Extract just some fields from XML]

Hi Gregor.

Here is a function that will collect all of the nodes in the
XML document whose names are in the vector elementNames

getElements =
function(elementNames)
{
els = list()

startElement = function(node, ...) {

 if(xmlName(node) %in% elementNames)
    els[[length(els) + 1]] <<- node

  node
}

 list(startElement = startElement, els = function() els)
}

So you can use it as

 myHandlers = getElements("PubDate")
 xmlTreeParse(URL, handlers = myHandlers)

And then
 myHandlers$els()

returns a list of the the three PubDate elements in the document.

If you wanted both PubDate and PubMedPubDate elements,
you could use

 myHandlers = getElements(c("PubDate", "PubMedPubDate")

[Note that XML is case-sensitive and pubdate won't work.]

The xmlEventParse is quite a bit more work as it is for
very low-level parsing, working at the parser level
of opening and closing XML elements.

The xmlTreeParse is a hybrid parser. It works at the higher
level of nodes, but provides an opportunity to process
nodes when they are "created" and before their parent
nodes have been processed.  So it works bottom up
(in one of its modes).

You can also use  xmlDOMApply() to iterate over all the
nodes of a parsed XML tree.  You give xmlDOMApply() a
function and it can do whatever it  wants, including
checking the name of the node to see if you want it
and then storing it somewhere. That's  where you'll
need closures (simply viewed the "functions within functions" part) again,
as in my example above.

But here is a simple example
 doc = xmlRoot(xmlTreeParse(URL))
 xmlDOMApply(doc, function(node, ...)
                     if(xmlName(node) == "PubDate")
                        print(node)
            )

Hello!

I am trying to get specific fields from an XML document and I am totally
puzzled. I hope someone can help me.

# URL
URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation"
# download a XML file
tmp <- xmlTreeParse(URL, isURL = TRUE)
tmp <- xmlRoot(tmp)

Now I want to extract only node 'pubdate' and its children, but I don't
know how to do that unless I try to dig into the structure of the XML
file. The problem is that structure can differ and then hardcoded set
of list indices i.e. tmp[[i]][[j]]... doesn't help me.

I've read xmlEventParse but I don't understand handlers part up to the
point that I could get anything usable from it. Here is something not
very usable ;)

  PubDate <- function(x, ...)
  {
    print(x)
  }
  xmlEventParse(URL, isURL = TRUE,
                handlers=list(PubDate=PubDate),
                addContext = FALSE)

Thanks in advance!

Lep pozdrav / With regards,
    Gregor Gorjanc

----------------------------------------------------------------------
University of Ljubljana
Biotechnical Faculty        URI: http://www.bfro.uni-lj.si/MR/ggorjan
Zootechnical Department     mail: gregor.gorjanc <at> bfro.uni-lj.si
Groblje 3                   tel: +386 (0)1 72 17 861
SI-1230 Domzale             fax: +386 (0)1 72 17 888
Slovenia, Europe
----------------------------------------------------------------------
"One must learn by doing the thing; for though you think you know it,
 you have no certainty until you try." Sophocles ~ 450 B.C.