class win(JFrame):
def __init__(self, title="Consumo Electrico"):
JFrame(title)
self.setLayout(None)
self.setBounds(10, 10, 300, 180)
self.show()
self.build()
def build(self):
self.label = JLabel("Cup")
self.label.setBounds(120, 10, 45, 15)
self.label2 = JLabel("KWh")
self.label2.setBounds(20, 10, 45, 15)
self.label3 = JLabel()
self.label3.setBounds(120, 30, 55, 15)
self.textfield = JTextField()
self.textfield.setBounds(15, 30, 75, 20)
self.textfield.addActionListener(lambda x: self.label3.setText(
str(calculate(self.textfield.getText()))))
button = JButton("Calcular")
button.setBounds(10, 55, 290, 35)
button.addActionListener(lambda x: self.label3.setText(
str(calculate(self.textfield.getText()))))
for var in [
self.label, self.label2, self.label3, self.textfield, button
]:
self.add(var)
def _buildInspectorGUI(self, beh):
"""Builds the inspector GUI for the given behaviour object.
@param beh: The behaviour object.
@type beh: C{Behaviour}
"""
inspectors = beh.getInspectors()
# ignore behaviours that don't provide any inspectors
if not inspectors:
return []
# class to modify the behaviour state from the GUI
class UpdateBehaviourState(ActionListener):
def __init__(self, modifier, component):
self._modifier = modifier
self._component = component
def actionPerformed(self, evt):
self._modifier(str(self._component.getText()))
# build the list
propertyList = LabelledList(beh.getName())
properties = []
for inspector in inspectors:
# create textfield if mutator is available
component = None
state_str = str(inspector[1]())
if inspector[2]:
component = JTextField(state_str)
# react on changes of values by the user
component.addActionListener(
UpdateBehaviourState(inspector[2], component))
else:
component = JLabel(state_str)
properties.append((component, inspector[1]))
propertyList.addLabelled("%s " % inspector[0], component)
# Needs to create an actual list of properties of class Properties
#propertyList.add(None,
# JLabel("%s " % inspector[0]),
# PropertyInspector(properties, index, guistate),
# component,
# None)
# add it to the GUI and return the list of properties with its
# accessors and components
# need to restrict maximum size to allow for glue at end of panel to
# expand
propertyList.setMaximumSize(
Dimension(int(propertyList.getMaximumSize().getWidth()),
int(propertyList.getMinimumSize().getHeight())))
self.add(propertyList)
return properties
def build(self):
#labels
cl = JLabel("Celcius")
cl.setBounds(10, 10, 60, 20)
fl = JLabel("Farenheit")
fl.setBounds(120, 10, 60, 20)
kl = JLabel("Kelvin")
kl.setBounds(230, 10, 60, 20)
#celcius textfield
c = JTextField()
c.setBounds(10, 40, 60, 20)
c.addActionListener(lambda x: log(x))
#farenheit textfield
f = JTextField()
f.setBounds(120, 40, 60, 20)
f.addActionListener(lambda x: log(x))
#kelvin textfield
k = JTextField()
k.setBounds(230, 40, 60, 20)
k.addActionListener(lambda x: log(x))
#buttons
cv = JButton("Convert")
cv.addActionListener(lambda x: self.convert(x))
cv.setBounds(10, 70, 300 - 10, 30)
clean = JButton("Clean")
clean.addActionListener(lambda x: self.clean())
clean.setBounds(10, 110, 300 - 10, 30)
#add vars to frame
list(map(lambda x: self.add(x), [cl, kl, fl, c, f, k, cv, clean]))
self.k = k
self.c = c
self.f = f
self.textfields = {self.c, self.f, self.k}
class EmulatorComponentProvider(ComponentProviderAdapter):
def __init__(self, plugin):
super(EmulatorComponentProvider,
self).__init__(plugin.getTool(), "Emulator", "emulate_function")
self.plugin = plugin
self.panel = JPanel(GridBagLayout())
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.gridy = 0
c.gridx = 0
c.weightx = 0.8
self.panel_label = JLabel("")
self.panel.add(self.panel_label, c)
c.gridx = 1
c.weightx = 0.2
self.panel_btn = JButton("Start")
self.panel_btn.addActionListener(EmulatorBtnAction(self))
self.panel.add(self.panel_btn, c)
c.gridy = 1
c.gridx = 0
c.gridwidth = 2
self.panel_input = JTextField()
self.panel_input.addActionListener(EmulatorInputAction(self))
self.panel.add(self.panel_input, c)
self.setStatus("Stopped")
def getComponent(self):
return self.panel
def setStatus(self, status):
self.panel_label.setText(status)
class CustomCellEditor(TreeCellEditor, ActionListener):
"""Renders the various tree edit controls (checkbox, tristate checkbox, text box etc.)"""
def __init__(self, tree):
TreeCellEditor.__init__(self)
self.editor = None
self.tree = tree
flowLayout = FlowLayout(FlowLayout.LEFT, 0, 0)
self.cbPanel = JPanel(flowLayout)
self.cb = JCheckBox(actionPerformed=self.checked)
self.cbPanel.add(self.cb)
self.cbLabel = JLabel()
self.cbPanel.add(self.cbLabel)
self.tcbPanel = JPanel(flowLayout)
self.tcb = TristateCheckBox(self.checked)
self.tcbPanel.add(self.tcb)
self.tcbLabel = JLabel()
self.tcbPanel.add(self.tcbLabel)
self.rbPanel = JPanel(flowLayout)
self.rb = JRadioButton(actionPerformed=self.checked)
self.rbPanel.add(self.rb)
self.rbLabel = JLabel()
self.rbPanel.add(self.rbLabel)
self.tfPanel = JPanel(flowLayout)
self.tfLabel = JLabel()
self.tfPanel.add(self.tfLabel)
self.tf = JTextField()
self.tf.setColumns(12)
self.tf.addActionListener(self)
self.tfPanel.add(self.tf)
def addCellEditorListener(self, l):
"""Register for edit events"""
self.listener = l
def isCellEditable(self, event):
if event != None and isinstance(
event.getSource(), JTree) and isinstance(event, MouseEvent):
tree = event.getSource()
path = tree.getPathForLocation(event.getX(), event.getY())
userData = path.getLastPathComponent().getUserObject()
if isinstance(userData,
TreeNodeData) and (not userData.getNodeType().isType(
[NodeType._comment, NodeType._menu
])) and (userData.getVisible() > 0):
return True
return False
def shouldSelectCell(self, event):
# log.info("shouldSelectCell")
return True
def cancelCellEditing(self):
# log.info("Cancel editing, please!")
# super(CustomCellEditor, self).cancelCellEditing()
pass
def stopCellEditing(self):
# log.info("stopCellEditing")
if self.nodeData.getNodeType().isType([NodeType._text]):
# log.info("stopCellEditing for sure!")
self.nodeData.setValue(str(self.tf.getText()))
return True
def getTreeCellEditorComponent(self, tree, value, selected, expanded, leaf,
row):
"""Return a swing edit control appropriate for the node type of the supplied value"""
self.nodeData = self.getNodeUserData(value)
if self.nodeData:
text = self.nodeData.getText()
t = self.nodeData.getNodeType()
# Boolean checkbox
if t.isType([NodeType._bool]):
self.editor = self.cbPanel
self.cbLabel.setText(text)
if self.nodeData.getTriValue() > 0:
self.cb.setSelected(True)
else:
self.cb.setSelected(False)
# Tristate checkbox
elif t.isType([NodeType._tri]):
# log.info("getTreeCellEditorComponent tristate")
self.editor = self.tcbPanel
self.tcbLabel.setText(text)
self.tcb.setTriState(self.nodeData.getTriValue())
# Radio button
elif t.isType([NodeType._radio]):
self.editor = self.rbPanel
self.rbLabel.setText(text)
if self.nodeData.getTriValue() > 0:
self.rb.setSelected(True)
else:
self.rb.setSelected(False)
# Text field
elif t.isType([NodeType._text]):
self.editor = self.tfPanel
self.tfLabel.setText(str(self.nodeData.getText()) + ":")
self.tf.setText(str(self.nodeData.getValue()))
else:
self.editor = self.tcb
self.editor.setText(text)
return self.editor
def getNodeUserData(self, value):
"""Gets the TreeNodeData from the tree node"""
if isinstance(value, DefaultMutableTreeNode):
nodeData = value.getUserObject()
if isinstance(nodeData, TreeNodeData):
return nodeData
return None
def getCellEditorValue(self):
newNode = TreeNodeData(self.nodeData.knode, self.tree)
if isinstance(self.editor, JTextField):
newNode.setValue(str(self.editor.getText()))
return newNode
def checked(self, e):
"""Updates the node data when a checkbox has been clicked"""
control = e.getSource()
if isinstance(control, TristateCheckBox):
# log.info("tristate checked")
self.nodeData.setTriValue(control.getTriState())
else:
# log.info("checkbox checked")
if control.isSelected():
self.nodeData.setValue(2)
else:
self.nodeData.setValue(0)
def actionPerformed(self, event):
""" ENTER pressed in text field, stop editing."""
