def __init__(self):
self.holdPanel = JPanel()
self.topPanel = JPanel()
self.bottomPanel = JPanel()
self.holdPanel.setBackground(Color.decode('#dddee6'))
self.topPanel.setBackground(Color.decode('#dddee6'))
self.bottomPanel.setBackground(Color.decode('#dddee6'))
self.topPanel.setPreferredSize(Dimension(300, 30))
self.regBar = JProgressBar()
self.gatePassBar = JProgressBar()
self.regLabel = JLabel('Register : ')
self.gatepassLabel = JLabel(' Gate Pass : '******'')
self.gatePercentlabel = JLabel('')
self.refreshButton = JButton('Refresh',
actionPerformed=self.updateProgress)
self.regBar.setMinimum(0)
self.regBar.setMaximum(100)
self.regBar.setStringPainted(True)
self.gatePassBar.setMinimum(0)
self.gatePassBar.setMaximum(100)
self.gatePassBar.setStringPainted(True)
self.setLayout(BorderLayout())
self.updateProgress(None)
def testJProgressBar(self):
percentCompleteDummy = DummyObject()
progressBar = JProgressBar(0, 10)
self.group.bind(progressBar, 'value', self.dummy, 'value')
self.group.bind(progressBar, 'percentComplete',
percentCompleteDummy, 'value')
assert self.dummy.value == 0
assert percentCompleteDummy.value == 0
progressBar.setValue(2)
assert self.dummy.value == 2
assert percentCompleteDummy.value == 0.2
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 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 __init__(self, parent, title, modal, app):
JDialog.__init__(self, parent, title, modal)
#Download and Read Dialog
border = BorderFactory.createEmptyBorder(5, 7, 5, 7)
self.getContentPane().setBorder(border)
self.setLayout(BoxLayout(self.getContentPane(), BoxLayout.Y_AXIS))
panel = JPanel()
panel.setAlignmentX(0.5)
panel.setLayout(BoxLayout(panel, BoxLayout.Y_AXIS))
panel.add(Box.createRigidArea(Dimension(0, 10)))
self.progressLbl = JLabel(
app.strings.getString("downloading_and_reading_errors"))
panel.add(self.progressLbl)
panel.add(Box.createRigidArea(Dimension(0, 10)))
self.progressBar = JProgressBar(0, 100, value=0)
panel.add(self.progressBar)
self.add(panel)
self.add(Box.createRigidArea(Dimension(0, 20)))
cancelBtn = JButton(app.strings.getString("cancel"),
ImageProvider.get("cancel"),
actionPerformed=app.on_cancelBtn_clicked)
cancelBtn.setAlignmentX(0.5)
self.add(cancelBtn)
self.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE)
self.pack()
def __init__(self, extender):
# Initialize self
super(FooterPanel, self).__init__()
self.extender = extender
self.setLayout(GridLayout(2, 1))
# Create children
self.progressInput = JProgressBar(0, 10000)
self.progressOutput = JProgressBar(0, 10000)
self.credit = JPanel()
# Configure children
self.progressInput.string = 'Ready'
self.progressOutput.string = 'Ready'
self.progressInput.stringPainted = True
self.progressOutput.stringPainted = True
# Add children
self.add(self.progressInput)
self.add(self.progressOutput)
def loadPanel(self):
panel = JPanel()
panel.setLayout(BoxLayout(panel, BoxLayout.Y_AXIS))
bottomButtonBarPanel = JPanel()
bottomButtonBarPanel.setLayout(BoxLayout(bottomButtonBarPanel, BoxLayout.X_AXIS))
bottomButtonBarPanel.setAlignmentX(1.0)
self.runButton = JButton("Run", actionPerformed=self.start)
self.cancelButton = JButton("Close", actionPerformed=self.cancel)
bottomButtonBarPanel.add(Box.createHorizontalGlue());
bottomButtonBarPanel.add(self.runButton)
bottomButtonBarPanel.add(self.cancelButton)
# Dimension(width,height)
bottom = JPanel()
bottom.setLayout(BoxLayout(bottom, BoxLayout.X_AXIS))
bottom.setAlignmentX(1.0)
self.progressBar = JProgressBar()
self.progressBar.setIndeterminate(False)
self.progressBar.setMaximum(100)
self.progressBar.setValue(0)
bottom.add(self.progressBar)
self.statusTextArea = JTextArea()
self.statusTextArea.setEditable(False)
scrollPane = JScrollPane(self.statusTextArea)
scrollPanel = JPanel()
scrollPanel.setLayout(BoxLayout(scrollPanel, BoxLayout.X_AXIS))
scrollPanel.setAlignmentX(1.0)
scrollPanel.add(scrollPane)
panel.add(scrollPanel)
panel.add(bottomButtonBarPanel)
panel.add(bottom)
self.add(panel)
self.setTitle("Determine Session Cookie(s)")
self.setSize(450, 300)
self.setLocationRelativeTo(None)
self.setVisible(True)
original_request_bytes = self.selected_message.getRequest()
http_service = self.selected_message.getHttpService()
helpers = self.callbacks.getHelpers()
request_info = helpers.analyzeRequest(http_service, original_request_bytes)
parameters = request_info.getParameters();
cookie_parameters = [parameter for parameter in parameters if parameter.getType() == IParameter.PARAM_COOKIE]
num_requests_needed = len(cookie_parameters) + 2
self.statusTextArea.append("This may require up to " + str(num_requests_needed) + " requests to be made. Hit 'Run' to begin.\n")
def _constructResultsPanel(self, insets):
resultsPanel = JPanel(GridBagLayout())
self._progressBar = JProgressBar()
self._progressBar.setStringPainted(True)
self._progressBar.setMinimum(0)
progressBarContraints = GridBagConstraints()
progressBarContraints.gridx = 0
progressBarContraints.gridy = 0
progressBarContraints.fill = GridBagConstraints.HORIZONTAL
resultsPanel.add(self._progressBar, progressBarContraints)
self._resultsTableModel = ResultsTableModel(COLUMNS, 0)
resultsTable = JTable(self._resultsTableModel)
resultsTable.setAutoCreateRowSorter(True)
cellRenderer = ColoredTableCellRenderer()
for index in [5, 6, 7, 8, 9]:
column = resultsTable.columnModel.getColumn(index)
column.cellRenderer = cellRenderer
resultsTable.getColumnModel().getColumn(0).setPreferredWidth(99999999)
resultsTable.getColumnModel().getColumn(1).setMinWidth(160)
resultsTable.getColumnModel().getColumn(2).setMinWidth(100)
resultsTable.getColumnModel().getColumn(3).setMinWidth(80)
resultsTable.getColumnModel().getColumn(4).setMinWidth(80)
resultsTable.getColumnModel().getColumn(5).setMinWidth(110)
resultsTable.getColumnModel().getColumn(6).setMinWidth(110)
resultsTable.getColumnModel().getColumn(7).setMinWidth(90)
resultsTable.getColumnModel().getColumn(8).setMinWidth(110)
resultsTable.getColumnModel().getColumn(9).setMinWidth(110)
resultsTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS)
resultsScrollPane = JScrollPane(resultsTable)
resultsScrollPaneConstraints = GridBagConstraints()
resultsScrollPaneConstraints.gridx = 0
resultsScrollPaneConstraints.gridy = 1
resultsScrollPaneConstraints.weightx = 1
resultsScrollPaneConstraints.weighty = 1
resultsScrollPaneConstraints.fill = GridBagConstraints.BOTH
resultsPanel.add(resultsScrollPane, resultsScrollPaneConstraints)
return resultsPanel
def run(self):
frame = JFrame('ProgressBar1',
size=(280, 125),
locationRelativeTo=None,
defaultCloseOperation=JFrame.EXIT_ON_CLOSE)
frame.getContentPane().setBorder(
BorderFactory.createEmptyBorder(20, 20, 20, 20))
panel = JPanel()
self.button = panel.add(JButton('Start', actionPerformed=self.start))
self.progressBar = panel.add(JProgressBar())
frame.add(panel, BorderLayout.NORTH)
frame.setVisible(1)
def __init__(self, parent, title, modal, app):
"""Restore the tools data by:
- downloading the tools list
- downloading the tools jar files
- extracting the tools data from jar files
"""
self.app = app
border = BorderFactory.createEmptyBorder(5, 7, 5, 7)
mainPane = self.getContentPane()
mainPane.setLayout(BorderLayout(5, 5))
mainPane.setBorder(border)
self.setPreferredSize(Dimension(400, 200))
self.taskOutput = JMultilineLabel(
self.app.strings.getString("checking_for_updates"))
self.taskOutput.setMaxWidth(350)
self.progressBar = JProgressBar(0, 100, value=0, stringPainted=True)
self.progressBar.setIndeterminate(True)
self.cancelBtn = JButton("Cancel",
actionPerformed=self.on_cancelBtn_clicked,
enabled=True)
self.okBtn = JButton("Ok",
actionPerformed=self.on_okBtn_clicked,
enabled=False)
mainPane.add(self.taskOutput, BorderLayout.CENTER)
bottomPanel = JPanel(BorderLayout(5, 5))
bottomPanel.add(self.progressBar, BorderLayout.PAGE_START)
buttonsPanel = JPanel()
buttonsPanel.add(self.okBtn)
buttonsPanel.add(self.cancelBtn)
bottomPanel.add(buttonsPanel, BorderLayout.PAGE_END)
mainPane.add(bottomPanel, BorderLayout.PAGE_END)
self.pack()
self.task = DownloaderTask(self)
self.task.addPropertyChangeListener(self)
self.task.execute()
def __init__(self):
self.mainDir = ""
self.frame = JFrame("Dots Quality Check", size=(250,300))
self.frame.setLocation(20,120)
self.Panel = JPanel(GridLayout(0,1))
self.frame.add(self.Panel)
self.openNextButton = JButton('Open Next Random',actionPerformed=openRandom)
self.Panel.add(self.openNextButton)
self.saveButton = JButton('Save',actionPerformed=save)
self.saveButton.setEnabled(False)
self.Panel.add(self.saveButton)
self.cropButton = JButton('Crop values from here', actionPerformed=cropVals)
self.Panel.add(self.cropButton)
self.DiscardButton = JButton('Discard cell', actionPerformed=discardCell)
self.DiscardButton.setEnabled(True)
self.Panel.add(self.DiscardButton)
self.quitButton = JButton('Quit script',actionPerformed=quit)
self.Panel.add(self.quitButton)
annoPanel = JPanel()
#add gridlayout
wtRButton = JRadioButton("wt", actionCommand="wt")
defectRButton = JRadioButton("Defect", actionCommand="defect")
annoPanel.add(wtRButton)
annoPanel.add(defectRButton)
self.aButtonGroup = ButtonGroup()
self.aButtonGroup.add(wtRButton)
self.aButtonGroup.add(defectRButton)
self.Panel.add(annoPanel)
self.ProgBar = JProgressBar()
self.ProgBar.setStringPainted(True)
self.ProgBar.setValue(0)
self.Panel.add(self.ProgBar)
self.pathLabel = JLabel("-- No main directory chosen --")
self.pathLabel.setHorizontalAlignment( SwingConstants.CENTER )
self.Panel.add(self.pathLabel)
WindowManager.addWindow(self.frame)
self.show()
def __init__(self):
self.mainDir = ""
self.setTitle("Dots Quality Check")
self.setSize(250, 300)
self.setLocation(20,120)
self.addWindowFocusListener(self)
self.Panel = JPanel(GridLayout(0,1))
self.add(self.Panel)
self.openNextButton = JButton("Open Next Random", actionPerformed=self.openRandom)
self.Panel.add(self.openNextButton)
self.saveButton = JButton("Save", actionPerformed=self.save, enabled=False)
self.Panel.add(self.saveButton)
self.cropButton = JButton("Crop values from here", actionPerformed=self.cropVals)
self.Panel.add(self.cropButton)
self.DiscardButton = JButton("Discard cell", actionPerformed=self.discardCell)
self.Panel.add(self.DiscardButton)
self.quitButton = JButton("Quit script",actionPerformed=self.quit)
self.Panel.add(self.quitButton)
annoPanel = JPanel()
#add gridlayout
self.wtRButton = JRadioButton("wt", actionCommand="wt")
self.wtRButton.addActionListener(self)
self.defectRButton = JRadioButton("Defect", actionCommand="defect")
self.defectRButton.addActionListener(self)
annoPanel.add(self.wtRButton)
annoPanel.add(self.defectRButton)
self.aButtonGroup = ButtonGroup()
self.aButtonGroup.add(self.wtRButton)
self.aButtonGroup.add(self.defectRButton)
self.Panel.add(annoPanel)
self.ProgBar = JProgressBar()
self.ProgBar.setStringPainted(True)
self.ProgBar.setValue(0)
self.Panel.add(self.ProgBar)
self.pathLabel = JLabel("-- No main directory chosen --")
self.pathLabel.setHorizontalAlignment( SwingConstants.CENTER )
self.Panel.add(self.pathLabel)
WindowManager.addWindow(self)
self.show()
def __init__(self, parent, title, modal, app):
"""Restore the tools data by:
- downloading the tools list
- downloading the tools jar files
- extracting the tools data from jar files
"""
self.app = app
border = BorderFactory.createEmptyBorder(5, 7, 5, 7)
mainPane = self.getContentPane()
mainPane.setLayout(BorderLayout(5, 5))
mainPane.setBorder(border)
self.setPreferredSize(Dimension(400, 200))
self.taskOutput = JMultilineLabel(self.app.strings.getString("checking_for_updates"))
self.taskOutput.setMaxWidth(350)
self.progressBar = JProgressBar(0, 100, value=0, stringPainted=True)
self.progressBar.setIndeterminate(True)
self.cancelBtn = JButton("Cancel",
actionPerformed=self.on_cancelBtn_clicked,
enabled=True)
self.okBtn = JButton("Ok",
actionPerformed=self.on_okBtn_clicked,
enabled=False)
mainPane.add(self.taskOutput, BorderLayout.CENTER)
bottomPanel = JPanel(BorderLayout(5, 5))
bottomPanel.add(self.progressBar, BorderLayout.PAGE_START)
buttonsPanel = JPanel()
buttonsPanel.add(self.okBtn)
buttonsPanel.add(self.cancelBtn)
bottomPanel.add(buttonsPanel, BorderLayout.PAGE_END)
mainPane.add(bottomPanel, BorderLayout.PAGE_END)
self.pack()
self.task = DownloaderTask(self)
self.task.addPropertyChangeListener(self)
self.task.execute()
class MenueFrame(object):
def __init__(self):
self.mainDir = ""
self.frame = JFrame("Dots Quality Check", size=(250,300))
self.frame.setLocation(20,120)
self.Panel = JPanel(GridLayout(0,1))
self.frame.add(self.Panel)
self.openNextButton = JButton('Open Next Random',actionPerformed=openRandom)
self.Panel.add(self.openNextButton)
self.saveButton = JButton('Save',actionPerformed=save)
self.saveButton.setEnabled(False)
self.Panel.add(self.saveButton)
self.cropButton = JButton('Crop values from here', actionPerformed=cropVals)
self.Panel.add(self.cropButton)
self.DiscardButton = JButton('Discard cell', actionPerformed=discardCell)
self.DiscardButton.setEnabled(True)
self.Panel.add(self.DiscardButton)
self.quitButton = JButton('Quit script',actionPerformed=quit)
self.Panel.add(self.quitButton)
annoPanel = JPanel()
#add gridlayout
wtRButton = JRadioButton("wt", actionCommand="wt")
defectRButton = JRadioButton("Defect", actionCommand="defect")
annoPanel.add(wtRButton)
annoPanel.add(defectRButton)
self.aButtonGroup = ButtonGroup()
self.aButtonGroup.add(wtRButton)
self.aButtonGroup.add(defectRButton)
self.Panel.add(annoPanel)
self.ProgBar = JProgressBar()
self.ProgBar.setStringPainted(True)
self.ProgBar.setValue(0)
self.Panel.add(self.ProgBar)
self.pathLabel = JLabel("-- No main directory chosen --")
self.pathLabel.setHorizontalAlignment( SwingConstants.CENTER )
self.Panel.add(self.pathLabel)
WindowManager.addWindow(self.frame)
self.show()
def show(self):
self.frame.visible = True
def getFrame(self):
return self.frame
def setSaveActive(self):
self.saveButton.setEnabled(True)
self.show()
def setSaveInactive(self):
self.saveButton.setEnabled(False)
self.show()
def setMainDir(self, path):
self.mainDir = path
self.pathLabel.setText("MainDir: " + os.path.basename(os.path.split(self.mainDir)[0]))
def getMainDir(self):
return self.mainDir
def setProgBarMax(self, maximum):
self.ProgBar.setMaximum(maximum)
def setProgBarVal(self, value):
self.ProgBar.setValue(value)
def close():
WindowManager.removeWindow(self.frame)
self.frame.dispose()
class BottomPanel(JPanel):
def __init__(self):
self.holdPanel = JPanel()
self.topPanel = JPanel()
self.bottomPanel = JPanel()
self.holdPanel.setBackground(Color.decode('#dddee6'))
self.topPanel.setBackground(Color.decode('#dddee6'))
self.bottomPanel.setBackground(Color.decode('#dddee6'))
self.topPanel.setPreferredSize(Dimension(300, 30))
self.regBar = JProgressBar()
self.gatePassBar = JProgressBar()
self.regLabel = JLabel('Register : ')
self.gatepassLabel = JLabel(' Gate Pass : '******'')
self.gatePercentlabel = JLabel('')
self.refreshButton = JButton('Refresh',
actionPerformed=self.updateProgress)
self.regBar.setMinimum(0)
self.regBar.setMaximum(100)
self.regBar.setStringPainted(True)
self.gatePassBar.setMinimum(0)
self.gatePassBar.setMaximum(100)
self.gatePassBar.setStringPainted(True)
self.setLayout(BorderLayout())
self.updateProgress(None)
def updateProgress(self, e):
progress = client.get_progress()
regTotal = progress[0]
regRecog = progress[1]
gateTotal = progress[2]
gateRecog = progress[3]
regPercent = int((regRecog * 100) / regTotal)
gatePercent = int((gateRecog * 100) / gateTotal)
self.regBar.setValue(regPercent)
self.gatePassBar.setValue(gatePercent)
self.regBar.setString(str(regPercent) + '%')
self.gatePassBar.setString(str(gatePercent) + '%')
self.regPercentlabel.setText(str(regRecog) + '/' + str(regTotal))
self.gatePercentlabel.setText(
str(gateRecog) + '/' + str(gateTotal) + ' ')
if regPercent <= 30:
regColor = Color.RED
elif regPercent > 30 and regPercent < 50:
regColor = Color.ORANGE
elif regPercent >= 50 and regPercent <= 100:
regColor = Color.GREEN
if gatePercent <= 30:
gateColor = Color.RED
elif gatePercent > 30 and gatePercent < 50:
gateColor = Color.ORANGE
elif gatePercent >= 50 and gatePercent <= 100:
