Class: Pubmed

Inherits:
Service show all
Includes:
MetadataHelper
Defined in:
app/service_adaptors/pubmed.rb

Overview

Looks up pmid from NLM api, and enhances referent with citation data.

If you use SFX, you prob don’t need/want this, as SFX does this already.

Constant Summary

Constants inherited from Service

Service::LinkOutFilterTask, Service::StandardTask

Instance Attribute Summary

Attributes inherited from Service

#group, #name, #priority, #request, #service_id, #status, #task, #url

Instance Method Summary collapse

Methods included from MetadataHelper

#get_doi, #get_epage, #get_gpo_item_nums, #get_identifier, #get_isbn, #get_issn, #get_lccn, #get_month, #get_oclcnum, #get_pmid, #get_search_creator, #get_search_terms, #get_search_title, #get_spage, #get_sudoc, #get_top_level_creator, #get_year, #normalize_lccn, #normalize_title, #raw_search_title, title_is_serial?

Methods included from MarcHelper

#add_856_links, #edition_statement, #get_title, #get_years, #gmd_values, #service_type_for_856, #should_skip_856_link?, #strip_gmd

Methods inherited from Service

#credits, #display_name, #handle_wrapper, #link_out_filter, #preempted_by, required_config_params, #response_url, #translate

Constructor Details

#initialize(config) ⇒ Pubmed

Returns a new instance of Pubmed.



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# File 'app/service_adaptors/pubmed.rb', line 11

def initialize(config)
  @display_name = "PubMed"
  @url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
  super(config)
end

Instance Method Details

#enhance_referent(body, request) ⇒ Object

Pull everything useful out of the Pubmed record



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# File 'app/service_adaptors/pubmed.rb', line 45

def enhance_referent(body, request)   
  doc = Nokogiri::XML(body)
  return unless cite = doc.at("PubmedArticleSet/PubmedArticle/MedlineCitation") # Nothing of interest here
  
  return unless article = cite.at("Article") # No more useful metadata   
  if abstract = article.at("Abstract/AbstractText")
    request.add_service_response(        
    :service=>self,
    :display_text => "Abstract from #{@display_name}",
    :content => abstract.inner_text,
    :service_type_value => 'abstract') unless abstract.inner_text.blank?      
  end
  
  if journal = article.at("Journal")
    if issn = journal.at('ISSN')
      if issn.attributes['issntype']=="Print"                  
        request.referent.enhance_referent('issn', issn.inner_html)
      else 
        request.referent.enhance_referent('eissn', issn.inner_html)        
      end
    end
    if jrnlissue = journal.at('JournalIssue')
      if volume = jrnlissue.at('Volume')
        request.referent.enhance_referent('volume', volume.inner_text)
      end
      if issue = jrnlissue.at('Issue')
        request.referent.enhance_referent('issue', issue.inner_text)
      end   
      if date = jrnlissue.at('PubDate')    
        
        request.referent.enhance_referent('date', openurl_date(date))
        
      end              
    end
    
    if jtitle = journal.at('Title')
      request.referent.enhance_referent('jtitle', jtitle.inner_text)          
    end
    if stitle = journal.at('ISOAbbreviation')
      request.referent.enhance_referent('stitle', stitle.inner_text)
    end       
    
    if atitle = article.at('ArticleTitle')
      request.referent.enhance_referent('atitle', atitle.inner_text)
    end   
    
    if pages = article.at('Pagination/MedlinePgn')
      page_str = pages.inner_text
      request.referent.enhance_referent('pages', page_str)
      if spage = page_str.split("-")[0]
        request.referent.enhance_referent('spage', spage.strip)
      end
    end                
    
    if author = article.at('AuthorList/Author')
      if last_name = author.at('LastName')
        request.referent.enhance_referent('aulast', last_name.inner_text)
      end
      if first_name = author.at('ForeName')
        request.referent.enhance_referent('aufirst', first_name.inner_text)
      end          
      if initials = author.at('Initials')
        request.referent.enhance_referent('auinit', initials.inner_text)
      end          
    end              
  end      

end

#fetch_record(pmid) ⇒ Object

Do the request. Takes the PMID as inputs



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# File 'app/service_adaptors/pubmed.rb', line 33

def fetch_record(pmid)  
  pmid_url = self.url + "?db=pubmed&retmode=xml&rettype=full&id="+pmid
  begin
    response = Net::HTTP.get_response(URI.parse(pmid_url))
  rescue
    return false
  end
  return false if response.body.match("<ERROR>Empty id list - nothing todo</ERROR>")
  return response.body
end

#handle(request) ⇒ Object 



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# File 'app/service_adaptors/pubmed.rb', line 17

def handle(request)
  return request.dispatched(self, true) unless pmid = get_pmid(request.referent)
      
  return request.dispatched(self, false) unless response = self.fetch_record(pmid)
  
  self.enhance_referent(response, request)
  
  return request.dispatched(self, true)    
end

#openurl_date(date_xml) ⇒ Object

input a PubMed <PubDate> element, return a string usable as rft.date yyyymmdd



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# File 'app/service_adaptors/pubmed.rb', line 116

def openurl_date(date_xml)
  date = ""
  
  if y = date_xml.at("Year")
    date << ("%04d" % y.inner_text.strip[0,4].to_i )
    if m = date_xml.at("Month")
      # Month name to number
      date << ( "%02d" % DateTime.parse(m.inner_text.strip).month )
      if d = date_xml.at("Day")
        date << ("%02d" % d.inner_text.strip[0,2].to_i)
      end
    end
  end
          
  return date             
end

#service_types_generated ⇒ Object 



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# File 'app/service_adaptors/pubmed.rb', line 27

def service_types_generated
  @service_types ||= [ServiceTypeValue["referent_enhance"]]
end