# -*- coding: utf-8 -*-
###############################################################################
# Copyright (c), Forschungszentrum Jülich GmbH, IAS-1/PGI-1, Germany. #
# All rights reserved. #
# This file is part of the Masci-tools package. #
# (Material science tools) #
# #
# The code is hosted on GitHub at https://github.com/judftteam/masci-tools. #
# For further information on the license, see the LICENSE.txt file. #
# For further information please visit http://judft.de/. #
# #
###############################################################################
"""
Functions for modifying the xml input file of Fleur with explicit xpath arguments
These can still use the schema dict for finding information about the xpath
"""
from lxml import etree
from masci_tools.util.xml.common_functions import eval_xpath
######################CREATING/DELETING TAGS###############################################
[docs]def xml_create_tag_schema_dict(xmltree,
schema_dict,
xpath,
base_xpath,
element,
create_parents=False,
occurrences=None):
"""
This method evaluates an xpath expression and creates a tag in a xmltree under the
returned nodes.
If there are no nodes evaluated the subtags can be created with `create_parents=True`
The tag is always inserted in the correct place if a order is enforced by the schema
:param xmltree: an xmltree that represents inp.xml
:param schema_dict: InputSchemaDict containing all information about the structure of the input
:param xpath: a path where to place a new tag
:param base_xpath: path where to place a new tag without complex syntax ([] conditions and so on)
:param element: a tag name or etree Element to be created
:param create_parents: bool optional (default False), if True and the given xpath has no results the
the parent tags are created recursively
:param occurrences: int or list of int. Which occurence of the parent nodes to create a tag.
By default all nodes are used.
:raises ValueError: If the nodes are missing and `create_parents=False`
:returns: xmltree with created tags
"""
from masci_tools.util.xml.xml_setters_basic import xml_create_tag
from masci_tools.util.xml.common_functions import check_complex_xpath, split_off_tag
check_complex_xpath(xmltree, base_xpath, xpath)
tag_info = schema_dict['tag_info'][base_xpath]
if not etree.iselement(element):
#Get original case of the tag
element_name = (tag_info['simple'] | tag_info['complex']).original_case[element]
try:
element = etree.Element(element_name)
except ValueError as exc:
raise ValueError(f"Failed to construct etree Element from '{element_name}'") from exc
else:
element_name = element.tag
if len(tag_info['order']) == 0:
tag_order = None
else:
tag_order = tag_info['order']
several_tags = element_name in tag_info['several']
parent_nodes = eval_xpath(xmltree, xpath, list_return=True)
if len(parent_nodes) == 0:
if create_parents:
parent_xpath, parent_name = split_off_tag(base_xpath)
complex_parent_xpath, _ = split_off_tag(xpath)
xmltree = xml_create_tag_schema_dict(xmltree,
schema_dict,
complex_parent_xpath,
parent_xpath,
parent_name,
create_parents=create_parents)
else:
raise ValueError(f"Could not create tag '{element_name}' because atleast one subtag is missing. "
'Use create=True to create the subtags')
return xml_create_tag(xmltree, xpath, element, tag_order=tag_order, occurrences=occurrences, several=several_tags)
[docs]def eval_xpath_create(xmltree,
schema_dict,
xpath,
base_xpath,
create_parents=False,
occurrences=None,
list_return=False):
"""
Evaluates and xpath and creates tag if the result is empty
:param xmltree: an xmltree that represents inp.xml
:param schema_dict: InputSchemaDict containing all information about the structure of the input
:param xpath: a path where to place a new tag
:param base_xpath: path where to place a new tag without complex syntax ([] conditions and so on)
:param create_parents: bool optional (default False), if True also the parents of the tag are created
if they are missing
:param occurrences: int or list of int. Which occurence of the parent nodes to create a tag if the tag is missing.
By default all nodes are used.
:param list_return: if True, the returned quantity is always a list even if only one element is in it
:returns: list of nodes from the result of the xpath expression
"""
from masci_tools.util.xml.common_functions import check_complex_xpath, split_off_tag
check_complex_xpath(xmltree, base_xpath, xpath)
nodes = eval_xpath(xmltree, xpath, list_return=True)
if len(nodes) == 0:
parent_xpath, tag_name = split_off_tag(base_xpath)
complex_parent_xpath, _ = split_off_tag(xpath)
xmltree = xml_create_tag_schema_dict(xmltree,
schema_dict,
complex_parent_xpath,
parent_xpath,
tag_name,
create_parents=create_parents,
occurrences=occurrences)
nodes = eval_xpath(xmltree, xpath, list_return=True)
if len(nodes) == 1 and not list_return:
nodes = nodes[0]
return nodes
[docs]def xml_set_attrib_value(xmltree,
schema_dict,
xpath,
base_xpath,
attributename,
attribv,
occurrences=None,
create=False):
"""
Sets an attribute in a xmltree to a given value. By default the attribute will be set
on all nodes returned for the specified xpath.
