Added main.py that now contains the One & Only Singleton instance of these classes:
- Navigator - Aplication - Workflow - Project - Options Corresponding changes have been added in lots of other files to account for this, but the access to these objects should now be a lot easier.
This commit is contained in:
parent
91abf12f51
commit
a45743c31e
15
bin/fluents
15
bin/fluents
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@ -3,7 +3,7 @@
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from getopt import getopt
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import os
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import sys
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from fluents import fluents, project, workflow
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from fluents import fluents, project, workflow, main
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import workflows
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import cfgparse, optparse
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@ -68,11 +68,16 @@ if __name__ == '__main__':
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if wf.ident == options.workflow:
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selected_wf = wf
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app = fluents.FluentApp(selected_wf)
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app.options = options
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fluents.app = app
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app.set_project(project.Project())
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main.set_workflow(selected_wf())
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main.set_options(options)
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app = fluents.FluentApp()
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main.set_application(app)
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main.set_project(project.Project())
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app.set_project(main.project)
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app.show()
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gtk.main()
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@ -0,0 +1,3 @@
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import main
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@ -17,9 +17,8 @@ class CreateProjectDruid(gtk.Window):
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Workflow, and asks the user to select one of these. A new project of
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the selected class is added to the application."""
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def __init__(self, app):
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def __init__(self):
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gtk.Window.__init__(self)
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self.app = app
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self.widget_tree = gtk.glade.XML(GLADEFILENAME, 'new_project_druid')
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self.workflows = self.make_workflow_list()
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self.selected = None
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@ -63,10 +62,12 @@ class CreateProjectDruid(gtk.Window):
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def finish(self, *rest):
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tree, it = self['workflow_list'].get_selection().get_selected()
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wf = self.workflows.get_value(it, 1)
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wf_class = self.workflows.get_value(it, 1)
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proj = project.Project()
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self.app.set_workflow(wf(self.app))
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self.app.set_project(proj)
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main.set_workflow(wf_class())
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# self.app.set_workflow(wf(self.app))
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# self.app.set_project(proj)
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main.set_project(proj)
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self.hide()
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self.destroy()
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@ -13,7 +13,7 @@ import gnome
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import gnome.ui
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import scipy
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import pango
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import project, workflow, dataset, logger, view, navigator, dialogs, selections
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import project, workflow, dataset, logger, view, navigator, dialogs, selections, main
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PROGRAM_NAME = 'fluents'
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@ -142,8 +142,8 @@ class ViewFrameToolButton (gtk.ToolItem):
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class FluentApp:
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def __init__(self, wf): # Application variables
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self.project = None
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def __init__(self): # Application variables
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# self.project = None
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self.current_data = None
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self._last_view = None
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self._plot_toolbar = None
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@ -151,7 +151,7 @@ class FluentApp:
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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 = wf(self)
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# self.workflow = wf
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self.idlist_crt = selections.IdListController(self['identifier_list'])
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self.sellist_crt = selections.SelectionListController(self['selection_tree'],
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@ -164,11 +164,11 @@ class FluentApp:
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self['appwindow'].set_size_request(800, 600)
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# Set up workflow
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self.wf_view = workflow.WorkflowView(self.workflow)
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self.wf_view = workflow.WorkflowView(main.workflow)
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self.wf_view.show()
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self['workflow_vbox'].pack_end(self.wf_view)
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self._wf_menu = workflow.WorkflowMenu(self.workflow)
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self._wf_menu = workflow.WorkflowMenu(main.workflow)
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self._wf_menu.show()
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wf_menuitem = gtk.MenuItem('Fu_nctions')
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wf_menuitem.set_submenu(self._wf_menu)
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@ -208,16 +208,16 @@ class FluentApp:
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def set_project(self, proj):
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logger.log('notice', 'Creating a new project')
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self.project = proj
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project.project = proj
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self.workflow.add_project(proj)
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# self.project = proj
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# project.project = proj
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# main.workflow.add_project(proj)
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self.navigator_view.add_project(proj)
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self.dimlist_crt.set_project(proj)
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self.sellist_crt.set_project(proj)
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def set_workflow(self, workflow):
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self.workflow = workflow
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self.wf_view.set_workflow(self.workflow)
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main.workflow = workflow
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self.wf_view.set_workflow(main.workflow)
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def show(self):
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self.init_gui()
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@ -226,7 +226,7 @@ class FluentApp:
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"""Sets the plot in the currently active ViewFrame. If the plot is
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already shown in another ViewFrame it will be moved from there."""
