def __init__(self):
# set up the layout
self.__component = JPanel(GridBagLayout())
self.__image = JLabel()
self.__album = JLabel()
self.__artist = JLabel()
self.__application = None
self.__image.setVerticalAlignment(SwingConstants.TOP)
self.__album.setVerticalAlignment(SwingConstants.TOP)
self.__artist.setVerticalAlignment(SwingConstants.TOP)
gbc = GridBagConstraints()
gbc.fill = GridBagConstraints.VERTICAL
gbc.anchor = GridBagConstraints.NORTHWEST
gbc.gridx = 0
gbc.gridy = 0
gbc.weighty = 2
gbc.gridheight = 2
self.__component.add(self.__image, gbc)
gbc.fill = GridBagConstraints.HORIZONTAL
gbc.anchor = GridBagConstraints.NORTHWEST
gbc.gridx = 1
gbc.gridy = 0
gbc.gridheight = 1
gbc.weighty = 0
gbc.insets = Insets(0, 10, 0, 10)
self.__component.add(self.__album, gbc)
gbc.fill = GridBagConstraints.BOTH
gbc.anchor = GridBagConstraints.NORTHWEST
gbc.gridx = 1
gbc.gridy = 1
gbc.weightx = 2
gbc.weighty = 2
gbc.gridheight = 1
self.__component.add(self.__artist, gbc)
def cachedBPROM(genome, fileName, frame):
"""
genome: Genome as a string.
fileName: File to save the BPROM results in.
swing: A JFrame or None. If this is None then messages will be printed, if it isn't then
they will also be put in a dialog box.
return: Results of the BPROM prediction stored in a list of Promoter objects.
If the file Specified by fileName already exists then this function simply parses the file
already there. Also, if a request is made to BPROM and nothing is returned, no file is
created, the user is warned, and an empty list is returned.
"""
offset = 25 if ".forward.bprom" in fileName else 50
direction = "forward" if offset == 50 else "reverse"
def getPromoters():
input = open(fileName, "r")
results = parseBPROM(input.read())
input.close()
return results
if not os.path.isfile(fileName):
results = urllib.urlopen("http://linux1.softberry.com/cgi-bin/programs/gfindb/bprom.pl",
urllib.urlencode({"DATA" : genome}))
resultString = results.read()
results.close()
resultString = resultString[resultString.find("<pre>"):resultString.find("</pre>")]
resultString = re.sub("<+.+>+", "", resultString).strip()
if resultString:
output = open(fileName, "w")
output.write(resultString)
output.close()
return getPromoters()
else:
if frame:
messageFrame = JFrame("BPROM Error",
defaultCloseOperation = WindowConstants.DISPOSE_ON_CLOSE)
messageFrame.setLocation(frame.location().x + offset, frame.location().y + offset)
messageFrame.contentPane.layout = GridBagLayout()
constraints = GridBagConstraints()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
messageFrame.contentPane.add(JLabel("<html>The pipeline will continue to run but BPROM<br/>did not process the request for promoters on the<br/>" + direction + " strand. Try again tomorrow.</html>"), constraints)
constraints.gridx, constraints.gridy = 0, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 1, 1
constraints.anchor = GridBagConstraints.LINE_END
messageFrame.contentPane.add(JButton("Ok", actionPerformed = lambda e: messageFrame.dispose()), constraints)
messageFrame.pack()
messageFrame.visible = True
print "BPROM Error:", "The pipeline will continue to run but BPROM did not process the request for promoters on the " + direction + " strand. Try again tomorrow"
return []
else:
return getPromoters()
def initializeDisplay(self, queries, swing):
"""
queries: A list of the fasts files to be processed.
swing: If true then updates about progress will be displayed in a swing window, otherwise they will be written to stdout.
Initializes the interface for telling the user about progress in the pipeline. Queries is used to count the
number of queries the pipeline will process and to size the swing display(if it is used) so that text
isn't cutoff at the edge of the window. The swing display is setup if swing is true.
"""
self.numJobs = len(queries)
if swing:
self.frame = JFrame("Neofelis")
self.frame.addWindowListener(PipelineWindowAdapter(self))
contentPane = JPanel(GridBagLayout())
self.frame.setContentPane(contentPane)
self.globalLabel = JLabel(max(queries, key = len))
self.globalProgress = JProgressBar(0, self.numJobs)
self.currentLabel = JLabel(max(self.messages, key = len))
self.currentProgress = JProgressBar(0, len(self.messages))
self.doneButton = JButton(DoneAction(self.frame))
self.doneButton.setEnabled(False)
constraints = GridBagConstraints()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.weightx = 1
constraints.fill = GridBagConstraints.HORIZONTAL
contentPane.add(self.globalLabel, constraints)
constraints.gridy = 1
contentPane.add(self.globalProgress, constraints)
constraints.gridy = 2
contentPane.add(self.currentLabel, constraints)
constraints.gridy = 3
contentPane.add(self.currentProgress, constraints)
constraints.gridy = 4
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.anchor = GridBagConstraints.LINE_END
contentPane.add(self.doneButton, constraints)
self.frame.pack()
self.frame.setResizable(False)
self.globalLabel.setText(" ")
self.currentLabel.setText(" ")
self.frame.setLocationRelativeTo(None)
self.frame.setVisible(True)
def p_build_ui(self, event):
"""
Adds a list of checkboxes, one for each loaded plugin
to the Selct plugins window
"""
if not self.loaded_p_list:
self.update_scroll("[!!] No plugins loaded!")
return
scroll_pane = JScrollPane()
scroll_pane.setPreferredSize(Dimension(200, 250))
check_frame = JPanel(GridBagLayout())
constraints = GridBagConstraints()
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.gridy = 0
constraints.anchor = GridBagConstraints.FIRST_LINE_START
for plug in self.loaded_p_list:
check_frame.add(JCheckBox(plug.get_name(), plug.enabled,
actionPerformed=self.update_box),
constraints)
constraints.gridy += 1
vport = JViewport()
vport.setView(check_frame)
scroll_pane.setViewport(vport)
self.window.contentPane.add(scroll_pane)
self.window.pack()
self.window.setVisible(True)
def __createDropDownConstraints(self):
constr = GridBagConstraints()
constr.fill = GridBagConstraints.HORIZONTAL
constr.weighty = 1
constr.gridwidth = 4
constr.gridx = 0
constr.gridy = 0
return constr
def __createTableConstraints(self):
constr = GridBagConstraints()
constr.fill = GridBagConstraints.BOTH
constr.weighty = 1000
constr.weightx = 2
constr.gridwidth = 4
constr.gridx = 0
constr.gridy = 2
return constr
def __createRadioConstraints(self, mode):
constr = GridBagConstraints()
constr.fill = GridBagConstraints.HORIZONTAL
constr.weighty = 1
constr.weightx = 1
if mode == 'cases': constr.gridx = 2
elif mode == 'commands': constr.gridx = 3
constr.gridy = 1
return constr
def __setupLayout(self):
self.setLayout(GridBagLayout())
constr = GridBagConstraints()
constr.weighty = 1
constr.weightx = 1
constr.gridx = 0
constr.gridy = 1
constr.fill = GridBagConstraints.BOTH
return constr
def _new_grid_bag(gridx, gridy, gridwidth=1):
"""Creates a new GridBagConstraints"""
g = GridBagConstraints()
g.gridx = gridx
g.gridy = gridy
g.gridwidth = gridwidth
g.fill = GridBagConstraints.BOTH
g.insets = Insets(2,2,5,5)
return g
def createAndShowGUI():
# Create the GUI and show it. As with all GUI code, this must run
# on the event-dispatching thread.
frame = JFrame("MAE ")
frame.setSize(1024, 768)
panel= JPanel()
panel.setLayout(GridBagLayout())
#Create and set up the content pane.
