Class: MESH::Tree

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

Constant Summary collapse

@@descriptor_classes = 
[:make_array_start_at_1, :topical_descriptor, :publication_type, :check_tag, :geographic_descriptor]
@@default_locale = 
:en_us

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Tree

Returns a new instance of Tree.



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# File 'lib/MESH/tree.rb', line 8

def initialize

  @headings = []
  @by_unique_id = {}
  @by_tree_number = {}
  @by_original_heading = {}
  @by_entry = {}
  @locales = [@@default_locale]

  filename = File.expand_path('../../../data/mesh_data_2014/d2014.bin.gz', __FILE__)
  gzipped_file = File.open(filename)
  file = Zlib::GzipReader.new(gzipped_file)

  current_heading = MESH::Heading.new(self)
  current_heading.default_locale = @@default_locale
  file.each_line do |line|

    case

      when line.match(/^\*NEWRECORD$/)
        unless current_heading.unique_id.nil?
          current_heading.entries.sort!
          @headings << current_heading
          @by_unique_id[current_heading.unique_id] = current_heading
          @by_original_heading[current_heading.original_heading] = current_heading
          current_heading.tree_numbers.each do |tree_number|
            raise if @by_tree_number[tree_number]
            @by_tree_number[tree_number] = current_heading
          end
          match_headings = current_heading.entries.map { |e| entry_match_key(e) }.uniq
          match_headings.each do |entry|
            raise "#{@by_entry[entry]} vs #{current_heading} on #{entry}\n\n#{@by_entry[entry].entries}\n\n#{current_heading.entries}" if @by_entry[entry]
            @by_entry[entry] = current_heading
          end
        end
        current_heading = MESH::Heading.new(self)
        current_heading.default_locale = @@default_locale

      when matches = line.match(/^UI = (.*)/)
        current_heading.unique_id = matches[1]

      when matches = line.match(/^MN = (.*)/)
        current_heading.tree_numbers << matches[1]
        current_heading.roots << matches[1][0] unless current_heading.roots.include?(matches[1][0])

      when matches = line.match(/^MS = (.*)/)
        current_heading.set_summary(matches[1])

      when matches = line.match(/^DC = (.*)/)
        current_heading.descriptor_class = @@descriptor_classes[matches[1].to_i]

      when matches = line.match(/^ST = (.*)/)
        current_heading.semantic_types << MESH::SemanticTypes[matches[1]]

      when matches = line.match(/^MH = (.*)/)
        mh = matches[1]
        current_heading.set_original_heading(mh)
        current_heading.entries << mh unless current_heading.entries.include? mh
        librarian_parts = mh.match(/(.*), (.*)/)
        nln = librarian_parts.nil? ? mh : "#{librarian_parts[2]} #{librarian_parts[1]}"
        current_heading.set_natural_language_name(nln)

      when matches = line.match(/^(?:PRINT )?ENTRY = ([^|]+)/)
        entry = matches[1].chomp
        current_heading.entries << entry unless current_heading.entries.include? entry

    end

  end

  @by_unique_id.each do |id, heading|
    heading.tree_numbers.each do |tree_number|
      #D03.438.221.173
      parts = tree_number.split('.')
      if parts.size > 1
        parts.pop
        parent_tree_number = parts.join '.'
        parent = @by_tree_number[parent_tree_number]
        heading.parents << parent unless parent.nil? || heading.parents.include?(parent)
        parent.children << heading unless parent.nil? || parent.children.include?(heading)
      end
    end
  end

end

Instance Method Details

#each ⇒ Object 



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# File 'lib/MESH/tree.rb', line 236

def each
  for i in 0 ... @headings.size
    yield @headings[i] if @headings[i].useful
  end
end

#entry_match_key(e) ⇒ Object 



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# File 'lib/MESH/tree.rb', line 94

def entry_match_key(e)
  e.strip.upcase
end

#find(unique_id) ⇒ Object

NO LONGER COVERED BY TESTS def translate(locale, tr)

return if @locales.include? locale
@headings.each_with_index do |h, i|
  h.set_original_heading(tr.translate(h.original_heading), locale)
  h.set_natural_language_name(tr.translate(h.natural_language_name), locale)
  h.set_summary(tr.translate(h.summary), locale)
  h.entries.each { |entry| h.entries(locale) << tr.translate(entry) }
  h.entries(locale).sort!
end