gateColor = Color.GREEN
self.regBar.setForeground(regColor)
self.gatePassBar.setForeground(gateColor)
self.holdPanel.add(self.regLabel)
self.holdPanel.add(self.regBar)
self.holdPanel.add(self.regPercentlabel)
self.holdPanel.add(self.gatepassLabel)
self.holdPanel.add(self.gatePassBar)
self.holdPanel.add(self.gatePercentlabel)
self.holdPanel.add(self.refreshButton)
self.add(self.holdPanel, BorderLayout.CENTER)
self.add(self.topPanel, BorderLayout.PAGE_START)
self.add(self.bottomPanel, BorderLayout.PAGE_END)
self.validate()
class BurpExtender(IBurpExtender, ITab, IExtensionStateListener):
# Define the global variables for the burp plugin
EXTENSION_NAME = "UPnP BHunter"
ipv4_selected = True
services_dict = {}
ip_service_dict = {}
STOP_THREAD = False
#Some SSDP m-search parameters are based upon "UPnP Device Architecture v2.0"
SSDP_MULTICAST_IPv4 = ["239.255.255.250"]
SSDP_MULTICAST_IPv6 = ["FF02::C", "FF05::C"]
SSDP_MULTICAST_PORT = 1900
ST_ALL = "ssdp:all"
ST_ROOTDEV = "upnp:rootdevice"
PLACEHOLDER = "FUZZ_HERE"
SSDP_TIMEOUT = 2
def registerExtenderCallbacks(self, callbacks):
# Get a reference to callbacks object
self.callbacks = callbacks
# Get the useful extension helpers object
self.helpers = callbacks.getHelpers()
# Set the extension name
self.callbacks.setExtensionName(self.EXTENSION_NAME)
self.callbacks.registerExtensionStateListener(self)
# Draw plugin user interface
self.drawPluginUI()
self.callbacks.addSuiteTab(self)
# Plugin loading message
print("[+] Burp plugin UPnP BHunter loaded successfully")
return
def drawPluginUI(self):
# Create the plugin user interface
self.pluginTab = JPanel()
self.uiTitle = JLabel('UPnP BHunter Load, Aim and Fire Console')
self.uiTitle.setFont(Font('Tahoma', Font.BOLD, 14))
self.uiTitle.setForeground(Color(250, 100, 0))
self.uiPanelA = JSplitPane(JSplitPane.VERTICAL_SPLIT)
self.uiPanelA.setMaximumSize(Dimension(2500, 1000))
self.uiPanelA.setDividerSize(2)
self.uiPanelB = JSplitPane(JSplitPane.VERTICAL_SPLIT)
self.uiPanelB.setDividerSize(2)
self.uiPanelA.setBottomComponent(self.uiPanelB)
self.uiPanelA.setBorder(BorderFactory.createLineBorder(Color.gray))
# Create and configure labels and text fields
self.labeltitle_step1 = JLabel("[1st STEP] Discover UPnP Locations")
self.labeltitle_step1.setFont(Font('Tahoma', Font.BOLD, 14))
self.labeltitle_step2 = JLabel(
"[2nd STEP] Select a UPnP Service and Action")
self.labeltitle_step2.setFont(Font('Tahoma', Font.BOLD, 14))
self.labeltitle_step3 = JLabel("[3rd STEP] Time to Attack it")
self.labeltitle_step3.setFont(Font('Tahoma', Font.BOLD, 14))
self.labelsubtitle_step1 = JLabel(
"Specify the IP version address in scope and start UPnP discovery")
self.labelsubtitle_step2 = JLabel(
"Select which of the found UPnP services will be probed")
self.labelsubtitle_step3 = JLabel(
"Review and modify the request, then send it to one of the attack tools"
)
self.label_step1 = JLabel("Target IP")
self.label_step2 = JLabel("Found UPnp Services")
self.labelstatus = JLabel(" Status")
self.labelempty_step1 = JLabel(" ")
self.labelempty_step2 = JLabel(" ")
self.labelupnp = JLabel("UPnP list")
self.labelip = JLabel("IP list")
self.labelactions = JLabel("Actions")
self.labelNoneServiceFound = JLabel(" ")
self.labelNoneServiceFound.setFont(Font('Tahoma', Font.BOLD, 12))
self.labelNoneServiceFound.setForeground(Color.red)
# Create combobox for IP version selection
self.ip_versions = ["IPv4", "IPv6"]
self.combo_ipversion = JComboBox(self.ip_versions)
self.combo_ipversion.setSelectedIndex(0)
self.combo_ipversion.setEnabled(True)
# Create and configure progress bar
self.progressbar = JProgressBar(0, 100)
self.progressbar.setString("Ready")
self.progressbar.setStringPainted(True)
# Create and configure buttons
self.startbutton = JButton("Start Discovery",
actionPerformed=self.startHunting)
self.clearbutton = JButton("Clear All", actionPerformed=self.clearAll)
self.intruderbutton = JButton("Send to Intruder",
actionPerformed=self.sendToIntruder)
self.repeaterbutton = JButton("Send to Repeater",
actionPerformed=self.sendToRepeater)
#self.WANrepeaterbutton = JButton("to Repeater", actionPerformed=self.sendWANUPnPToRepeater)
self.textarea_request = JTextArea(18, 90)
self.intruderbutton.setEnabled(False)
self.repeaterbutton.setEnabled(False)
# Class neeeded to handle the target combobox in second step panel
class TargetComboboxListener(ActionListener):
def __init__(self, upnpcombo_targets, upnpcombo_services,
ip_service_dict):
self.upnpcombo_targets = upnpcombo_targets
self.upnpcombo_services = upnpcombo_services
self.ip_service_dict = ip_service_dict
def actionPerformed(self, event):
try:
# Update the location url combobox depending on the IP combobox
selected_target = self.upnpcombo_targets.getSelectedItem()
if self.ip_service_dict and selected_target:
self.upnpcombo_services.removeAllItems()
for service_url in self.ip_service_dict[
selected_target]:
self.upnpcombo_services.addItem(service_url)
self.upnpcombo_services.setSelectedIndex(0)
except BaseException as e:
print("[!] Exception selecting service: \"%s\" ") % e
# Class neeeded to handle the service combobox in second step panel
class ServiceComboboxListener(ActionListener):
def __init__(self, upnpcombo_services, upnpcombo_actions,
services_dict):
self.upnpcombo_services = upnpcombo_services
self.upnpcombo_actions = upnpcombo_actions
self.services = services_dict
def actionPerformed(self, event):
try:
# Update the location url combobox depending on the IP combobox
selected_service = self.upnpcombo_services.getSelectedItem(
)
if self.services and selected_service:
self.upnpcombo_actions.removeAllItems()
actions = self.services[selected_service]
for action in actions:
self.upnpcombo_actions.addItem(action)
self.upnpcombo_actions.setSelectedIndex(0)
except BaseException as e:
print("[!] Exception selecting service: \"%s\" ") % e
# Class neeeded to handle the action combobox in second step panel
class ActionComboboxListener(ActionListener):
def __init__(self, upnpcombo_services, upnpcombo_actions,
textarea_request, services_dict):
self.upnpcombo_services = upnpcombo_services
self.upnpcombo_actions = upnpcombo_actions
self.textarea_request = textarea_request
self.services = services_dict
def actionPerformed(self, event):
try:
# Update the location url combobox depending on the IP combobox
selected_action = self.upnpcombo_actions.getSelectedItem()
selected_service = self.upnpcombo_services.getSelectedItem(
)
if self.services and selected_action:
self.textarea_request.setText(
self.services[selected_service][selected_action])
except BaseException as e:
print("[!] Exception selecting action: \"%s\" ") % e
self.upnpactions = [" "]
self.upnpcombo_actions = JComboBox(self.upnpactions)
self.upnpcombo_actions.setSelectedIndex(0)
self.upnpcombo_actions.setEnabled(False)
# Create the combo box, select item at index 0 (first item in list)
self.upnpservices = [" "]
self.upnpcombo_services = JComboBox(self.upnpservices)
self.upnpcombo_services.setSelectedIndex(0)
self.upnpcombo_services.setEnabled(False)
# Create the combo box, select item at index 0 (first item in list)
self.upnptargets = [" "]
self.upnpcombo_targets = JComboBox(self.upnptargets)
self.upnpcombo_targets.setSelectedIndex(0)
self.upnpcombo_targets.setEnabled(False)
# Set the action listeners for all the comboboxes
self.upnpcombo_targets.addActionListener(
TargetComboboxListener(self.upnpcombo_targets,
self.upnpcombo_services,
self.ip_service_dict))
self.upnpcombo_services.addActionListener(
ServiceComboboxListener(self.upnpcombo_services,
self.upnpcombo_actions,
self.services_dict))
self.upnpcombo_actions.addActionListener(
ActionComboboxListener(self.upnpcombo_services,
self.upnpcombo_actions,
self.textarea_request, self.services_dict))
# Configuring first step panel
self.panel_step1 = JPanel()
self.panel_step1.setPreferredSize(Dimension(2250, 100))
self.panel_step1.setBorder(EmptyBorder(10, 10, 10, 10))
self.panel_step1.setLayout(BorderLayout(15, 15))
self.titlepanel_step1 = JPanel()
self.titlepanel_step1.setLayout(BorderLayout())
self.titlepanel_step1.add(self.labeltitle_step1, BorderLayout.NORTH)
self.titlepanel_step1.add(self.labelsubtitle_step1)
self.targetpanel_step1 = JPanel()
self.targetpanel_step1.add(self.label_step1)
self.targetpanel_step1.add(self.combo_ipversion)
self.targetpanel_step1.add(self.startbutton)
self.targetpanel_step1.add(self.clearbutton)
self.targetpanel_step1.add(self.labelstatus)
self.targetpanel_step1.add(self.progressbar)
self.emptypanel_step1 = JPanel()
self.emptypanel_step1.setLayout(BorderLayout())
self.emptypanel_step1.add(self.labelempty_step1, BorderLayout.WEST)
# Assembling first step panel components
self.panel_step1.add(self.titlepanel_step1, BorderLayout.NORTH)
self.panel_step1.add(self.targetpanel_step1, BorderLayout.WEST)
self.panel_step1.add(self.emptypanel_step1, BorderLayout.SOUTH)
self.uiPanelA.setTopComponent(self.panel_step1)
# Configure second step panel
self.panel_step2 = JPanel()
self.panel_step2.setPreferredSize(Dimension(2250, 100))
self.panel_step2.setBorder(EmptyBorder(10, 10, 10, 10))
self.panel_step2.setLayout(BorderLayout(15, 15))
self.titlepanel_step2 = JPanel()
self.titlepanel_step2.setLayout(BorderLayout())
self.titlepanel_step2.add(self.labeltitle_step2, BorderLayout.NORTH)
self.titlepanel_step2.add(self.labelsubtitle_step2)
self.selectpanel_step2 = JPanel()
self.selectpanel_step2.add(self.labelip)
self.selectpanel_step2.add(self.upnpcombo_targets)
self.selectpanel_step2.add(self.labelupnp)
self.selectpanel_step2.add(self.upnpcombo_services)
self.selectpanel_step2.add(self.labelactions)
self.selectpanel_step2.add(self.upnpcombo_actions)
self.emptypanel_step2 = JPanel()
self.emptypanel_step2.setLayout(BorderLayout())
self.emptypanel_step2.add(self.labelempty_step2, BorderLayout.WEST)
self.emptypanel_step2.add(self.labelNoneServiceFound)
# Assembling second step panel components
self.panel_step2.add(self.titlepanel_step2, BorderLayout.NORTH)
self.panel_step2.add(self.selectpanel_step2, BorderLayout.WEST)
self.panel_step2.add(self.emptypanel_step2, BorderLayout.SOUTH)
self.uiPanelB.setTopComponent(self.panel_step2)
# Configuring third step panel
self.panel_step3 = JPanel()
self.panel_step3.setPreferredSize(Dimension(2250, 100))
self.panel_step3.setBorder(EmptyBorder(10, 10, 10, 10))
self.panel_step3.setLayout(BorderLayout(15, 15))
self.titlepanel_step3 = JPanel()
self.titlepanel_step3.setLayout(BorderLayout())
self.titlepanel_step3.add(self.labeltitle_step3, BorderLayout.NORTH)
self.titlepanel_step3.add(self.labelsubtitle_step3)
self.underpanel_step3 = JPanel()
self.underpanel_step3.setLayout(BorderLayout())
self.underpanel_step3.add((JScrollPane(self.textarea_request)),
BorderLayout.NORTH)
self.actionpanel_step3 = JPanel()
self.actionpanel_step3.add(self.intruderbutton)
self.actionpanel_step3.add(self.repeaterbutton)
self.extrapanel_step3 = JPanel()
self.extrapanel_step3.setLayout(BorderLayout())
self.extrapanel_step3.add(self.actionpanel_step3, BorderLayout.WEST)
# Assembling thirdd step panel components
self.panel_step3.add(self.titlepanel_step3, BorderLayout.NORTH)
self.panel_step3.add(self.underpanel_step3, BorderLayout.WEST)
self.panel_step3.add(self.extrapanel_step3, BorderLayout.SOUTH)
self.uiPanelB.setBottomComponent(self.panel_step3)
# Assembling the group of all panels
layout = GroupLayout(self.pluginTab)
self.pluginTab.setLayout(layout)
layout.setHorizontalGroup(
layout.createParallelGroup(GroupLayout.Alignment.LEADING).addGroup(
layout.createSequentialGroup().addGap(10, 10, 10).addGroup(
layout.createParallelGroup(
GroupLayout.Alignment.LEADING).addComponent(
self.uiTitle).addGap(15, 15, 15).addComponent(
self.uiPanelA)).addContainerGap(
26, Short.MAX_VALUE)))
layout.setVerticalGroup(
layout.createParallelGroup(GroupLayout.Alignment.LEADING).addGroup(
layout.createSequentialGroup().addGap(15, 15, 15).addComponent(
self.uiTitle).addGap(15, 15, 15).addComponent(
self.uiPanelA).addGap(20, 20, 20).addGap(20, 20, 20)))
def extensionUnloaded(self):
# Unload the plugin, and if running stop the background thread
if self.upnpcombo_services.isEnabled():
if self.th.isAlive():
print("[+] Stopping thread %s") % self.th.getName()
self.STOP_THREAD = True
self.th.join()
else:
print("Thread %s already dead") % self.th.getName()
print("[+] Burp plugin UPnP BHunter successfully unloaded")
return
def getTabCaption(self):
return self.EXTENSION_NAME
def getUiComponent(self):
return self.pluginTab
def clearAll(self, e=None):
# Reset all data of the plugin
self.services_dict.clear()
self.progressbar.setString("Ready")
self.progressbar.setValue(0)
self.upnpcombo_targets.removeAllItems()
self.upnpcombo_targets.setEnabled(False)
self.upnpcombo_services.removeAllItems()
self.upnpcombo_services.setEnabled(False)
self.upnpcombo_actions.removeAllItems()
self.upnpcombo_actions.setEnabled(False)
self.intruderbutton.setEnabled(False)
self.repeaterbutton.setEnabled(False)
self.labelNoneServiceFound.setText(" ")
self.textarea_request.setText(" ")
print("[+] Clearing all data")
return
def startHunting(self, e=None):
# Starting the UPnP hunt
def startHunting_run():
# Initialize the internal parameters every time the start-discovery button is clicked
self.services_dict.clear()
found_loc = []
discovery_files = []
self.labelNoneServiceFound.setText(" ")
self.intruderbutton.setEnabled(False)
self.repeaterbutton.setEnabled(False)
# Then determine if targerting IPv4 or IPv6 adresses
if self.combo_ipversion.getSelectedItem() == "IPv4":
self.ipv4_selected = True
print("[+] Selected IPv4 address scope")
else:
self.ipv4_selected = False
print("[+] Selected IPv6 address scope")
# And here finally the hunt could start
self.progressbar.setString("Running...")
self.progressbar.setValue(20)
found_loc = self.discoverUpnpLocations()
self.progressbar.setValue(40)
discovery_files = self.downloadXMLfiles(found_loc)
self.progressbar.setValue(60)
self.buildSOAPs(discovery_files)
self.progressbar.setValue(80)
self.progressbar.setString("Done")
self.progressbar.setValue(100)
self.updateComboboxList(self.services_dict)
# Update the comboboxes list with the discovered UPnPs
if (self.services_dict):
self.upnpcombo_targets.setEnabled(True)
self.upnpcombo_services.setEnabled(True)
self.upnpcombo_actions.setEnabled(True)
self.intruderbutton.setEnabled(True)
self.repeaterbutton.setEnabled(True)
if self.STOP_THREAD:
return
# Start a background thread to run the above nested function in order to prevent the blocking of plugin UI
self.th = threading.Thread(target=startHunting_run)
#self.th.daemon = True # This does not seem to be useful
self.th.setName("th-BHunter")
self.th.start()
def ssdpReqBuilder(self, ssdp_timeout, st_type, ssdp_ip, ssdp_port):
# Builder of the two ssdp msearch request types
msearch_req = "M-SEARCH * HTTP/1.1\r\n" \
"HOST: {0}:{1}\r\n" \
"MAN: \"ssdp:discover\"\r\n" \
"MX: {2}\r\n" \
"ST: {3}\r\n" \
"\r\n" \
.format(ssdp_ip, ssdp_port, ssdp_timeout, st_type)
return msearch_req
def sendMsearch(self, ssdp_req, ssdp_ip, ssdp_port):
# Send the ssdp request and retrieve response
buf_resp = set()
if self.ipv4_selected:
print("[+] Creating IPv4 SSDP multicast request")
sock = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
else:
print("[+] Creating IPv6 SSDP multicast request")
sock = socket.socket(socket.AF_INET6, socket.SOCK_DGRAM)
sock.setblocking(0)
# Sending ssdp requests
while len(ssdp_req):
# Blocking socket client until the request is completely sent
try:
sent = sock.sendto(ssdp_req.encode("ASCII"),
(ssdp_ip, ssdp_port))
ssdp_req = ssdp_req[sent:]
except socket.error, exc:
if exc.errno != errno.EAGAIN:
print("[E] Got error %s with socket when sending") % exc
sock.close()
raise exc
print("[!] Blocking socket until ", len(ssdp_req), " is sent.")
select.select([], [sock], [])
continue
# Retrieving ssdp responses
num_resp = 0
while sock:
# Blocking socket until there are ssdp responses to be read or timeout is reached
readable, __, __ = select.select([sock], [], [], self.SSDP_TIMEOUT)
if not readable:
# Timeout reached without receiving any ssdp response
if num_resp == 0:
print(
"[!] Got timeout without receiving any ssdp response.")
