| xmlTreeParse {XML} | R Documentation |
Parses an XML or HTML file or string containing XML/HTML content, and generates an R
structure representing the XML/HTML tree. Use htmlTreeParse when the content is known
to be (potentially malformed) HTML.
This function has numerous parameters/options and operates quite differently
based on their values.
It can create trees in R or using internal C-level nodes, both of
which are useful in different contexts.
It can perform conversion of the nodes into R objects using
caller-specified handler functions and this can be used to
map the XML document directly into R data structures,
by-passing the conversion to an R-level tree which would then
be processed recursively or with multiple descents to extract the
information of interest.
xmlParse and htmlParse are equivalent to the
xmlTreeParse and htmlTreeParse respectively,
except they both use a default value for the useInternalNodes parameter
of TRUE, i.e. they working with and return internal
nodes/C-level nodes. These can then be searched using
XPath expressions via xpathApply and
getNodeSet.
xmlSchemaParse is a convenience function for parsing an XML schema.
xmlTreeParse(file, ignoreBlanks=TRUE, handlers=NULL, replaceEntities=FALSE,
asText=FALSE, trim=TRUE, validate=FALSE, getDTD=TRUE,
isURL=FALSE, asTree = FALSE, addAttributeNamespaces = FALSE,
useInternalNodes = FALSE, isSchema = FALSE,
fullNamespaceInfo = FALSE, encoding = character(),
useDotNames = length(grep("^\\.", names(handlers))) > 0,
xinclude = TRUE, addFinalizer = TRUE, error = xmlErrorCumulator(),
isHTML = FALSE, options = integer(), parentFirst = FALSE)
xmlInternalTreeParse(file, ignoreBlanks=TRUE, handlers=NULL, replaceEntities=FALSE,
asText=FALSE, trim=TRUE, validate=FALSE, getDTD=TRUE,
isURL=FALSE, asTree = FALSE, addAttributeNamespaces = FALSE,
useInternalNodes = TRUE, isSchema = FALSE,
fullNamespaceInfo = FALSE, encoding = character(),
useDotNames = length(grep("^\\.", names(handlers))) > 0,
xinclude = TRUE, addFinalizer = TRUE, error = xmlErrorCumulator(),
isHTML = FALSE, options = integer(), parentFirst = FALSE)
xmlNativeTreeParse(file, ignoreBlanks=TRUE, handlers=NULL, replaceEntities=FALSE,
asText=FALSE, trim=TRUE, validate=FALSE, getDTD=TRUE,
isURL=FALSE, asTree = FALSE, addAttributeNamespaces = FALSE,
useInternalNodes = TRUE, isSchema = FALSE,
fullNamespaceInfo = FALSE, encoding = character(),
useDotNames = length(grep("^\\.", names(handlers))) > 0,
xinclude = TRUE, addFinalizer = TRUE, error = xmlErrorCumulator(),
isHTML = FALSE, options = integer(), parentFirst = FALSE)
htmlTreeParse(file, ignoreBlanks=TRUE, handlers=NULL, replaceEntities=FALSE,
asText=FALSE, trim=TRUE, validate=FALSE, getDTD=TRUE,
isURL=FALSE, asTree = FALSE, addAttributeNamespaces = FALSE,
useInternalNodes = FALSE, isSchema = FALSE,
fullNamespaceInfo = FALSE, encoding = character(),
useDotNames = length(grep("^\\.", names(handlers))) > 0,
xinclude = TRUE, addFinalizer = TRUE, error = htmlErrorHandler,
isHTML = TRUE, options = integer(), parentFirst = FALSE)
htmlParse(file, ignoreBlanks = TRUE, handlers = NULL, replaceEntities = FALSE,
asText = FALSE, trim = TRUE, validate = FALSE, getDTD = TRUE,
isURL = FALSE, asTree = FALSE, addAttributeNamespaces = FALSE,
useInternalNodes = TRUE, isSchema = FALSE, fullNamespaceInfo = FALSE,
encoding = character(),
useDotNames = length(grep("^\\.", names(handlers))) > 0,
xinclude = TRUE, addFinalizer = TRUE,
error = htmlErrorHandler, isHTML = TRUE,
options = integer(), parentFirst = FALSE)
xmlSchemaParse(file, asText = FALSE, xinclude = TRUE, error = xmlErrorCumulator())
file |
The name of the file containing the XML contents.
This can contain \~ which is expanded to the user's
home directory.
