Some stuff on tasks.

fluents/workflow.py

@@ -88,12 +88,6 @@ class Workflow:
             for fun in stage.functions:
                 print '        %s' % fun.name
 
-#    def add_project(self,project):
-#        if project == None:
-#            logger.log('notice','Proejct is empty')
-#        logger.log('notice','Project added in : %s' %self.name)
-#        self.project = project
-
 
 class EmptyWorkflow(Workflow):
     name = 'Empty Workflow'
@@ -122,24 +116,32 @@ class Stage:
         self.functions_by_id[fun.id] = fun
 
 
-class Function:
+class Task:
     """A Function object encapsulates a function on a data set.
 
     Each Function instance encapsulates some function that can be applied
     to one or more types of data.
     """
 
-    def __init__(self, id, name):
+    title = ""
-        self.id = id
+
-        self.name = name
+    def __init__(self, input):
+        self.input = input
+        self.options = Options()
+
+        self.datasets = {}
+        self.arrays = {}
+        self.plots = {}
 
     # just return a Validation object
     def validate_input(input):
         return Validation(True,"Validation Not Implemented")
 
     def run(self):
-        pass
+        print self.input
 
+    def show_options_gui(self, editable=False):
+        pass
 
 class Validation:
     def __init__(self,result, reason):
@@ -461,3 +463,9 @@ class WorkflowMenu (gtk.Menu):
         menuitem.show()
         return menuitem
 
+
+class Options():
+    def __init__(self):
+        pass
+
+

workflows/test_workflow.py

@@ -10,113 +10,28 @@ class TestWorkflow (workflow.Workflow):
 
     name = 'Test Workflow'
     ident = 'test'
-    description = 'Test Gene Ontology Workflow. This workflow currently serves as a general testing workflow.'
+    description = 'This workflow currently serves as a general testing workflow.'
 
     def __init__(self, app):
         workflow.Workflow.__init__(self, app)
 
-        load = workflow.Stage('load', 'Load Data')
+        load = workflow.Stage('load', 'Test Data')
-        load.add_function(CelFileImportFunction())
-        load.add_function(DataLoadTestFunction(self))
         load.add_function(TestDataFunction())
-        load.add_function(DatasetLoadFunction())
-        load.add_function(SelectFunction())
         self.add_stage(load)
 
-        preproc = workflow.Stage('preprocess', 'Preprocessing')
-        preproc.add_function(DatasetLog())
-        preproc.add_function(workflow.Function('rma', 'RMA'))
-        self.add_stage(preproc)
-
-        go = workflow.Stage('go', 'Gene Ontology Data')
-        go.add_function(GODistanceFunction())
-        go.add_function(ImagePlotFunction())
-        self.add_stage(go)
-
-        regression = workflow.Stage('regression', 'Regression')
-        regression.add_function(workflow.Function('pls', 'PLS'))
-        self.add_stage(regression)
-
-        explore = workflow.Stage('explore', 'Explorative analysis')
-        explore.add_function(PCAFunction(self))
-        self.add_stage(explore)
-
-        save = workflow.Stage('save', 'Save Data')
-        save.add_function(DatasetSaveFunction())
-        self.add_stage(save)
         
-        
+class TestDataTask(workflow.Task):  
-class LoadAnnotationsFunction(workflow.Function):
+    title = "Test data"
 
     def __init__(self):
-        workflow.Function.__init__(self, 'load-go-ann', 'Load Annotations')
+        workflow.Task.__init__(self)
-        self.annotations = None
-
-    def load_file(self, filename):
-        f = open(filename)
-        self.annotations = Annotations('genes', 'go-terms')
-        logger.log('notice', 'Loading annotation file: %s' % filename)
-
-        for line in f.readlines():
-            val = line.split(' \t')
-
-            if len(val) > 1:
-                val = [v.strip() for v in val]
-                retval.add_annotations('genes', val[0], 
-                                       'go-terms', set(val[1:]))
-            
-    def on_response(self, dialog, response):
-        if response == gtk.RESPONSE_OK:
-            logger.log('notice', 'Reading file: %s' % dialog.get_filename())
-            self.load_file(dialog.get_filename())
-
-    def run(self):
-        btns = ('Open', gtk.RESPONSE_OK, \
-                'Cancel', gtk.RESPONSE_CANCEL)
-        dialog = gtk.FileChooserDialog('Open GO Annotation File',
-                                       buttons=btns)
-        dialog.connect('response', self.on_response)
-        dialog.run()
-        dialog.destroy()
-        return [self.annotations]
-
-class GODistanceFunction(workflow.Function):
-
-    def __init__(self):
-        workflow.Function.__init__(self, 'go_diatance', 'GO Distances')
-        self.output = None
-
-    def run(self, data):
-        logger.log('debug', 'datatype: %s' % type(data))
-        if not type(data) == Annotations:
-            return None
-
-        logger.log('debug', 'dimensions: %s' % data.dimensions)
-        
-        genes = data.get_ids('genes')
-        gene_distances = array((len(genes), len(genes)))
-
-        return gene_distances
-
-
-class ImagePlotFunction(workflow.Function):
-    def __init__(self):
-        workflow.Function.__init__(self, 'image', 'Show Image')
-
-    def run(self, data):
-        return [plots.ImagePlot(data, name='foo')]
-
-
-class TestDataFunction(workflow.Function):  
-    def __init__(self):
-        workflow.Function.__init__(self, 'test_data', 'Generate Test Data')
 