break
else:
num_resp = num_resp + 1
# Almost an ssdp response was received
if readable[0]:
try:
data = sock.recv(1024)
if data:
buf_resp.add(data.decode('ASCII'))
except socket.error, exc:
print("[E] Got error %s with socket when receiving"
) % exc
sock.close()
raise exc
def drawPluginUI(self):
# Create the plugin user interface
self.pluginTab = JPanel()
self.uiTitle = JLabel('UPnP BHunter Load, Aim and Fire Console')
self.uiTitle.setFont(Font('Tahoma', Font.BOLD, 14))
self.uiTitle.setForeground(Color(250, 100, 0))
self.uiPanelA = JSplitPane(JSplitPane.VERTICAL_SPLIT)
self.uiPanelA.setMaximumSize(Dimension(2500, 1000))
self.uiPanelA.setDividerSize(2)
self.uiPanelB = JSplitPane(JSplitPane.VERTICAL_SPLIT)
self.uiPanelB.setDividerSize(2)
self.uiPanelA.setBottomComponent(self.uiPanelB)
self.uiPanelA.setBorder(BorderFactory.createLineBorder(Color.gray))
# Create and configure labels and text fields
self.labeltitle_step1 = JLabel("[1st STEP] Discover UPnP Locations")
self.labeltitle_step1.setFont(Font('Tahoma', Font.BOLD, 14))
self.labeltitle_step2 = JLabel(
"[2nd STEP] Select a UPnP Service and Action")
self.labeltitle_step2.setFont(Font('Tahoma', Font.BOLD, 14))
self.labeltitle_step3 = JLabel("[3rd STEP] Time to Attack it")
self.labeltitle_step3.setFont(Font('Tahoma', Font.BOLD, 14))
self.labelsubtitle_step1 = JLabel(
"Specify the IP version address in scope and start UPnP discovery")
self.labelsubtitle_step2 = JLabel(
"Select which of the found UPnP services will be probed")
self.labelsubtitle_step3 = JLabel(
"Review and modify the request, then send it to one of the attack tools"
)
self.label_step1 = JLabel("Target IP")
self.label_step2 = JLabel("Found UPnp Services")
self.labelstatus = JLabel(" Status")
self.labelempty_step1 = JLabel(" ")
self.labelempty_step2 = JLabel(" ")
self.labelupnp = JLabel("UPnP list")
self.labelip = JLabel("IP list")
self.labelactions = JLabel("Actions")
self.labelNoneServiceFound = JLabel(" ")
self.labelNoneServiceFound.setFont(Font('Tahoma', Font.BOLD, 12))
self.labelNoneServiceFound.setForeground(Color.red)
# Create combobox for IP version selection
self.ip_versions = ["IPv4", "IPv6"]
self.combo_ipversion = JComboBox(self.ip_versions)
self.combo_ipversion.setSelectedIndex(0)
self.combo_ipversion.setEnabled(True)
# Create and configure progress bar
self.progressbar = JProgressBar(0, 100)
self.progressbar.setString("Ready")
self.progressbar.setStringPainted(True)
# Create and configure buttons
self.startbutton = JButton("Start Discovery",
actionPerformed=self.startHunting)
self.clearbutton = JButton("Clear All", actionPerformed=self.clearAll)
self.intruderbutton = JButton("Send to Intruder",
actionPerformed=self.sendToIntruder)
self.repeaterbutton = JButton("Send to Repeater",
actionPerformed=self.sendToRepeater)
#self.WANrepeaterbutton = JButton("to Repeater", actionPerformed=self.sendWANUPnPToRepeater)
self.textarea_request = JTextArea(18, 90)
self.intruderbutton.setEnabled(False)
self.repeaterbutton.setEnabled(False)
# Class neeeded to handle the target combobox in second step panel
class TargetComboboxListener(ActionListener):
def __init__(self, upnpcombo_targets, upnpcombo_services,
ip_service_dict):
self.upnpcombo_targets = upnpcombo_targets
self.upnpcombo_services = upnpcombo_services
self.ip_service_dict = ip_service_dict
def actionPerformed(self, event):
try:
# Update the location url combobox depending on the IP combobox
selected_target = self.upnpcombo_targets.getSelectedItem()
if self.ip_service_dict and selected_target:
self.upnpcombo_services.removeAllItems()
for service_url in self.ip_service_dict[
selected_target]:
self.upnpcombo_services.addItem(service_url)
self.upnpcombo_services.setSelectedIndex(0)
except BaseException as e:
print("[!] Exception selecting service: \"%s\" ") % e
# Class neeeded to handle the service combobox in second step panel
class ServiceComboboxListener(ActionListener):
def __init__(self, upnpcombo_services, upnpcombo_actions,
services_dict):
self.upnpcombo_services = upnpcombo_services
self.upnpcombo_actions = upnpcombo_actions
self.services = services_dict
def actionPerformed(self, event):
try:
# Update the location url combobox depending on the IP combobox
selected_service = self.upnpcombo_services.getSelectedItem(
)
if self.services and selected_service:
self.upnpcombo_actions.removeAllItems()
actions = self.services[selected_service]
for action in actions:
self.upnpcombo_actions.addItem(action)
self.upnpcombo_actions.setSelectedIndex(0)
except BaseException as e:
print("[!] Exception selecting service: \"%s\" ") % e
# Class neeeded to handle the action combobox in second step panel
class ActionComboboxListener(ActionListener):
def __init__(self, upnpcombo_services, upnpcombo_actions,
textarea_request, services_dict):
self.upnpcombo_services = upnpcombo_services
self.upnpcombo_actions = upnpcombo_actions
self.textarea_request = textarea_request
self.services = services_dict
def actionPerformed(self, event):
try:
# Update the location url combobox depending on the IP combobox
selected_action = self.upnpcombo_actions.getSelectedItem()
selected_service = self.upnpcombo_services.getSelectedItem(
)
if self.services and selected_action:
self.textarea_request.setText(
self.services[selected_service][selected_action])
except BaseException as e:
print("[!] Exception selecting action: \"%s\" ") % e
self.upnpactions = [" "]
self.upnpcombo_actions = JComboBox(self.upnpactions)
self.upnpcombo_actions.setSelectedIndex(0)
self.upnpcombo_actions.setEnabled(False)
# Create the combo box, select item at index 0 (first item in list)
self.upnpservices = [" "]
self.upnpcombo_services = JComboBox(self.upnpservices)
self.upnpcombo_services.setSelectedIndex(0)
self.upnpcombo_services.setEnabled(False)
# Create the combo box, select item at index 0 (first item in list)
self.upnptargets = [" "]
self.upnpcombo_targets = JComboBox(self.upnptargets)
self.upnpcombo_targets.setSelectedIndex(0)
self.upnpcombo_targets.setEnabled(False)
# Set the action listeners for all the comboboxes
self.upnpcombo_targets.addActionListener(
TargetComboboxListener(self.upnpcombo_targets,
self.upnpcombo_services,
self.ip_service_dict))
self.upnpcombo_services.addActionListener(
ServiceComboboxListener(self.upnpcombo_services,
self.upnpcombo_actions,
self.services_dict))
self.upnpcombo_actions.addActionListener(
ActionComboboxListener(self.upnpcombo_services,
self.upnpcombo_actions,
self.textarea_request, self.services_dict))
# Configuring first step panel
self.panel_step1 = JPanel()
self.panel_step1.setPreferredSize(Dimension(2250, 100))
self.panel_step1.setBorder(EmptyBorder(10, 10, 10, 10))
self.panel_step1.setLayout(BorderLayout(15, 15))
self.titlepanel_step1 = JPanel()
self.titlepanel_step1.setLayout(BorderLayout())
self.titlepanel_step1.add(self.labeltitle_step1, BorderLayout.NORTH)
self.titlepanel_step1.add(self.labelsubtitle_step1)
self.targetpanel_step1 = JPanel()
self.targetpanel_step1.add(self.label_step1)
self.targetpanel_step1.add(self.combo_ipversion)
self.targetpanel_step1.add(self.startbutton)
self.targetpanel_step1.add(self.clearbutton)
self.targetpanel_step1.add(self.labelstatus)
self.targetpanel_step1.add(self.progressbar)
self.emptypanel_step1 = JPanel()
self.emptypanel_step1.setLayout(BorderLayout())
self.emptypanel_step1.add(self.labelempty_step1, BorderLayout.WEST)
# Assembling first step panel components
self.panel_step1.add(self.titlepanel_step1, BorderLayout.NORTH)
self.panel_step1.add(self.targetpanel_step1, BorderLayout.WEST)
self.panel_step1.add(self.emptypanel_step1, BorderLayout.SOUTH)
self.uiPanelA.setTopComponent(self.panel_step1)
# Configure second step panel
self.panel_step2 = JPanel()
self.panel_step2.setPreferredSize(Dimension(2250, 100))
self.panel_step2.setBorder(EmptyBorder(10, 10, 10, 10))
self.panel_step2.setLayout(BorderLayout(15, 15))
self.titlepanel_step2 = JPanel()
self.titlepanel_step2.setLayout(BorderLayout())
self.titlepanel_step2.add(self.labeltitle_step2, BorderLayout.NORTH)
self.titlepanel_step2.add(self.labelsubtitle_step2)
self.selectpanel_step2 = JPanel()
self.selectpanel_step2.add(self.labelip)
self.selectpanel_step2.add(self.upnpcombo_targets)
self.selectpanel_step2.add(self.labelupnp)
self.selectpanel_step2.add(self.upnpcombo_services)
self.selectpanel_step2.add(self.labelactions)
self.selectpanel_step2.add(self.upnpcombo_actions)
self.emptypanel_step2 = JPanel()
self.emptypanel_step2.setLayout(BorderLayout())
self.emptypanel_step2.add(self.labelempty_step2, BorderLayout.WEST)
self.emptypanel_step2.add(self.labelNoneServiceFound)
# Assembling second step panel components
self.panel_step2.add(self.titlepanel_step2, BorderLayout.NORTH)
self.panel_step2.add(self.selectpanel_step2, BorderLayout.WEST)
self.panel_step2.add(self.emptypanel_step2, BorderLayout.SOUTH)
self.uiPanelB.setTopComponent(self.panel_step2)
# Configuring third step panel
self.panel_step3 = JPanel()
self.panel_step3.setPreferredSize(Dimension(2250, 100))
self.panel_step3.setBorder(EmptyBorder(10, 10, 10, 10))
self.panel_step3.setLayout(BorderLayout(15, 15))
self.titlepanel_step3 = JPanel()
self.titlepanel_step3.setLayout(BorderLayout())
self.titlepanel_step3.add(self.labeltitle_step3, BorderLayout.NORTH)
self.titlepanel_step3.add(self.labelsubtitle_step3)
self.underpanel_step3 = JPanel()
self.underpanel_step3.setLayout(BorderLayout())
self.underpanel_step3.add((JScrollPane(self.textarea_request)),
BorderLayout.NORTH)
self.actionpanel_step3 = JPanel()
self.actionpanel_step3.add(self.intruderbutton)
self.actionpanel_step3.add(self.repeaterbutton)
self.extrapanel_step3 = JPanel()
self.extrapanel_step3.setLayout(BorderLayout())
self.extrapanel_step3.add(self.actionpanel_step3, BorderLayout.WEST)
# Assembling thirdd step panel components
self.panel_step3.add(self.titlepanel_step3, BorderLayout.NORTH)
self.panel_step3.add(self.underpanel_step3, BorderLayout.WEST)
self.panel_step3.add(self.extrapanel_step3, BorderLayout.SOUTH)
self.uiPanelB.setBottomComponent(self.panel_step3)
# Assembling the group of all panels
layout = GroupLayout(self.pluginTab)
self.pluginTab.setLayout(layout)
layout.setHorizontalGroup(
layout.createParallelGroup(GroupLayout.Alignment.LEADING).addGroup(
layout.createSequentialGroup().addGap(10, 10, 10).addGroup(
layout.createParallelGroup(
GroupLayout.Alignment.LEADING).addComponent(
self.uiTitle).addGap(15, 15, 15).addComponent(
self.uiPanelA)).addContainerGap(
26, Short.MAX_VALUE)))
layout.setVerticalGroup(
layout.createParallelGroup(GroupLayout.Alignment.LEADING).addGroup(
layout.createSequentialGroup().addGap(15, 15, 15).addComponent(
self.uiTitle).addGap(15, 15, 15).addComponent(
self.uiPanelA).addGap(20, 20, 20).addGap(20, 20, 20)))
class BurpExtender(
IBurpExtender, ITab, IContextMenuFactory, IMessageEditorController):
# Implement IBurpExtender
def registerExtenderCallbacks(self, callbacks):
callbacks.registerContextMenuFactory(self)
self._callbacks = callbacks
self._helpers = callbacks.getHelpers()
callbacks.setExtensionName(EXTENSION_NAME)
# Construct UI
insets = Insets(3, 3, 3, 3)
self._messageEditor = callbacks.createMessageEditor(self, True)
attackPanel = self._constructAttackPanel(
insets, self._messageEditor.getComponent())
resultsPanel = self._constructResultsPanel(insets)
aboutPanel = self._constructAboutPanel(insets)
self._tabbedPane = JTabbedPane()
self._tabbedPane.addTab("Attack", attackPanel)
self._tabbedPane.addTab("Results", resultsPanel)
self._tabbedPane.addTab("About", aboutPanel)
callbacks.addSuiteTab(self)
# Implement ITab
def getTabCaption(self):
return EXTENSION_NAME
def getUiComponent(self):
return self._tabbedPane
# Implement IMessageEditorController
def getHttpService(self):
self._updateClassFromUI()
return self._httpService
def getRequest(self):
self._updateClassFromUI()
return self._request
def getResponse(self):
return None
# Implement IContextMenuFactory
def createMenuItems(self, contextMenuInvocation):
messages = contextMenuInvocation.getSelectedMessages()
# Only add menu item if a single request is selected
if len(messages) == 1:
self._contextMenuData = messages
menu_item = JMenuItem(
"Send to {}".format(EXTENSION_NAME),
actionPerformed=self._contextMenuItemClicked
)
return [menu_item]
def _contextMenuItemClicked(self, _):
httpRequestResponse = self._contextMenuData[0]
# Update instance variables with request data
self._httpService = httpRequestResponse.getHttpService()
self._request = httpRequestResponse.getRequest()
# Update fields in tab
self._hostTextField.setText(self._httpService.getHost())
self._portTextField.setText(str(self._httpService.getPort()))
self._protocolCheckBox.setSelected(
True if self._httpService.getProtocol() == "https" else False)
self._messageEditor.setMessage(self._request, True)
def _startAttack(self, _):
# Switch to results tab
self._tabbedPane.setSelectedIndex(1)
# Clear results table
self._resultsTableModel.setRowCount(0)
# Set progress bar to 0%
self._progressBar.setValue(0)
Thread(target=self._makeHttpRequests).start()
def _makeHttpRequests(self):
# Set class variables from values in UI
self._updateClassFromUI()
self._responses = {}
# Set progress bar max to number of requests
self._progressBar.setMaximum(len(self._payloads) * self._numReq)
for payload in self._payloads:
self._responses[payload] = []
# Stick payload into request at specified position
# Use lambda function for replacement string to stop slashes being
# escaped
request = sub("\xa7[^\xa7]*\xa7", lambda x: payload, self._request)
request = self._updateContentLength(request)
for _ in xrange(self._numReq):
# Make request and work out how long it took in ms. This method
# is crude, but it's as good as we can get with current Burp
# APIs.
# See https://support.portswigger.net/customer/portal/questions/16227838-request-response-timing # noqa: E501
startTime = time()
response = self._callbacks.makeHttpRequest(
self._httpService, request)
endTime = time()
duration = (endTime - startTime) * 1000
self._progressBar.setValue(self._progressBar.getValue() + 1)
self._responses[payload].append(duration)
# If all responses for this payload have
# been added to array, add to results table.
results = self._responses[payload]
numReqs = self._numReq
statusCode = response.getStatusCode()
analysis = self._helpers.analyzeResponse(
response.getResponse())
for header in analysis.getHeaders():
if header.lower().startswith("content-length"):
content_length = int(header.split(": ")[1])
meanTime = round(mean(results), 3)
medianTime = round(median(results), 3)
stdDevTime = round(stdDev(results), 3)
minTime = int(min(results))
maxTime = int(max(results))
rowData = [
payload, numReqs, statusCode,
len(response.getResponse()), content_length, minTime,
maxTime, meanTime, medianTime, stdDevTime]
self._resultsTableModel.addRow(rowData)
def _updateClassFromUI(self):
host = self._hostTextField.text
port = int(self._portTextField.text)
protocol = "https" if self._protocolCheckBox.isSelected() else "http"
