* The New project toolbar button now works. A druid will display the
available workflows and ask you to select one of them. There are still a couple of unresolved issues, but it works, so i upload it to ease the use of the program.
This commit is contained in:
parent
357cd1a1a6
commit
efcdafe843
50
fluent
50
fluent
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@ -4,6 +4,7 @@ import sys
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sys.path.append('system')
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sys.path.append('workflows')
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import dialogs
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import pygtk
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pygtk.require('2.0')
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import gtk
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@ -18,7 +19,7 @@ import dataset
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import logger
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import plots
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import navigator
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import go_workflow
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#import go_workflow
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#import pca_workflow
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import scipy
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@ -30,25 +31,23 @@ class FluentApp:
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def __init__(self):
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# Application variables
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self.project = project.Project()
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# add test data ##################
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x = scipy.rand(200,3)
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def_list = [ ['samples',[]], ['genes',['a','b','c']] ]
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test_data1 = dataset.Dataset(x,def_list)
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self.project.add_dataset(test_data1)
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#y = scipy.rand(200,2)
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#def_list = [ ['samples',[]], ['yclasses',['C','N']] ]
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#test_data2 = dataset.Dataset(y,def_list)
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####################
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self.project = None
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self.current_data = None
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gtk.glade.set_custom_handler(self.custom_object_factory)
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self.widget_tree = gtk.glade.XML(GLADEFILENAME, 'appwindow')
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# self.workflow = pca_workflow.PCAWorkflow(self)
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self.workflow = go_workflow.EinarsWorkflow(self)
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self.workflow = workflow.EmptyWorkflow(self)
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# self.workflow.add_project(self.project)
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def set_project(self, project):
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logger.log('notice', 'Creating a new project')
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self.project = project
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self.workflow.add_project(self.project)
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self.navigator_view.add_project(self.project)
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def set_workflow(self, workflow):
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self.workflow = workflow
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self.wf_menu.set_workflow(self.workflow)
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def custom_object_factory(self, glade, function_name, widget_name,\
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str1, str2, int1, int2):
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@ -77,8 +76,8 @@ class FluentApp:
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return self.large_view
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def create_navigator_view(self, str1, str2, int1, int2):
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tree = self.project.data_tree
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self.navigator_view = navigator.NavigatorView(self.project, self)
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# tree = self.project.data_tree
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self.navigator_view = navigator.NavigatorView(None, self)
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self.navigator_view.show()
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return self.navigator_view
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@ -89,9 +88,9 @@ class FluentApp:
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self['appwindow'].set_size_request(800, 600)
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# Set up workflow
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wf_menu = workflow.WorkflowView(self.workflow)
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wf_menu.show()
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self['workflow_vbox'].pack_end(wf_menu)
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self.wf_menu = workflow.WorkflowView(self.workflow)
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self.wf_menu.show()
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self['workflow_vbox'].pack_end(self.wf_menu)
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# Set up plot toolbar
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# self['plot_toolbar_dock'].add(plot.get_toolbar(self.app))
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@ -100,7 +99,9 @@ class FluentApp:
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signals = {'on_quit1_activate' : (gtk.main_quit),
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'on_appwindow_delete_event' : (gtk.main_quit),
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'on_zoom_in_button_clicked' : (self.on_single_view),
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'on_zoom_out_button_clicked' : (self.on_multiple_view)}
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'on_zoom_out_button_clicked' : (self.on_multiple_view),
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'on_new1_activated' : (self.on_create_project),
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'on_button_new_clicked' : (self.on_create_project)}
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self.widget_tree.signal_autoconnect(signals)
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# Log that we've set up the app now
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@ -121,6 +122,11 @@ class FluentApp:
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def __getitem__(self, key):
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return self.widget_tree.get_widget(key)
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def on_create_project(self, *rest):
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logger.log('error', 'FIXME: Create project')
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d = dialogs.CreateProjectDruid(self)
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d.run()
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if __name__ == '__main__':
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gnome.program_init(PROGRAM_NAME, VERSION)
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app = FluentApp()
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@ -225,13 +225,14 @@
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<property name="show_arrow">False</property>
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<child>
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<widget class="GtkToolButton" id="toolbutton1">
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<widget class="GtkToolButton" id="button_new">
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<property name="visible">True</property>
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<property name="tooltip" translatable="yes">Ny fil</property>
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<property name="stock_id">gtk-new</property>
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<property name="visible_horizontal">True</property>
