import gtk, gobject import sys import os import inspect import logger def _workflow_classes(modname): """Returns a list of all subclasses of Workflow in a given module""" workflow_classes = [] __import__('workflows.%s' % modname) module = sys.modules['workflows.%s' % modname] d = module.__dict__ for wf in d.values(): try: if issubclass(wf, Workflow): workflow_classes.append(wf) except TypeError, e: pass return workflow_classes def workflow_list(): """Returns a ListStore containing all new workflows""" retval = [] # List all .py files that can contain workflow classes wf_path = sys.modules['workflows'].__path__ wf_files = [] for dir in wf_path: for fn in os.listdir(dir): if fn.endswith('.py') and ('#' not in fn): wf_files.append(fn[:-3]) # Try to load each file and look for Workflow derived classes for fn in wf_files: try: for wf in _workflow_classes(fn): retval.append(wf) except Exception, e: logger.log('warning', 'Cannot load workflow: %s' % fn) logger.log('warning', e) return retval class Workflow: """Defines a workflow that contains a set of analysis stages. A Workflow is a set of analysis stages for a certain type of analysis. Each stage contains some possible operations to do accomplish that task. """ name = "Workflow" ident = None description = "Workflow Description" def __init__(self, app): self.stages = [] self.stages_by_id = {} self.app = app def add_stage(self, stage): self.stages.append(stage) self.stages_by_id[stage.id] = stage def print_tree(self): print self.name for stage in self.stages: print ' %s' % stage.name 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' def __init__(self, app): Workflow.__init__(self, None) class Stage: """A stage is a part of the data analysis process. Each stage contains a set of functions that can be used to accomplish the task. A typical early stage is 'preprocessing', which can be done in several ways, each represented by a function. """ def __init__(self, id, name): self.id = id self.name = name self.functions = [] self.functions_by_id = {} def add_function(self, fun): self.functions.append(fun) self.functions_by_id[fun.id] = fun class Function: """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): self.id = id self.name = name # ,ust return a Validation object def validate_input(input): return Validation(True,"Validation Not Implemented") def run(self): pass class Validation: def __init__(self,result, reason): self.succeeded = result self.reason = reason class WorkflowView (gtk.VBox): def __init__(self, wf): gtk.VBox.__init__(self) self.workflow = wf self.setup_workflow(wf) def setup_workflow(self, wf): # Add stage in the process for stage in wf.stages: exp = gtk.Expander(stage.name) btn_box = gtk.VBox() btn_box.show() exp.add(btn_box) # Add functions in each stage for fun in stage.functions: btn = gtk.Button(fun.name) btn.connect('clicked', lambda button, f=fun : self.run_function(f)) btn_box.add(btn) btn.show() exp.show() self.pack_start(exp, expand=False, fill=False) def remove_workflow(self): for c in self.get_children(): c.hide() self.remove(c) def set_workflow(self, workflow): self.workflow = workflow self.remove_workflow() self.setup_workflow(workflow) def run_function(self, function): logger.log('debug', 'Starting function: %s' % function.name) project = self.workflow.app.project parent_data = project.current_data validation = function.validate_input() if not validation.succeeded: logger.log('warning','Invalid Inputdata: ' + str(reason)) return args, varargs, varkw, defaults = inspect.getargspec(function.run) # first argument is 'self' and second should be the selection # and we don't care about those... args.remove('self') if "selection" in args: pass_selection = True args.remove('selection') else: pass_selection = False if varargs and len(parent_data) < len(args): logger.log('warning', "Function requires minimum %d datasets selected." % len(args)) return elif not varargs and args and len(args) != len(parent_data): # functions requiring datasets have to have the right number logger.log('warning', "Function requires %d datasets, but only %d selected." % (len(args), len(parent_data))) return if not args: # we allow functions requiring no data to be run even if a # dataset is is selected data = [] else: data = parent_data if pass_selection: # if the function has a 'selection' argument, we pass in # the selection new_data = function.run(selection=project.get_selection(), *data) else: new_data = function.run(*data) if new_data != None: project.add_data(parent_data, new_data, function.name) logger.log('debug', 'Function ended: %s' % function.name) class Options(dict): """Options base class. """ def __init__(self, *args,**kw): dict.