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.

bin/fluents

@@ -3,7 +3,7 @@
 from getopt import getopt
 import os
 import sys
-from fluents import fluents, project, workflow
+from fluents import fluents, project, workflow, main
 import workflows
 import cfgparse, optparse
 
@@ -68,11 +68,16 @@ if __name__ == '__main__':
         if wf.ident == options.workflow:
             selected_wf = wf            
 
-    app = fluents.FluentApp(selected_wf)
-    app.options = options
-    fluents.app = app
 
-    app.set_project(project.Project())
+    main.set_workflow(selected_wf())
+    main.set_options(options)
+    app = fluents.FluentApp()
+
+    main.set_application(app)
+    main.set_project(project.Project())
+
+
+    app.set_project(main.project)
     app.show()
     gtk.main()
 

fluents/__init__.py

@@ -0,0 +1,3 @@
+
+import main
+

fluents/dialogs.py

@@ -17,9 +17,8 @@ class CreateProjectDruid(gtk.Window):
     Workflow, and asks the user to select one of these. A new project of
     the selected class is added to the application."""
     
-    def __init__(self, app):
+    def __init__(self):
         gtk.Window.__init__(self)
-        self.app = app
         self.widget_tree = gtk.glade.XML(GLADEFILENAME, 'new_project_druid')
         self.workflows = self.make_workflow_list()
         self.selected = None
@@ -63,10 +62,12 @@ class CreateProjectDruid(gtk.Window):
         
     def finish(self, *rest):
         tree, it = self['workflow_list'].get_selection().get_selected()
-        wf = self.workflows.get_value(it, 1)
+        wf_class = self.workflows.get_value(it, 1)
         proj = project.Project()
-        self.app.set_workflow(wf(self.app))
+        main.set_workflow(wf_class())
-        self.app.set_project(proj)
+#        self.app.set_workflow(wf(self.app))
+#        self.app.set_project(proj)
+        main.set_project(proj)
         self.hide()
         self.destroy()
 

fluents/fluents.py

@@ -13,7 +13,7 @@ import gnome
 import gnome.ui
 import scipy
 import pango
-import project, workflow, dataset, logger, view, navigator, dialogs, selections
+import project, workflow, dataset, logger, view, navigator, dialogs, selections, main
 
 
 PROGRAM_NAME = 'fluents'
@@ -142,8 +142,8 @@ class ViewFrameToolButton (gtk.ToolItem):
 
 class FluentApp:
 
-    def __init__(self, wf): # Application variables
+    def __init__(self): # Application variables
-        self.project = None
+#        self.project = None
         self.current_data = None
         self._last_view = None
         self._plot_toolbar = None
@@ -151,7 +151,7 @@ class FluentApp:
         
         gtk.glade.set_custom_handler(self.custom_object_factory)
         self.widget_tree = gtk.glade.XML(GLADEFILENAME, 'appwindow')
-        self.workflow = wf(self)
+#        self.workflow = wf
     
         self.idlist_crt = selections.IdListController(self['identifier_list'])
         self.sellist_crt = selections.SelectionListController(self['selection_tree'],
@@ -164,11 +164,11 @@ class FluentApp:
         self['appwindow'].set_size_request(800, 600)
 
         # Set up workflow
-        self.wf_view = workflow.WorkflowView(self.workflow)
+        self.wf_view = workflow.WorkflowView(main.workflow)
         self.wf_view.show()
         self['workflow_vbox'].pack_end(self.wf_view)
 