tf = event.getSource()
self.listener.editingStopped(ChangeEvent(tf))
class BobGui(JFrame):
def choose_dir_al(self, e):
dc = DirectoryChooser('Choose a bob_py experiment folder')
self.dir_path = dc.getDirectory()
self.choose_dir_textField.setText(self.dir_path)
def textField_al(self, e):
self.dir_path = self.choose_dir_textField.getText()
def run_button_al(self, e):
print('run button al')
self.exper = bob_py.Exper(self.dir_path)
# self.exper.hsegs()[0].nuc_bin().show()
self.make_tree()
def make_tree(self):
root = DefaultMutableTreeNode(self.exper.name)
for hseg in self.exper.hsegs():
hseg_node = DefaultMutableTreeNode(hseg.name)
root.add(hseg_node)
for file_suf in hseg.file_dict():
hseg_node.add(DefaultMutableTreeNode(file_suf))
self.tree = JTree(root)
scrollPane = JScrollPane()
scrollPane.getViewport().setView((self.tree))
# scrollPane.setPreferredSize(Dimension(300,250))
tree_panel = JPanel()
tree_panel.add(scrollPane)
box_layout = BoxLayout(self.panel, BoxLayout.Y_AXIS)
self.panel.setLayout(box_layout)
self.panel.add(tree_panel)
self.revalidate()
def __init__(self):
self.dir_path = ''
self.panel = JPanel()
box_layout = BoxLayout(self.panel, BoxLayout.Y_AXIS)
self.panel.setLayout(box_layout)
self.panel.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10))
self.choose_dir_label = JLabel('Experiment Folder:')
self.choose_dir_textField = JTextField(30)
self.choose_dir_textField.addActionListener(
ActionListenerFactory(self, self.textField_al))
self.choose_dir_button = JButton('open')
self.choose_dir_button.addActionListener(
ActionListenerFactory(self, self.choose_dir_al))
self.choose_dir_panel = JPanel()
self.choose_dir_panel.add(self.choose_dir_label)
self.choose_dir_panel.add(self.choose_dir_textField)
self.choose_dir_panel.add(self.choose_dir_button)
self.panel.add(self.choose_dir_panel)
# root = DefaultMutableTreeNode()
# self.meta_data_mode_label = JLabel('Autogenerated meta_data file mode')
# self.raw_stack_mode = JRadioButton('raw stack mode')
# self.projection_mode = JRadioButton('projection files mode')
#
# self.meta_data_mode = ButtonGroup()
# self.meta_data_mode.add(self.raw_stack_mode)
# self.meta_data_mode.add(self.projection_mode)
#
# self.meta_data_mode_panel = JPanel(GridLayout(0, 1))
# self.meta_data_mode_panel.add(self.meta_data_mode_label)
# self.meta_data_mode_panel.add(self.raw_stack_mode)
# self.meta_data_mode_panel.add(self.projection_mode)
#
# self.panel.add(self.meta_data_mode_panel)
self.run_button = JButton('Run')
self.run_button.addActionListener(
ActionListenerFactory(self, self.run_button_al))
self.panel.add(self.run_button)
super(BobGui, self).__init__("BobPy")
self.getContentPane().add(self.panel)
self.pack()
self.setLocationRelativeTo(None)
self.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE)
self.setVisible(True)
class BobGui(JFrame):
def choose_dir_al(self, e):
dc = DirectoryChooser('Choose a bob_py experiment folder')
self.dir_path = dc.getDirectory()
self.choose_dir_textField.setText(self.dir_path)
self.got_exper(self.dir_path)
def textField_al(self, e):
self.dir_path = self.choose_dir_textField.getText()
self.got_exper(self.dir_path)
def got_exper(self, dir_path):
self.exper = bob_py.Exper(dir_path)
self.make_tree()
def make_tree(self):
print('make_tree')
root = DefaultMutableTreeNode(self.exper.name)
sb = br.SimilarityBuilder()
for hseg in self.exper.hsegs():
all_file_dict = hseg.file_dict()
all_file_dict.update(hseg.cell_file_dict())
all_file_dict.update(hseg.bin_file_dict())
sb.add_group(hseg.name, all_file_dict)
simprofile, comparisons = sb.simprofile_comparison()
sim_str = ''
for val in simprofile:
sim_str += str(val) + '\n'
tp = JTextArea(sim_str)
stp = JScrollPane()
stp.getViewport().setView(tp)
#
# stp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
# stp.setPreferredSize(Dimension(250, 250));
# tp.setPreferredSize(Dimension(250, 250))
stp_panel = JPanel(BorderLayout())
stp_panel.add(tp, BorderLayout.CENTER)
# self.add(stp_panel, 'grow')
for hseg in self.exper.hsegs():
hseg_node = DefaultMutableTreeNode(hseg.name)
root.add(hseg_node)
if len(comparisons[hseg.name]) > 0:
for definer, file_names in comparisons[hseg.name].items():
for file_name in file_names:
node_str = definer + ': ' + file_name
hseg_node.add(DefaultMutableTreeNode(node_str))
# for file_suf in hseg.file_dict() :
# hseg_node.add(DefaultMutableTreeNode(file_suf))
self.tree = JTree(root)
scrollPane = JScrollPane()
scrollPane.getViewport().setView((self.tree))
# scrollPan
# scrollPane.setPreferredSize(Dimension(300,250))
tree_panel = JPanel(BorderLayout())
tree_panel.add(scrollPane, BorderLayout.CENTER)
combo_panel = JPanel(GridLayout(0, 2, 10, 10))
# combo_panel.setLayout(BoxLayout(combo_panel, BoxLayout.X_AXIS))
combo_panel.add(stp_panel) #, BorderLayout.LINE_START)
combo_panel.add(tree_panel) #, BorderLayout.LINE_END)
self.panel.add(combo_panel)
# self.add(scrollPane, 'grow')
self.revalidate()
def __init__(self):
super(BobGui, self).__init__("BobPy")
self.dir_path = ''
# ml = MigLayout('fill')
# self.setLayout(ml)
self.panel = JPanel()
self.panel.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10))
box_layout = BoxLayout(self.panel, BoxLayout.Y_AXIS)
self.panel.setLayout(box_layout)
self.choose_dir_label = JLabel('Experiment Folder:')
self.choose_dir_textField = JTextField(20)
self.choose_dir_textField.addActionListener(
ActionListenerFactory(self, self.textField_al))
self.choose_dir_button = JButton('open')
self.choose_dir_button.addActionListener(
ActionListenerFactory(self, self.choose_dir_al))
self.choose_dir_panel = JPanel()
self.choose_dir_panel.add(self.choose_dir_label)
self.choose_dir_panel.add(self.choose_dir_textField)
self.choose_dir_panel.add(self.choose_dir_button)
self.panel.add(self.choose_dir_panel)
self.add(self.panel)
self.setPreferredSize(Dimension(500, 300))
self.pack()
self.setLocationRelativeTo(None)
self.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE)
self.setVisible(True)
class ConsolePanel(Panel):
def __init__(self):
self.console = None
self.outText = None
self.inText = None
self.outTextScroller = None
self.nestedInputPanel = None
self.directoryText = None
Panel.__init__(self, "insets 0 0 0 0")
def sendCommand(self, command):
print str(self)
oldText = self.inText.getText()
self.inText.setText(command)
self.inText.getActionListeners()[0].actionPerformed(None)
self.inText.setText(oldText)
def setDirectoryText(self, dirText):
self.directoryText.setText(dirText)
self.nestedInputPanel.revalidate()
def write_out(self,text):
if not self.outText:
return
self.outText.setText(self.outText.getText() + text)
def initUI(self):
font = Font("Courier New", Font.BOLD, 14)
#create the output text panel
self.outText = JTextArea()
self.outText.setEditable(False)
self.outText.setFont(font)
self.outText.setWrapStyleWord(True)
self.outText.setLineWrap(True)
#self.outText.setLineWrap(True)
#self.outText.setWrapStyleWord(True)
class NoGhostScroller(JScrollPane):
def paintComponent(self, g):
g.setColor(self.getBackground())
g.fillRect(0, 0, self.getWidth(), self.getHeight())
#super(NoGhostScroller, self).paintComponent(g)
self.outTextScroller = JScrollPane(self.outText)
self.outTextScroller.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER)
self.outTextScroller.getVerticalScrollBar().setForeground(Color(255, 0, 0))
#self.outText.setOpaque(False)
self.outText.setBackground(Color(0, 20, 0))
self.outText.setForeground(Color.WHITE)
#self.outTextScroller.setOpaque(False)
self.outTextScroller.setBackground(Color(0, 20, 0))
#self.outText.repaint()
#self.layered = JLayeredPane()
#self.layered.setLayer(self.outTextScroller, 0)
#create the input text box
self.inText = JTextField()
self.inText.setFocusTraversalKeysEnabled(False)
self.inText.setFont(font)
self.inText.setBackground(Color(0, 20, 0))
self.inText.setForeground(Color.WHITE)
self.inText.getCaret().setVisible(True)
self.inText.getCaret().setBlinkRate(500)
self.inText.setCaretColor(Color(200,255,200))
class InFocusAdapter(FocusAdapter):
def focusLost(adap, e):
self.inText.setVisible(True)
self.inText.addFocusListener(InFocusAdapter())
self.nestedInputPanel = Panel("Insets 0 0 0 0")
#create the directory text box
self.directoryText = JTextField()
self.directoryText.setEditable(False)
self.directoryText.setFont(font)
self.directoryText.setBackground(Color(0, 20, 0))
self.directoryText.setForeground(Color.WHITE)
#set up the console
sys.stdout = FakeOut(self.outText)
self.console = BashED_Console(stdout=sys.stdout)
self.directoryText.setText(self.console.get_prompt())
self.revalidate();
dirTex = self.directoryText;
#create the listener that fires when the 'return' key is pressed
class InputTextActionListener(ActionListener):
def __init__(self,parent,inp,out,console):
self.parent = parent
self.inp = inp
self.out = out
self.console = console
def actionPerformed(self, e):
#print self.getCommandText()
# print(self.console.get_prompt())
# self.console.onecmd(self.inp.getText())
# self.parent.write_out("\n" + self.inp.getText())
# dirTex.setText(self.console.get_prompt())
# self.inp.setText("")
self.parent.write_out(self.console.get_prompt() + self.inp.getText() + '\n')
if 'clear' in self.inp.getText().split(' ')[0]:
self.out.setText("") #clear the screen
else:
self.console.onecmd(self.inp.getText())
dirTex.setText(self.console.get_prompt())
self.inp.setText("")
#create the listener that fires whenever a user hits a key
class InputKeyActionListener(KeyAdapter):
def __init__(self,parent,inp,out,console):
self.parent = parent
self.inp = inp
self.out = out
self.console = console
def keyReleased(self, k):
inp = self.inp.getText()
if k.getKeyCode() == 9: #tab character
autos = self.console.tabcomplete(self.inp.getText())
if len(autos) == 1:
self.inp.setText(autos[0])
else:
i = 0
for option in autos:
self.parent.write_out(option)
if i % 3 == 0:
print('\n')
else:
print('\t')
hist = None
if k.getKeyCode() == 38:
hist = self.console.next_hist()
if k.getKeyCode() == 40:
hist = self.console.last_hist()
if hist:
self.inp.setText(hist.rstrip('\n'))#prevent from firing
self.inText.addActionListener(InputTextActionListener(self,self.inText,self.outText,self.console))
self.inText.addKeyListener(InputKeyActionListener(self,self.inText,self.outText,self.console))
def addUI(self):
self.add(self.outTextScroller, "cell 0 0, push, grow")
self.add(self.nestedInputPanel, "cell 0 1, pushx, growx")
self.nestedInputPanel.add(self.directoryText, "cell 0 0")
self.nestedInputPanel.add(self.inText, "cell 1 0, spanx, pushx, growx")
class BobGui(JFrame):
def __init__(self):
super(BobGui, self).__init__('BobPy')