@locales << locale

end



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# File 'lib/MESH/tree.rb', line 212

def find(unique_id)
  return @by_unique_id[unique_id]
end

#find_by_entry(entry) ⇒ Object 



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# File 'lib/MESH/tree.rb', line 224

def find_by_entry(entry)
  return @by_entry[entry_match_key(entry)]
end

#find_by_original_heading(heading) ⇒ Object 



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# File 'lib/MESH/tree.rb', line 220

def find_by_original_heading(heading)
  return @by_original_heading[heading]
end

#find_by_tree_number(tree_number) ⇒ Object 



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# File 'lib/MESH/tree.rb', line 216

def find_by_tree_number(tree_number)
  return @by_tree_number[tree_number]
end

#linkify_summaries(&block) ⇒ Object 



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# File 'lib/MESH/tree.rb', line 192

def linkify_summaries &block
  @headings.each do |h|
    h.linkify_summary &block
  end
end

#load_translation(locale) ⇒ Object 



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# File 'lib/MESH/tree.rb', line 98

def load_translation(locale)
  return if @locales.include? locale
  filename = File.expand_path("../../../data/mesh_data_2014/d2014.#{locale}.bin.gz", __FILE__)
  gzipped_file = File.open(filename)
  file = Zlib::GzipReader.new(gzipped_file)

  entries = []
  original_heading = nil
  natural_language_name = nil
  summary = nil
  unique_id = nil
  file.each_line do |line|

    case

      when line.match(/^\*NEWRECORD$/)
        unless unique_id.nil?
          entries.sort!
          entries.uniq!
          if heading = find(unique_id)
            heading.set_original_heading(original_heading, locale) unless original_heading.nil?
            heading.set_natural_language_name(natural_language_name, locale) unless natural_language_name.nil?
            heading.set_summary(summary, locale) unless summary.nil?
            entries.each { |entry| heading.entries(locale) << entry }
          end

          entries = []
          original_heading = nil
          summary = nil
          unique_id = nil
        end

      when matches = line.match(/^UI = (.*)/)
        unique_id = matches[1]

      when matches = line.match(/^MS = (.*)/)
        summary = matches[1]

      when matches = line.match(/^MH = (.*)/)
        mh = matches[1]
        original_heading = mh
        entries << mh
        librarian_parts = mh.match(/(.*), (.*)/)
        natural_language_name = librarian_parts.nil? ? mh : "#{librarian_parts[2]} #{librarian_parts[1]}"

      when matches = line.match(/^(?:PRINT )?ENTRY = ([^|]+)/)
        entry = matches[1].chomp
        entries << entry

    end

  end
  @locales << locale
end

#load_wikipedia ⇒ Object 



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# File 'lib/MESH/tree.rb', line 153

def load_wikipedia
  return if @wikipedia_loaded
  filename = File.expand_path("../../../data/mesh_data_2014/d2014.wikipedia.bin.gz", __FILE__)
  gzipped_file = File.open(filename)
  file = Zlib::GzipReader.new(gzipped_file)

  unique_id = nil
  wikipedia_links = []
  file.each_line do |line|

    case

      when line.match(/^\*NEWRECORD$/)
        unless unique_id.nil?
          if heading = find(unique_id)
            wikipedia_links.each do |wl|
              wl[:score] = (wl[:score].to_f / heading.entries.length.to_f).round(2)
            end
            heading.wikipedia_links = wikipedia_links
          end

          wikipedia_links = []
          unique_id = nil
        end

      when matches = line.match(/^UI = (.*)/)
        unique_id = matches[1]

      when matches = line.match(/^WK = (.*)/)
        hash = JSON.parse(matches[1], symbolize_names: true)
        wikipedia_links << hash

    end

  end
  @wikipedia_loaded = true
end

#match_in_text(text) ⇒ Object 



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# File 'lib/MESH/tree.rb', line 242

def match_in_text(text)
  return [] if text.nil?
  downcased = text.downcase
  matches = []
  @headings.each do |heading|
    next unless heading.useful
    @locales.each do |locale|
      heading.entries(locale).each do |entry|
        if downcased.include? entry.downcase #This is a looser check than the regex but much, much faster
          if /^[A-Z0-9]+$/ =~ entry
            regex = /(^|\W)#{Regexp.quote(entry)}(\W|$)/
          else
            regex = /(^|\W)#{Regexp.quote(entry)}(\W|$)/i
          end
          text.to_enum(:scan, regex).map do |m,|
            matches << {heading: heading, matched: entry, index: $`.size}
          end
        end
      end
    end
  end
  confirmed_matches = []
  matches.combination(2) do |l, r|
    if (r[:index] >= l[:index]) && (r[:index] + r[:matched].length <= l[:index] + l[:matched].length)
      #r is within l
      r[:delete] = true
    elsif (l[:index] >= r[:index]) && (l[:index] + l[:matched].length <= r[:index] + r[:matched].length)
      #l is within r
      l[:delete] = true
    end
  end
  matches.delete_if { |match| match[:delete] }
end

#where(conditions) ⇒ Object 



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# File 'lib/MESH/tree.rb', line 228

def where(conditions)
  matches = []
  @headings.each do |heading|
    matches << heading if heading.matches(conditions)
  end
  matches
end