# In an effort to prevent DNS queries introducing a delay, an attempt
# was made to use the IP address of the destination web server instead
# of the hostname when building the HttpService. Unfortunately it
# caused issues with HTTPS requests, probably because of SNIs. As an
# alternative, the hostname is resolved in the next line and hopefully
# it will be cached at that point.
gethostbyname(host)
self._httpService = self._helpers.buildHttpService(
host, port, protocol)
self._request = self._messageEditor.getMessage()
self._numReq = int(self._requestsNumTextField.text)
self._payloads = set(self._payloadTextArea.text.split("\n"))
def _addPayload(self, _):
request = self._messageEditor.getMessage()
selection = self._messageEditor.getSelectionBounds()
if selection[0] == selection[1]:
# No text selected so in/out points are same
request.insert(selection[0], 0xa7)
request.insert(selection[1], 0xa7)
else:
request.insert(selection[0], 0xa7)
request.insert(selection[1]+1, 0xa7)
self._messageEditor.setMessage(request, True)
def _clearPayloads(self, _):
request = self._messageEditor.getMessage()
request = self._helpers.bytesToString(request).replace("\xa7", "")
self._messageEditor.setMessage(request, True)
def _updateContentLength(self, request):
messageSize = len(request)
bodyOffset = self._helpers.analyzeRequest(request).getBodyOffset()
contentLength = messageSize - bodyOffset
contentLengthHeader = "Content-Length: {}".format(contentLength)
request = sub("Content-Length: \\d+", contentLengthHeader, request)
return request
def _constructAttackPanel(self, insets, messageEditorComponent):
attackPanel = JPanel(GridBagLayout())
targetHeadingLabel = JLabel("<html><b>Target</b></html>")
targetHeadingLabelConstraints = GridBagConstraints()
targetHeadingLabelConstraints.gridx = 0
targetHeadingLabelConstraints.gridy = 0
targetHeadingLabelConstraints.gridwidth = 4
targetHeadingLabelConstraints.anchor = GridBagConstraints.LINE_START
targetHeadingLabelConstraints.insets = insets
attackPanel.add(targetHeadingLabel, targetHeadingLabelConstraints)
startAttackButton = JButton("<html><b>Start Attack</b></html>",
actionPerformed=self._startAttack)
startAttackButtonConstraints = GridBagConstraints()
startAttackButtonConstraints.gridx = 4
startAttackButtonConstraints.gridy = 0
startAttackButtonConstraints.insets = insets
attackPanel.add(startAttackButton, startAttackButtonConstraints)
hostLabel = JLabel("Host:")
hostLabelConstraints = GridBagConstraints()
hostLabelConstraints.gridx = 0
hostLabelConstraints.gridy = 1
hostLabelConstraints.anchor = GridBagConstraints.LINE_START
hostLabelConstraints.insets = insets
attackPanel.add(hostLabel, hostLabelConstraints)
self._hostTextField = JTextField(25)
self._hostTextField.setMinimumSize(
self._hostTextField.getPreferredSize())
hostTextFieldConstraints = GridBagConstraints()
hostTextFieldConstraints.gridx = 1
hostTextFieldConstraints.gridy = 1
hostTextFieldConstraints.weightx = 1
hostTextFieldConstraints.gridwidth = 2
hostTextFieldConstraints.anchor = GridBagConstraints.LINE_START
hostTextFieldConstraints.insets = insets
attackPanel.add(self._hostTextField, hostTextFieldConstraints)
portLabel = JLabel("Port:")
portLabelConstraints = GridBagConstraints()
portLabelConstraints.gridx = 0
portLabelConstraints.gridy = 2
portLabelConstraints.anchor = GridBagConstraints.LINE_START
portLabelConstraints.insets = insets
attackPanel.add(portLabel, portLabelConstraints)
self._portTextField = JTextField(5)
self._portTextField.setMinimumSize(
self._portTextField.getPreferredSize())
portTextFieldConstraints = GridBagConstraints()
portTextFieldConstraints.gridx = 1
portTextFieldConstraints.gridy = 2
portTextFieldConstraints.gridwidth = 2
portTextFieldConstraints.anchor = GridBagConstraints.LINE_START
portTextFieldConstraints.insets = insets
attackPanel.add(self._portTextField, portTextFieldConstraints)
self._protocolCheckBox = JCheckBox("Use HTTPS")
protocolCheckBoxConstraints = GridBagConstraints()
protocolCheckBoxConstraints.gridx = 0
protocolCheckBoxConstraints.gridy = 3
protocolCheckBoxConstraints.gridwidth = 3
protocolCheckBoxConstraints.anchor = GridBagConstraints.LINE_START
protocolCheckBoxConstraints.insets = insets
attackPanel.add(self._protocolCheckBox, protocolCheckBoxConstraints)
requestHeadingLabel = JLabel("<html><b>Request</b></html>")
requestHeadingLabelConstraints = GridBagConstraints()
requestHeadingLabelConstraints.gridx = 0
requestHeadingLabelConstraints.gridy = 4
requestHeadingLabelConstraints.gridwidth = 4
requestHeadingLabelConstraints.anchor = GridBagConstraints.LINE_START
requestHeadingLabelConstraints.insets = insets
attackPanel.add(requestHeadingLabel, requestHeadingLabelConstraints)
messageEditorComponentConstraints = GridBagConstraints()
messageEditorComponentConstraints.gridx = 0
messageEditorComponentConstraints.gridy = 5
messageEditorComponentConstraints.weightx = 1
messageEditorComponentConstraints.weighty = .75
messageEditorComponentConstraints.gridwidth = 4
messageEditorComponentConstraints.gridheight = 2
messageEditorComponentConstraints.fill = GridBagConstraints.BOTH
messageEditorComponentConstraints.insets = insets
attackPanel.add(
messageEditorComponent, messageEditorComponentConstraints)
addPayloadButton = JButton(
"Add \xa7", actionPerformed=self._addPayload)
addPayloadButtonConstraints = GridBagConstraints()
addPayloadButtonConstraints.gridx = 4
addPayloadButtonConstraints.gridy = 5
addPayloadButtonConstraints.fill = GridBagConstraints.HORIZONTAL
addPayloadButtonConstraints.insets = insets
attackPanel.add(addPayloadButton, addPayloadButtonConstraints)
clearPayloadButton = JButton(
"Clear \xa7", actionPerformed=self._clearPayloads)
clearPayloadButtonConstraints = GridBagConstraints()
clearPayloadButtonConstraints.gridx = 4
clearPayloadButtonConstraints.gridy = 6
clearPayloadButtonConstraints.anchor = GridBagConstraints.PAGE_START
clearPayloadButtonConstraints.fill = GridBagConstraints.HORIZONTAL
clearPayloadButtonConstraints.insets = insets
attackPanel.add(clearPayloadButton, clearPayloadButtonConstraints)
payloadHeadingLabel = JLabel("<html><b>Payloads<b></html>")
payloadHeadingLabelConstraints = GridBagConstraints()
payloadHeadingLabelConstraints.gridx = 0
payloadHeadingLabelConstraints.gridy = 7
payloadHeadingLabelConstraints.gridwidth = 4
payloadHeadingLabelConstraints.anchor = GridBagConstraints.LINE_START
payloadHeadingLabelConstraints.insets = insets
attackPanel.add(payloadHeadingLabel, payloadHeadingLabelConstraints)
self._payloadTextArea = JTextArea()
payloadScrollPane = JScrollPane(self._payloadTextArea)
payloadScrollPaneConstraints = GridBagConstraints()
payloadScrollPaneConstraints.gridx = 0
payloadScrollPaneConstraints.gridy = 8
payloadScrollPaneConstraints.weighty = .25
payloadScrollPaneConstraints.gridwidth = 3
payloadScrollPaneConstraints.fill = GridBagConstraints.BOTH
payloadScrollPaneConstraints.insets = insets
attackPanel.add(payloadScrollPane, payloadScrollPaneConstraints)
requestsNumLabel = JLabel("Number of requests for each payload:")
requestsNumLabelConstraints = GridBagConstraints()
requestsNumLabelConstraints.gridx = 0
requestsNumLabelConstraints.gridy = 9
requestsNumLabelConstraints.gridwidth = 2
requestsNumLabelConstraints.anchor = GridBagConstraints.LINE_START
requestsNumLabelConstraints.insets = insets
attackPanel.add(requestsNumLabel, requestsNumLabelConstraints)
self._requestsNumTextField = JTextField("100", 4)
self._requestsNumTextField.setMinimumSize(
self._requestsNumTextField.getPreferredSize())
requestsNumTextFieldConstraints = GridBagConstraints()
requestsNumTextFieldConstraints.gridx = 2
requestsNumTextFieldConstraints.gridy = 9
requestsNumTextFieldConstraints.anchor = GridBagConstraints.LINE_START
requestsNumTextFieldConstraints.insets = insets
attackPanel.add(
self._requestsNumTextField, requestsNumTextFieldConstraints)
return attackPanel
def _constructResultsPanel(self, insets):
resultsPanel = JPanel(GridBagLayout())
self._progressBar = JProgressBar()
self._progressBar.setStringPainted(True)
self._progressBar.setMinimum(0)
progressBarContraints = GridBagConstraints()
progressBarContraints.gridx = 0
progressBarContraints.gridy = 0
progressBarContraints.fill = GridBagConstraints.HORIZONTAL
resultsPanel.add(self._progressBar, progressBarContraints)
self._resultsTableModel = ResultsTableModel(COLUMNS, 0)
resultsTable = JTable(self._resultsTableModel)
resultsTable.setAutoCreateRowSorter(True)
cellRenderer = ColoredTableCellRenderer()
for index in [5, 6, 7, 8, 9]:
column = resultsTable.columnModel.getColumn(index)
column.cellRenderer = cellRenderer
resultsTable.getColumnModel().getColumn(0).setPreferredWidth(99999999)
resultsTable.getColumnModel().getColumn(1).setMinWidth(160)
resultsTable.getColumnModel().getColumn(2).setMinWidth(100)
resultsTable.getColumnModel().getColumn(3).setMinWidth(80)
resultsTable.getColumnModel().getColumn(4).setMinWidth(80)
resultsTable.getColumnModel().getColumn(5).setMinWidth(110)
resultsTable.getColumnModel().getColumn(6).setMinWidth(110)
resultsTable.getColumnModel().getColumn(7).setMinWidth(90)
resultsTable.getColumnModel().getColumn(8).setMinWidth(110)
resultsTable.getColumnModel().getColumn(9).setMinWidth(110)
resultsTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS)
resultsScrollPane = JScrollPane(resultsTable)
resultsScrollPaneConstraints = GridBagConstraints()
resultsScrollPaneConstraints.gridx = 0
resultsScrollPaneConstraints.gridy = 1
resultsScrollPaneConstraints.weightx = 1
resultsScrollPaneConstraints.weighty = 1
resultsScrollPaneConstraints.fill = GridBagConstraints.BOTH
resultsPanel.add(resultsScrollPane, resultsScrollPaneConstraints)
return resultsPanel
def _constructAboutPanel(self, insets):
aboutPanel = JPanel(GridBagLayout())
with open("about.html") as file:
aboutBody = file.read()
aboutLabel = JLabel(
aboutBody.format(extension_name=EXTENSION_NAME))
aboutLabelConstraints = GridBagConstraints()
aboutLabelConstraints.weightx = 1
aboutLabelConstraints.weighty = 1
aboutLabelConstraints.insets = insets
aboutLabelConstraints.fill = GridBagConstraints.HORIZONTAL
aboutLabelConstraints.anchor = GridBagConstraints.PAGE_START
aboutPanel.add(aboutLabel, aboutLabelConstraints)
return aboutPanel
class ToolsProgressDialog(JDialog, PropertyChangeListener):
def __init__(self, parent, title, modal, app):
"""Restore the tools data by:
- downloading the tools list
- downloading the tools jar files
- extracting the tools data from jar files
"""
self.app = app
border = BorderFactory.createEmptyBorder(5, 7, 5, 7)
mainPane = self.getContentPane()
mainPane.setLayout(BorderLayout(5, 5))
mainPane.setBorder(border)
self.setPreferredSize(Dimension(400, 200))
self.taskOutput = JMultilineLabel(self.app.strings.getString("checking_for_updates"))
self.taskOutput.setMaxWidth(350)
self.progressBar = JProgressBar(0, 100, value=0, stringPainted=True)
self.progressBar.setIndeterminate(True)
self.cancelBtn = JButton("Cancel",
actionPerformed=self.on_cancelBtn_clicked,
enabled=True)
self.okBtn = JButton("Ok",
actionPerformed=self.on_okBtn_clicked,
enabled=False)
mainPane.add(self.taskOutput, BorderLayout.CENTER)
bottomPanel = JPanel(BorderLayout(5, 5))
bottomPanel.add(self.progressBar, BorderLayout.PAGE_START)
buttonsPanel = JPanel()
buttonsPanel.add(self.okBtn)
buttonsPanel.add(self.cancelBtn)
bottomPanel.add(buttonsPanel, BorderLayout.PAGE_END)
mainPane.add(bottomPanel, BorderLayout.PAGE_END)
self.pack()
self.task = DownloaderTask(self)
self.task.addPropertyChangeListener(self)
self.task.execute()
def propertyChange(self, e):
# Invoked when task's progress property changes.
if e.propertyName == "progress":
if e.newValue == 2:
text = self.app.strings.getString("downloading_tools_list")
elif e.newValue == 3:
text = self.app.strings.getString("tools_not_downloaded_warning")
elif e.newValue == 5:
text = self.app.strings.getString("downloading_tools_data")
elif e.newValue == 6:
text = self.app.strings.getString("i_cannot_download_the_tool_files")
elif e.newValue == 7:
text = self.app.strings.getString("extracting_jar_files")
elif e.newValue == 8:
text = self.app.strings.getString("tools_updated")
self.taskOutput.setText("<html>" + text + "</html>")
def on_cancelBtn_clicked(self, e):
self.dispose()
self.task.cancel(True)
def on_okBtn_clicked(self, e):
self.dispose()
def __init__(self, imgData):
n = imgData.size()
win = JFrame("Point Marker Panel")
win.setPreferredSize(Dimension(350, 590))
win.setSize(win.getPreferredSize())
pan = JPanel()
pan.setLayout(BoxLayout(pan, BoxLayout.Y_AXIS))
win.getContentPane().add(pan)
progressPanel = JPanel()
progressPanel.setLayout(BoxLayout(progressPanel, BoxLayout.Y_AXIS))
positionBar = JProgressBar()
positionBar.setMinimum(0)
positionBar.setMaximum(n)
positionBar.setStringPainted(True)
progressPanel.add(Box.createGlue())
progressPanel.add(positionBar)
progressBar = JProgressBar()
progressBar.setMinimum(0)
progressBar.setMaximum(n)
progressBar.setStringPainted(True)
progressPanel.add(progressBar)
progressPanel.setBorder(BorderFactory.createEmptyBorder(0,10,0,10))
pan.add(progressPanel)
pan.add(Box.createRigidArea(Dimension(5,5)))
savePanel = JPanel()
savePanel.setLayout(BoxLayout(savePanel, BoxLayout.Y_AXIS))
saveMessageLabel = JLabel("<html><u>Save Often</u></html>")
savePanel.add(saveMessageLabel)
savePanel.setAlignmentX(Component.CENTER_ALIGNMENT)
savePanel.setBorder(BorderFactory.createEmptyBorder(0,10,0,10))
pan.add(savePanel)
# pan.add(saveMessageLabel)
pan.add(Box.createRigidArea(Dimension(5,5)))
calPanel = JPanel()
calPanel.setLayout(BoxLayout(calPanel, BoxLayout.Y_AXIS))
calPanelIn = JPanel()
calPanelIn.setLayout(BoxLayout(calPanelIn, BoxLayout.X_AXIS))
pixelSizeText = JTextField(12)
pixelSizeText.setHorizontalAlignment(JTextField.RIGHT)
# pixelSizeText.setMaximumSize(pixelSizeText.getPreferredSize())
unitText = JTextField(10)
# unitText.setMaximumSize(unitText.getPreferredSize())
pixelSizeText.setText("Enter Pixel Size Here")
calPanelIn.add(pixelSizeText)
unitText.setText("Unit")
calPanelIn.add(unitText)
calPanelIn.setAlignmentX(Component.CENTER_ALIGNMENT)
calPanelIn.setBorder(BorderFactory.createTitledBorder("Custom Calibration"))
calPanel.add(calPanelIn)
calPanelIn.setAlignmentX(Component.CENTER_ALIGNMENT)
calPanel.setBorder(BorderFactory.createEmptyBorder(0,10,0,10))
pan.add(calPanel)
pan.add(Box.createRigidArea(Dimension(5,5)))
helpPanel = JPanel()
helpPanel.setLayout(BoxLayout(helpPanel, BoxLayout.Y_AXIS))
helpLable = JLabel("<html><ul>\
<li>Focus on Image Window</li>\
<li>Select multi-point Tool</li>\
<li>Click to Draw Points</li>\
<li>Drag to Move Points</li>\
<li>\"Alt\" + Click to Erase Points</li>\
<li>Optional: Customize Calibration Above\
and Refresh Images\
(won't be written to files)</li>\
</html>")
helpLable.setBorder(BorderFactory.createTitledBorder("Usage"))
keyTagOpen = "<span style=\"background-color: #FFFFFF\"><b><kbd>"
keyTagClose = "</kbd></b></span>"
keyLable = JLabel("<html><ul>\
<li>Next Image --- " + keyTagOpen + "<" + \
keyTagClose + "</li>\
<li>Previous Image --- " + keyTagOpen + ">" + \
keyTagClose + "</li>\
<li>Save --- " + keyTagOpen + "`" + keyTagClose + \
" (upper-left to TAB key)</li>\
<li>Next Unmarked Image --- " + keyTagOpen + \
"TAB" + keyTagClose + "</li></ul>\
</html>")
keyLable.setBorder(BorderFactory.createTitledBorder("Keyboard Shortcuts"))
helpPanel.add(helpLable)
helpPanel.add(keyLable)
helpPanel.setAlignmentX(Component.CENTER_ALIGNMENT)
helpPanel.setBorder(BorderFactory.createEmptyBorder(0,10,0,10))
pan.add(helpPanel)
# pan.add(Box.createRigidArea(Dimension(0, 10)))
infoPanel = JPanel()
infoPanel.setLayout(BoxLayout(infoPanel, BoxLayout.Y_AXIS))
infoLabel = JLabel()
infoLabel.setBorder(BorderFactory.createTitledBorder("Project Info"))
infoPanel.add(infoLabel)
infoPanel.setAlignmentX(Component.CENTER_ALIGNMENT)
infoPanel.setBorder(BorderFactory.createEmptyBorder(0,10,0,10))
pan.add(infoPanel)
win.setVisible(True)
self.imgData = imgData
self.win = win
# self.progressPanel = progressPanel
self.positionBar = positionBar
self.progressBar = progressBar
self.saveMessageLabel = saveMessageLabel
self.infoLabel = infoLabel
self.pixelSizeText = pixelSizeText
self.unitText = unitText
self.update()
class Pipeline():
def __init__(self):
#If a swing interface is asked for this will be the JFrame.
self.frame = None
#Keeps track of the number of queries processed.
self.jobCount = 0
#Keeps track of the query currently being processed.
self.currentJob = ""
#Keeps track of the massage to be displayed.
self.message = 0
#Messages to be displayed at each stage in the processing of a single query.
self.messages = ["Searching for genes via genemark",
"Extending genes found via genemark",
"Searching for intergenic genes",
"Removing overlapping genes",
"Searching for promoters",
"Using transterm to find terminators",
"Removing transcription signals which conflict with genes",
"Using tRNAscan to find transfer RNAs",
"Writing Artemis file",
"Writing summary .xml, .html, and .xls files"]
self.exception = None
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 updateProgress(self, job):
"""
query: Name of the query currently being processed.
This function use used for updating the progress shown in the interface. If job is not equal to currentJob then
global progress is incremented and shown and the currentProgress is reset and shown. If job is equal to currentJob
then the globalProgress does not change and currentProgress is increased.
"""
if self.exception:
raise self.exception
if self.frame:
if job != self.currentJob:
self.currentProgress.setValue(self.currentProgress.getMaximum())
self.globalLabel.setText(job)
self.globalProgress.setValue(self.jobCount)
print "Processing %s, %.2f%% done" % (job, 100.0*self.jobCount/self.numJobs)
self.jobCount += 1
self.currentJob = job
self.message = -1
self.message += 1
print " %s, %.2f%% done" % (self.messages[self.message], 100.0*self.message/len(self.messages))
self.currentProgress.setValue(self.message)
self.currentLabel.setText(self.messages[self.message])
else:
if job != self.currentJob:
print "Processing %s, %.2f%% done" % (job, 100.0*self.jobCount/self.numJobs)
self.jobCount += 1
self.currentJob = job
self.message = -1
self.message += 1
print " %s, %.2f%% done" % (self.messages[self.message], 100.0*self.message/len(self.messages))
def finished(self):
"""
This function is to be called at the end of the pipeline. Informs the user that the pipeline is finished
and if a swing interface is being used the Done button is enabled.
"""
print "Processing 100.00% done"
if self.frame:
self.globalLabel.setText("Finished")
self.globalProgress.setValue(self.globalProgress.getMaximum())
self.currentLabel.setText(" ")
self.currentProgress.setValue(self.currentProgress.getMaximum())
self.doneButton.setEnabled(True)
while self.frame.isVisible():
pass
def run(self, blastLocation, genemarkLocation, transtermLocation, tRNAscanLocation, database, eValue, matrix, minLength, scaffoldingDistance, promoterScoreCutoff, queries, swing = False, email = ""):
"""
blastLocation: Directory blast was installed in.
genemarkLocation: Directory genemark was installed in.
transtermLocation: Directory transterm was installed in.
tRNAscanLocation: Directory tRNAscan was installed in.
database: Name of the blast database to use.
eValue: The e value used whenever a blast search is done.
matrix: The matrix to use when running genemark. If None then genemark is run heuristically.
minLength: Minimum length of any genes included in the resulting annotation.
scaffoldingDistance: The maximum length allowed between genes when contiguous regions of genes are being identified
promoterScoreCutoff: Minimum score allowed for any promoters included in the resulting annotation
queries: A list of faster files to process.
swing: If true a swing window will be used to updated the user about the pipeline's progress.
email: If this is a non-empty string an email will be sent to the address in the string when the pipeline is done. This will be attempted with the sendmail command on the local computer.
The main pipeline function. For every query genemark is used to predict genes, these genes are then extended to any preferable starts. Then the pipeline searches
for any intergenic genes(genes between those found by genemark) and these are combined with the extended genemark genes. Then the genes are pruned to remove
any undesirable genes found in the intergenic stage. BPROM and Transterm are used to find promoters and terminators, which are then pruned to remove any
signals which are inside or too far away from any genes. Next, tRNAscan is used to find any transfer RNAs in the genome. Finally, all the remaining genes,
promoters, and terminators are written to an artemis file in the directory of the query with the same name but with a .art extension, and .xml, .html, and
.xls files will be generating describing the blast results of the final genes.
