Error parsing XML document with Ruby's Nokogiri

Question

Using Ruby's Nokogiri library, I want to parse an XML document as follows, extracting from it some elements (like "tsn" or "kingdom"):

<ns:searchByScientificNameResponse xmlns:ns="http://itis_service.itis.usgs.gov">
<ns:return xmlns:ax21="http://data.itis_service.itis.usgs.gov/xsd" xmlns:ax23="http://metadata.itis_service.itis.usgs.gov/xsd" xmlns:ax26="http://itis_service.itis.usgs.gov/xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ax21:SvcScientificNameList">
<ax21:scientificNames xsi:type="ax21:SvcScientificName">
<ax21:tsn>26339</ax21:tsn>
<ax21:author>L.</ax21:author>
<ax21:combinedName>Vicia faba</ax21:combinedName>
<ax21:kingdom>Plantae</ax21:kingdom>
<ax21:unitInd1 xsi:nil="true" />
<ax21:unitInd2 xsi:nil="true" />
<ax21:unitInd3 xsi:nil="true" />
<ax21:unitInd4 xsi:nil="true" />
<ax21:unitName1>Vicia</ax21:unitName1>
<ax21:unitName2>faba</ax21:unitName2>
<ax21:unitName3 xsi:nil="true" />
<ax21:unitName4 xsi:nil="true" />
</ax21:scientificNames>
</ns:return>
</ns:searchByScientificNameResponse>

After opening the document with

doc = Nokogiri::XML(File.open("sample.xml"))

if I use

tsn = doc.at_xpath("//tsn")
puts tsn

I get a nil value, and if I use

tsn = doc.at_xpath("//:tsn")

I get an error: Nokogiri::XML::XPath::SyntaxError (ERROR: Invalid expression: //:tsn)

Could someone out there give me some help?

Answer 1

So the issue is that your XML contains namespaces.

There are 2 options:

1. Remove the namespaces

doc.remove_namespaces! 
doc.at_xpath("//tsn") 
#=> #<Nokogiri::XML::Element:0x2add795ea3b8 name="tsn" children=[#<Nokogiri::XML::Text:0x2add795e5f70 "26339">]>

2. Reference the namespace:

doc.at_xpath("//ax21:tsn", 'ax21' => "http://data.itis_service.itis.usgs.gov/xsd") 
#=> #<Nokogiri::XML::Element:0x2add795ea3b8 name="tsn" children=[#<Nokogiri::XML::Text:0x2add795e5f70 "26339">]>

Based on the comments it seems you are really only interested in the text for that node. You can retrieve that in multiple ways:

doc.at_xpath("//tsn").text()
#=> "26339"
doc.at_xpath("//tsn/text()").to_s
#=> "26339"
# If you want tsn and kingdom at the same time 
doc.xpath('//tsn/text() | //kingdom/text()').map(&:to_s)
#=> ["26339", "Plantae"]

Example

Answer 2

here's what I came up with

require 'nokogiri'

doc = Nokogiri::XML(File.open("sample.xml"))

node_names = []
doc.xpath('//*').each do |node|
    node_names << node.name
end

print node_names
#=>["ns:searchByScientificNameResponse", "ns:return", "ax21:scientificNames", "ax21:tsn", "ax21:author", "ax21:combinedName", "ax21:kingdom", "ax21:unitInd1", "ax21:unitInd2", "ax21:unitInd3", "ax21:unitInd4", "ax21:unitName1", "ax21:unitName2", "ax21:unitName3", "ax21:unitName4"]


node_names.each do |elem|
  if elem == "ax21:kingdom"
    puts elem
  elsif
    elem == ("ax21:tsn")
    puts elem
  end
end
#=>ax21:tsn
#=>ax21:kingdom

Not sure if this is what you want, so I will include link to documentation that gave me this solution: https://gist.github.com/carolineartz/10276637