Node Modification

Modifying Existing XML

Modifying existing XML can be done in xml2 by using the replacement functions of the accessors. They all have methods for both individual xml_node objects as well as xml_nodeset objects. If a vector of values is provided it is applied piecewise over the nodeset, otherwise the value is recycled.

Text Modification

Text modification only happens on text nodes. If a given node has more than one text node only the first will be affected. If you want to modify additional text nodes you need to select them explicitly with /text().

x <- read_xml("<p>This is some <b>text</b>. This is more.</p>")
xml_text(x)
#> [1] "This is some text. This is more."

xml_text(x) <- "This is some other text."
xml_text(x)
#> [1] "This is some other text.text. This is more."

# You can avoid this by explicitly selecting the text node.
x <- read_xml("<p>This is some text. This is <b>bold!</b></p>")
text_only <- xml_find_all(x, "//text()")

xml_text(text_only) <- c("This is some other text. ", "Still bold!")
xml_text(x)
#> [1] "This is some other text. Still bold!"
xml_structure(x)
#> <p>
#>   {text}
#>   <b>
#>     {text}

Attribute and Namespace Definition Modification

Attributes and namespace definitions are modified one at a time with xml_attr() or all at once with xml_attrs(). In both cases using NULL as the value will remove the attribute completely.

x <- read_xml("<a href='invalid!'>xml2</a>")
xml_attr(x, "href")
#> [1] "invalid!"

xml_attr(x, "href") <- "https://github.com/r-lib/xml2"
xml_attr(x, "href")
#> [1] "https://github.com/r-lib/xml2"

xml_attrs(x) <- c(id = "xml2", href = "https://github.com/r-lib/xml2")
xml_attrs(x)
#>                            href                              id 
#> "https://github.com/r-lib/xml2"                          "xml2"
x
#> {xml_document}
#> <a href="https://github.com/r-lib/xml2" id="xml2">

xml_attrs(x) <- NULL
x
#> {xml_document}
#> <a>

# Namespaces are added with as a xmlns or xmlns:prefix attribute
xml_attr(x, "xmlns") <- "http://foo"
x
#> {xml_document}
#> <a xmlns="http://foo">

xml_attr(x, "xmlns:bar") <- "http://bar"
x
#> {xml_document}
#> <a xmlns="http://foo" xmlns:bar="http://bar">

Name Modification

Node names are modified with xml_name().

x <- read_xml("<a><b/></a>")
x
#> {xml_document}
#> <a>
#> [1] <b/>
xml_name(x)
#> [1] "a"
xml_name(x) <- "c"
x
#> {xml_document}
#> <c>
#> [1] <b/>

All of these functions have a .copy argument. If this is set to FALSE they will remove the new node from its location before inserting it into the new location. Otherwise they make a copy of the node before insertion.

Replacing existing nodes

x <- read_xml("<parent><child>1</child><child>2<child>3</child></child></parent>")
children <- xml_children(x)
t1 <- children[[1]]
t2 <- children[[2]]
t3 <- xml_children(children[[2]])[[1]]

xml_replace(t1, t3)
#> {xml_node}
#> <child>
x
#> {xml_document}
#> <parent>
#> [1] <child>3</child>
#> [2] <child>2<child>3</child></child>

Add a sibling

x <- read_xml("<parent><child>1</child><child>2<child>3</child></child></parent>")
children <- xml_children(x)
t1 <- children[[1]]
t2 <- children[[2]]
t3 <- xml_children(children[[2]])[[1]]

xml_add_sibling(t1, t3)
x
#> {xml_document}
#> <parent>
#> [1] <child>1</child>
#> [2] <child>3</child>
#> [3] <child>2<child>3</child></child>

xml_add_sibling(t3, t1, where = "before")
x
#> {xml_document}
#> <parent>
#> [1] <child>1</child>
#> [2] <child>3</child>
#> [3] <child>2<child>3</child><child>1</child></child>

Add a child

x <- read_xml("<parent><child>1</child><child>2<child>3</child></child></parent>")
children <- xml_children(x)
t1 <- children[[1]]
t2 <- children[[2]]
t3 <- xml_children(children[[2]])[[1]]

xml_add_child(t1, t3)
x
#> {xml_document}
#> <parent>
#> [1] <child>1<child>3</child></child>
#> [2] <child>2<child>3</child></child>

xml_add_child(t1, read_xml("<test/>"))
x
#> {xml_document}
#> <parent>
#> [1] <child>1<child>3</child><test/></child>
#> [2] <child>2<child>3</child></child>

Removing nodes

The xml_remove() can be used to remove a node (and its children) from a tree. The default behavior is to unlink the node from the tree, but does not free the memory for the node, so R objects pointing to the node are still valid.

This allows code like the following to work without crashing R

x <- read_xml("<foo><bar><baz/></bar></foo>")
x1 <- x %>%
  xml_children() %>%
  .[[1]]
x2 <- x1 %>%
  xml_children() %>%
  .[[1]]

xml_remove(x1)
rm(x1)
gc()
#>           used (Mb) gc trigger (Mb) max used (Mb)
#> Ncells  673203   36    1327711   71  1327711 71.0
#> Vcells 1168848    9    8388608   64  2560784 19.6

x2
#> {xml_node}
#> <baz>

If you are not planning on referencing these nodes again this memory is wasted. Calling xml_remove(free = TRUE) will remove the nodes and free the memory used to store them. Note In this case any node which previously pointed to the node or its children will instead be pointing to free memory and may cause R to crash. xml2 can’t figure this out for you, so it’s your responsibility to remove any objects which are no longer valid.

In particular xml_find_*() results are easy to overlook, for example

x <- read_xml("<a><b /><b><b /></b></a>")
bees <- xml_find_all(x, "//b")
xml_remove(xml_child(x), free = TRUE)
# bees[[1]] is no longer valid!!!
rm(bees)
gc()
#>           used (Mb) gc trigger (Mb) max used (Mb)
#> Ncells  673207   36    1327711   71  1327711 71.0
#> Vcells 1168845    9    8388608   64  2560784 19.6

Namespaces

We want to construct a document with the following namespace layout. (From https://stackoverflow.com/questions/32939229/creating-xml-in-r-with-namespaces/32941524#32941524).

<?xml version = "1.0" encoding="UTF-8"?>
<sld xmlns="http://www.opengis.net/sld"
     xmlns:ogc="http://www.opengis.net/ogc"
     xmlns:se="http://www.opengis.net/se"
     version="1.1.0" >
<layer>
<se:Name>My Layer</se:Name>
</layer>
</sld>

d <- xml_new_root("sld",
  "xmlns" = "http://www.opengis.net/sld",
  "xmlns:ogc" = "http://www.opengis.net/ogc",
  "xmlns:se" = "http://www.opengis.net//se",
  version = "1.1.0"
) %>%
  xml_add_child("layer") %>%
  xml_add_child("se:Name", "My Layer") %>%
  xml_root()

d
#> {xml_document}
#> <sld version="1.1.0" xmlns="http://www.opengis.net/sld" xmlns:ogc="http://www.opengis.net/ogc" xmlns:se="http://www.opengis.net//se">
#> [1] <layer>\n  <se:Name>My Layer</se:Name>\n</layer>

Node Modification

Jim Hester

2023-12-04

Modifying Existing XML

Text Modification

Attribute and Namespace Definition Modification

Name Modification