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

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.add_function(Function('load', 'Load Microarrays'))
+        load = workflow.Stage('load', 'Load Data')
         load.add_function(CelFileImportFunction())
         load.add_function(TestDataFunction())
         load.add_function(DatasetLoadFunction())
         self.add_stage(load)
 
-        preproc = Stage('preprocess', 'Preprocessing')
-        preproc.add_function(Function('rma', 'RMA'))
+        preproc = workflow.Stage('preprocess', 'Preprocessing')
+        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.add_function(Function('pls', 'PLS'))
+        regression = workflow.Stage('regression', 'Regression')
+        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):
-        Function.__init__(self, 'pca', 'PCA')
-        self._workflow = workflow
+    def __init__(self, wf):
+        workflow.Function.__init__(self, 'pca', 'PCA')
+        self._workflow = wf
 
     def run(self, data):
         import rpy