Class: PubMed

Inherits:
Citation::Article show all
Defined in:
lib/pubmed.rb

Overview

given the html page where the display is specified as xml extracts out the requested pieces

Instance Attribute Summary collapse

Attributes inherited from Citation::Article

#issue, #month, #pages, #title, #vol, #year

Attributes included from JournalLike

#journal_full, #journal_iso, #journal_medline

Attributes inherited from Citation

#abstract, #authors, #bibtype, #ident, #quotes

Instance Method Summary collapse

Methods inherited from Citation::Article

#==, #pages_full

Methods included from JournalLike

#has_journal?, #set_journal_from_medline

Methods inherited from Citation

#to_hash, #to_yaml

Constructor Details

#initialize(pmid = nil, identifier = nil) ⇒ PubMed

also takes pmid=hash of values to set



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# File 'lib/pubmed.rb', line 13

def initialize(pmid=nil, identifier=nil)
  @quotes = []
  if pmid.is_a? Hash
    ########## THIS WHOLE MESS SHOULD BE ENCAPSULATED/INHERITED! but can't get
    #inheritance with authors= working for some reason
    @authors = []
    pmid.each do |k,v|
      if k == 'authors'
        v.each do |auth|
        if auth.is_a? String
          authors.push( Citation::Author.from_s(auth) )
        else
          authors.push( auth )
        end
        end
      else
        send("#{k}=".to_sym, v)
      end
    end
    ############ <-- END MESS
  else
    @authors = []
    @pmid = pmid
    @bibtype = :article
    if pmid
      begin
        url = query_builder(pmid)
        xml_string = get_xml(url)
        extract_attrs_from_xml(xml_string)
      end
    end
    if identifier
      @ident = identifier
    else
      if pmid
        @ident = create_id
      end
    end
  end
end

Instance Attribute Details

#pmid ⇒ Object

Returns the value of attribute pmid.



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# File 'lib/pubmed.rb', line 10

def pmid
  @pmid
end

Instance Method Details

#create_id ⇒ Object

first author’s last name + year collapsing any spaces



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# File 'lib/pubmed.rb', line 64

def create_id
  (@authors[0].last.to_s + @year.to_s).sub(/\s+/,'')
end

#get_xml(query) ⇒ Object

returns xml from online (parses html output). No internet connection gives nil



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# File 'lib/pubmed.rb', line 56

def get_xml(query)
  handle = open(query)
  xml = handle.read
  handle.close
  xml
end

#inspect ⇒ Object 



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# File 'lib/pubmed.rb', line 68

def inspect
  st = "<#{self.class}:##{self.__id__} "
  st << ( %w(authors ident quotes abstract journal_medline title year month vol issue pages).reject{|v| (v == :authors || v == :url)}.push(:bibtype).map {|v| ":#{v}=>#{send(v).inspect}"}.join(", ") )
  st << " @authors=[#{authors.map{|g| g.inspect }.join(", ")}]"
  st << ">"
  st
end