rpy2.robjects.methods — rpy2 3.5.13 documentation (original) (raw)
import abc from types import SimpleNamespace from rpy2.robjects.robject import RObjectMixin import rpy2.rinterface as rinterface from rpy2.rinterface import StrSexpVector from rpy2.robjects import help as rhelp from rpy2.robjects import conversion
_get_exported_value = rinterface.baseenv['::'] getmethod = _get_exported_value('methods', 'getMethod')
require = rinterface.baseenv.find('require') require(StrSexpVector(('methods', )), quietly=rinterface.BoolSexpVector((True, )))
[docs]class RS4(RObjectMixin, rinterface.SexpS4): """ Python representation of an R instance of class 'S4'. """
[docs] def slotnames(self): """ Return the 'slots' defined for this object """ return methods_env'slotNames'
def do_slot(self, name):
return (conversion.get_conversion()
.rpy2py(super(RS4, self).do_slot(name)))[docs] def extends(self): """Return the R classes this extends.
This calls the R function methods::extends()."""
return methods_env['extends'](self.rclass)[docs] @staticmethod def isclass(name): """ Return whether the given name is a defined class. """ name = conversion.get_conversion().py2rpy(name) return methods_env'isClass'[0]
[docs] def validobject(self, test=False, complete=False): """ Return whether the instance is 'valid' for its class. """ cv = conversion.get_conversion() test = cv.py2rpy(test) complete = cv.py2rpy(complete) return methods_env['validObject'](self, test=test, complete=complete)[0]
class ClassRepresentation(RS4): """ Definition of an R S4 class """ slots = property(lambda x: [y[0] for y in x.do_slot('slots')], None, None, "Slots (attributes) for the class")
basenames = property(lambda x: [y[0] for y in x.do_slot('contains')],
None, None,
"Parent classes")
contains = basenames
isabstract = property(lambda x: x.do_slot('virtual')[0],
None, None,
"Is the class an abstract class ?")
virtual = isabstract
packagename = property(lambda x: x.do_slot('package')[0],
None, None,
"R package in which the class is defined")
package = packagename
classname = property(lambda x: x.do_slot('className')[0],
None, None,
"Name of the R class")def getclassdef(cls_name: str, packagename=rinterface.MissingArg): cls_def = methods_env'getClassDef', package=StrSexpVector((packagename, )) ) cls_def = ClassRepresentation(cls_def) cls_def.rname = cls_name return cls_def
class RS4_Type(abc.ABCMeta):
def __new__(mcs, name, bases, cls_dict):
try:
cls_rname = cls_dict['__rname__']
except KeyError:
cls_rname = name
try:
accessors = cls_dict['__accessors__']
except KeyError:
accessors = []
for rname, where, \
python_name, as_property, \
docstring in accessors:
if where is None:
where = rinterface.globalenv
else:
where = StrSexpVector(('package:%s' % where, ))
if python_name is None:
python_name = rname
signature = StrSexpVector((cls_rname, ))
r_meth = getmethod(StrSexpVector((rname, )),
signature=signature,
where=where)
r_meth = conversion.get_conversion().rpy2py(r_meth)
if as_property:
cls_dict[python_name] = property(r_meth, None, None,
doc=docstring)
else:
cls_dict[python_name] = lambda self: r_meth(self)
return type.__new__(mcs, name, bases, cls_dict)playground to experiment with more metaclass-level automation
[docs]class RS4Auto_Type(abc.ABCMeta): """ This type (metaclass) takes an R S4 class and create a Python class out of it, copying the R documention page into the Python docstring. A class with this metaclass has the following optional attributes: rname, rpackagename, __attr__translation, meth_translation. """ def new(mcs, name, bases, cls_dict): try: cls_rname = cls_dict['rname'] except KeyError: cls_rname = name
try:
cls_rpackagename = cls_dict['__rpackagename__']
except KeyError:
cls_rpackagename = None
try:
cls_attr_translation = cls_dict['__attr_translation__']
except KeyError:
cls_attr_translation = {}
try:
cls_meth_translation = cls_dict['__meth_translation__']
except KeyError:
cls_meth_translation = {}
cls_def = getclassdef(cls_rname, cls_rpackagename)
# documentation / help
if cls_rpackagename is None:
cls_dict['__doc__'] = "Undocumented class from the R workspace."