psimures= SimoutPanel()
psimures.setOpaque(True)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridx = 0
c.gridy = 0
panel.add(psimures, c);
pmeasure= MeasPanel()
pmeasure.setOpaque(True)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridx = 0
c.gridy = 1
panel.add(pmeasure, c);
preport = ReportPanel()
preport.setOpaque(True)
c = GridBagConstraints()
c.fill = GridBagConstraints.VERTICAL
c.weighty = 1
c.gridx = 1
c.gridy = 0
c.gridheight= 2
panel.add(preport,c)
# show the GUI
frame.add(panel)
# frame.add(pmeasure)
# frame.add(preport)
frame.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE)
frame.setVisible(True)
def __init__(self):
self.frame = JFrame('Hello, Jython!',
defaultCloseOperation=JFrame.EXIT_ON_CLOSE,
size=(400, 600))
bag_layout = GridBagLayout()
self.frame.layout = bag_layout
grid_constraints = GridBagConstraints()
format_1_string_label = JLabel("Format 1 string:")
grid_constraints.weightx = 0.1
grid_constraints.weighty = 0.1
grid_constraints.gridy = 0
grid_constraints.fill = GridBagConstraints.NONE
self._add_component(format_1_string_label, bag_layout, grid_constraints)
self.input_textbox = JTextArea()
grid_constraints.weightx = 1
grid_constraints.weighty = 1
grid_constraints.gridy = 1
grid_constraints.fill = GridBagConstraints.BOTH
input_scroll_pane = JScrollPane(self.input_textbox)
input_scroll_pane.verticalScrollBarPolicy = ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS
self._add_component(input_scroll_pane, bag_layout, grid_constraints)
output_string_label = JLabel("Output:")
grid_constraints.weightx = 0.1
grid_constraints.weighty = 0.1
grid_constraints.gridy = 2
grid_constraints.fill = GridBagConstraints.NONE
self._add_component(output_string_label, bag_layout, grid_constraints)
self.output_textbox = JTextArea()
grid_constraints.weightx = 1
grid_constraints.weighty = 1
grid_constraints.gridy = 3
grid_constraints.fill = GridBagConstraints.BOTH
self.output_textbox.editable = False
output_scroll_pane = JScrollPane(self.output_textbox)
output_scroll_pane.verticalScrollBarPolicy = ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS
self._add_component(output_scroll_pane, bag_layout, grid_constraints)
def __init__(self):
self.running = True
menuBar = JMenuBar()
menu = JMenu("File")
menu.add(OpenAction(self))
menu.add(CloseAction(self))
menu.addSeparator()
menu.add(QuitAction(self))
self.addWindowListener(ProfelisWindowAdapter(self))
menuBar.add(menu)
self.setJMenuBar(menuBar)
self.contentPane = JPanel()
self.contentPane.layout = GridBagLayout()
constraints = GridBagConstraints()
self.blastLocation = JTextField(System.getProperty("user.home") + "/blast")
self.databaseLocation = JTextField(System.getProperty("user.home") + "/blast/db")
self.projects = JTabbedPane()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JLabel("Blast Location"), constraints)
constraints.gridx, constraints.gridy = 1, 0
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.weightx, constraints.weighty = 1, 0
self.contentPane.add(self.blastLocation, constraints)
constraints.gridx, constraints.gridy = 2, 0
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JButton(BlastAction(self)), constraints)
constraints.gridx, constraints.gridy = 3, 0
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JLabel("Database Location"), constraints)
constraints.gridx, constraints.gridy = 4, 0
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.weightx, constraints.weighty = 1, 0
self.contentPane.add(self.databaseLocation, constraints)
constraints.gridx, constraints.gridy = 5, 0
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JButton(DatabaseAction(self)), constraints)
constraints.gridx, constraints.gridy = 0, 1
constraints.gridwidth, constraints.gridheight = 6, 1
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.contentPane.add(self.projects, constraints)
def __fillQuestions(self):
panel = JPanel()
panel.setLayout(GridBagLayout())
panel.setBorder(None)
c = GridBagConstraints()
c.gridx = 0
c.gridy = 0
c.weightx = 1.0
c.fill = GridBagConstraints.HORIZONTAL
c.anchor = GridBagConstraints.PAGE_START
line = 0
for question in self.test.getQuestions():
c.gridy = line
panel.add(question.getPanel().asJComponent(),c)
line += 1
scrollPanel = JScrollPane(panel)
scrollPanel.setBorder(None)
self.questionsContainer.setLayout(BorderLayout())
self.questionsContainer.add(scrollPanel, BorderLayout.CENTER)
def getGridBagConstraints(game,node):
c = GridBagConstraints()
for str in node.getAttribute("constraints").split(","):
a = str.split(":")
if a[0]=="fill":
c.fill = int(a[1])
elif a[0]=="gridwidth":
c.gridwidth = int(a[1])
elif a[0]=="gridheight":
c.gridheight = int(a[1])
elif a[0]=="gridx":
c.gridx = int(a[1])
elif a[0]=="gridy":
c.gridy = int(a[1])
elif a[0]=="weightx":
c.weightx = int(a[1])
elif a[0]=="weighty":
c.weighty = int(a[1])
else:
print a[0]+"was not found"
return c
def arrange_plots(regplot, plotm, plotd):
"""
arranges the plots in a certain order,
regplot and plotm in first row next to each other
plotd in second row
"""
from javax.swing import JPanel,JFrame
from java.awt import GridBagLayout, GridBagConstraints
mainPanel = JPanel()
mainPanel.setLayout(GridBagLayout())
c=GridBagConstraints()
c.fill=c.BOTH
c.weightx,c.weighty=0.5,1
c.gridx,c.gridy,c.gridwidth,c.gridheight=0,0,10,4
c.weightx,c.weighty=0.5,1
c.gridx,c.gridy,c.gridwidth,c.gridheight=0,0,10,4
mainPanel.add(regplot)
c.gridx,c.gridy,c.gridwidth,c.gridheight=0,0,10,4
c.weightx,c.weighty=1,1
mainPanel.add(plotm,c)
c.gridx,c.gridy,c.gridwidth,c.gridheight=0,4,10,6
mainPanel.add(plotd,c)
return mainPanel
def __init__(self, frame, name):
self.frame = frame
self.exception = None
self.name = name
self.searchTerm = None
self.searchIndex = -1
self.searchField = JTextField("")
self.searchField.addActionListener(SearchListener(self))
self.newGeneFrom = JTextField("")
self.newGeneTo = JTextField("")
self.newGeneButton = JButton("New Gene")
newGeneActionListener = NewGeneActionListener(self)
self.newGeneFrom.addActionListener(newGeneActionListener)
self.newGeneTo.addActionListener(newGeneActionListener)
self.newGeneButton.addActionListener(newGeneActionListener)
self.markForRemovalButton = JButton("Mark For Removal")
self.markForRemovalButton.addActionListener(MarkForRemovalListener(self))
self.inGenes = JList(DefaultListModel())
self.inGenes.selectionMode = ListSelectionModel.SINGLE_SELECTION
self.inGenes.cellRenderer = ProfelisCellRenderer()
self.markButtonLabelerTimer = Timer(100, MarkButtonLabeler(self))
self.markButtonLabelerTimer.start()
self.loadFile()
self.outGenes = JList(DefaultListModel())
self.outGenes.selectionMode = ListSelectionModel.SINGLE_SELECTION
self.outGenes.cellRenderer = ProfelisCellRenderer()
constraints = GridBagConstraints()
self.layout = GridBagLayout()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.add(JLabel("Genes In Artemis File"), constraints)
constraints.gridx, constraints.gridy = 0, 1
self.add(JButton(RemoveAction(self)), constraints)
constraints.gridx, constraints.gridy = 1, 1
self.add(self.markForRemovalButton, constraints)
constraints.gridx, constraints.gridy = 2, 1
self.add(JLabel("Search"), constraints)
constraints.gridx, constraints.gridy = 3, 1
constraints.fill = GridBagConstraints.HORIZONTAL
self.add(self.searchField, constraints)
constraints.gridx, constraints.gridy = 0, 2
constraints.gridwidth, constraints.gridheight = 4, 2
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.add(JScrollPane(self.inGenes), constraints)
constraints.gridx, constraints.gridy = 4, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.add(JLabel("Genes To Add To Artemis File"), constraints)
constraints.gridx, constraints.gridy = 4, 1
self.add(self.newGeneButton, constraints)
constraints.weightx = 1
constraints.fill = GridBagConstraints.BOTH
constraints.gridx, constraints.gridy = 5, 1
self.add(self.newGeneFrom, constraints)
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.gridx, constraints.gridy = 6, 1
self.add(JLabel("To"), constraints)
constraints.weightx = 1
constraints.fill = GridBagConstraints.BOTH
constraints.gridx, constraints.gridy = 7, 1
self.add(self.newGeneTo, constraints)
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.gridx, constraints.gridy = 4, 2
self.add(JButton(AddGenesAction(self)), constraints)
constraints.gridx, constraints.gridy = 4, 3
constraints.gridwidth, constraints.gridheight = 4, 1
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.add(JScrollPane(self.outGenes), constraints)
def doall(locations, fileobs,filerun1,filerun2,stime,etime,imageDir='d:/temp',weights=None,filter_type="AVE",normalize=False):
obs=HecDss.open(fileobs,True)
obs.setTimeWindow(stime,etime)
run1=HecDss.open(filerun1,True)
run1.setTimeWindow(stime,etime)
if filerun2 != None:
run2=HecDss.open(filerun2,True)
run2.setTimeWindow(stime,etime)
else:
run2=None
rms1=0
rms1_min,rms1_max=0,0
rms2=0
rms2_min,rms2_max=0,0
rmsmap={}
#run2=None
sumwts=0
average_interval=None;
for l in locations:
data1=get_matching(obs,'A=%s C=%s E=15MIN'%(l,type))
if data1 == None:
data1=get_matching(obs,'A=%s C=%s E=1DAY'%(l,type))
if data1 == None:
data1=get_matching(obs,'A=%s C=%s E=IR-DAY'%(l,type))
if data1 == None:
data1=get_matching(obs,'A=%s C=%s E=1HOUR'%(l,type))
drun1=get_matching(run1,'B=%s C=%s'%(l,type))
if run2 != None:
drun2=get_matching(run2, 'B=%s C=%s'%(l,type))
else:
drun2=None
avg_intvl="1DAY"
if data1 != None:
if average_interval != None:
dobsd=TimeSeriesMath(data1).transformTimeSeries(average_interval, None, filter_type, 0)
else:
dobsd=TimeSeriesMath(data1)
if normalize:
dobsd=dobsd.divide(TimeSeriesMath(data1).mean())
dobsm=TimeSeriesMath(data1).transformTimeSeries(avg_intvl, None, filter_type, 0)
dobsm_max=TimeSeriesMath(data1).transformTimeSeries(avg_intvl, None, "MAX", 0)
dobsm_max.data.fullName=dobsm_max.data.fullName+"MAX"
dobsm_min=TimeSeriesMath(data1).transformTimeSeries(avg_intvl, None, "MIN", 0)
dobsm_min.data.fullName=dobsm_min.data.fullName+"MIN"
if normalize:
dobsm=dobsm.divide(TimeSeriesMath(data1).mean())
if drun1==None:
continue;
else:
if average_interval != None:
drun1d=TimeSeriesMath(drun1).transformTimeSeries(average_interval, None, filter_type, 0)
else:
drun1d=TimeSeriesMath(drun1)
if normalize:
drun1d=drun1d.divide(TimeSeriesMath(drun1).mean())
if drun2 != None:
if average_interval != None:
drun2d=TimeSeriesMath(drun2).transformTimeSeries(average_interval, None, filter_type, 0)
else:
drun2d=TimeSeriesMath(drun2)
if normalize:
drun2d=drun2d.divide(TimeSeriesMath(drun2).mean())
drun1m=TimeSeriesMath(drun1).transformTimeSeries(avg_intvl, None, filter_type, 0)
drun1m_max=TimeSeriesMath(drun1).transformTimeSeries(avg_intvl, None, "MAX", 0)
drun1m_min=TimeSeriesMath(drun1).transformTimeSeries(avg_intvl, None, "MIN", 0)
if normalize:
drun1m=drun1m.divide(TimeSeriesMath(drun1).mean())
if drun2 != None:
drun2m=TimeSeriesMath(drun2).transformTimeSeries(avg_intvl, None, filter_type, 0)
drun2m_max=TimeSeriesMath(drun2).transformTimeSeries(avg_intvl, None, "MAX", 0)
drun2m_min=TimeSeriesMath(drun2).transformTimeSeries(avg_intvl, None, "MIN", 0)
if normalize:
drun2m=drun2m.divide(TimeSeriesMath(drun2).mean())
else:
drun2m=None
if weights != None:
sumwts=sumwts+weights[l]
lrms1 = calculate_rms(drun1m.data, dobsm.data)*weights[l]
lrms1_min=calculate_rms(drun1m_min.data,dobsm_min.data)*weights[l]
lrms1_max=calculate_rms(drun1m_max.data,dobsm_max.data)*weights[l]
rms1=rms1+lrms1
rms1_min=rms1_min+lrms1_min
rms1_max=rms1_max+lrms1_max
lrms2 = calculate_rms(drun2m.data,dobsm.data)*weights[l]
lrms2_min=calculate_rms(drun2m_min.data,dobsm_min.data)*weights[l]
lrms2_max=calculate_rms(drun2m_max.data,dobsm_max.data)*weights[l]
rmsmap[l] = lrms1,lrms2,lrms1_min,lrms2_min,lrms1_max,lrms2_max
rms2=rms2+lrms2
rms2_min=rms2_min+lrms2_min
rms2_max=rms2_max+lrms2_max
plotd = newPlot("Hist vs New Geom [%s]"%l)
if data1 != None:
plotd.addData(dobsd.data)
plotd.addData(drun1d.data)
if drun2 != None:
plotd.addData(drun2d.data)
plotd.showPlot()
legend_label = plotd.getLegendLabel(drun1d.data)
legend_label.setText(legend_label.getText()+" ["+str(int(lrms1*100)/100.)+","+str(int(lrms1_min*100)/100.)+","+str(int(lrms1_max*100)/100.)+"]")
legend_label = plotd.getLegendLabel(drun2d.data)
legend_label.setText(legend_label.getText()+" ["+str(int(lrms2*100)/100.)+","+str(int(lrms2_min*100)/100.)+","+str(int(lrms2_max*100)/100.)+"]")
plotd.setVisible(False)
xaxis=plotd.getViewport(0).getAxis("x1")
vmin =xaxis.getViewMin()+261500. # hardwired to around july 1, 2008
xaxis.setViewLimits(vmin,vmin+10000.)
