot("")
def on_actionNew_triggered(self):
"""
This is a slot. It's automatically connected to the actionNew
created in the QtDesigner.
"""
self.new_model()
@Slot("")
def on_actionOpen_triggered(self):
"""
This is a slot. It's automatically connected to the actionOpen
created in the QtDesigner.
"""
homeDir = filehelpers.getHomeDir()
filenameTuple = QFileDialog.getOpenFileName(
parent=self, directory=homeDir, filter="SBML files (*.sbml *.xml)", caption="Open SBML file..."
)
if (
filenameTuple and filenameTuple[0]
): # if user presses cancel, the tuple exists but is two empty unicode strings.
filename = filenameTuple[0]
self.load_model(filename)
else:
logging.info("No file selected. Didn't load anything.")
@Slot("")
def on_actionClose_Model_triggered(self):
# self.on_modelClosed(self.ActiveModelController)
self.modelClosed.emit(self.ActiveModelController)
@Slot("")
def on_actionSave_triggered(self):
"""
This is a slot. It's automatically connected to the actionSave
created in the QtDesigner.
"""
self.saveActiveNetwork(filename=None)
@Slot("")
def on_actionSave_as_triggered(self):
"""
This is a slot. It's automatically connected to the actionSaveAs
created in the QtDesigner.
"""
if not self.ActiveModelController:
logging.info("Can't save anything. No model loaded.")
return
filenameTuple = QFileDialog.getSaveFileName(
parent=self,
dir=self.ActiveModelController.filename,
caption="Save as...",
filter="SBML file (*.sbml *.xml)",
)
if filenameTuple:
self.saveActiveNetwork(filenameTuple[0])
def saveActiveNetwork(self, filename=None):
"""
Tell the currently active network controller to
save to a file.
@param filename: Filename of the network.
@type filename: str
"""
if self.ActiveModelController is None:
logging.warning("No model loaded. Can't save anything.")
return
self.ActiveModelController.save(filename=filename)
@Slot("")
def on_actionShow_Data_Manager_triggered(self):
"""
This is a slot. It's automatically connected to the actionShowDataManager
created in the QtDesigner.
"""
self.DataManagementController.show()
@Slot("")
def on_actionODEGenerator_triggered(self):
"""
Open the ODE Generator information dialog.
"""
if self.ActiveModelController and self.ActiveModelController.sbmlModel:
self.odeViewer = ODEViewer(self, self.ActiveModelController.sbmlModel)
self.odeViewer.show()
else:
logging.info("ODEs can't be shown. No model selected.")
def closeEvent(self, event):
"""
Override the close event to handle file saving.
"""
if self.okToContinue(): # files will be saved in self.okToContinue()
settings = QSettings()
settings.setValue("Geometry", self.saveGeometry())
settings.setValue("MainWindow/State", self.saveState())
settings.setValue("RecentFiles", self.recentFiles)
event.accept()
else:
event.ignore()
def okToContinue(self):
"""
Checks if it is ok to close the application.
The user will be prompted to save files.
@return: True, if it is ok to continue (e.g. close the app); False, otherwise
@rtype: bool
@todo: Make a smart save dialog to allow the user to save only certain files.
"""
dirtyFilenames = []
for filename, networkController in self.ModelControllers.items():
if networkController.Dirty:
dirtyFilenames.append(
networkController.filename
) # we don't use the filename key because it might be outdated
if len(dirtyFilenames) == 0: # nothing to save
return True
reply = QMessageBox.question(
self,
"BioParkin - Unsaved Changes",
"Unsaved changes in these files:\n\n%s\n\nDo you want to save them?" % "\n".join(dirtyFilenames),
buttons=QMessageBox.SaveAll | QMessageBox.Discard | QMessageBox.Cancel,
)
if reply == QMessageBox.Cancel:
return False
elif reply == QMessageBox.SaveAll:
for networkController in self.ModelControllers:
if networkController.Dirty:
networkController.save()
return True
############ SLOTS for SimulationWorkbenchWidget ##############
@Slot("")
def on_actionSimulate_triggered(self):
self.SimulationWorkbenchController.actionSimulate.trigger()
@Slot("")
def on_actionComputeSensitivityOverview_triggered(self):
self.SimulationWorkbenchController.actionComputeSensitivityOverview.trigger()
@Slot("")
def on_actionCompute_Detailed_Sensitivities_triggered(self):
self.SimulationWorkbenchController.actionCompute_Detailed_Sensitivities.trigger()
@Slot("")
def on_actionEstimateParameterValues_triggered(self):
self.SimulationWorkbenchController.actionEstimateParameterValues.trigger()
@Slot("")
def on_actionAbout_triggered(self):
self.aboutDialog = AboutDialog(self)
self.aboutDialog.show()
@Slot("")
def on_actionShow_Results_Window_triggered(self):
if self.SimulationWorkbenchController and self.SimulationWorkbenchController.resultsWindow:
self.SimulationWorkbenchController.resultsWindow.show()
else:
logging.info("Cannot show Results Window. Nothing has been simulated, yet.")
