Fast and elegant XML generation for R
xmlwriter is an R package that provides a fast and simple interface
for creating XML documents and fragments from R. It has a simple elegant
syntax for creating xml_fragments.
xmlwriter’s XML generation from R lists is fast, implemented in C++
using Rcpp. Curious for the
benchmarks? Check the performance section.
xmlwriter can be used as a companion to R packages
XML or
xml2 which are both
wonderful packages optimized for parsing, querying and manipulating XML
documents. Both XML and xml2 provide several ways for creating XML
documents, but they are not optimized for generating and writing XML.
Creating XML documents with XML and xml2 can be a bit cumbersome,
mostly because it
forces the author to manipulate the XML document tree, obscuring the XML
structure of the document, and making it hard to read the XML that is
being generated. xml2 does provide a way to create XML documents from
R data structures using nested lists which is a powerful feature, but it
is not optimized for speed or readability.
xmlwriter provides an intuitive interface for creating XML documents,
that mimics how XML is written in a text editor.
It has two different ways to create XML documents:
- a light weight R syntax using
tag,frag,+,/anddata_frag, creating anxml_fragment, that can be easily translated into acharacterorxml2::xml_documentobject, or be used as a flexible building block for generating a larger XML document. - an
xmlbuilderobject that allows you to create XML documents in a feed-forward manner, withstartandendmethods, giving you more control on the XML document structure, including XML comment, prolog etc.
You can install the development version of xmlwriter from:w
GitHub with:
# install.packages("devtools")
devtools::install_github("edwindj/xmlwriter")xml_fragments allow to write XML using readable R syntax. tag and
frag are function that create XML elements that can be combined using
+ and / operators resulting in an xml_fragment.
xml_fragments can be used to create an character with valid XML, a
xml2::xml_document or as a building block for more complex XML
documents. An xml_fragment is a list object that is identical to the
output of xml2::as_list, and can be converted to a character or an
xml2::xml_document object but xmlwriter provides a much faster
implementation (see performance).
tag is a function that creates a simple xml_fragment element with a
given tag name, text, and attributes. It allows for creating elements
with a tag name using a character, which gives flexibility.
library(xmlwriter)
# tag creates a simple xml_fragment, with text and named attributes
tag("person", "John Doe", id = 1, state="CA")
#> {xml_fragment}
#> <person id="1" state="CA">John Doe</person>frag is a function that allows for specifying nested elements and
attributes, thus creating a more complex xml_fragment.
An argument to frag is either:
- a named element in which case the name is used as the tag name for
that element. The element can be a value or a nested
frag. - an unnamed element in which case the element is added as a text node.
- a
.attrargument that is used to add attributes to the parent element.
# a frag can contain multiple elements
frag(
name = "John Doe",
age = 30
)
#> {xml_fragment (2)}
#> [1]<name>John Doe</name>
#> [2]<age>30</age>
#> ...
# and can nest frags
frag(
person = frag(
# attributes on person are specified using .attr
.attr = c(id = 1, state = "CA"),
name = "John Doe",
age = 30
)
)
#> {xml_fragment}
#> <person id="1" state="CA">
#> <name>John Doe</name>
#> <age>30</age>
#> </person>The xml_fragment function is a restricted version of frag that does
not allow .attr on its top level.
# xml_fragment is more strict version of a frag
fragment <- xml_fragment(
person = frag(
.attr = c(id = 1, state="CA"),
name = "John Doe",
age = 30,
address = frag(
street = "123 Main St",
city = "Anytown",
state = "CA",
zip = 12345
)
)
)cat(as.character(fragment))<person id="1" state="CA">
<name>John Doe</name>
<age>30</age>
<address>
<street>123 Main St</street>
<city>Anytown</city>
<state>CA</state>
<zip>12345</zip>
</address>
</person>data_frag is function that converts a data.frame to an xml_fragment:
data <- data.frame(
name = c("John Doe", "Jane Doe"),
age = c(30, 25),
stringsAsFactors = FALSE
)
# create an xml_fragment from a data.frame
data_frag(data, row_tag = "person")
#> {xml_fragment (2)}
#> [1]<person>
#> <name>John Doe</name>
#> <age>30</age>
#> </person>
#> [2]<person>
#> <name>Jane Doe</name>
#> <age>25</age>
#> </person>
#> ...Or you can use it within an xml_fragment:
# but you can also use it within an xml_fragment
doc <- xml_fragment(
homeless = data_frag(data, row_tags = "person")
)
doc<homeless>
<person>
<name>John Doe</name>
<age>30</age>
</person>
<person>
<name>Jane Doe</name>
<age>25</age>
</person>
</homeless>xml_fragments such as tag, frag and data_frag can be combined
with the + operator, which is equivalent to the append() and c()
function: it creates sibling XML nodes.