# IJ.log('okay?')
# print('okay??')
self.setLayout(BorderLayout())
self.main_panel = JPanel()
# self.main_panel.setLayout(MigLayout('insets 1 10 1 1'))
self.main_panel.setLayout(MigLayout())
dir_panel = JPanel()
dir_panel.setLayout(BoxLayout(dir_panel, BoxLayout.X_AXIS))
dir_label = JLabel('Experiment Folder:')
dir_panel.add(dir_label)
self.dir_text_field = JTextField(10)
self.dir_text_field.addActionListener(
ActionListenerFactory(self, self.text_field_al))
dir_panel.add(self.dir_text_field)
dir_button = JButton('open')
dir_button.addActionListener(
ActionListenerFactory(self, self.choose_dir_al))
dir_panel.add(dir_button)
self.main_panel.add(dir_panel, 'wrap, growx, spanx, pushx')
add_key_args(self.main_panel, 'close_w',
ActionListenerFactory(self, self.close_al), KeyEvent.VK_W,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask())
self.add(self.main_panel, BorderLayout.CENTER)
self.setPreferredSize(Dimension(650, 600))
self.pack()
self.setLocationRelativeTo(None)
self.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE)
self.setVisible(True)
def show_exper_info(self):
chf_panel = self.make_chf_panel()
hseg_tree_panel = self.make_hseg_tree_panel()
self.split_pane = JSplitPane(JSplitPane.HORIZONTAL_SPLIT)
self.split_pane.setOneTouchExpandable(True)
self.split_pane.setContinuousLayout(True)
self.split_pane.setResizeWeight(0.5)
self.split_pane.add(chf_panel)
self.split_pane.add(hseg_tree_panel)
self.main_panel.add(self.split_pane, 'grow, wrap')
# self.log_text = JTextArea()
self.main_panel.add(self.log_text, 'grow, wrap')
self.log_text.setLineWrap(True)
self.log_text.setWrapStyleWord(True)
self.revalidate()
def make_chf_panel(self):
""" chf --> common hseg files """
chf_panel = JPanel()
chf_panel.setLayout(MigLayout('insets 0'))
chf_files_label = JLabel('Hemisegment cells')
chf_files_text = JTextArea(
BobGui.archetype_to_str(
self.exper.hseg_cell_files_cab().archetype))
chf_panel.add(chf_files_label, 'growx, wrap')
chf_panel.add(chf_files_text, 'grow, wrap')
chf_files_label = JLabel('Hemisegment binary image files')
chf_files_text = JTextArea(
BobGui.archetype_to_str(self.exper.hseg_bin_files_cab().archetype))
chf_panel.add(chf_files_label, 'growx, wrap')
chf_panel.add(chf_files_text, 'grow, wrap')
chf_files_label = JLabel('Intensity Image Files')
# chf_files_text = JTextArea(BobGui.archetype_to_str(self.exper.hseg_intens_im_files_cab().archetype))
# print(self.exper.hseg_intens_im_files_cab().archetype)
# chf_panel.add(chf_files_label, 'growx, wrap')
# chf_panel.add(chf_files_text, 'grow, wrap')
self.intens_im_boxes = []
intens_im_panel = JPanel()
intens_im_panel.setLayout(MigLayout('insets 0'))
for poss_im_file in self.exper.hseg_intens_im_files_cab().archetype:
self.intens_im_boxes.append(JCheckBox(poss_im_file))
intens_im_panel.add(self.intens_im_boxes[-1], 'wrap')
chf_panel.add(chf_files_label, 'growx, wrap')
chf_panel.add(intens_im_panel, 'grow, wrap')
mdf_create_button = JButton(
'Create meta_data file from default outline')
# mdf_create_button = JButton('<html>Create meta_data file<br>from default outline</html>')
mdf_create_button.addActionListener(
ActionListenerFactory(self, self.mdf_create_al))
mdf_open_button = JButton('Open existing meta_data file')
mdf_open_button.addActionListener(
ActionListenerFactory(self, self.mdf_open_al))
# meta_data_file_buttton = JButton('Open/Create meta_data file')
# meta_data_file_buttton.addActionListener(ActionListenerFactory(self, self.meta_data_al))
# chf_panel.add(meta_data_file_buttton)
chf_panel.add(mdf_create_button, 'wrap')
chf_panel.add(mdf_open_button, 'wrap')
chf_scroll_pane = JScrollPane()
chf_scroll_pane.getViewport().setView(chf_panel)
return chf_scroll_pane
@staticmethod
def archetype_to_str(archetype):
at_str = ''
for val in archetype:
at_str += str(val) + '\n'
return at_str
def make_hseg_tree_panel(self):
root = DefaultMutableTreeNode(self.exper.name)
for hseg in self.exper.hsegs():
hseg_node = DefaultMutableTreeNode(hseg.name)
root.add(hseg_node)
hseg_at_deviations = self.exper.hseg_files_cab(
).archetype_deviations
if len(hseg_at_deviations[hseg.name]) > 0:
for definer, file_names in hseg_at_deviations[
hseg.name].items():
for file_name in file_names:
node_str = definer + ': ' + file_name
temp = DefaultMutableTreeNode(node_str)
hseg_node.add(temp)
hseg_tree = JTree(root)
hseg_tree.setCellRenderer(BobPyTreeCellRenderer())
hseg_scroll_pane = JScrollPane()
hseg_scroll_pane.getViewport().setView((hseg_tree))
hseg_panel = JPanel(MigLayout('insets 0'))
hseg_panel.add(hseg_scroll_pane, 'grow, span, push, wrap')
run_button = JButton('Run')
run_button.addActionListener(ActionListenerFactory(self, self.run_al))
rerun_button = JButton('Rerun')
rerun_button.addActionListener(
ActionListenerFactory(self, self.rerun_al))
hseg_panel.add(run_button)
hseg_panel.add(rerun_button)
return hseg_panel
def log(self, text):
self.log_text.append(str(text) + '\n')
def text_field_al(self, e):
# self.dir_path =
self.got_exper(self.dir_text_field.getText())
def choose_dir_al(self, e):
dc = DirectoryChooser('Choose a bob_py experiment folder')
# self.dir_path = dc.getDirectory()
# self.dir_text_field.setText(self.dir_path)
# self.dir_text_field.setText('blerg')
# IJ.log('blerg')
# print('boop')
self.got_exper(dc.getDirectory())
def close_al(self, e):
self.dispatchEvent(WindowEvent(self, WindowEvent.WINDOW_CLOSING))
def run_al(self, e):
# dt = br.dtic('Processed experiment {}'.format(self.exper.name))
t = br.tic()
self.exper.make_data()
self.exper.output_cell_cols_def()
self.exper.output_nuc_cols_def()
self.exper.output_new_hdings()
self.exper.log('Processed experiment {} in {:.3f} seconds'.format(
self.exper.name, br.toc(t)))
# br.dtoc(dt)
def rerun_al(self, e):
# dt = br.dtic('Processed experiment {}'.format(self.exper.name))
# t = br.tic()
self.exper = None
self.got_exper(self.dir_path)
self.run_al(None)
# self.exper =
# self.exper.make_data()
# self.exper.output_cell_cols_def()
# self.exper.output_nuc_cols_def()
# self.exper.output_new_hdings()
#
# self.exper.log('Created and processed experiment {} in {:.3f} seconds'.format(self.exper.name, br.toc(t)))
# br.dtoc(dt)
# def meta_data_al(self, e) :
# meta_data_path = self.exper.meta_data_path()
# if not os.path.exists(meta_data_path) :
# txt = make_meta_data_str(self.exper)
# with open(meta_data_path, 'w') as f :
# f.write(txt)
#
# IJ.open(meta_data_path)
def mdf_create_al(self, e):
meta_data_path = self.exper.meta_data_path()
# if not os.path.exists(meta_data_path) :
intens_im_list = []
for check_box in self.intens_im_boxes:
if check_box.isSelected():
intens_im_list.append(check_box.getLabel())
txt = make_meta_data_str2(self.exper, intens_im_list)
with open(meta_data_path, 'w') as f:
f.write(txt)
# IJ.open(meta_data_path)
def mdf_open_al(self, e):
meta_data_path = self.exper.meta_data_path()
IJ.open(meta_data_path)
def got_exper(self, dir_path):
# IJ.log('exper')
self.dir_path = dir_path
self.dir_text_field.setText(self.dir_path)
self.log_text = JTextArea()
self.exper = bob_py.Exper(dir_path, gui=self)
self.show_exper_info()
class BurpExtender(IBurpExtender, ITab, IHttpListener,
IMessageEditorController, AbstractTableModel,
IContextMenuFactory, IScannerCheck):
name = "Femida XSS"
conf_path = "./config.py"
_jTabbedPane = JTabbedPane()
_jPanel = JPanel()
_jAboutPanel = JPanel()
_jPanelConstraints = GridBagConstraints()
_jLabelParameters = None
_jTextFieldParameters = None
_jLabelTechniques = None
_jTextFieldURL = None
_jLabelFuzzFactor = None
_jTextFieldFuzzFactor = None
_jLabelAdditionalCmdLine = None
_jTextFieldAdditionalCmdLine = None
_jButtonSetCommandLine = None
_jLabelAbout = None
_overwriteHeader = False
_overwriteParam = False
_forkRequestParam = False
def doActiveScan(self, baseRequestResponse, insertionPoint):
scan_issues = []
try:
requestString = str(baseRequestResponse.getRequest().tostring())
newRequestString = self.prepareRequest(requestString)
vulnerable, verifyingRequestResponse = self.quickCheckScan(
newRequestString, baseRequestResponse)
except Exception as msg:
print(msg)
return []
def quickCheckScan(self, preparedRequest, requestResponse):
check = self._callbacks.makeHttpRequest(
requestResponse.getHttpService(),
self._helpers.stringToBytes(preparedRequest))
vulner = self._helpers.analyzeResponse(
check.getResponse()).getStatusCode() == 200
return vulner, check
#
# implement IBurpExtender
#
def registerExtenderCallbacks(self, callbacks):
self._callbacks = callbacks
self._helpers = callbacks.getHelpers()
self._callbacks.setExtensionName(self.name)
self._callbacks.registerScannerCheck(self)
self._dictPayloads = {}
self._dictHeaders = {}
self._dictParams = {}
self.status_flag = False
self.jfc = JFileChooser("./")
self.jfc.setDialogTitle("Upload Payloads")
self.jfc.setFileFilter(FileNameExtensionFilter("TXT file", ["txt"]))
self._layout = GridBagLayout()
self._jPanel.setLayout(self._layout)
self._jLabelTechniques = JLabel("Press to start:")
self.createAnyView(self._jLabelTechniques, 0, 0, 3, 1,
Insets(0, 0, 10, 0))
self.submitSearchButton = swing.JButton(
'Run proxy', actionPerformed=self.active_flag)
self.submitSearchButton.setBackground(Color.WHITE)
self.createAnyView(self.submitSearchButton, 3, 0, 6, 1,
Insets(0, 0, 10, 0))
self._jPanel.setBounds(0, 0, 1000, 1000)
self._jLabelTechniques = JLabel("Your URL (my.burpcollaborator.net):")
self.createAnyView(self._jLabelTechniques, 0, 1, 3, 1,