if data1 != None:
pline = plotd.getCurve(dobsd.data)
pline.setLineVisible(1)
pline.setLineColor("blue")
pline.setSymbolType(Symbol.SYMBOL_CIRCLE)
pline.setSymbolsVisible(0)
pline.setSymbolSize(3)
pline.setSymbolSkipCount(0)
pline.setSymbolFillColor(pline.getLineColorString())
pline.setSymbolLineColor(pline.getLineColorString())
g2dPanel = plotd.getPlotpanel()
g2dPanel.revalidate();
g2dPanel.paintGfx();
plotm = newPlot("Hist vs New Geom Monthly [%s]"%l)
plotm.setSize(1800,1200)
if data1 != None:
plotm.addData(dobsm.data)
#plotm.addData(dobsm_max.data)
#plotm.addData(dobsm_min.data)
plotm.addData(drun1m.data)
#plotm.addData(drun1m_max.data)
#plotm.addData(drun1m_min.data)
if drun2 != None:
plotm.addData(drun2m.data)
#plotm.addData(drun2m_max.data)
#plotm.addData(drun2m_min.data)
plotm.showPlot()
if data1 != None:
pline = plotm.getCurve(dobsm.data)
pline.setLineVisible(1)
pline.setLineColor("blue")
pline.setSymbolType(Symbol.SYMBOL_CIRCLE)
pline.setSymbolsVisible(0)
pline.setSymbolSize(3)
pline.setSymbolSkipCount(0)
pline.setSymbolFillColor(pline.getLineColorString())
pline.setSymbolLineColor(pline.getLineColorString())
plotm.setVisible(False)
if data1 != None:
plots=do_regression_plots(dobsm,drun1m,drun2m)
if plots != None:
spanel = plots.getPlotpanel()
removeToolbar(spanel)
mpanel = plotm.getPlotpanel()
removeToolbar(mpanel)
dpanel = plotd.getPlotpanel()
removeToolbar(dpanel)
from javax.swing import JPanel,JFrame
from java.awt import GridBagLayout, GridBagConstraints
mainPanel = JPanel()
mainPanel.setLayout(GridBagLayout())
c=GridBagConstraints()
c.fill=c.BOTH
c.weightx,c.weighty=0.5,1
c.gridx,c.gridy,c.gridwidth,c.gridheight=0,0,10,4
if data1 != None:
if plots != None:
pass
#mainPanel.add(spanel,c)
c.gridx,c.gridy,c.gridwidth,c.gridheight=0,0,10,4
c.weightx,c.weighty=1,1
mainPanel.add(mpanel,c)
c.gridx,c.gridy,c.gridwidth,c.gridheight=0,4,10,6
mainPanel.add(dpanel,c)
fr=JFrame()
fr.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE)
fr.getContentPane().add(mainPanel)
fr.setSize(1100,850);
fr.show();
mainPanel.setSize(1100,850);
mainPanel.setBackground(Color.WHITE);
#import time; time.sleep(5)
saveToPNG(mainPanel,imageDir+l+".png")
if weights != None:
rms1=(rms1+rms1_min+rms1_max)/sumwts
rms2=(rms2+rms2_min+rms2_max)/sumwts
print 'RMS Run 1: %f'%rms1
print 'RMS Run 2: %f'%rms2
for loc in rmsmap.keys():
print loc, rmsmap[loc]
pass # none editable
# Create the GUI: a 3-column table and a text area next to it
# to show and write notes for any selected row, plus some buttons and a search field
all = JPanel()
all.setBackground(Color.white)
gb = GridBagLayout()
all.setLayout(gb)
c = GridBagConstraints()
# Top-left element: a text field for filtering rows by regular expression match
c.gridx = 0
c.gridy = 0
c.anchor = GridBagConstraints.CENTER
c.fill = GridBagConstraints.HORIZONTAL
search_field = JTextField("")
gb.setConstraints(search_field, c)
all.add(search_field)
# Bottom left element: the table, wrapped in a scrollable component
table = JTable(TableModel())
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION)
#table.setCellSelectionEnabled(True)
table.setAutoCreateRowSorter(
True) # to sort the view only, not the data in the underlying TableModel
c.gridx = 0
c.gridy = 1
c.anchor = GridBagConstraints.NORTHWEST
c.fill = GridBagConstraints.BOTH # resize with the frame
c.weightx = 1.0
def registerExtenderCallbacks(self, callbacks):
self.callbacks = callbacks
self.helpers = callbacks.getHelpers()
callbacks.setExtensionName("Session Authentication Tool")
self.out = callbacks.getStdout()
# definition of suite tab
self.tab = JPanel(GridBagLayout())
self.tabledata = MappingTableModel(callbacks)
self.table = JTable(self.tabledata)
#self.table.getColumnModel().getColumn(0).setPreferredWidth(50);
#self.table.getColumnModel().getColumn(1).setPreferredWidth(100);
self.tablecont = JScrollPane(self.table)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.anchor = GridBagConstraints.FIRST_LINE_START
c.gridx = 0
c.gridy = 0
c.gridheight = 6
c.weightx = 0.3
c.weighty = 0.5
self.tab.add(self.tablecont, c)
c = GridBagConstraints()
c.weightx = 0.1
c.anchor = GridBagConstraints.FIRST_LINE_START
c.gridx = 1
c.gridy = 0
label_id = JLabel("Identifier:")
self.tab.add(label_id, c)
self.input_id = JTextField(20)
self.input_id.setToolTipText(
"Enter the identifier which is used by the application to identifiy a particular test user account, e.g. a numerical user id or a user name."
)
c.gridy = 1
self.tab.add(self.input_id, c)
c.gridy = 2
label_content = JLabel("Content:")
self.tab.add(label_content, c)
self.input_content = JTextField(20, actionPerformed=self.btn_add_id)
self.input_content.setToolTipText(
"Enter some content which is displayed in responses of the application and shows that the current session belongs to a particular user, e.g. the full name of the user."