"""
self.initializeDisplay(queries, swing)
try:
for query in queries:
name = os.path.splitext(query)[0]
queryDirectory, name = os.path.split(name)
genome = utils.loadGenome(query)
swapFileName = "query" + str(id(self)) + ".fas"
queryFile = open(swapFileName, "w")
queryFile.write(">" + name + "\n")
for i in range(0, len(genome), 50):
queryFile.write(genome[i:min(i+50, len(genome))] + "\n")
queryFile.close()
self.updateProgress(query)
initialGenes = genemark.findGenes(swapFileName, name, blastLocation, database, eValue, genemarkLocation, matrix, self)
self.updateProgress(query)
extendedGenes = extend.extendGenes(swapFileName, initialGenes, name, blastLocation, database, eValue, self)
self.updateProgress(query)
intergenicGenes = intergenic.findIntergenics(swapFileName, extendedGenes, name, minLength, blastLocation, database, eValue, self)
genes = {}
for k, v in extendedGenes.items() + intergenicGenes.items():
genes[k] = v
self.updateProgress(query)
scaffolded = scaffolds.refineScaffolds(genes, scaffoldingDistance)
self.updateProgress(query)
initialPromoters = promoters.findPromoters(swapFileName, name, promoterScoreCutoff, self.frame)
self.updateProgress(query)
initialTerminators = terminators.findTerminators(swapFileName, name, genes.values(), transtermLocation)
self.updateProgress(query)
filteredSignals = signals.filterSignals(scaffolded.values(), initialPromoters + initialTerminators)
filteredPromoters = filter(lambda x: isinstance(x, promoters.Promoter), filteredSignals)
filteredTerminators = filter(lambda x: isinstance(x, terminators.Terminator), filteredSignals)
self.updateProgress(query)
transferRNAs = rna.findtRNAs(tRNAscanLocation, swapFileName)
os.remove(swapFileName)
self.updateProgress(query)
artemis.writeArtemisFile(os.path.splitext(query)[0] + ".art", genome, scaffolded.values(), filteredPromoters, filteredTerminators, transferRNAs)
self.updateProgress(query)
report.report(name, scaffolded, os.path.splitext(query)[0])
if email:
if not os.path.isfile("EMAIL_MESSAGE"):
message = open("EMAIL_MESSAGE", "w")
message.write("Subject: Annotation Complete\nYour genome has been annotated.\n")
message.close()
sent = False
while not sent:
message = open("EMAIL_MESSAGE", "r")
sendmailProcess = subprocess.Popen(["/usr/sbin/sendmail", "-F", "Neofelis", "-f", "*****@*****.**", email],
stdin = message,
stdout = subprocess.PIPE)
result = ""
nextRead = sendmailProcess.stdout.read()
while nextRead:
result += nextRead
nextRead = sendmailProcess.stdout.read()
sent = not result.strip()
message.close()
self.finished()
except PipelineException:
return
class DetermineCookieFrame(JFrame):
""" This is the GUI for for the user to control the actions when
determining which cookie is the session cookie.
"""
def __init__(self, callbacks, selected_message):
super(DetermineCookieFrame, self).__init__()
self.callbacks = callbacks
self.selected_message = selected_message
self.windowClosing = self.close
def loadPanel(self):
panel = JPanel()
panel.setLayout(BoxLayout(panel, BoxLayout.Y_AXIS))
bottomButtonBarPanel = JPanel()
bottomButtonBarPanel.setLayout(BoxLayout(bottomButtonBarPanel, BoxLayout.X_AXIS))
bottomButtonBarPanel.setAlignmentX(1.0)
self.runButton = JButton("Run", actionPerformed=self.start)
self.cancelButton = JButton("Close", actionPerformed=self.cancel)
bottomButtonBarPanel.add(Box.createHorizontalGlue());
bottomButtonBarPanel.add(self.runButton)
bottomButtonBarPanel.add(self.cancelButton)
# Dimension(width,height)
bottom = JPanel()
bottom.setLayout(BoxLayout(bottom, BoxLayout.X_AXIS))
bottom.setAlignmentX(1.0)
self.progressBar = JProgressBar()
self.progressBar.setIndeterminate(False)
self.progressBar.setMaximum(100)
self.progressBar.setValue(0)
bottom.add(self.progressBar)
self.statusTextArea = JTextArea()
self.statusTextArea.setEditable(False)
scrollPane = JScrollPane(self.statusTextArea)
scrollPanel = JPanel()
scrollPanel.setLayout(BoxLayout(scrollPanel, BoxLayout.X_AXIS))
scrollPanel.setAlignmentX(1.0)
scrollPanel.add(scrollPane)
panel.add(scrollPanel)
panel.add(bottomButtonBarPanel)
panel.add(bottom)
self.add(panel)
self.setTitle("Determine Session Cookie(s)")
self.setSize(450, 300)
self.setLocationRelativeTo(None)
self.setVisible(True)
original_request_bytes = self.selected_message.getRequest()
http_service = self.selected_message.getHttpService()
helpers = self.callbacks.getHelpers()
request_info = helpers.analyzeRequest(http_service, original_request_bytes)
parameters = request_info.getParameters();
cookie_parameters = [parameter for parameter in parameters if parameter.getType() == IParameter.PARAM_COOKIE]
num_requests_needed = len(cookie_parameters) + 2
self.statusTextArea.append("This may require up to " + str(num_requests_needed) + " requests to be made. Hit 'Run' to begin.\n")
def start(self, event):
global cancelThread
cancelThread = False
self.runButton.setEnabled(False)
self.cancelButton.setText("Cancel")
thread = ThreadDetermineCookie(self.callbacks, self.selected_message, self.statusTextArea, self.progressBar)
thread.start()
def cancel(self, event):
self.setVisible(False);
self.dispose();
def close(self, event):
global cancelThread
cancelThread = True
class JythonGui(ItemListener):
def __init__(self, instructionsURI=''):
self.instructionsURI = instructionsURI
self.logger = logging.getLogger('sasi_runner_gui')
self.logger.addHandler(logging.StreamHandler())
def log_fn(msg):
self.log_msg(msg)
self.logger.addHandler(FnLogHandler(log_fn))
self.logger.setLevel(logging.DEBUG)
self.selected_input_file = None
self.selected_output_file = None
self.frame = JFrame(
"SASI Runner",
defaultCloseOperation = WindowConstants.EXIT_ON_CLOSE,
)
self.frame.size = (650, 600,)
self.main_panel = JPanel()
self.main_panel.layout = BoxLayout(self.main_panel, BoxLayout.Y_AXIS)
self.frame.add(self.main_panel)
self.top_panel = JPanel(SpringLayout())
self.top_panel.alignmentX = Component.CENTER_ALIGNMENT
self.main_panel.add(self.top_panel)
self.stageCounter = 1
def getStageLabel(txt):
label = JLabel("%s. %s" % (self.stageCounter, txt))
self.stageCounter += 1
return label
# Instructions link.
self.top_panel.add(getStageLabel("Read the instructions:"))
instructionsButton = JButton(
('<HTML><FONT color="#000099">'
'<U>open instructions</U></FONT><HTML>'),
actionPerformed=self.browseInstructions)
instructionsButton.setHorizontalAlignment(SwingConstants.LEFT);
instructionsButton.setBorderPainted(False);
instructionsButton.setOpaque(False);
instructionsButton.setBackground(Color.WHITE);
instructionsButton.setToolTipText(self.instructionsURI);
self.top_panel.add(instructionsButton)
# 'Select input' elements.
self.top_panel.add(getStageLabel(
"Select a SASI .zip file or data folder:"))
self.top_panel.add(
JButton("Select input...", actionPerformed=self.openInputChooser))
# 'Select output' elements.
self.top_panel.add(getStageLabel("Specify an output file:"))
self.top_panel.add(
JButton("Specify output...", actionPerformed=self.openOutputChooser))
# 'Set result fields' elements.
result_fields = [
{'id': 'gear_id', 'label': 'Gear', 'selected': True,
'enabled': False},
{'id': 'substrate_id', 'label': 'Substrate', 'selected': True},
{'id': 'energy_id', 'label': 'Energy', 'selected': False},
{'id': 'feature_id', 'label': 'Feature', 'selected': False},
{'id': 'feature_category_id', 'label': 'Feature Category',
'selected': False}
]
self.selected_result_fields = {}
resolutionLabelPanel = JPanel(GridLayout(0,1))
resolutionLabelPanel.add(getStageLabel("Set result resolution:"))
resolutionLabelPanel.add(
JLabel(("<html><i>This sets the specificity with which<br>"
"results will be grouped. Note that enabling<br>"
"more fields can *greatly* increase resulting<br>"
"output sizes and run times.</i>")))
#self.top_panel.add(getStageLabel("Set result resolution:"))
self.top_panel.add(resolutionLabelPanel)
checkPanel = JPanel(GridLayout(0, 1))
self.top_panel.add(checkPanel)
self.resultFieldCheckBoxes = {}
for result_field in result_fields:
self.selected_result_fields.setdefault(
result_field['id'], result_field['selected'])
checkBox = JCheckBox(
result_field['label'], result_field['selected'])
checkBox.setEnabled(result_field.get('enabled', True))
checkBox.addItemListener(self)
checkPanel.add(checkBox)
self.resultFieldCheckBoxes[checkBox] = result_field
# 'Run' elements.
self.top_panel.add(getStageLabel("Run SASI: (this might take a while)"))
self.run_button = JButton("Run...", actionPerformed=self.runSASI)
self.top_panel.add(self.run_button)
SpringUtilities.makeCompactGrid(
self.top_panel, self.stageCounter - 1, 2, 6, 6, 6, 6)
# Progress bar.
self.progressBar = JProgressBar(0, 100)
self.main_panel.add(self.progressBar)
# Log panel.
self.log_panel = JPanel()
self.log_panel.alignmentX = Component.CENTER_ALIGNMENT
self.log_panel.setBorder(EmptyBorder(10,10,10,10))
self.main_panel.add(self.log_panel)
self.log_panel.setLayout(BorderLayout())
self.log = JTextArea()
self.log.editable = False
self.logScrollPane = JScrollPane(self.log)
self.logScrollPane.setVerticalScrollBarPolicy(
JScrollPane.VERTICAL_SCROLLBAR_ALWAYS)
self.logScrollBar = self.logScrollPane.getVerticalScrollBar()
self.log_panel.add(self.logScrollPane, BorderLayout.CENTER)
# File selectors
self.inputChooser = JFileChooser()
self.inputChooser.fileSelectionMode = JFileChooser.FILES_AND_DIRECTORIES
self.outputChooser = JFileChooser()
defaultOutputFile = os.path.join(System.getProperty("user.home"),
"sasi_project.zip")
self.outputChooser.setSelectedFile(File(defaultOutputFile));
self.outputChooser.fileSelectionMode = JFileChooser.FILES_ONLY
self.frame.setLocationRelativeTo(None)
self.frame.visible = True
def browseInstructions(self, event):
""" Open a browser to the instructions page. """
browseURI(self.instructionsURI)
def itemStateChanged(self, event):
""" Listen for checkbox changes. """
checkBox = event.getItemSelectable()
is_selected = (event.getStateChange() == ItemEvent.SELECTED)
result_field = self.resultFieldCheckBoxes[checkBox]
self.selected_result_fields[result_field['id']] = is_selected
def log_msg(self, msg):
""" Print message to log and scroll to bottom. """
self.log.append(msg + "\n")
self.log.setCaretPosition(self.log.getDocument().getLength())
def openInputChooser(self, event):
ret = self.inputChooser.showOpenDialog(self.frame)
if ret == JFileChooser.APPROVE_OPTION:
self.selected_input_file = self.inputChooser.selectedFile
self.log_msg("Selected '%s' as input." % self.selected_input_file.path)
def openOutputChooser(self, event):
ret = self.outputChooser.showSaveDialog(self.frame)
if ret == JFileChooser.APPROVE_OPTION:
selectedPath = self.outputChooser.selectedFile.path
if not selectedPath.endswith('.zip'):
zipPath = selectedPath + '.zip'
self.outputChooser.setSelectedFile(File(zipPath))
self.selected_output_file = self.outputChooser.selectedFile
self.log_msg(
"Selected '%s' as output." % self.selected_output_file.path)
def runSASI(self, event):
try:
self.validateParameters()
except Exception as e:
self.log_msg("ERROR: '%s'" % e)
# Run task in a separate thread, so that log
# messages will be shown as task progresses.
def run_task():
self.tmp_dir = tempfile.mkdtemp(prefix="sasi_runner.")
self.db_file = os.path.join(self.tmp_dir, "sasi_runner.db")
self.progressBar.setValue(0)
self.progressBar.setIndeterminate(True)
def get_connection():
engine = create_engine('h2+zxjdbc:////%s' % self.db_file)
con = engine.connect()
return con
try:
# Set result fields.
result_fields = []
for field_id, is_selected in self.selected_result_fields.items():
if is_selected: result_fields.append(field_id)
task = RunSasiTask(
input_path=self.selected_input_file.path,
output_file=self.selected_output_file.path,
logger=self.logger,
get_connection=get_connection,
config={
'result_fields': result_fields,
'run_model': {
'run': {
'batch_size': 'auto',
}
},
'output': {
'batch_size': 'auto',
},
}
)
task.call()
except Exception as e:
self.logger.exception("Could not complete task")
self.progressBar.setIndeterminate(False)
self.progressBar.setValue(100)
try:
shutil.rmtree(self.tmp_dir)
except:
pass
Thread(target=run_task).start()
def validateParameters(self):
return True
def __init__(self, instructionsURI=""):
self.instructionsURI = instructionsURI
self.logger = logging.getLogger("sasi_gridder_gui")
self.logger.addHandler(logging.StreamHandler())
def log_fn(msg):
self.log_msg(msg)
self.logger.addHandler(FnLogHandler(log_fn))
self.logger.setLevel(logging.DEBUG)
self.selected_input_file = None
self.selected_output_file = None
self.frame = JFrame("SASI Gridder", defaultCloseOperation=WindowConstants.EXIT_ON_CLOSE)
self.frame.size = (650, 600)
self.main_panel = JPanel()
self.main_panel.layout = BoxLayout(self.main_panel, BoxLayout.Y_AXIS)
self.frame.add(self.main_panel)
self.top_panel = JPanel(SpringLayout())
self.top_panel.alignmentX = Component.CENTER_ALIGNMENT
self.main_panel.add(self.top_panel)
self.stageCounter = 1
def getStageLabel(txt):
label = JLabel("%s. %s" % (self.stageCounter, txt))
self.stageCounter += 1
return label
# Instructions link.
self.top_panel.add(getStageLabel("Read the instructions:"))
instructionsButton = JButton(
('<HTML><FONT color="#000099">' "<U>open instructions</U></FONT><HTML>"),
actionPerformed=self.browseInstructions,
)
instructionsButton.setHorizontalAlignment(SwingConstants.LEFT)
instructionsButton.setBorderPainted(False)
instructionsButton.setOpaque(False)
instructionsButton.setBackground(Color.WHITE)
instructionsButton.setToolTipText(self.instructionsURI)
self.top_panel.add(instructionsButton)
# Select input elements.
self.top_panel.add(getStageLabel("Select an input data folder:"))
self.top_panel.add(JButton("Select input...", actionPerformed=self.openInputChooser))
# Select output elements.
self.top_panel.add(getStageLabel("Specify an output file:"))
self.top_panel.add(JButton("Specify output...", actionPerformed=self.openOutputChooser))
# Run elements.
self.top_panel.add(getStageLabel("Run SASI Gridder: (this might take a hwile"))
self.run_button = JButton("Run...", actionPerformed=self.runSASIGridder)
self.top_panel.add(self.run_button)
SpringUtilities.makeCompactGrid(self.top_panel, self.stageCounter - 1, 2, 6, 6, 6, 6)
# Progress bar.
self.progressBar = JProgressBar(0, 100)
self.main_panel.add(self.progressBar)
# Log panel.
self.log_panel = JPanel()
self.log_panel.alignmentX = Component.CENTER_ALIGNMENT
self.log_panel.setBorder(EmptyBorder(10, 10, 10, 10))
self.main_panel.add(self.log_panel)
self.log_panel.setLayout(BorderLayout())
self.log = JTextArea()
self.log.editable = False
self.logScrollPane = JScrollPane(self.log)
self.logScrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS)
self.log_panel.add(self.logScrollPane, BorderLayout.CENTER)
# File selectors
self.inputChooser = JFileChooser()
self.inputChooser.fileSelectionMode = JFileChooser.FILES_AND_DIRECTORIES
self.outputChooser = JFileChooser()
self.outputChooser.fileSelectionMode = JFileChooser.FILES_ONLY
defaultOutputFile = os.path.join(System.getProperty("user.home"), "gridded_efforts.csv")
self.outputChooser.setSelectedFile(File(defaultOutputFile))
self.frame.setLocationRelativeTo(None)
self.frame.visible = True
class DetermineCookieFrame(JFrame):
""" This is the GUI for for the user to control the actions when
determining which cookie is the session cookie.
