* fluent, *.py: Data and plots returned from functions will now show up in

the navigator window.

fluent

@@ -24,8 +24,6 @@ import scipy
 PROGRAM_NAME = 'fluent'
 VERSION = '0.1.0'
 GLADEFILENAME = 'system/fluent.glade'
-WF_BOX = 'workflow_vbox'
-DATA_BOX = 'data_vbox'
 
 class FluentApp:
 
@@ -44,8 +42,6 @@ class FluentApp:
 
         ####################
 
-        
-        self.navigator = navigator.NavigatorStore(self.project)
         self.current_data = None
         gtk.glade.set_custom_handler(self.custom_object_factory)
         self.widget_tree = gtk.glade.XML(GLADEFILENAME, 'appwindow')
@@ -78,7 +74,8 @@ class FluentApp:
         return self.large_view
 
     def create_navigator_view(self, str1, str2, int1, int2):
-        self.navigator_view = navigator.NavigatorView(self.navigator, self)
+        tree = self.project.data_tree
+        self.navigator_view = navigator.NavigatorView(tree, self)
         self.navigator_view.show()
         return self.navigator_view
 
@@ -128,4 +125,3 @@ if __name__ == '__main__':
     gtk.main()
 
 
-

system/navigator.py

@@ -4,29 +4,6 @@ import gobject
 import plots
 import logger
 
-class NavigatorStore (gtk.TreeStore):
-    def __init__(self,project):
-        gtk.TreeStore.__init__(self, gobject.TYPE_STRING, plots.Plot)
-        self.project = project
-        iter = self.append(None)
-        self.set_value(iter, 0, ('Sine Plot'))
-        self.set_value(iter, 1, (plots.SinePlot(project)))
-
-        iter = self.append(None)
-        self.set_value(iter, 0, ('Scatter Plot'))
-        self.set_value(iter, 1, (plots.ScatterPlot(project)))
-
-        iter = self.append(None)
-        self.set_value(iter, 0, ('Scatter Plot 2'))
-        self.set_value(iter, 1, (plots.ScatterPlot(project)))
-
-    def plot_at(self, path):
-        iter = self.get_iter(path)
-        plot = self.get_value(iter, 1)
-        if plot:
-            plot.show()
-        return plot
-
 class NavigatorView (gtk.TreeView):
     def __init__(self, nav, app):
         gtk.TreeView.__init__(self, nav)
@@ -43,6 +20,8 @@ class NavigatorView (gtk.TreeView):
         logger.log('debug', 'Initializing naviagor window')
 
     def row_activated_handler(self, widget, path, column):
-        plot = self.navigator.plot_at(path)
+            
+        iter = self.navigator.get_iter(path)
+        object = self.navigator.get_value(iter, 2)
         logger.log('notice', 'Button pressed')
-        self.app.change_plot(plot)
+        self.app.change_plot(object)

system/plots.py

@@ -73,7 +73,6 @@ class SmallView (gtk.Table):
     def set_child(self, child, col, row):
         cur_widget = self.child_views[col][row]
         cur_widget.disconnect(cur_widget.parent_signalling)
-        print cur_widget
         self.remove(cur_widget)
         self.attach(child, col, col+1, row, row+1)
         child.parent_signalling = child.connect('button_press_event', self.__view_button_event__)

system/project.py

@@ -1,8 +1,15 @@
 import dataset
+import plots
 import scipy
+import gobject
+import gtk
 
 class Project:
     def __init__(self,name="Testing"):
+        self.data_tree = gtk.TreeStore(gobject.TYPE_STRING, 
+                                       gobject.TYPE_STRING, 
+                                       gobject.TYPE_PYOBJECT)
+
         self.name = name
         self.dim_names = []
         self._observers = {}
@@ -39,6 +46,26 @@ class Project:
         """Returns the current selection object"""
         return self.sel_obj.current_selection
     
+    def add_data(self, parent, data):
+        """Adds a set of data and plots to the navigator.
+
+        This method is usually called after a Function in a workflow
+        has finished and returns its output."""
+        for d in data:
+            if isinstance(d, dataset.Dataset):
+                self.add_dataset(d)
+                self.data_tree_insert(None, 'data', d)
+            elif isinstance(d, plots.Plot):
+#                self.add_view(d)
+                self.data_tree_insert(None, 'view', d)
+
+    def data_tree_insert(self, parent, text, data):
+        tree = self.data_tree
+        iter = tree.append(parent)
+        tree.set_value(iter, 0, text)
+        tree.set_value(iter, 1, type(data))
+        tree.set_value(iter, 2, data)
+
     def add_dataset(self,dataset):
         """Appends a new Dataset to the project."""
         self.datasets.append(dataset)
@@ -52,6 +79,11 @@ class Project:
             dim_name = dim_name + "_t" 
         return dim_name
         
-
+    def object_at(self, path):
-
+        "Returns the object at a given path in the tree."
+        iter = self.get_iter(path)
+        object = self.get_value(iter, 2)
+        if object:
+            object.show()
+        return object
 

system/workflow.py

@@ -92,7 +92,7 @@ class WorkflowView (gtk.VBox):
         project = self.workflow.app.project
         new_data = function.run(project.current_data)
         if new_data != None:
-            project.current_data = new_data
+            project.add_data(None, new_data)
         logger.log('debug', 'Function ended: %s' % function.name)
         
     def button_click_handler(self, button):

workflows/go_workflow.py

@@ -2,6 +2,7 @@ import gtk
 import logger
 from annotations import Annotations
 from workflow import *
+import plots
 #import geneontology
 #import gostat
 from scipy import array
@@ -14,6 +15,7 @@ class EinarsWorkflow (Workflow):
 
         load = Stage('load', 'Load Data')
         load.add_function(Function('load', 'Load Microarrays'))
+        load.add_function(TestDataFunction())
         self.add_stage(load)
 
         preproc = Stage('preprocess', 'Preprocessing')
@@ -83,3 +85,12 @@ class GODistanceFunction(Function):
 
         return gene_distances
 
+class TestDataFunction(Function):
+    
+    def __init__(self):
+        Function.__init__(self, 'test_data', 'Generate Test Data')
+
+    def run(self, data):
+        logger.log('notice', 'Injecting foo test data')
+        return [plots.SinePlot(None)]
+