)
c.gridy = 3
self.tab.add(self.input_content, c)
self.btn_add = JButton("Add/Edit Identity",
actionPerformed=self.btn_add_id)
c.gridy = 4
self.tab.add(self.btn_add, c)
self.btn_del = JButton("Delete Identity",
actionPerformed=self.btn_del_id)
c.gridy = 5
self.tab.add(self.btn_del, c)
callbacks.customizeUiComponent(self.tab)
callbacks.customizeUiComponent(self.table)
callbacks.customizeUiComponent(self.tablecont)
callbacks.customizeUiComponent(self.btn_add)
callbacks.customizeUiComponent(self.btn_del)
callbacks.customizeUiComponent(label_id)
callbacks.customizeUiComponent(self.input_id)
callbacks.addSuiteTab(self)
callbacks.registerScannerCheck(self)
callbacks.registerIntruderPayloadGeneratorFactory(self)
callbacks.registerContextMenuFactory(self)
def doall(locations,
fileobs,
filerun1,
filerun2,
stime,
etime,
imageDir='d:/temp',
weights=None,
filter_type="AVE",
normalize=False):
obs = HecDss.open(fileobs, True)
obs.setTimeWindow(stime, etime)
run1 = HecDss.open(filerun1, True)
run1.setTimeWindow(stime, etime)
if filerun2 != None:
run2 = HecDss.open(filerun2, True)
run2.setTimeWindow(stime, etime)
else:
run2 = None
rms1 = 0
rms1_min, rms1_max = 0, 0
rms2 = 0
rms2_min, rms2_max = 0, 0
rmsmap = {}
#run2=None
sumwts = 0
average_interval = None
for l in locations:
data1 = get_matching(obs, 'A=%s C=%s E=15MIN' % (l, type))
if data1 == None:
data1 = get_matching(obs, 'A=%s C=%s E=1DAY' % (l, type))
if data1 == None:
data1 = get_matching(obs, 'A=%s C=%s E=IR-DAY' % (l, type))
if data1 == None:
data1 = get_matching(obs, 'A=%s C=%s E=1HOUR' % (l, type))
drun1 = get_matching(run1, 'B=%s C=%s' % (l, type))
if run2 != None:
drun2 = get_matching(run2, 'B=%s C=%s' % (l, type))
else:
drun2 = None
avg_intvl = "1DAY"
if data1 != None:
if average_interval != None:
dobsd = TimeSeriesMath(data1).transformTimeSeries(
average_interval, None, filter_type, 0)
else:
dobsd = TimeSeriesMath(data1)
if normalize:
dobsd = dobsd.divide(TimeSeriesMath(data1).mean())
dobsm = TimeSeriesMath(data1).transformTimeSeries(
avg_intvl, None, filter_type, 0)
dobsm_max = TimeSeriesMath(data1).transformTimeSeries(
avg_intvl, None, "MAX", 0)
dobsm_max.data.fullName = dobsm_max.data.fullName + "MAX"
dobsm_min = TimeSeriesMath(data1).transformTimeSeries(
avg_intvl, None, "MIN", 0)
dobsm_min.data.fullName = dobsm_min.data.fullName + "MIN"
if normalize:
dobsm = dobsm.divide(TimeSeriesMath(data1).mean())
if drun1 == None:
continue
else:
if average_interval != None:
drun1d = TimeSeriesMath(drun1).transformTimeSeries(
average_interval, None, filter_type, 0)
else:
drun1d = TimeSeriesMath(drun1)
if normalize:
drun1d = drun1d.divide(TimeSeriesMath(drun1).mean())
if drun2 != None:
if average_interval != None:
drun2d = TimeSeriesMath(drun2).transformTimeSeries(
average_interval, None, filter_type, 0)
else:
drun2d = TimeSeriesMath(drun2)
if normalize:
drun2d = drun2d.divide(TimeSeriesMath(drun2).mean())
drun1m = TimeSeriesMath(drun1).transformTimeSeries(
avg_intvl, None, filter_type, 0)
drun1m_max = TimeSeriesMath(drun1).transformTimeSeries(
avg_intvl, None, "MAX", 0)
drun1m_min = TimeSeriesMath(drun1).transformTimeSeries(
avg_intvl, None, "MIN", 0)
if normalize:
drun1m = drun1m.divide(TimeSeriesMath(drun1).mean())
if drun2 != None:
drun2m = TimeSeriesMath(drun2).transformTimeSeries(
avg_intvl, None, filter_type, 0)
drun2m_max = TimeSeriesMath(drun2).transformTimeSeries(
avg_intvl, None, "MAX", 0)
drun2m_min = TimeSeriesMath(drun2).transformTimeSeries(
avg_intvl, None, "MIN", 0)
if normalize:
drun2m = drun2m.divide(TimeSeriesMath(drun2).mean())
else:
drun2m = None
if weights != None:
sumwts = sumwts + weights[l]
lrms1 = calculate_rms(drun1m.data, dobsm.data) * weights[l]
lrms1_min = calculate_rms(drun1m_min.data,
dobsm_min.data) * weights[l]
lrms1_max = calculate_rms(drun1m_max.data,
dobsm_max.data) * weights[l]
rms1 = rms1 + lrms1
rms1_min = rms1_min + lrms1_min
rms1_max = rms1_max + lrms1_max
lrms2 = calculate_rms(drun2m.data, dobsm.data) * weights[l]
lrms2_min = calculate_rms(drun2m_min.data,
dobsm_min.data) * weights[l]
lrms2_max = calculate_rms(drun2m_max.data,
dobsm_max.data) * weights[l]
rmsmap[
l] = lrms1, lrms2, lrms1_min, lrms2_min, lrms1_max, lrms2_max
rms2 = rms2 + lrms2
rms2_min = rms2_min + lrms2_min
rms2_max = rms2_max + lrms2_max
plotd = newPlot("Hist vs New Geom [%s]" % l)
if data1 != None:
plotd.addData(dobsd.data)
plotd.addData(drun1d.data)
if drun2 != None:
plotd.addData(drun2d.data)
plotd.showPlot()
legend_label = plotd.getLegendLabel(drun1d.data)
legend_label.setText(legend_label.getText() + " [" +
str(int(lrms1 * 100) / 100.) + "," +
str(int(lrms1_min * 100) / 100.) + "," +
str(int(lrms1_max * 100) / 100.) + "]")
legend_label = plotd.getLegendLabel(drun2d.data)
legend_label.setText(legend_label.getText() + " [" +
str(int(lrms2 * 100) / 100.) + "," +
str(int(lrms2_min * 100) / 100.) + "," +
str(int(lrms2_max * 100) / 100.) + "]")
plotd.setVisible(False)
xaxis = plotd.getViewport(0).getAxis("x1")
vmin = xaxis.getViewMin() + 261500. # hardwired to around july 1, 2008
xaxis.setViewLimits(vmin, vmin + 10000.)
if data1 != None:
pline = plotd.getCurve(dobsd.data)
pline.setLineVisible(1)
pline.setLineColor("blue")
pline.setSymbolType(Symbol.SYMBOL_CIRCLE)
pline.setSymbolsVisible(0)
pline.setSymbolSize(3)
pline.setSymbolSkipCount(0)
pline.setSymbolFillColor(pline.getLineColorString())
pline.setSymbolLineColor(pline.getLineColorString())
g2dPanel = plotd.getPlotpanel()
g2dPanel.revalidate()
g2dPanel.paintGfx()
plotm = newPlot("Hist vs New Geom Monthly [%s]" % l)
plotm.setSize(1800, 1200)
if data1 != None:
plotm.addData(dobsm.data)
#plotm.addData(dobsm_max.data)
#plotm.addData(dobsm_min.data)
plotm.addData(drun1m.data)
#plotm.addData(drun1m_max.data)
#plotm.addData(drun1m_min.data)
if drun2 != None:
plotm.addData(drun2m.data)
#plotm.addData(drun2m_max.data)
#plotm.addData(drun2m_min.data)
plotm.showPlot()
if data1 != None:
pline = plotm.getCurve(dobsm.data)
pline.setLineVisible(1)
pline.setLineColor("blue")
pline.setSymbolType(Symbol.SYMBOL_CIRCLE)
pline.setSymbolsVisible(0)
pline.setSymbolSize(3)
pline.setSymbolSkipCount(0)
pline.setSymbolFillColor(pline.getLineColorString())
pline.setSymbolLineColor(pline.getLineColorString())
plotm.setVisible(False)
if data1 != None:
plots = do_regression_plots(dobsm, drun1m, drun2m)
if plots != None:
spanel = plots.getPlotpanel()
removeToolbar(spanel)
mpanel = plotm.getPlotpanel()
removeToolbar(mpanel)
dpanel = plotd.getPlotpanel()
removeToolbar(dpanel)
from javax.swing import JPanel, JFrame
from java.awt import GridBagLayout, GridBagConstraints
mainPanel = JPanel()
mainPanel.setLayout(GridBagLayout())
c = GridBagConstraints()
c.fill = c.BOTH
c.weightx, c.weighty = 0.5, 1
c.gridx, c.gridy, c.gridwidth, c.gridheight = 0, 0, 10, 4
if data1 != None:
if plots != None:
pass
#mainPanel.add(spanel,c)
c.gridx, c.gridy, c.gridwidth, c.gridheight = 0, 0, 10, 4
c.weightx, c.weighty = 1, 1
mainPanel.add(mpanel, c)
c.gridx, c.gridy, c.gridwidth, c.gridheight = 0, 4, 10, 6
mainPanel.add(dpanel, c)
fr = JFrame()
fr.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE)
fr.getContentPane().add(mainPanel)
fr.setSize(1100, 850)
fr.show()
mainPanel.setSize(1100, 850)
mainPanel.setBackground(Color.WHITE)
#import time; time.sleep(5)
saveToPNG(mainPanel, imageDir + l + ".png")
if weights != None:
rms1 = (rms1 + rms1_min + rms1_max) / sumwts
rms2 = (rms2 + rms2_min + rms2_max) / sumwts
print 'RMS Run 1: %f' % rms1
print 'RMS Run 2: %f' % rms2
for loc in rmsmap.keys():
print loc, rmsmap[loc]
def __init__(self):
''' Configuration Panel '''
# pconfig = JPanel(GridBagLayout())
# pconfig.setSize(Dimension(500,300))
self.setLayout(GridBagLayout())
# super(self,GridBagLayout())
self.setSize(Dimension(500,300))
''' fila 1 '''
label = JLabel('Configuration panel')
c1 = GridBagConstraints()
c1.fill = GridBagConstraints.HORIZONTAL
c1.weightx = 0.5
c1.gridwidth = 4
c1.gridx = 0
c1.gridy = 0
self.add(label, c1)
''' fila 2 '''
self.radioBtnOMC = JRadioButton('OpenModelica')
c2 = GridBagConstraints()
c2.fill = GridBagConstraints.HORIZONTAL
c2.weightx = 0.5
c2.gridx = 0
c2.gridy = 1
self.add(self.radioBtnOMC, c2)
self.radioBtnJM = JRadioButton('JModelica')
c3 = GridBagConstraints()
c3.fill = GridBagConstraints.HORIZONTAL
c3.weightx = 0.5
c3.gridx = 1
c3.gridy = 1
self.add(self.radioBtnJM, c3)
self.radioBtnDY = JRadioButton('Dymola')
c4 = GridBagConstraints()
c4.fill = GridBagConstraints.HORIZONTAL