"""
def __init__(self, callbacks, selected_message):
super(DetermineCookieFrame, self).__init__()
self.callbacks = callbacks
self.selected_message = selected_message
self.windowClosing = self.close
def loadPanel(self):
panel = JPanel()
panel.setLayout(BoxLayout(panel, BoxLayout.Y_AXIS))
bottomButtonBarPanel = JPanel()
bottomButtonBarPanel.setLayout(
BoxLayout(bottomButtonBarPanel, BoxLayout.X_AXIS))
bottomButtonBarPanel.setAlignmentX(1.0)
self.runButton = JButton("Run", actionPerformed=self.start)
self.cancelButton = JButton("Close", actionPerformed=self.cancel)
bottomButtonBarPanel.add(Box.createHorizontalGlue())
bottomButtonBarPanel.add(self.runButton)
bottomButtonBarPanel.add(self.cancelButton)
# Dimension(width,height)
bottom = JPanel()
bottom.setLayout(BoxLayout(bottom, BoxLayout.X_AXIS))
bottom.setAlignmentX(1.0)
self.progressBar = JProgressBar()
self.progressBar.setIndeterminate(False)
self.progressBar.setMaximum(100)
self.progressBar.setValue(0)
bottom.add(self.progressBar)
self.statusTextArea = JTextArea()
self.statusTextArea.setEditable(False)
scrollPane = JScrollPane(self.statusTextArea)
scrollPanel = JPanel()
scrollPanel.setLayout(BoxLayout(scrollPanel, BoxLayout.X_AXIS))
scrollPanel.setAlignmentX(1.0)
scrollPanel.add(scrollPane)
panel.add(scrollPanel)
panel.add(bottomButtonBarPanel)
panel.add(bottom)
self.add(panel)
self.setTitle("Determine Session Cookie(s)")
self.setSize(450, 300)
self.setLocationRelativeTo(None)
self.setVisible(True)
original_request_bytes = self.selected_message.getRequest()
http_service = self.selected_message.getHttpService()
helpers = self.callbacks.getHelpers()
request_info = helpers.analyzeRequest(http_service,
original_request_bytes)
parameters = request_info.getParameters()
cookie_parameters = [
parameter for parameter in parameters
if parameter.getType() == IParameter.PARAM_COOKIE
]
num_requests_needed = len(cookie_parameters) + 2
self.statusTextArea.append(
"This may require up to " + str(num_requests_needed) +
" requests to be made. Hit 'Run' to begin.\n")
def start(self, event):
global cancelThread
cancelThread = False
self.runButton.setEnabled(False)
self.cancelButton.setText("Cancel")
thread = ThreadDetermineCookie(self.callbacks, self.selected_message,
self.statusTextArea, self.progressBar)
thread.start()
def cancel(self, event):
self.setVisible(False)
self.dispose()
def close(self, event):
global cancelThread
cancelThread = True
class ToolsProgressDialog(JDialog, PropertyChangeListener):
def __init__(self, parent, title, modal, app):
"""Restore the tools data by:
- downloading the tools list
- downloading the tools jar files
- extracting the tools data from jar files
"""
self.app = app
border = BorderFactory.createEmptyBorder(5, 7, 5, 7)
mainPane = self.getContentPane()
mainPane.setLayout(BorderLayout(5, 5))
mainPane.setBorder(border)
self.setPreferredSize(Dimension(400, 200))
self.taskOutput = JMultilineLabel(
self.app.strings.getString("checking_for_updates"))
self.taskOutput.setMaxWidth(350)
self.progressBar = JProgressBar(0, 100, value=0, stringPainted=True)
self.progressBar.setIndeterminate(True)
self.cancelBtn = JButton("Cancel",
actionPerformed=self.on_cancelBtn_clicked,
enabled=True)
self.okBtn = JButton("Ok",
actionPerformed=self.on_okBtn_clicked,
enabled=False)
mainPane.add(self.taskOutput, BorderLayout.CENTER)
bottomPanel = JPanel(BorderLayout(5, 5))
bottomPanel.add(self.progressBar, BorderLayout.PAGE_START)
buttonsPanel = JPanel()
buttonsPanel.add(self.okBtn)
buttonsPanel.add(self.cancelBtn)
bottomPanel.add(buttonsPanel, BorderLayout.PAGE_END)
mainPane.add(bottomPanel, BorderLayout.PAGE_END)
self.pack()
self.task = DownloaderTask(self)
self.task.addPropertyChangeListener(self)
self.task.execute()
def propertyChange(self, e):
# Invoked when task's progress property changes.
if e.propertyName == "progress":
if e.newValue == 2:
text = self.app.strings.getString("downloading_tools_list")
elif e.newValue == 3:
text = self.app.strings.getString(
"tools_not_downloaded_warning")
elif e.newValue == 5:
text = self.app.strings.getString("downloading_tools_data")
elif e.newValue == 6:
text = self.app.strings.getString(
"i_cannot_download_the_tool_files")
elif e.newValue == 7:
text = self.app.strings.getString("extracting_jar_files")
elif e.newValue == 8:
text = self.app.strings.getString("tools_updated")
self.taskOutput.setText("<html>" + text + "</html>")
def on_cancelBtn_clicked(self, e):
self.dispose()
self.task.cancel(True)
def on_okBtn_clicked(self, e):
self.dispose()
lbl2.setBounds(40,50,200,20)
f2_btn_label = JButton("Browse", actionPerformed = f2_clic_browse2)
f2_btn_label.setBounds(170,50,100,20)
f2_txt2 = JTextField(10)
f2_txt2.setBounds(280, 50, 120,20)
# Button Previous
f2_btn_prev = JButton("Previous", actionPerformed = f2_clic_prev)
f2_btn_prev.setBounds(40,120,100,20)
# Button Next
f2_btn_next = JButton("Next", actionPerformed = f2_clic_next)
f2_btn_next.setBounds(300,120,100,20)
# Progress Bar
progressBar = JProgressBar(0, 100, value=0, stringPainted=True)
progressBar.setBounds(40,85,360,20)
frame2.add(lbl1)
frame2.add(f2_btn_original)
frame2.add(f2_txt1)
frame2.add(lbl2)
frame2.add(f2_btn_label)
frame2.add(f2_txt2)
frame2.add(f2_btn_prev)
frame2.add(f2_btn_next)
frame2.add(progressBar)
def drawPluginUI(self):
# Create the plugin user interface
self.pluginTab = JPanel()
self.uiTitle = JLabel('UPnP BHunter Load, Aim and Fire Console')
self.uiTitle.setFont(Font('Tahoma', Font.BOLD, 14))
self.uiTitle.setForeground(Color(250, 100, 0))
self.uiPanelA = JSplitPane(JSplitPane.VERTICAL_SPLIT)
self.uiPanelA.setMaximumSize(Dimension(2500, 1000))
self.uiPanelA.setDividerSize(2)
self.uiPanelB = JSplitPane(JSplitPane.VERTICAL_SPLIT)
self.uiPanelB.setDividerSize(2)
self.uiPanelA.setBottomComponent(self.uiPanelB)
self.uiPanelA.setBorder(BorderFactory.createLineBorder(Color.gray))
# Create and configure labels and text fields
self.labeltitle_step1 = JLabel("[1st STEP] Discover UPnP Locations")
self.labeltitle_step1.setFont(Font('Tahoma', Font.BOLD, 14))
self.labeltitle_step2 = JLabel("[2nd STEP] Select an UPnP Service")
self.labeltitle_step2.setFont(Font('Tahoma', Font.BOLD, 14))
self.labeltitle_step3 = JLabel("[3rd STEP] Time to Attack it")
self.labeltitle_step3.setFont(Font('Tahoma', Font.BOLD, 14))
self.labelsubtitle_step1 = JLabel(
"Specify the IP version address in scope and start UPnP discovery")
self.labelsubtitle_step2 = JLabel(
"Select which of the found UPnP services will be probed")
self.labelsubtitle_step3 = JLabel(
"Select how to test the extracted UPnP SOAP requests having input arguments"
)
self.label_step1 = JLabel("Target IP")
self.label_step2 = JLabel("Found UPnp Services")
self.label_step3 = JLabel("Send all the extracted SOAP requests ")
self.labelstatus = JLabel(" Status")
self.labelempty_step1 = JLabel(" ")
self.labelempty_step2 = JLabel(" ")
self.labelupnp = JLabel("UPnP list")
self.labelip = JLabel("IP list")
self.labelLANHOST = JLabel(
"Send the interesting LANHostConfigManagement SOAP requests ")
self.labelWANCONNECTION = JLabel(
"Send the interesting WANIP/PPPConnection SOAP requests ")
self.labelSOAPnum = JLabel("0")
self.labelLANHOSTnum = JLabel("0")
self.labelWANCONNECTIONnum = JLabel("0")
self.labelNoneServiceFound = JLabel(" ")
self.labelNoneServiceFound.setFont(Font('Tahoma', Font.BOLD, 12))
self.labelNoneServiceFound.setForeground(Color.red)
# Create combobox for IP version selection
self.ip_versions = ["IPv4", "IPv6"]
self.combo_ipversion = JComboBox(self.ip_versions)
self.combo_ipversion.setSelectedIndex(0)
self.combo_ipversion.setEnabled(True)
# Create and configure progress bar
self.progressbar = JProgressBar(0, 100)
self.progressbar.setString("Ready")
self.progressbar.setStringPainted(True)
# Create and configure buttons
self.startbutton = JButton("Start Discovery",
actionPerformed=self.startHunting)
self.clearbutton = JButton("Clear All", actionPerformed=self.clearAll)
self.confirmbutton = JButton("Confirm Selection",
actionPerformed=self.selectUPnPService)
self.intruderbutton = JButton("to Intruder",
actionPerformed=self.sendUPnPToIntruder)
self.LANrepeaterbutton = JButton(
"to Repeater", actionPerformed=self.sendLANUPnPToRepeater)
self.WANrepeaterbutton = JButton(
"to Repeater", actionPerformed=self.sendWANUPnPToRepeater)
self.confirmbutton.setEnabled(False)
self.intruderbutton.setEnabled(False)
self.LANrepeaterbutton.setEnabled(False)
self.WANrepeaterbutton.setEnabled(False)
# Create the combo box, select item at index 0 (first item in list)
self.upnpservices = [" "]
self.upnpcombo_services = JComboBox(self.upnpservices)
self.upnpcombo_services.setSelectedIndex(0)
self.upnpcombo_services.setEnabled(False)
# Class neeeded to handle the combobox in second step panel
class ComboboxListener(ActionListener):
def __init__(self, upnpcombo_targets, upnpcombo_services,
scope_dict):
self.upnpcombo_targets = upnpcombo_targets
self.upnpcombo_services = upnpcombo_services
self.scope_dict = scope_dict
def actionPerformed(self, event):
# Update the location url combobox depending on the IP combobox
selected_target = self.upnpcombo_targets.getSelectedItem()
if self.scope_dict and selected_target:
self.upnpcombo_services.removeAllItems()
for scope_url in self.scope_dict[selected_target]:
self.upnpcombo_services.addItem(scope_url)
self.upnpcombo_services.setSelectedIndex(0)
# Create the combo box, select item at index 0 (first item in list)
self.upnptargets = [" "]
self.upnpcombo_targets = JComboBox(self.upnptargets)
self.upnpcombo_targets.setSelectedIndex(0)
self.upnpcombo_targets.setEnabled(False)
self.upnpcombo_targets.addActionListener(
ComboboxListener(self.upnpcombo_targets, self.upnpcombo_services,
self.scope_dict))
# Configuring first step panel
self.panel_step1 = JPanel()
self.panel_step1.setPreferredSize(Dimension(2250, 100))
self.panel_step1.setBorder(EmptyBorder(10, 10, 10, 10))
self.panel_step1.setLayout(BorderLayout(15, 15))
self.titlepanel_step1 = JPanel()
self.titlepanel_step1.setLayout(BorderLayout())
self.titlepanel_step1.add(self.labeltitle_step1, BorderLayout.NORTH)
self.titlepanel_step1.add(self.labelsubtitle_step1)
self.targetpanel_step1 = JPanel()
self.targetpanel_step1.add(self.label_step1)
self.targetpanel_step1.add(self.combo_ipversion)
self.targetpanel_step1.add(self.startbutton)
self.targetpanel_step1.add(self.clearbutton)
self.targetpanel_step1.add(self.labelstatus)
self.targetpanel_step1.add(self.progressbar)
self.emptypanel_step1 = JPanel()
self.emptypanel_step1.setLayout(BorderLayout())
self.emptypanel_step1.add(self.labelempty_step1, BorderLayout.WEST)
# Assembling first step panel components
self.panel_step1.add(self.titlepanel_step1, BorderLayout.NORTH)
self.panel_step1.add(self.targetpanel_step1, BorderLayout.WEST)
self.panel_step1.add(self.emptypanel_step1, BorderLayout.SOUTH)
self.uiPanelA.setTopComponent(self.panel_step1)
# Configure second step panel
self.panel_step2 = JPanel()
self.panel_step2.setPreferredSize(Dimension(2250, 100))
self.panel_step2.setBorder(EmptyBorder(10, 10, 10, 10))
self.panel_step2.setLayout(BorderLayout(15, 15))
self.titlepanel_step2 = JPanel()
self.titlepanel_step2.setLayout(BorderLayout())
self.titlepanel_step2.add(self.labeltitle_step2, BorderLayout.NORTH)
self.titlepanel_step2.add(self.labelsubtitle_step2)
self.selectpanel_step2 = JPanel()
self.selectpanel_step2.add(self.labelip)
self.selectpanel_step2.add(self.upnpcombo_targets)
self.selectpanel_step2.add(self.labelupnp)
self.selectpanel_step2.add(self.upnpcombo_services)
self.selectpanel_step2.add(self.confirmbutton)
self.emptypanel_step2 = JPanel()
self.emptypanel_step2.setLayout(BorderLayout())
self.emptypanel_step2.add(self.labelempty_step2, BorderLayout.WEST)
self.emptypanel_step2.add(self.labelNoneServiceFound)
# Assembling second step panel components
self.panel_step2.add(self.titlepanel_step2, BorderLayout.NORTH)
self.panel_step2.add(self.selectpanel_step2, BorderLayout.WEST)
self.panel_step2.add(self.emptypanel_step2, BorderLayout.SOUTH)
self.uiPanelB.setTopComponent(self.panel_step2)
# Configuring third step panel
self.panel_step3 = JPanel()
self.panel_step3.setPreferredSize(Dimension(2250, 100))
self.panel_step3.setBorder(EmptyBorder(10, 10, 10, 10))
self.panel_step3.setLayout(BorderLayout(15, 15))
self.titlepanel_step3 = JPanel()
self.titlepanel_step3.setLayout(BorderLayout())
self.titlepanel_step3.add(self.labeltitle_step3, BorderLayout.NORTH)
self.titlepanel_step3.add(self.labelsubtitle_step3)
self.underpanel_step3 = JPanel()
underlayout = GroupLayout(self.underpanel_step3)
self.underpanel_step3.setLayout(underlayout)
underlayout.setAutoCreateGaps(True)
underlayout.setAutoCreateContainerGaps(True)
left2right = underlayout.createSequentialGroup()
firstcolumn = underlayout.createParallelGroup()
firstcolumn.addComponent(self.label_step3, GroupLayout.PREFERRED_SIZE,
GroupLayout.PREFERRED_SIZE,
GroupLayout.PREFERRED_SIZE)
firstcolumn.addComponent(self.labelLANHOST, GroupLayout.PREFERRED_SIZE,
GroupLayout.PREFERRED_SIZE,
GroupLayout.PREFERRED_SIZE)
firstcolumn.addComponent(self.labelWANCONNECTION,
GroupLayout.PREFERRED_SIZE,
GroupLayout.PREFERRED_SIZE,
GroupLayout.PREFERRED_SIZE)
secondcolumn = underlayout.createParallelGroup()
secondcolumn.addComponent(self.labelSOAPnum)
secondcolumn.addComponent(self.labelLANHOSTnum)
secondcolumn.addComponent(self.labelWANCONNECTIONnum)
thirdcolumn = underlayout.createParallelGroup()
thirdcolumn.addComponent(self.intruderbutton)
thirdcolumn.addComponent(self.LANrepeaterbutton)
thirdcolumn.addComponent(self.WANrepeaterbutton)
left2right.addGroup(firstcolumn)
left2right.addGroup(secondcolumn)
left2right.addGroup(thirdcolumn)
top2bottom = underlayout.createSequentialGroup()
firstrow = underlayout.createParallelGroup()
firstrow.addComponent(self.label_step3, GroupLayout.PREFERRED_SIZE,
GroupLayout.PREFERRED_SIZE,
GroupLayout.PREFERRED_SIZE)
firstrow.addComponent(self.labelSOAPnum)
firstrow.addComponent(self.intruderbutton)
secondrow = underlayout.createParallelGroup()
secondrow.addComponent(self.labelLANHOST, GroupLayout.PREFERRED_SIZE,
GroupLayout.PREFERRED_SIZE,
GroupLayout.PREFERRED_SIZE)
secondrow.addComponent(self.labelLANHOSTnum)
secondrow.addComponent(self.LANrepeaterbutton)
thirdrow = underlayout.createParallelGroup()
thirdrow.addComponent(self.labelWANCONNECTION,
GroupLayout.PREFERRED_SIZE,
GroupLayout.PREFERRED_SIZE,
GroupLayout.PREFERRED_SIZE)
thirdrow.addComponent(self.labelWANCONNECTIONnum)
thirdrow.addComponent(self.WANrepeaterbutton)
top2bottom.addGroup(firstrow)
top2bottom.addGroup(secondrow)
top2bottom.addGroup(thirdrow)
underlayout.setHorizontalGroup(left2right)
underlayout.setVerticalGroup(top2bottom)
# Assembling thirdd step panel components
self.panel_step3.add(self.titlepanel_step3, BorderLayout.NORTH)
self.panel_step3.add(self.underpanel_step3, BorderLayout.WEST)
self.uiPanelB.setBottomComponent(self.panel_step3)
# Assembling the group of all panels
layout = GroupLayout(self.pluginTab)
self.pluginTab.setLayout(layout)
layout.setHorizontalGroup(
layout.createParallelGroup(GroupLayout.Alignment.LEADING).addGroup(
layout.createSequentialGroup().addGap(10, 10, 10).addGroup(
layout.createParallelGroup(
GroupLayout.Alignment.LEADING).addComponent(
self.uiTitle).addGap(15, 15, 15).addComponent(
self.uiPanelA)).addContainerGap(
26, Short.MAX_VALUE)))
layout.setVerticalGroup(
layout.createParallelGroup(GroupLayout.Alignment.LEADING).addGroup(
layout.createSequentialGroup().addGap(15, 15, 15).addComponent(
self.uiTitle).addGap(15, 15, 15).addComponent(
self.uiPanelA).addGap(20, 20, 20).addGap(20, 20, 20)))
class JythonGui(object):
def __init__(self, instructionsURI=""):
self.instructionsURI = instructionsURI
self.logger = logging.getLogger("sasi_gridder_gui")
self.logger.addHandler(logging.StreamHandler())
def log_fn(msg):
self.log_msg(msg)
self.logger.addHandler(FnLogHandler(log_fn))
self.logger.setLevel(logging.DEBUG)
self.selected_input_file = None
self.selected_output_file = None
self.frame = JFrame("SASI Gridder", defaultCloseOperation=WindowConstants.EXIT_ON_CLOSE)
self.frame.size = (650, 600)
self.main_panel = JPanel()
self.main_panel.layout = BoxLayout(self.main_panel, BoxLayout.Y_AXIS)
self.frame.add(self.main_panel)
self.top_panel = JPanel(SpringLayout())
self.top_panel.alignmentX = Component.CENTER_ALIGNMENT
self.main_panel.add(self.top_panel)
self.stageCounter = 1
def getStageLabel(txt):
label = JLabel("%s. %s" % (self.stageCounter, txt))
self.stageCounter += 1
return label
# Instructions link.
self.top_panel.add(getStageLabel("Read the instructions:"))
instructionsButton = JButton(
('<HTML><FONT color="#000099">' "<U>open instructions</U></FONT><HTML>"),
actionPerformed=self.browseInstructions,
)
instructionsButton.setHorizontalAlignment(SwingConstants.LEFT)
instructionsButton.setBorderPainted(False)
instructionsButton.setOpaque(False)
instructionsButton.setBackground(Color.WHITE)
instructionsButton.setToolTipText(self.instructionsURI)
self.top_panel.add(instructionsButton)
# Select input elements.
self.top_panel.add(getStageLabel("Select an input data folder:"))
self.top_panel.add(JButton("Select input...", actionPerformed=self.openInputChooser))
# Select output elements.
self.top_panel.add(getStageLabel("Specify an output file:"))
self.top_panel.add(JButton("Specify output...", actionPerformed=self.openOutputChooser))
# Run elements.
self.top_panel.add(getStageLabel("Run SASI Gridder: (this might take a hwile"))
self.run_button = JButton("Run...", actionPerformed=self.runSASIGridder)
self.top_panel.add(self.run_button)
SpringUtilities.makeCompactGrid(self.top_panel, self.stageCounter - 1, 2, 6, 6, 6, 6)
# Progress bar.
self.progressBar = JProgressBar(0, 100)
self.main_panel.add(self.progressBar)