Insets(0, 0, 10, 0))
self._jTextFieldURL = JTextField("", 30)
self._jTextFieldURL.addActionListener(self.setCallbackUrl)
self.createAnyView(self._jTextFieldURL, 3, 1, 5, 1,
Insets(0, 0, 10, 0))
self._forkRequestButton = swing.JButton(
'Parallel Request', actionPerformed=self.forkRequest)
self._forkRequestButton.setBackground(Color.WHITE)
self.createAnyView(self._forkRequestButton, 8, 1, 1, 1,
Insets(0, 0, 10, 0))
self._tableModelPayloads = DefaultTableModel()
self._tableModelPayloads.addColumn("Payload")
self._tableModelPayloads.addColumn("Active")
self._tableModelHeaders = DefaultTableModel()
self._tableModelHeaders.addColumn("Header")
self._tableModelHeaders.addColumn("Active")
self._tableModelParams = DefaultTableModel()
self._tableModelParams.addColumn("Parameter")
self._tableModelParams.addColumn("Active")
self._payloadTable = self.createAnyTable(self._tableModelPayloads, 1,
Dimension(300, 200))
self.createAnyView(self._payloadTable, 0, 2, 3, 1, Insets(0, 0, 0, 10))
self._headerTable = self.createAnyTable(self._tableModelHeaders, 2,
Dimension(300, 200))
self.createAnyView(self._headerTable, 3, 2, 3, 1, Insets(0, 0, 0, 10))
self._paramTable = self.createAnyTable(self._tableModelParams, 3,
Dimension(300, 200))
self.createAnyView(self._paramTable, 6, 2, 3, 1, Insets(0, 0, 0, 0))
deletePayloadButton = swing.JButton(
'Delete', actionPerformed=self.deleteToPayload)
deletePayloadButton.setBackground(Color.WHITE)
self.createAnyView(deletePayloadButton, 0, 3, 1, 1, Insets(3, 0, 0, 0))
deletePayloadButton = swing.JButton(
'Upload', actionPerformed=self.uploadToPayload)
deletePayloadButton.setBackground(Color.WHITE)
self.createAnyView(deletePayloadButton, 1, 3, 1, 1, Insets(3, 0, 0, 0))
addPayloadButton = swing.JButton('Add',
actionPerformed=self.addToPayload)
addPayloadButton.setBackground(Color.WHITE)
self.createAnyView(addPayloadButton, 2, 3, 1, 1, Insets(3, 0, 0, 10))
deleteHeaderButton = swing.JButton('Delete',
actionPerformed=self.deleteToHeader)
deleteHeaderButton.setBackground(Color.WHITE)
self.createAnyView(deleteHeaderButton, 3, 3, 1, 1, Insets(3, 0, 0, 0))
self._overwriteHeaderButton = swing.JButton(
'Overwrite', actionPerformed=self.overwriteHeader)
self._overwriteHeaderButton.setBackground(Color.WHITE)
self.createAnyView(self._overwriteHeaderButton, 4, 3, 1, 1,
Insets(3, 0, 0, 0))
addHeaderButton = swing.JButton('Add',
actionPerformed=self.addToHeader)
addHeaderButton.setBackground(Color.WHITE)
self.createAnyView(addHeaderButton, 5, 3, 1, 1, Insets(3, 0, 0, 10))
deleteParamsButton = swing.JButton('Delete',
actionPerformed=self.deleteToParams)
deleteParamsButton.setBackground(Color.WHITE)
self.createAnyView(deleteParamsButton, 6, 3, 1, 1, Insets(3, 0, 0, 0))
self._overwriteParamButton = swing.JButton(
'Overwrite', actionPerformed=self.overwriteParam)
self._overwriteParamButton.setBackground(Color.WHITE)
self.createAnyView(self._overwriteParamButton, 7, 3, 1, 1,
Insets(3, 0, 0, 0))
addParamsButton = swing.JButton('Add',
actionPerformed=self.addToParams)
addParamsButton.setBackground(Color.WHITE)
self.createAnyView(addParamsButton, 8, 3, 1, 1, Insets(3, 0, 0, 0))
self._resultsTextArea = swing.JTextArea()
resultsOutput = swing.JScrollPane(self._resultsTextArea)
resultsOutput.setMinimumSize(Dimension(800, 200))
self.createAnyView(resultsOutput, 0, 4, 9, 1, Insets(10, 0, 0, 0))
self.clearSearchButton = swing.JButton(
'Clear Search Output', actionPerformed=self.clearOutput)
self.createAnyView(self.clearSearchButton, 3, 6, 3, 1,
Insets(3, 0, 0, 0))
self._callbacks.customizeUiComponent(self._jPanel)
self._callbacks.addSuiteTab(self)
self.starterPack()
self._callbacks.registerHttpListener(self)
self._callbacks.registerContextMenuFactory(self)
return
def createAnyTable(self, table_model, table_number, min_size):
_table = JTable(table_model)
_table.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS)
for i in range(2):
column = _table.getColumnModel().getColumn(i)
if i == 0:
column.setPreferredWidth(250)
else:
column.setPreferredWidth(50)
_scrolltable = JScrollPane(_table)
_scrolltable.setMinimumSize(min_size)
return _scrolltable
def insertAnyTable(self, table, data):
def detectTable(table):
name = table.getColumnName(0)
if name == 'Payloads':
return 0
elif name == 'Headers':
return 1
elif name == 'Parameters':
return 2
tableNum = detectTable(table)
new_data = [str(x) for x in data]
table.insertRow(table.getRowCount(), new_data)
return table.getRowCount()
def replaceLine(self, file_path, new_line):
from tempfile import mkstemp
from shutil import move
from os import fdopen, remove
#Create temp file
fh, abs_path = mkstemp()
with fdopen(fh, 'w') as new_file:
with open(file_path) as old_file:
for line in old_file:
a = re.findall('^Callback_url[ =]+(.+)$', line)
if a:
for k in a:
temp = k.replace("\'", "").replace("\"", "")
new_file.write(line.replace(temp, new_line))
else:
new_file.write(line)
#Remove original file
remove(file_path)
#Move new file
move(abs_path, file_path)
def createAnyView(self, _component, gridx, gridy, gridwidth, gridheight,
insets):
self._jPanelConstraints.fill = GridBagConstraints.HORIZONTAL
self._jPanelConstraints.gridx = gridx
self._jPanelConstraints.gridy = gridy
self._jPanelConstraints.gridwidth = gridwidth
self._jPanelConstraints.gridheight = gridheight
self._jPanelConstraints.insets = insets
self._jPanel.add(_component, self._jPanelConstraints)
def createMenuItems(self, contextMenuInvocation):
context = contextMenuInvocation.getInvocationContext()
filterMenu = JMenu("Femida XSS")
self._contextMenuData = contextMenuInvocation
if (context == 0 or context == 1 or context == 2 or context == 3
or context == 8 or context == 9):
filterMenu.add(
JMenuItem("Add to Headers",
actionPerformed=self.addToHeadersItem))
filterMenu.add(
JMenuItem("Add to Parameters",
actionPerformed=self.addToParametersItem))
return Arrays.asList(filterMenu)
return Arrays.asList([])
def addToHeadersItem(self, event):
start, end = self._contextMenuData.getSelectionBounds()
message = self._contextMenuData.getSelectedMessages()[0]
ctx = self._contextMenuData.getInvocationContext()
if ctx == 0 or ctx == 2:
message = message.getRequest()
elif ctx == 1 or ctx == 3:
message = message.getResponse()
else:
print(ctx)
return
try:
selected_text = self._helpers.bytesToString(message)[start:end]
self.insertAnyTable(self._tableModelHeaders,
[str(selected_text), '1'])
except Exception:
pass
def addToParametersItem(self, event):
start, end = self._contextMenuData.getSelectionBounds()
message = self._contextMenuData.getSelectedMessages()[0]
ctx = self._contextMenuData.getInvocationContext()
if ctx == 0 or ctx == 2:
message = message.getRequest()
elif ctx == 1 or ctx == 3:
message = message.getResponse()
else:
print(ctx)
return
try:
selected_text = self._helpers.bytesToString(message)[start:end]
self.insertAnyTable(self._tableModelParams,
[str(selected_text), '1'])
except Exception:
pass
def starterPack(self):
self.addFromFileAsync(config.Payloads, self._tableModelPayloads)
self.addFromFileAsync(config.Headers, self._tableModelHeaders)
self.addFromFileAsync(config.Parameters, self._tableModelParams)
self._jTextFieldURL.setText(config.Callback_url)
self._tableModelPayloads.addTableModelListener(
MyTableModelListener(self._tableModelPayloads, self,
self._dictPayloads, config.Payloads))
self._tableModelHeaders.addTableModelListener(
MyTableModelListener(self._tableModelHeaders, self,
self._dictHeaders, config.Headers))
self._tableModelParams.addTableModelListener(
MyTableModelListener(self._tableModelParams, self,
self._dictParams, config.Parameters))
def setCallbackUrl(self, event):
self.replaceLine(self.conf_path, self._jTextFieldURL.getText())
self.appendToResults('New url={} saved.'.format(
self._jTextFieldURL.getText()))
def addToPayload(self, button):
self.insertAnyTable(self._tableModelPayloads, ['', '1'])
def addToHeader(self, button):
self.insertAnyTable(self._tableModelHeaders, ['', '1'])
def addToParams(self, button):
self.insertAnyTable(self._tableModelParams, ['', '1'])
def uploadToPayload(self, button):
self._returnFileChooser = self.jfc.showDialog(None, "Open")
if (self._returnFileChooser == JFileChooser.APPROVE_OPTION):
selectedFile = self.jfc.getSelectedFile()
self.fileUpload(selectedFile, self._tableModelPayloads)
def deleteToPayload(self, button):
try:
val = self._tableModelPayloads.getValueAt(
self._tableModelPayloads.getRowCount() - 1, 0)
self._tableModelPayloads.removeRow(
self._tableModelPayloads.getRowCount() - 1)
self._dictPayloads.pop(val)
self.saveToFileAsync(config.Payloads, self._dictPayloads)
except Exception as msg:
# print(msg)
pass
def deleteToHeader(self, button):
try:
val = self._tableModelHeaders.getValueAt(
self._tableModelHeaders.getRowCount() - 1, 0)
self._tableModelHeaders.removeRow(
self._tableModelHeaders.getRowCount() - 1)
self._dictHeaders.pop(val)
self.saveToFileAsync(config.Headers, self._dictHeaders)
except Exception as msg:
# print(msg)
pass
def deleteToParams(self, button):
try:
val = self._tableModelParams.getValueAt(
self._tableModelParams.getRowCount() - 1, 0)
self._tableModelParams.removeRow(
self._tableModelParams.getRowCount() - 1)
self._dictParams.pop(val)
self.saveToFileAsync(config.Parameters, self._dictParams)
except Exception as msg:
# print(msg)
pass
def clearOutput(self, button):
self._resultsTextArea.setText("")