If there are no nodes under the specified xpath a tag can be created with `create=True`.
The attribute values are converted automatically according to the types of the attribute
with :py:func:`~masci_tools.util.xml.converters.convert_attribute_to_xml()` if they
are not `str` already.
:param xmltree: an xmltree that represents inp.xml
:param schema_dict: InputSchemaDict containing all information about the structure of the input
:param xpath: a path where to set the attributes
:param base_xpath: path where to place a new tag without complex syntax ([] conditions and so on)
:param attributename: the attribute name to set
:param attribv: value or list of values to set
:param occurrences: int or list of int. Which occurence of the node to set. By default all are set.
:param create: bool optional (default False), if True the tag is created if is missing
:raises ValueError: If the conversion to string failed
:raises ValueError: If the tag is missing and `create=False`
:raises ValueError: If the attributename is not allowed on the base_xpath
:returns: xmltree with set attribute
"""
from masci_tools.util.xml.xml_setters_basic import xml_set_attrib_value_no_create
from masci_tools.util.xml.converters import convert_attribute_to_xml
from masci_tools.util.xml.common_functions import check_complex_xpath, split_off_tag
check_complex_xpath(xmltree, base_xpath, xpath)
if create:
nodes = eval_xpath_create(xmltree,
schema_dict,
xpath,
base_xpath,
create_parents=True,
occurrences=occurrences,
list_return=True)
else:
nodes = eval_xpath(xmltree, xpath, list_return=True)
if len(nodes) == 0:
raise ValueError(f"Could not set attribute '{attributename}' on path '{xpath}' "
'because atleast one subtag is missing. '
'Use create=True to create the subtags')
_, tag_name = split_off_tag(base_xpath)
attribs = schema_dict['tag_info'][base_xpath]['attribs']
if attributename not in attribs:
raise ValueError(
f"The key '{attributename}' is not expected for this version of the input for the '{tag_name}' tag. "
f'Allowed attributes are: {attribs.original_case.values()}')
attributename = attribs.original_case[attributename]
converted_attribv, suc = convert_attribute_to_xml(attribv, schema_dict['attrib_types'][attributename])
if '/fleurInput/forceTheorem/' in base_xpath and attributename in ('theta', 'phi', 'ef_shift'):
#Special case for theta and phi attributes on forceTheorem tags
#In Max5/5.1 They are entered as FleurDouble but can be a list. Since
#the attribute setting so far does not support this we convert the values explicitely
#here
if isinstance(converted_attribv, list):
converted_attribv = ' '.join(converted_attribv)
return xml_set_attrib_value_no_create(xmltree, xpath, attributename, converted_attribv, occurrences=occurrences)
[docs]def xml_set_first_attrib_value(xmltree, schema_dict, xpath, base_xpath, attributename, attribv, create=False):
"""
Sets the first occurrence attribute in a xmltree to a given value.
If there are no nodes under the specified xpath a tag can be created with `create=True`.
The attribute values are converted automatically according to the types of the attribute
with :py:func:`~masci_tools.util.xml.converters.convert_attribute_to_xml()` if they
are not `str` already.
:param xmltree: an xmltree that represents inp.xml
:param schema_dict: InputSchemaDict containing all information about the structure of the input
:param xpath: a path where to set the attribute
:param base_xpath: path where to place a new tag without complex syntax ([] conditions and so on)
:param attributename: the attribute name to set
:param attribv: value or list of values to set
:param create: bool optional (default False), if True the tag is created if is missing
:raises ValueError: If the conversion to string failed
:raises ValueError: If the tag is missing and `create=False`
:raises ValueError: If the attributename is not allowed on the base_xpath
:returns: xmltree with set attribute
"""
return xml_set_attrib_value(xmltree,
schema_dict,
xpath,
base_xpath,
attributename,
attribv,
create=create,
occurrences=0)
[docs]def xml_set_text(xmltree, schema_dict, xpath, base_xpath, text, occurrences=None, create=False):
"""
Sets the text on tags in a xmltree to a given value. By default the text will be set
on all nodes returned for the specified xpath.
If there are no nodes under the specified xpath a tag can be created with `create=True`.