# Log panel.
self.log_panel = JPanel()
self.log_panel.alignmentX = Component.CENTER_ALIGNMENT
self.log_panel.setBorder(EmptyBorder(10, 10, 10, 10))
self.main_panel.add(self.log_panel)
self.log_panel.setLayout(BorderLayout())
self.log = JTextArea()
self.log.editable = False
self.logScrollPane = JScrollPane(self.log)
self.logScrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS)
self.log_panel.add(self.logScrollPane, BorderLayout.CENTER)
# File selectors
self.inputChooser = JFileChooser()
self.inputChooser.fileSelectionMode = JFileChooser.FILES_AND_DIRECTORIES
self.outputChooser = JFileChooser()
self.outputChooser.fileSelectionMode = JFileChooser.FILES_ONLY
defaultOutputFile = os.path.join(System.getProperty("user.home"), "gridded_efforts.csv")
self.outputChooser.setSelectedFile(File(defaultOutputFile))
self.frame.setLocationRelativeTo(None)
self.frame.visible = True
def browseInstructions(self, event):
""" Open a browser to the instructions page. """
browseURI(self.instructionsURI)
return
def log_msg(self, msg):
self.log.append(msg + "\n")
self.log.setCaretPosition(self.log.getDocument().getLength())
def openInputChooser(self, event):
ret = self.inputChooser.showOpenDialog(self.frame)
if ret == JFileChooser.APPROVE_OPTION:
self.selected_input_file = self.inputChooser.selectedFile
self.log_msg("Selected '%s' as input." % self.selected_input_file.path)
def openOutputChooser(self, event):
ret = self.outputChooser.showSaveDialog(self.frame)
if ret == JFileChooser.APPROVE_OPTION:
self.selected_output_file = self.outputChooser.selectedFile
self.log_msg("Selected '%s' as output." % self.selected_output_file.path)
def runSASIGridder(self, event):
try:
self.validateParameters()
except Exception as e:
self.log_msg("ERROR: '%s'" % e)
# Run task in a separate thread, so that log
# messages will be shown as task progresses.
def run_task():
self.progressBar.setValue(0)
self.progressBar.setIndeterminate(True)
try:
input_dir = self.selected_input_file.path
output_path = self.selected_output_file.path
grid_path = os.path.join(input_dir, "grid", "grid.shp")
stat_areas_path = os.path.join(input_dir, "stat_areas", "stat_areas.shp")
raw_efforts_path = os.path.join(input_dir, "raw_efforts.csv")
gear_mappings_path = os.path.join(input_dir, "gear_mappings.csv")
gear_mappings = {}
with open(gear_mappings_path, "rb") as f:
r = csv.DictReader(f)
for mapping in r:
gear_mappings[mapping["trip_type"]] = mapping["gear_code"]
task = SASIGridderTask(
grid_path=grid_path,
raw_efforts_path=raw_efforts_path,
stat_areas_path=stat_areas_path,
output_path=output_path,
logger=self.logger,
gear_mappings=gear_mappings,
effort_limit=None,
)
task.call()
except Exception as e:
self.logger.exception("Could not complete task")
self.progressBar.setIndeterminate(False)
self.progressBar.setValue(100)
Thread(target=run_task).start()
def validateParameters(self):
return True
def main():
all_files = currentSelectedItems
total = len(all_files)
jprog = JProgressBar(0, total)
jprog.setStringPainted(True)
jframe.getContentPane().add(jprog)
jframe.getContentPane().add(jbutton)
jframe.setVisible(True)
try:
statusLabel.setText("Selected " + str(total) + " items")
discovered = 0
for idx, item in enumerate(all_files):
if cancelled:
return "User cancelled"
jprog.setValue(idx)
statusLabel.setText("Processing %d of %d" % (idx, total))
md5 = item.digests.md5
# Item needs an md5 to check against, so move on if there isn't one
if not md5:
continue
response = send_request(md5)
if not response:
return
cm = item.getCustomMetadata()
if response == "404":
cm.putText("VirusTotal", "Item md5 not matched in database")
else:
data = json.load(response)
malicious = data["data"]["attributes"]["last_analysis_stats"]["malicious"]
if malicious > 0:
discovered += 1
cm.putInteger("AVs identifying item as malicious", malicious)
for scanner, res in data["data"]["attributes"]["last_analysis_results"].iteritems():
if res["result"] is not None:
cm.putText("VirusTotal " + scanner, res["result"])
# vHash
if SET_VHASH and ("vhash" in data["data"]["attributes"]):
cm.putText("vHash", data["data"]["attributes"]["vhash"])
# Import Hash
if SET_IMPHASH and ("pe_info" in data["data"]["attributes"]) and \
("imphash" in data["data"]["attributes"]["pe_info"]):
cm.putText("Import Hash", data["data"]["attributes"]["pe_info"]["imphash"])
# Authentihash
if SET_AUTHENTIHASH and ("authentihash" in data["data"]["attributes"]):
cm.putText("Authentihash", data["data"]["attributes"]["authentihash"])
# Crowd sourced yara results
if SET_YARA and ("crowdsourced_yara_results" in data["data"]["attributes"]):
yara_matches = []
for yara in data["data"]["attributes"]["crowdsourced_yara_results"]:
yara_matches += [yara["rule_name"]]
cm.putText("Matched Yara Rules", ", ".join(yara_matches))
# Virus Total defined tags. Often this can be a list that needs to be looped through
if SET_TAGS and ("tags" in data["data"]["attributes"]):
for tag in data["data"]["attributes"]["tags"]:
item.addTag("VirusTotal|" + tag)
time.sleep(SLEEP_TIME)
jprog.setValue(total)
statusLabel.setText("Done")
return "VirusTotal Search has finished. %d potentially malicious items found from the %d selected." % (discovered, total)
except Exception:
import traceback
print('generic exception: ' + traceback.format_exc())
return
class Pipeline():
def __init__(self):
#If a swing interface is asked for this will be the JFrame.
self.frame = None
#Keeps track of the number of queries processed.
self.jobCount = 0
#Keeps track of the query currently being processed.
self.currentJob = ""
#Keeps track of the massage to be displayed.
self.message = 0
#Messages to be displayed at each stage in the processing of a single query.
self.messages = [
"Searching for genes via genemark",
"Extending genes found via genemark",
"Searching for intergenic genes", "Removing overlapping genes",
"Searching for promoters", "Using transterm to find terminators",
"Removing transcription signals which conflict with genes",
"Writing Artemis file", "Writing summary file"
]
self.exception = None
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 updateProgress(self, job):
"""
query: Name of the query currently being processed.
This function use used for updating the progress shown in the interface. If job is not equal to currentJob then
global progress is incremented and shown and the currentProgress is reset and shown. If job is equal to currentJob
then the globalProgress does not change and currentProgress is incremented.
"""
if self.exception:
raise self.exception
if self.frame:
if job != self.currentJob:
self.currentProgress.setValue(
self.currentProgress.getMaximum())
self.globalLabel.setText(job)
self.globalProgress.setValue(self.jobCount)
print "Processing %s, %.2f%% done" % (
job, 100.0 * self.jobCount / self.numJobs)
self.jobCount += 1
self.currentJob = job
self.message = -1
self.message += 1
print " %s, %.2f%% done" % (self.messages[self.message], 100.0 *
self.message / len(self.messages))
self.currentProgress.setValue(self.message)
self.currentLabel.setText(self.messages[self.message])
else:
if job != self.currentJob:
print "Processing %s, %.2f%% done" % (
job, 100.0 * self.jobCount / self.numJobs)
self.jobCount += 1
self.currentJob = job
self.message = -1
self.message += 1
print " %s, %.2f%% done" % (self.messages[self.message], 100.0 *
self.message / len(self.messages))
def finished(self):
"""
This function is to be called at the end of the pipeline. Informs the user that the pipeline is finished
and if a swing interface is being used the Done button is enabled.
"""
print "Processing 100.00% done"
if self.frame:
self.globalLabel.setText("Finished")
self.globalProgress.setValue(self.globalProgress.getMaximum())
self.currentLabel.setText(" ")
self.currentProgress.setValue(self.currentProgress.getMaximum())
self.doneButton.setEnabled(True)
while self.frame.isVisible():
pass
def run(self,
blastLocation,
genemarkLocation,
transtermLocation,
database,
eValue,
matrix,
minLength,
scaffoldingDistance,
ldfCutoff,
queries,
swing=False,
email=""):
"""
blastLocation: Directory blast was installed in.
genemarkLocation: Directory genemark was installed in.
transtermLocation: Directory transterm was installed in.
database: Name of the blast database to use.
eValue: The e value used whenever a blast search is done.
matrix: The matrix to use when running genemark. If None then genemark is run heuristically.
minLength: Minimum length of any genes included in the resulting annotation.
scaffoldingDistance: The maximum length allowed between genes when contiguous regions of genes are being identified
ldfCutoff: Minimum LDF allowed for any promoters included in the resulting annotation
queries: A list of faster files to process.
swing: If true a swing window will be used to updated the user about the pipeline's progress.
email: If this is a non-empty string an email will be sent to the address in the string when the pipeline is done. The local machine will be used as
an SMTP server and this will not work if it isn't.
The main pipeline function. For every query genemark is used to predict genes, these genes are then extended to any preferable starts. Then the pipeline searches
for any intergenic genes(genes between those found by genemark) and these are combined with the extended genemark genes. Then the genes are pruned to remove
any undesirable genes found in the intergenic stage. BPROM and Transterm are used to find promoters and terminators, which are then pruned to remove any
signals which are inside or too far away from any genes. Finally, all the remaining genes, promoters, and terminators ar written to an artemis file in the directory
of the query with the same name but with a .art extension, and .dat and .xls files will be generating describing the blast results of the final genes.
"""
self.initializeDisplay(queries, swing)
try:
for query in queries:
name = os.path.splitext(query)[0]
queryDirectory, name = os.path.split(name)
genome = utils.loadGenome(query)
swapFileName = "query" + str(id(self)) + ".fas"
queryFile = open(swapFileName, "w")
queryFile.write(">" + name + "\n")
for i in range(0, len(genome), 50):
queryFile.write(genome[i:min(i + 50, len(genome))] + "\n")
queryFile.close()
self.updateProgress(query)
initialGenes = genemark.findGenes(swapFileName, name,
blastLocation, database,
eValue, genemarkLocation,
matrix, self)
#artemis.writeArtemisFile(os.path.splitext(query)[0] + ".genemark.art", genome, initialGenes.values())
self.updateProgress(query)
extendedGenes = extend.extendGenes(swapFileName, initialGenes,
name, blastLocation,
database, eValue, self)
#artemis.writeArtemisFile(os.path.splitext(query)[0] + ".extended.art", genome, extendedGenes.values())
self.updateProgress(query)
intergenicGenes = intergenic.findIntergenics(
swapFileName, extendedGenes, name, minLength,
blastLocation, database, eValue, self)
#artemis.writeArtemisFile(os.path.splitext(query)[0] + ".intergenic.art", genome, intergenicGenes.values())
genes = {}
for k, v in extendedGenes.items() + intergenicGenes.items():
genes[k] = v
self.updateProgress(query)
scaffolded = scaffolds.refineScaffolds(genes,
scaffoldingDistance)
self.updateProgress(query)
initialPromoters = promoters.findPromoters(swapFileName, name)
self.updateProgress(query)
initialTerminators = terminators.findTerminators(
swapFileName, name, genes.values(), transtermLocation)
self.updateProgress(query)
filteredSignals = signals.filterSignals(
scaffolded.values(), initialPromoters + initialTerminators)
filteredPromoters = filter(
lambda x: isinstance(x, promoters.Promoter),
filteredSignals)
filteredTerminators = filter(
lambda x: isinstance(x, terminators.Terminator),
filteredSignals)
self.updateProgress(query)
artemis.writeArtemisFile(
os.path.splitext(query)[0] + ".art", genome,
scaffolded.values(), filteredPromoters,
filteredTerminators)
self.updateProgress(query)
report.report(name, scaffolded, os.path.splitext(query)[0])
if email:
message = MIMEText("Your genome has been annotated.")
message["Subject"] = "Annotation complete"
message["From"] = "Neofelis"
message["To"] = email
smtp = smtplib.SMTP("tmpl.arizona.edu", 587)
smtp.ehlo()
smtp.starttls()
smtp.ehlo
smtp.sendmail("Neofelis", [email], message.as_string())
smtp.close()
self.finished()
except PipelineException:
return
class Gui(JFrame):
'''
classdocs
'''
def __init__(self, pP):
'''
Constructor
'''
self.pP = pP
self.annotationType = self.pP.getAnnotationType()
self.setTitle("Random Picture Picker")
#annotation Panel
annoPanel = JPanel()
annoPanel.setBorder(BorderFactory.createTitledBorder("Annotations"))
annoPLayout = GroupLayout(annoPanel)
annoPanel.setLayout(annoPLayout)
annoPLayout.setAutoCreateContainerGaps(True)
annoPLayout.setAutoCreateGaps(True)
# dynamic creation of annotation panel
# yesNoIgnore, int, number, list
if len(self.pP.getAnnotationType()) == 1:
self.annoField = JTextField("", 16)
annoPLayout.setHorizontalGroup(annoPLayout.createParallelGroup().addComponent(self.annoField))
annoPLayout.setVerticalGroup(annoPLayout.createSequentialGroup().addComponent(self.annoField))
elif len(self.pP.getAnnotationType()) > 1:
choices = pP.getAnnotationType()
print "choices", choices
choiceBtns = []
self.annoField = ButtonGroup()
for c in choices:
Btn = JRadioButton(c, actionCommand=c)
self.annoField.add(Btn)
choiceBtns.append(Btn)
h = annoPLayout.createParallelGroup()
for b in choiceBtns:
h.addComponent(b)
annoPLayout.setHorizontalGroup(h)
v = annoPLayout.createSequentialGroup()
for b in choiceBtns:
v.addComponent(b)
annoPLayout.setVerticalGroup(v)
# Control Panel
ctrlPanel = JPanel()
ctrlPLayout = GroupLayout(ctrlPanel, autoCreateContainerGaps=True, autoCreateGaps=True)
ctrlPanel.setLayout(ctrlPLayout)
nextImgButton = JButton("Next >", actionPerformed=self.nextPicture)
prevImgButton = JButton("< Prev", actionPerformed=self.pP.prevPicture)
quitButton = JButton("Quit", actionPerformed=self.exit)
ctrlPLayout.setHorizontalGroup(ctrlPLayout.createParallelGroup(GroupLayout.Alignment.CENTER)
.addGroup(ctrlPLayout.createSequentialGroup()
.addComponent(prevImgButton)
.addComponent(nextImgButton))
.addComponent(quitButton))
ctrlPLayout.setVerticalGroup(ctrlPLayout.createSequentialGroup()
.addGroup(ctrlPLayout.createParallelGroup()
.addComponent(prevImgButton)
.addComponent(nextImgButton))
.addComponent(quitButton))
ctrlPLayout.linkSize(SwingConstants.HORIZONTAL, quitButton)
statusPanel = JPanel() # contains status information: progress bar
self.progressBar = JProgressBar()
self.progressBar.setStringPainted(True)
self.progressBar.setValue(0)
statusPanel.add(self.progressBar)
#MainLayout
mainLayout = GroupLayout(self.getContentPane())
self.getContentPane().setLayout(mainLayout)
mainLayout.setHorizontalGroup(mainLayout.createParallelGroup(GroupLayout.Alignment.CENTER)
.addComponent(annoPanel)
.addComponent(ctrlPanel)
.addComponent(statusPanel)
)
mainLayout.setVerticalGroup(mainLayout.createSequentialGroup()
.addComponent(annoPanel)
.addComponent(ctrlPanel)
.addComponent(statusPanel)
)
mainLayout.linkSize(SwingConstants.HORIZONTAL, annoPanel, ctrlPanel, statusPanel)
self.pack()
self.setVisible(True)
self.pP.nextPicture()
def nextPicture(self, event):
percent = (float(len(self.pP.usedList))/len(self.pP.pictureList))*100
self.progressBar.setValue(int(percent))
self.setAnnotation()
self.pP.nextPicture()
#try:
# self.setAnnotation()
# self.pP.nextPicture()
#except AttributeError:
# print "Please choose something!"
def setAnnotationField(self, a):
if len(self.pP.getAnnotationType()) > 1:
[Rbutton.setSelected(True) for Rbutton in self.annoField.getElements() if Rbutton.getActionCommand()==a]
if len(self.pP.getAnnotationType()) == 1:
self.annoField.setText(a)
#rename this method to something clearer!
def setAnnotation(self):
if len(self.pP.getAnnotationType()) > 1:
annotation = self.annoField.getSelection().getActionCommand()
if len(self.pP.getAnnotationType()) == 1:
annotation = self.annoField.getText()
self.annoField.setText(None)
self.pP.getCurrentPicture().annotate(annotation)
def getAnnotation(self):
return self.annotation
def exit(self, event):
self.pP.exit()
self.dispose()
def __init__(self, instructionsURI=''):
self.instructionsURI = instructionsURI
self.logger = logging.getLogger('sasi_runner_gui')
self.logger.addHandler(logging.StreamHandler())
def log_fn(msg):
self.log_msg(msg)
self.logger.addHandler(FnLogHandler(log_fn))
self.logger.setLevel(logging.DEBUG)
self.selected_input_file = None
self.selected_output_file = None
self.frame = JFrame(
"SASI Runner",
defaultCloseOperation = WindowConstants.EXIT_ON_CLOSE,
)
self.frame.size = (650, 600,)
self.main_panel = JPanel()
self.main_panel.layout = BoxLayout(self.main_panel, BoxLayout.Y_AXIS)
self.frame.add(self.main_panel)
self.top_panel = JPanel(SpringLayout())
self.top_panel.alignmentX = Component.CENTER_ALIGNMENT
self.main_panel.add(self.top_panel)
self.stageCounter = 1
def getStageLabel(txt):
label = JLabel("%s. %s" % (self.stageCounter, txt))
self.stageCounter += 1
return label
# Instructions link.
self.top_panel.add(getStageLabel("Read the instructions:"))
instructionsButton = JButton(
('<HTML><FONT color="#000099">'
'<U>open instructions</U></FONT><HTML>'),
actionPerformed=self.browseInstructions)
instructionsButton.setHorizontalAlignment(SwingConstants.LEFT);
instructionsButton.setBorderPainted(False);
instructionsButton.setOpaque(False);
instructionsButton.setBackground(Color.WHITE);
instructionsButton.setToolTipText(self.instructionsURI);
self.top_panel.add(instructionsButton)
# 'Select input' elements.
self.top_panel.add(getStageLabel(
"Select a SASI .zip file or data folder:"))
self.top_panel.add(
JButton("Select input...", actionPerformed=self.openInputChooser))
# 'Select output' elements.
self.top_panel.add(getStageLabel("Specify an output file:"))
self.top_panel.add(
JButton("Specify output...", actionPerformed=self.openOutputChooser))
# 'Set result fields' elements.
result_fields = [
{'id': 'gear_id', 'label': 'Gear', 'selected': True,
'enabled': False},
{'id': 'substrate_id', 'label': 'Substrate', 'selected': True},
{'id': 'energy_id', 'label': 'Energy', 'selected': False},
{'id': 'feature_id', 'label': 'Feature', 'selected': False},
{'id': 'feature_category_id', 'label': 'Feature Category',
'selected': False}
]
self.selected_result_fields = {}
resolutionLabelPanel = JPanel(GridLayout(0,1))
resolutionLabelPanel.add(getStageLabel("Set result resolution:"))
resolutionLabelPanel.add(
JLabel(("<html><i>This sets the specificity with which<br>"
"results will be grouped. Note that enabling<br>"
"more fields can *greatly* increase resulting<br>"
"output sizes and run times.</i>")))
#self.top_panel.add(getStageLabel("Set result resolution:"))
self.top_panel.add(resolutionLabelPanel)
checkPanel = JPanel(GridLayout(0, 1))
self.top_panel.add(checkPanel)
self.resultFieldCheckBoxes = {}
for result_field in result_fields:
self.selected_result_fields.setdefault(
result_field['id'], result_field['selected'])
checkBox = JCheckBox(
result_field['label'], result_field['selected'])
checkBox.setEnabled(result_field.get('enabled', True))
checkBox.addItemListener(self)
checkPanel.add(checkBox)