-        self._wf_menu = workflow.WorkflowMenu(self.workflow)
+        self._wf_menu = workflow.WorkflowMenu(main.workflow)
         self._wf_menu.show()
         wf_menuitem = gtk.MenuItem('Fu_nctions')
         wf_menuitem.set_submenu(self._wf_menu)
@@ -208,16 +208,16 @@ class FluentApp:
 
     def set_project(self, proj):
         logger.log('notice', 'Creating a new project')
-        self.project = proj
+#        self.project = proj
-        project.project = proj
+#        project.project = proj
-        self.workflow.add_project(proj)
+#        main.workflow.add_project(proj)
         self.navigator_view.add_project(proj)
         self.dimlist_crt.set_project(proj)
         self.sellist_crt.set_project(proj)
         
     def set_workflow(self, workflow):
-        self.workflow = workflow
+        main.workflow = workflow
-        self.wf_view.set_workflow(self.workflow)
+        self.wf_view.set_workflow(main.workflow)
 
     def show(self):
         self.init_gui()
@@ -226,7 +226,7 @@ class FluentApp:
         """Sets the plot in the currently active ViewFrame. If the plot is 
         already shown in another ViewFrame it will be moved from there."""
         # Set current selection in the plot before showing it.
-        plot.selection_changed(None, self.project.get_selection())
+        plot.selection_changed(None, main.project.get_selection())
 
         self['main_view'].insert_view(plot)
         self._update_toolbar(plot)
@@ -287,7 +287,7 @@ class FluentApp:
         return self.main_view
 
     def create_navigator_view(self, str1, str2, int1, int2):
-        self.navigator_view = navigator.NavigatorView(None, self)
+        self.navigator_view = navigator.NavigatorView()
         self.navigator_view.show()
         return self.navigator_view
 
@@ -336,7 +336,7 @@ class FluentApp:
 
     def on_workflow_refresh_clicked(self, *ignored):
         try:
-            reload(sys.modules[self.workflow.__class__.__module__])
+            reload(sys.modules[main.workflow.__class__.__module__])
         except Exception, e:
             logger.log('warning', 'Cannot reload workflow')
             logger.log('warning', e)

fluents/main.py

@@ -0,0 +1,90 @@
+    
+import sys
+
+#: Dictionary of observers
+_observers = {}
+
+#: The current Navigator object.
+navigator = None
+
+#: The current application
+application = None
+
+#: The current project
+project = None
+
+#: The current workflow
+workflow = None
+
+#: A cfgparse/optparse options object.
+options = None
+        
+def notify_observers(name):
+    call = "%s_changed" % name
+    for s in _observers.get(name, []):
+        getattr(s, call)(getattr(sys.modules[__name__], name))
+
+def _add_observer(name, observer):
+    """Adds observer as an observer of the named object."""
+    if not _observers.has_key(name):
+        _observers[name] = []
+    _observers[name].append(observer)
+    
+def _remove_observer(name, observer):
+    """Removes observer as an observer of the named object."""
+    if not _observers.has_key(name):
+        return
+    _observers.remove(observer)
+
+def add_navigator_observer(observer):
+    _add_observer('navigator', observer)
+
+def add_project_observer(observer):
+    _add_observer('project', observer)
+
+def add_workflow_observer(observer):
+    _add_observer('workflow', observer)
+
+def add_application_observer(observer):
+    _add_observer('application', observer)
+
+def remove_navigator_observer(observer):
+    _remove_observer('navigator', observer)
+
+def remove_project_observer(observer):
+    _remove_observer('project', observer)
+
+def remove_workflow_observer(observer):
+    _remove_observer('workflow', observer)
+
+def remove_application_observer(observer):
+    _remove_observer('application', observer)
+
+def remove_options_observer(observer):
+    _remove_observer('options', observer)
+
+def set_navigator(nav):
+    global navigator
+    navigator = nav
+    notify_observers('navigator')
+
+def set_application(app):
+    global application
+    application = app
+    notify_observers('application')
+
+def set_project(p):
+    global project
+    project = p
+    notify_observers('project')
+
+def set_workflow(wf):
+    global workflow
+    workflow = wf
+    notify_observers('workflow')
+
+def set_options(opt):
+    global options 
+    options = opt
+    notify_observers('options')
+

fluents/navigator.py

@@ -4,14 +4,14 @@ import gobject
 import plots
 import time
 import fluents
-import dataset, logger, plots, project, workflow
+import dataset, logger, plots, project, workflow, main
 
 class NavigatorView (gtk.TreeView):
-    def __init__(self, project, app):
+    def __init__(self):
-        self.project = project
+#        self.project = project
-        self.app = app
+#        self.app = app
-        if project:
+        if main.project:
-            self.data_tree = project.data_tree
+            self.data_tree = main.project.data_tree
         else:
             self.data_tree = None
         