c4.weightx = 0.5
c4.gridx = 2
c4.gridy = 1
self.add(self.radioBtnDY, c4)
rbBtnGroup = ButtonGroup()
rbBtnGroup.add(self.radioBtnOMC)
rbBtnGroup.add(self.radioBtnJM)
rbBtnGroup.add(self.radioBtnDY)
''' fila 2 '''
label = JLabel('Start time')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 2
self.add(label, c)
self.txtstart= JTextField('0')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 2
self.add(self.txtstart, c)
label = JLabel('Stop time')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 2
c.gridy = 2
self.add(label, c)
self.txtstop= JTextField('0')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 3
c.gridy = 2
self.add(self.txtstop, c)
''' fila 3 '''
label = JLabel('Solver')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 3
self.add(label, c)
self.cbsolver= JComboBox(['dassl','rkfix2'])
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 3
self.add(self.cbsolver, c)
label = JLabel('Algorithm (JM)')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 2
c.gridy = 3
self.add(label, c)
self.cbalgorithm= JComboBox(['AssimuloAlg'])
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 3
c.gridy = 3
self.add(self.cbalgorithm, c)
''' fila 4 '''
label = JLabel('Interval')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 4
self.add(label, c)
self.txtinterval= JTextField('0')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 4
self.add(self.txtinterval, c)
''' fila 5 '''
label = JLabel('Tolerance')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 5
self.add(label, c)
self.txttolerance= JTextField('0')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 5
self.add(self.txttolerance, c)
''' fila 6 '''
label = JLabel('Output format')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 6
self.add(label, c)
self.cboutformat= JComboBox(['.mat','.h5','.csv'])
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 6
self.add(self.cboutformat, c)
label = JLabel('Initialize (JM)')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 2
c.gridy = 6
self.add(label, c)
self.cbinitialize= JComboBox(['True','False'])
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 3
c.gridy = 6
self.add(self.cbinitialize, c)
''' fila 7 '''
bSaveCfg= JButton('Save Configuration', actionPerformed= self.saveConfiguration)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridwidth = 2
c.gridx = 0
c.gridy = 7
self.add(bSaveCfg, c)
self.bSimulation= JButton('Load Configuration', actionPerformed= self.loadConfiguration)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridwidth = 2
c.gridx = 2
c.gridy = 7
self.add(self.bSimulation, c)
''' fila 8 '''
self.bSimulation= JButton('Simulate', actionPerformed= self.startSimlation)
self.bSimulation.enabled= 0
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridwidth = 4
c.gridx = 0
c.gridy = 8
self.add(self.bSimulation, c)
''' file 9 '''
simProgress= JProgressBar(0, self.getWidth(), value=0, stringPainted=True)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridwidth = 4
c.gridx = 0
c.gridy = 9
self.add(simProgress, c)
''' fila 10 '''
self.lblResult= JLabel('Simulation information')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridwidth = 4
c.gridx = 0
c.gridy = 10
self.add(self.lblResult, c)
def getArguments(self):
"""
This function brings up a window to retreive any required arguments. It uses a window with fields for each argument, filled with any arguments already given.
While this window is visible the program will wait, once it is no longer visible all the arguments will be filled with the entries in the fields.
"""
class LocationAction(AbstractAction):
"""
Action to set the text of a text field to a folder or directory.
"""
def __init__(self, field):
AbstractAction.__init__(self, "...")
self.field = field
def actionPerformed(self, event):
fileChooser = JFileChooser()
fileChooser.fileSelectionMode = JFileChooser.FILES_AND_DIRECTORIES
if fileChooser.showOpenDialog(None) == JFileChooser.APPROVE_OPTION:
self.field.text = fileChooser.selectedFile.absolutePath
class HelpAction(AbstractAction):
"""
Displays a help page in a web browser.
"""
def __init__(self):
AbstractAction.__init__(self, "Help")
def actionPerformed(self, event):
browsers = ["google-chrome", "firefox", "opera", "epiphany", "konqueror", "conkeror", "midori", "kazehakase", "mozilla"]
osName = System.getProperty("os.name")
helpHTML = ClassLoader.getSystemResource("help.html").toString()
if osName.find("Mac OS") == 0:
Class.forName("com.apple.eio.FileManager").getDeclaredMethod( "openURL", [String().getClass()]).invoke(None, [helpHTML])
elif osName.find("Windows") == 0:
Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + helpHTML)
else:
browser = None
for b in browsers:
if browser == None and Runtime.getRuntime().exec(["which", b]).getInputStream().read() != -1:
browser = b
Runtime.getRuntime().exec([browser, helpHTML])
class OKAction(AbstractAction):
"""
Action for starting the pipeline. This action will simply make the window invisible.
"""
def __init__(self):
AbstractAction.__init__(self, "Ok")
def actionPerformed(self, event):
frame.setVisible(False)
class CancelAction(AbstractAction):
"""
Action for canceling the pipeline. Exits the program.
"""
def __init__(self):
AbstractAction.__init__(self, "Cancel")
def actionPerformed(self, event):
sys.exit(0)
frame = JFrame("Neofelis")
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE)
constraints = GridBagConstraints()
contentPane = JPanel(GridBagLayout())
frame.setContentPane(contentPane)
blastField = JTextField(self.blastLocation)
genemarkField = JTextField(self.genemarkLocation)
transtermField = JTextField(self.transtermLocation)
tRNAscanField = JTextField(self.tRNAscanLocation)
databaseLocationField = JTextField(os.path.split(self.database)[0])
databaseField = JTextField(os.path.split(self.database)[1])
matrixField = JTextField(str(self.matrix))
eValueField = JTextField(str(self.eValue))
minLengthField = JTextField(str(self.minLength))
scaffoldingDistanceField = JTextField(str(self.scaffoldingDistance))
promoterScoreField = JTextField(str(self.promoterScoreCutoff))
queryField = JTextField(self.sources[0])
constraints.gridx = 0
constraints.gridy = 0
constraints.gridwidth = 1
constraints.gridheight = 1
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.weightx = 0
constraints.weighty = 0
contentPane.add(JLabel("Blast Location"), constraints)
constraints.gridy = 1
contentPane.add(JLabel("Genemark Location"), constraints)
constraints.gridy = 2
contentPane.add(JLabel("Transterm Location"), constraints)
constraints.gridy = 3
contentPane.add(JLabel("tRNAscan Location"), constraints)
constraints.gridy = 4
contentPane.add(JLabel("Databases Location"), constraints)
constraints.gridy = 5
contentPane.add(JLabel("Database"), constraints)
constraints.gridy = 6
contentPane.add(JLabel("Matrix(Leave blank to use heuristic matrix)"), constraints)
constraints.gridy = 7
contentPane.add(JLabel("E Value"), constraints)
constraints.gridy = 8
contentPane.add(JLabel("Minimum Intergenic Length"), constraints)
constraints.gridy = 9
contentPane.add(JLabel("Scaffold Distance"), constraints)
constraints.gridy = 10
contentPane.add(JLabel("Promoter Score Cutoff"), constraints)
constraints.gridy = 11
contentPane.add(JLabel("Query"), constraints)
constraints.gridx = 1
constraints.gridy = 0
constraints.weightx = 1
contentPane.add(blastField, constraints)
constraints.gridy = 1
contentPane.add(genemarkField, constraints)
constraints.gridy = 2
contentPane.add(transtermField, constraints)
constraints.gridy = 3
contentPane.add(tRNAscanField, constraints)
constraints.gridy = 4
contentPane.add(databaseLocationField, constraints)
constraints.gridy = 5
contentPane.add(databaseField, constraints)
constraints.gridy = 6
contentPane.add(matrixField, constraints)
constraints.gridy = 7
contentPane.add(eValueField, constraints)
constraints.gridy = 8
contentPane.add(minLengthField, constraints)
constraints.gridy = 9
contentPane.add(scaffoldingDistanceField, constraints)
constraints.gridy = 10
contentPane.add(promoterScoreField, constraints)
constraints.gridy = 11
contentPane.add(queryField, constraints)
constraints.gridx = 2
constraints.gridy = 0
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.anchor = GridBagConstraints.LINE_END
contentPane.add(JButton(LocationAction(blastField)), constraints)
constraints.gridy = 1
contentPane.add(JButton(LocationAction(genemarkField)), constraints)
constraints.gridy = 2