def __init__(self, args, parent=None):
"""
This initialization does a lot of stuff. :)
* State variables are set up
* Views are created and tied to UI parts (e.g. Docks)
* Logging is set up
* Services (StatusBar, Data, ...) are started
* Necessary slots are connected
"""
super(BioParkinController, self).__init__(parent)
#locale.setlocale(locale.LC_ALL, 'de_DE')
# locale.setlocale(locale.LC_ALL, 'deu_deu')
self.startTime = time.localtime()
# set file logger
self.rotatingFileHandler = logging.handlers.RotatingFileHandler(_LOG_FILENAME,
maxBytes=1000000,
backupCount=5)
self.rotatingFileHandler.setFormatter(logging.Formatter("%(asctime)s | %(levelname)s | %(message)s"))
self.logger = logging.getLogger() #gets root logger
self.logger.addHandler(self.rotatingFileHandler)
# Status bar logger
self.statusBarLoggingHandler = StatusBarLoggingHandler()
self.statusBarLoggingHandler.setLevel(logging.INFO) # only log on info level
self.logger.addHandler(self.statusBarLoggingHandler)
# set GUI logger
# self.loggingView = QtLoggingView(self)
# loggingHandler = QtLoggingHandler(self.loggingView)
# loggingHandler.setLevel(logging.INFO)
# self.logger.addHandler(loggingHandler)
# filling log dock area (was set up in QtDesigner)
# self._logDockWidget.setWidget(self.loggingView)
# self._logDockWidget.hide()
# parse command line arguments
parser = OptionParser()
parser.add_option("-d", "--debug",
action="store_true", dest=OPTION_DEBUG, default=False,
help="Include debugging information in console and file log")
self.options, args = parser.parse_args()
self.optionsService = OptionsService()
self.optionsService.setDebug(self.options.debug)
# set logging options
if self.options.debug:
self.logger.setLevel(logging.DEBUG)
self.rotatingFileHandler.setLevel(logging.DEBUG)
logging.info("Debug logging active.")
else:
self.logger.setLevel(logging.INFO)
self.rotatingFileHandler.setLevel(logging.INFO)
logging.info("Debug logging not active.")
logging.debug("Starting BioPARKIN... %s" % self.startTime)
##### LOGGING #####
logging.info("BioPARKIN started (version %s)" % BioParkinController.__version__)
logging.info("Command line arguments: %s" % args)
logging.info("Python version: %s" % sys.version)
# logging.info("SIP version: %s" % sip.SIP_VERSION_STR)
#logging.info("PyQt version: %s" % PYQT_VERSION_STR)
logging.info("PySide version: %s" % PySide.__version__)
logging.info("libSBML version: %s" % LIBSBML_VERSION_STRING)
logging.info("Matplotlib version: %s" % matplotlib.__version__)
# logging.info("NetworkX version: %s" % networkx.__version__)
logging.info("Python Image Library version: %s" % Image.VERSION)
self.setupUi(self)
self._mdiArea.hide()
self.setWindowTitle("BioPARKIN v%s" % BioParkinController.__version__)
# restore previous settings
settings = QSettings()
try:
self.recentFiles = settings.value("RecentFiles", [])
# handles the case if only one file is in the "list" in Linux (it's retrieved as unicode string in this case)
if type(self.recentFiles) is str or type(self.recentFiles) is unicode:
self.recentFiles = [self.recentFiles]
logging.info("Recently opened files: %s" % self.recentFiles)
except:
logging.warning("Can't access list of recently opened files. Resetting the list.")
self.recentFiles = []
self.updateFileMenu()
self.aboutDialog = None
geometry = settings.value("Geometry")
if geometry:
self.restoreGeometry(geometry)
state = settings.value("MainWindow/State")
if state:
self.restoreState(state)
self.ModelControllers = {}
# self.SubWindowToModelControllers = {}
# self.NetworkWindowCount = 0
# self.ActiveNetworkWindow = None
self.ActiveModelController = None
# self.networkSubWindows = {}
self.integrator = None
self.odeViewer = None
self.ModelView = ModelView(self.masterDetailSplitter, self)
self.ModelTreeView = SBMLEntityWidget(self.masterDetailSplitter)
self.EntityTableView = EntityTableView(self.masterDetailSplitter)
# self.masterDetailSplitter.widget(0).destroy()
# logging.debug("1st Child of Splitter: %s" % self.masterDetailSplitter.widget(0))
self.mainWindowViews = [self.ModelTreeView, self.EntityTableView] #used to iterate over Views
# set up Data Service and Data Viewer
datahandling.parkinController = self
self.dataService = DataService()
# debugging#############
BASE_PATH = reduce(lambda l, r: l + os.path.sep + r,
os.path.dirname(os.path.realpath(__file__)).split(os.path.sep)[:-1])
#BASE_PATH = os.path.dirname(os.path.realpath(__file__))
# add ../../templates (relative to the file (!) and not to the CWD)
dataPath = os.path.join(BASE_PATH, "data")
#######################
self.SimulationWorkbenchController = SimulationWorkbenchController(parent=None, parkinController=self)
self.mainTabWidget.addTab(self.SimulationWorkbenchController, "Workbench")
# hook up status bar with progress service (that threads can connect to)
self.statusBarService = StatusBarService(self.statusBar()) # first time, service is instantiated => give statusBar reference!
