Reading xml data from oracle table column and parsing it in R - r

Question

I have one scenario in R.
I have connected the oracle database with R through RODBC package and in one column of table there is xml data. Now when I am using xmlParse function its showing error as XML content does not seem to be XML. and class(xmldata) is data frame.
When i am copying the xml data and put it into new xml file and parsing though xmlParse function its getting parsed correctly and class(sourcefile) as XMLInternalDocument.

Answer 1

Error is raised because you are running XML::xmlParse on a dataframe object which is the returned value of RODBC::sqlQuery(), and not underlying XML content. Simply index the column and row value for specific XML content.
As example, below reads an XML (top 5 StackOverflow users in R tag) into a dataframe and runs xmlParse to reproduce error and another xmlParse call to resolve error.
Dataframe Build (replicating sqlQuery)
txt <- '<?xml version="1.0"?>
<stackoverflow>
<group lang="r">
<topusers>
<user>akrun</user>
<link>https://stackoverflow.com/users/3732271/akrun</link>
<location>Bengaluru, Karnataka, India</location>
<year_rep>15,900</year_rep>
<total_rep>328,573</total_rep>
<tag1>r</tag1>
<tag2>dataframe</tag2>
<tag3>dplyr</tag3>
</topusers>
<topusers>
<user>Dirk Eddelbuettel</user>
<link>https://stackoverflow.com/users/143305/dirk-eddelbuettel</link>
<location>Chicago, IL, United States </location>
<year_rep>5,588</year_rep>
<total_rep>253,481</total_rep>
<tag1>r</tag1>
<tag2>rcpp</tag2>
<tag3>c++</tag3>
</topusers>
<topusers>
<user>42-</user>
<link>https://stackoverflow.com/users/1855677/42</link>
<location>Alameda, CA</location>
<year_rep>4,143</year_rep>
<total_rep>193,407</total_rep>
<tag1>r</tag1>
<tag2>dataframe</tag2>
<tag3>plot</tag3>
</topusers>
<topusers>
<user>A5C1D2H2I1M1N2O1R2T1</user>
<link>https://stackoverflow.com/users/1270695/a5c1d2h2i1m1n2o1r2t1</link>
<location>Chennai, India</location>
<year_rep>3,982</year_rep>
<total_rep>141,425</total_rep>
<tag1>r</tag1>
<tag2>dataframe</tag2>
<tag3>reshape</tag3>
</topusers>
<topusers>
<user>Gavin Simpson</user>
<link>https://stackoverflow.com/users/429846/gavin-simpson</link>
<location>Regina, Canada </location>
<year_rep>2,780</year_rep>
<total_rep>124,779</total_rep>
<tag1>r</tag1>
<tag2>plot</tag2>
<tag3>dataframe</tag3>
</topusers>
</group>
</stackoverflow>'
res <- data.frame(Col1 = txt)
Error line
result1 <- xmlParse(res, asText=TRUE)
# Error: XML content does not seem to be XML: '1'
Resolved line (which yields no error)
# SINGLE XML
result1 <- xmlParse(res$Col1[[1]], asText=TRUE)
# MULTIPLE XML (ACROSS ALL ROWS)
result_list <- lapply(res$Col1, xmlParse, asText=TRUE)