@@ -65,7 +65,7 @@ class NavigatorView (gtk.TreeView):
             self.data_tree.drag_data_get(paths[0], selection)
 
     def add_project(self, project):
-        self.project = project
+#        self.project = project
         self.data_tree = project.data_tree
         self.set_model(project.data_tree)
         self.data_tree.connect('row-changed',self.row_changed_handler)
@@ -101,10 +101,10 @@ class NavigatorView (gtk.TreeView):
 
         if objs and isinstance(objs[0], dataset.Dataset):
             logger.log('debug', 'Selecting dataset')
-            self.project.set_current_data(objs)
+            main.project.set_current_data(objs)
         else:
             logger.log('debug', 'Deselecting dataset')
-            self.project.set_current_data([])
+            main.project.set_current_data([])
 
 
     # TreeView changed. Set correct focus and colours
@@ -142,7 +142,7 @@ class NavigatorView (gtk.TreeView):
         
         if isinstance(obj, plots.Plot):
             logger.log('debug', 'Activating plot')
-            self.app.change_plot(obj)
+            main.application.change_plot(obj)
         elif isinstance(obj, dataset.Dataset):
             self.display_data_info(obj)
         elif obj == None:
@@ -153,7 +153,7 @@ class NavigatorView (gtk.TreeView):
                 if isinstance(child, plots.Plot):
                     children.append(child)
                 i = self.data_tree.iter_next(i)
-            self.app.change_plots(children)
+            main.application.change_plots(children)
         else:
             t = type(obj)
             logger.log('debug', 'Activated datatype was %s. Don\'t know what to do.' % t)
@@ -248,9 +248,8 @@ class NavigatorMenu(gtk.Menu):
                 else:
                     icon = fluents.icon_factory.get("dataset")
 
-                project = navigator.project
+                main.project.add_dataset(ds)
-                project.add_dataset(ds)
+                main.project.data_tree_insert(None, ds.get_name(), ds, None, "black", icon)
-                project.data_tree_insert(None, ds.get_name(), ds, None, "black", icon)
         else:
             print "unknown; ", retval 
         dialog.destroy()
@@ -273,10 +272,9 @@ class NavigatorMenu(gtk.Menu):
         dialog.destroy()
 
     def on_plot_image(self, item, navigator):
-        project = navigator.project
         plot = plots.ImagePlot(self.dataset, name='Image Plot')
         icon = fluents.icon_factory.get("line_plot")
-        project.data_tree_insert(self.tree_iter, 'Image Plot', plot, None, "black", icon)
+        main.project.data_tree_insert(self.tree_iter, 'Image Plot', plot, None, "black", icon)
         # fixme: image plot selections are not well defined
         #plot.set_selection_listener(project.set_selection)
         #project._selection_observers.append(plot)

fluents/project.py

@@ -136,7 +136,3 @@ class Project:
         self.current_data = obj
 
 
-## Singleton project.
-## This is the current and only project in the application.
-project = None
-

fluents/selections.py

@@ -6,7 +6,7 @@ import gnome
 import gnome.ui
 import gobject
 
-import logger, dataset
+import logger, dataset, main
 import annotations
 from lib import hypergeom
 
