# -*- 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/. #
# #
###############################################################################
"""
Basic functions for modifying the xml input file of Fleur. These functions DO NOT
have the ability to create missing tags on the fly. This functionality is added on top
in :py:mod:`~masci_tools.util.xml.xml_setters_xpaths` since we need the schema dictionary
to do these operations robustly
"""
from lxml import etree
from masci_tools.util.xml.common_functions import eval_xpath
import warnings
[docs]def xml_replace_tag(xmltree, xpath, newelement, occurrences=None):
"""
replaces xml tags by another tag on an xmletree in place
:param xmltree: an xmltree that represents inp.xml
:param xpath: a path to the tag to be replaced
:param newelement: a new tag
:param occurrences: int or list of int. Which occurence of the parent nodes to create a tag.
By default all nodes are used.
:returns: xmltree with replaced tag
"""
import copy
from masci_tools.io.common_functions import is_sequence
root = xmltree.getroot()
nodes = eval_xpath(root, xpath, list_return=True)
if occurrences is not None:
if not is_sequence(occurrences):
occurrences = [occurrences]
try:
nodes = [nodes[occ] for occ in occurrences]
except IndexError as exc:
raise ValueError('Wrong value for occurrences') from exc
for node in nodes:
parent = node.getparent()
index = parent.index(node)
parent.remove(node)
parent.insert(index, copy.deepcopy(newelement))
etree.indent(xmltree)
return xmltree
[docs]def xml_delete_att(xmltree, xpath, attrib, occurrences=None):
"""
Deletes an xml attribute in an xmletree.
:param xmltree: an xmltree that represents inp.xml
:param xpath: a path to the attribute to be deleted
:param attrib: the name of an attribute
:param occurrences: int or list of int. Which occurence of the parent nodes to create a tag.
By default all nodes are used.
:returns: xmltree with deleted attribute
"""
from masci_tools.io.common_functions import is_sequence
root = xmltree.getroot()
nodes = eval_xpath(root, xpath, list_return=True)
if occurrences is not None:
if not is_sequence(occurrences):
occurrences = [occurrences]
try:
nodes = [nodes[occ] for occ in occurrences]
except IndexError as exc:
raise ValueError('Wrong value for occurrences') from exc
for node in nodes:
node.attrib.pop(attrib, None)
return xmltree
[docs]def xml_delete_tag(xmltree, xpath, occurrences=None):
"""
Deletes a xml tag in an xmletree.
:param xmltree: an xmltree that represents inp.xml
:param xpath: a path to the tag to be deleted
:param occurrences: int or list of int. Which occurence of the parent nodes to create a tag.
By default all nodes are used.
:returns: xmltree with deleted tag
"""
from masci_tools.io.common_functions import is_sequence
root = xmltree.getroot()
nodes = eval_xpath(root, xpath, list_return=True)
if occurrences is not None:
if not is_sequence(occurrences):
occurrences = [occurrences]
try:
nodes = [nodes[occ] for occ in occurrences]
except IndexError as exc:
raise ValueError('Wrong value for occurrences') from exc
for node in nodes:
parent = node.getparent()
parent.remove(node)
etree.indent(xmltree)
return xmltree
[docs]def xml_create_tag(xmltree,
xpath,
element,
place_index=None,
tag_order=None,
occurrences=None,
correct_order=True,
several=True):
"""
This method evaluates an xpath expression and creates a tag in a xmltree under the
returned nodes.
If there are no nodes under the specified xpath an error is raised.
The tag is appended by default, but can be inserted at a certain index (`place_index`)
or can be inserted according to a given order of tags
:param xmltree: an xmltree that represents inp.xml
:param xpath: a path where to place a new tag
:param element: a tag name or etree Element to be created
:param place_index: defines the place where to put a created tag
:param tag_order: defines a tag order
:param occurrences: int or list of int. Which occurence of the parent nodes to create a tag.
By default all nodes are used.
:param correct_order: bool, if True (default) and a tag_order is given, that does not correspond to the given order
in the xmltree (only order wrong no unknown tags) it will be corrected and a warning is given
This is necessary for some edge cases of the xml schemas of fleur
:param several: bool, if True multiple tags od the given name are allowed
:raises ValueError: If the insertion failed in any way (tag_order does not match, failed to insert, ...)
