Class: Jekyll::Jekyll_Pubmed

Inherits:
Generator
  • Object
show all
Defined in:
lib/jekyll-pubmed.rb

Instance Method Summary collapse

Instance Method Details

#generate(site) ⇒ Object 



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# File 'lib/jekyll-pubmed.rb', line 16

def generate(site)
  config = site.config['jekyll_pubmed']
  if !config
    return
  end
  if !config.kind_of?(Array)
    config = [config]
  end
  config.each do |d|
    begin
      target = site.data[d['data']]
      search_term = URI.escape(d['term'])          
      file_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=#{search_term}&format=json"
      source = JSON.load(open(file_url))
      if target
        HashJoiner.deep_merge target, source
      else
        site.data[d['data']] = source
      end
      if d['data'] == "publications"
        pub_ids = source["esearchresult"]["idlist"]
        #site.data["abstracts"] = @pub_ids
        id_var = pub_ids.join(",")
        esummary_url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=#{id_var}&retmode=xml"
        #doc = Nokogiri::XML(open(esummary_url))
        doc = Crack::XML.parse(open(esummary_url))
        site.data["abstracts"] = make_pubmed_json(doc)
        #.PubmedArticle.MedlineCitation.Article.Journal.JournalIssue.PubDate.Year
      end
      if d['cache']
        data_source = (site.config['data_source'] || '_data')
        path = "#{data_source}/#{d['data']}.json"
        open(path, 'wb') do |file|
          file << JSON.generate(site.data[d['data']])
        end
      end
    rescue
      next
    end
  end
end

#make_pubmed_json(doc) ⇒ Object 



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# File 'lib/jekyll-pubmed.rb', line 57

def make_pubmed_json(doc)
  h = Hash.new
  sorted_pmid = Hash.new
  years = Array.new
  #puts "Hello World #{doc}"
  doc["PubmedArticleSet"].each do |key,array|
    puts "#{key}---"
    array.each do |array2|
      year = array2["MedlineCitation"]["Article"]["Journal"]["JournalIssue"]["PubDate"]["Year"]
      month = array2["MedlineCitation"]["Article"]["Journal"]["JournalIssue"]["PubDate"]["Month"]
      date = array2["MedlineCitation"]["Article"]["Journal"]["JournalIssue"]["PubDate"]["Day"]
      pub_date = Time.new(year,month,date)

      pmid = array2["MedlineCitation"]["PMID"]
      authors = Array.new
      array2["MedlineCitation"]["Article"]["AuthorList"]["Author"].each do |author|
        authors = authors << author["LastName"] + " " + author["Initials"]
      end

      journal = array2["MedlineCitation"]["Article"]["Journal"]["ISOAbbreviation"]

      aritcle_title = array2["MedlineCitation"]["Article"]["ArticleTitle"]
      article_abstract = array2["MedlineCitation"]["Article"]["Abstract"]["AbstractText"]
      #puts article_abstract

      #tmp_record[pmid] = Hash.new

      tmp_record = {"pub_date" => pub_date, "authors" => authors, "journal" => journal, "title"=>aritcle_title, "abstract"=>article_abstract}
      sorted_pmid[pub_date] = pmid
      h["#{pmid}"] = tmp_record
      years = years << year
     #pp tmp_record
    end
  end
  sorted_pmid =  sorted_pmid.sort.reverse.to_h
  sorted_years = years.uniq.sort.reverse.to_a
  #return doc["PubmedArticleSet"]
  out_hash =  {"pmids" => sorted_pmid, "articles" => h, "years" => sorted_years}
  #pp out_hash
  return out_hash
end