def fileUpload(self, path, table):
with open(str(path), "r") as f:
for line in f:
self.insertAnyTable(table, [str(line), '1'])
def active_flag(self, button):
if not self.status_flag:
self.status_flag = True
self.submitSearchButton.setBackground(Color.GRAY)
self.appendToResults("Proxy start...\n")
else:
self.status_flag = False
self.submitSearchButton.setBackground(Color.WHITE)
self.appendToResults("Proxy stop...\n")
def overwriteHeader(self, button):
if not self._overwriteHeader:
self._overwriteHeader = True
self._overwriteHeaderButton.setBackground(Color.GRAY)
else:
self._overwriteHeader = False
self._overwriteHeaderButton.setBackground(Color.WHITE)
def overwriteParam(self, button):
if not self._overwriteParam:
self._overwriteParam = True
self._overwriteParamButton.setBackground(Color.GRAY)
else:
self._overwriteParam = False
self._overwriteParamButton.setBackground(Color.WHITE)
def forkRequest(self, button):
if not self._forkRequestParam:
self._forkRequestParam = True
self._forkRequestButton.setBackground(Color.GRAY)
else:
self._forkRequestParam = False
self._forkRequestButton.setBackground(Color.WHITE)
def prepareRequest(self, requestString, messageInfo=None):
requestString = str(requestString)
listHeader = re.findall('([\w-]+):\s?(.*)', requestString)
dictRealHeaders = {x[0].lower(): x[1] for x in listHeader}
selectedPayloads = {}
for ind, k in enumerate(self._dictPayloads):
if self._dictPayloads[k] == '1':
selectedPayloads[k] = '1'
else:
continue
for index, key in enumerate(self._dictHeaders):
if key.lower() in dictRealHeaders.keys(
) and self._dictHeaders[key] == '1':
if len(self._dictPayloads.keys()) == 0:
pass
elif self._overwriteHeader:
payload = random.choice(selectedPayloads.keys())
payload = payload.replace(r"{URL}",
self._jTextFieldURL.getText(), 1)
requestString = requestString.replace(
dictRealHeaders.get(key.lower()), payload, 1)
elif not self._overwriteHeader:
payload = random.choice(selectedPayloads.keys())
payload = payload.replace(r"{URL}",
self._jTextFieldURL.getText(), 1)
payload = dictRealHeaders.get(key.lower()) + payload
requestString = requestString.replace(
dictRealHeaders.get(key.lower()), payload, 1)
else:
pass
for index, key in enumerate(self._dictParams):
analyzed = self._helpers.analyzeRequest(requestString.encode())
param = analyzed.getParameters()
dictRealParams = {
x.getName().lower():
[x.getValue(),
x.getValueStart(),
x.getValueEnd()]
for x in param
}
if key.lower() in dictRealParams.keys(
) and self._dictParams[key] == '1':
if len(self._dictPayloads.keys()) == 0:
pass
elif self._overwriteParam:
payload = random.choice(selectedPayloads.keys())
payload = payload.replace(r"{URL}",
self._jTextFieldURL.getText(), 1)
start_word = dictRealParams[key.lower()][1]
end_word = dictRealParams[key.lower()][2]
requestString = requestString[:
start_word] + payload + requestString[
end_word:]
elif not self._overwriteParam:
payload = random.choice(selectedPayloads.keys())
payload = payload.replace(r"{URL}",
self._jTextFieldURL.getText(), 1)
payload = dictRealParams[key.lower()][0] + payload
start_word = dictRealParams[key.lower()][1]
end_word = dictRealParams[key.lower()][2]
requestString = requestString[:
start_word] + payload + requestString[
end_word:]
else:
pass
return requestString
def processHttpMessage(self, toolFlag, messageIsRequest, messageInfo):
if not self.status_flag:
return
# only process requests
if not messageIsRequest:
return
if self._forkRequestParam:
requestString = messageInfo.getRequest().tostring()
# SOOOO HARD FIX! It should be better
if requestString[0] == '@':
messageInfo.setRequest(
self._helpers.stringToBytes(requestString[1:]))
else:
newRequestString = self.prepareRequest(requestString,
messageInfo)
self.appendToResults('Parallel Request:')
self.appendToResults(newRequestString.encode())
newRequestString = '@' + newRequestString
func = self._callbacks.makeHttpRequest
thread = Thread(
target=func,
args=(messageInfo.getHttpService(),
self._helpers.stringToBytes(newRequestString)))
thread.start()
else:
requestString = messageInfo.getRequest().tostring()
newRequestString = self.prepareRequest(requestString, messageInfo)
self.appendToResults(newRequestString.encode())
messageInfo.setRequest(
self._helpers.stringToBytes(newRequestString))
# Fnction to provide output to GUI
def appendToResults(self, s):
def appendToResults_run(s):
self._resultsTextArea.append(s)
self._resultsTextArea.append('\n')
swing.SwingUtilities.invokeLater(
PyRunnable(appendToResults_run, str(s)))
def addFromFileAsync(self, file, table):
def addFromFile_run(file, table):
if os.path.exists(file):
with open(file, 'r') as f:
for row in f.readlines():
if row != '':
temp = row[:-1] if row[-1] == '\n' else row
self.insertAnyTable(table, [str(temp), '1'])
swing.SwingUtilities.invokeLater(
PyRunnable(addFromFile_run, file, table))
def saveToFileAsync(self, file, data, isAppend=False):
def saveToFile_run(file, data, isAppend):
isAppend = 'w'
with open(file, isAppend) as f:
for i, k in enumerate(data):
f.write("{}\n".format(k))
f.seek(-1, os.SEEK_END)
f.truncate()
swing.SwingUtilities.invokeLater(
PyRunnable(saveToFile_run, file, data, isAppend))
def getTabCaption(self):
return self.name
def getUiComponent(self):
return self._jPanel
class ConsolePanel(Panel):
def __init__(self):
self.console = None
self.outText = None
self.inText = None
self.outTextScroller = None
self.nestedInputPanel = None
self.directoryText = None
Panel.__init__(self, "insets 0 0 0 0")
def sendCommand(self, command):
print str(self)
oldText = self.inText.getText()
self.inText.setText(command)
self.inText.getActionListeners()[0].actionPerformed(None)
self.inText.setText(oldText)
def setDirectoryText(self, dirText):
self.directoryText.setText(dirText)
self.nestedInputPanel.revalidate()
def write_out(self, text):
if not self.outText:
return
self.outText.setText(self.outText.getText() + text)
def initUI(self):
font = Font("Courier New", Font.BOLD, 14)
#create the output text panel
self.outText = JTextArea()
self.outText.setEditable(False)
self.outText.setFont(font)
self.outText.setWrapStyleWord(True)
self.outText.setLineWrap(True)
#self.outText.setLineWrap(True)
#self.outText.setWrapStyleWord(True)
class NoGhostScroller(JScrollPane):
def paintComponent(self, g):
g.setColor(self.getBackground())
g.fillRect(0, 0, self.getWidth(), self.getHeight())
#super(NoGhostScroller, self).paintComponent(g)
self.outTextScroller = JScrollPane(self.outText)
self.outTextScroller.setHorizontalScrollBarPolicy(
ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER)
self.outTextScroller.getVerticalScrollBar().setForeground(
Color(255, 0, 0))
#self.outText.setOpaque(False)
self.outText.setBackground(Color(0, 20, 0))
self.outText.setForeground(Color.WHITE)
#self.outTextScroller.setOpaque(False)
self.outTextScroller.setBackground(Color(0, 20, 0))
#self.outText.repaint()
#self.layered = JLayeredPane()
#self.layered.setLayer(self.outTextScroller, 0)
#create the input text box
self.inText = JTextField()
self.inText.setFocusTraversalKeysEnabled(False)
self.inText.setFont(font)
self.inText.setBackground(Color(0, 20, 0))
self.inText.setForeground(Color.WHITE)
self.inText.getCaret().setVisible(True)
self.inText.getCaret().setBlinkRate(500)
self.inText.setCaretColor(Color(200, 255, 200))
class InFocusAdapter(FocusAdapter):
def focusLost(adap, e):
self.inText.setVisible(True)
self.inText.addFocusListener(InFocusAdapter())
self.nestedInputPanel = Panel("Insets 0 0 0 0")
#create the directory text box
self.directoryText = JTextField()
self.directoryText.setEditable(False)
self.directoryText.setFont(font)
self.directoryText.setBackground(Color(0, 20, 0))
self.directoryText.setForeground(Color.WHITE)
#set up the console
sys.stdout = FakeOut(self.outText)
self.console = BashED_Console(stdout=sys.stdout)
self.directoryText.setText(self.console.get_prompt())
self.revalidate()
dirTex = self.directoryText
#create the listener that fires when the 'return' key is pressed
class InputTextActionListener(ActionListener):
def __init__(self, parent, inp, out, console):
self.parent = parent
self.inp = inp
self.out = out
self.console = console
def actionPerformed(self, e):
#print self.getCommandText()
# print(self.console.get_prompt())
# self.console.onecmd(self.inp.getText())
# self.parent.write_out("\n" + self.inp.getText())
# dirTex.setText(self.console.get_prompt())
# self.inp.setText("")
self.parent.write_out(self.console.get_prompt() +
self.inp.getText() + '\n')
if 'clear' in self.inp.getText().split(' ')[0]:
self.out.setText("") #clear the screen
else:
self.console.onecmd(self.inp.getText())
dirTex.setText(self.console.get_prompt())
self.inp.setText("")
#create the listener that fires whenever a user hits a key
class InputKeyActionListener(KeyAdapter):
def __init__(self, parent, inp, out, console):
self.parent = parent
self.inp = inp
self.out = out
self.console = console
def keyReleased(self, k):
inp = self.inp.getText()
if k.getKeyCode() == 9: #tab character
autos = self.console.tabcomplete(self.inp.getText())
if len(autos) == 1:
self.inp.setText(autos[0])
else:
i = 0
for option in autos:
self.parent.write_out(option)
if i % 3 == 0:
print('\n')
else:
print('\t')
hist = None
if k.getKeyCode() == 38:
hist = self.console.next_hist()
if k.getKeyCode() == 40:
hist = self.console.last_hist()
if hist:
self.inp.setText(hist.rstrip('\n')) #prevent from firing