contentPane.add(JButton(LocationAction(transtermField)), constraints)
constraints.gridy = 3
contentPane.add(JButton(LocationAction(tRNAscanField)), constraints)
constraints.gridy = 4
contentPane.add(JButton(LocationAction(databaseLocationField)), constraints)
constraints.gridy = 11
contentPane.add(JButton(LocationAction(queryField)), constraints)
constraints.gridx = 0
constraints.gridy = 12
constraints.anchor = GridBagConstraints.LINE_START
contentPane.add(JButton(HelpAction()), constraints)
constraints.gridx = 1
constraints.anchor = GridBagConstraints.LINE_END
contentPane.add(JButton(OKAction()), constraints)
constraints.gridx = 2
contentPane.add(JButton(CancelAction()), constraints)
frame.pack()
frame.setLocationRelativeTo(None)
frame.setVisible(True)
while frame.isVisible():
pass
self.blastLocation = blastField.getText()
self.genemarkLocation = genemarkField.getText()
self.transtermLocation = transtermField.getText()
self.database = databaseLocationField.getText() + "/" + databaseField.getText()
self.matrix = matrixField.getText()
self.eValue = float(eValueField.getText())
self.minLength = int(minLengthField.getText())
self.scaffoldingDistance = int(scaffoldingDistanceField.getText())
self.promoterScoreCutoff = float(promoterScoreField.getText())
self.sources = [queryField.getText()]
def __init__(self, extender, *rows, **kwargs):
self.extender = extender
if 'title' in kwargs:
self.setBorder(
BorderFactory.createCompoundBorder(
BorderFactory.createTitledBorder(kwargs.get('title', '')),
BorderFactory.createEmptyBorder(5, 5, 5, 5)))
self.table = table = JTable(ParameterProcessingRulesTableModel(*rows))
table.setPreferredScrollableViewportSize(Dimension(500, 70))
table.setRowSorter(TableRowSorter(table.getModel()))
table.setFillsViewportHeight(True)
gridBagLayout = GridBagLayout()
gridBagLayout.columnWidths = [0, 0, 25, 0]
gridBagLayout.rowHeights = [0, 0, 0, 0]
gridBagLayout.columnWeights = [0.0, 1.0, 1.0, Double.MIN_VALUE]
gridBagLayout.rowWeights = [0.0, 0.0, 0.0, Double.MIN_VALUE]
self.setLayout(gridBagLayout)
addButton = JButton("Add")
addButton.addActionListener(AddRemoveParameterListener(table))
addButtonConstraints = GridBagConstraints()
addButtonConstraints.fill = GridBagConstraints.HORIZONTAL
addButtonConstraints.insets = Insets(0, 0, 5, 5)
addButtonConstraints.gridx = 0
addButtonConstraints.gridy = 0
self.add(addButton, addButtonConstraints)
removeButton = JButton("Remove")
removeButton.addActionListener(AddRemoveParameterListener(table))
removeButtonConstraints = GridBagConstraints()
removeButtonConstraints.fill = GridBagConstraints.HORIZONTAL
removeButtonConstraints.insets = Insets(0, 0, 5, 5)
removeButtonConstraints.gridx = 0
removeButtonConstraints.gridy = 1
self.add(removeButton, removeButtonConstraints)
upButton = JButton("Up")
upButton.addActionListener(AddRemoveParameterListener(table))
upButtonConstraints = GridBagConstraints()
upButtonConstraints.fill = GridBagConstraints.HORIZONTAL
upButtonConstraints.insets = Insets(0, 0, 5, 5)
upButtonConstraints.gridx = 0
upButtonConstraints.gridy = 2
self.add(upButton, upButtonConstraints)
downButton = JButton("Down")
downButton.addActionListener(AddRemoveParameterListener(table))
downButtonConstraints = GridBagConstraints()
downButtonConstraints.fill = GridBagConstraints.HORIZONTAL
downButtonConstraints.anchor = GridBagConstraints.NORTH
downButtonConstraints.insets = Insets(0, 0, 5, 5)
downButtonConstraints.gridx = 0
downButtonConstraints.gridy = 3
self.add(downButton, downButtonConstraints)
scrollPane = JScrollPane(table)
scrollPaneConstraints = GridBagConstraints()
scrollPaneConstraints.gridwidth = 2
scrollPaneConstraints.gridheight = 5
scrollPaneConstraints.insets = Insets(0, 0, 5, 5)
scrollPaneConstraints.anchor = GridBagConstraints.NORTHWEST
scrollPaneConstraints.gridx = 1
scrollPaneConstraints.gridy = 0
self.add(scrollPane, scrollPaneConstraints)
self.initParameterColumn(table)
self.initColumnSizes(table)
def registerExtenderCallbacks(self, callbacks):
self.callbacks = callbacks
self.helpers = callbacks.getHelpers()
callbacks.setExtensionName("Session Authentication Tool")
self.out = callbacks.getStdout()
# definition of suite tab
self.tab = JPanel(GridBagLayout())
self.tabledata = MappingTableModel(callbacks)
self.table = JTable(self.tabledata)
#self.table.getColumnModel().getColumn(0).setPreferredWidth(50);
#self.table.getColumnModel().getColumn(1).setPreferredWidth(100);
self.tablecont = JScrollPane(self.table)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.anchor = GridBagConstraints.FIRST_LINE_START
c.gridx = 0
c.gridy = 0
c.gridheight = 6
c.weightx = 0.3
c.weighty = 0.5
self.tab.add(self.tablecont, c)
c = GridBagConstraints()
c.weightx = 0.1
c.anchor = GridBagConstraints.FIRST_LINE_START
c.gridx = 1
c.gridy = 0
label_id = JLabel("Identifier:")
self.tab.add(label_id, c)
self.input_id = JTextField(20)
self.input_id.setToolTipText("Enter the identifier which is used by the application to identifiy a particular test user account, e.g. a numerical user id or a user name.")
c.gridy = 1
self.tab.add(self.input_id, c)
c.gridy = 2
label_content = JLabel("Content:")
self.tab.add(label_content, c)
self.input_content = JTextField(20, actionPerformed=self.btn_add_id)
self.input_content.setToolTipText("Enter some content which is displayed in responses of the application and shows that the current session belongs to a particular user, e.g. the full name of the user.")
c.gridy = 3
self.tab.add(self.input_content, c)
self.btn_add = JButton("Add/Edit Identity", actionPerformed=self.btn_add_id)
c.gridy = 4
self.tab.add(self.btn_add, c)
self.btn_del = JButton("Delete Identity", actionPerformed=self.btn_del_id)
c.gridy = 5
self.tab.add(self.btn_del, c)
callbacks.customizeUiComponent(self.tab)
callbacks.customizeUiComponent(self.table)
callbacks.customizeUiComponent(self.tablecont)
callbacks.customizeUiComponent(self.btn_add)
callbacks.customizeUiComponent(self.btn_del)
callbacks.customizeUiComponent(label_id)
callbacks.customizeUiComponent(self.input_id)
callbacks.addSuiteTab(self)
callbacks.registerScannerCheck(self)
callbacks.registerIntruderPayloadGeneratorFactory(self)
callbacks.registerContextMenuFactory(self)
def build_welcome_panel(self):
'''
Construct the welcome panel here.
'''
panel = JPanel(GridBagLayout())
constraints = GridBagConstraints()
constraints.insets = Insets(10, 10, 10, 10)
message = ('<html><body>'
'<h1>Welcome to Nammu</h1>'
'<h2>An editor for the ORACC project<h2>'
'<p>'
'<a href=\'oracc\'>Click here</a> for help with ORACC.'
'</p>'
'<p>Learn more about Nammu <a href=\'nammu\'>here</a>.</p>'
'</body></html>')
# Configure a JEditorPane to display HTML for our welcome message
msg_pane = JEditorPane()
msg_pane.setEditable(False)
kit = HTMLEditorKit()
msg_pane.setEditorKit(kit)
scrollPane = JScrollPane(msg_pane)
# This handles the stylesheet applied to the welcome message
styleSheet = kit.getStyleSheet()
styleSheet.addRule('body {color:black; font-size: 16 pt; }')
styleSheet.addRule('h1 {text-align:center; }')
styleSheet.addRule('h2 {text-align:center; }')
# Set the JEditorPane background to match the rest of the window
msg_pane.border = BorderFactory.createEmptyBorder(4, 4, 4, 4)
msg_pane.background = Color(238, 238, 238)
# Add the message and the css and to the JEditorPane
doc = kit.createDefaultDocument()
msg_pane.setDocument(doc)
msg_pane.setText(message)
# Set up a hyperlink listener
listener = addEventListener(msg_pane, HyperlinkListener,
'hyperlinkUpdate', self.handleEvent)
# Configure the placement of the JEditorPane
constraints.gridx = 1
constraints.gridy = 1
constraints.fill = GridBagConstraints.BOTH
constraints.anchor = GridBagConstraints.CENTER
panel.add(msg_pane, constraints)
# Build and place the checkbox
self.checkbox = JCheckBox('Don\'t show this message again.',
selected=False)
constraints.gridx = 1
constraints.gridy = 2
panel.add(self.checkbox, constraints)
# Build and place the close button
close_button = JButton('Close', actionPerformed=self.close_action)
constraints.gridx = 2
constraints.gridy = 2
panel.add(close_button, constraints)
return panel
def __init__(self, callbacks, parent):
# Initialze self stuff
self._callbacks = callbacks
self.config = {}
self.ext_stats = {}
self.url_reqs = []
self.parse_files = False
self.tab = JPanel(GridBagLayout())
self.view_port_text = JTextArea("===SpyDir===")
self.delim = JTextField(30)
self.ext_white_list = JTextField(30)