:returns: xmltree with created tags
"""
import copy
from more_itertools import unique_justseen
from masci_tools.io.common_functions import is_sequence
if not etree.iselement(element):
element_name = element
try:
element = etree.Element(element)
except ValueError as exc:
raise ValueError(f"Failed to construct etree Element from '{element_name}'") from exc
else:
element_name = element.tag
parent_nodes = eval_xpath(xmltree, xpath, list_return=True)
if len(parent_nodes) == 0:
raise ValueError(f"Could not create tag '{element_name}' because atleast one subtag is missing. "
'Use create=True to create the subtags')
if occurrences is not None:
if not is_sequence(occurrences):
occurrences = [occurrences]
try:
parent_nodes = [parent_nodes[occ] for occ in occurrences]
except IndexError as exc:
raise ValueError('Wrong value for occurrences') from exc
for parent in parent_nodes:
element_to_write = copy.deepcopy(element)
if tag_order is not None:
try:
tag_index = tag_order.index(element_name)
except ValueError as exc:
raise ValueError(f"The tag '{element_name}' was not found in the order list. "
f'Allowed tags are: {tag_order}') from exc
behind_tags = tag_order[:tag_index]
child_tags = [child.tag for child in parent.iterchildren()]
#This ignores serial duplicates. With this out of order tags will be obvious e.g ['ldaU', 'lo','lo', 'ldaU']
#will result in ['ldaU', 'lo', 'ldaU']
existing_order = list(unique_justseen(child_tags))
#Does the input file have unknown tags
extra_tags = set(existing_order).difference(set(tag_order))
if extra_tags:
raise ValueError(f'Did not find existing elements in the tag_order list: {extra_tags}')
if element_name in existing_order and not several:
raise ValueError(f'The given tag {element_name} is not allowed to appear multiple times')
#Is the existing order in line with the given tag_order
if sorted(existing_order, key=tag_order.index) != existing_order:
if not correct_order:
raise ValueError('Existing order does not correspond to tag_order list\n'
f'Expected order: {tag_order}\n'
f'Actual order: {existing_order}')
else:
#Here we know that there are no unexpected tags in the order, so we can 'repair' the order
warnings.warn('Existing order does not correspond to tag_order list. Correcting it\n'
f'Expected order: {tag_order}\n'
f'Actual order: {existing_order}')
new_tag = copy.deepcopy(parent)
#Remove all child nodes from new_tag (deepcopied so they are still on parent)
for node in new_tag.iterchildren():
new_tag.remove(node)
for tag in tag_order:
#Iterate over all children with the given tag on the parent and append to the new_tag
for node in parent.iterchildren(tag=tag):
new_tag.append(node)
#Now replace the parent node with the reordered node
parent_of_parent = parent.getparent()
index = parent_of_parent.index(parent)
parent_of_parent.remove(parent)
parent_of_parent.insert(index, new_tag)
parent = new_tag
for tag in reversed(behind_tags):
existing_tags = list(parent.iterchildren(tag=tag))
if len(existing_tags) != 0:
insert_index = parent.index(existing_tags[-1]) + 1
try:
parent.insert(insert_index, element_to_write)
except ValueError as exc:
raise ValueError(f"Failed to insert element '{element_name}' behind '{tag}' tag") from exc
break
else: #This is the construct for reaching the end of the loop without breaking
try:
parent.insert(0, element_to_write)
except ValueError as exc:
raise ValueError(
f"Failed to insert element '{element_name}' at the beginning of the order") from exc
elif place_index is not None:
#We just try to insert the new element at the index
try:
parent.insert(place_index, element_to_write)
except ValueError as exc:
raise ValueError(f"Failed to create element '{element_name}' at the place index '{place_index}' "
f"to the parent '{parent.tag}'") from exc
else:
#We append the node and hope nothing breaks
try:
parent.append(element_to_write)
except ValueError as exc:
raise ValueError(f"Failed to append element '{element_name}' to the parent '{parent.tag}'") from exc
etree.indent(xmltree)
return xmltree
[docs]def xml_set_attrib_value_no_create(xmltree, xpath, attributename, attribv, occurrences=None):
"""
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.
:param xmltree: an xmltree that represents inp.xml
:param xpath: a path where to set the attributes
:param attributename: the attribute name to set
:param attribv: value or list of values to set (if not str they will be converted with `str(value)`)
:param occurrences: int or list of int. Which occurence of the node to set. By default all are set.
:raises ValueError: If the lengths of attribv or occurrences do not match number of nodes
:returns: xmltree with set attribute
"""
from masci_tools.io.common_functions import is_sequence
root = xmltree.getroot()
nodes = eval_xpath(root, xpath, list_return=True)
if len(nodes) == 0:
return xmltree
if occurrences is not None:
if not is_sequence(occurrences):
occurrences = [occurrences]
try:
nodes = [nodes[occ] for occ in occurrences]
except IndexError as exc:
raise ValueError('Wrong value for occurrences') from exc
if is_sequence(attribv):
if len(attribv) != len(nodes):
raise ValueError(f'Wrong length for attribute values. Expected {len(nodes)} items. Got: {len(attribv)}')
else:
attribv = [attribv] * len(nodes)
attribv = [val if isinstance(val, str) else str(val) for val in attribv]
for node, value in zip(nodes, attribv):
node.set(attributename, value)
return xmltree
[docs]def xml_set_text_no_create(xmltree, xpath, text, occurrences=None):
"""
Sets the text of a tag in a xmltree to a given value.
By default the text will be set on all nodes returned for the specified xpath.
:param xmltree: an xmltree that represents inp.xml
:param xpath: a path where to set the text
:param text: value or list of values to set (if not str they will be converted with `str(value)`)
:param occurrences: int or list of int. Which occurrence of the node to set. By default all are set.
:raises ValueError: If the lengths of text or occurrences do not match number of nodes
:returns: xmltree with set text
"""
from masci_tools.io.common_functions import is_sequence
root = xmltree.getroot()
nodes = eval_xpath(root, xpath, list_return=True)
if len(nodes) == 0:
return xmltree
if occurrences is not None:
if not is_sequence(occurrences):
occurrences = [occurrences]
try:
nodes = [nodes[occ] for occ in occurrences]
except IndexError as exc:
raise ValueError('Wrong value for occurrences') from exc
if is_sequence(text):
if len(text) != len(nodes):
raise ValueError(f'Wrong length for text values. Expected {len(nodes)} items. Got: {text}')
else:
text = [text] * len(nodes)
for node, text_val in zip(nodes, text):
node.text = text_val
return xmltree