use eutils url for pubmed scraping

griffithlab · Jun 20, 2017 · 726dc52 · 726dc52
1 parent fd86310
commit 726dc52
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/lib/scrapers/pub_med.rb b/lib/scrapers/pub_med.rb
@@ -57,7 +57,7 @@ def self.call_pubmed_api(pubmed_id)
 
     private
     def self.url_for_pubmed_id(pubmed_id)
-      "https://www.ncbi.nlm.nih.gov/pubmed/#{pubmed_id}?report=xml&format=text"
+      "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=#{pubmed_id}&retmode=xml"
     end
   end
 end
diff --git a/lib/scrapers/pub_med_response.rb b/lib/scrapers/pub_med_response.rb
@@ -2,7 +2,7 @@ module Scrapers
   class PubMedResponse
     attr_reader :xml
     def initialize(response_body)
-      @xml = Nokogiri::XML(Nokogiri::XML(response_body).text)
+      @xml = Nokogiri::XML(response_body)
     end
 
     def citation