Add children to existing node using R XML - r

Question

I have the following XML file test.graphml that I am trying to manipulate using the XML package in R.
<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<graph id="G" edgedefault="directed">
<node id="n0"/>
<node id="n1"/>
<node id="n2"/>
<node id="n3"/>
<node id="n4"/>
<edge source="n0" target="n1"/>
<edge source="n0" target="n2"/>
<edge source="n2" target="n3"/>
<edge source="n1" target="n3"/>
<edge source="n3" target="n4"/>
</graph>
</graphml>
I would like to nest nodes n0, n1, n2, and n3 into a new graph node as shown below.
<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<graph id="G" edgedefault="directed">
<graph id="g1">
<node id="n0"/>
<node id="n1"/>
<node id="n2"/>
<node id="n3"/>
</graph>
<node id="n4"/>
<edge source="n0" target="n1"/>
<edge source="n0" target="n2"/>
<edge source="n2" target="n3"/>
<edge source="n1" target="n3"/>
<edge source="n3" target="n4"/>
</graph>
</graphml>
The code I have written has unknowns and errors that I am unable to resolve due to lack of experience with XML processing. I would greatly appreciate some pointers to that will help me proceed.
library(XML)
# Read file
x <- xmlParse("test.graphml")
ns <- c(graphml ="http://graphml.graphdrawing.org/xmlns")
# Create new graph node
ng <- xmlNode("graph", attrs = c("id" = "g1"))
# Add n0-n3 as children of new graph node
n0_n1_n2_n3 <- getNodeSet(x,"//graphml:node[#id = 'n0' or #id='n1' or #id='n2' or #id='n3']", namespaces = ns)
ng <- append.xmlNode(ng, n0_n1_n2_n3)
# Get only graph node
g <- getNodeSet(x,"//graphml:graph", namespaces = ns)
# Remove nodes n0-n3 from the only graph node
# How I do this?
# This did not work: removeNodes(g, n0_n1_n2_n3)
# Add new graph node as child of only graph node
g <- append.xmlNode(g, ng)
#! Error message:
Error in UseMethod("append") :
no applicable method for 'append' applied to an object of class "XMLNodeSet"

Answer 1

Consider XSLT, the special-purpose language to transform XML files. Since you require modification of the XML (adding parent node in a select group of children) and have to navigate through an undeclared namespace prefix (xmlns="http://graphml.graphdrawing.org/xmlns"), XSLT is an optimal solution.
However, to date R does not have a fully compliant XSL module to run XSLT 1.0 scripts like other general purpose languages (Java, PHP, Python). Nonetheless, R can call external programs (including aforementioned languages), or dedicated XSLT processors (Xalan, Saxon), or call command line interpreters including PowerShell and terminal's xsltproc using system(). Below are latter solutions.
XSLT (save as .xsl, to be referenced in R script)
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
xmlns:doc="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<xsl:output method="xml" omit-xml-declaration="no" indent="yes"/>
<xsl:strip-space elements="*"/>
<xsl:template match="doc:graphml">
<xsl:copy>
<xsl:copy-of select="document('')/*/#xsi:schemaLocation"/>
<xsl:apply-templates select="doc:graph"/>
</xsl:copy>
</xsl:template>
<xsl:template match="doc:graph">
<xsl:element name="{local-name()}" namespace="http://graphml.graphdrawing.org/xmlns">
<xsl:apply-templates select="#*"/>
<xsl:element name="graph" namespace="http://graphml.graphdrawing.org/xmlns">
<xsl:attribute name="id">g1</xsl:attribute>
<xsl:apply-templates select="doc:node[position() < 5]"/>
</xsl:element>
<xsl:apply-templates select="doc:node[#id='n4']|doc:edge"/>
</xsl:element>
</xsl:template>
<xsl:template match="doc:graph/#*">
<xsl:attribute name="{local-name()}"><xsl:value-of select="."/></xsl:attribute>
</xsl:template>
<xsl:template match="doc:node|doc:edge">
<xsl:element name="{local-name()}" namespace="http://graphml.graphdrawing.org/xmlns">
<xsl:attribute name="{local-name(#*)}"><xsl:value-of select="#*"/></xsl:attribute>
</xsl:element>
</xsl:template>
</xsl:stylesheet>
PowerShell script (for Windows PC users, save as XMLTransform.ps1)
param ($xml, $xsl, $output)
if (-not $xml -or -not $xsl -or -not $output) {
Write-Host "& .\xslt.ps1 [-xml] xml-input [-xsl] xsl-input [-output] transform-output"
exit;
}
trap [Exception]{
Write-Host $_.Exception;
}
$xslt = New-Object System.Xml.Xsl.XslCompiledTransform;
$xslt.Load($xsl);
$xslt.Transform($xml, $output);
Write-Host "generated" $output;
R Script (calling command line operations)
library(XML)
# WINDOWS USERS
ps <- '"C:\\Path\\To\\XMLTransform.ps1"' # POWER SHELL SCRIPT
input <- '"C:\\Path\\To\\Input.xml"' # XML SOURCE
xsl <- '"C:\\Path\\To\\XSLTScript.xsl"' # XSLT SCRIPT
output <- '"C:\\Path\\To\\Output.xml"' # BLANK, EMPTY FILE PATH TO BE CREATED
system(paste('Powershell.exe -executionpolicy remotesigned -File',
ps, input, xsl, output)) # NOTE SECURITY BYPASS ARGS
doc <- xmlParse("C:\\Path\\To\\Output.xml")
# UNIX (MAC/LINUX) USERS
system("xsltproc /path/to/XSLTScript.xsl /path/to/input.xml -o /path/to/output.xml")
doc <- xmlParse("/path/to/output.xml")
print(doc)
# <?xml version="1.0" encoding="utf-8"?>
# <graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
# <graph id="G" edgedefault="directed">
# <graph id="g1">
# <node id="n0"/>
# <node id="n1"/>
# <node id="n2"/>
# <node id="n3"/>
# </graph>
# <node id="n4"/>
# <edge source="n0"/>
# <edge source="n0"/>
# <edge source="n2"/>
# <edge source="n1"/>
# <edge source="n3"/>
# </graph>
# </graphml>