It can also be a URL. See |
ignoreBlanks |
logical value indicating whether text elements made up entirely of white space should be included in the resulting ‘tree’. |
handlers |
Optional collection of functions used to map the different XML nodes to R objects. Typically, this is a named list of functions, and a closure can be used to provide local data. This provides a way of filtering the tree as it is being created in R, adding or removing nodes, and generally processing them as they are constructed in the C code. In a recent addition to the package (version 0.99-8), if this is specified as a single function object, we call that function for each node (of any type) in the underlying DOM tree. It is invoked with the new node and its parent node. This applies to regular nodes and also comments, processing instructions, CDATA nodes, etc. So this function must be sufficiently general to handle them all. |
replaceEntities |
logical value indicating whether to substitute entity references with their text directly. This should be left as False. The text still appears as the value of the node, but there is more information about its source, allowing the parse to be reversed with full reference information. |
asText |
logical value indicating that the first argument, ‘file’, should be treated as the XML text to parse, not the name of a file. This allows the contents of documents to be retrieved from different sources (e.g. HTTP servers, XML-RPC, etc.) and still use this parser. |
trim |
whether to strip white space from the beginning and end of text strings. |
validate |
logical indicating whether to use a validating parser or not, or in other words check the contents against the DTD specification. If this is true, warning messages will be displayed about errors in the DTD and/or document, but the parsing will proceed except for the presence of terminal errors. This is ignored when parsing an HTML document. |
getDTD |
logical flag indicating whether the DTD (both internal and external) should be returned along with the document nodes. This changes the return type. This is ignored when parsing an HTML document. |
isURL |
indicates whether the |
asTree |
this only applies when on passes a value for
the |
addAttributeNamespaces |
a logical value indicating whether to
return the namespace in the names of the attributes within a node
or to omit them. If this is |
useInternalNodes |
a logical value indicating whether
to call the converter functions with objects of class
If this argument is This is ignored when parsing an HTML document. |
isSchema |
a logical value indicating whether the document
is an XML schema ( |
fullNamespaceInfo |
a logical value indicating whether
to provide the namespace URI and prefix on each node
or just the prefix. The latter ( This is ignored when parsing an HTML document. |
encoding |
a character string (scalar) giving the encoding for the document. This is optional as the document should contain its own encoding information. However, if it doesn't, the caller can specify this for the parser. If the XML/HTML document does specify its own encoding that value is used regardless of any value specified by the caller. (That's just the way it goes!) So this is to be used as a safety net in case the document does not have an encoding and the caller happens to know theactual encoding. |
useDotNames |
a logical value
indicating whether to use the
newer format for identifying general element function handlers
with the '.' prefix, e.g. .text, .comment, .startElement.
If this is |
xinclude |
a logical value indicating whether
to process nodes of the form |
addFinalizer |
a logical value indicating whether the
default finalizer routine should be registered to
free the internal xmlDoc when R no longer has a reference to this
external pointer object. This is only relevant when
|
error |
a function that is invoked when the XML parser reports
an error.
When an error is encountered, this is called with 7 arguments.
See If parsing completes and no document is generated, this function is called again with only argument which is a character vector of length 0. This gives the function an opportunity to report all the errors and raise an exception rather than doing this when it sees th first one. This function can do what it likes with the information. It can raise an R error or let parser continue and potentially find further errors. The default value of this argument supplies a function that cumulates the errors If this is |
isHTML |
a logical value that allows this function to be used for parsing HTML documents.
This causes validation and processing of a DTD to be turned off.
This is currently experimental so that we can implement
|
options |
an integer value or vector of values that are combined
(OR'ed) together
to specify options for the XML parser. This is the same as the
|
parentFirst |
a logical value for use when we have handler functions and are traversing the tree. This controls whether we process the node before processing its children, or process the children before their parent node. |
The handlers argument is used similarly
to those specified in xmlEventParse.
When an XML tag (element) is processed,
we look for a function in this collection
with the same name as the tag's name.
If this is not found, we look for one named
startElement. If this is not found, we use the default
built in converter.
The same works for comments, entity references, cdata, processing instructions,
etc.
The default entries should be named
comment, startElement,
externalEntity,
processingInstruction,
text, cdata and namespace.
All but the last should take the XMLnode as their first argument.
In the future, other information may be passed via ...,
for example, the depth in the tree, etc.
Specifically, the second argument will be the parent node into which they
are being added, but this is not currently implemented,
so should have a default value (NULL).