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<property name="visible_vertical">True</property>
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<property name="is_important">False</property>
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<signal name="clicked" handler="on_button_new_clicked" last_modification_time="Fri, 21 Apr 2006 13:46:38 GMT"/>
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</widget>
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<packing>
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<property name="expand">False</property>
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@ -268,30 +269,6 @@
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<property name="homogeneous">True</property>
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</packing>
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</child>
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</widget>
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</child>
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</widget>
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<packing>
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<property name="placement">BONOBO_DOCK_TOP</property>
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<property name="band">1</property>
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<property name="position">0</property>
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<property name="offset">2</property>
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<property name="behavior">BONOBO_DOCK_ITEM_BEH_NORMAL</property>
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</packing>
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</child>
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<child>
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<widget class="BonoboDockItem" id="bonobodockitem3">
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<property name="visible">True</property>
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<property name="shadow_type">GTK_SHADOW_OUT</property>
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<child>
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<widget class="GtkToolbar" id="toolbar2">
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<property name="visible">True</property>
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<property name="orientation">GTK_ORIENTATION_HORIZONTAL</property>
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<property name="toolbar_style">GTK_TOOLBAR_ICONS</property>
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<property name="tooltips">True</property>
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<property name="show_arrow">False</property>
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<child>
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<widget class="GtkToolButton" id="zoom_in_button">
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@ -322,18 +299,14 @@
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<property name="homogeneous">True</property>
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</packing>
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</child>
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<child>
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<placeholder/>
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</child>
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</widget>
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</child>
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</widget>
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<packing>
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<property name="placement">BONOBO_DOCK_TOP</property>
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<property name="band">1</property>
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<property name="position">1</property>
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<property name="offset">0</property>
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<property name="position">0</property>
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<property name="offset">2</property>
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<property name="behavior">BONOBO_DOCK_ITEM_BEH_NORMAL</property>
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</packing>
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</child>
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@ -350,7 +323,7 @@
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<packing>
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<property name="placement">BONOBO_DOCK_TOP</property>
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<property name="band">1</property>
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<property name="position">2</property>
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<property name="position">1</property>
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<property name="offset">0</property>
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<property name="behavior">BONOBO_DOCK_ITEM_BEH_NORMAL</property>
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</packing>
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@ -580,4 +553,188 @@
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</child>
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</widget>
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<widget class="GtkWindow" id="new_project_druid">
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<property name="visible">True</property>
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<property name="title" translatable="yes">Create project</property>
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<property name="type">GTK_WINDOW_TOPLEVEL</property>
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<property name="window_position">GTK_WIN_POS_NONE</property>
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<property name="modal">True</property>
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<property name="default_width">550</property>
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<property name="default_height">320</property>
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<property name="resizable">True</property>
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<property name="destroy_with_parent">False</property>
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<property name="decorated">True</property>
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<property name="skip_taskbar_hint">False</property>
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<property name="skip_pager_hint">False</property>
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<property name="type_hint">GDK_WINDOW_TYPE_HINT_NORMAL</property>
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<property name="gravity">GDK_GRAVITY_NORTH_WEST</property>
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<property name="focus_on_map">True</property>
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<property name="urgency_hint">False</property>
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<child>
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<widget class="GnomeDruid" id="druid">
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<property name="border_width">3</property>
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<property name="width_request">510</property>
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<property name="height_request">228</property>
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<property name="visible">True</property>
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<property name="show_help">False</property>
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<child>
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<widget class="GnomeDruidPageEdge" id="druidpagestart1">
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<property name="visible">True</property>
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<property name="position">GNOME_EDGE_START</property>
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<property name="title" translatable="yes">Create new project</property>
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<property name="text" translatable="yes">You have to select the workflow you want the new project to be based on.
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A workflow is a collection of steps that are commonly needed to accomplish a task. For each step a set of relevant functions are available.