The text values are converted automatically according to the types
with :py:func:`~masci_tools.util.xml.converters.convert_text_to_xml()` if they
are not `str` already.
:param xmltree: an xmltree that represents inp.xml
:param schema_dict: InputSchemaDict containing all information about the structure of the input
:param xpath: a path where to set the text
:param base_xpath: path where to place a new tag without complex syntax ([] conditions and so on)
:param text: value or list of values to set
:param occurrences: int or list of int. Which occurence of the node to set. By default all are set.
:param create: bool optional (default False), if True the tag is created if is missing
:raises ValueError: If the conversion to string failed
:raises ValueError: If the tag is missing and `create=False`
:returns: xmltree with set text
"""
from masci_tools.util.xml.xml_setters_basic import xml_set_text_no_create
from masci_tools.util.xml.converters import convert_text_to_xml
from masci_tools.util.xml.common_functions import check_complex_xpath, split_off_tag
check_complex_xpath(xmltree, base_xpath, xpath)
if create:
nodes = eval_xpath_create(xmltree,
schema_dict,
xpath,
base_xpath,
create_parents=True,
occurrences=occurrences,
list_return=True)
else:
nodes = eval_xpath(xmltree, xpath, list_return=True)
if len(nodes) == 0:
raise ValueError(f"Could not set text on path '{xpath}' because atleast one subtag is missing. "
'Use create=True to create the subtags')
_, tag_name = split_off_tag(base_xpath)
possible_definitions = schema_dict['simple_elements'][tag_name]
converted_text, suc = convert_text_to_xml(text, possible_definitions)
return xml_set_text_no_create(xmltree, xpath, converted_text, occurrences=occurrences)
[docs]def xml_set_first_text(xmltree, schema_dict, xpath, base_xpath, text, create=False):
"""
Sets the text on the first occurrence of a tag in a xmltree to a given value.
If there are no nodes under the specified xpath a tag can be created with `create=True`.
The text values are converted automatically according to the types
with :py:func:`~masci_tools.util.xml.converters.convert_text_to_xml()` if they
are not `str` already.
:param xmltree: an xmltree that represents inp.xml
:param schema_dict: InputSchemaDict containing all information about the structure of the input
:param xpath: a path where to set the text
:param base_xpath: path where to place a new tag without complex syntax ([] conditions and so on)
:param text: value or list of values to set
:param create: bool optional (default False), if True the tag is created if is missing
:raises ValueError: If the conversion to string failed
:raises ValueError: If the tag is missing and `create=False`
:returns: xmltree with set text
"""
return xml_set_text(xmltree, schema_dict, xpath, base_xpath, text, create=create, occurrences=0)
[docs]def xml_add_number_to_attrib(xmltree,
schema_dict,
xpath,
base_xpath,
attributename,
add_number,
mode='abs',
occurrences=None):
"""
Adds a given number to the attribute value in a xmltree. By default the attribute will be shifted
on all nodes returned for the specified xpath.
If there are no nodes under the specified xpath an error is raised
:param xmltree: an xmltree that represents inp.xml
:param schema_dict: InputSchemaDict containing all information about the structure of the input
:param xpath: a path where to set the attributes
:param base_xpath: path where to place a new tag without complex syntax ([] conditions and so on)
:param attributename: the attribute name to change
:param add_number: number to add/multiply with the old attribute value
:param mode: str (either `rel` or `abs`).
`rel` multiplies the old value with `add_number`
`abs` adds the old value and `add_number`
:param occurrences: int or list of int. Which occurence of the node to set. By default all are set.