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# Set current selection in the plot before showing it.
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plot.selection_changed(None, self.project.get_selection())
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plot.selection_changed(None, main.project.get_selection())
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self['main_view'].insert_view(plot)
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self._update_toolbar(plot)
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@ -287,7 +287,7 @@ class FluentApp:
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return self.main_view
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def create_navigator_view(self, str1, str2, int1, int2):
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self.navigator_view = navigator.NavigatorView(None, self)
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self.navigator_view = navigator.NavigatorView()
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self.navigator_view.show()
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return self.navigator_view
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@ -336,7 +336,7 @@ class FluentApp:
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def on_workflow_refresh_clicked(self, *ignored):
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try:
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reload(sys.modules[self.workflow.__class__.__module__])
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reload(sys.modules[main.workflow.__class__.__module__])
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except Exception, e:
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logger.log('warning', 'Cannot reload workflow')
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logger.log('warning', e)
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@ -0,0 +1,90 @@
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import sys
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#: Dictionary of observers
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_observers = {}
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#: The current Navigator object.
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navigator = None
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#: The current application
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application = None
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#: The current project
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project = None
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#: The current workflow
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workflow = None
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#: A cfgparse/optparse options object.
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options = None
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def notify_observers(name):
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call = "%s_changed" % name
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for s in _observers.get(name, []):
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getattr(s, call)(getattr(sys.modules[__name__], name))
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def _add_observer(name, observer):
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"""Adds observer as an observer of the named object."""
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if not _observers.has_key(name):
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_observers[name] = []
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_observers[name].append(observer)
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def _remove_observer(name, observer):
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"""Removes observer as an observer of the named object."""
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if not _observers.has_key(name):
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return
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_observers.remove(observer)
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def add_navigator_observer(observer):
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_add_observer('navigator', observer)
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def add_project_observer(observer):
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_add_observer('project', observer)
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def add_workflow_observer(observer):
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_add_observer('workflow', observer)
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def add_application_observer(observer):
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_add_observer('application', observer)
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def remove_navigator_observer(observer):
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_remove_observer('navigator', observer)
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def remove_project_observer(observer):
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_remove_observer('project', observer)
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def remove_workflow_observer(observer):
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_remove_observer('workflow', observer)
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def remove_application_observer(observer):
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_remove_observer('application', observer)
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def remove_options_observer(observer):
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_remove_observer('options', observer)
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def set_navigator(nav):
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global navigator
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navigator = nav
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notify_observers('navigator')
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def set_application(app):
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global application
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application = app
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notify_observers('application')
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def set_project(p):
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global project
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project = p
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notify_observers('project')
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def set_workflow(wf):
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global workflow
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workflow = wf
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notify_observers('workflow')
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def set_options(opt):
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global options
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options = opt
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notify_observers('options')
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@ -4,14 +4,14 @@ import gobject
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import plots
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import time
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import fluents
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import dataset, logger, plots, project, workflow
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import dataset, logger, plots, project, workflow, main
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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.app = app
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if project:
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self.data_tree = project.data_tree
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def __init__(self):
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# self.project = project
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# self.app = app
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if main.project:
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self.data_tree = main.project.data_tree
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else:
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self.data_tree = None
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@ -65,7 +65,7 @@ class NavigatorView (gtk.TreeView):
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self.data_tree.drag_data_get(paths[0], selection)
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def add_project(self, project):
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self.project = 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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self.data_tree.connect('row-changed',self.row_changed_handler)
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@ -101,10 +101,10 @@ class NavigatorView (gtk.TreeView):
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if objs and isinstance(objs[0], dataset.Dataset):
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logger.log('debug', 'Selecting dataset')
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self.project.set_current_data(objs)
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main.project.set_current_data(objs)
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else:
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logger.log('debug', 'Deselecting dataset')
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self.project.set_current_data([])