__init__(self, *args, **kw) self['out_plots'] = None self['out_data'] = None def _copy_from_list(self, key_list): """Returns suboptions (dictionary) from a list of keys. """ d = {} for key in key_list: d[key] = self.get(key, None) return d class OptionsDialog(gtk.Dialog): """The basic input/output dialog box. This defines the first page of the function options-gui. Any function that invokes a option-gui will inherit from this class. """ def __init__(self, data, options, input_names=['X','Y']): gtk.Dialog.__init__(self, 'Input-Output dialog', None, gtk.DIALOG_DESTROY_WITH_PARENT, (gtk.STOCK_OK, gtk.RESPONSE_OK, gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL)) self._options = options self._data = data self._editable = True self.set_size_request(300,400) # create notebook nb = gtk.Notebook() # 1. page: input/output # #inputs input_frame = gtk.Frame("Input") hbox = gtk.HBox(True, 8) align = gtk.Alignment(1, 1, 1, 1) align.set_padding(8, 8, 8, 8) align.add(hbox) input_frame.add(align) for i, name in enumerate(input_names): frame = gtk.Frame(name) frame.set_label_align(0.5, 0.5) label = gtk.Label(data[i]._name + "\n" + str(data[i]._array.shape)) frame.add(label) hbox.add(frame) #outputs output_frame = gtk.Frame("Output") output_hbox = gtk.HBox(True,4) output_align = gtk.Alignment(1, 1, 1, 1) output_align.set_padding(8, 8, 8, 8) #left padding:8 output_align.add(output_hbox) output_frame.add(output_align) # plots plot_list = gtk.ListStore(gobject.TYPE_STRING, gobject.TYPE_BOOLEAN) plot_treeview = gtk.TreeView(plot_list) # Add plots for plt, name, use in self._options['all_plots']: plot_list.append((name, use)) # Renderer for active toggle. active_renderer = gtk.CellRendererToggle() active_renderer.set_property('mode', gtk.CELL_RENDERER_MODE_ACTIVATABLE) active_renderer.connect('toggled', toggled, plot_list) active_column = gtk.TreeViewColumn('Use', active_renderer, active=1) # Renderer for plot title. title_renderer = gtk.CellRendererText() title_renderer.set_property('mode', gtk.CELL_RENDERER_MODE_EDITABLE) title_column = gtk.TreeViewColumn('Plot', title_renderer, text=0) # Add columns to tree view. plot_treeview.append_column(active_column) plot_treeview.append_column(title_column) ## datasets dataset_list = gtk.ListStore(gobject.TYPE_STRING, gobject.TYPE_BOOLEAN) dataset_treeview = gtk.TreeView(dataset_list) # Add datasets for dat, name, use in self._options['all_data']: dataset_list.append((name, use)) # Renderer for active toggle. active_renderer = gtk.CellRendererToggle() active_renderer.set_property('mode', gtk.CELL_RENDERER_MODE_ACTIVATABLE) active_renderer.connect('toggled', toggled, dataset_list) active_column = gtk.TreeViewColumn('Use', active_renderer, active=1) # Renderer for plot title. title_renderer = gtk.CellRendererText() title_renderer.set_property('mode', gtk.CELL_RENDERER_MODE_EDITABLE) title_column = gtk.TreeViewColumn('Dataset', title_renderer, text=0) # Add columns to tree view. dataset_treeview.append_column(active_column) dataset_treeview.append_column(title_column) # add treeviews to output frame output_hbox.add(plot_treeview) output_hbox.add(dataset_treeview) # vbox for input/spacer/output vbox1 = gtk.VBox() vbox1.add(input_frame) vbox1.add(gtk.HSeparator()) vbox1.add(output_frame) # add vbox to notebook nb.append_page(vbox1, gtk.Label("I/O")) self.vbox.add(nb) #keep ref to liststores self.dataset_list = dataset_list self.plot_list = plot_list def run(self): self.vbox.show_all() return gtk.Dialog.run(self) def set_options(self, options): self._options = options def update_options(self, options): self._options.update(options) def set_output(self): # get marked output data out_data = [item[0] for name, mark in self.dataset_list for item in self._options['all_data'] if mark==True and name==item[1]] # get marked plots out_plots = [item[0] for name, mark in self.plot_list for item in self._options['all_plots'] if mark==True and name==item[1]] # update options self._options['out_data'] = out_data self._options['out_plots'] = out_plots def set_editable(self, editable): self._editable = True def set_data(self, data): self._data = data def get_data(self): return self._data def get_options(self): return self._options def toggled(renderer, path, store): it = store.get_iter(path) old_value = store.get_value(it, 1) store.set_value(it, 1, not old_value)