The navigator now displays the plots and data in a tree that shows the ancestry information.

fluent

@@ -53,6 +53,7 @@ class FluentApp:
     def create_logview(self, str1, str2, int1, int2):
         # Set up log view
         self.log_view = logger.LogView(logger.logger)
+        self.log_view.set_level('notice')
         self.log_view.show()
         return self.log_view
 

system/logger.py

@@ -58,7 +58,10 @@ class LogView(gtk.TreeView):
         #self.connect('button_release_event', None)
 
         # Make sure tree view displays bottom entry when entered
-        self.model.connect('row-changed', lambda model, path, iter : self.scroll_to_cell(path))
+        def scroll_to_last(model, path, it):
+            if path:
+                self.scroll_to_cell(path)
+        self.model.connect('row-changed', scroll_to_last)
 
     def set_level(self, level):
         self.level = level

system/plots.py

@@ -161,13 +161,17 @@ class LargeView (gtk.Frame):
 
 class Plot (gtk.Frame):
 
-    def __init__(self):
+    def __init__(self, title):
         gtk.Frame.__init__(self)
         self.mark_active(False)
         self.connect('button_press_event', self.on_button_press)
         self.sel_obj = None
         self.active = False
-        
+        self.title = title
+
+    def get_title(self):
+        return self.title
+
     def on_button_press(self, *rest):
 #        logger.log('debug', 'button pressed in plot')
         self.mark_active(True)
@@ -188,7 +192,7 @@ class Plot (gtk.Frame):
     
 class EmptyView (Plot):
     def __init__(self):
-        Plot.__init__(self)
+        Plot.__init__(self, 'Empty view')
         
         label = gtk.Label('No view')
         ebox = gtk.EventBox()
@@ -213,20 +217,22 @@ class EmptyView (Plot):
 
 class SinePlot(Plot):
     def __init__(self):
-        Plot.__init__(self)
+        Plot.__init__(self, 'Sine plot')
+
         fig = Figure(figsize=(5,4), dpi=72)
         ax = fig.add_subplot(111)
         t = arange(0.0,3.0,0.01)
         s = sin(2*pi*t)
         ax.plot(t,s)
+
         self.canvas = FigureCanvas(fig)
         self.add(self.canvas)
         self.canvas.show()
 
 
 class ScatterPlot(Plot):
-    def __init__(self, dataset, id_dim, sel_dim, id_1, id_2):
+    def __init__(self, dataset,id_dim, sel_dim,id_1,id_2):
-        Plot.__init__(self)
+        Plot.__init__(self, 'Scatter plot')
         fig = Figure(figsize=(5,4), dpi=72)
         self.ax = ax = fig.add_subplot(111)
         self.current_dim = id_dim

system/project.py

@@ -45,28 +45,42 @@ class Project:
     def get_selection(self):
         """Returns the current selection object"""
         return self.sel_obj.current_selection
-    
+ 
+    def get_data_iter(self, obj):
+        """Retuns an iterator to data."""
+        retval = [None]
+        def is_obj(m, p, i, d):
+            if obj == m.get_value(i, 2):
+                d.append(i)
+                return True
+
+        self.data_tree.foreach(is_obj, retval)
+        return retval[-1]
+
     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."""
+        
+        parent_iter = self.get_data_iter(parent)
+
         for d in data:
             if isinstance(d, dataset.Dataset):
                 self.add_dataset(d)
-                self.data_tree_insert(None, d.get_name(), d)
+                self.data_tree_insert(parent_iter, d.get_name(), d)
             elif isinstance(d, plots.Plot):
 #                self.add_view(d)
-                self.data_tree_insert(None, 'view', d)
+                self.data_tree_insert(parent_iter, d.get_title(), d)
                 d.set_project(self)
                 self.attach(d, 'selection_update')
 
     def data_tree_insert(self, parent, text, data):
         tree = self.data_tree
-        iter = tree.append(parent)
+        it = tree.append(parent)
-        tree.set_value(iter, 0, text)
+        tree.set_value(it, 0, text)
-        tree.set_value(iter, 1, type(data))
+        tree.set_value(it, 1, type(data))
-        tree.set_value(iter, 2, data)
+        tree.set_value(it, 2, data)
 
     def add_dataset(self,dataset):
         """Appends a new Dataset to the project."""

system/workflow.py

@@ -116,9 +116,12 @@ class WorkflowView (gtk.VBox):
     def run_function(self, function):
         logger.log('debug', 'Starting function: %s' % function.name)
         project = self.workflow.app.project
+        parent_data = project.current_data
+
         new_data = function.run(project.current_data)
         if new_data != None:
-            project.add_data(None, new_data)
+            project.add_data(parent_data, new_data)
+
         logger.log('debug', 'Function ended: %s' % function.name)
         
     def button_click_handler(self, button):

workflows/go_workflow.py

@@ -1,55 +1,55 @@
 import gtk
 import logger
 from annotations import Annotations
-from workflow import *
+import workflow
 import plots
 import dataset
 #import geneontology
 #import gostat
-from scipy import array,randn
+from scipy import array,randn,log
 import cPickle
 
-class EinarsWorkflow (Workflow):
+class EinarsWorkflow (workflow.Workflow):
 
     name = 'Test Workflow'
     description = 'Gene Ontology Workflow. This workflow currently serves as a general testing workflow.'
     def __init__(self, app):
-        Workflow.__init__(self, app)
+        workflow.Workflow.__init__(self, app)
 