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main.project.set_current_data([])
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# TreeView changed. Set correct focus and colours
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@ -142,7 +142,7 @@ class NavigatorView (gtk.TreeView):
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if isinstance(obj, plots.Plot):
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logger.log('debug', 'Activating plot')
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self.app.change_plot(obj)
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main.application.change_plot(obj)
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elif isinstance(obj, dataset.Dataset):
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self.display_data_info(obj)
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elif obj == None:
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@ -153,7 +153,7 @@ class NavigatorView (gtk.TreeView):
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if isinstance(child, plots.Plot):
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children.append(child)
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i = self.data_tree.iter_next(i)
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self.app.change_plots(children)
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main.application.change_plots(children)
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else:
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t = type(obj)
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logger.log('debug', 'Activated datatype was %s. Don\'t know what to do.' % t)
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@ -248,9 +248,8 @@ class NavigatorMenu(gtk.Menu):
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else:
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icon = fluents.icon_factory.get("dataset")
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project = navigator.project
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project.add_dataset(ds)
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project.data_tree_insert(None, ds.get_name(), ds, None, "black", icon)
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main.project.add_dataset(ds)
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main.project.data_tree_insert(None, ds.get_name(), ds, None, "black", icon)
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else:
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print "unknown; ", retval
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dialog.destroy()
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@ -273,10 +272,9 @@ class NavigatorMenu(gtk.Menu):
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dialog.destroy()
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def on_plot_image(self, item, navigator):
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project = navigator.project
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plot = plots.ImagePlot(self.dataset, name='Image Plot')
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icon = fluents.icon_factory.get("line_plot")
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project.data_tree_insert(self.tree_iter, 'Image Plot', plot, None, "black", icon)
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main.project.data_tree_insert(self.tree_iter, 'Image Plot', plot, None, "black", icon)
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# fixme: image plot selections are not well defined
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#plot.set_selection_listener(project.set_selection)
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#project._selection_observers.append(plot)
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@ -136,7 +136,3 @@ class Project:
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self.current_data = obj
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## Singleton project.
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## This is the current and only project in the application.
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project = None
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@ -6,7 +6,7 @@ import gnome
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import gnome.ui
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import gobject
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import logger, dataset
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import logger, dataset, main
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import annotations
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from lib import hypergeom
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@ -243,8 +243,7 @@ class SelectionListController:
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def set_project(self, project):
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"""Dependency injection."""
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self.project = project
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project.add_selection_observer(self)
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main.project.add_selection_observer(self)
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def set_dimlist_controller(self, dimlist_controller):
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"""Dependency injection of the dimension list controller."""
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@ -292,7 +291,7 @@ class SelectionListController:
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di = self._get_dataset_iter(dataset)
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if not di:
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n_tot = dataset.shape[0]
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selection = self.project.get_selection().get(dim_name)
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selection = main.project.get_selection().get(dim_name)
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ds_idents = dataset.get_identifiers(dim_name)
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n_cs = len(selection.intersection(ds_idents))
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values = (dataset.get_name(), dataset, dim_name, n_cs, n_tot, 2)
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@ -363,7 +362,7 @@ class SelectionListController:
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"""
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dim_name = dataset.get_dim_name(0)
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sel_store = self._sel_stores[dim_name]
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selection_obj = self.project.get_selection()
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selection_obj = main.project.get_selection()
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current_selection = selection_obj.get(dim_name)
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if current_selection==None: return
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@ -427,7 +426,7 @@ class SelectionListController:
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else:
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seltree.expand_row(path, True)
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elif isinstance(obj, dataset.Selection):
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self.project.set_selection(self._dimension,
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main.project.set_selection(self._dimension,
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obj[self._dimension])
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def _on_button_pressed(self, widget, event):
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@ -486,7 +485,7 @@ class DimListController:
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##
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def set_project(self, project):
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"""Dependency injection."""
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self.project = project
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# self.project = project
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self.dim_names = project.dim_names
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self.update_dims()
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project.add_dataset_observer(self)
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@ -4,6 +4,7 @@ import os
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import inspect
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import logger
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import fluents
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import main
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def _workflow_classes(modname):
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"""Returns a list of all subclasses of Workflow in a given module"""
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@ -58,20 +59,20 @@ class Workflow:
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ident = None
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description = "Workflow Description"
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def __init__(self, app):
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def __init__(self):
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print "Setting stages"
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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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def get_data_file_name(self, filename):
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"""Checks if a file with the given name exists in the data directory.