# self.statusBarService.setStatusBar(self.statusBar())
self.progressBarService = ProgressBarService(self, self.statusBarService)
self.statusBarLoggingHandler.setStatusBar(self.statusBarService)
self.warningsService = WarningService.getInstance()
self.warningsDialog = WarningsDialog(self, self.actionShow_Warnings, self.warningsService)
# register signals
# self.connect(self._mdiArea, SIGNAL("subWindowActivated(QMdiSubWindow*)"), self.on_networkwindow_raised)
self.activeModelChanged.connect(self.on_activeModelChanged)
# self.activeModelChanged.connect(self.selectNetworkView) # put into own method -> easier to put in own class later
self.modelClosed.connect(self.on_modelClosed)
# self.modelClosed.connect(self.closeNetworkWindow) # put into own method -> easier to put in own class later
self.menuFile.aboutToShow.connect(self.updateFileMenu)
# for debugging
self.dummyThread = None
try: # try to set correct taskbar icon in Windows 7
myappid = 'ZIB.BioPARKIN' # arbitrary string
ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
except:
pass
class BioParkinController(QMainWindow, Ui_MainWindow):
"""
This is the heart of BioParkin. It sets up the general UI
(MainWindow, some Views, ...), handles creation and management of
individual network windows, and instantiates needed services
(for easy access to data, status bar, ...).
This class inherits from QMainWindow for its functionality and from
the (automatically generated) Ui_MainWindow for the design of the UI
(including the self.setupUi() method).
@param parent: The standard Qt parent.
@type parent: QWidget
@organization: Zuse Insitute Berlin
"""
__version__ = "1.2.13"
__author__ = "Moritz Wade & Thomas Dierkes"
__contact__ = "[email protected] or [email protected]"
__copyright__ = "Zuse Institute Berlin 2011"
newNetworkWindowCreated = Signal()
networkWindowRaised = Signal()
activeModelChanged = Signal(ModelController)
modelClosed = Signal(ModelController)
def __init__(self, args, parent=None):
"""
This initialization does a lot of stuff. :)
* State variables are set up
* Views are created and tied to UI parts (e.g. Docks)
* Logging is set up
* Services (StatusBar, Data, ...) are started
* Necessary slots are connected
"""
super(BioParkinController, self).__init__(parent)
#locale.setlocale(locale.LC_ALL, 'de_DE')
# locale.setlocale(locale.LC_ALL, 'deu_deu')
self.startTime = time.localtime()
# set file logger
self.rotatingFileHandler = logging.handlers.RotatingFileHandler(_LOG_FILENAME,
maxBytes=1000000,
backupCount=5)
self.rotatingFileHandler.setFormatter(logging.Formatter("%(asctime)s | %(levelname)s | %(message)s"))
self.logger = logging.getLogger() #gets root logger
self.logger.addHandler(self.rotatingFileHandler)
# Status bar logger
self.statusBarLoggingHandler = StatusBarLoggingHandler()
self.statusBarLoggingHandler.setLevel(logging.INFO) # only log on info level
self.logger.addHandler(self.statusBarLoggingHandler)
# set GUI logger
# self.loggingView = QtLoggingView(self)
# loggingHandler = QtLoggingHandler(self.loggingView)
# loggingHandler.setLevel(logging.INFO)
# self.logger.addHandler(loggingHandler)
# filling log dock area (was set up in QtDesigner)
# self._logDockWidget.setWidget(self.loggingView)
# self._logDockWidget.hide()
# parse command line arguments
parser = OptionParser()
parser.add_option("-d", "--debug",
action="store_true", dest=OPTION_DEBUG, default=False,
help="Include debugging information in console and file log")
self.options, args = parser.parse_args()
self.optionsService = OptionsService()
self.optionsService.setDebug(self.options.debug)
# set logging options
if self.options.debug:
self.logger.setLevel(logging.DEBUG)
self.rotatingFileHandler.setLevel(logging.DEBUG)
logging.info("Debug logging active.")
else:
self.logger.setLevel(logging.INFO)
self.rotatingFileHandler.setLevel(logging.INFO)
logging.info("Debug logging not active.")
logging.debug("Starting BioPARKIN... %s" % self.startTime)
##### LOGGING #####
logging.info("BioPARKIN started (version %s)" % BioParkinController.__version__)
logging.info("Command line arguments: %s" % args)
logging.info("Python version: %s" % sys.version)
# logging.info("SIP version: %s" % sip.SIP_VERSION_STR)
#logging.info("PyQt version: %s" % PYQT_VERSION_STR)
logging.info("PySide version: %s" % PySide.__version__)
logging.info("libSBML version: %s" % LIBSBML_VERSION_STRING)
logging.info("Matplotlib version: %s" % matplotlib.__version__)
# logging.info("NetworkX version: %s" % networkx.__version__)
logging.info("Python Image Library version: %s" % Image.VERSION)
self.setupUi(self)
self._mdiArea.hide()
self.setWindowTitle("BioPARKIN v%s" % BioParkinController.__version__)
# restore previous settings
settings = QSettings()
try:
self.recentFiles = settings.value("RecentFiles", [])
# handles the case if only one file is in the "list" in Linux (it's retrieved as unicode string in this case)
if type(self.recentFiles) is str or type(self.recentFiles) is unicode:
self.recentFiles = [self.recentFiles]
logging.info("Recently opened files: %s" % self.recentFiles)
except:
logging.warning("Can't access list of recently opened files. Resetting the list.")
