Removed need to provide plots with project/workflow on creation, is instead injected by project itself when added to it.

system/plots.py

@@ -161,15 +161,12 @@ class LargeView (gtk.Frame):
 
 class Plot (gtk.Frame):
 
-    def __init__(self,project):
+    def __init__(self):
         gtk.Frame.__init__(self)
-        self.project = project
         self.mark_active(False)
         self.connect('button_press_event', self.on_button_press)
         self.sel_obj = None
         self.active = False
-        if project!=None: #its not an Emptyview
-            project.attach(self,'selection_update')
         
     def on_button_press(self, *rest):
 #        logger.log('debug', 'button pressed in plot')
@@ -182,12 +179,16 @@ class Plot (gtk.Frame):
             self.set_shadow_type(gtk.SHADOW_OUT)
         self.active = active
 
-    def update(self,project,key):
+    def update(self, key):
         pass
 
+    def set_project(self, project):
+        self.project = project
+        
+    
 class EmptyView (Plot):
     def __init__(self):
-        Plot.__init__(self,None)
+        Plot.__init__(self)
         
         label = gtk.Label('No view')
         ebox = gtk.EventBox()
@@ -211,8 +212,8 @@ class EmptyView (Plot):
         
 
 class SinePlot(Plot):
-    def __init__(self,project):
-        Plot.__init__(self,project)
+    def __init__(self):
+        Plot.__init__(self)
         fig = Figure(figsize=(5,4), dpi=72)
         ax = fig.add_subplot(111)
         t = arange(0.0,3.0,0.01)
@@ -224,9 +225,8 @@ class SinePlot(Plot):
 
 
 class ScatterPlot(Plot):
-    def __init__(self,project,dataset,id_dim,sel_dim,id_1,id_2):
-        Plot.__init__(self,project)
-        self.project = project
+    def __init__(self, dataset, id_dim, sel_dim, id_1, id_2):
+        Plot.__init__(self)
         fig = Figure(figsize=(5,4), dpi=72)
         self.ax = ax = fig.add_subplot(111)
         self.current_dim = id_dim
@@ -272,8 +272,8 @@ class ScatterPlot(Plot):
         ids = [id for id,ind in self.dataset[self.current_dim].items() if ind in index]
         self.project.set_selection(self.current_dim,ids)
 
-    def update(self,project,key):
-        curr_sel = project.get_selection() # get selection object
+    def update(self, key):
+        curr_sel = self.project.get_selection() # get selection object
         ids = curr_sel[self.current_dim] # current identifiers
         
         index = [ind for id,ind in self.dataset[self.current_dim].items() if id in ids] #conversion to index
@@ -283,5 +283,3 @@ class ScatterPlot(Plot):
         self.ax.plot(self.xaxis_data,self.yaxis_data,'og')
         self.ax.plot(xdata_new,ydata_new,'or')
         self.canvas.draw()
-
-

system/project.py

@@ -35,7 +35,7 @@ class Project:
         """Notifies observers"""
         for observer in self._observers[key]:
             if modifier != observer:
-                observer.update(self,key)
+                observer.update(key)
 
     def set_selection(self,dim_name,selection):
         """Sets a current selection and notify observers"""
@@ -58,6 +58,8 @@ class Project:
             elif isinstance(d, plots.Plot):
 #                self.add_view(d)
                 self.data_tree_insert(None, 'view', d)
+                d.set_project(self)
+                self.attach(d, 'selection_update')
 
     def data_tree_insert(self, parent, text, data):
         tree = self.data_tree

workflows/go_workflow.py

@@ -107,7 +107,7 @@ class TestDataFunction(Function):
         logger.log('notice', 'Injecting foo test data')
         x = randn(20,30)
         X = dataset.Dataset(x)
-        return [X, plots.SinePlot(None)]
+        return [X, plots.SinePlot()]
 
 
 class DatasetLoadFunction(Function):
@@ -239,8 +239,8 @@ class PCAFunction(Function):
         # cleanup
         rpy.r.rm(["t", "m"])
 
-        loading_plot1 = plots.ScatterPlot(self._workflow.project,P,'ids','component','1','2')
-        loading_plot2 = plots.ScatterPlot(self._workflow.project,P,'ids','component','3','4')
-        score_plot = plots.ScatterPlot(self._workflow.project,T,'filename','component','1','2')     
+        loading_plot1 = plots.ScatterPlot(P,'ids','component','1','2')
+        loading_plot2 = plots.ScatterPlot(P,'ids','component','3','4')
+        score_plot = plots.ScatterPlot(T,'filename','component','1','2')     
         
         return [T, P, loading_plot1, loading_plot2, score_plot]

workflows/pca_workflow.py

@@ -102,9 +102,9 @@ class PCAFunction(Function):
         #tsq = dataset.Dataset(tsq,[singel_def,data_ids[1])
         
         ## plots
-        loading_plot1 = plots.ScatterPlot(self.workflow.project,P,'genes','comp','1','2')
-        loading_plot2 = plots.ScatterPlot(self.workflow.project,P,'genes','comp','3','4')
-        score_plot = plots.ScatterPlot(self.workflow.project,T,'samples','comp','1','2')
+        loading_plot1 = plots.ScatterPlot(P,'genes','comp','1','2')
+        loading_plot2 = plots.ScatterPlot(P,'genes','comp','3','4')
+        score_plot = plots.ScatterPlot(T,'samples','comp','1','2')
         
         return [T,P,E,loading_plot1,loading_plot2,score_plot]