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The functions of the workflow you select will be available on the right part of the application window.</property>
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</widget>
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</child>
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<child>
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<widget class="GnomeDruidPageStandard" id="druidpagestandard1">
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<property name="visible">True</property>
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<property name="title" translatable="yes">Select workflow</property>
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<child internal-child="vbox">
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<widget class="GtkVBox" id="druid-vbox1">
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<property name="border_width">16</property>
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<property name="visible">True</property>
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<property name="homogeneous">False</property>
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<property name="spacing">6</property>
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<child>
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<widget class="GtkHBox" id="hbox1">
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<property name="visible">True</property>
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<property name="homogeneous">False</property>
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<property name="spacing">0</property>
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<child>
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<widget class="GtkScrolledWindow" id="scrolledwindow4">
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<property name="visible">True</property>
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<property name="can_focus">True</property>
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<property name="hscrollbar_policy">GTK_POLICY_NEVER</property>
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<property name="vscrollbar_policy">GTK_POLICY_AUTOMATIC</property>
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<property name="shadow_type">GTK_SHADOW_IN</property>
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<property name="window_placement">GTK_CORNER_TOP_LEFT</property>
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<child>
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<widget class="GtkTreeView" id="workflow_list">
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<property name="border_width">2</property>
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<property name="visible">True</property>
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<property name="can_focus">True</property>
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<property name="headers_visible">True</property>
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<property name="rules_hint">False</property>
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<property name="reorderable">False</property>
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<property name="enable_search">True</property>
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<property name="fixed_height_mode">False</property>
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<property name="hover_selection">False</property>
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<property name="hover_expand">False</property>
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<signal name="select_cursor_row" handler="on_workflow_list_select_cursor_row" last_modification_time="Sat, 22 Apr 2006 19:34:03 GMT"/>
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</widget>
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</child>
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</widget>
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<packing>
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<property name="padding">0</property>
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<property name="expand">True</property>
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<property name="fill">True</property>
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</packing>
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</child>
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<child>
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<widget class="GtkVSeparator" id="vseparator1">
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<property name="visible">True</property>
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</widget>
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<packing>
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<property name="padding">10</property>
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<property name="expand">False</property>
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<property name="fill">True</property>
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</packing>
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</child>
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<child>
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<widget class="GtkScrolledWindow" id="scrolledwindow3">
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<property name="visible">True</property>
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<property name="can_focus">True</property>
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<property name="hscrollbar_policy">GTK_POLICY_NEVER</property>
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<property name="vscrollbar_policy">GTK_POLICY_AUTOMATIC</property>
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<property name="shadow_type">GTK_SHADOW_IN</property>
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<property name="window_placement">GTK_CORNER_TOP_LEFT</property>
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<child>
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<widget class="GtkTextView" id="workflow_info">
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<property name="visible">True</property>
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<property name="can_focus">True</property>
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<property name="editable">False</property>
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<property name="overwrite">False</property>
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<property name="accepts_tab">True</property>
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<property name="justification">GTK_JUSTIFY_LEFT</property>
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<property name="wrap_mode">GTK_WRAP_WORD</property>
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<property name="cursor_visible">True</property>
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<property name="pixels_above_lines">0</property>
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<property name="pixels_below_lines">0</property>
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<property name="pixels_inside_wrap">0</property>
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<property name="left_margin">0</property>
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<property name="right_margin">0</property>
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<property name="indent">0</property>
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<property name="text" translatable="yes"></property>
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</widget>
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</child>
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</widget>
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<packing>
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<property name="padding">0</property>
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<property name="expand">True</property>
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<property name="fill">True</property>
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</packing>
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</child>
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</widget>
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<packing>
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<property name="padding">0</property>
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<property name="expand">True</property>
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<property name="fill">True</property>
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</packing>
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</child>