self.recentFiles = []
self.updateFileMenu()
self.aboutDialog = None
geometry = settings.value("Geometry")
if geometry:
self.restoreGeometry(geometry)
state = settings.value("MainWindow/State")
if state:
self.restoreState(state)
self.ModelControllers = {}
# self.SubWindowToModelControllers = {}
# self.NetworkWindowCount = 0
# self.ActiveNetworkWindow = None
self.ActiveModelController = None
# self.networkSubWindows = {}
self.integrator = None
self.odeViewer = None
self.ModelView = ModelView(self.masterDetailSplitter, self)
self.ModelTreeView = SBMLEntityWidget(self.masterDetailSplitter)
self.EntityTableView = EntityTableView(self.masterDetailSplitter)
# self.masterDetailSplitter.widget(0).destroy()
# logging.debug("1st Child of Splitter: %s" % self.masterDetailSplitter.widget(0))
self.mainWindowViews = [self.ModelTreeView, self.EntityTableView] #used to iterate over Views
# set up Data Service and Data Viewer
datahandling.parkinController = self
self.dataService = DataService()
# debugging#############
BASE_PATH = reduce(lambda l, r: l + os.path.sep + r,
os.path.dirname(os.path.realpath(__file__)).split(os.path.sep)[:-1])
#BASE_PATH = os.path.dirname(os.path.realpath(__file__))
# add ../../templates (relative to the file (!) and not to the CWD)
dataPath = os.path.join(BASE_PATH, "data")
#######################
self.SimulationWorkbenchController = SimulationWorkbenchController(parent=None, parkinController=self)
self.mainTabWidget.addTab(self.SimulationWorkbenchController, "Workbench")
# hook up status bar with progress service (that threads can connect to)
self.statusBarService = StatusBarService(self.statusBar()) # first time, service is instantiated => give statusBar reference!
# self.statusBarService.setStatusBar(self.statusBar())
self.progressBarService = ProgressBarService(self, self.statusBarService)
self.statusBarLoggingHandler.setStatusBar(self.statusBarService)
self.warningsService = WarningService.getInstance()
self.warningsDialog = WarningsDialog(self, self.actionShow_Warnings, self.warningsService)
# register signals
# self.connect(self._mdiArea, SIGNAL("subWindowActivated(QMdiSubWindow*)"), self.on_networkwindow_raised)
self.activeModelChanged.connect(self.on_activeModelChanged)
# self.activeModelChanged.connect(self.selectNetworkView) # put into own method -> easier to put in own class later
self.modelClosed.connect(self.on_modelClosed)
# self.modelClosed.connect(self.closeNetworkWindow) # put into own method -> easier to put in own class later
self.menuFile.aboutToShow.connect(self.updateFileMenu)
# for debugging
self.dummyThread = None
try: # try to set correct taskbar icon in Windows 7
myappid = 'ZIB.BioPARKIN' # arbitrary string
ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
except:
pass
def updateFileMenu(self):
"""
Updates the file menu dynamically, so that recent files can be shown.
"""
self.menuFile.clear()
# self.menuFile.addAction(self.actionNew) # disable for now
self.menuFile.addAction(self.actionOpen)
self.menuFile.addAction(self.actionSave)
self.menuFile.addAction(self.actionSave_as)
self.menuFile.addAction(self.actionClose_Model)
recentFiles = []
for filename in self.recentFiles:
if QFile.exists(filename):
recentFiles.append(filename)
if len(self.recentFiles) > 0:
self.menuFile.addSeparator()
for i, filename in enumerate(recentFiles):
action = QAction("&%d %s" % (i + 1, QFileInfo(filename).fileName()), self)
action.setData(filename)
action.setStatusTip("Opens recent file %s" % QFileInfo(filename).fileName())
action.setShortcut(QKeySequence(Qt.CTRL | (Qt.Key_1+i)))
action.triggered.connect(self.load_model)
#self.connect(action, SIGNAL("triggered()"), self.load_model)
self.menuFile.addAction(action)
self.menuFile.addSeparator()
self.menuFile.addAction(self.actionQuit)
#pass
def new_model(self):
"""
Just calls load_model without a filename
to create a new model.
"""
#self.load_model(filename = None)
# debugging
#self.load_model(filename = "/home/bzfwadem/bin/SBMLeditor/data/biomodels-release-20090902/curated/BIOMD0000000231.xml")
BASE_PATH = reduce(lambda l, r: l + os.path.sep + r,
os.path.dirname(os.path.realpath(__file__)).split(os.path.sep)[:-1])
#BASE_PATH = os.path.dirname(os.path.realpath(__file__))
# add ../../templates (relative to the file (!) and not to the CWD)
dataPath = os.path.join(BASE_PATH, "data")
#self.load_model(filename = "/home/bzfwadem/workspace/BioParkin/data/gyncyc_0.2.sbml")
#self.load_model(filename=os.path.join(dataPath, "femcyc/pfizer02.xml"))
def load_model(self, filename=None):
"""
Loads a given SBML file, thereby creating a new subwindow
on the main MDI Area.
If filename is None, it creates a new model.
There are a lot of reference variables, so that the system knows the
currently active subwindow, etc.
@param filename: The filename of the model. If None, a new model is created.
@type filename: str
"""
if not filename:
action = self.sender()
if type(action) == QAction:
filename = action.data()
else:
return
# note: this has been (temporarily added) to allow only one file to be open at the same time
# We will probably change this behaviour again later, once we have decided how to handle
# multiple-model results, etc. intelligently
if len(self.ModelControllers) > 0:
# show warning dialog
msgBox = QMessageBox()
infoText =\
"""<b>Another model is currently loaded.</b><br>
"""
msgBox.setText(infoText)
infoTextShort = "Do you want to save the current model (you will be prompted to enter a new filename)?"
