以下代码用于解析XML，以便将节点，父级，类型等信息提取到数据框中。它适用于小行的XML文件，但是当使用大于25,000行的文件时，需要几分钟的时间来处理。因此，我打算优化代码以便更快地处理。该函数的目的是读取任何XML文件并根据数据框的要求生成数据。
示例XML：
<?xml version="1.0" encoding="UTF-8"?>
<CATALOG>
<PLANT id="1" required="false">
<COMMON Source="NLM">Bloodroot</COMMON>
<BOTANICAL>Aquilegia canadensis</BOTANICAL>
<DATE>
<Year>2013</Year>
</DATE>
</PLANT>
<PLANT id="2" required="true">
<COMMON Source="LNP">Columbine</COMMON>
<BOTANICAL>Aquilegia canadensis</BOTANICAL>
<DATE>
<Year>2014</Year>
</DATE>
</PLANT>
</CATALOG>
输出：
path node value parent type
1 CATALOG CATALOG NULL NULL element
2 CATALOG/PLANT PLANT NULL CATALOG element
3 CATALOG/PLANT id 1 PLANT attribute
4 CATALOG/PLANT required false PLANT attribute
5 CATALOG/PLANT/COMMON COMMON Bloodroot PLANT text
6 CATALOG/PLANT/COMMON Source NLM COMMON attribute
7 CATALOG/PLANT/BOTANICAL BOTANICAL Aquilegia canadensis PLANT text
8 CATALOG/PLANT/DATE DATE NULL PLANT element
9 CATALOG/PLANT/DATE/Year Year 2013 DATE text
10 CATALOG/PLANT PLANT NULL CATALOG element
11 CATALOG/PLANT id 2 PLANT attribute
12 CATALOG/PLANT required true PLANT attribute
13 CATALOG/PLANT/COMMON COMMON Columbine PLANT text
14 CATALOG/PLANT/COMMON Source LNP COMMON attribute
15 CATALOG/PLANT/BOTANICAL BOTANICAL Aquilegia canadensis PLANT text
16 CATALOG/PLANT/DATE DATE NULL PLANT element
17 CATALOG/PLANT/DATE/Year Year 2014 DATE text
代码段：
library(XML)
library(plyr)
## helper function of xPathApply
getValues <- function(x) {
List <- list()
# find all ancestors of a given node
ancestorNames <- character()
ancestorNamesList <- xmlAncestors(x, fun = function(y) {
ancestorNames <- c(ancestorNames, xmlName(y))})
pathName <- paste(ancestorNamesList, collapse = "/")
# find the parent of a given node
parentNode <- xmlParent(x)
parentName <- "NULL"
if(!is.null(parentNode)) {
parentName <- xmlName(parentNode)
}
if(inherits(x, "XMLInternalElementNode")) {
# check if the value of the given node exists i.e. text
if(length(xmlValue(x, recursive=FALSE)) != 0) {
List <- append(List, list(path = pathName, node = xmlName(x), value = xmlValue(x, recursive=FALSE), parent = parentName, type = "text"))
} else {
List <- append(List, list(path = pathName, node = xmlName(x), value = "NULL", parent = parentName, type = "element"))
}
}
## attributes
if(!is.null(xmlAttrs(x))) {
num.attributes = xmlSize(xmlAttrs(x))
for (i in seq_len(num.attributes)) {
# get the attribute name
attributeName <- names(xmlAttrs(x)[i])
# get the attribute value
attributeValue <- xmlAttrs(x)[[i]]
List <- append(List, list(path = pathName, node = attributeName, value = attributeValue, parent = parentName, type = "attribute"))
}
}
return(List)
}
## recursive function
visitNode <- function(node, xpath) {
if (is.null(node)) {
return()
}
# number of children of a node
num.children <- xmlSize(node)
bypass <- function(n = num.children) {
if(num.children == 0) {
xpathSApply(node, path = xpath, getValues)
} else {
return(num.children)
}
}
# recursive call to visitNode
for (i in seq_len(num.children)) {
visitNode(node[[i]], xpath)
}
# add list type result to data frame
if(is.list(result <- bypass())) {
dt <<- do.call(rbind.fill, lapply(result, data.frame))
}
}