-        load = Stage('load', 'Load Data')
+        load = workflow.Stage('load', 'Load Data')
-        load.add_function(Function('load', 'Load Microarrays'))
         load.add_function(CelFileImportFunction())
         load.add_function(TestDataFunction())
         load.add_function(DatasetLoadFunction())
         self.add_stage(load)
 
-        preproc = Stage('preprocess', 'Preprocessing')
+        preproc = workflow.Stage('preprocess', 'Preprocessing')
-        preproc.add_function(Function('rma', 'RMA'))
+        preproc.add_function(DatasetLog())
+        preproc.add_function(workflow.Function('rma', 'RMA'))
         self.add_stage(preproc)
 
-        go = Stage('go', 'Gene Ontology Data')
+        go = workflow.Stage('go', 'Gene Ontology Data')
         go.add_function(LoadAnnotationsFunction())
         go.add_function(GODistanceFunction())
         self.add_stage(go)
 
-        regression = Stage('regression', 'Regression')
+        regression = workflow.Stage('regression', 'Regression')
-        regression.add_function(Function('pls', 'PLS'))
+        regression.add_function(workflow.Function('pls', 'PLS'))
         self.add_stage(regression)
 
-        explore = Stage('explore', 'Explorative analysis')
+        explore = workflow.Stage('explore', 'Explorative analysis')
         explore.add_function(PCAFunction(self))
         self.add_stage(explore)
 
-        save = Stage('save', 'Save Data')
+        save = workflow.Stage('save', 'Save Data')
         save.add_function(DatasetSaveFunction())
         self.add_stage(save)
         
         logger.log('debug', '\tEinar\'s workflow is now active')
 
-class LoadAnnotationsFunction(Function):
+class LoadAnnotationsFunction(workflow.Function):
 
     def __init__(self):
-        Function.__init__(self, 'load-go-ann', 'Load Annotations')
+        workflow.Function.__init__(self, 'load-go-ann', 'Load Annotations')
         self.annotations = None
 
     def load_file(self, filename):
@@ -80,10 +80,10 @@ class LoadAnnotationsFunction(Function):
         dialog.destroy()
         return [self.annotations]
 
-class GODistanceFunction(Function):
+class GODistanceFunction(workflow.Function):
 
     def __init__(self):
-        Function.__init__(self, 'go_diatance', 'GO Distances')
+        workflow.Function.__init__(self, 'go_diatance', 'GO Distances')
         self.output = None
 
     def run(self, data):
@@ -99,9 +99,9 @@ class GODistanceFunction(Function):
         return gene_distances
 
 
-class TestDataFunction(Function):  
+class TestDataFunction(workflow.Function):  
     def __init__(self):
-        Function.__init__(self, 'test_data', 'Generate Test Data')
+        workflow.Function.__init__(self, 'test_data', 'Generate Test Data')
 
     def run(self, data):
         logger.log('notice', 'Injecting foo test data')
@@ -109,11 +109,20 @@ class TestDataFunction(Function):
         X = dataset.Dataset(x)
         return [X, plots.SinePlot()]
 
+class DatasetLog(workflow.Function):
+    def __init__(self):
+        workflow.Function.__init__(self, 'log', 'Log')
 
-class DatasetLoadFunction(Function):
+    def run(self, data):
+        logger.log('notice', 'Taking the log of dataset %s' % data.get_name())
+        d = data.asarray()
+        d = log(d)
+        return [dataset.Dataset(d)]
+
+class DatasetLoadFunction(workflow.Function):
     """Loader for previously pickled Datasets."""
     def __init__(self):
-        Function.__init__(self, 'load_data', 'Load Pickled Dataset')
+        workflow.Function.__init__(self, 'load_data', 'Load Pickled Dataset')
 
     def run(self, data):
         chooser = gtk.FileChooserDialog(title="Select cel files...", parent=None,
@@ -136,10 +145,10 @@ class DatasetLoadFunction(Function):
             chooser.destroy()
 
 
-class DatasetSaveFunction(Function):
+class DatasetSaveFunction(workflow.Function):
     """QND way to save data to file for later import to this program."""
     def __init__(self):
-        Function.__init__(self, 'save_data', 'Save Pickled Dataset')
+        workflow.Function.__init__(self, 'save_data', 'Save Pickled Dataset')
 
     def run(self, data):
         if not data:
@@ -168,10 +177,10 @@ class DatasetSaveFunction(Function):
             chooser.destroy()
                 
 
-class CelFileImportFunction(Function):
+class CelFileImportFunction(workflow.Function):
     """Loads AffyMetrix .CEL-files into matrix."""
     def __init__(self):
-        Function.__init__(self, 'cel_import', 'Import Affy')
+        workflow.Function.__init__(self, 'cel_import', 'Import Affy')
 
     def run(self, data):
         import rpy
@@ -214,11 +223,11 @@ class CelFileImportFunction(Function):
             chooser.destroy()
 
 
-class PCAFunction(Function):
+class PCAFunction(workflow.Function):
     """Generic PCA function."""
-    def __init__(self, workflow):
+    def __init__(self, wf):
-        Function.__init__(self, 'pca', 'PCA')
+        workflow.Function.__init__(self, 'pca', 'PCA')
-        self._workflow = workflow
+        self._workflow = wf
 
     def run(self, data):
         import rpy