self.inText.addActionListener(
InputTextActionListener(self, self.inText, self.outText,
self.console))
self.inText.addKeyListener(
InputKeyActionListener(self, self.inText, self.outText,
self.console))
def addUI(self):
self.add(self.outTextScroller, "cell 0 0, push, grow")
self.add(self.nestedInputPanel, "cell 0 1, pushx, growx")
self.nestedInputPanel.add(self.directoryText, "cell 0 0")
self.nestedInputPanel.add(self.inText, "cell 1 0, spanx, pushx, growx")
class BobGui(JFrame):
def __init__(self):
super(BobGui, self).__init__('BobPy')
# cls = self.getClass()
# print(cls)
# self.setLayout(MigLayout())
self.setLayout(BorderLayout())
self.main_panel = JPanel()
self.main_panel.setLayout(MigLayout())
dir_panel = JPanel()
dir_panel.setLayout(BoxLayout(dir_panel, BoxLayout.X_AXIS))
dir_label = JLabel('Experiment Folder:')
dir_panel.add(dir_label)
self.dir_text_field = JTextField(10)
self.dir_text_field.addActionListener(
ActionListenerFactory(self, self.text_field_al))
dir_panel.add(self.dir_text_field)
dir_button = JButton('open')
dir_button.addActionListener(
ActionListenerFactory(self, self.choose_dir_al))
dir_panel.add(dir_button)
self.main_panel.add(dir_panel, 'growx, spanx, pushx, wrap')
add_key_args(self.main_panel, 'close_w',
ActionListenerFactory(self, self.close_al), KeyEvent.VK_W,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask())
self.add(self.main_panel, BorderLayout.CENTER)
self.setPreferredSize(Dimension(500, 400))
self.pack()
self.setLocationRelativeTo(None)
self.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE)
self.setVisible(True)
def show_exper_info_old(self):
# sb = br.SimilarityBuilder()
cab = br.CollectionArchetypeBuilder()
for hseg in self.exper.hsegs():
all_file_dict = hseg.file_dict()
all_file_dict.update(hseg.cell_file_dict())
all_file_dict.update(hseg.bin_file_dict())
cab.add_collection(hseg.name, all_file_dict)
hseg_at, hseg_at_deviations = cab.get_archetype_info()
at_str = ''
for val in hseg_at:
at_str += str(val) + '\n'
chf_panel = self.make_chf_panel(at_str)
hseg_tree_panel = self.make_hseg_tree_panel(hseg_at_deviations)
self.split_pane = JSplitPane(JSplitPane.HORIZONTAL_SPLIT)
self.split_pane.setOneTouchExpandable(True)
self.split_pane.setContinuousLayout(True)
self.split_pane.setResizeWeight(0.5)
self.split_pane.add(chf_panel)
self.split_pane.add(hseg_tree_panel)
self.main_panel.add(self.split_pane, 'grow')
self.revalidate()
def show_exper_info(self):
# sb = br.SimilarityBuilder()
# cab = br.CollectionArchetypeBuilder()
#
# for hseg in self.exper.hsegs() :
# all_file_dict = hseg.file_dict()
# all_file_dict.update(hseg.cell_file_dict())
# all_file_dict.update(hseg.bin_file_dict())
# cab.add_collection(hseg.name, all_file_dict)
#
# hseg_at, hseg_at_deviations = cab.get_archetype_info()
#
# at_str = ''
# for val in hseg_at :
# at_str += str(val) + '\n'
chf_panel = self.make_chf_panel()
hseg_tree_panel = self.make_hseg_tree_panel()
self.split_pane = JSplitPane(JSplitPane.HORIZONTAL_SPLIT)
self.split_pane.setOneTouchExpandable(True)
self.split_pane.setContinuousLayout(True)
self.split_pane.setResizeWeight(0.5)
self.split_pane.add(chf_panel)
self.split_pane.add(hseg_tree_panel)
self.main_panel.add(self.split_pane, 'grow')
self.revalidate()
def make_chf_panel_old(self, at_str):
""" cf --> common hseg files """
chf_panel = JPanel()
# chf_panel.setLayout(BoxLayout(chf_panel, BoxLayout.Y_AXIS))
chf_panel.setLayout(MigLayout('insets 0'))
# chf_panel.setAlignmentX(Component.LEFT_ALIGNMENT)
chf_label = JLabel('Common Hemeisegment Files')
# chf_label.setAlignmentX(Component.LEFT_ALIGNMENT)
chf_panel.add(chf_label, 'grow, wrap')
chf_text_area = JTextArea(at_str)
chf_panel.add(chf_text_area, 'grow, push, span')
return chf_panel
def make_chf_panel(self):
""" chf --> common hseg files """
chf_panel = JPanel()
# chf_panel.setLayout(BoxLayout(chf_panel, BoxLayout.Y_AXIS))
chf_panel.setLayout(MigLayout('insets 0'))
# chf_panel.setAlignmentX(Component.LEFT_ALIGNMENT)
chf_files_label = JLabel('Hemisegment cells')
chf_files_text = JTextArea(
BobGui.archetype_to_str(
self.exper.hseg_cell_files_cab().archetype))
chf_panel.add(chf_files_label, 'growx, wrap')
chf_panel.add(chf_files_text, 'grow, wrap')
chf_files_label = JLabel('Hemisegment binary image files')
chf_files_text = JTextArea(
BobGui.archetype_to_str(self.exper.hseg_bin_files_cab().archetype))
chf_panel.add(chf_files_label, 'growx, wrap')
chf_panel.add(chf_files_text, 'grow, wrap')
chf_files_label = JLabel('Other hemisegment files')
chf_files_text = JTextArea(
BobGui.archetype_to_str(self.exper.hseg_files_cab().archetype))
chf_panel.add(chf_files_label, 'growx, wrap')
chf_panel.add(chf_files_text, 'grow')
# chf_label = JLabel('Common Hemeisegment Files')
# # chf_label.setAlignmentX(Component.LEFT_ALIGNMENT)
#
# chf_panel.add(chf_label, 'grow, wrap')
#
# chf_text_area = JTextArea(at_str)
# chf_panel.add(chf_text_area, 'grow, push, span')
return chf_panel
@staticmethod
def archetype_to_str(archetype):
at_str = ''
for val in archetype:
at_str += str(val) + '\n'
return at_str
# def make_hseg_tree_panel(self, hseg_at_deviations) :
def make_hseg_tree_panel(self):
root = DefaultMutableTreeNode(self.exper.name)
for hseg in self.exper.hsegs():
hseg_node = DefaultMutableTreeNode(hseg.name)
root.add(hseg_node)
hseg_at_deviations = self.exper.hseg_all_files_cab(
).archetype_deviations
if len(hseg_at_deviations[hseg.name]) > 0:
for definer, file_names in hseg_at_deviations[
hseg.name].items():
for file_name in file_names:
node_str = definer + ': ' + file_name
temp = DefaultMutableTreeNode(node_str)
hseg_node.add(temp)
hseg_tree = JTree(root)
hseg_tree.setCellRenderer(BobPyTreeCellRenderer())
hseg_scroll_pane = JScrollPane()
hseg_scroll_pane.getViewport().setView((hseg_tree))
return hseg_scroll_pane
def text_field_al(self, e):
self.dir_path = self.dir_text_field.getText()
self.got_exper(self.dir_path)
def choose_dir_al(self, e):
dc = DirectoryChooser('Choose a bob_py experiment folder')
self.dir_path = dc.getDirectory()
self.dir_text_field.setText(self.dir_path)
self.got_exper(self.dir_path)
def close_al(self, e):
self.dispatchEvent(WindowEvent(self, WindowEvent.WINDOW_CLOSING))
def got_exper(self, dir_path):
self.exper = bob_py.Exper(dir_path)
self.show_exper_info()
class ProfelisPanel(JPanel):
def __init__(self, frame, name):
self.frame = frame
self.exception = None
self.name = name
self.searchTerm = None
self.searchIndex = -1
self.searchField = JTextField("")
self.searchField.addActionListener(SearchListener(self))
self.newGeneFrom = JTextField("")
self.newGeneTo = JTextField("")
self.newGeneButton = JButton("New Gene")
newGeneActionListener = NewGeneActionListener(self)
self.newGeneFrom.addActionListener(newGeneActionListener)
self.newGeneTo.addActionListener(newGeneActionListener)
self.newGeneButton.addActionListener(newGeneActionListener)
self.markForRemovalButton = JButton("Mark For Removal")
self.markForRemovalButton.addActionListener(
MarkForRemovalListener(self))
self.inGenes = JList(DefaultListModel())
self.inGenes.selectionMode = ListSelectionModel.SINGLE_SELECTION
self.inGenes.cellRenderer = ProfelisCellRenderer()
self.markButtonLabelerTimer = Timer(100, MarkButtonLabeler(self))
self.markButtonLabelerTimer.start()
self.loadFile()
self.outGenes = JList(DefaultListModel())
self.outGenes.selectionMode = ListSelectionModel.SINGLE_SELECTION
self.outGenes.cellRenderer = ProfelisCellRenderer()
constraints = GridBagConstraints()
self.layout = GridBagLayout()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.add(JLabel("Genes In Artemis File"), constraints)
constraints.gridx, constraints.gridy = 0, 1
self.add(JButton(RemoveAction(self)), constraints)
constraints.gridx, constraints.gridy = 1, 1
self.add(self.markForRemovalButton, constraints)
constraints.gridx, constraints.gridy = 2, 1
self.add(JLabel("Search"), constraints)
constraints.gridx, constraints.gridy = 3, 1
constraints.fill = GridBagConstraints.HORIZONTAL
self.add(self.searchField, constraints)
constraints.gridx, constraints.gridy = 0, 2
constraints.gridwidth, constraints.gridheight = 4, 2
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.add(JScrollPane(self.inGenes), constraints)
constraints.gridx, constraints.gridy = 4, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.add(JLabel("Genes To Add To Artemis File"), constraints)
constraints.gridx, constraints.gridy = 4, 1
self.add(self.newGeneButton, constraints)
constraints.weightx = 1
constraints.fill = GridBagConstraints.BOTH
constraints.gridx, constraints.gridy = 5, 1
self.add(self.newGeneFrom, constraints)
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.gridx, constraints.gridy = 6, 1
self.add(JLabel("To"), constraints)
constraints.weightx = 1
constraints.fill = GridBagConstraints.BOTH
constraints.gridx, constraints.gridy = 7, 1
self.add(self.newGeneTo, constraints)
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.gridx, constraints.gridy = 4, 2
self.add(JButton(AddGenesAction(self)), constraints)
constraints.gridx, constraints.gridy = 4, 3
constraints.gridwidth, constraints.gridheight = 4, 1
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.add(JScrollPane(self.outGenes), constraints)
def loadFile(self):
self.inGenes.model.clear()
self.database, self.evalue, genes = utils.parseBlast(self.name +
".blastp.xml")
[self.inGenes.model.addElement(gene) for gene in genes]
