Class: Bibliography

Inherits:
Object
  • Object
show all
Defined in:
lib/bibliography.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(citations = nil) ⇒ Bibliography

Returns a new instance of Bibliography.



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# File 'lib/bibliography.rb', line 8

def initialize(citations=nil)
  if citations
    @citations = citations
  end
end

Instance Attribute Details

#citations ⇒ Object

Returns the value of attribute citations.



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# File 'lib/bibliography.rb', line 6

def citations
  @citations
end

Class Method Details

.from_yaml(file_or_string) ⇒ Object

if file, loads it



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# File 'lib/bibliography.rb', line 61

def self.from_yaml(file_or_string)
  hash = 
    if File.exist? file_or_string
      YAML.load_file(file_or_string)
    else
      YAML.load(file_or_string)
    end
  # we were given a nonexistent file and the yaml is not a hash
  # in this case we need to create an empty bib object
  unless hash.is_a? Hash
    hash = {}
  end
  citations = hash.map do |id,vals|
    vals['ident'] = id 
    bibtype = vals['bibtype']
    klass = 
      if vals.key? 'pmid'
        PubMed
      else
        Citation.const_get(bibtype.capitalize)
      end
      #when 'article'
      #  else
      #    Citation::Article
      #  end
      #when 'book'
      #  Citation::Book
      #else
      #  abort "Unrecognized bibtype!"
      #end
    vals['bibtype'] = bibtype.to_sym
    cit = klass.new(vals)
    #if cit.authors =~ /Paris/
    #  p cit.authors
    #  abort
    #end
    #if cit.authors.is_a? Array
    #  cit.authors = cit.author_strings_to_objects
    #end
    cit
  end
  bib = Bibliography.new(citations)
end

Instance Method Details

#add(*citations) ⇒ Object

adds a list of citations. It will ONLY add citations whose identifiers do not already exist. Citations which already have a duplicate identifier will be returned. nil is returned if no citation objects have clashing id’s



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# File 'lib/bibliography.rb', line 43

def add(*citations)
  clashing = []
  hsh = to_hash
  citations.each do |cit|
    if hsh.key? cit.ident
      clashing << cit
    else
      @citations.push(cit)
    end
  end
  if clashing.size > 0
    clashing
  else
    nil
  end
end

#not_uniq(other) ⇒ Object

returns an array of citations from other that are not uniq compared self



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# File 'lib/bibliography.rb', line 15

def not_uniq(other)
  scit = self.citations
  ocit = other.citations
  pass_id = not_uniq_by(scit, ocit, :ident)
  passed = [scit, ocit].map do |ar|
    ar.select {|v| v.respond_to? :pmid}
  end
  passed.push( *(not_uniq_by(passed[0], passed[1], :ident)) )
  passed.uniq!
  passed
end

#not_uniq_by(cits1, cits2, att) ⇒ Object 



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# File 'lib/bibliography.rb', line 27

def not_uniq_by(cits1, cits2, att)
  self_by_att = cits1.group_by(&att)
  other_by_att = cits2.group_by(&att)
  not_un = [] 
  other_by_att.each do |k,v| 
    if self_by_att.key? k
      not_un.push( *v )
    end
  end
  not_un 
end

#select_by_id!(ids) ⇒ Object

selects as internal citations only those matching the array of idents returns the citations



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# File 'lib/bibliography.rb', line 107

def select_by_id!(ids)
  # should mimic index_by
  hash = @citations.group_by(&:ident) ; hash.each {|k,v| hash[k] = v.last }
  new_cits = ids.map do |id|
    unless hash.key? id ; abort "Cannot find '#{id}' in citations!" end
    hash[id]
  end
  @citations = new_cits
end

#to_hash ⇒ Object

hashes by ident



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# File 'lib/bibliography.rb', line 118

def to_hash
  hsh = {}
  @citations.each do |cit|
     cthash = cit.to_hash
     cthash.delete('ident')
     hsh[cit.ident] = cthash
  end
  hsh
end

#to_yaml(file = nil) ⇒ Object

if given a file, writes to the file, otherwise returns the string



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# File 'lib/bibliography.rb', line 129

def to_yaml(file=nil)
  hsh = to_hash
  string = hsh.to_yaml
  if file
    File.open(file, 'w') {|v| v.print string }
  end
  string
end

#write(format_obj) ⇒ Object

a format_obj can respond to the call obj.format(citation, format_type) and :header and :footer



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# File 'lib/bibliography.rb', line 140

def write(format_obj)
  format_obj.header + format_obj.format(@citations) + format_obj.footer
end