| getNodeSet {XML} | R Documentation |
These functions provide a way to find XML nodes that match a particular criterion. It uses the XPath syntax and allows quite powerful expressions for identifying nodes. The XPath language requires some knowledge, but tutorials are available on the Web and in books. XPath queries can result in different types of values such as numbers, strings, and node sets.
These sets of matching nodes are returned in R as a list. And then one can iterate over these elements to process the nodes in whatever way one wants. Unfortunately, this involves two loops - one in the XPath query over the entire tree, and another in R. Typically, this is fine as the number of matching nodes is reasonably small. However, if repeating this on numerous files, speed may become an issue. We can avoid the second loop (i.e. the one in R) by applying a function to each node before it is returned to R as part of the node set. The result of the function call is then returned, rather than the node itself.
One can provide an expression rather than a function. This is expected to be a call and the first argument of the call will be replaced with the node.
getNodeSet(doc, path, namespaces = getDefaultNamespace(xmlRoot(doc)), fun = NULL, ...) xpathApply(doc, path, fun, ... , namespaces = getDefaultNamespace(xmlRoot(doc)))
doc |
an object of class XMLInternalDocument |
path |
a string (character vector of length 1) giving the XPath expression to evaluate. |
namespaces |
a named character vector giving the namespace prefix and URI pairs that are to be used in the XPath expression and matching of nodes. The prefix is just a simple string that acts as a short-hand or alias for the URI that is the unique identifier for the namespace. The URI is the element in this vector and the prefix is the corresponding element name. One only needs to specify the namespaces in the XPath expression and for the nodes of interest rather than requiring all the namespaces for the entire document. Also note that the prefix used in this vector is local only to the path. It does not have to be the same as the prefix used in the document to identify the namespace. However, the URI in this argument must be identical to the target namespace URI in the document. It is the namespace URIs that are matched (exactly) to find correspondence. The prefixes are used only to refer to that URI. |
fun |
a function object, or an expression or call, which is used when the result is a node set and evaluated for each node element in the node set. If this is a call, the first argument is replaced with the current node. |
... |
any additional arguments to be passed to fun for each node in the node set. |
This calls the libxml routine xmlXPathEval.
The results can currently be different based on the returned value from the XPath expression evaluation:
list |
a node set |
numeric |
a number |
logical |
a boolean |
character |
a string, i.e. a single character element. |
If fun is supplied and the result of the XPath query is a node set,
the result in R is a list.
In order to match nodes in the default name space for
documents with a non-trivial default namespace, e.g. given as
xmlns="http://www.omegahat.org", you will need to use a prefix
for the default namespace in this call.
When specifying the namespaces, give a name - any name - to the
default namespace URI and then use this as the prefix in the
XPath expression, e.g.
getNodeSet(d, "//d:myNode", c(d = "http://www.omegahat.org"))
to match myNode in the default name space
http://www.omegahat.org.
This default namespace of the document is now computed for us and is the default value for the namespaces argument. It can be referenced using the prefix 'd', standing for default but sufficiently short to be easily used within the XPath expression.
More of the XPath functionality provided by libxml can and may be made available to the R package. Facilities such as compiled XPath expressions, functions, ordered node information are examples.
Please send requests to the package maintainer.
Duncan Temple Lang <duncan@wald.ucdavis.edu>
http://xmlsoft.org, http://www.w3.org/xml http://www.w3.org/TR/xpath http://www.omegahat.org/RSXML
xmlTreeParse with useInternalNodes as TRUE.
doc = xmlTreeParse(system.file("exampleData", "tagnames.xml", package = "XML"), useInternalNodes = TRUE)
getNodeSet(doc, "/doc//b[@status]")
getNodeSet(doc, "/doc//b[@status='foo']")
els = getNodeSet(doc, "/doc//a[@status]")
sapply(els, function(el) xmlGetAttr(el, "status"))
# Using a namespace
f = system.file("exampleData", "SOAPNamespaces.xml", package = "XML")
z = xmlTreeParse(f, useInternal = TRUE)
getNodeSet(z, "/a:Envelope/a:Body", c("a" = "http://schemas.xmlsoap.org/soap/envelope/"))
getNodeSet(z, "//a:Body", c("a" = "http://schemas.xmlsoap.org/soap/envelope/"))
# Get two items back with namespaces
f = system.file("exampleData", "gnumeric.xml", package = "XML")
z = xmlTreeParse(f, useInternal = TRUE)
getNodeSet(z, "//gmr:Item/gmr:name", c(gmr="http://www.gnome.org/gnumeric/v2"))
#####
# European Central Bank (ECB) exchange rate data
# Data is available from "http://www.ecb.int/stats/eurofxref/eurofxref-hist.xml"
# or locally.
uri = system.file("exampleData", "eurofxref-hist.xml.gz", package = "XML")
doc = xmlTreeParse(uri, useInternalNodes = TRUE)
# The default namespace for all elements is given by
namespaces <- c(ns="http://www.ecb.int/vocabulary/2002-08-01/eurofxref")
# Get the data for Slovenian currency for all time periods.
# Find all the nodes of the form <Cube currency="SIT"...>
slovenia = getNodeSet(doc, "//ns:Cube[@currency='SIT']", namespaces )
# Now we have a list of such nodes, loop over them
# and get the rate attribute
rates = as.numeric( sapply(slovenia, xmlGetAttr, "rate") )
# Now put the date on each element
# find nodes of the form <Cube time=".." ... >
# and extract the time attribute
names(rates) = sapply(getNodeSet(doc, "//ns:Cube[@time]", namespaces ),
xmlGetAttr, "time")
# Or we could turn these into dates with strptime()
strptime(names(rates), "%Y-%m-%d")
# Using xpathApply, we can do
rates = xpathApply(doc, "//ns:Cube[@currency='SIT']", xmlGetAttr, "rate", namespaces = namespaces )
rates = as.numeric(unlist(rates))
# Using an expression rather than a function and ...
rates = xpathApply(doc, "//ns:Cube[@currency='SIT']", quote(xmlGetAttr(x, "rate")), namespaces = namespaces )
#
uri = system.file("exampleData", "namespaces.xml", package = "XML")
d = xmlTreeParse(uri, useInternalNodes = TRUE)
getNodeSet(d, "//c:c", c(c="http://www.c.org"))
# the following, perhaps unexpectedly but correctly, returns an empty
# with no matches
getNodeSet(d, "//defaultNs", "http://www.omegahat.org")
# But if we create our own prefix for the evaluation of the XPath
# expression and use this in the expression, things work as one
# might hope.
getNodeSet(d, "//dummy:defaultNs", c(dummy = "http://www.omegahat.org"))
# And since the default value for the namespaces argument is the
# default namespace of the document with the prefix 'd', we can use
getNodeSet(d, "//d:defaultNs")
# And the syntactic sugar is
d["//d:defaultNs"]