The namespace function is called with a single argument which
is an object of class XMLNameSpace. This contains
the namespace identifier as used to qualify tag names;
the value of the namespace identifier, i.e. the URI identifying the namespace.
a logical value indicating whether the definition is local to the document being parsed.
One should note that the namespace handler is called before the
node in which the namespace definition occurs and its children are
processed. This is different than the other handlers which are called
after the child nodes have been processed.
Each of these functions can return arbitrary values that are then
entered into the tree in place of the default node passed to the
function as the first argument. This allows the caller to generate
the nodes of the resulting document tree exactly as they wish. If the
function returns NULL, the node is dropped from the resulting
tree. This is a convenient way to discard nodes having processed their
contents.
By default ( when useInternalNodes is FALSE,
getDTD is TRUE, and no
handler functions are provided), the return value is, an object of
(S3) class XMLDocument.
This has two fields named doc and dtd
and are of class DTDList and XMLDocumentContent respectively.
If getDTD is FALSE, only the doc object is returned.
The doc object has three fields of its own:
file, version and children.
|
The (expanded) name of the file containing the XML. |
|
A string identifying the version of XML used by the document. |
|
A list of the XML nodes at the top of the document.
Each of these is of class
Some nodes specializations of If the value of the argument getDTD is TRUE and the document refers
to a DTD via a top-level DOCTYPE element, the DTD and its information
will be available in the If a list of functions is given via If If If internal nodes are used and the internal tree returned directly,
all the nodes are returned as-is and no attempt to
trim white space, remove “empty” nodes (i.e. containing only white
space), etc. is done. This is potentially quite expensive and so is
not done generally, but should be done during the processing
of the nodes. When using XPath queries, such nodes are easily
identified and/or ignored and so do not cause any difficulties.
They do become an issue when dealing with a node's chidren
directly and so one can use simple filtering techniques such as
|
Make sure that the necessary 3rd party libraries are available.
Duncan Temple Lang <duncan@wald.ucdavis.edu>
http://xmlsoft.org, http://www.w3.org/xml
xmlEventParse,
free for releasing the memory when
an XMLInternalDocument object is returned.
fileName <- system.file("exampleData", "test.xml", package="XML")
# parse the document and return it in its standard format.
xmlTreeParse(fileName)
# parse the document, discarding comments.
xmlTreeParse(fileName, handlers=list("comment"=function(x,...){NULL}), asTree = TRUE)
# print the entities
invisible(xmlTreeParse(fileName,
handlers=list(entity=function(x) {
cat("In entity",x$name, x$value,"\n")
x}
), asTree = TRUE
)
)
# Parse some XML text.
# Read the text from the file
xmlText <- paste(readLines(fileName), "\n", collapse="")
print(xmlText)
xmlTreeParse(xmlText, asText=TRUE)
# with version 1.4.2 we can pass the contents of an XML
# stream without pasting them.
xmlTreeParse(readLines(fileName), asText=TRUE)
# Read a MathML document and convert each node
# so that the primary class is
# <name of tag>MathML
# so that we can use method dispatching when processing
# it rather than conditional statements on the tag name.
# See plotMathML() in examples/.
fileName <- system.file("exampleData", "mathml.xml",package="XML")
m <- xmlTreeParse(fileName,
handlers=list(
startElement = function(node){
cname <- paste(xmlName(node),"MathML", sep="",collapse="")
class(node) <- c(cname, class(node));
node
}))
