fluents/fluents.py

@@ -22,6 +22,7 @@ DATADIR = os.path.dirname(sys.modules['fluents'].__file__)
 ICONDIR = os.path.join(DATADIR,"..","icons")
 GLADEFILENAME = os.path.join(DATADIR, 'fluents.glade')
 
+
 class IconFactory:
     """Factory for icons that ensures that each icon is only loaded once."""
 
@@ -43,6 +44,7 @@ class IconFactory:
 
 icon_factory = IconFactory(ICONDIR)
 
+
 class TableSizeSelection(gtk.Window):
     
     def __init__(self):

fluents/workflow.py

@@ -60,9 +60,7 @@ class Workflow:
     description = "Workflow Description"
 
     def __init__(self):
-        print "Setting stages"
         self.stages = []
-        self.stages_by_id = {}
 
     def get_data_file_name(self, filename):
         """Checks if a file with the given name exists in the data directory.
@@ -79,7 +77,7 @@ class Workflow:
 
     def add_stage(self, stage):
         self.stages.append(stage)
-        self.stages_by_id[stage.id] = stage
+        #self.stages_by_id[stage.id] = stage
 
     def print_tree(self):
         print self.name
@@ -109,11 +107,9 @@ class Stage:
         self.id = id
         self.name = name
         self.tasks = []
-        self.tasks_by_id = {}
 
     def add_task(self, task):
         self.tasks.append(task)
-        #self.tasks_by_id[task.id] = task
 
 
 class Task:
@@ -151,7 +147,6 @@ class Validation:
 
 
 class WorkflowView (gtk.VBox):
-   
     def __init__(self, wf):
         gtk.VBox.__init__(self)
         self.workflow = wf
@@ -201,8 +196,7 @@ class WorkflowView (gtk.VBox):
             return
 
         task_result = task.run()
-        
-            
+                    
         if task_result != None:
             main.project.add_data(parent_data, task_result, task.name)
         else:

workflows/test_workflow.py

@@ -1,11 +1,11 @@
 import gtk
 from fluents import dataset, logger, plots, workflow
-#import geneontology
-#import gostat
+
 from scipy import array, randn, log, ones, newaxis
 import cPickle
 import networkx
 
+
 class TestWorkflow (workflow.Workflow):
 
     name = 'Test Workflow'
@@ -15,15 +15,14 @@ class TestWorkflow (workflow.Workflow):
     def __init__(self):
         workflow.Workflow.__init__(self)
 
-        load = workflow.Stage('load', 'Test Data')
-        load.add_task(TestDataTask)
-        load.add_task(TestPlot)
-        self.add_stage(load)
+        test_stage = workflow.Stage('test', 'Test Data')
+        test_stage.tasks.append(TestDataTask)
+        test_stage.tasks.append(TestPlot)
+        self.stages.append(test_stage)
 
         
 class TestDataTask(workflow.Task):  
     name = "Test data"
-
     def __init__(self, input):
         workflow.Task.__init__(self, input)
 
@@ -56,10 +55,10 @@ class TestPlot(workflow.Task):
         workflow.Task.__init__(self, input)
 
     def run(self):
-        logger.log('notice', 'Injecting foo test data')
-        x = randn(500,15)
-        X = dataset.Dataset(x)
-        ii = X.get_dim_name()
-        p = plots.ScatterPlot(X, X, ii[0], ii[0], '0_1', '0_2',name='scatter')
+        #logger.log('notice', 'Injecting % dataset') %self.input[0].get_name()
+        X = self.input[0]
+        ii = X.get_dim_name()[0]
+        ids = X.get_identifiers(ii, indices=[0,1])
+        p = plots.ScatterPlot(X, X, ii, ii, ids[0], ids[1],name='scatter')
         
         return [p]