library(xmlwriter)
john <- tag("person", "John", id = 1)
jane <- tag("person", "Jane", id = 2)
john + jane
#> {xml_fragment (2)}
#> [1]<person id="1">John</person>
#> [2]<person id="2">Jane</person>
#> ...
john + tag("person", "Jane", id = 2)
#> {xml_fragment (2)}
#> [1]<person id="1">John</person>
#> [2]<person id="2">Jane</person>
#> ...
john + xml_fragment(
person = frag(
.attr = c(id = 2),
"Jane"
)
)
#> {xml_fragment (2)}
#> [1]<person id="1">John</person>
#> [2]<person id="2">Jane</person>
#> ...- the
/operator, which is equivalent to theadd_child_fragmentfunction which creates a child XML node of the last XML node in anxml_fragment.
tag("person", id = 1) / (
tag("name", "John Doe")
)
#> {xml_fragment}
#> <person id="1">
#> <name>John Doe</name>
#> </person>
tag("person", id = 1) / frag(
name = "John Doe",
age = 30
)
#> {xml_fragment}
#> <person id="1">
#> <name>John Doe</name>
#> <age>30</age>
#> </person>
tag("person", id = 1) |>
add_child_fragment(
name = "John Doe",
age = 30
)
#> {xml_fragment}
#> <person id="1">
#> <name>John Doe</name>
#> <age>30</age>
#> </person>Using the tag, frag, + and / functions, one can create complex
XML documents in a very flexible manner.
# overly complex, but shows flexible construction of XML
fragment <-
tag("person", id = "1") / # adds child nodes to person
( frag(
name = "John Doe",
age = 30
) + # add an extra child node to person, with subnodes
tag("address") |> add_child_fragment(
street = "123 Main St",
city = "Anytown",
state = "CA",
zip = 12345
)
)
fragment
#> {xml_fragment}
#> <person id="1">
#> <name>John Doe</name>
#> <age>30</age>
#> <address>
#> <street>...A cleaner version of the above:
tag("person", id = 1) / frag(
name = "John Doe",
age = 30,
address = frag(
street = "123 Main St",
city = "Anytown",
state = "CA",
zip = 12345
)
)
#> {xml_fragment}
#> <person id="1">
#> <name>John Doe</name>
#> <age>30</age>
#> <address>
#> <street>...xml_writer does not have a hard dependency on xml2, but the output
of xml_writer can be converted to a xml2::xml_document object. An
xml_fragment is identical to the output of xml2::as_list, so it can
be converted to a xml2::xml_document object.
xml_fragment supports the following xml2 methods:
xml2::as_xml_document, calls thexml2::read_xmlmethodxml2::as_list, removes thexml_fragmentclassxml2::write_xml, writes the xml to a file or console
One can also use the as_xml_nodeset function to convert the
xml_fragment to a xml2::xml_nodeset object.
fragment |> xml2::as_xml_document()
#> {xml_document}
#> <person id="1">
#> [1] <name>John Doe</name>
#> [2] <age>30</age>
#> [3] <address>\n <street>123 Main St</street>\n <city>Anytown</city>\n <sta ...
