a very basic Pubmed search API in ruby

LICENSE

Copyright (c) 2012 Heath Anderson

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

pubmed_api.rb

class PubmedApi # a very basic Pubmed API
  require "net/http"
  require "uri"
  require "nokogiri"

  def self.find(ids) # can accept an array of ids or a single id or a string of ids separated by commas
    param = ids.class == Array ? ids.join(",") : ids

    uri = URI.parse("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=#{param}")
    response = Net::HTTP.get_response(uri)

    documents = []

     if response.code_type.to_s == "Net::HTTPOK"

      parsedDoc = Nokogiri::XML(response.body)
      parsedDoc = parsedDoc.css("eSummaryResult DocSum")

      parsedDoc.each do |pd|
        doc = {}
        doc[:title] =pd.css("Item[Name=Title]")[0].text
        doc[:id] = pd.at_css("Item[Name=ArticleIds] Item[Name=pubmed]").text
        doc[:date] =pd.css("Item[Name=PubDate]")[0].text
        doc[:source] =pd.css("Item[Name=FullJournalName]")[0].text
        doc[:url] = "http://www.ncbi.nlm.nih.gov/pubmed/#{doc[:id]}"
        doc[:db] = "pubmed"

        doc[:authors] = []
        pd.css("Item[Name=AuthorList] Item[Name=Author]").each do |author|
          doc[:authors] << author.text
        end

        documents << doc
      end
    end

    documents
  end

  def self.search(terms)
    # see # http://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.Search_Field_Descrip for help with terms

    # A search query can be build by going to http://www.ncbi.nlm.nih.gov/pubmed and then using the filters provided. The search terms can then be copied from the "Search details" section on the right-hand side and used here.
    
    terms = URI.escape(terms, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]")) 
    uri = URI.parse("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=#{terms}")
    response = Net::HTTP.get_response(uri)

    ids = []

     if response.code_type.to_s == "Net::HTTPOK"

        parsedDoc = Nokogiri::XML(response.body)
        parsedDoc = parsedDoc.css("eSearchResult")

        if parsedDoc.at_css("Count").text.to_i > 0
          parsedDoc.css("IdList Id").each do |id|
            ids << id.text
          end
        end
      end
   self.find(ids)
  end

end