else:
pack_help = rhelp.Package(cls_rpackagename)
page_help = None
try:
# R's classes are sometimes documented with a prefix 'class.'
page_help = pack_help.fetch('%s-class' % cls_def.__rname__)
except rhelp.HelpNotFoundError:
pass
if page_help is None:
try:
page_help = pack_help.fetch(cls_def.__rname__)
except rhelp.HelpNotFoundError:
pass
if page_help is None:
cls_dict['__doc__'] = ('Unable to fetch R documentation '
'for the class')
else:
cls_dict['__doc__'] = ''.join(page_help.to_docstring())
for slt_name in cls_def.slots:
# TODO: sanity check on the slot name
try:
slt_name = cls_attr_translation[slt_name]
except KeyError:
# no translation: abort
pass
# TODO: isolate the slot documentation and have it here
cls_dict[slt_name] = property(lambda self: self.do_slot(slt_name),
None, None,
None)
# Now tackle the methods
all_generics = methods_env['getGenerics']()
findmethods = methods_env['findMethods']
# does not seem elegant, but there is probably nothing else to do
# than loop across all generics
r_cls_rname = StrSexpVector((cls_rname, ))
for funcname in all_generics:
all_methods = findmethods(StrSexpVector((funcname, )),
classes=r_cls_rname)
# skip if no methods (issue #301). R's findMethods() result
# does not have an attribute "names" if of length zero.
if len(all_methods) == 0:
continue
# all_methods contains all method/signature pairs
# having the class we are considering somewhere in the signature
# (the R/S4 systems allows multiple dispatch)
for name, meth in zip(all_methods.do_slot("names"), all_methods):
# R/S4 is storing each method/signature as a string,
# with the argument type separated by the character '#'
# We will re-use that name for the Python name
# (no multiple dispatch in python, the method name
# will not be enough), replacing the '#'s with '__'s.
signature = name.split("#")
meth_name = '__'.join(signature)
# function names ending with '<-' indicate that the function
# is a setter of some sort. We reflect that by adding a 'set_'
# prefix to the Python name (and of course remove the
# suffix '<-').
if funcname.endswith('<-'):
meth_name = 'set_%s__%s' % (funcname[:-2], meth_name)
else:
meth_name = '%s__%s' % (funcname, meth_name)
# finally replace remaining '.'s in the Python name with '_'s
meth_name = meth_name.replace('.', '_')
# TODO: sanity check on the function name
try:
meth_name = cls_meth_translation[meth_name]
except KeyError:
# no translation: abort
pass
# TODO: isolate the slot documentation and have it here
if meth_name in cls_dict:
raise Exception("Duplicated attribute/method name.")
cls_dict[meth_name] = meth
return abc.ABCMeta.__new__(mcs, name, bases, cls_dict)def set_accessors(cls, cls_name, where, acs): # set accessors (to be abandonned for the metaclass above ?)
if where is None:
where = rinterface.globalenv
else:
where = "package:" + str(where)
where = StrSexpVector((where, ))
for r_name, python_name, as_property, docstring in acs:
if python_name is None:
python_name = r_name
r_meth = getmethod(StrSexpVector((r_name, )),
signature=StrSexpVector((cls_name, )),
where=where)
r_meth = conversion.get_conversion().rpy2py(r_meth)
if as_property:
setattr(cls, python_name, property(r_meth, None, None))
else:
setattr(cls, python_name, lambda self: r_meth(self))def get_classnames(packname): res = methods_env['getClasses']( where=StrSexpVector(("package:%s" % packname, )) ) return tuple(res)
Namespace to store the definition of RS4 classes
rs4classes = SimpleNamespace()
def _getclass(rclsname): if hasattr(rs4classes, rclsname): rcls = getattr(rs4classes, rclsname) else: # dynamically create a class rcls = type(rclsname, (RS4, ), dict()) setattr(rs4classes, rclsname, rcls) return rcls
def rs4instance_factory(robj):
"""
Return an RS4 objects (R objects in the 'S4' class system)
as a Python object of type inheriting from robjects.methods.RS4.
The types are located in the namespace `robjects.methods.rs4classes`,
and a dummy type is dynamically created whenever necessary.
"""
clslist = None
if len(robj.rclass) > 1:
raise ValueError(
'Currently unable to handle more than one class per object'
)
for rclsname in robj.rclass:
rcls = _getclass(rclsname)
return rcls(robj)
if clslist is None:
return robjmethods_env = rinterface.baseenv.find('as.environment')( StrSexpVector(('package:methods', )) )