artemisInput = open(self.name + ".art", "r")
lines = artemisInput.readlines()
artemisInput.close()
self.restOfFile = self.genome = []
while lines:
if re.match("\s+CDS\s+(complement\()?\d+\.\.\d+\)?\n", lines[0]):
lines = lines[4:]
elif lines[0].find("ORIGIN") == 0:
self.genome = map(lambda x: re.sub("\s+", "", x), lines[1:])
lines = []
else:
if lines[0].strip():
self.restOfFile.append(lines[0])
lines = lines[1:]
self.genome = "".join(self.genome)
self.restOfFile = "".join(self.restOfFile)
def writeArtemisFile(self):
output = open(self.name + ".art", "w")
output.write(self.restOfFile)
for element in self.inGenes.model.elements():
output.write(element.toArtemis())
output.write("\nORIGIN\n\n")
for i in range(0, len(self.genome), 50):
output.write(self.genome[i:min(i + 50, len(self.genome))] + "\n")
output.close()
class FEA_BC_ConfigPanel(JPanel):
cbBlockchainCheck = None
tbHitlist = None
blockchainCheck = True
hitlist = "testlist"
maxTimeout = 5
tbMaxBCHits = None
def __init__(self):
self.initComponents()
#get previous settings selected by the user
if (ModuleSettings.getConfigSetting("FEA", "hitlist") != None) and (
ModuleSettings.getConfigSetting("FEA", "hitlist") != ""):
if ModuleSettings.getConfigSetting("FEA", "hitlist"):
self.tbHitlist.text = ModuleSettings.getConfigSetting(
"FEA", "hitlist")
else:
self.tbHitlist.text = "testlist"
if (ModuleSettings.getConfigSetting("FEA", "maxTimeout") != None) and (
ModuleSettings.getConfigSetting("FEA", "maxTimeout") != ""):
if ModuleSettings.getConfigSetting("FEA", "maxTimeout"):
self.tbMaxBCHits.text = ModuleSettings.getConfigSetting(
"FEA", "maxTimeout")
else:
self.tbMaxBCHits.text = "5"
if (ModuleSettings.getConfigSetting("FEA", "blockchainCheck") !=
None) and (ModuleSettings.getConfigSetting(
"FEA", "blockchainCheck") != ""):
if ModuleSettings.getConfigSetting("FEA", "blockchainCheck"):
self.cbBlockchainCheck.setSelected(True)
self.blockchainCheck = True
else:
self.cbBlockchainCheck.setSelected(False)
self.blockchainCheck = False
def addStatusLabel(self, msg):
gbc = GridBagConstraints()
gbc.anchor = GridBagConstraints.NORTHWEST
gbc.gridx = 0
gbc.gridy = 7
lab = JLabel(msg)
self.add(lab, gbc)
def getHitlist(self):
return self.hitlist
def getBlockchainCheck(self):
return self.blockchainCheck
def getMaxTimeout(self):
return self.maxTimeout
def initComponents(self):
self.setLayout(GridBagLayout())
gbc = GridBagConstraints()
gbc.anchor = GridBagConstraints.NORTHWEST
gbc.gridx = 0
gbc.gridy = 0
descriptionLabel = JLabel("FEA - BitCoin Validation module")
self.add(descriptionLabel, gbc)
tlHitlist = JLabel("Base list of hashes to analyze: ")
gbc.gridy = 1
self.add(tlHitlist, gbc)
self.tbHitlist = JTextField("testlist", 20)
self.tbHitlist.addActionListener(self.tbHitlistActionPerformed)
gbc.gridx = 1
self.add(self.tbHitlist, gbc)
gbc.gridx = 0
self.cbBlockchainCheck = JCheckBox(
"Query Blockchain.info",
actionPerformed=self.cbBlockchainCheckActionPerformed)
self.cbBlockchainCheck.setSelected(True)
gbc.gridy = 2
self.add(self.cbBlockchainCheck, gbc)
tlBCMaxHits = JLabel(
"Timeout (in seconds) between calls to Blockchain.info: ")
gbc.gridy = 3
self.add(tlBCMaxHits, gbc)
self.tbMaxBCHits = JTextField("5", 5)
self.tbMaxBCHits.addActionListener(self.tbMaxBCHitsActionPerformed)
gbc.gridx = 1
self.add(self.tbMaxBCHits, gbc)
def tbMaxBCHitsActionPerformed(self, event):
source = event.getSource()
self.maxTimeout = int(float(source.getText()))
ModuleSettings.setConfigSetting("FEA", "maxTimeout", self.maxTimeout)
def tbHitlistActionPerformed(self, event):
source = event.getSource()
self.hitlist = source.getText()
ModuleSettings.setConfigSetting("FEA", "hitlist", self.hitlist)
def cbBlockchainCheckActionPerformed(self, event):
source = event.getSource()
if (source.isSelected()):
ModuleSettings.setConfigSetting("FEA", "blockchainCheck", "true")
self.blockchainCheck = True
else:
ModuleSettings.setConfigSetting("FEA", "blockchainCheck", "false")
self.blockchainCheck = False
class spyTailMonitor(JPanel, ActionListener):
length = 10 # Number of words per line
def __init__(self, parentCrate=None):
JPanel.__init__(self)
self.spy = None
self.parentCrate = parentCrate
self.nw = 10 # Number of words (total)
self.upperPanel = JPanel()
self.lowerPanel = JPanel()
self.add(self.upperPanel)
self.add(self.lowerPanel)
self.nameLabel = JLabel("n/a")
self.slotLabel = JLabel("n/a")
self.textArea = JTextArea("n/a", 1, 70, editable=0)
self.scrollPane = JScrollPane(self.textArea)
self.textField = JTextField(3,
actionCommand="textField",
text=("%d" % self.nw))
self.textField.addActionListener(self)
self.clearButton = JButton("Stop", actionCommand="button")
self.clearButton.addActionListener(self)
self.border = BorderFactory.createEmptyBorder(5, 5, 5, 5)
self.layout = BoxLayout(self, BoxLayout.Y_AXIS)
self.upperPanel.layout = BoxLayout(self.upperPanel, BoxLayout.X_AXIS)
self.lowerPanel.layout = BoxLayout(self.lowerPanel, BoxLayout.X_AXIS)
self.upperPanel.add(self.clearButton)
self.upperPanel.add(Box.createRigidArea(Dimension(20, 0)))
self.upperPanel.add(JLabel("Spy:"))
self.upperPanel.add(Box.createRigidArea(Dimension(5, 0)))
self.upperPanel.add(self.nameLabel)
self.upperPanel.add(Box.createRigidArea(Dimension(20, 0)))
self.upperPanel.add(JLabel("Slot:"))
self.upperPanel.add(Box.createRigidArea(Dimension(5, 0)))
self.upperPanel.add(self.slotLabel)
self.upperPanel.add(Box.createRigidArea(Dimension(20, 0)))
self.upperPanel.add(JLabel("Number of words:"))
self.upperPanel.add(Box.createRigidArea(Dimension(5, 0)))
self.upperPanel.add(self.textField)
self.upperPanel.add(Box.createHorizontalGlue())
self.lowerPanel.add(JLabel("Tail contents:"))
self.lowerPanel.add(Box.createRigidArea(Dimension(5, 0)))
self.lowerPanel.add(self.scrollPane)
self.lowerPanel.add(Box.createHorizontalGlue())
def setSpy(self, spy):
self.spy = spy
self.nameLabel.text = spy.name
self.slotLabel.text = "%d" % spy.board.slot
self.textArea.text = "n/a"
def update(self):
if self.spy != None:
array = self.spy.readTail(self.nw)
text = "%6.6x" % array[0]
for i in range(1, len(array)): # len(array) = len(array[1:])+1
if i % 10:
text = text + " %6.6x" % array[i]
else:
text = text + "\n%6.6x" % array[i]
self.textArea.text = text
def actionPerformed(self, event):
if event.actionCommand == "button":
self.spy = None
self.nameLabel.text = "n/a"
self.slotLabel.text = "n/a"
self.textArea.text = "n/a"
self.textArea.rows = 1
elif event.actionCommand == "textField":
self.nw = eval(self.textField.text)
self.textArea.rows = min(
[int(math.ceil(self.nw / self.length)), 10])
if self.parentCrate != None:
self.parentCrate.frame.pack()
###########################################################################
##### Main code #####
###########################################################################
# Set up the fields for the SWING interface
minField = JFormattedTextField( 0 )
minField.addActionListener( ChangedMin(minField) )
maxField = JFormattedTextField( 255 )
maxField.addActionListener( ChangedMax(maxField) )
scoreField = JTextField( "" )
scoreField.addActionListener( NextImage(scoreField) )
scoreField.addActionListener( WriteScore(scoreField) )
button = JButton("Previous image")
button.addActionListener( PreviousImage(scoreField) )
# Pack all the fields into a JPanel
all = JPanel()
layout = GridLayout(4, 1)
all.setLayout(layout)
all.add( JLabel(" ") )
all.add( button )
all.add( JLabel("Min") )
all.add( minField )
all.add( JLabel("Max") )
all.add(maxField )
class ConsoleController:
def __init__(self, parent):
self._parent = parent
self._sessions = self._parent.sessions()
self._request = None #TODO I'll need a request in order to connect to something
self._position = None #TODO I'll need a position, something to change in the header to insert the command
self._pwd = None
self._commandHistory = []
self._historyIndex = 0
self._tabComplete = []
def getMainComponent(self):
self._mainPanel = JPanel(BorderLayout())
# input
self._consolePwd = JTextField()
self._consolePwd.setEditable(False)
self._consolePwd.setText("Not initialized")
self._consoleInput = JTextField()
#Remove 'tab' low-level tab-function of jumping to other component, so I can use it
self._consoleInput.setFocusTraversalKeys(KeyboardFocusManager.FORWARD_TRAVERSAL_KEYS, Collections.EMPTY_SET)
self._consoleInput.addActionListener(self.EnterPress())
self._consoleInput.addKeyListener(self.KeyPress())
self._inputPanel = JPanel(BorderLayout())
self._inputPanel.add(self._consolePwd, BorderLayout.WEST)
self._inputPanel.add(self._consoleInput, BorderLayout.CENTER)
# output
self._consoleOutput = JTextArea()
self._consoleOutput.setEditable(False)
self._consoleOutput.setForeground(Color.WHITE)
self._consoleOutput.setBackground(Color.BLACK)
self._consoleOutput.setFont(self._consoleOutput.getFont().deriveFont(12.0))
self._scrollPaneConsoleOutput = JScrollPane(self._consoleOutput)
# Add to main panel and return the main panel
self._mainPanel.add(self._scrollPaneConsoleOutput, BorderLayout.CENTER)
self._mainPanel.add(self._inputPanel, BorderLayout.SOUTH)
return self._mainPanel
def sendCommand(self, requestId, cmd, directTo):
Utils.out("ConsoleController > sendCommand > 'cmd'")
Utils.out(cmd)
if cmd == 'clear':
self.resetOutput()
self._commandHistory.append(cmd)
self.resetHistoryIndex()
self.clearCmd()
return
cmdModified = cmd
requestHttpMethod = self._parent.getRequestHttpService(requestId)
