# -*- coding: utf-8 -*-
"""
This is a simple plugin that takes two node inputs, both of type ParameterData,
with the following labels: template and parameters.
You can also add other SinglefileData nodes as input, that will be copied according to
what is written in 'template' (see below).
* parameters: a set of parameters that will be used for substitution.
* template: can contain the following parameters:
* input_file_template: a string with substitutions to be managed with the format()\
function of python, i.e. if you want to substitute a variable called 'varname', you write\
{varname} in the text. See http://www.python.org/dev/peps/pep-3101/ for more\
details. The replaced file will be the input file.
* input_file_name: a string with the file name for the input. If it is not provided, no\
file will be created.
* output_file_name: a string with the file name for the output. If it is not provided, no\
redirection will be done and the output will go in the scheduler output file.
* cmdline_params: a list of strings, to be passed as command line parameters.\
Each one is substituted with the same rule of input_file_template. Optional
* input_through_stdin: if True, the input file name is passed via stdin. Default is\
False if missing.
* files_to_copy: if defined, a list of tuple pairs, with format ('link_name', 'dest_rel_path');\
for each tuple, an input link to this calculation is looked for, with link labeled 'link_label',\
and with file type 'Singlefile', and the content is copied to a remote file named 'dest_rel_path'\
Errors are raised in the input links are non-existent, or of the wrong type, or if there are \
unused input files.
TODO: probably use Python's Template strings instead??
TODO: catch exceptions
"""
from aiida.orm.calculation.job import JobCalculation
from aiida.common.exceptions import InputValidationError
from aiida.common.datastructures import CalcInfo
# TODO: write a 'input_type_checker' routine to automatically check the existence
# and type of inputs + default values etc.
__copyright__ = u"Copyright (c), 2015, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland and ROBERT BOSCH LLC, USA. All rights reserved."
__license__ = "MIT license, see LICENSE.txt file"
__version__ = "0.4.1"
__contributors__ = "Andrea Cepellotti, Giovanni Pizzi"
[docs]class TemplatereplacerCalculation(JobCalculation):
"""
Simple stub of a plugin that can be used to replace some text in a given
template. Can be used for many different codes, or as a starting point
to develop a new plugin.
"""
def _prepare_for_submission(self,tempfolder,inputdict):
"""
This is the routine to be called when you want to create
the input files and related stuff with a plugin.
This is the routine to be called when you want to create
the input files and related stuff with a plugin.
:param tempfolder: a aiida.common.folders.Folder subclass where
the plugin should put all its files.
:param inputdict: a dictionary with the input nodes, as they would
be returned by get_inputdata_dict (without the Code!)
"""
import StringIO
from aiida.orm.data.parameter import ParameterData
from aiida.orm.data.singlefile import SinglefileData
from aiida.orm.data.remote import RemoteData
from aiida.common.utils import validate_list_of_string_tuples
from aiida.common.exceptions import ValidationError
parameters_node = inputdict.pop('parameters', None)
if parameters_node is None:
parameters = {}
else:
if not isinstance(parameters_node,ParameterData):
raise InputValidationError("'parameters' data is not of type ParameterData")
parameters = dict(parameters_node.iterattrs())
template_node = inputdict.pop('template', None)
if template_node is None:
raise InputValidationError("No 'template' input data")
if not isinstance(template_node,ParameterData):
raise InputValidationError("'template' data is not of type ParameterData")
template = dict(template_node.iterattrs())
input_file_template = template.pop('input_file_template', "")
input_file_name = template.pop('input_file_name', None)
output_file_name = template.pop('output_file_name', None)
cmdline_params_tmpl = template.pop('cmdline_params', [])
input_through_stdin = template.pop('input_through_stdin', False)
files_to_copy = template.pop('files_to_copy',[])
if template:
raise InputValidationError("The following keys could not be "
"used in the template node: {}".format(
template.keys()))
try:
validate_list_of_string_tuples(files_to_copy, tuple_length = 2)
except ValidationError as e:
raise InputValidationError("invalid file_to_copy format: {}".format(e.message))
local_copy_list = []
remote_copy_list = []
for link_name, dest_rel_path in files_to_copy:
try:
fileobj = inputdict.pop(link_name)
except KeyError:
raise InputValidationError("You are asking to copy a file link {}, "
"but there is no input link with such a name".format(link_name))
if isinstance(fileobj, SinglefileData):
local_copy_list.append((fileobj.get_file_abs_path(),dest_rel_path))
elif isinstance(fileobj, RemoteData): # can be a folder
remote_copy_list.append(
(fileobj.get_computer().uuid, fileobj.get_remote_path(),dest_rel_path)
)
else:
raise InputValidationError("If you ask to copy a file link {}, "
"it must be either a SinglefileData or a RemoteData; it is instead of type {}".format(
link_name, fileobj.__class__.__name__))
if len(inputdict) > 0:
raise InputValidationError("The input nodes with the following labels could not be "
"used by the templatereplacer plugin: {}".format(
inputdict.keys()))
if input_file_name is not None and not input_file_template:
raise InputValidationError("If you give an input_file_name, you "
"must also specify a input_file_template")
if input_through_stdin and input_file_name is None:
raise InputValidationError("If you ask for input_through_stdin you have to "
"specify a input_file_name")
input_file = StringIO.StringIO(input_file_template.format(**parameters))
if input_file_name:
tempfolder.create_file_from_filelike(input_file, input_file_name)
else:
if input_file_template:
self.logger.warning("No input file name passed, but a input file template is present")
cmdline_params = [i.format(**parameters) for i in cmdline_params_tmpl]
calcinfo = CalcInfo()
calcinfo.retrieve_list = []
calcinfo.uuid = self.uuid
calcinfo.cmdline_params = cmdline_params
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
if input_through_stdin is not None:
calcinfo.stdin_name = input_file_name
if output_file_name:
calcinfo.stdout_name = output_file_name
calcinfo.retrieve_list.append(output_file_name)
# TODO: implement
# 'job_environment',
# 'prepend_text',
# 'append_text',
# 'stderr_name',
# 'join_files',
return calcinfo