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Initial import. 

* fluent: The application program.
 * system: The core system.
 * workflows: Directory for workflow modules.
This commit is contained in:
Einar Ryeng 2006-04-16 18:25:54 +00:00
parent bb246a77d7
commit 5853216df4
6 changed files with 1084 additions and 0 deletions
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117
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#!/usr/bin/python
import sys
sys.path.append('system')
sys.path.append('workflows')
import pygtk
pygtk.require('2.0')
import gtk
import gtk.gdk
import gtk.glade
import gnome
import gnome.ui
import pango
import workflow
import logger
import plots
import navigator
PROGRAM_NAME = 'fluent'
VERSION = '0.1.0'
GLADEFILENAME = 'system/fluent.glade'
APP = 'appwindow'
WF_BOX = 'workflow_vbox'
DATA_BOX = 'data_vbox'
class FluentApp:
def __init__(self):
# Application variables
self.navigator = navigator.NavigatorStore()
self.current_data = None
gtk.glade.set_custom_handler(self.custom_object_factory)
self.widget_tree = gtk.glade.XML(GLADEFILENAME, APP)
self.workflow = workflow.EinarsWorkflow(self)
def custom_object_factory(self, glade, function_name, widget_name,\
str1, str2, int1, int2):
handler = getattr(self, function_name)
return handler(str1, str2, int1, int2)
def create_logview(self, str1, str2, int1, int2):
# Set up log view
self.log_view = logger.LogView(logger.logger)
self.log_view.show()
return self.log_view
def create_navigator_view(self, str1, str2, int1, int2):
self.navigator_view = navigator.NavigatorView(self.navigator, self)
self.navigator_view.show()
return self.navigator_view
def show(self):
self.init_gui()
def init_gui(self):
self.app = self.widget_tree.get_widget(APP)
self.app.set_size_request(800, 600)
# Set up workflow
wf_box = self.widget_tree.get_widget(WF_BOX)
wf_menu = workflow.WorkflowView(self.workflow)
wf_menu.show()
wf_box.pack_end(wf_menu)
# Set up plot
pt = self.widget_tree.get_widget('plot_table')
plot = plots.SinePlot()
plot.show()
plot.mark_active(True)
pt.add(plot)
plot2 = plots.EmptyPlot()
plot2.show()
pt.attach(plot2, 1, 2, 0, 1)
plot3 = plots.EmptyPlot()
plot3.show()
pt.attach(plot3, 0, 1, 1, 2)
plot4 = plots.EmptyPlot()
plot4.show()
pt.attach(plot4, 1, 2, 1, 2)
# Set up plot toolbar
dock = self.widget_tree.get_widget('plot_toolbar_dock')
dock.add(plot.get_toolbar(self.app))
# Connect signals
signals = {'on_quit1_activate' : (gtk.main_quit),
'on_appwindow_delete_event' : (gtk.main_quit),
'on_view_log_activate' : (self.toggle_view_log)}
self.widget_tree.signal_autoconnect(signals)
# Log that we've set up the app now
logger.log('debug', 'Program started')
def change_plot(self, plot):
pt = self.widget_tree.get_widget('plot_table')
pt.attach(plot, 1, 2, 1, 2)
def toggle_view_log(self, menu_item):
lw = self.widget_tree.get_widget('logview')
if menu_item.get_active():
lw.show()
else:
lw.unparent()
logger.log('debug', 'Toggling log window visibility')
if __name__ == '__main__':
gnome.program_init(PROGRAM_NAME, VERSION)
app = FluentApp()
app.show()
gtk.main()

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<?xml version="1.0" standalone="no"?> <!--*- mode: xml -*-->
<!DOCTYPE glade-interface SYSTEM "http://glade.gnome.org/glade-2.0.dtd">
<glade-interface>
<requires lib="gnome"/>
<requires lib="bonobo"/>
<widget class="GnomeApp" id="appwindow">
<property name="visible">True</property>
<property name="title" translatable="yes">Fluent</property>
<property name="type">GTK_WINDOW_TOPLEVEL</property>
<property name="window_position">GTK_WIN_POS_NONE</property>
<property name="modal">False</property>
<property name="default_width">800</property>
<property name="default_height">600</property>
<property name="resizable">True</property>
<property name="destroy_with_parent">False</property>
<property name="decorated">True</property>
<property name="skip_taskbar_hint">False</property>
<property name="skip_pager_hint">False</property>
<property name="type_hint">GDK_WINDOW_TYPE_HINT_NORMAL</property>
<property name="gravity">GDK_GRAVITY_NORTH_WEST</property>
<property name="enable_layout_config">True</property>