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Returns the file name if the file exists in the data directory, which
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is defined as datadir/workflowname. If the file does not exist, or the
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workflow does not have an identificator, this method returns None."""
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print os.path.join(self.app.options.datadir, self.ident, filename)
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print os.path.join(main.options.datadir, self.ident, filename)
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if self.ident == None:
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return None
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fn = os.path.join(self.app.options.datadir, self.ident, filename)
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fn = os.path.join(main.options.datadir, self.ident, filename)
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if os.path.isfile(fn):
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return fn
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return None
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@ -87,18 +88,19 @@ class Workflow:
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for fun in stage.functions:
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print ' %s' % fun.name
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def add_project(self,project):
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if project == None:
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logger.log('notice','Proejct is empty')
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logger.log('notice','Project added in : %s' %self.name)
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self.project = project
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# def add_project(self,project):
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# if project == None:
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# logger.log('notice','Proejct is empty')
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# logger.log('notice','Project added in : %s' %self.name)
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# self.project = project
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class EmptyWorkflow(Workflow):
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name = 'Empty Workflow'
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def __init__(self, app):
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Workflow.__init__(self, None)
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def __init__(self):
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print "initing empty workflow"
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Workflow.__init__(self)
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class Stage:
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@ -188,8 +190,7 @@ class WorkflowView (gtk.VBox):
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def run_function(self, function):
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logger.log('debug', 'Starting function: %s' % function.name)
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project = self.workflow.app.project
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parent_data = project.current_data
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parent_data = main.project.current_data
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|
||||
validation = function.validate_input()
|
||||
|
||||
|
|
@ -226,12 +227,12 @@ class WorkflowView (gtk.VBox):
|
|||
if pass_selection:
|
||||
# if the function has a 'selection' argument, we pass in
|
||||
# the selection
|
||||
new_data = function.run(selection=project.get_selection(), *data)
|
||||
new_data = function.run(selection=main.project.get_selection(), *data)
|
||||
else:
|
||||
new_data = function.run(*data)
|
||||
|
||||
if new_data != None:
|
||||