self.resultFieldCheckBoxes[checkBox] = result_field
# 'Run' elements.
self.top_panel.add(getStageLabel("Run SASI: (this might take a while)"))
self.run_button = JButton("Run...", actionPerformed=self.runSASI)
self.top_panel.add(self.run_button)
SpringUtilities.makeCompactGrid(
self.top_panel, self.stageCounter - 1, 2, 6, 6, 6, 6)
# Progress bar.
self.progressBar = JProgressBar(0, 100)
self.main_panel.add(self.progressBar)
# Log panel.
self.log_panel = JPanel()
self.log_panel.alignmentX = Component.CENTER_ALIGNMENT
self.log_panel.setBorder(EmptyBorder(10,10,10,10))
self.main_panel.add(self.log_panel)
self.log_panel.setLayout(BorderLayout())
self.log = JTextArea()
self.log.editable = False
self.logScrollPane = JScrollPane(self.log)
self.logScrollPane.setVerticalScrollBarPolicy(
JScrollPane.VERTICAL_SCROLLBAR_ALWAYS)
self.logScrollBar = self.logScrollPane.getVerticalScrollBar()
self.log_panel.add(self.logScrollPane, BorderLayout.CENTER)
# File selectors
self.inputChooser = JFileChooser()
self.inputChooser.fileSelectionMode = JFileChooser.FILES_AND_DIRECTORIES
self.outputChooser = JFileChooser()
defaultOutputFile = os.path.join(System.getProperty("user.home"),
"sasi_project.zip")
self.outputChooser.setSelectedFile(File(defaultOutputFile));
self.outputChooser.fileSelectionMode = JFileChooser.FILES_ONLY
self.frame.setLocationRelativeTo(None)
self.frame.visible = True
def __init__(self, pP):
'''
Constructor
'''
self.pP = pP
self.annotationType = self.pP.getAnnotationType()
self.setTitle("Random Picture Picker")
#annotation Panel
annoPanel = JPanel()
annoPanel.setBorder(BorderFactory.createTitledBorder("Annotations"))
annoPLayout = GroupLayout(annoPanel)
annoPanel.setLayout(annoPLayout)
annoPLayout.setAutoCreateContainerGaps(True)
annoPLayout.setAutoCreateGaps(True)
# dynamic creation of annotation panel
# yesNoIgnore, int, number, list
if len(self.pP.getAnnotationType()) == 1:
self.annoField = JTextField("", 16)
annoPLayout.setHorizontalGroup(annoPLayout.createParallelGroup().addComponent(self.annoField))
annoPLayout.setVerticalGroup(annoPLayout.createSequentialGroup().addComponent(self.annoField))
elif len(self.pP.getAnnotationType()) > 1:
choices = pP.getAnnotationType()
print "choices", choices
choiceBtns = []
self.annoField = ButtonGroup()
for c in choices:
Btn = JRadioButton(c, actionCommand=c)
self.annoField.add(Btn)
choiceBtns.append(Btn)
h = annoPLayout.createParallelGroup()
for b in choiceBtns:
h.addComponent(b)
annoPLayout.setHorizontalGroup(h)
v = annoPLayout.createSequentialGroup()
for b in choiceBtns:
v.addComponent(b)
annoPLayout.setVerticalGroup(v)
# Control Panel
ctrlPanel = JPanel()
ctrlPLayout = GroupLayout(ctrlPanel, autoCreateContainerGaps=True, autoCreateGaps=True)
ctrlPanel.setLayout(ctrlPLayout)
nextImgButton = JButton("Next >", actionPerformed=self.nextPicture)
prevImgButton = JButton("< Prev", actionPerformed=self.pP.prevPicture)
quitButton = JButton("Quit", actionPerformed=self.exit)
ctrlPLayout.setHorizontalGroup(ctrlPLayout.createParallelGroup(GroupLayout.Alignment.CENTER)
.addGroup(ctrlPLayout.createSequentialGroup()
.addComponent(prevImgButton)
.addComponent(nextImgButton))
.addComponent(quitButton))
ctrlPLayout.setVerticalGroup(ctrlPLayout.createSequentialGroup()
.addGroup(ctrlPLayout.createParallelGroup()
.addComponent(prevImgButton)
.addComponent(nextImgButton))
.addComponent(quitButton))
ctrlPLayout.linkSize(SwingConstants.HORIZONTAL, quitButton)
statusPanel = JPanel() # contains status information: progress bar
self.progressBar = JProgressBar()
self.progressBar.setStringPainted(True)
self.progressBar.setValue(0)
statusPanel.add(self.progressBar)
#MainLayout
mainLayout = GroupLayout(self.getContentPane())
self.getContentPane().setLayout(mainLayout)
mainLayout.setHorizontalGroup(mainLayout.createParallelGroup(GroupLayout.Alignment.CENTER)
.addComponent(annoPanel)
.addComponent(ctrlPanel)
.addComponent(statusPanel)
)
mainLayout.setVerticalGroup(mainLayout.createSequentialGroup()
.addComponent(annoPanel)
.addComponent(ctrlPanel)
.addComponent(statusPanel)
)
mainLayout.linkSize(SwingConstants.HORIZONTAL, annoPanel, ctrlPanel, statusPanel)
self.pack()
self.setVisible(True)
self.pP.nextPicture()
def __init__(self, imgData):
n = imgData.size()
win = JFrame("Point Marker Panel")
win.setPreferredSize(Dimension(350, 590))
win.setSize(win.getPreferredSize())
pan = JPanel()
pan.setLayout(BoxLayout(pan, BoxLayout.Y_AXIS))
win.getContentPane().add(pan)
progressPanel = JPanel()
progressPanel.setLayout(BoxLayout(progressPanel, BoxLayout.Y_AXIS))
positionBar = JProgressBar()
positionBar.setMinimum(0)
positionBar.setMaximum(n)
positionBar.setStringPainted(True)
progressPanel.add(Box.createGlue())
progressPanel.add(positionBar)
progressBar = JProgressBar()
progressBar.setMinimum(0)
progressBar.setMaximum(n)
progressBar.setStringPainted(True)
progressPanel.add(progressBar)
progressPanel.setBorder(BorderFactory.createEmptyBorder(0, 10, 0, 10))
pan.add(progressPanel)
pan.add(Box.createRigidArea(Dimension(5, 5)))
savePanel = JPanel()
savePanel.setLayout(BoxLayout(savePanel, BoxLayout.Y_AXIS))
saveMessageLabel = JLabel("<html><u>Save Often</u></html>")
savePanel.add(saveMessageLabel)
savePanel.setAlignmentX(Component.CENTER_ALIGNMENT)
savePanel.setBorder(BorderFactory.createEmptyBorder(0, 10, 0, 10))
pan.add(savePanel)
# pan.add(saveMessageLabel)
pan.add(Box.createRigidArea(Dimension(5, 5)))
calPanel = JPanel()
calPanel.setLayout(BoxLayout(calPanel, BoxLayout.Y_AXIS))
calPanelIn = JPanel()
calPanelIn.setLayout(BoxLayout(calPanelIn, BoxLayout.X_AXIS))
pixelSizeText = JTextField(12)
pixelSizeText.setHorizontalAlignment(JTextField.RIGHT)
# pixelSizeText.setMaximumSize(pixelSizeText.getPreferredSize())
unitText = JTextField(10)
# unitText.setMaximumSize(unitText.getPreferredSize())
pixelSizeText.setText("Enter Pixel Size Here")
calPanelIn.add(pixelSizeText)
unitText.setText("Unit")
calPanelIn.add(unitText)
calPanelIn.setAlignmentX(Component.CENTER_ALIGNMENT)
calPanelIn.setBorder(
BorderFactory.createTitledBorder("Custom Calibration"))
calPanel.add(calPanelIn)
calPanelIn.setAlignmentX(Component.CENTER_ALIGNMENT)
calPanel.setBorder(BorderFactory.createEmptyBorder(0, 10, 0, 10))
pan.add(calPanel)
pan.add(Box.createRigidArea(Dimension(5, 5)))
helpPanel = JPanel()
helpPanel.setLayout(BoxLayout(helpPanel, BoxLayout.Y_AXIS))
helpLable = JLabel("<html><ul>\
<li>Focus on Image Window</li>\
<li>Select multi-point Tool</li>\
<li>Click to Draw Points</li>\
<li>Drag to Move Points</li>\
<li>\"Alt\" + Click to Erase Points</li>\
<li>Optional: Customize Calibration Above\
and Refresh Images\
(won't be written to files)</li>\
</html>")
helpLable.setBorder(BorderFactory.createTitledBorder("Usage"))
keyTagOpen = "<span style=\"background-color: #FFFFFF\"><b><kbd>"
keyTagClose = "</kbd></b></span>"
keyLable = JLabel("<html><ul>\
<li>Next Image --- " + keyTagOpen + "<" + \
keyTagClose + "</li>\
<li>Previous Image --- " + keyTagOpen + ">" + \
keyTagClose + "</li>\
<li>Save --- " + keyTagOpen + "`" + keyTagClose + \
" (upper-left to TAB key)</li>\
<li>Next Unmarked Image --- " + keyTagOpen + \
"TAB" + keyTagClose + "</li></ul>\
</html>" )
keyLable.setBorder(
BorderFactory.createTitledBorder("Keyboard Shortcuts"))
helpPanel.add(helpLable)
helpPanel.add(keyLable)
helpPanel.setAlignmentX(Component.CENTER_ALIGNMENT)
helpPanel.setBorder(BorderFactory.createEmptyBorder(0, 10, 0, 10))
pan.add(helpPanel)
# pan.add(Box.createRigidArea(Dimension(0, 10)))
infoPanel = JPanel()
infoPanel.setLayout(BoxLayout(infoPanel, BoxLayout.Y_AXIS))
infoLabel = JLabel()
infoLabel.setBorder(BorderFactory.createTitledBorder("Project Info"))
infoPanel.add(infoLabel)
infoPanel.setAlignmentX(Component.CENTER_ALIGNMENT)
infoPanel.setBorder(BorderFactory.createEmptyBorder(0, 10, 0, 10))
pan.add(infoPanel)
win.setVisible(True)
self.imgData = imgData
self.win = win
# self.progressPanel = progressPanel
self.positionBar = positionBar
self.progressBar = progressBar
self.saveMessageLabel = saveMessageLabel
self.infoLabel = infoLabel
self.pixelSizeText = pixelSizeText
self.unitText = unitText
self.update()
def loadPanel(self):
panel = JPanel()
panel.setLayout(BoxLayout(panel, BoxLayout.Y_AXIS))
bottomButtonBarPanel = JPanel()
bottomButtonBarPanel.setLayout(
BoxLayout(bottomButtonBarPanel, BoxLayout.X_AXIS))
bottomButtonBarPanel.setAlignmentX(1.0)
self.runButton = JButton("Run", actionPerformed=self.start)
self.cancelButton = JButton("Close", actionPerformed=self.cancel)
bottomButtonBarPanel.add(Box.createHorizontalGlue())
bottomButtonBarPanel.add(self.runButton)
bottomButtonBarPanel.add(self.cancelButton)
# Dimension(width,height)
bottom = JPanel()
bottom.setLayout(BoxLayout(bottom, BoxLayout.X_AXIS))
bottom.setAlignmentX(1.0)
self.progressBar = JProgressBar()
self.progressBar.setIndeterminate(False)
self.progressBar.setMaximum(100)
self.progressBar.setValue(0)
bottom.add(self.progressBar)
self.statusTextArea = JTextArea()
self.statusTextArea.setEditable(False)
scrollPane = JScrollPane(self.statusTextArea)
scrollPanel = JPanel()
scrollPanel.setLayout(BoxLayout(scrollPanel, BoxLayout.X_AXIS))
scrollPanel.setAlignmentX(1.0)
scrollPanel.add(scrollPane)
panel.add(scrollPanel)
panel.add(bottomButtonBarPanel)
panel.add(bottom)
self.add(panel)
self.setTitle("Determine Session Cookie(s)")
self.setSize(450, 300)
self.setLocationRelativeTo(None)
self.setVisible(True)
original_request_bytes = self.selected_message.getRequest()
http_service = self.selected_message.getHttpService()
helpers = self.callbacks.getHelpers()
request_info = helpers.analyzeRequest(http_service,
original_request_bytes)
parameters = request_info.getParameters()
cookie_parameters = [
parameter for parameter in parameters
if parameter.getType() == IParameter.PARAM_COOKIE
]
num_requests_needed = len(cookie_parameters) + 2
self.statusTextArea.append(
"This may require up to " + str(num_requests_needed) +
" requests to be made. Hit 'Run' to begin.\n")
class MenueFrame(JFrame, ActionListener, WindowFocusListener): # should extend JFrame
def __init__(self):
self.mainDir = ""
self.setTitle("Dots Quality Check")
self.setSize(250, 300)
self.setLocation(20,120)
self.addWindowFocusListener(self)
self.Panel = JPanel(GridLayout(0,1))
self.add(self.Panel)
self.openNextButton = JButton("Open Next Random", actionPerformed=self.openRandom)
self.Panel.add(self.openNextButton)
self.saveButton = JButton("Save", actionPerformed=self.save, enabled=False)
self.Panel.add(self.saveButton)
self.cropButton = JButton("Crop values from here", actionPerformed=self.cropVals)
self.Panel.add(self.cropButton)
self.DiscardButton = JButton("Discard cell", actionPerformed=self.discardCell)
self.Panel.add(self.DiscardButton)
self.quitButton = JButton("Quit script",actionPerformed=self.quit)
self.Panel.add(self.quitButton)
annoPanel = JPanel()
#add gridlayout
self.wtRButton = JRadioButton("wt", actionCommand="wt")
self.wtRButton.addActionListener(self)
self.defectRButton = JRadioButton("Defect", actionCommand="defect")
self.defectRButton.addActionListener(self)
annoPanel.add(self.wtRButton)
annoPanel.add(self.defectRButton)
self.aButtonGroup = ButtonGroup()
self.aButtonGroup.add(self.wtRButton)
self.aButtonGroup.add(self.defectRButton)
self.Panel.add(annoPanel)
self.ProgBar = JProgressBar()
self.ProgBar.setStringPainted(True)
self.ProgBar.setValue(0)
self.Panel.add(self.ProgBar)
self.pathLabel = JLabel("-- No main directory chosen --")
self.pathLabel.setHorizontalAlignment( SwingConstants.CENTER )
self.Panel.add(self.pathLabel)
WindowManager.addWindow(self)
self.show()
# - - - - B U T T O N M E T H O D S - - - -
# - - - - - - - - - - - - - - - - - - - - - - -
def openRandom(self, event): # when click here: get random cell and meas.measure(csv, tif, savePath)
if self.mainDir == "":
self.mainDir = DirectoryChooser("Random QC - Please choose main directory containing ctrl and test folders").getDirectory()
self.pathLabel.setText("MainDir: " + os.path.basename(os.path.split(self.mainDir)[0]))
try:
# should be complete disposal!
self.cT.closeWindows()
finally:
inFiles = glob.glob(os.path.join(self.mainDir, "*", G_OPENSUBDIR, "val_*.csv")) # glob.glob returns list of paths
uncheckedCells = [cell(csvPath) for csvPath in inFiles if cell(csvPath).processed == False]
if len(uncheckedCells) > 0:
self.cell = random.choice(uncheckedCells)
#update progressbar
self.ProgBar.setMaximum(len(inFiles)-1)
self.ProgBar.setValue(len(inFiles)-len(uncheckedCells))
# open imp and resultstable
self.cT = correctionTable(self.cell, self) #self, openPath_csv, mF
self.RBActionListener.setCell(self.cell)
# delete previous Radiobutton annotation
self.wtRButton.setSelected(False)
self.defectRButton.setSelected(True)
else:
print "All cells measured!"
def save(self, event):
savepath = self.cell.getQcCsvPath()
anaphase = self.cell.getAnOn()
timeInterval = self.cT.getImp().getCalibration().frameInterval
annotation = self.getAnnotation()
position = str(self.cell.position)
cellIndex = str(self.cell.cellNo)
if not os.path.exists(os.path.split(savepath)[0]): # check if save folder present.
os.makedirs(os.path.split(savepath)[0]) # create save folder, if not present
f = open(savepath, "w")
# Position Cell Phenotype Frame Time AnOn Distance ch0x ch0y ch0z ch0vol ch1x ch1y ch1z ch1vol
f.write("Position,Cell,Phenotype,Frame,Time,Anaphase,Distance,ch0x,ch0y,ch0z,ch0vol,ch1x,ch1y,ch1z,ch1vol\n")
for i in range(self.cT.getLineCount()):
frame, distance, a = self.cT.getLine(i).split("\t")
corrFrame = str(int(frame)-int(anaphase))
time = "%.f" % (round(timeInterval) * int(corrFrame))
if distance == "NA":
ch0x, ch0y, ch0z, ch0vol, ch1x, ch1y, ch1z, ch1vol = ("NA," * 7 + "NA\n").split(",")
else:
ch0x, ch0y, ch0z, ch0vol, ch1x, ch1y, ch1z, ch1vol = self.cT.getXYZtable()[i]
f.write(position+","+cellIndex+","+annotation+","+corrFrame+","+time+","+anaphase+","+distance+","+ch0x+","+ch0y+","+ch0z+","+ch0vol+","+ch1x+","+ch1y+","+ch1z+","+ch1vol)
f.close()
print "Successfully saved!"
def cropVals(self, event): #"this function deletes all values with frame > current cursor"
for line in range(self.cT.getSelectionEnd(), self.cT.getLineCount(), 1):
frame, distance, AOCol = self.cT.getLine(line).split("\t")
self.cT.setLine(line, frame + "\tNA" + "\t" + AOCol)
def discardCell(self, event):
if not os.path.exists(os.path.split(self.cell.getQcCsvPath() )[0]): # check if save folder present.
os.makedirs(os.path.split(self.cell.getQcCsvPath() )[0]) # create save folder, if not present.
f = open(self.cell.getQcCsvPath() ,"w")
# Write dummy header. Position Cell Phenotype Frame Time AnOn Distance ch0x ch0y ch0z ch0vol ch1x ch1y ch1z ch1vol
f.write("Position,Cell,Phenotype,Frame,Time,AnOn,Distance,ch0x,ch0y,ch0z,ch0vol,ch1x,ch1y,ch1z,ch1vol\n")
f.close()
print "Discarded cell - saved dummy"
def quit(self, event):
try:
self.cT.closeWindows()
finally:
WindowManager.removeWindow(self)
self.dispose()
# Methods implementing ActionListener interfaces:
def actionPerformed(self, e):
# this function is called when RadioButtons are changed
self.cell.annotate( e.getSource().getActionCommand() )
self.setSaveActive()
def windowGainedFocus(self, e):
pass
def windowLostFocus(self, e):
pass
# - - - - - - - - - - - - -
# - get and set methods - -
# - - - - - - - - - - - - -
def getAnnotation(self):
return self.aButtonGroup.getSelection().getActionCommand()
def getMainDir(self):
return self.mainDir
def setSaveActive(self):
if (self.cell.getAnnotation() != None and self.cell.getAnOn() != None):
self.saveButton.setEnabled(True)
self.show()
def setSaveInactive(self):
self.saveButton.setEnabled(False)
self.show()
def setMainDir(self, path):
self.mainDir = path
self.pathLabel.setText("MainDir: " + os.path.basename(os.path.split(self.mainDir)[0]))