<signal name="delete_event" handler="on_appwindow_delete_event" last_modification_time="Thu, 13 Apr 2006 18:54:58 GMT"/>
<child internal-child="dock">
<widget class="BonoboDock" id="bonobodock1">
<property name="visible">True</property>
<property name="allow_floating">True</property>
<child>
<widget class="BonoboDockItem" id="bonobodockitem1">
<property name="visible">True</property>
<property name="shadow_type">GTK_SHADOW_NONE</property>
<child>
<widget class="GtkMenuBar" id="menubar1">
<property name="visible">True</property>
<child>
<widget class="GtkMenuItem" id="file1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_FILE_TREE</property>
<child>
<widget class="GtkMenu" id="file1_menu">
<child>
<widget class="GtkImageMenuItem" id="new1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_NEW_ITEM</property>
<property name="label" translatable="yes">_Ny</property>
<property name="use_underline">True</property>
<signal name="activate" handler="on_new1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="open1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_OPEN_ITEM</property>
<signal name="activate" handler="on_open1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="save1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_SAVE_ITEM</property>
<signal name="activate" handler="on_save1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="save_as1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_SAVE_AS_ITEM</property>
<signal name="activate" handler="on_save_as1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
</widget>
</child>
<child>
<widget class="GtkSeparatorMenuItem" id="separator1">
<property name="visible">True</property>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="quit1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_EXIT_ITEM</property>
<signal name="activate" handler="on_quit1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
</widget>
</child>
</widget>
</child>
</widget>
</child>
<child>
<widget class="GtkMenuItem" id="edit1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_EDIT_TREE</property>
<child>
<widget class="GtkMenu" id="edit1_menu">
<child>
<widget class="GtkImageMenuItem" id="cut1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_CUT_ITEM</property>
<signal name="activate" handler="on_cut1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="copy1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_COPY_ITEM</property>
<signal name="activate" handler="on_copy1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="paste1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_PASTE_ITEM</property>
<signal name="activate" handler="on_paste1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="clear1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_CLEAR_ITEM</property>
<signal name="activate" handler="on_clear1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
</widget>
</child>
<child>
<widget class="GtkSeparatorMenuItem" id="separator2">
<property name="visible">True</property>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="properties1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_PROPERTIES_ITEM</property>
<signal name="activate" handler="on_properties1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
</widget>
</child>
<child>
<widget class="GtkSeparatorMenuItem" id="separator3">
<property name="visible">True</property>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="preferences1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_PREFERENCES_ITEM</property>
<signal name="activate" handler="on_preferences1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
</widget>
</child>
</widget>
</child>
</widget>
</child>
<child>
<widget class="GtkMenuItem" id="view1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_VIEW_TREE</property>
<child>
<widget class="GtkMenu" id="view1_menu">
<child>
<widget class="GtkCheckMenuItem" id="view_log">
<property name="visible">True</property>
<property name="label" translatable="yes">Log</property>
<property name="use_underline">True</property>
<property name="active">True</property>