:raises ValueError: If the attribute is unknown or cannot be float or int
:raises ValueError: If the evaluation of the old values failed
:raises ValueError: If a float result is written to a integer attribute
:returns: xmltree with shifted attribute
"""
from masci_tools.util.schema_dict_util import read_constants
from masci_tools.util.xml.converters import convert_xml_attribute
from masci_tools.io.common_functions import is_sequence
from masci_tools.util.xml.common_functions import check_complex_xpath, split_off_attrib, split_off_tag
check_complex_xpath(xmltree, base_xpath, xpath)
if attributename not in schema_dict['attrib_types']:
raise ValueError(
f"You try to shift the attribute:'{attributename}' , but the key is unknown to the fleur plug-in")
possible_types = schema_dict['attrib_types'][attributename]
if not etree.iselement(xmltree):
constants = read_constants(xmltree.getroot(), schema_dict)
else:
constants = read_constants(xmltree, schema_dict)
if 'float' not in possible_types and \
'float_expression' not in possible_types and \
'int' not in possible_types:
raise ValueError(f"Given attribute name '{attributename}' is not float or int")
attribs = schema_dict['tag_info'][base_xpath]['attribs']
_, tag_name = split_off_tag(base_xpath)
if attributename not in attribs:
raise ValueError(
f"The key '{attributename}' is not expected for this version of the input for the '{tag_name}' tag. "
f'Allowed attributes are: {attribs.original_case.values()}')
attributename = attribs.original_case[attributename]
if not xpath.endswith(f'/@{attributename}'):
xpath = '/@'.join([xpath, attributename])
stringattribute = eval_xpath(xmltree, xpath, list_return=True)
tag_xpath, attributename = split_off_attrib(xpath)
if len(stringattribute) == 0:
raise ValueError(f"No attribute values found for '{attributename}'. Cannot add number")
attribvalues, _ = convert_xml_attribute(stringattribute, possible_types, constants=constants, list_return=True)
if occurrences is not None:
if not is_sequence(occurrences):
occurrences = [occurrences]
try:
attribvalues = [attribvalues[occ] for occ in occurrences]
except IndexError as exc:
raise ValueError('Wrong value for occurrences') from exc
if mode == 'abs':
attribvalues = [value + float(add_number) for value in attribvalues]
elif mode == 'rel':
attribvalues = [value * float(add_number) for value in attribvalues]
if 'float' in possible_types or 'float_expression' in possible_types:
pass
elif 'int' in possible_types:
if any(not value.is_integer() for value in attribvalues):
raise ValueError('You are trying to write a float to an integer attribute')
attribvalues = [int(value) for value in attribvalues]
xmltree = xml_set_attrib_value(xmltree,
schema_dict,
tag_xpath,
base_xpath,
attributename,
attribvalues,
occurrences=occurrences)
return xmltree
[docs]def xml_add_number_to_first_attrib(xmltree, schema_dict, xpath, base_xpath, attributename, add_number, mode='abs'):
"""
Adds a given number to the first occurrence of a attribute value in a xmltree.
If there are no nodes under the specified xpath an error is raised
:param xmltree: an xmltree that represents inp.xml
:param schema_dict: InputSchemaDict containing all information about the structure of the input
:param xpath: a path where to set the attributes
:param base_xpath: path where to place a new tag without complex syntax ([] conditions and so on)
:param attributename: the attribute name to change
:param add_number: number to add/multiply with the old attribute value
:param mode: str (either `rel` or `abs`).
`rel` multiplies the old value with `add_number`
`abs` adds the old value and `add_number`
:raises ValueError: If the attribute is unknown or cannot be float or int
:raises ValueError: If the evaluation of the old values failed
:raises ValueError: If a float result is written to a integer attribute
:returns: xmltree with shifted attribute
"""
return xml_add_number_to_attrib(xmltree,
schema_dict,
xpath,
base_xpath,
attributename,
add_number,
mode=mode,
occurrences=0)
[docs]def xml_set_simple_tag(xmltree, schema_dict, xpath, base_xpath, tag_name, changes, create_parents=False):
"""
Sets one or multiple `simple` tag(s) in an xmltree. A simple tag can only hold attributes and has no
subtags.
If the tag can occur multiple times all existing tags are DELETED and new ones are written.
If the tag only occurs once it will automatically be created if its missing.
:param xmltree: an xmltree that represents inp.xml
:param schema_dict: InputSchemaDict containing all information about the structure of the input
:param xpath: a path where to set the attributes
:param base_xpath: path where to place a new tag without complex syntax ([] conditions and so on)
:param tag_name: name of the tag to set
:param changes: list of dicts or dict with the changes. Elements in list describe multiple tags.
Keys in the dictionary correspond to {'attributename': attributevalue}
:param create_parents: bool optional (default False), if True and the path, where the simple tags are
set does not exist it is created
:returns: xmltree with set simple tags
"""
from masci_tools.util.xml.xml_setters_basic import xml_delete_tag
from masci_tools.util.xml.common_functions import check_complex_xpath
check_complex_xpath(xmltree, base_xpath, xpath)
tag_info = schema_dict['tag_info'][base_xpath]
tag_xpath = f'{xpath}/{tag_name}'
tag_base_xpath = f'{base_xpath}/{tag_name}'
if tag_name in tag_info['several']:
#change_dict can either be a list or a dict
if isinstance(changes, dict):
changes = [changes]