msgBox.setInformativeText(infoTextShort)
msgBox.setWindowTitle(infoTextShort)
msgBox.setStandardButtons(QMessageBox.Save | QMessageBox.Discard)
msgBox.setDefaultButton(QMessageBox.Save)
msgBox.setIcon(QMessageBox.Warning)
# msgBox.setWindowIcon(None)
clickedButton = msgBox.exec_()
if clickedButton == QMessageBox.Save:
self.actionSave_as.trigger()
for modelController in self.ModelControllers.values(): # close all models (in theory, there should be only one :)
self.modelClosed.emit(modelController)
# self.NetworkWindowCount += 1
# self.setStatusTip("Opening file %s..." % filename)
self.statusBar().showMessage("Opening file %s..." % filename, 2000)
modelController = ModelController(filename=filename, views=self.mainWindowViews)
# # create NetworkViewController
# networkViewController = NetworkViewController(modelController=modelController)
# networkView = networkViewController.createNetworkView(self) # sets networkController.networkView internally
# networkView.setMinimumSize(400, 300)
# modelController.setViews(networkViewController=networkViewController)
# # Create Subwindow to hold the NetworkView
# subWindow = QMdiSubWindow(parent=self._mdiArea)
# networkViewController.subWindow = subWindow
# subWindow.setAttribute(Qt.WA_DeleteOnClose)
# subWindow.setWidget(networkView)
# subWindow.setOption(QMdiSubWindow.RubberBandResize, True)
# self._mdiArea.addSubWindow(subWindow)
# subWindow.activateWindow()
#
# # why do these not work to emit a self._mdiArea.networkWindowActivated Signal?
# # self._mdiArea.setActiveSubWindow(subWindow)
# # self._mdiArea.activateNextSubWindow()
# # self._mdiArea.subWindowActivated()
#
# subWindow.show() # important!
# networkView.show()
# handle references
filename = modelController.filename
# self.SubWindowToModelControllers[subWindow] = modelController
# self.networkSubWindows[modelController] = subWindow #networkView
self.ModelControllers[filename] = modelController
# self.ActiveNetworkWindow = networkWindow
self.ActiveModelController = modelController
# self.connectNetworkWindowSignals(networkView, subWindow)
# emit custom Signal so that e.g. Simulationworkbench are notified of the new subwindow
# self.newNetworkWindowCreated.emit()
self.activeModelChanged.emit(modelController)
# handle recent files list
if filename in self.recentFiles:
self.recentFiles.remove(filename)
self.recentFiles.insert(0, filename)
if len(self.recentFiles) > NUM_RECENT_FILES: # cap list at length of NUM_RECENT_FILES
self.recentFiles = self.recentFiles[:NUM_RECENT_FILES]
# def getMdiArea(self):
# return self._mdiArea
# @Slot("QWidget")
# def connectNetworkWindowSignals(self, networkWindow, subWindow):
# """
# Connect the signals of network windows (e.g. network is about to be destroyed, etc.)
#
# @param networkWindow: A network view
# @type networkWindow: NetworkView
#
# @param subWindow: A Qt QMdiArea sub window
# @type subWindow: QMdiSubWindow
# """
# #self.connect(button3, SIGNAL("clicked()"), lambda who="Three": self.anyButton(who))
#
# self.connect(networkWindow, SIGNAL("destroyed()"),
# lambda who=networkWindow: self.on_networkwindow_destroyed(who))
def dragEnterEvent(self, event):
if event.mimeData().hasFormat('Filename'):
event.accept()
else:
event.ignore()
def dropEvent(self, event):
# get filename
uris = event.mimeData().urls() # support opening several models at once
# note: uncomment this, to enable drag'n'dropping of multiple models, again
# for uri in uris:
# filename = uri.toLocalFile()
# #open file
# self.load_model(filename)
filename = uris[0].toLocalFile()
self.load_model(filename)
if len(uris)>1:
logging.info("You dragged more than one model to BioPARKIN. Currently, only one model is supported to be opened at the same time. Only the first dragged model was loaded.")
def on_modelClosed(self, modelController):
"""
Whenever the Signal self.modelClosed is emitted, this
method is called.
It removes the modelController of the closed model from
the managemend dicitionary and updates all local Views.
"""
if not modelController:
logging.info("Can't close the model. No model selected.")
#### abusing this place for testing ####
# self.dummyThread = DummyProgressThread()
# self.progressBarService.connect_to_thread(self.dummyThread)
# self.dummyThread.start()
# self.dummyThread = DummyThrobberThread()
# self.progressBarService.connect_to_thread(self.dummyThread)
# self.dummyThread.start()
########################################
return
if self.ModelControllers.has_key(
modelController.filename): # we do this to remove the model controller from the management dict
self.ModelControllers.pop(modelController.filename)
if len(self.ModelControllers) == 0:
# self.dataService.remove_all_simulated_data()
self.ActiveModelController = None
for view in self.mainWindowViews:
view.setModel(None)
# def on_networkwindow_destroyed(self, networkWindow):
# """
# This is a slot. It's called to clean things up when a network
# window is destroyed. Basically, it just gets the correct ModelController
# and passes it on using the modelClosed signal of the BioPARKIN controller.
#
# @param networkWindow: A network view
# @type networkWindow: NetworkView
# """
# logging.debug("Destroying a NetworkWindow: %s" % networkWindow)
# modelController = networkWindow.controller.modelController
# self.modelClosed.emit(modelController)
#
# def closeNetworkWindow(self, modelController):
# if self.networkSubWindows.has_key(modelController): # might have been removed already
# self.networkSubWindows.pop(modelController).close() #removes window from dict and closes it
def on_activeModelChanged(self, activeModelController):
"""
Whenever the active model changes, the appropriate Signal
self.activeModelChanged should be emitted. When that is done, this method
is called.