<signal name="activate" handler="on_view_log_activate" last_modification_time="Sat, 15 Apr 2006 10:37:30 GMT"/>
</widget>
</child>
</widget>
</child>
</widget>
</child>
<child>
<widget class="GtkMenuItem" id="help1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_HELP_TREE</property>
<child>
<widget class="GtkMenu" id="help1_menu">
<child>
<widget class="GtkImageMenuItem" id="about1">
<property name="visible">True</property>
<property name="stock_item">GNOMEUIINFO_MENU_ABOUT_ITEM</property>
<signal name="activate" handler="on_about1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
</widget>
</child>
</widget>
</child>
</widget>
</child>
</widget>
</child>
</widget>
<packing>
<property name="placement">BONOBO_DOCK_TOP</property>
<property name="band">0</property>
<property name="position">0</property>
<property name="offset">0</property>
<property name="behavior">BONOBO_DOCK_ITEM_BEH_EXCLUSIVE|BONOBO_DOCK_ITEM_BEH_NEVER_VERTICAL|BONOBO_DOCK_ITEM_BEH_LOCKED</property>
</packing>
</child>
<child>
<widget class="BonoboDockItem" id="bonobodockitem2">
<property name="visible">True</property>
<property name="shadow_type">GTK_SHADOW_OUT</property>
<child>
<widget class="GtkToolbar" id="toolbar1">
<property name="visible">True</property>
<property name="orientation">GTK_ORIENTATION_HORIZONTAL</property>
<property name="toolbar_style">GTK_TOOLBAR_ICONS</property>
<property name="tooltips">True</property>
<property name="show_arrow">False</property>
<child>
<widget class="GtkToolButton" id="toolbutton1">
<property name="visible">True</property>
<property name="tooltip" translatable="yes">Ny fil</property>
<property name="stock_id">gtk-new</property>
<property name="visible_horizontal">True</property>
<property name="visible_vertical">True</property>
<property name="is_important">False</property>
</widget>
<packing>
<property name="expand">False</property>
<property name="homogeneous">True</property>
</packing>
</child>
<child>
<widget class="GtkToolButton" id="toolbutton2">
<property name="visible">True</property>
<property name="tooltip" translatable="yes">Åpne fil</property>
<property name="stock_id">gtk-open</property>
<property name="visible_horizontal">True</property>
<property name="visible_vertical">True</property>
<property name="is_important">False</property>
</widget>
<packing>
<property name="expand">False</property>
<property name="homogeneous">True</property>
</packing>
</child>
<child>
<widget class="GtkToolButton" id="toolbutton3">
<property name="visible">True</property>
<property name="tooltip" translatable="yes">Lagre fil</property>
<property name="stock_id">gtk-save</property>
<property name="visible_horizontal">True</property>
<property name="visible_vertical">True</property>
<property name="is_important">False</property>
</widget>
<packing>
<property name="expand">False</property>
<property name="homogeneous">True</property>
</packing>
</child>
</widget>
</child>
</widget>
<packing>
<property name="placement">BONOBO_DOCK_TOP</property>
<property name="band">1</property>
<property name="position">0</property>
<property name="offset">2</property>
<property name="behavior">BONOBO_DOCK_ITEM_BEH_NORMAL</property>
</packing>
</child>
<child>
<widget class="BonoboDockItem" id="bonobodockitem3">
<property name="visible">True</property>
<property name="shadow_type">GTK_SHADOW_OUT</property>
<child>
<widget class="GtkToolbar" id="toolbar2">
<property name="visible">True</property>
<property name="orientation">GTK_ORIENTATION_HORIZONTAL</property>
<property name="toolbar_style">GTK_TOOLBAR_ICONS</property>
<property name="tooltips">True</property>
<property name="show_arrow">False</property>
<child>
<widget class="GtkToolButton" id="toolbutton4">
<property name="visible">True</property>
<property name="stock_id">gtk-zoom-in</property>
<property name="visible_horizontal">True</property>
<property name="visible_vertical">True</property>
<property name="is_important">False</property>
</widget>
<packing>
<property name="expand">False</property>
<property name="homogeneous">True</property>
</packing>
</child>
<child>
<widget class="GtkToolButton" id="toolbutton5">