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</widget>
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</child>
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</widget>
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</child>
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<child>
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<widget class="GnomeDruidPageEdge" id="druidpagefinish1">
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<property name="visible">True</property>
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<property name="position">GNOME_EDGE_FINISH</property>
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<property name="title" translatable="yes">Finished</property>
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<property name="text" translatable="yes">A project will now be created.</property>
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<signal name="finish" handler="on_druidpagefinish1_finish" last_modification_time="Sat, 22 Apr 2006 19:28:28 GMT"/>
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</widget>
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</child>
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</widget>
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</child>
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</widget>
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<widget class="GtkAboutDialog" id="aboutdialog">
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<property name="visible">True</property>
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<property name="destroy_with_parent">True</property>
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<property name="name" translatable="yes">Fluent</property>
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<property name="copyright" translatable="yes">Copyright (C) 2006 the Fluents Team
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</property>
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<property name="comments" translatable="yes">From WordNet (r) 2.0 [wn]: fluent (adj)
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1: easy and graceful in shape; "a yacht with long, fluent curves"
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2: smooth and unconstrained in movement; "a long, smooth stride"; "the fluid motion of a cat"; "the liquid grace of a ballerina"; "liquid prose" [syn:{flowing}, {fluid}, {liquid}, {smooth}]
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3: expressing yourself readily, clearly, effectively; "able to dazzle with his facile tongue"; "silver speech" [syn: {eloquent}, {facile}, {silver}, {silver-tongued}, {smooth-spoken}]
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</property>
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<property name="license" translatable="yes"></property>
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<property name="wrap_license">False</property>
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<property name="website">https://dev.pvv.ntnu.no/projects/fluent</property>
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<property name="website_label" translatable="yes">The Fluent project website</property>
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<property name="authors">Arnar Flatberg
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Einar Ryeng
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Truls A. Tangstad</property>
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<property name="translator_credits" translatable="yes" comments="TRANSLATORS: Replace this string with your names, one name per line.">translator-credits</property>
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</widget>
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</glade-interface>
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@ -9,10 +9,13 @@ import project
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class NavigatorView (gtk.TreeView):
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def __init__(self, project, app):
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self.project = project
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self.data_tree = project.data_tree
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self.app = app
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if project:
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self.data_tree = project.data_tree
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else:
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self.data_tree = None
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gtk.TreeView.__init__(self, self.data_tree)
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gtk.TreeView.__init__(self) #, self.data_tree)
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self.set_headers_visible(False)
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self.connect('cursor_changed', self.cursor_changed_handler)
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@ -24,6 +27,11 @@ class NavigatorView (gtk.TreeView):
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logger.log('debug', 'Initializing navigator window.')
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def add_project(self, project):
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self.project = project
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self.data_tree = project.data_tree
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self.set_model(project.data_tree)
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def cursor_changed_handler(self, widget):
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selection = widget.get_selection()
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model, tree_iter = selection.get_selected()
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@ -172,7 +172,7 @@ class Plot (gtk.Frame):
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project.attach(self,'selection_update')
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def on_button_press(self, *rest):
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logger.log('debug', 'button pressed in plot')
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# logger.log('debug', 'button pressed in plot')
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self.mark_active(True)
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def mark_active(self, active):
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@ -10,8 +10,9 @@ class Workflow:
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task.
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"""
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name = "Workflow"
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def __init__(self, app):
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self.name = ''
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self.stages = []
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self.stages_by_id = {}
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self.app = app
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@ -30,6 +31,12 @@ class Workflow:
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def add_project(self,project):
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self.project = project
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class EmptyWorkflow(Workflow):
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name = 'Empty Workflow'
|
||||
|
||||
def __init__(self, app):
|
||||
Workflow.__init__(self, None)
|
||||
|
||||
class Stage:
|
||||
"""A stage is a part of the data analysis process.
|
||||
|
||||
|
|
@ -70,7 +77,9 @@ class WorkflowView (gtk.VBox):
|
|||
def __init__(self, wf):
|
||||
gtk.VBox.__init__(self)
|
||||
self.workflow = wf
|
||||
self.setup_workflow(wf)
|
||||
|
||||
def setup_workflow(self, wf):
|
||||
# Add stage in the process
|
||||
for stage in wf.stages:
|
||||
exp = gtk.Expander(stage.name)
|
||||
|
|
@ -90,6 +99,19 @@ class WorkflowView (gtk.VBox):
|
|||
exp.show()
|
||||
self.pack_start(exp, expand=False, fill=False)
|
||||
|
||||
def remove_workflow(self):
|
||||
print self.get_children()
|
||||
for c in self.get_children():
|
||||
c.hide()
|
||||
self.remove(c)
|
||||
|
||||
def set_workflow(self, workflow):
|
||||
self.workflow = workflow
|
||||
self.remove_workflow()
|
||||
self.setup_workflow(workflow)
|
||||
print workflow
|
||||
logger.log('notice', 'Created new workflow')
|
||||
|
||||
def run_function(self, function):
|
||||
logger.log('debug', 'Starting function: %s' % function.name)
|
||||
project = self.workflow.app.project
|
||||
|
|
|
|||
|
|
@ -144,3 +144,5 @@ class LoadMoothaData(Function):
|
|||
sample_def = ['samples', sample_names]
|
||||
X = dataset.Dataset(x,[sample_def,gene_def]) # samples x genes
|
||||
return [X]
|
||||
|
||||
PCAWorkflow.name = 'PCA Workflow'
|
||||
|
|
|
|||
Reference in New Issue