Class: Pubmed

Inherits:
Service show all
Defined in:
lib/service_adaptors/pubmed.rb

Overview

FIXME This service is not working For starters it needs the method service_types_generated()

Constant Summary

Constant Summary

Constants inherited from Service

Service::LinkOutFilterTask, Service::StandardTask

Instance Attribute Summary (collapse)

Attributes inherited from Service

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

Instance Method Summary (collapse)

Methods inherited from Service

#display_name, #handle_wrapper, #initialize, #link_out_filter, #preempted_by, required_config_params, #response_to_view_data, #response_url, #service_types_generated, #session, #update_session, #view_data_from_service_type

Constructor Details

This class inherits a constructor from Service

Instance Attribute Details

- (Object) atitle (readonly)

Returns the value of attribute atitle



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# File 'lib/service_adaptors/pubmed.rb', line 9

def atitle
  @atitle
end

- (Object) aufirst (readonly)

Returns the value of attribute aufirst



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# File 'lib/service_adaptors/pubmed.rb', line 9

def aufirst
  @aufirst
end

- (Object) auinit (readonly)

Returns the value of attribute auinit



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# File 'lib/service_adaptors/pubmed.rb', line 9

def auinit
  @auinit
end

- (Object) aulast (readonly)

Returns the value of attribute aulast



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# File 'lib/service_adaptors/pubmed.rb', line 9

def aulast
  @aulast
end

- (Object) date (readonly)

Returns the value of attribute date



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# File 'lib/service_adaptors/pubmed.rb', line 9

def date
  @date
end

- (Object) description (readonly)

Returns the value of attribute description



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# File 'lib/service_adaptors/pubmed.rb', line 9

def description
  @description
end

- (Object) eissn (readonly)

Returns the value of attribute eissn



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# File 'lib/service_adaptors/pubmed.rb', line 9

def eissn
  @eissn
end

- (Object) issn (readonly)

Returns the value of attribute issn



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# File 'lib/service_adaptors/pubmed.rb', line 9

def issn
  @issn
end

- (Object) issue (readonly)

Returns the value of attribute issue



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# File 'lib/service_adaptors/pubmed.rb', line 9

def issue
  @issue
end

- (Object) jtitle (readonly)

Returns the value of attribute jtitle



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# File 'lib/service_adaptors/pubmed.rb', line 9

def jtitle
  @jtitle
end

- (Object) pages (readonly)

Returns the value of attribute pages



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# File 'lib/service_adaptors/pubmed.rb', line 9

def pages
  @pages
end

- (Object) stitle (readonly)

Returns the value of attribute stitle



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# File 'lib/service_adaptors/pubmed.rb', line 9

def stitle
  @stitle
end

- (Object) subjects (readonly)

Returns the value of attribute subjects



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# File 'lib/service_adaptors/pubmed.rb', line 9

def subjects
  @subjects
end

- (Object) volume (readonly)

Returns the value of attribute volume



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# File 'lib/service_adaptors/pubmed.rb', line 9

def volume
  @volume
end

Instance Method Details

- (Boolean) can_resolve?(req)

Only request for things with PMIDs

Returns:

  • (Boolean) 


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# File 'lib/service_adaptors/pubmed.rb', line 21

def can_resolve?(req)    
  req.referent.referent_values.find(:all, :conditions=>['key_name = ?', 'identifier']).each do | val |
    # PMIDs can come in with either of these prefixes
    return val.value if val.value.match(/^(info:pmid\/)|(pmid:)/)          
  end    
  return false
end

- (Object) fetch_record(id)

Do the request. Takes the PMID as inputs



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# File 'lib/service_adaptors/pubmed.rb', line 30

def fetch_record(id)    
  id.sub!(/^(info:pmid\/)|(pmid:)/, "")
  pmid_url = self.url + "?db=pubmed&retmode=xml&rettype=full&id="+id
  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

- (Object) handle(request) 