"""
logging.info("Active Model: %s" % activeModelController.filename)
if activeModelController is not None:
self.ActiveModelController = activeModelController
for view in self.mainWindowViews:
view.setModel(self.ActiveModelController.proxyModel, mainModel=self.ActiveModelController.sbmlModel)
view.setSelectionModel(self.ActiveModelController.selectionModel)
# def selectNetworkView(self, modelController):
# subwindow = self.networkSubWindows[modelController]
## subwindow.show()
# subwindow.raise_()
# subwindow.activateWindow()
## subwindow.setFocus()
# def on_networkwindow_raised(self, subWindow):
# """
# This is a slot. It's called when a network window gets focus.
# Some references have to be set, and most importantly, all the Views
# have to be switched so that they use the data model behind the
# newly focused network window.
#
# @param subWindow: A sub window
# @type subWindow: QMdiSubWindow
# """
# if subWindow is None:
# return
# if not self.SubWindowToModelControllers.has_key(subWindow):
# return
#
# activeModelController = self.SubWindowToModelControllers[subWindow]
## self.ActiveNetworkWindow = self.ActiveModelController.getNetworkView()
#
## self.on_activeModelChanged()
# self.activeModelChanged.emit(activeModelController)
## self.networkWindowRaised.emit()
#
## logging.debug("Leaving on_networkwindow_raised()")
@Slot("")
def on_actionNew_triggered(self):
"""
This is a slot. It's automatically connected to the actionNew
created in the QtDesigner.
"""
self.new_model()
@Slot("")
def on_actionOpen_triggered(self):
"""
This is a slot. It's automatically connected to the actionOpen
created in the QtDesigner.
"""
homeDir = filehelpers.getHomeDir()
filenameTuple = QFileDialog.getOpenFileName(parent=self,
directory=homeDir,
filter="SBML files (*.sbml *.xml)",
caption="Open SBML file...")
if filenameTuple and filenameTuple[0]: # if user presses cancel, the tuple exists but is two empty unicode strings.
filename = filenameTuple[0]
self.load_model(filename)
else:
logging.info("No file selected. Didn't load anything.")
@Slot("")
def on_actionClose_Model_triggered(self):
# self.on_modelClosed(self.ActiveModelController)
self.modelClosed.emit(self.ActiveModelController)
@Slot("")
def on_actionSave_triggered(self):
"""
This is a slot. It's automatically connected to the actionSave
created in the QtDesigner.
"""
self.saveActiveNetwork(filename=None)
@Slot("")
def on_actionSave_as_triggered(self):
"""
This is a slot. It's automatically connected to the actionSaveAs
created in the QtDesigner.
"""
if not self.ActiveModelController:
logging.info("Can't save anything. No model loaded.")
return
filenameTuple = QFileDialog.getSaveFileName(parent=self,
dir=self.ActiveModelController.filename,
caption="Save as...",
filter="SBML file (*.sbml)")
if filenameTuple:
self.saveActiveNetwork(filenameTuple[0])
def saveActiveNetwork(self, filename=None):
"""
Tell the currently active network controller to
save to a file.
@param filename: Filename of the network.
@type filename: str
"""
if self.ActiveModelController is None:
logging.warning("No model loaded. Can't save anything.")
return
self.ActiveModelController.save(filename=filename)
@Slot("")
def on_actionShow_Data_Manager_triggered(self):
"""
This is a slot. It's automatically connected to the actionShowDataManager
created in the QtDesigner.
"""
self.DataManagementController.show()
@Slot("")
def on_actionODEGenerator_triggered(self):
"""
Open the ODE Generator information dialog.
"""
if self.ActiveModelController and self.ActiveModelController.sbmlModel:
self.odeViewer = ODEViewer(self, self.ActiveModelController.sbmlModel)
self.odeViewer.show()
else:
logging.info("ODEs can't be shown. No model selected.")
def closeEvent(self, event):
"""
Override the close event to handle file saving.
"""
if self.okToContinue(): # files will be saved in self.okToContinue()
settings = QSettings()
settings.setValue("Geometry", self.saveGeometry())
settings.setValue("MainWindow/State", self.saveState())
settings.setValue("RecentFiles", self.recentFiles)
event.accept()
else:
event.ignore()
def okToContinue(self):
"""
Checks if it is ok to close the application.
The user will be prompted to save files.
@return: True, if it is ok to continue (e.g. close the app); False, otherwise
@rtype: bool
@todo: Make a smart save dialog to allow the user to save only certain files.
"""
dirtyFilenames = []
for filename, networkController in self.ModelControllers.items():
if networkController.Dirty:
dirtyFilenames.append(
networkController.filename) # we don't use the filename key because it might be outdated
if len(dirtyFilenames) == 0: #nothing to save
return True
reply = QMessageBox.question(self,
"BioParkin - Unsaved Changes",
"Unsaved changes in these files:\n\n%s\n\nDo you want to save them?" % "\n".join(
dirtyFilenames),
buttons=QMessageBox.SaveAll | QMessageBox.Discard | QMessageBox.Cancel)
if reply == QMessageBox.Cancel:
return False
elif reply == QMessageBox.SaveAll:
for networkController in self.ModelControllers:
if networkController.Dirty:
networkController.save()
return True
############ SLOTS for SimulationWorkbenchWidget ##############
@Slot("")
def on_actionSimulate_triggered(self):
self.SimulationWorkbenchController.actionSimulate.trigger()
@Slot("")
def on_actionComputeSensitivityOverview_triggered(self):
self.SimulationWorkbenchController.actionComputeSensitivityOverview.trigger()
@Slot("")
def on_actionCompute_Detailed_Sensitivities_triggered(self):
self.SimulationWorkbenchController.actionCompute_Detailed_Sensitivities.trigger()
@Slot("")
def on_actionEstimateParameterValues_triggered(self):
self.SimulationWorkbenchController.actionEstimateParameterValues.trigger()
@Slot("")
def on_actionAbout_triggered(self):
self.aboutDialog = AboutDialog(self)
self.aboutDialog.show()
@Slot("")
def on_actionShow_Results_Window_triggered(self):
if self.SimulationWorkbenchController and self.SimulationWorkbenchController.resultsWindow:
self.SimulationWorkbenchController.resultsWindow.show()
else:
logging.info("Cannot show Results Window. Nothing has been simulated, yet.")