# I'm not sure if these fields are necessary still
# why not just use Burp func to handle this?
# leaving them in case I need it for the HTTP handler later
# self.cookies = JTextField(30)
# self.headers = JTextField(30)
self.url = JTextField(30)
self.parent_window = parent
self.plugins = {}
self.loaded_p_list = set()
self.loaded_plugins = False
self.config['Plugin Folder'] = None
self.double_click = False
self.source_input = ""
self.print_stats = True
self.curr_conf = JLabel()
self.window = JFrame("Select plugins",
preferredSize=(200, 250),
windowClosing=self.p_close)
self.window.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE)
self.window.setVisible(False)
self.path_vars = JTextField(30)
# Initialize local stuff
tab_constraints = GridBagConstraints()
status_field = JScrollPane(self.view_port_text)
# Configure view port
self.view_port_text.setEditable(False)
labels = self.build_ui()
# Add things to rows
tab_constraints.anchor = GridBagConstraints.FIRST_LINE_END
tab_constraints.gridx = 1
tab_constraints.gridy = 0
tab_constraints.fill = GridBagConstraints.HORIZONTAL
self.tab.add(JButton(
"Resize screen", actionPerformed=self.resize),
tab_constraints)
tab_constraints.gridx = 0
tab_constraints.gridy = 1
tab_constraints.anchor = GridBagConstraints.FIRST_LINE_START
self.tab.add(labels, tab_constraints)
tab_constraints.gridx = 1
tab_constraints.gridy = 1
tab_constraints.fill = GridBagConstraints.BOTH
tab_constraints.weightx = 1.0
tab_constraints.weighty = 1.0
tab_constraints.anchor = GridBagConstraints.FIRST_LINE_END
self.tab.add(status_field, tab_constraints)
try:
self._callbacks.customizeUiComponent(self.tab)
except Exception:
pass
def __init__(self):
''' Resources Panel '''
# psimures= JPanel(GridBagLayout())
# psimures.setSize(Dimension(500,300))
self.setLayout(GridBagLayout())
# super(self,GridBagLayout())
self.setSize(Dimension(500,300))
''' fila 1 '''
label = JLabel('Resources panel')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridwidth = 4
c.gridx = 0
c.gridy = 0
self.add(label, c)
''' fila 2 '''
self.dModelFile = []
self.cbMoFile = JComboBox(self.dModelFile)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.75
c.gridwidth = 3
c.gridx = 0
c.gridy = 1
self.add(self.cbMoFile, c)
bloadmodel= JButton('Load Model',actionPerformed=self.onOpenFile)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.25
# c.gridwidth = 1
c.gridx = 3
c.gridy = 1
self.add(bloadmodel, c)
''' fila 3 '''
self.dLibFile = []
self.cbMoLib = JComboBox(self.dLibFile)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.75
c.gridwidth = 3
c.gridx = 0
c.gridy = 2
self.add(self.cbMoLib, c)
bloadlib= JButton('Load Library',actionPerformed=self.onOpenFile)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.25
# c.gridwidth = 1
c.gridx = 3
c.gridy = 2
self.add(bloadlib, c)
''' fila 4 '''
self.dModel = []
self.cbModel = JComboBox(self.dModel)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.75
c.gridwidth = 3
c.gridx = 0
c.gridy = 3
self.add(self.cbModel, c)
bselectmodel= JButton('Select Model',actionPerformed=self.onOpenModel)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.25
# c.gridwidth = 1
c.gridx = 3
c.gridy = 3
self.add(bselectmodel, c)
''' fila 5 '''
self.dOutPath = []
self.cbOutDir = JComboBox(self.dOutPath)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.75
c.gridwidth = 3
c.gridx = 0
c.gridy = 4
self.add(self.cbOutDir, c)
bloadoutpath= JButton('Output Path',actionPerformed=self.onOpenFolder)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.25
# c.gridwidth = 1
c.gridx = 3
c.gridy = 4
self.add(bloadoutpath, c)
''' fila 6 '''
bsaveSource= JButton('Save Resources',actionPerformed=self.saveResources)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridwidth = 2
c.gridx = 0
c.gridy = 5
self.add(bsaveSource, c)
bloadSource= JButton('Load Resources',actionPerformed=self.loadResources)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridwidth = 2
c.gridx = 2
c.gridy = 5
self.add(bloadSource, c)
def tag_3_1(self, c):
# 输入框-标题
lblParams = JLabel(u'请填写域名:')
self.setFontBold(lblParams)
lblParams.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 0
c.insets = Insets(5, 5, 5, 5)
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.FIRST_LINE_END
self.white_list_domain_settings.add(lblParams, c)
# 输入框
self.white_list_text_field = JTextField()
c.fill = GridBagConstraints.BOTH
c.gridx = 1
c.gridy = 0
self.white_list_domain_settings.add(self.white_list_text_field, c)
lblParamsNote = JLabel(u"白名单域名列表")
self.setFontItalic(lblParamsNote)
c.fill = GridBagConstraints.NONE
c.gridx = 0
c.gridy = 1
self.white_list_domain_settings.add(lblParamsNote, c)
# 添加 文本框
self.white_list_text_area = JTextArea()
self.white_list_text_area.setColumns(20)
self.white_list_text_area.setRows(10)
self.white_list_text_area.setEditable(False)
c.fill = GridBagConstraints.BOTH
self.white_list_mouse_listener = TextAreaMouseListener(
self.white_list_text_area)
self.white_list_text_area.addMouseListener(
self.white_list_mouse_listener)
# 向文本框添加数据
for name in white_list_names:
self.white_list_text_area.append(name + linesep())
c.gridx = 1
c.gridy = 1
sp = JScrollPane(self.white_list_text_area)
self.white_list_domain_settings.add(sp, c)
# 添加 删除 重置
buttonsPanel = JPanel(GridBagLayout())
_c = GridBagConstraints()
_c.insets = Insets(3, 3, 3, 3)
_c.gridx = 0
_c.fill = GridBagConstraints.BOTH
_c.weightx = 1
_c.gridwidth = 1
handlers = ButtonHandlers(self.white_list_text_field,
self.white_list_text_area,
self.white_list_mouse_listener,
white_list_names)
# 添加按钮
self.white_list_add_button = JButton(
u'添加', actionPerformed=handlers.handler_add)
_c.gridy = 1
buttonsPanel.add(self.white_list_add_button, _c)
# 删除按钮
self.white_list_rm_button = JButton(
u'删除', actionPerformed=handlers.handler_rm)
_c.gridy = 2
buttonsPanel.add(self.white_list_rm_button, _c)
# 重置按钮
self.white_list_restore_button = JButton(
u'重置', actionPerformed=handlers.handler_restore)
_c.gridy = 3
buttonsPanel.add(self.white_list_restore_button, _c)
c.gridx = 2
c.gridy = 1
c.fill = GridBagConstraints.NONE
self.white_list_domain_settings.add(buttonsPanel, c)
def __init__(self, extender=None, *rows):
self.extender = extender
self.table = table = JTable(ParameterProcessingRulesTableModel(*rows))
table.setPreferredScrollableViewportSize(Dimension(500, 70))
table.setRowSorter(TableRowSorter(table.getModel()))
table.setFillsViewportHeight(True)
gridBagLayout = GridBagLayout()
gridBagLayout.columnWidths = [0, 0, 25, 0 ]
gridBagLayout.rowHeights = [0, 0, 0, 0]
gridBagLayout.columnWeights = [0.0, 1.0, 1.0, Double.MIN_VALUE]
gridBagLayout.rowWeights = [0.0, 0.0, 0.0, Double.MIN_VALUE]
self.setLayout(gridBagLayout)
addButton = JButton("Add")
addButton.addActionListener(AddRemoveParameterListener(table))
addButtonConstraints = GridBagConstraints()
addButtonConstraints.fill = GridBagConstraints.HORIZONTAL
addButtonConstraints.insets = Insets(0, 0, 5, 5)
addButtonConstraints.gridx = 0
addButtonConstraints.gridy = 0
self.add(addButton, addButtonConstraints)
removeButton = JButton("Remove")
removeButton.addActionListener(AddRemoveParameterListener(table))
removeButtonConstraints = GridBagConstraints()
removeButtonConstraints.fill = GridBagConstraints.HORIZONTAL
removeButtonConstraints.insets = Insets(0, 0, 5, 5)
removeButtonConstraints.gridx = 0
removeButtonConstraints.gridy = 1
self.add(removeButton, removeButtonConstraints)
upButton = JButton("Up")
upButton.addActionListener(AddRemoveParameterListener(table))
upButtonConstraints = GridBagConstraints()
upButtonConstraints.fill = GridBagConstraints.HORIZONTAL
upButtonConstraints.insets = Insets(0, 0, 5, 5)
upButtonConstraints.gridx = 0
upButtonConstraints.gridy = 2
self.add(upButton, upButtonConstraints)
downButton = JButton("Down")
downButton.addActionListener(AddRemoveParameterListener(table))
downButtonConstraints = GridBagConstraints()
downButtonConstraints.fill = GridBagConstraints.HORIZONTAL
downButtonConstraints.anchor = GridBagConstraints.NORTH
downButtonConstraints.insets = Insets(0, 0, 5, 5)
downButtonConstraints.gridx = 0
downButtonConstraints.gridy = 3
self.add(downButton, downButtonConstraints)
scrollPane = JScrollPane(table)
scrollPaneConstraints = GridBagConstraints()
scrollPaneConstraints.gridwidth = 2
scrollPaneConstraints.gridheight = 5
scrollPaneConstraints.insets = Insets(0, 0, 5, 5)
scrollPaneConstraints.anchor = GridBagConstraints.NORTHWEST
scrollPaneConstraints.gridx = 1
scrollPaneConstraints.gridy = 0
self.add(scrollPane, scrollPaneConstraints)
self.initParameterColumn(table)
self.initColumnSizes(table)
def __init__(self, callbacks, parent):
# Initialze self stuff
self._callbacks = callbacks
self.config = {}
self.ext_stats = {}
self.url_reqs = []
self.parse_files = False
self.tab = JPanel(GridBagLayout())
self.view_port_text = JTextArea("===SpyDir===")
self.delim = JTextField(30)
self.ext_white_list = JTextField(30)