# policy: we DELETE all existing tags, and create new ones from the given parameters.
xml_delete_tag(xmltree, tag_xpath)
for indx in range(0, len(changes)):
xml_create_tag_schema_dict(xmltree, schema_dict, xpath, base_xpath, tag_name, create_parents=create_parents)
for indx, change in enumerate(changes):
for attrib, value in change.items():
occurrences = [
k * len(changes) + indx
for k in range(len(eval_xpath(xmltree, tag_xpath, list_return=True)) // len(changes))
]
xml_set_attrib_value(xmltree,
schema_dict,
tag_xpath,
tag_base_xpath,
attrib,
value,
occurrences=occurrences)
else:
if not isinstance(changes, dict):
raise ValueError(f"Tag '{tag_name}' can only occur once. But 'set_simple_tag' got a list")
#eval and ggf. create tag
eval_xpath_create(xmltree, schema_dict, tag_xpath, tag_base_xpath, create_parents=create_parents)
for attrib, value in changes.items():
xml_set_attrib_value(xmltree, schema_dict, tag_xpath, tag_base_xpath, attrib, value)
return xmltree
[docs]def xml_set_complex_tag(xmltree, schema_dict, xpath, base_xpath, attributedict, create=False):
"""
Recursive Function to correctly set tags/attributes for a given tag.
Goes through the attributedict and decides based on the schema_dict, how the corresponding
key has to be handled.
Supports:
- attributes
- tags with text only
- simple tags, i.e. only attributes (can be optional single/multiple)
- complex tags, will recursively create/modify them
:param xmltree: an xmltree that represents inp.xml
:param schema_dict: InputSchemaDict containing all information about the structure of the input
:param xpath: a path where to set the attributes
:param base_xpath: path where to place a new tag without complex syntax ([] conditions and so on)
:param tag_name: name of the tag to set
:param attributedict: Keys in the dictionary correspond to names of tags and the values are the modifications
to do on this tag (attributename, subdict with changes to the subtag, ...)
:param create: bool optional (default False), if True and the path, where the complex tag is
set does not exist it is created
:returns: xmltree with changes to the complex tag
"""
from masci_tools.util.xml.xml_setters_basic import xml_delete_tag
from masci_tools.util.xml.common_functions import check_complex_xpath, split_off_tag
check_complex_xpath(xmltree, base_xpath, xpath)
tag_info = schema_dict['tag_info'][base_xpath]
_, tag_name = split_off_tag(base_xpath)
if create:
#eval complex tag and ggf create
eval_xpath_create(xmltree, schema_dict, xpath, base_xpath, create_parents=True)
for key, val in attributedict.items():
if key not in tag_info['complex'] | tag_info['simple'] | tag_info['attribs']:
raise ValueError(
f"The key '{key}' is not expected for this version of the input for the '{tag_name}' tag. "
f"Allowed tags are: {sorted((tag_info['complex']|tag_info['simple']).original_case.values())}"
f"Allowed attributes are: {sorted(tag_info['attribs'].original_case.values())}")
key = (tag_info['complex'] | tag_info['simple'] | tag_info['attribs']).original_case[key]
sub_xpath = f'{xpath}/{key}'
sub_base_xpath = f'{base_xpath}/{key}'
if key in tag_info['attribs']:
xml_set_attrib_value(xmltree, schema_dict, xpath, base_xpath, key, val, create=create)
elif key in tag_info['text']:
xml_set_text(xmltree, schema_dict, sub_xpath, sub_base_xpath, val, create=create)
elif key in tag_info['simple']:
xml_set_simple_tag(xmltree, schema_dict, xpath, base_xpath, key, val, create_parents=create)
elif key not in tag_info['several']: #Complex tag but only one (electronConfig)
# eval and ggf create tag at right place.
eval_xpath_create(xmltree, schema_dict, sub_xpath, sub_base_xpath, create_parents=create)
xmltree = xml_set_complex_tag(xmltree, schema_dict, sub_xpath, sub_base_xpath, val, create=create)
else:
# policy: we DELETE all existing tags, and create new ones from the given parameters.
xml_delete_tag(xmltree, sub_xpath)
if isinstance(val, dict):
val = [val]
for indx in range(0, len(val)):
xml_create_tag_schema_dict(xmltree, schema_dict, xpath, base_xpath, key, create_parents=create)
for indx, tagdict in enumerate(val):
for k in range(len(eval_xpath(xmltree, sub_xpath, list_return=True)) // len(val)):
current_elem_xpath = f'{sub_xpath}[{k*len(val)+indx+1}]'
xmltree = xml_set_complex_tag(xmltree,
schema_dict,
current_elem_xpath,
sub_base_xpath,
tagdict,
create=create)
return xmltree