class DataBrowser(QWidget, Ui_DataBrowser):
"""
@since: 2011-08-24
"""
__author__ = "Moritz Wade"
__contact__ = "*****@*****.**"
__copyright__ = "Zuse Institute Berlin 2011"
def __init__(self, parent, id, dataSet):
super(DataBrowser, self).__init__(parent)
self.setupUi(self)
self._simWorkbench = None
self.dataService = None
self.id = id
self.data = dataSet
self.optionsService = OptionsService()
# create the custom selectable table header
self.selectableHeader = SelectableTableHeader(Qt.Horizontal, self.tableView)
self.selectableHeader.setNonSelectableIndexes([0])
self.selectableHeader.sectionSelectionChanged.connect(self.on_columnSelectionChanged)
self.tableView.setHorizontalHeader(self.selectableHeader)
# create the data model
self.dataModel = DataBrowserModel(self, self.id, self.data)
self.tableView.setModel(self.dataModel)
self._setUpSelectionCheckBox()
self._updateInfoPane()
if not self.optionsService.getDebug():
self.groupBoxPerturbation.setVisible(False)
def getId(self):
return self.id
def setSimulationWorkbench(self, simWorkbench):
self._simWorkbench = simWorkbench
def getSelectionCheckBox(self):
return self._selectionCheckBox
def isSelected(self):
checkState = self._selectionCheckBox.checkState()
return True if checkState == Qt.Checked else False
def _setUpSelectionCheckBox(self):
self._selectionCheckBox = QCheckBox()
self._selectionCheckBox.setChecked(True)
infoText = "Select or deselect this data (e.g. to be included in plots and computations)."
self._selectionCheckBox.setStatusTip(infoText)
self._selectionCheckBox.setToolTip(infoText)
self._selectionCheckBox.stateChanged.connect(self._selectionChanged)
def _updateInfoPane(self):
"""
Updates the info pane with basic info about the loaded data
and the data file (if any).
"""
self.lineEditInfoSpecies.setText(str(self.data.getNumOfRealData()))
self.lineEditInfoDataType.setText(self.data.type)
# self.lineEditInfoFormat.setText(self.data.format)
filepath = self.data.filename
if filepath and os.path.exists(filepath):
self.lineEditInfoPath.setText(filepath)
filesize = os.path.getsize(filepath)
filesize = filesize / 1024 # displaying kB
self.lineEditInfoFilesize.setText("%s kB" % filesize)
timeLastModifiedEpoch = os.path.getmtime(filepath)
timeLastModified = time.strftime("%a, %d %b %Y %H:%M:%S", time.localtime(timeLastModifiedEpoch))
self.lineEditInfoLastModified.setText(str(timeLastModified))
else:
noFileText = "No File"
self.lineEditInfoPath.setText(noFileText)
self.lineEditInfoFilesize.setText(noFileText)
self.lineEditInfoLastModified.setText(noFileText)
def remove(self):
"""
Cleans up stuff then destroys self.
It's not sure whether this is really needed
but it might serve to close some memory holes
(e.g. dangling references somewhere).
"""
del self.dataModel
del self
@Slot()
def on_actionPlot_triggered(self):
dataDict = {self.data.getId(): self.data}
self._simWorkbench.plotExpData(dataDict)
@Slot()
def on_buttonPerturb_clicked(self):
"""
Perturbs the data by the % given
in self.spinBoxPerturb.
"""
percentage = self.spinBoxPerturb.value()
factor = percentage / 100.0
for entity, entityData in self.data.getData().items():
if not entityData.isSelected():
continue
id = entity.getId() if type(entity) == EntityData else str(entity)
logging.debug("Perturbing data of EntityData: %s" % id)
for i in xrange(len(entityData.datapoints)):
value = entityData.datapoints[i]
if not value: # for None values
continue
fraction = value * factor # fraction of value that will be added or substracted
#newValue = value + random.uniform(-1 * fraction, fraction)
newValue = value + random.uniform(-1, 1) * fraction
# newValue = value - fraction if random.random() < 0.5 else value + fraction
entityData.setDatapoint(i, newValue)
@Slot("")
def on_buttonSaveAs_clicked(self):
logging.debug("Saving data. Displaying file chooser...")
file_choices = "Tab-Delimited Text File *.txt (*.txt)"
path = unicode(QFileDialog.getSaveFileName(self, 'Save file', '', file_choices)[0])
if not path.endswith(".txt"):
path += ".txt"
if path:
if not self.dataService:
self.dataService = DataService()
id = self.data.getId()
self.dataService.save_data_as_csv(id, path)
logging.info("Saved data to %s" % path)
@Slot()
def on_buttonTimeshift_clicked(self):
"""
Timeshift data within this DataBrowser (i.e. DataSet).
