import gtk
import logger
from annotations import Annotations
from workflow import *

class EinarsWorkflow (Workflow):

    def __init__(self, app):
        Workflow.__init__(self, app)
        self.name = 'Einar\'s Workflow'

        load = Stage('load', 'Load Data')
        load.add_function(Function('load', 'Load Microarrays'))
        self.add_stage(load)

        preproc = Stage('preprocess', 'Preprocessing')
        preproc.add_function(Function('rma', 'RMA'))
        self.add_stage(preproc)

        go = Stage('go', 'Gene Ontology Data')
        go.add_function(LoadAnnotationsFunction())
        go.add_function(Function('godist', 'GO Distances'))
        self.add_stage(go)

        regression = Stage('regression', 'Regression')
        regression.add_function(Function('pls', 'PLS'))
        self.add_stage(regression)
        
        logger.log('debug', '\tEinar\'s workflow is now active')

class LoadAnnotationsFunction(Function):

    def __init__(self):
        Function.__init__(self, 'load-go-ann', 'Load Annotations')
        self.annotations = None

    def load_file(self, filename):
        f = open(filename)
        self.annotations = Annotations('genes', 'go-terms')

        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, data):
        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]