<property name="visible">True</property>
<property name="stock_id">gtk-zoom-out</property>
<property name="visible_horizontal">True</property>
<property name="visible_vertical">True</property>
<property name="is_important">False</property>
</widget>
<packing>
<property name="expand">False</property>
<property name="homogeneous">True</property>
</packing>
</child>
<child>
<placeholder/>
</child>
</widget>
</child>
</widget>
<packing>
<property name="placement">BONOBO_DOCK_TOP</property>
<property name="band">1</property>
<property name="position">1</property>
<property name="offset">0</property>
<property name="behavior">BONOBO_DOCK_ITEM_BEH_NORMAL</property>
</packing>
</child>
<child>
<widget class="BonoboDockItem" id="plot_toolbar_dock">
<property name="visible">True</property>
<property name="shadow_type">GTK_SHADOW_OUT</property>
<child>
<placeholder/>
</child>
</widget>
<packing>
<property name="placement">BONOBO_DOCK_TOP</property>
<property name="band">1</property>
<property name="position">2</property>
<property name="offset">0</property>
<property name="behavior">BONOBO_DOCK_ITEM_BEH_NORMAL</property>
</packing>
</child>
<child>
<widget class="GtkVPaned" id="vpaned1">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="position">300</property>
<child>
<widget class="GtkHPaned" id="hpaned1">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="position">700</property>
<child>
<widget class="GtkHPaned" id="hpaned2">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="position">200</property>
<child>
<widget class="GtkVBox" id="data_vbox">
<property name="visible">True</property>
<property name="homogeneous">False</property>
<property name="spacing">0</property>
<child>
<widget class="GtkLabel" id="label4">
<property name="visible">True</property>
<property name="label" translatable="yes">&lt;b&gt;Navigator&lt;/b&gt;</property>
<property name="use_underline">False</property>
<property name="use_markup">True</property>
<property name="justify">GTK_JUSTIFY_LEFT</property>
<property name="wrap">False</property>
<property name="selectable">False</property>
<property name="xalign">0.5</property>
<property name="yalign">0.5</property>
<property name="xpad">0</property>
<property name="ypad">0</property>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">False</property>
<property name="fill">True</property>
</packing>
</child>
<child>
<widget class="Custom" id="navigator_view">
<property name="visible">True</property>
<property name="creation_function">create_navigator_view</property>
<property name="int1">0</property>
<property name="int2">0</property>
<property name="last_modification_time">Sat, 15 Apr 2006 12:34:23 GMT</property>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">True</property>
<property name="fill">True</property>
</packing>
</child>
</widget>
<packing>
<property name="shrink">False</property>
<property name="resize">False</property>
</packing>
</child>
<child>
<widget class="GtkTable" id="plot_table">
<property name="visible">True</property>
<property name="n_rows">2</property>
<property name="n_columns">2</property>
<property name="homogeneous">True</property>
<property name="row_spacing">3</property>
<property name="column_spacing">3</property>
</widget>
<packing>
<property name="shrink">True</property>
<property name="resize">True</property>
</packing>
</child>
</widget>
<packing>
<property name="shrink">True</property>
<property name="resize">False</property>
</packing>
</child>
<child>
<widget class="GtkVBox" id="workflow_vbox">
<property name="visible">True</property>
<property name="homogeneous">False</property>
<property name="spacing">0</property>
<child>
<widget class="GtkLabel" id="label14">
<property name="visible">True</property>
<property name="label" translatable="yes">&lt;b&gt;Workflow&lt;/b&gt;</property>
<property name="use_underline">False</property>
<property name="use_markup">True</property>
<property name="justify">GTK_JUSTIFY_LEFT</property>
<property name="wrap">False</property>
<property name="selectable">False</property>
<property name="xalign">0.5</property>
