def __init__(self, dir, permissions=0, create=False):
self.directory = full_path(dir)
if create:
if not os.path.exists(self.directory):
os.makedirs(self.directory)
if not os.path.isdir(self.directory):
raise OSError("{0} is not a directory.")
elif not os.access(self.directory, os.R_OK|permissions):
raise OSError("directory {0} cannot be accessed with sufficient permissions")
def __init__(self, dir, permissions=0, create=False):
self.directory = full_path(dir)
if create:
if not os.path.exists(self.directory):
os.makedirs(self.directory)
if not os.path.isdir(self.directory):
raise OSError("{0} is not a directory.")
elif not os.access(self.directory, os.R_OK | permissions):
raise OSError(
"directory {0} cannot be accessed with sufficient permissions")
def __enter__(self):
self.return_directory = full_path(os.curdir)
os.chdir(self.directory)
def __new__(cls, **kwargs):
"""
"""
def get_kwarg(arg, cls, subclass=False):
gotten = pop_kwarg(kwargs, arg)
if not subclass:
if gotten is not None and not isinstance(gotten, cls):
if not isinstance(cls, tuple):
raise TypeError("#{0} argument given to Computation() "\
"must be an instance of the #{1} class.".format(arg, classname(cls)))
else:
raise TypeError("#{0} argument given to Computation() "\
"must be one of (#{1}) .".format(arg, ', '.join(classname(cl) for cl in cls)))
else:
if gotten is not None and not issubclass(gotten, cls):
if not isinstance(cls, tuple):
raise TypeError("#{0} argument given to Computation() "\
"must be an subclass of the #{1} class.".format(arg, classname(cls)))
else:
raise TypeError("#{0} argument given to Computation() "\
"must be subclass of one of (#{1}) .".format(arg, ', '.join(classname(cl) for cl in cls)))
return gotten
#--------------------------------------------------------------------------------#
# Handle molecule, make a ResultGetter
molecule = get_kwarg('molecule', Molecule)
res_getter = get_kwarg('result_getter', ComputationResultGetter)
if res_getter is None:
res_getter = ComputationResultGetter(**kwargs)
molecule.result_getters.append(res_getter)
#--------------------------------------------------------------------------------#
# Now see what package we're using
package = get_kwarg('package', (basestring, PackageInterface))
comp_class = cls
interface = None
if isinstance(package, PackageInterface):
interface = package
elif isinstance(package, basestring):
interface = PackageInterface.load_package(
package,
input_generator=get_kwarg('input_generator', InputGenerator, True),
runner=get_kwarg('runner', Runner, True),
output_parser=get_kwarg('output_parser', OutputParser, True),
details_class=get_kwarg('details_class', ComputationDetails, True),
computation_class=get_kwarg('computation_class', cls, True)
)
if interface.computation_class is not None:
comp_class = cls
ret_val = object.__new__(comp_class)
#--------------------------------------------------------------------------------#
ret_val.molecule = molecule
res_getter.add_computation(ret_val)
ret_val.input_generator = interface.input_generator(ret_val)
ret_val.output_parser = interface.output_parser(ret_val)
#TODO accept option for directory to put input/output files in
#TODO accept option for input/output filenames
#TODO support for runners that don't follow the input/output pattern
ret_val.runner = interface.runner(input_file='input.dat', output_file='output.dat')
#--------------------------------------------------------------------------------#
ret_val.details = get_kwarg('details', interface.details_class)
ret_val.properties = pop_kwarg(kwargs, 'property')
if isinstance(ret_val.properties, Iterable):
ret_val.properties = list(ret_val.properties)
else:
ret_val.properties = [ret_val.properties]
if not all(issubclass(prop, MolecularProperty) or isinstance(prop, MolecularProperty) for prop in ret_val.properties):
raise TypeError("property argument given to Computation() must be a list of MolecularProperty subclasses or instances.".format(classname(cls)))
fixed_properties = []
for prop in ret_val.properties:
if isinstance(prop, MolecularProperty):
fixed_properties.append(prop)
prop.details = ret_val.details
elif issubclass(prop, MolecularProperty):
fixed_properties.append(prop(molecule=ret_val.molecule, details=ret_val.details))
ret_val.properties = fixed_properties
#--------------------------------------------------------------------------------#
