Пример #1
0
    def phyloviz(self, trans, id=None, dataset_id=None, tree_index=0, **kwargs):
        config = None
        data = None

        # if id, then this is a saved visualization; get its config and the dataset_id from there
        if id:
            visualization = self.get_visualization(trans, id)
            config = self.get_visualization_config(trans, visualization)
            dataset_id = config.get('dataset_id', None)

        # get the hda if we can, then its data using the phyloviz parsers
        if dataset_id:
            decoded_id = self.decode_id(dataset_id)
            hda = self.hda_manager.get_accessible(decoded_id, trans.user)
            hda = self.hda_manager.error_if_uploading(hda)
        else:
            return trans.show_message("Phyloviz couldn't find a dataset_id")

        pd = PhylovizDataProvider(original_dataset=hda)
        data = pd.get_data(tree_index=tree_index)

        # ensure at least a default configuration (gen. an new/unsaved visualization)
        if not config:
            config = {
                'dataset_id': dataset_id,
                'title'     : hda.display_name(),
                'ext'       : hda.datatype.file_ext,
                'treeIndex' : tree_index,
                'saved_visualization' : False
            }
        return trans.fill_template_mako("visualization/phyloviz.mako", data=data, config=config)
Пример #2
0
    def phyloviz( self, trans, id=None, dataset_id=None, tree_index=0, **kwargs ):
        config = None
        data = None

        # if id, then this is a saved visualization; get its config and the dataset_id from there
        if id:
            visualization = self.get_visualization( trans, id )
            config = self.get_visualization_config( trans, visualization )
            dataset_id = config.get( 'dataset_id', None )

        # get the hda if we can, then its data using the phyloviz parsers
        if dataset_id:
            hda = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True )
        else:
            return trans.show_message( "Phyloviz couldn't find a dataset_id" )

        pd = PhylovizDataProvider( original_dataset=hda )
        data = pd.get_data( tree_index=tree_index )

        # ensure at least a default configuration (gen. an new/unsaved visualization)
        if not config:
            config = {
                'dataset_id': dataset_id,
                'title'     : hda.display_name(),
                'ext'       : hda.datatype.file_ext,
                'treeIndex' : tree_index,
                'saved_visualization' : False
            }
        return trans.fill_template_mako( "visualization/phyloviz.mako", data=data, config=config )
Пример #3
0
    def phyloviz( self, trans, dataset_id, tree_index=0, **kwargs ):
        # Get HDA.
        hda = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True )

        # Get data.
        pd = PhylovizDataProvider( original_dataset=hda )
        config = pd.get_data( tree_index=tree_index )
        
        config["title"] = hda.display_name()
        config["ext"] = hda.datatype.file_ext
        config["dataset_id"] = dataset_id
        config["treeIndex"] = tree_index
        config["saved_visualization"] = False

        # Return viz.
        return trans.fill_template_mako( "visualization/phyloviz.mako", data = config[ "data" ], config=config )