<property name="yalign">0.5</property>
<property name="xpad">0</property>
<property name="ypad">0</property>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">False</property>
<property name="fill">False</property>
</packing>
</child>
<child>
<placeholder/>
</child>
</widget>
<packing>
<property name="shrink">False</property>
<property name="resize">False</property>
</packing>
</child>
</widget>
<packing>
<property name="shrink">True</property>
<property name="resize">True</property>
</packing>
</child>
<child>
<widget class="GtkNotebook" id="notebook1">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="show_tabs">True</property>
<property name="show_border">True</property>
<property name="tab_pos">GTK_POS_TOP</property>
<property name="scrollable">False</property>
<property name="enable_popup">False</property>
<child>
<widget class="GtkScrolledWindow" id="scrolledwindow1">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="hscrollbar_policy">GTK_POLICY_NEVER</property>
<property name="vscrollbar_policy">GTK_POLICY_ALWAYS</property>
<property name="shadow_type">GTK_SHADOW_NONE</property>
<property name="window_placement">GTK_CORNER_TOP_LEFT</property>
<child>
<widget class="Custom" id="logview">
<property name="visible">True</property>
<property name="creation_function">create_logview</property>
<property name="int1">0</property>
<property name="int2">0</property>
<property name="last_modification_time">Fri, 14 Apr 2006 20:23:55 GMT</property>
</widget>
</child>
</widget>
<packing>
<property name="tab_expand">False</property>
<property name="tab_fill">True</property>
</packing>
</child>
<child>
<widget class="GtkLabel" id="label1">
<property name="visible">True</property>
<property name="label" translatable="yes">Log</property>
<property name="use_underline">False</property>
<property name="use_markup">False</property>
<property name="justify">GTK_JUSTIFY_LEFT</property>
<property name="wrap">False</property>
<property name="selectable">False</property>
<property name="xalign">0.5</property>
<property name="yalign">0.5</property>
<property name="xpad">0</property>
<property name="ypad">0</property>
</widget>
<packing>
<property name="type">tab</property>
</packing>
</child>
</widget>
<packing>
<property name="shrink">True</property>
<property name="resize">False</property>
</packing>
</child>
</widget>
</child>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">True</property>
<property name="fill">True</property>
</packing>
</child>
<child internal-child="appbar">
<widget class="GnomeAppBar" id="appbar1">
<property name="visible">True</property>
<property name="has_progress">True</property>
<property name="has_status">True</property>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">True</property>
<property name="fill">True</property>
</packing>
</child>
</widget>
</glade-interface>

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import gobject
import gtk
import time
class Logger:
def __init__(self):
self.store = gtk.ListStore(gobject.TYPE_STRING,
gobject.TYPE_STRING,
gobject.TYPE_STRING)
self.levels = ['debug', 'notice', 'warning', 'error']
self.level_text = {'debug': 'Debug',
'notice': 'Notice',
'warning': 'Warning',
'error': 'Error'}
self.components = {}
self.colors = { 'debug': 'grey',
'notice': 'black',
'warning': 'brown',
'error': 'red' }
def log(self, level, message):
iter = self.store.append()
self.store.set_value(iter, 0, level)
self.store.set_value(iter, 1, message)
self.store.set_value(iter, 2, self.colors[level])
class LogView(gtk.TreeView):
def __init__(self, logger=None, level='notice'):
self.logger = logger
self.model = logger.store
# Set up filter
self.filter = self.model.filter_new()
gtk.TreeView.__init__(self, self.filter)
self.filter.set_visible_func(self.level_filter)
self.set_level(level)
# Set up log level column
renderer = gtk.CellRendererText()
self.level_col = gtk.TreeViewColumn('Level', renderer, text=0)
self.level_col.add_attribute(renderer, "foreground", 2)
self.append_column(self.level_col)
# Set up message column
renderer = gtk.CellRendererText()
self.message_col = gtk.TreeViewColumn('Message', renderer, text=1)