Not only shift the global timepoints but also the timepoint lists
within the individiual EntityData objects.
"""
try:
shiftValue = float(self.lineEditTimeshift.text())
self.dataModel.doTimeshift(shiftValue)
except Exception, e:
logging.error("DataBrowser.on_buttonTimeshift_clicked(): Error while timeshifting the data: %s" % e)
class DataBrowser(QWidget, Ui_DataBrowser):
"""
@since: 2011-08-24
"""
__author__ = "Moritz Wade"
__contact__ = "*****@*****.**"
__copyright__ = "Zuse Institute Berlin 2011"
def __init__(self, parent, id, dataSet):
super(DataBrowser, self).__init__(parent)
self.setupUi(self)
self._simWorkbench = None
self.dataService = None
self.id = id
self.data = dataSet
self.optionsService = OptionsService()
# create the custom selectable table header
self.selectableHeader = SelectableTableHeader(Qt.Horizontal,
self.tableView)
self.selectableHeader.setNonSelectableIndexes([0])
self.selectableHeader.sectionSelectionChanged.connect(
self.on_columnSelectionChanged)
self.tableView.setHorizontalHeader(self.selectableHeader)
# create the data model
self.dataModel = DataBrowserModel(self, self.id, self.data)
self.tableView.setModel(self.dataModel)
self._setUpSelectionCheckBox()
self._updateInfoPane()
if not self.optionsService.getDebug():
self.groupBoxPerturbation.setVisible(False)
def getId(self):
return self.id
def setSimulationWorkbench(self, simWorkbench):
self._simWorkbench = simWorkbench
def getSelectionCheckBox(self):
return self._selectionCheckBox
def isSelected(self):
checkState = self._selectionCheckBox.checkState()
return True if checkState == Qt.Checked else False
def _setUpSelectionCheckBox(self):
self._selectionCheckBox = QCheckBox()
self._selectionCheckBox.setChecked(True)
infoText = "Select or deselect this data (e.g. to be included in plots and computations)."
self._selectionCheckBox.setStatusTip(infoText)
self._selectionCheckBox.setToolTip(infoText)
self._selectionCheckBox.stateChanged.connect(self._selectionChanged)
def _updateInfoPane(self):
"""
Updates the info pane with basic info about the loaded data
and the data file (if any).
"""
self.lineEditInfoSpecies.setText(str(self.data.getNumOfRealData()))
self.lineEditInfoDataType.setText(self.data.type)
# self.lineEditInfoFormat.setText(self.data.format)
filepath = self.data.filename
if filepath and os.path.exists(filepath):
self.lineEditInfoPath.setText(filepath)
filesize = os.path.getsize(filepath)
filesize = filesize / 1024 # displaying kB
self.lineEditInfoFilesize.setText("%s kB" % filesize)
timeLastModifiedEpoch = os.path.getmtime(filepath)
timeLastModified = time.strftime(
"%a, %d %b %Y %H:%M:%S", time.localtime(timeLastModifiedEpoch))
self.lineEditInfoLastModified.setText(str(timeLastModified))
else:
noFileText = "No File"
self.lineEditInfoPath.setText(noFileText)
self.lineEditInfoFilesize.setText(noFileText)
self.lineEditInfoLastModified.setText(noFileText)
def remove(self):
"""
Cleans up stuff then destroys self.
It's not sure whether this is really needed
but it might serve to close some memory holes
(e.g. dangling references somewhere).
"""
del self.dataModel
del self
@Slot()
def on_actionPlot_triggered(self):
dataDict = {self.data.getId(): self.data}
self._simWorkbench.plotExpData(dataDict)
@Slot()
def on_buttonPerturb_clicked(self):
"""
Perturbs the data by the % given
in self.spinBoxPerturb.
"""
percentage = self.spinBoxPerturb.value()
factor = percentage / 100.0
for entity, entityData in self.data.getData().items():
if not entityData.isSelected():
continue
id = entity.getId() if type(entity) == EntityData else str(entity)
logging.debug("Perturbing data of EntityData: %s" % id)
for i in xrange(len(entityData.datapoints)):
value = entityData.datapoints[i]
if not value: # for None values
continue
fraction = value * factor # fraction of value that will be added or substracted
#newValue = value + random.uniform(-1 * fraction, fraction)
newValue = value + random.uniform(-1, 1) * fraction
# newValue = value - fraction if random.random() < 0.5 else value + fraction
entityData.setDatapoint(i, newValue)
@Slot("")
def on_buttonSaveAs_clicked(self):
logging.debug("Saving data. Displaying file chooser...")
file_choices = "Tab-Delimited Text File *.txt (*.txt)"
path = unicode(
QFileDialog.getSaveFileName(self, 'Save file', '',
file_choices)[0])
if not path.endswith(".txt"):
path += ".txt"
if path:
if not self.dataService:
self.dataService = DataService()
id = self.data.getId()
self.dataService.save_data_as_csv(id, path)
logging.info("Saved data to %s" % path)
@Slot()
def on_buttonTimeshift_clicked(self):
"""
Timeshift data within this DataBrowser (i.e. DataSet).
Not only shift the global timepoints but also the timepoint lists
within the individiual EntityData objects.
"""
try:
shiftValue = float(self.lineEditTimeshift.text())
self.dataModel.doTimeshift(shiftValue)
except Exception, e:
logging.error(
"DataBrowser.on_buttonTimeshift_clicked(): Error while timeshifting the data: %s"
% e)