Parse XML Files (>1 megabyte) in R

问题

Currently I have ~20,000 XML files that range in size from a couple of KB to a few MB. Although it may not be ideal, I am using the "xmlTreeParse" function in the XML package to loop through each of the files and extract the text that I need and save the document as a csv file.

The code below works fine for files <1 MB in size:

files <- list.files()
for (i in files) {
    doc <- xmlTreeParse(i, useInternalNodes = TRUE)
    root <- xmlRoot(doc)

    name <- xmlValue(root[[8]][[1]][[1]]) # Name
    data <- xmlValue(root[[8]][[1]]) # Full text

    x <- data.frame(c(name))
    x$data <- data

    write.csv(x, paste(i, ".csv"), row.names=FALSE, na="")
}

The trouble is that any file >1 MB gives me the following error:

Excessive depth in document: 256 use XML_PARSE_HUGE option
Extra content at the end of the document
Error: 1: Excessive depth in document: 256 use XML_PARSE_HUGE option
2: Extra content at the end of the document

Please forgive my ignorance, however I have tried searching for the "XML_PARSE_HUGE" function in the XML package and can't seem to find it. Has anyone had any experience using this function? If so, I would greatly appreciate any advice as to how to get this code to handle slightly larger XML files.

Thanks!

回答1:

To choose "XML_PARSE_HUGE" you need to stipulate it in the options. XML:::parserOptions lists the option choices:

> XML:::parserOptions
   RECOVER      NOENT    DTDLOAD    DTDATTR   DTDVALID    NOERROR  NOWARNING 
         1          2          4          8         16         32         64 
  PEDANTIC   NOBLANKS       SAX1   XINCLUDE      NONET     NODICT    NSCLEAN 
       128        256        512       1024       2048       4096       8192 
   NOCDATA NOXINCNODE    COMPACT      OLD10  NOBASEFIX       HUGE     OLDSAX 
     16384      32768      65536     131072     262144     524288    1048576

for example

> HUGE
[1] 524288

It is suffiecient to declare a vector of integers with any of these options. In your case

xmlTreeParse(i, useInternalNodes = TRUE, options = HUGE)

来源：https://stackoverflow.com/questions/17154308/parse-xml-files-1-megabyte-in-r

标签

xml

xml-parsing