# read XML data from the given file
xtree <- xmlParse("test.xml")
# retrieve the root of the XML
root <- xmlRoot(xtree)
# define data frame which is to hold the data interpreted from XML
dt <- data.frame(path = NA, node = NA, value = NA, parent = NA, type = NA)
# call to recursive function
visitNode(root, xpath <- "//node()")
dt
答案 0 :(得分：4)
我真的希望有很好的XSLT支持，但我似乎无法找到一个很棒的软件包。另一种策略是将xml转换为更简单的数据文件，您可以使用read.table或其他内容轻松阅读。您可以使用xmlEventParse轻松传递它。这是一个自定义处理程序，似乎可以创建您想要的数据
getHandler<-function(file="", sep=",") {
list(.startDocument = function(.state) {
cat("path","node","value","parent","type", file=file, sep=sep)
cat("\n", file=file, sep=sep, append=T)
.state
}, .startElement=function(name, atts, .state) {
.state$path <- c(.state$path, name)
cat(paste(.state$path, collapse="/"), name, NA, .state$path[length(.state$path)-1], "element", sep=sep, file=file, append=T)
cat("\n", file=file, append=T)
if(!is.null(atts)) {
cat(paste(paste(.state$path, collapse="/"), names(atts), atts, .state$path[length(.state$path)-1], "attribute", sep=sep, collapse="\n"), file=file, append=T)
cat("\n",file=file, append=T)
}
.state
}, .endElement=function(name, .state) {
.state$path <- .state$path[-length(.state$path)]
.state
}, .text=function(value, .state) {
value <- gsub("^\\s+|\\s+$", "", value)
if(nchar(value)>0) {
cat(paste(.state$path, collapse="/"), .state$path[length(.state$path)], value, .state$path[length(.state$path)-1], "text", sep=sep, file=file, append=T)
cat("\n", file=file, append=T)
}
.state
})
}
所以它并不完全漂亮，但它基本上只是用cat()构建一个字符串。然后我们可以将它与
zz <- xmlEventParse("test.xml",
handlers = getHandler(),
state = list(path=character(0)), useDotNames=TRUE)
这将以逗号分隔值的数据输出到屏幕。要保存到文件，您可以执行
zz <- xmlEventParse("test.xml",
handlers = getHandler(file="ok.txt", sep="\t"),
state = list(path=character(0)), useDotNames=TRUE)
将数据分隔为名为＆＃34; ok.txt＆＃34;的文件。然后，您可以使用
读取数据read.table("ok.txt", sep="\t", header=T)
返回
path node value parent type
1 CATALOG CATALOG <NA> element
2 CATALOG/PLANT PLANT <NA> CATALOG element
3 CATALOG/PLANT id 1 CATALOG attribute
4 CATALOG/PLANT required false CATALOG attribute
5 CATALOG/PLANT/COMMON COMMON <NA> PLANT element
6 CATALOG/PLANT/COMMON Source NLM PLANT attribute
7 CATALOG/PLANT/COMMON COMMON Bloodroot PLANT text
8 CATALOG/PLANT/BOTANICAL BOTANICAL <NA> PLANT element
9 CATALOG/PLANT/BOTANICAL BOTANICAL Aquilegia canadensis PLANT text
10 CATALOG/PLANT/DATE DATE <NA> PLANT element
11 CATALOG/PLANT/DATE/Year Year <NA> DATE element
12 CATALOG/PLANT/DATE/Year Year 2013 DATE text
13 CATALOG/PLANT PLANT <NA> CATALOG element
14 CATALOG/PLANT id 2 CATALOG attribute
15 CATALOG/PLANT required true CATALOG attribute
16 CATALOG/PLANT/COMMON COMMON <NA> PLANT element
17 CATALOG/PLANT/COMMON Source LNP PLANT attribute
18 CATALOG/PLANT/COMMON COMMON Columbine PLANT text
19 CATALOG/PLANT/BOTANICAL BOTANICAL <NA> PLANT element
20 CATALOG/PLANT/BOTANICAL BOTANICAL Aquilegia canadensis PLANT text
21 CATALOG/PLANT/DATE DATE <NA> PLANT element
22 CATALOG/PLANT/DATE/Year Year <NA> DATE element
23 CATALOG/PLANT/DATE/Year Year 2014 DATE text
现在您的样本中有更多行，但有些选择规则对我来说并不清楚。
主要思想是xmlEventParse比xmlParse更有效，因为它不必加载整个树。此外，通过使用cat()转储到文件，我不必立即担心内存管理（但它并不完全像写入磁盘一样好。）
无论如何，它至少是另一个需要考虑的选择。