#If I use virtual persistence and there's already a pwd set
if Utils.shellController._virtualPersistence and self.pwd():
#Then always prepend 'cd <pwd>' to any command executed. In reality we
# always enter in the same directory, but because this shell keeps track
# of where the user thinks he is, and always goes to that directory first
# the illusion of a persistence is created
cmdVirtual = "cd " + self.pwd()
cmdModified = cmdVirtual + "; " + cmd
requestWithCommand = self._parent.getRequestWithCommand(requestId, cmdModified)
Thread(GetThreadForRequest(requestHttpMethod, requestWithCommand, directTo)).start()
self._commandHistory.append(cmd)
self.resetHistoryIndex()
self.clearCmd()
if Utils.shellController._virtualPersistence:
if cmd.startswith('cd '):
Utils.out("ConsoleController > sendCommand: detected 'cd '")
#ask for pwd
cmdPwd = cmdModified + "; " + Commands.pwd(Commands.OS_LINUX)
requestWithCommand = self._parent.getRequestWithCommand(requestId, cmdPwd)
Thread(GetThreadForRequest(requestHttpMethod, requestWithCommand, 'pwd')).start()
if Utils.shellController._tabCompletion:
#ask 'ls -1a' for tab-completion
# The first command, pwd is set here, but cmdVirtual ain't. But this
# also means we are at the entry directory anyway, so we can just ask ls
# and get the correct tab completion anyway
try:
cmdTabComplete = cmdVirtual + "; " + Commands.ls(Commands.OS_LINUX)
except:
cmdTabComplete = Commands.ls(Commands.OS_LINUX)
requestWithCommand = self._parent.getRequestWithCommand(requestId, cmdTabComplete)
Thread(GetThreadForRequest(requestHttpMethod, requestWithCommand, 'tabComplete')).start()
else:
if Utils.shellController._tabCompletion:
cmdTabComplete = Commands.ls(Commands.OS_LINUX)
requestWithCommand = self._parent.getRequestWithCommand(requestId, cmdTabComplete)
Thread(GetThreadForRequest(requestHttpMethod, requestWithCommand, 'tabComplete')).start()
#either way execute the requested command
def startSession(self):
#TODO when starting a session I want to test for a number of things:
# if I can reform the request to a post request and still have it work
# if base 64 is available
# if bash is available
self.setPwd(None)
if Utils.shellController._virtualPersistence and Utils.shellController._outputIsolator:
Utils.out("startSession > virtualPersistence enabled > Requesting pwd")
self.sendCommand(self._parent.currentRequestId(), Commands.pwd(Commands.OS_LINUX), 'pwd')
def appendOutput(self, text, printCommand=True):
try:
if printCommand:
self.printCommand(self._commandHistory[-1])
except:
pass
self._consoleOutput.append("\n" + text)
#auto scroll down if needed
self._consoleOutput.setCaretPosition(self._consoleOutput.getDocument().getLength())
def resetOutput(self):
Utils.setConsole('')
def printCommand(self, cmd):
self._consoleOutput.append("\n" + self._pwd + "# " + cmd)
def printCurrentCommand(self):
self.printCommand(self.cmd())
def setPwd(self, pwd):
self._pwd = pwd
if pwd is None:
self._consolePwd.setText('')
else:
self._consolePwd.setText(pwd)
Utils.consoleController._mainPanel.revalidate()
def pwd(self):
return self._pwd
def cmdHistoryCount(self):
return len(self._commandHistory) #TODO - 1
def setCmd(self, cmd):
self._consoleInput.setText(cmd)
def cmd (self):
return self._consoleInput.getText()
def clearCmd(self):
self._consoleInput.setText('')
def resetHistoryIndex(self):
self._historyIndex = self.cmdHistoryCount()
def previousCommand(self):
if self._historyIndex > 0:
self._historyIndex -= 1
self.setCmd(self._commandHistory[self._historyIndex])
def nextCommand(self):
if self._historyIndex < self.cmdHistoryCount():
self._historyIndex += 1
self.setCmd(self._commandHistory[self._historyIndex])
else:
self.clearCmd()
self.resetHistoryIndex()
def setTabComplete(self, text):
self._tabComplete = text.splitlines()
def findTabComplete(self, beginCharacters=''):
suggestions = []
if beginCharacters:
for suggestion in self._tabComplete:
Utils.debug("suggestion", suggestion)
Utils.debug("text", beginCharacters)
if suggestion[0:len(beginCharacters)] == beginCharacters:
suggestions.append(suggestion)
else:
suggestions = self._tabComplete
return suggestions
def tabComplete(self):
currentCommand = self.cmd()
Utils.debug("currentCommand", currentCommand)
if currentCommand:
commandArray = currentCommand.split(' ')
lastword = commandArray.pop()
Utils.debug("lastword", lastword)
suggestions = self.findTabComplete(lastword)
if suggestions:
if len(suggestions) > 1:
self.printCurrentCommand()
for suggestion in suggestions:
self.appendOutput(suggestion, False)
if len(suggestions) == 1:
self.setCmd(' '.join(commandArray) + ' ' + suggestions.pop())
else:
suggestions = self.findTabComplete()
if len(suggestions) > 1:
self.printCurrentCommand()
for suggestion in suggestions:
self.appendOutput(suggestion, False)
class EnterPress(ActionListener): #TODO remove: AbstractAction
def actionPerformed(self, e):
Utils.consoleController.sendCommand(Utils.shellController.currentRequestId(), Utils.consoleInput.getText(), 'console')
def keyPressed(self, e):
Utils.out("key pressed")
class KeyPress(KeyListener):
def keyTyped(self, e):
pass
def keyReleased(self, e):
if e.getKeyCode() == e.VK_DOWN:
Utils.consoleController.nextCommand()
Utils.out("released down")
if e.getKeyCode() == e.VK_UP:
Utils.consoleController.previousCommand()
Utils.out("released up")
if e.getKeyCode() == e.VK_TAB:
Utils.out("pressed tab")
Utils.consoleController.tabComplete()
def keyPressed(self, e):
pass
class ProfelisPanel(JPanel):
def __init__(self, frame, name):
self.frame = frame
self.exception = None
self.name = name
self.searchTerm = None
self.searchIndex = -1
self.searchField = JTextField("")
self.searchField.addActionListener(SearchListener(self))
self.newGeneFrom = JTextField("")
self.newGeneTo = JTextField("")
self.newGeneButton = JButton("New Gene")
newGeneActionListener = NewGeneActionListener(self)
self.newGeneFrom.addActionListener(newGeneActionListener)
self.newGeneTo.addActionListener(newGeneActionListener)
self.newGeneButton.addActionListener(newGeneActionListener)
self.markForRemovalButton = JButton("Mark For Removal")
self.markForRemovalButton.addActionListener(MarkForRemovalListener(self))
self.inGenes = JList(DefaultListModel())
self.inGenes.selectionMode = ListSelectionModel.SINGLE_SELECTION
self.inGenes.cellRenderer = ProfelisCellRenderer()
self.markButtonLabelerTimer = Timer(100, MarkButtonLabeler(self))
self.markButtonLabelerTimer.start()
self.loadFile()
self.outGenes = JList(DefaultListModel())
self.outGenes.selectionMode = ListSelectionModel.SINGLE_SELECTION
self.outGenes.cellRenderer = ProfelisCellRenderer()
constraints = GridBagConstraints()
self.layout = GridBagLayout()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.add(JLabel("Genes In Artemis File"), constraints)
constraints.gridx, constraints.gridy = 0, 1
self.add(JButton(RemoveAction(self)), constraints)
constraints.gridx, constraints.gridy = 1, 1
self.add(self.markForRemovalButton, constraints)
constraints.gridx, constraints.gridy = 2, 1
self.add(JLabel("Search"), constraints)
constraints.gridx, constraints.gridy = 3, 1
constraints.fill = GridBagConstraints.HORIZONTAL
self.add(self.searchField, constraints)
constraints.gridx, constraints.gridy = 0, 2
constraints.gridwidth, constraints.gridheight = 4, 2
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.add(JScrollPane(self.inGenes), constraints)
constraints.gridx, constraints.gridy = 4, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.add(JLabel("Genes To Add To Artemis File"), constraints)
constraints.gridx, constraints.gridy = 4, 1
self.add(self.newGeneButton, constraints)
constraints.weightx = 1
constraints.fill = GridBagConstraints.BOTH
constraints.gridx, constraints.gridy = 5, 1
self.add(self.newGeneFrom, constraints)
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.gridx, constraints.gridy = 6, 1
self.add(JLabel("To"), constraints)
constraints.weightx = 1
constraints.fill = GridBagConstraints.BOTH
constraints.gridx, constraints.gridy = 7, 1
self.add(self.newGeneTo, constraints)
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.gridx, constraints.gridy = 4, 2
self.add(JButton(AddGenesAction(self)), constraints)
constraints.gridx, constraints.gridy = 4, 3
constraints.gridwidth, constraints.gridheight = 4, 1
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.add(JScrollPane(self.outGenes), constraints)
def loadFile(self):
self.inGenes.model.clear()
self.database, self.evalue, genes = utils.parseBlast(self.name + ".blastp.xml")
[self.inGenes.model.addElement(gene) for gene in genes]
artemisInput = open(self.name + ".art", "r")
lines = artemisInput.readlines()
artemisInput.close()
self.restOfFile = self.genome = []
while lines:
if re.match("\s+CDS\s+(complement\()?\d+\.\.\d+\)?\n", lines[0]):
lines = lines[4:]
elif lines[0].find("ORIGIN") == 0:
self.genome = map(lambda x: re.sub("\s+", "", x), lines[1:])
lines = []
else:
if lines[0].strip():
self.restOfFile.append(lines[0])
lines = lines[1:]
self.genome = "".join(self.genome)
self.restOfFile = "".join(self.restOfFile)
def writeArtemisFile(self):
output = open(self.name + ".art", "w")
output.write(self.restOfFile)
for element in self.inGenes.model.elements():
output.write(element.toArtemis())
output.write("\nORIGIN\n\n")
for i in range(0, len(self.genome), 50):
output.write(self.genome[i:min(i+50, len(self.genome))] + "\n")
output.close()
