Prototype delayed IO generalized containers

qiime_containers.py

#!/usr/bin/env python

__author__ = "Daniel McDonald"
__copyright__ = "Copyright 2013, The QIIME Project"
__credits__ = ["Daniel McDonald", "Greg Caporaso", "Doug Wendel",
               "Jai Ram Rideout"]
__license__ = "GPL"
__version__ = "0.1.0-dev"
__maintainer__ = "Daniel McDonald"
__email__ = "[email protected]"

from biom.parse import parse_biom_table

class ContainerError(Exception):
    pass

class CannotReadError(ContainerError):
    pass

class CannotWriteError(ContainerError):
    pass

class Container(object):
    _reserved = set(['_reserved','TypeName', 'Info'])
    TypeName = "Container"
    Info = None

    def __init__(self, *args, **kwargs):
        if 'Info' in kwargs:
            super(Container, self).__setattr__('Info',  kwargs['Info'])

    def _load_if_needed(self):
        pass

    def __getattr__(self, attr):
        if attr in super(Container, self).__getattribute__('_reserved'):
            return super(Container, self).__getattribute__(attr)
        
        self._load_if_needed()
        
        return getattr(self._object, attr)

    def __setattr__(self, attr, val):
        if attr in super(Container, self).__getattribute__('_reserved'):
            return super(Container, self).__setattr__(attr, val)
       
        self._load_if_needed()

        setattr(self._object, attr, val)

    def __hasattr__(self, attr):
        if attr in super(Container, self).__getattribute__('_reserved'):
            return True

        self._load_if_needed()
        
        return hasattr(self._object, attr)

class IOContainer(Container):
    _reserved = set(['_reserved', 'TypeName', '_reader', '_writer',
                     '_object', 'InPath', 'OutPath','read', 'write',
                     '_load_if_needed', 'Info'])
    TypeName = "IOContainer"
    _object = None
    InPath = None
    OutPath = None
    Info = None

    def __init__(self, *args, **kwargs):
        if 'Object' in kwargs:
            super(IOContainer, self).__setattr__('_object',  kwargs['Object'])
        if 'InPath' in kwargs:
            super(IOContainer, self).__setattr__('InPath',  kwargs['InPath'])
        if 'OutPath' in kwargs:
            super(IOContainer, self).__setattr__('OutPath',  kwargs['OutPath'])
        super(IOContainer, self).__init__(*args, **kwargs)

    def _load_if_needed(self):
        if self._object is None:
            if self.InPath is not None:
                self._object = self._reader(self.InPath)
            else:
                raise CannotReadError("No object and InPath is None!")
    
    def write(self):
        if self._object is not None:
            if self.OutPath is None:
                raise CannotWriteError("OutPath is None!")
            self._writer(self.OutPath)

    def read(self):
        if self._object is None:
            if self.InPath is None:
                raise CannotReadError("InPath is None!")
            self._object = self._reader(self.InPath)

class QIIMEInt(Container, int):
    TypeName = "Int"

class QIIMEFloat(Container, float):
    TypeName = "Float"

class QIIMEStr(Container, str):
    TypeName = "String"

def write_biom_table(path, s):
    f = open(path, 'w')
    f.write(s)
    f.close()

class BIOMTable(IOContainer):
    TypeName = "BIOMTable"
    _reader = lambda self, x: parse_biom_table(open(x))
    _writer = lambda self, x: write_biom_table(x, 
                                self.getBiomFormatJsonString('asd'))