project.add_data(parent_data, new_data, function.name)
|
||||
main.project.add_data(parent_data, new_data, function.name)
|
||||
|
||||
logger.log('debug', 'Function ended: %s' % function.name)
|
||||
|
||||
|
|
|
|||
|
|
@ -164,17 +164,12 @@ def read_gene_ontology(fd):
|
|||
section = s
|
||||
if s == 'Term':
|
||||
term = GOTerm()
|
||||
# print "[Term]"
|
||||
else:
|
||||
term = None
|
||||
#print "ignoring: %s" %s
|
||||
print "ignoring: %s" %s
|
||||
else:
|
||||
if term:
|
||||
_add_term_attribute(term, k, v, c)
|
||||
# print " %s: %s" % (k, v)
|
||||
# else:
|
||||
# print "no term: ignoring: %s" %line
|
||||
# print '.',
|
||||
line = fd.readline()
|
||||
|
||||
if term:
|
||||
|
|
@ -182,6 +177,18 @@ def read_gene_ontology(fd):
|
|||
|
||||
return go
|
||||
|
||||
|
||||
def pickle_gene_ontology(go, fn):
|
||||
fd = open(fn, 'wb')
|
||||
pickle.dump(go, fd)
|
||||
fd.close()
|
||||
|
||||
def load_pickled_ontology(fn):
|
||||
fd = open(fn, 'rb')
|
||||
go = pickle.load(fd)
|
||||
fd.close()
|
||||
return go
|
||||
|
||||
def read_default_go():
|
||||
f = open("/usr/share/gene-ontology/gene_ontology.obo")
|
||||
go = read_gene_ontology(f)
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@ class GoTermView (gtk.Frame):
|
|||
|
||||
def __init__(self):
|
||||
gtk.Frame.__init__(self)
|
||||
tab = gtk.Table(2, 2, False)
|
||||
tab = gtk.Table(2, 3, False)
|
||||
self._table = tab
|
||||
|
||||
self._name = gtk.Label('')
|
||||
|
|
@ -48,6 +48,11 @@ class GoTermView (gtk.Frame):
|
|||
tab.attach(name_label, 0, 1, 0, 1, gtk.FILL, gtk.FILL, 5, 5)
|
||||
tab.attach(self._name, 1, 2, 0, 1, gtk.FILL|gtk.EXPAND, gtk.FILL, 5, 5)
|
||||
|
||||
self._isa_parents = gtk.HBox()
|
||||
isa_parents_label = gtk.Label('Is a:')
|
||||
tab.attach(isa_parents_label, 0, 1, 1, 2, gtk.FILL, gtk.FILL, 5, 5)
|
||||
tab.attach(self._isa_parents, 1, 2, 1, 2, gtk.FILL, gtk.FILL, 5, 5)
|
||||
|
||||
self._def = gtk.TextBuffer()
|
||||
textview = gtk.TextView(self._def)
|
||||
textview.set_wrap_mode(gtk.WRAP_WORD)
|
||||
|
|
@ -55,9 +60,10 @@ class GoTermView (gtk.Frame):
|
|||
scrolled_window.add(textview)
|
||||
def_label = gtk.Label('Def:')
|
||||
def_label.set_alignment(0.0, 0.0)
|
||||
tab.attach(def_label, 0, 1, 1, 2, gtk.FILL, gtk.FILL, 5, 5)
|
||||
tab.attach(scrolled_window, 1, 2, 1, 2, gtk.FILL|gtk.EXPAND, gtk.FILL|gtk.EXPAND, 5, 5)
|
||||
tab.attach(def_label, 0, 1, 2, 3, gtk.FILL, gtk.FILL, 5, 5)
|
||||
tab.attach(scrolled_window, 1, 2, 2, 3, gtk.FILL|gtk.EXPAND, gtk.FILL|gtk.EXPAND, 5, 5)
|
||||
|
||||
self._tab = tab
|
||||
self.add(tab)
|
||||
self.set_go_term(None)
|
||||
|
||||
|
|
@ -66,16 +72,28 @@ class GoTermView (gtk.Frame):
|
|||
self.set_label(term['id'])
|
||||
self._name.set_text(term['name'])
|
||||
self._def.set_text(term['def'])
|
||||
self._tab.remove(self._isa_parents)
|
||||
self._isa_parents = gtk.HBox()
|
||||
for p in term['is_a']:
|
||||
btn = gtk.Button(p)
|
||||
btn.show()
|
||||
self._isa_parents.add(btn)
|
||||
self._isa_parents.show()
|
||||
self._tab.attach(self._isa_parents, 1, 2, 1, 2, gtk.FILL, gtk.FILL, 5, 5)
|
||||
else:
|
||||
self.set_label('GO Term')
|
||||
self._name.set_text('')
|
||||
self._def.set_text('')
|
||||
|
||||
self._tab.remove(self._isa_parents)
|
||||
self._isa_parents = gtk.HBox()
|
||||
self._tab.attach(self._isa_parents, 1, 2, 1, 2, gtk.FILL, gtk.FILL, 5, 5)
|
||||
|
||||
|
||||
class GeneOntologyTree (gtk.HPaned):
|
||||
|
||||
def __init__(self, network):
|
||||
gtk.HPaned.__init__(self)
|
||||
self.set_position(400)
|
||||
|
||||
treemodel = geneontology.get_go_treestore(network)
|
||||
self._treemodel = treemodel
|
||||
|
|
|
|||
|
|
@ -13,8 +13,8 @@ class SmallTestWorkflow(workflow.Workflow):
|
|||
ident = 'smokers'
|
||||
description = 'A small test workflow for gene expression analysis.'
|
||||
|
||||
def __init__(self, app):
|
||||
workflow.Workflow.__init__(self, app)
|
||||
def __init__(self):
|
||||
workflow.Workflow.__init__(self)
|
||||
|
||||
# DATA IMPORT
|
||||
load = workflow.Stage('load', 'Data')
|
||||
|
|
|
|||
Reference in New Issue