self.message_col.add_attribute(renderer, "foreground", 2)
self.append_column(self.message_col)
# Activate context menu
self.menu = LogMenu(self.logger, self)
self.connect('popup_menu', self.popup_menu)
self.connect('button_press_event', self.mouse_popup_menu)
#self.connect('button_release_event', None)
def set_level(self, level):
self.level = level
self.level_no = self.logger.levels.index(level)
self.filter.refilter()
self.queue_draw()
def popup_menu(self, *rest):
self.menu.popup(None, None, None, 0, 0)
def mouse_popup_menu(self, widget, event):
if event.button == 3:
self.menu.popup(None, None, None, event.button, event.time)
def level_filter(self, store, iter):
if store.get_value(iter,0):
value = self.logger.levels.index(store.get_value(iter, 0))
return value >= self.level_no
else:
return False
class LogLevelMenu(gtk.Menu):
def __init__(self, logger, view):
self.logger = logger
self.view = view
items = []
gtk.Menu.__init__(self)
for level in logger.levels:
if len(items) == 0:
group = None
else:
group = items[0]
item = gtk.RadioMenuItem(group, logger.level_text[level], level)
item.connect('activate', self.set_log_level, level)
items.append(item)
self.append(item)
item.show()
items[0].set_active(True)
def set_log_level(self, widget, level, *rest):
if widget.active:
self.view.set_level(level)
class LogComponentMenu(gtk.Menu):
def __init__(self, logger, view):
gtk.Menu.__init__(self)
components = logger.components.keys()
components.sort(str.__gt__)
for c in components:
item = gtk.MenuItem(c)
self.append(item)
item.show()
# for component in logger.components
class LogMenu(gtk.Menu):
def __init__(self, logger, view):
gtk.Menu.__init__(self)
self.logger = logger
# View Log Level
self.view_menu = LogLevelMenu(logger, view)
self.view_item = gtk.MenuItem('View Log Level')
self.view_item.set_submenu(self.view_menu)
self.append(self.view_item)
self.view_item.show()
# View Components
self.component_menu = LogComponentMenu(logger, view)
self.component_item = gtk.MenuItem('View Components')
self.component_item.set_submenu(self.component_menu)
self.append(self.component_item)
self.component_item.show()
# Clear Log
clear_item = gtk.MenuItem('Clear Log')
clear_item.connect('activate', self.activate_clear_button)
self.append(clear_item)
clear_item.show()
def activate_clear_button(self, item):
self.logger.store.clear()
logger = Logger()
log = logger.log

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system/navigator.py Normal file
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import gtk
import gobject
import plots
import logger
class NavigatorStore (gtk.TreeStore):
def __init__(self):
gtk.TreeStore.__init__(self, gobject.TYPE_STRING, plots.Plot)
iter = self.append(None)
self.set_value(iter, 0, ('Sine Plot'))
self.set_value(iter, 1, (plots.SinePlot()))
iter = self.append(None)
self.set_value(iter, 0, ('Sine Plot 1'))
self.set_value(iter, 1, (plots.EmptyPlot()))
def plot_at(self, path):
iter = self.get_iter(path)
plot = self.get_value(iter, 1)
if plot:
plot.show()
return plot
class NavigatorView (gtk.TreeView):
def __init__(self, nav, app):
gtk.TreeView.__init__(self, nav)
self.navigator = nav
self.app = app
self.set_headers_visible(False)
self.connect('row-activated', self.row_activated_handler)
renderer = gtk.CellRendererText()
self.object_col = gtk.TreeViewColumn('Object', renderer, text=0)
self.append_column(self.object_col)
logger.log('debug', 'Initializing naviagor window')
def row_activated_handler(self, widget, path, column):
#self.app.change_window(
#
plot = self.navigator.plot_at(path)
logger.log('notice', 'Button pressed')
self.app.change_plot(plot)

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system/plots.py Normal file
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import pygtk
import gtk
import matplotlib
from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas
from matplotlib.axes import Subplot
from matplotlib.figure import Figure
from matplotlib.numerix import arange, sin, pi
from matplotlib.backends.backend_gtk import NavigationToolbar2GTK as NavigationToolbar
import scipy
import logger
