LIST to data.frame in XML file - r

Question

I am working on XML files and I am trying to transform them into data.frame. However, during the transformation process the file is “LIST”, as seen below:
My Code:
require(tidyverse)
require(xml2)
page<-read_xml('<?xml version="1.0" encoding="ISO-8859-1" ?>
<test2:TASS xmlns="http://www.vvv.com/schemas"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.vvv.com/schemas http://www.vvv.com/schemas/testV2_02_03.xsd"
xmlns:test2="http://www.vvv.com/schemas" >
<test2:billing>
<test2:proceduresummary>
<test2:guidenumber>Z4088</test2:guidenumber>
<test2:diagnosis>
<test2:table>ICD-10</test2:table>
<test2:diagnosiscod>G93</test2:diagnosiscod>
<test2:description>DISORDER OF BRAIN, UNSPECIFIED</test2:description>
</test2:diagnosis>
<test2:procedure>
<test2:procedure>
<test2:description>HOSPITAL</test2:description>
</test2:procedure>
<test2:amount>15</test2:amount>
</test2:procedure>
</test2:proceduresummary>
</test2:billing>
</test2:TASS>')
t1<-if ("test2" %in% names(xml_ns(page))) {
ns<-xml_ns_rename(xml_ns(page), test2 = "test")
} else {
ns<- xml_ns(page)
}
MYFILE<- ifelse(names(xml_ns(page)) %in% "d1",
page %>% xml_find_all(".//d1:billing"),
page %>% xml_find_all(".//test:billing", ns))
MYFILE<-xml2::as_list(MYFILE) %>% jsonlite::toJSON() %>% jsonlite::fromJSON()
My "LIST"
**List of 1
$ :List of 2
..$ node:<externalptr>
..$ doc :<externalptr>
..- attr(*, "class")= chr "xml_node"**
I'm using the code below to transform it, but it's giving an error:
MYFILE <- xml2 :: as_list (MYFILE)%>% jsonlite :: toJSON ()%>% jsonlite :: fromJSON ()
This is the error.
Error in UseMethod("as_list") :
no applicable method for 'as_list' applied to an object of class "list"
How do I turn it into data.frame/tibble?

Answer 1

It looks like the ifelse statement is causing the file to be parsed three times. This is causing a problem. If you need this line try this instead ifelse("d1" %in% names(xml_ns(page)), . . .
This script works on the above sample. If there are more than 1 billing node then part of the below script will need modification. I highlighted that in the comments.
t1<-if ("test2" %in% names(xml_ns(page))) {
ns<-xml_ns_rename(xml_ns(page), test2 = "test")
} else {
ns<- xml_ns(page)
}
MYFILE<- ifelse(names(xml_ns(page)) %in% "d1",
page %>% xml_find_all(".//d1:billing"),
page %>% xml_find_all(".//test:billing", ns))
#To prevent repeating reading the file multiple times
# MYFILE<- if ("d1" %in% names(xml_ns(page))) {
# page %>% xml_find_all(".//d1:billing")
# } else {
# page %>% xml_find_all(".//test:billing", ns)
# }
OUTPUT<-lapply(MYFILE, function(MYFILE){
#convert all of the nodes to named vector
output<-as_list(MYFILE) %>% unlist()
#Shorten the names
names(output) <- gsub("^(.+?\\.)", "", names(output))
#depending on your next steps will determine the disired output
#create a long format dataframe
# long_answer<-data.frame(Name=names(output), output, row.names = NULL)
#create a wide format dataframe
wide_answer<-data.frame( t(output))
})
bind_rows(OUTPUT)