     def run(self):
         logger.log('notice', 'Injecting foo test data')
         x = randn(500,15)
         X = dataset.Dataset(x)
         p = plots.ScatterPlot(X, X, 'rows', 'rows', '0_1', '0_2',name='scatter')
-        p2 = plots.ScatterMarkerPlot(X, X, 'rows', 'rows', '0_1', '0_2',name='marker')
+#        p2 = plots.ScatterMarkerPlot(X, X, 'rows', 'rows', '0_1', '0_2',name='marker')
         graph = networkx.XGraph()
         for x in 'ABCDEF':
             for y in 'ADE':
@@ -125,181 +40,11 @@ class TestDataFunction(workflow.Function):
         ds_plot = plots.NetworkPlot(ds)
 
         cds = dataset.CategoryDataset(ones([3, 3]))
-        ds_scatter = plots.ScatterMarkerPlot(ds, ds, 'rows_0', 'rows_0', '0_1', '0_2')
+        ds_scatter = plots.ScatterMarkerPlot(ds, ds, 
+                                             'rows_0', 'rows_0', 
+                                             '0_1', '0_2')
         lp = plots.LineViewPlot(X,major_axis=0)
         vp = plots.VennPlot()
+        self.datasets = [p]
         return [X, ds, p, ds_plot, ds_scatter, p2, cds, lp, vp]
 
