Added text-input for contrast-matrix creator for affymetrics workflow.

system/dialogs.py

@@ -79,3 +79,30 @@ class CreateProjectDruid(gtk.Window):
         wf = self.workflows.get_value(it, 1)
         self.wf_info.set_text(wf.description) 
 
+
+def get_text(title, text):
+    """Allow user to type in a string for text."""
+    dlg = gtk.Dialog(title)
+    dlg.show()
+
+    text = gtk.Label(text)
+    text.show()
+
+    entry = gtk.Entry()
+    entry.show()
+    entry.set_activates_default(True)
+    dlg.vbox.pack_start(text)
+    dlg.vbox.pack_start(entry)
+
+    dlg.add_button(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL)
+    dlg.add_button(gtk.STOCK_OK, gtk.RESPONSE_OK)
+    dlg.set_default_response(gtk.RESPONSE_OK)
+    response = dlg.run()
+
+    retval = None
+
+    if response == gtk.RESPONSE_OK:
+        retval = entry.get_text()
+    dlg.destroy()
+    return retval
+    

workflows/affy_workflow.py

@@ -1,5 +1,5 @@
 import gtk
-from system import dataset, logger, plots, workflow
+from system import dataset, logger, plots, workflow, dialogs
 from scipy import randn, array, transpose, zeros
 import cPickle
 
@@ -17,6 +17,7 @@ class AffyWorkflow (workflow.Workflow):
         load.add_function(PhenotypeImportFunction())
         load.add_function(TestDataFunction())
         load.add_function(DatasetLoadFunction())
+        load.add_function(ContrastMatrixGenerateFunction())
         self.add_stage(load)
 
         explore = workflow.Stage('explore', 'Explorative analysis')
@@ -105,6 +106,19 @@ class DatasetSaveFunction(workflow.Function):
             chooser.destroy()
 
 
+class ContrastMatrixGenerateFunction(workflow.Function):
+    def __init__(self):
+        workflow.Function.__init__(self, 'contrast_create', 'Create contrast matrix')
+
+    def run(self, data):
+        response = dialogs.get_text('Enter contrasts...', """\
+Enter comma-separated list of contrasts.
+Available categories: %s
+
+Example: Y-N, M-F""" % ", ".join(data.get_categories()))
+        logger.log("notice", "contrasts selected: %s" % response)
+
+
 class CelFileImportFunction(workflow.Function):
     """Loads Affymetrics .CEL-files into matrix."""
     def __init__(self):