# In this example, we extract _just_ the names of the
# variables in the mtcars.xml file.
# The names are the contents of the <variable>
# tags. We discard all other tags by returning NULL
# from the startElement handler.
#
# We cumulate the names of variables in a character
# vector named `vars'.
# We define this within a closure and define the
# variable function within that closure so that it
# will be invoked when the parser encounters a <variable>
# tag.
# This is called with 2 arguments: the XMLNode object (containing
# its children) and the list of attributes.
# We get the variable name via call to xmlValue().
# Note that we define the closure function in the call and then
# create an instance of it by calling it directly as
# (function() {...})()
# Note that we can get the names by parsing
# in the usual manner and the entire document and then executing
# xmlSApply(xmlRoot(doc)[[1]], function(x) xmlValue(x[[1]]))
# which is simpler but is more costly in terms of memory.
fileName <- system.file("exampleData", "mtcars.xml", package="XML")
doc <- xmlTreeParse(fileName, handlers = (function() {
vars <- character(0) ;
list(variable=function(x, attrs) {
vars <<- c(vars, xmlValue(x[[1]]));
NULL},
startElement=function(x,attr){
NULL
},
names = function() {
vars
}
)
})()
)
# Here we just print the variable names to the console
# with a special handler.
doc <- xmlTreeParse(fileName, handlers = list(
variable=function(x, attrs) {
print(xmlValue(x[[1]])); TRUE
}), asTree=TRUE)
# This should raise an error.
try(xmlTreeParse(
system.file("exampleData", "TestInvalid.xml", package="XML"),
validate=TRUE))
## Not run:
# Parse an XML document directly from a URL.
# Requires Internet access.
xmlTreeParse("http://www.omegahat.net/Scripts/Data/mtcars.xml", asText=TRUE)
## End(Not run)
counter = function() {
counts = integer(0)
list(startElement = function(node) {
name = xmlName(node)
if(name %in% names(counts))
counts[name] <<- counts[name] + 1
else
counts[name] <<- 1
},
counts = function() counts)
}
h = counter()
xmlParse(system.file("exampleData", "mtcars.xml", package="XML"), handlers = h)
h$counts()
f = system.file("examples", "index.html", package = "XML")
htmlTreeParse(readLines(f), asText = TRUE)
htmlTreeParse(readLines(f))
# Same as
htmlTreeParse(paste(readLines(f), collapse = "\n"), asText = TRUE)
getLinks = function() {
links = character()
list(a = function(node, ...) {
links <<- c(links, xmlGetAttr(node, "href"))
node
},
links = function()links)
}
h1 = getLinks()
htmlTreeParse(system.file("examples", "index.html", package = "XML"),
handlers = h1)
h1$links()
h2 = getLinks()
htmlTreeParse(system.file("examples", "index.html", package = "XML"),
handlers = h2, useInternalNodes = TRUE)
all(h1$links() == h2$links())
# Using flat trees
tt = xmlHashTree()
f = system.file("exampleData", "mtcars.xml", package="XML")
xmlTreeParse(f, handlers = list(.startElement = tt[[".addNode"]]))
xmlRoot(tt)
doc = xmlTreeParse(f, useInternalNodes = TRUE)
sapply(getNodeSet(doc, "//variable"), xmlValue)
#free(doc)
# character set encoding for HTML
f = system.file("exampleData", "9003.html", package = "XML")
# we specify the encoding
d = htmlTreeParse(f, encoding = "UTF-8")
# get a different result if we do not specify any encoding
d.no = htmlTreeParse(f)
# document with its encoding in the HEAD of the document.
d.self = htmlTreeParse(system.file("exampleData", "9003-en.html",package = "XML"))
# XXX want to do a test here to see the similarities between d and
# d.self and differences between d.no
# include
f = system.file("exampleData", "nodes1.xml", package = "XML")
xmlRoot(xmlTreeParse(f, xinclude = FALSE))
xmlRoot(xmlTreeParse(f, xinclude = TRUE))
f = system.file("exampleData", "nodes2.xml", package = "XML")
xmlRoot(xmlTreeParse(f, xinclude = TRUE))
# Errors
try(xmlTreeParse("<doc><a> & < <?pi > </doc>"))
# catch the error by type.
tryCatch(xmlTreeParse("<doc><a> & < <?pi > </doc>"),
"XMLParserErrorList" = function(e) {
cat("Errors in XML document\n", e$message, "\n")
})
# terminate on first error
try(xmlTreeParse("<doc><a> & < <?pi > </doc>", error = NULL))
# see xmlErrorCumulator in the XML package
f = system.file("exampleData", "book.xml", package = "XML")
doc.trim = xmlInternalTreeParse(f, trim = TRUE)
doc = xmlInternalTreeParse(f, trim = FALSE)
xmlSApply(xmlRoot(doc.trim), class)
# note the additional XMLInternalTextNode objects
xmlSApply(xmlRoot(doc), class)
top = xmlRoot(doc)
textNodes = xmlSApply(top, inherits, "XMLInternalTextNode")
sapply(xmlChildren(top)[textNodes], xmlValue)
# Storing nodes
f = system.file("exampleData", "book.xml", package = "XML")
titles = list()
xmlTreeParse(f, handlers = list(title = function(x)
titles[[length(titles) + 1]] <<- x))
sapply(titles, xmlValue)
rm(titles)