-class SelectFunction(workflow.Function):
-    def __init__(self):
-        workflow.Function.__init__(self, 'select', 'Select')
-
-    def run(self, data):
-        s = dataset.Selection('Arbitrary selection')
-        s.select('rows', ['0_1', '0_2'])
-        return [s]
-
-class DatasetLog(workflow.Function):
-    def __init__(self):
-        workflow.Function.__init__(self, 'log', 'Log')
-
-    def run(self, data):
-        logger.log('notice', 'Taking the log of dataset %s' % data.get_name())
-        d = data.asarray()
-        d = log(d)
-        new_data_name = 'log(%s)' % data.get_name()
-        ds = dataset.Dataset(d, name=new_data_name)
-        return [ds]
-
-class DatasetLoadFunction(workflow.Function):
-    """Loader for previously pickled Datasets."""
-    def __init__(self):
-        workflow.Function.__init__(self, 'load_data', 'Load Pickled Dataset')
-
-    def run(self):
-        chooser = gtk.FileChooserDialog(title="Select cel files...", parent=None,
-                                        action=gtk.FILE_CHOOSER_ACTION_OPEN,
-                                        buttons=(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL,
-                                                 gtk.STOCK_OPEN, gtk.RESPONSE_OK))
-        pkl_filter = gtk.FileFilter()
-        pkl_filter.set_name("Python pickled data files (*.pkl)")
-        pkl_filter.add_pattern("*.[pP][kK][lL]")
-        all_filter = gtk.FileFilter()
-        all_filter.set_name("All Files (*.*)")
-        all_filter.add_pattern("*")
-        chooser.add_filter(pkl_filter)
-        chooser.add_filter(all_filter)
-
-        try:
-            if chooser.run() == gtk.RESPONSE_OK:
-                return [cPickle.load(open(chooser.get_filename()))]
-        finally:
-            chooser.destroy()
-
-
-class DatasetSaveFunction(workflow.Function):
-    """QND way to save data to file for later import to this program."""
-    def __init__(self):
-        workflow.Function.__init__(self, 'save_data', 'Save Pickled Dataset')
-
-    def run(self):
-        if not data:
-            logger.log("notice", "No data to save.")
-            return
-        else:
-            data = data[0]
-        chooser = gtk.FileChooserDialog(title="Save pickled data...", parent=None,
-                                        action=gtk.FILE_CHOOSER_ACTION_SAVE,
-                                        buttons=(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL,
-                                                 gtk.STOCK_SAVE, gtk.RESPONSE_OK))
-        pkl_filter = gtk.FileFilter()
-        pkl_filter.set_name("Python pickled data files (*.pkl)")
-        pkl_filter.add_pattern("*.[pP][kK][lL]")
-        all_filter = gtk.FileFilter()
-        all_filter.set_name("All Files (*.*)")
-        all_filter.add_pattern("*")
-        chooser.add_filter(pkl_filter)
-        chooser.add_filter(all_filter)
-        chooser.set_current_name(data.get_name() + ".pkl")
-
-        try:
-            if chooser.run() == gtk.RESPONSE_OK:
-                cPickle.dump(data, open(chooser.get_filename(), "w"), protocol=2)
-                logger.log("notice", "Saved data to %r." % chooser.get_filename())
-        finally:
-            chooser.destroy()
-                
-
-class CelFileImportFunction(workflow.Function):
-    """Loads AffyMetrix .CEL-files into matrix."""
-    def __init__(self):
-        workflow.Function.__init__(self, 'cel_import', 'Import Affy')
-
-    def run(self, data):
-        import rpy
-        chooser = gtk.FileChooserDialog(title="Select cel files...", parent=None,
-                                        action=gtk.FILE_CHOOSER_ACTION_OPEN,
-                                        buttons=(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL,
-                                                 gtk.STOCK_OPEN, gtk.RESPONSE_OK))
-        chooser.set_select_multiple(True)
-        cel_filter = gtk.FileFilter()
-        cel_filter.set_name("Cel Files (*.cel)")
-        cel_filter.add_pattern("*.[cC][eE][lL]")
-        all_filter = gtk.FileFilter()
-        all_filter.set_name("All Files (*.*)")
-        all_filter.add_pattern("*")
-        chooser.add_filter(cel_filter)
-        chooser.add_filter(all_filter)
-
-        try:
-            if chooser.run() == gtk.RESPONSE_OK:
-                rpy.r.library("affy")
-    
-                silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r)
-                silent_eval('E <- ReadAffy(filenames=c("%s"))' % '", "'.join(chooser.get_filenames()))
-                silent_eval('E <- rma(E)')
-
-                m = rpy.r('m <- E@exprs')
-    
-                vector_eval = rpy.with_mode(rpy.VECTOR_CONVERSION, rpy.r)
-                rownames = vector_eval('rownames(m)') 
-                colnames = vector_eval('colnames(m)') 
-
-                # We should be nice and clean up after ourselves
-                rpy.r.rm(["E", "m"])
-                
-                if m:
-                    data = dataset.Dataset(m, (('ids', rownames), ('filename', colnames)), name="AffyMatrix Data")
-                    plot = plots.LinePlot(data, "Gene profiles")
-                    return [data, plot]
-                else:
-                    logger.log("notice", "No data loaded from importer.")
-        finally:
-            chooser.destroy()
-
-
-class DataLoadTestFunction(workflow.Function):
-    def __init__(self, wf):
-        workflow.Function.__init__(self, 'datadirload', 'Load from datadir')
-        self._wf = wf
-    
-    def run(self):
-        print self._wf.get_data_file_name('smoker-x.ftsv')
-        fn = self._wf.get_data_file_name('smoker-x.ftsv')
-        if fn:
-            fd = open(fn)
-            ds = dataset.read_ftsv(fd)
-            return [ds]
-        else:
-            print "Cannot find file %s" % fn
-            return []
-
-class PCAFunction(workflow.Function):
-    """Generic PCA function."""
-    def __init__(self, wf):
-        workflow.Function.__init__(self, 'pca', 'PCA')
-        self._workflow = wf
-
-    def run(self, data):
-        import rpy
-        
-        dim_2, dim_1 = data.get_dim_names()
-        
-    
-        silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r)
-        rpy.with_mode(rpy.NO_CONVERSION, rpy.r.assign)("m", data.asarray())
-        silent_eval("t = prcomp(t(m))")
-
-        T_ids = map(str, range(1, rpy.r("dim(t$x)")[1]+1))
-        T = dataset.Dataset(rpy.r("t$x"), [(dim_1, data.get_identifiers(dim_1)),
-                                   ("component", T_ids)], name="T")
-        P = dataset.Dataset(rpy.r("t$rotation"), [(dim_2, data.get_identifiers(dim_2)),
-                                          ("component", T_ids)], name="P")
-
-        # cleanup
-        rpy.r.rm(["t", "m"])
-
-        loading_plot = plots.ScatterMarkerPlot(P, P, 'ids','component','1','2', "Loadings")
-        score_plot = plots.ScatterMarkerPlot(T, T,'filename','component','1','2', "Scores")
-        
-        return [T, P, loading_plot, score_plot]