# I'm not sure if these fields are necessary still
# why not just use Burp func to handle this?
# leaving them in case I need it for the HTTP handler later
# self.cookies = JTextField(30)
# self.headers = JTextField(30)
self.url = JTextField(30)
self.parent_window = parent
self.plugins = {}
self.loaded_p_list = set()
self.loaded_plugins = False
self.config['Plugin Folder'] = None
self.double_click = False
self.source_input = ""
self.print_stats = True
self.curr_conf = JLabel()
self.window = JFrame("Select plugins",
preferredSize=(200, 250),
windowClosing=self.p_close)
self.window.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE)
self.window.setVisible(False)
# Initialize local stuff
tab_constraints = GridBagConstraints()
status_field = JScrollPane(self.view_port_text)
# Configure view port
self.view_port_text.setEditable(False)
labels = self.build_ui()
# Add things to rows
tab_constraints.anchor = GridBagConstraints.FIRST_LINE_END
tab_constraints.gridx = 1
tab_constraints.gridy = 0
tab_constraints.fill = GridBagConstraints.HORIZONTAL
self.tab.add(JButton(
"Resize screen", actionPerformed=self.resize),
tab_constraints)
tab_constraints.gridx = 0
tab_constraints.gridy = 1
tab_constraints.anchor = GridBagConstraints.FIRST_LINE_START
self.tab.add(labels, tab_constraints)
tab_constraints.gridx = 1
tab_constraints.gridy = 1
tab_constraints.fill = GridBagConstraints.BOTH
tab_constraints.weightx = 1.0
tab_constraints.weighty = 1.0
tab_constraints.anchor = GridBagConstraints.FIRST_LINE_END
self.tab.add(status_field, tab_constraints)
try:
self._callbacks.customizeUiComponent(self.tab)
except Exception:
pass
def registerExtenderCallbacks(self, callbacks):
# Initialize the global stdout stream
global stdout
# Keep a reference to our callbacks object
self._callbacks = callbacks
# Obtain an extension helpers object
self._helpers = callbacks.getHelpers()
# set our extension name
callbacks.setExtensionName("Burpsuite Yara Scanner")
# Create the log and a lock on which to synchronize when adding log entries
self._log = ArrayList()
self._lock = Lock()
# main split pane
splitpane = JSplitPane(JSplitPane.VERTICAL_SPLIT)
# table of log entries
logTable = Table(self)
scrollPane = JScrollPane(logTable)
splitpane.setLeftComponent(scrollPane)
# Options panel
optionsPanel = JPanel()
optionsPanel.setLayout(GridBagLayout())
constraints = GridBagConstraints()
yara_exe_label = JLabel("Yara Executable Location:")
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.gridx = 0
constraints.gridy = 0
optionsPanel.add(yara_exe_label, constraints)
self._yara_exe_txtField = JTextField(25)
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.gridx = 1
constraints.gridy = 0
optionsPanel.add(self._yara_exe_txtField, constraints)
yara_rules_label = JLabel("Yara Rules File:")
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.gridx = 0
constraints.gridy = 1
optionsPanel.add(yara_rules_label, constraints)
self._yara_rules_files = Vector()
self._yara_rules_files.add("< None >")
self._yara_rules_fileList = JList(self._yara_rules_files)
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.gridx = 1
constraints.gridy = 1
optionsPanel.add(self._yara_rules_fileList, constraints)
self._yara_rules_select_files_button = JButton("Select Files")
self._yara_rules_select_files_button.addActionListener(self)
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.gridx = 1
constraints.gridy = 2
optionsPanel.add(self._yara_rules_select_files_button, constraints)
self._yara_clear_button = JButton("Clear Yara Results Table")
self._yara_clear_button.addActionListener(self)
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.gridx = 1
constraints.gridy = 3
optionsPanel.add(self._yara_clear_button, constraints)
# Tabs with request/response viewers
viewerTabs = JTabbedPane()
self._requestViewer = callbacks.createMessageEditor(self, False)
self._responseViewer = callbacks.createMessageEditor(self, False)
viewerTabs.addTab("Request", self._requestViewer.getComponent())
viewerTabs.addTab("Response", self._responseViewer.getComponent())
splitpane.setRightComponent(viewerTabs)
# Tabs for the Yara output and the Options
self._mainTabs = JTabbedPane()
self._mainTabs.addTab("Yara Output", splitpane)
self._mainTabs.addTab("Options", optionsPanel)
# customize our UI components
callbacks.customizeUiComponent(splitpane)
callbacks.customizeUiComponent(logTable)
callbacks.customizeUiComponent(scrollPane)
callbacks.customizeUiComponent(viewerTabs)
callbacks.customizeUiComponent(self._mainTabs)
# add the custom tab to Burp's UI
callbacks.addSuiteTab(self)
# add ourselves as a context menu factory
callbacks.registerContextMenuFactory(self)
# Custom Menu Item
self.menuItem = JMenuItem("Scan with Yara")
self.menuItem.addActionListener(self)
# obtain our output stream
stdout = PrintWriter(callbacks.getStdout(), True)
# Print a startup notification
stdout.println("Burpsuite Yara scanner initialized.")
def registerExtenderCallbacks(self, callbacks):
self.out = callbacks.getStdout()
self.callbacks = callbacks
self.helpers = callbacks.getHelpers()
callbacks.setExtensionName("WhatsApp Decoder")
self.banner = JLabel("WHATSAPP DECRYPTION AND ENCRYPTION EXTENSION BY DIKLA BARDA, ROMAN ZAIKIN", SwingConstants.CENTER)
self.banner.setFont(Font("Serif", Font.PLAIN, 17))
self.banner.setBorder(BorderFactory.createLineBorder(Color.BLACK))
self.statusConn = JLabel("CONNECTION STATUS: ")
self.statusConnField = JLabel("NOT CONNECTED")
self.statusAct = JLabel("ACTION STATUS: ")
self.statusActField = JLabel("OK")
self.ref = JLabel("Ref object: ")
self.refField = JTextField("", 80)
self.refField.setToolTipText("Copy the Ref from burpsuit WebSocket, make sure that the parameter 'secret' is there and you copy only the 'ref' without the connection and other data, if not logout from your whatsapp web and login again.")
self.privateKey = JLabel("Private Key:")
self.privateKeyField = JTextField("", 80)
self.privateKeyField.setToolTipText("Copy the private key list from your whatsapp web according to our blog post.")
self.publicKey = JLabel("Public Key: ")
self.publicKeyField = JTextField("", 80)
self.publicKeyField.setToolTipText("Copy the public key list from your whatsapp web according to our blog post.")
self.statusPanel1 = JPanel()
self.statusPanel1.add(self.statusConn)
self.statusPanel1.add(self.statusConnField)
self.statusPanel2 = JPanel()
self.statusPanel2.add(self.statusAct)
self.statusPanel2.add(self.statusActField)
self.privateKeyPanel = JPanel()
self.privateKeyPanel.add(self.privateKey)
self.privateKeyPanel.add(self.privateKeyField)
self.publicKeyPanel = JPanel()
self.publicKeyPanel.add(self.publicKey)
self.publicKeyPanel.add(self.publicKeyField)
self.refPanel = JPanel()
self.refPanel.add(self.ref)
self.refPanel.add(self.refField)
self.messageField = JTextArea('["action", {"add": "relay"}, [{"message": {"conversation": "WhatsApp Protocol Decryption!"}, "participant": "*****@*****.**", "messageTimestamp": "1565193325", "key": {"fromMe": false, "remoteJid": "*****@*****.**", "id": "78CECC5019E81B84B64ED2F6A57217AK"}, "status": "ERROR"}]]', 5, 90)
self.messageField.setLineWrap(True)
self.messageField.setToolTipText("Incoming traffic is from burp suite websocket, The outgoing traffic is the list from aesCbcEncrypt")
self.messageTag = JLabel("Message Tag:")
self.messageTagField = JTextField("", 80)
self.messageTagField.setToolTipText("Copy the message tag from WebSocket it's the text until first ',' ")
self.messageTagFieldButton = JButton("Update Tag", actionPerformed=self.performUpdateTag)
self.whatsAppMessagesPanel = JPanel()
self.whatsAppMessagesPanel.add(self.messageField)
self.messageTagPanel = JPanel()
self.messageTagPanel.add(self.messageTag)
self.messageTagPanel.add(self.messageTagField)
self.messageTagPanel.add(self.messageTagFieldButton)
self.btnSave = JButton("Connect", actionPerformed=self.saveConfig)
self.btnRestore = JButton("Clear", actionPerformed=self.clearConfig)
self.grpConfig = JPanel()
self.grpConfig.add(self.btnSave)
self.grpConfig.add(self.btnRestore)
self.btnIncoming = JButton("Incoming", actionPerformed=self.performAction)
self.btnOutgoing = JButton("Outgoing", actionPerformed=self.performAction)
self.btnEncrypt = JButton("Encrypt", actionPerformed=self.performAction)
self.btnEncrypt.setEnabled(False) # Can't send data without a direction
self.btnDecrypt = JButton("Decrypt", actionPerformed=self.performAction)
self.btnDecrypt.setEnabled(False) # Can't send data without a direction
self.btnCrypt = JPanel()
self.btnCrypt.add(self.btnIncoming)
self.btnCrypt.add(self.btnEncrypt)
self.btnCrypt.add(self.btnDecrypt)
self.btnCrypt.add(self.btnOutgoing)
self.tab = JPanel()
layout = GridBagLayout()
self.tab.setLayout(layout)
c = GridBagConstraints()
c.ipadx = 0
c.ipady = 0
c.fill = GridBagConstraints.BOTH
#c.weightx = 0 # gap between the x items
#c.weighty = 0 # gap between the y items
c.anchor = GridBagConstraints.NORTHWEST
c.gridx = 0
c.gridy = 0
self.tab.add(self.banner, c)
c.gridx = 0
c.gridy = 1
self.tab.add(self.refPanel, c)
c.gridx = 0
c.gridy = 2
self.tab.add(self.privateKeyPanel, c)
c.gridx = 0
c.gridy = 3
self.tab.add(self.publicKeyPanel, c)
c.gridx = 0
c.gridy = 4
c.anchor = GridBagConstraints.CENTER
self.tab.add(self.grpConfig, c)
c.gridx = 0
c.gridy = 5
self.tab.add(self.whatsAppMessagesPanel, c)
c.gridx = 0
c.gridy = 6
self.tab.add(self.messageTagPanel, c)
c.gridx = 0
c.gridy = 7
self.tab.add(self.btnCrypt, c)
c.gridx = 0
c.gridy = 8
self.tab.add(self.statusPanel1, c)
c.gridx = 0
c.gridy = 9
self.tab.add(self.statusPanel2, c)
# restore config
self.restoreConfig()
callbacks.addSuiteTab(self)