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

def handle(request)
  return request.dispatched(self, true) unless id = self.can_resolve?(request)
  unless request.dispatched?(self)
    return request.dispatched(self, false) unless response = self.fetch_record(id)
    self.parse_record(response, request)
    return request.dispatched(self, true)
  end
end

- (Object) parse_record(body, request)

Pull everything useful out of the Pubmed record



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# File 'lib/service_adaptors/pubmed.rb', line 43

def parse_record(body, request)   
  require 'hpricot'
  doc = Hpricot(body)
  return unless cite = (doc/"/PubmedArticleSet/PubmedArticle/MedlineCitation") # Nothing of interest here
  
  # Get the MeSH subject headings
  @subjects = {}
  (cite/'/MeshHeadingList/MeshHeading').each do | mesh |
    @subjects["mesh"] = [] unless @subjects["mesh"]
    subjects = []
    major = ''
    if dn = (mesh/'/DescriptorName').first
      subjects << dn.inner_html
      major = '*' if dn.attributes['majortopicyn'] == "Y"                              
    end
    if qn = (mesh/'/QualifierName').first
      subjects << qn.inner_html
      major = '*' if qn.attributes['majortopicyn'] == "Y"                      
    end  
    @subjects["mesh"] << subjects.join("/")+major 
    request.add_service_response({:service=>self,:key=>'subject',:value_string=>subjects.join("/")+major,:value_alt_string=>'mesh'}, ['subject'])             
  end
  
  return unless article = (cite/"/Article").first # No more useful metadata   
  if abstract = (article/"/Abstract/AbstractText").first
    @description = abstract.inner_html 
  end
  request.add_service_response({:service=>self,:key=>'abstract',:value_text=>@description}, ['abstract']) unless @description.blank?
  if journal = (article/"/journal").first
    if issn = (journal/'/ISSN').first
      if issn.attributes['issntype']=="Print"                  
        request.referent.enhance_referent('issn', issn.inner_html, true, false)
      else 
        request.referent.enhance_referent('eissn', issn.inner_html, true, false)        
      end
    end
    if jrnlissue = (journal/'/JournalIssue').first
      if (jrnlissue/'/Volume').first
        request.referent.enhance_referent('volume', (jrnlissue/'/Volume').first.inner_html, true, false)
      end
      if (jrnlissue/'/Issue').first
        request.referent.enhance_referent('issue', (jrnlissue/'/Issue').first.inner_html, true, false)
      end   
      if (jrnlissue/'/PubDate').first
        if (jrnlissue/'/PubDate/Year').first
          request.referent.enhance_referent('date', (jrnlissue/'/PubDate/Year').first.inner_html, true, false)
        end
      end              
    end
    
    if (journal/'/Title').first
      request.referent.enhance_referent('jtitle', (journal/'/Title').first.inner_html, true, false)          
    end
    if (journal/'/ISOAbbreviation').first
      request.referent.enhance_referent('stitle', (journal/'/ISOAbbreviation').first.inner_html, true, false)
    end         
    if (journal/'/ArticleTitle').first
      request.referent.enhance_referent('atitle', (journal/'/ArticleTitle').first.inner_html, true, false)
    end   
    
    if (article/'/Pagination/MedlinePgn').first
      request.referent.enhance_referent('pages', (article/'/Pagination/MedlinePgn').first.inner_html, true, false)        
    end                

    if (article/'/AuthorList/Author').first
      if (article/'/AuthorList/Author/LastName').first
        request.referent.enhance_referent('aulast', (article/'/AuthorList/Author/LastName').first.inner_html, true, false)
      end
      if (article/'/AuthorList/Author/ForeName').first
        request.referent.enhance_referent('aufirst', (article/'/AuthorList/Author/ForeName').first.inner_html, true, false)
      end          
      if (article/'AuthorList/Author/Initials').first
        request.referent.enhance_referent('auinit', (article/'AuthorList/Author/Initials').first.inner_html, true, false)
      end          
    end   
    request.referent.save
    request.save     
  end      

end