xmlTreeParse {XML}R Documentation

XML Parser

Description

Parses an XML or HTML file or string, and generates an R structure representing the XML/HTML tree. Use htmlTreeParse when the content is known to be (potentially malformed) HTML.

Usage

xmlTreeParse(file, ignoreBlanks=TRUE, handlers=NULL, replaceEntities=FALSE,
              asText=FALSE, trim=TRUE, validate=FALSE, getDTD=TRUE,
               isURL=FALSE, asTree = FALSE, addAttributeNamespaces = FALSE)
htmlTreeParse(file, ignoreBlanks = TRUE, handlers = NULL,
               replaceEntities = FALSE, asText = FALSE, trim = TRUE,
                isURL = FALSE, asTree = FALSE) 

Arguments

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 isURL. Additionally, the file can be compressed (gzip) and is read directly without the user having to de-compress (gunzip) it.
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. 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, adding or removing nodes, and generally processing them as they are constructed in the C code.
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.
getDTD logical flag indicating whether the DTD (both internal and external) should be returned along with the document nodes. This changes the return type.
isURL indicates whether the file argument refers to a URL (accessible via ftp or http) or a regular file on the system. If asText is TRUE, this should not be specified. The function attempts to determine whether the data source is a URL by using grep to look for http or ftp at the start of the string. The libxml parser handles the connection to servers, not the R facilities (e.g. scan).
asTree this only applies when on passes a value for the handlers argument and is used then to determine whether the DOM tree should be returned or the handlers object.
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 TRUE, an attribute such as xsi:type="xsd:string"

is reported with the name xsi:type. If it is FALSE, the name of the attribute is type.

Details

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 begin{description} item[id] the namespace identifier as used to qualify tag names; item[uri] the value of the namespace identifier, i.e. the URI identifying the namespace. item[local] a logical value indicating whether the definition is local to the document being parsed. end{description}

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.

Value

By default, an object of class XML doc is returned, which contains fields/slots named file, version and children.

file The (expanded) name of the file containing the XML.
version A string identifying the version of XML used by the document.
children A list of the XML nodes at the top of the document. Each of these is of class XMLNode. These are made up of 4 fields.
name
The name of the element.
attributes
For regular elements, a named list of XML attributes converted from the <tag x="1" y="abc">
children
List of sub-nodes.
value
Used only for text entries.
Some nodes specializations of XMLNode, such as XMLComment, XMLProcessingInstruction, XMLEntityRef are used.
If the value of the argument getDTD is TRUE, the return value is a list of length 2. The first element is as the document as described above. The second element is a list containing the external and internal DTDs. Each of these contains 2 lists - one for elements and another for entities. See parseDTD.

Note

Make sure that the necessary 3rd party libraries are available.

Author(s)

Duncan Temple Lang

References

http://xmlsoft.org, http://www.w3.org/xml

See Also

xmlEventParse

Examples

 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="")

 xmlTreeParse(xmlText, 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.org/Scripts/Data/mtcars.xml", asText=TRUE)
## End(Not run)

[Package XML version 0.97-0 Index]