fragment |> as_xml_nodeset()
#> {xml_nodeset (1)}
#> [1] <person id="1">\n <name>John Doe</name>\n <age>30</age>\n <address>\n ...xml_fragment implements the xml2::write_xml method
xml2::write_xml(fragment, file="") # print to the consoleresults in:
<person id="1">
<name>John Doe</name>
<age>30</age>
<address>
<street>123 Main St</street>
<city>Anytown</city>
<state>CA</state>
<zip>12345</zip>
</address>
</person>xmlwriter is optimized for generating xml documents and fragments from
a R list structure that is identical to the xml2::as_list output.
library(microbenchmark)
library(xml2)
library(xmlwriter)
# read in a sample 600k xml file as a R list str
doc <- xml2::read_xml("./example/DataGeneric.xml")
doc_list <- xml2::as_list(doc)
# just copy the list and set an extra attribute class="xml_fragment"
# making it a xml_fragment object
doc_fragment <- structure(doc_list, class = "xml_fragment")
# see how long it takes to create an xml document with xml2 and xmlwriter
(m <- microbenchmark(
xml2 = xml2::as_xml_document(doc_list),
xmlwriter = xml2::as_xml_document(doc_fragment),
times = 10
))
#> Warning in microbenchmark(xml2 = xml2::as_xml_document(doc_list), xmlwriter =
#> xml2::as_xml_document(doc_fragment), : less accurate nanosecond times to avoid
#> potential integer overflows
#> Unit: milliseconds
#> expr min lq mean median uq max
#> xml2 2399.64796 2447.8843 2473.02250 2459.12949 2519.27686 2559.83217
#> xmlwriter 39.46873 40.6877 42.48128 41.46744 44.61841 46.35956
#> neval
#> 10
#> 10xmlwriter is about 58.2 times faster than xml2 for creating an xml
document from an R list. Note that xmlwriter includes a round trip,
since xmlwriter first generates a character vector which is then
read using xml2::read_xml().
xmlbuilder is an object that allows you to create xml documents in a
feed-forward manner.
With xml_fragment one creates the xml document structure as one
(large) R list and then converts it to a xml string or
xml2::xml_document, with xmlbuilder one incremently builds the xml
document, without having the whole list structure in memory. It also
provides more functions for the output xml document, like adding a
prolog or comment.
It provides the following methods:
startto start a new elementendto end the current elementelementto add an element with a valuecommentto add a commentprologto add a prologfragmentto add a fragment
library(xmlwriter)
b <- xmlbuilder(allow_fragments = FALSE)
b$comment("This is an xml comment")
b$start("homeless")
b$start("person", id = "1")
b$element("name", "John Doe")
b$element("age", 30)
b$start("address")
b$element("street", "123 Main St")
b$element("city", "Anytown")
b$element("state", "CA")
b$element("zip", 12345)
b$end("address")
b$end("person")
b$start("person", id = "2")
b$element("name", "Jane Doe")
b$element("age", 25)
b$start("address")
b$element("street", "321 Main St")
b$element("city", "Anytown")
b$element("state", "CA")
b$element("zip", 54321)
b$end("address")
b$end("person")
b$fragment(
person = frag(
.attr = c(id = "3"),
name = "Jim Doe",
age = 35
)
)
b$end("homeless")
# includes a xml prolog and comment
b
#> {xmlbuilder}
as.character(b)
#> [1] "<?xml version='1.0' encoding='UTF-8'?><!--This is an xml comment--><homeless><person id=\"1\"><name>John Doe</name><age>30</age><address><street>123 Main St</street><city>Anytown</city><state>CA</state><zip>12345</zip></address></person><person id=\"2\"><name>Jane Doe</name><age>25</age><address><street>321 Main St</street><city>Anytown</city><state>CA</state><zip>54321</zip></address></person><person id=\"3\">\n <name>Jim Doe</name>\n <age>35</age>\n</person></homeless>"
# only contains the actual nodes
xml2::as_xml_document(b)
#> {xml_document}
#> <homeless>
#> [1] <person id="1">\n <name>John Doe</name>\n <age>30</age>\n <address>\n ...
#> [2] <person id="2">\n <name>Jane Doe</name>\n <age>25</age>\n <address>\n ...
#> [3] <person id="3">\n <name>Jim Doe</name>\n <age>35</age>\n</person>