class Plot (gtk.Frame):
def __init__(self):
gtk.Frame.__init__(self)
self.canvas = None
self.mark_active(False)
self.connect('button_press_event', self.on_button_press)
def on_button_press(self, *rest):
logger.log('debug', 'button pressed in plot')
self.mark_active(True)
def get_toolbar(self, window):
self.toolbar = NavigationToolbar(self.canvas, window)
self.toolbar.set_property('show-arrow', False)
return self.toolbar
def mark_active(self, active):
if active:
self.set_shadow_type(gtk.SHADOW_IN)
else:
self.set_shadow_type(gtk.SHADOW_ETCHED_IN)
class EmptyPlot (Plot):
def __init__(self):
Plot.__init__(self)
label = gtk.Label('No plot')
label.show()
self.add(label)
def get_toolbar(self, window):
return None
class SinePlot (Plot):
def __init__(self):
Plot.__init__(self)
fig = Figure(figsize=(5,4), dpi=72)
ax = fig.add_subplot(111)
t = arange(0.0,3.0,0.01)
s = sin(2*pi*t)
ax.plot(t,s)
self.canvas = FigureCanvas(fig)
self.add(self.canvas)
self.canvas.show()
class ScatterPlot (Plot):
def __init__(self):
Plot.__init__(self)
fig = Figure(figsize=(5,4), dpi=72)
ax = fig.add_subplot(111)
t = arange(0.0, 3.0, 0.01)
a = scipy.randn(200, 300)
fig.plot(a)
self.canvas = FigureCanvas(fig)
self.add(self.canvas)
self.canvas.show()

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system/workflow.py Normal file
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import gtk
import logger
class Workflow:
"""Defines a workflow that contains a set of analysis stages.
A Workflow is a set of analysis stages for a certain type of analysis.
Each stage contains some possible operations to do accomplish that
task.
"""
def __init__(self, app):
self.name = ''
self.stages = []
self.stages_by_id = {}
self.app = app
def add_stage(self, stage):
self.stages.append(stage)
self.stages_by_id[stage.id] = stage
def print_tree(self):
print self.name
for stage in self.stages:
print ' %s' % stage.name
for fun in stage.functions:
print ' %s' % fun.name
class Stage:
"""A stage is a part of the data analysis process.
Each stage contains a set of functions that can be used to
accomplish the task. A typical early stage is 'preprocessing', which
can be done in several ways, each represented by a function.
"""
def __init__(self, id, name):
self.id = id
self.name = name
self.functions = []
self.functions_by_id = {}
def add_function(self, fun):
self.functions.append(fun)
self.functions_by_id[fun.id] = fun
class Function:
"""A Function object encapsulates a function on a data set.
Each Function instance encapsulates some function that can be applied
to one or more types of data.
"""
def __init__(self, id, name):
self.id = id
self.name = name
def valid_input(input):
return True
def run(self, data):
pass
def foo():
print "foo"
class EinarsWorkflow (Workflow):
def __init__(self, app):
Workflow.__init__(self, app)
self.name = 'Einar\'s Workflow'
load = Stage('load', 'Load Data')
load.add_function(Function('load', 'Load Microarrays'))
self.add_stage(load)
preproc = Stage('preprocess', 'Preprocessing')
preproc.add_function(Function('rma', 'RMA'))
self.add_stage(preproc)
go = Stage('go', 'Gene Ontology Data')
go.add_function(Function('godist', 'GO Distances'))
self.add_stage(go)
regression = Stage('regression', 'Regression')
regression.add_function(Function('pls', 'PLS'))
self.add_stage(regression)
logger.log('debug', 'Einar\'s workflow is now active')
class WorkflowView (gtk.VBox):
def __init__(self, wf):
gtk.VBox.__init__(self)
self.workflow = wf
# Add stage in the process
for stage in wf.stages:
exp = gtk.Expander(stage.name)
btn_box = gtk.VBox()
btn_box.show()
exp.add(btn_box)
# Add functions in each stage
for fun in stage.functions:
btn = gtk.Button(fun.name)
btn.connect('clicked', self.button_click_handler)
# btn.connect('clicked', lambda(w): logger.log('notice', fun.name))
btn.function = fun
btn_box.add(btn)
btn.show()
exp.show()
self.pack_start(exp, expand=False, fill=False)
def button_click_handler(self, button):
function = button.function
logger.log('debug', 'Starting function: %s' % function.name)
function.run(self.workflow.app.current_data)
logger.log('debug', 'Function ended: %s' % function.name)