@@ -243,8 +243,7 @@ class SelectionListController:
 
     def set_project(self, project):
         """Dependency injection."""
-        self.project = project
+        main.project.add_selection_observer(self)
-        project.add_selection_observer(self)
         
     def set_dimlist_controller(self, dimlist_controller):
         """Dependency injection of the dimension list controller."""
@@ -292,7 +291,7 @@ class SelectionListController:
         di = self._get_dataset_iter(dataset)
         if not di:
             n_tot = dataset.shape[0]
-            selection = self.project.get_selection().get(dim_name)
+            selection = main.project.get_selection().get(dim_name)
             ds_idents = dataset.get_identifiers(dim_name)
             n_cs = len(selection.intersection(ds_idents))
             values = (dataset.get_name(), dataset, dim_name, n_cs, n_tot, 2)
@@ -363,7 +362,7 @@ class SelectionListController:
         """
         dim_name = dataset.get_dim_name(0)
         sel_store = self._sel_stores[dim_name]
-        selection_obj = self.project.get_selection()
+        selection_obj = main.project.get_selection()
         current_selection = selection_obj.get(dim_name)
         if current_selection==None: return
 
@@ -427,7 +426,7 @@ class SelectionListController:
             else:
                 seltree.expand_row(path, True)
         elif isinstance(obj, dataset.Selection):
-            self.project.set_selection(self._dimension,
+            main.project.set_selection(self._dimension,
                                        obj[self._dimension])
 
     def _on_button_pressed(self, widget, event):
@@ -486,7 +485,7 @@ class DimListController:
     ##
     def set_project(self, project):
         """Dependency injection."""
-        self.project = project
+#        self.project = project
         self.dim_names = project.dim_names
         self.update_dims()
         project.add_dataset_observer(self)

fluents/workflow.py

@@ -4,6 +4,7 @@ import os
 import inspect
 import logger
 import fluents
+import main
 
 def _workflow_classes(modname):
     """Returns a list of all subclasses of Workflow in a given module"""
@@ -58,20 +59,20 @@ class Workflow:
     ident = None
     description = "Workflow Description"
 
-    def __init__(self, app):
+    def __init__(self):
+        print "Setting stages"
         self.stages = []
         self.stages_by_id = {}
-        self.app = app
 
     def get_data_file_name(self, filename):
         """Checks if a file with the given name exists in the data directory.
         Returns the file name if the file exists in the data directory, which
         is defined as datadir/workflowname. If the file does not exist, or the
         workflow does not have an identificator, this method returns None."""
-        print os.path.join(self.app.options.datadir, self.ident, filename)
+        print os.path.join(main.options.datadir, self.ident, filename)
         if self.ident == None:
             return None
-        fn = os.path.join(self.app.options.datadir, self.ident, filename)
+        fn = os.path.join(main.options.datadir, self.ident, filename)
         if os.path.isfile(fn):
             return fn
         return None
@@ -87,18 +88,19 @@ class Workflow:
             for fun in stage.functions:
                 print '        %s' % fun.name
 
-    def add_project(self,project):
+#    def add_project(self,project):
-        if project == None:
+#        if project == None:
-            logger.log('notice','Proejct is empty')
+#            logger.log('notice','Proejct is empty')
-        logger.log('notice','Project added in : %s' %self.name)
+#        logger.log('notice','Project added in : %s' %self.name)
-        self.project = project
+#        self.project = project
 
 
 class EmptyWorkflow(Workflow):
     name = 'Empty Workflow'
 
-    def __init__(self, app):
+    def __init__(self):
-        Workflow.__init__(self, None)
+        print "initing empty workflow"
+        Workflow.__init__(self)
     
 
 class Stage:
@@ -188,8 +190,7 @@ class WorkflowView (gtk.VBox):
 
     def run_function(self, function):
         logger.log('debug', 'Starting function: %s' % function.name)
-        project = self.workflow.app.project
+        parent_data = main.project.current_data
-        parent_data = project.current_data
 
         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)
 

workflows/geneontology.py

@@ -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)

workflows/gobrowser.py

@@ -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(def_label, 0, 1, 2, 3, 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(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

workflows/smokers.py

@@ -13,8 +13,8 @@ class SmallTestWorkflow(workflow.Workflow):
     ident = 'smokers'
     description = 'A small test workflow for gene expression analysis.'
 
-    def __init__(self, app):
+    def __init__(self):
-        workflow.Workflow.__init__(self, app)        
+        workflow.Workflow.__init__(self)        
 
         # DATA IMPORT
         load = workflow.Stage('load', 'Data')