# Get input_filename and output_filename, if specified. Make sure that neither
# is a path.
# first get input_filename
input_filename = pop_kwarg(kwargs, 'input_filename')
if input_filename:
if os.path.split(input_filename)[0] != '':
raise ValueError("File name '{0}' given for argument 'input_filename' of Computation constructor "
"must be a single file, not a path. Use the 'directory' argument to specify "
"a directory.".format(input_filename))
ret_val.runner.input_file = input_filename
else:
ret_val.runner.input_file = Runner.default_input_filename
#----------------------------------------#
# now get output_filename
output_filename = pop_kwarg(kwargs, 'output_filename')
if output_filename:
if os.path.split(output_filename)[0] != '':
raise ValueError("File name '{0}' given for argument 'output_filename' of Computation constructor "
"must be a single file, not a path. Use the 'directory' argument to specify "
"a directory.".format(output_filename))
ret_val.runner.output_file = output_filename
else:
ret_val.runner.output_file = Runner.default_output_filename
#--------------------------------------------------------------------------------#
# Find out the desired directory and make new ones if necessary and allowed.
ret_val.directory = pop_kwarg(kwargs, 'directory')
used_template = False
if ret_val.directory is not None:
ret_val.directory = full_path(ret_val.directory)
elif cls.directory_template is not None:
ret_val.directory = cls.directory_template
used_template = True
else:
ret_val.directory = full_path(os.curdir)
#----------------------------------------#
# Do mako-template style replacement, if the user has mako
try:
from mako.template import Template
from mako import exceptions
# Start with some obvious standard things to add...
variables = dict(
mol = ret_val.molecule, molecule = ret_val.molecule,
calc = ret_val, calculation = ret_val,
rg = res_getter, result_getter = res_getter,
details = ret_val.details
)
# Get all of the known details, as strings
det_strs = dict()
for k, v in ret_val.details._known_details.items():
det_strs[str(k)] = str(v)
det_strs[str(k).lower()] = str(v)
det_strs[str(k).upper()] = str(v)
if k in Computation.attribute_aliases:
for alias in Computation.attribute_aliases[k]:
alias = make_safe_identifier(alias)
det_strs[str(alias)] = str(v)
det_strs[str(alias).lower()] = str(v)
det_strs[str(alias).upper()] = str(v)
variables.update(det_strs)
# Get any additional keywords specified by the user (advanced feature)
additional = kwargs.pop('directory_creation_vars', dict())
variables.update(additional)
# Now run mako on the template...
try:
ret_val.directory = Template(
text=ret_val.directory,
strict_undefined=True
).render(
**variables
)
except:
raise ValueError(
"invalid MAKO template:\n{}\nMako came back with error:\n{}".format(
indent(ret_val.directory),
indent(exceptions.text_error_template().render())
)
)
# and make it into a "url safe string":
ret_val.directory = urllib.quote_plus(
ret_val.directory,
safe='/' + cls.additional_safe_directory_characters
)
except ImportError:
# Can't do mako parsing of path. Oh well...
# But if the user specified additional args, they probably thought they did have
# mako installed...
additional = kwargs.pop('directory_creation_vars', None)
if additional is not None:
raise
# and if they have a ${ in the directory name or a <% in the directory name,
# they probably also thought that they had mako.
# (Note: this could be an issue in the unlikely scenario that the user is using
# e.g. zsh and specifying environment variables from within Python as ${ }.
# If someone is having that problem, they probably have enough intelligence
# also to figure out how to get around it.)
if '${' in ret_val.directory or '<%' in ret_val.directory:
raise
# if they're using a class-level template, they also need to have mako installed
if used_template:
raise
#----------------------------------------#
ret_val.directory = full_path(ret_val.directory)
#----------------------------------------#
# Now create the directory if we're allowed to and need to
create_dirs = kwargs.pop('create_directories', cls.always_create_missing)
if create_dirs:
if not os.path.isdir(ret_val.directory):
if os.path.exists(ret_val.directory):
raise OSError(
"path '{}' exists and is not a directory".format(
ret_val.directory
)
)
os.makedirs(ret_val.directory)
else:
if not os.path.isdir(ret_val.directory):
raise OSError(
"'{0}' is not a valid directory, and will not be created. Set the "
"'create_directories' argument of computation to True to do directory "
"creation automatically.".format(
ret_val.directory
))
#----------------------------------------#
# now set the input_file and output_file values
ret_val.runner.input_file = os.path.join(ret_val.directory, ret_val.runner.input_file)
ret_val.runner.output_file = os.path.join(ret_val.directory, ret_val.runner.output_file)
ret_val.runner.working_directory = ret_val.directory
#--------------------------------------------------------------------------------#
# Pass the remaining kwargs on to the initialization, which may have been customized for the particular package.
ret_val.__init__(**kwargs)
return ret_val
def __enter__(self):
self.return_directory = full_path(os.curdir)
os.chdir(self.directory)
