Class: ChemScanner::Interpreter::ReactionTextGroup

Inherits:
Object
  • Object
show all
Includes:
BoldGroup
Defined in:
lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from BoldGroup

#extract_alphabet_number, #extract_range_number, #group_combinations, #line_bold_groups, #normalize_bold, #normalize_bold_groups, #text_bold_groups

Constructor Details

#initialize(reaction, alias_info, scheme) ⇒ ReactionTextGroup

Returns a new instance of ReactionTextGroup.



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 12

def initialize(reaction, alias_info, scheme)
  @reaction = reaction
  @alias_info = alias_info
  @scheme = scheme
  @mol_map = scheme.mol_map
  @text_map = scheme.text_map

  # List of aliases, ex: ["R1", "R2"]
  @alias_groups = []

  # final list if text-groups and label
  @text_groups = []

  @reactants = {}
  @reagents = {}
  @products = {}

  retrieve_alias_groups
end

Instance Attribute Details

#alias_groups ⇒ Object

Returns the value of attribute alias_groups.



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 10

def alias_groups
  @alias_groups
end

#bold_groups ⇒ Object

Returns the value of attribute bold_groups.



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 10

def bold_groups
  @bold_groups
end

#plain_groups ⇒ Object

Returns the value of attribute plain_groups.



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 10

def plain_groups
  @plain_groups
end

#text_groups ⇒ Object

Returns the value of attribute text_groups.



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 10

def text_groups
  @text_groups
end

Instance Method Details

#generate_from_bold_groups ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 129

def generate_from_bold_groups
  max = max_group_size
  genr_arr = []
  used_groups = []

  (0..max - 1).each do |idx|
    new_r = false
    genr = @reaction.clone

    [@reactants, @reagents, @products].each do |group|
      group.select { |k, _| @alias_info.key?(k) }.each do |k, v|
        next if v.bold_groups.empty?

        mg = v.bold_groups[idx] || v.bold_groups.last
        mg_info = mg

        if mg[:group].empty? && !mg[:bold].nil?
          mgs = @bold_groups.select do |bg|
            bg[:bold] == mg[:bold] && !bg[:group].empty?
          end
          next unless mgs.count == 1

          mg_info = mg.merge(mgs.first)
        end

        is_used = used_groups.detect do |x|
          (
            x[:bold] == mg_info[:bold] &&
            x[:group].to_a == mg_info[:group].to_a
          )
        end
        next unless is_used.nil?

        new_r = true
        mtg = MoleculeTextGroup.new(@mol_map[k], @alias_info, @scheme)
        used_groups.push(mg_info)
        mtg.text_groups = [mg_info]
        gmol = mtg.generate_molecule.first

        genr.replace_molecule(k, gmol)
      end
    end

    genr_arr.push(genr) if new_r
  end

  genr_arr
end

#generate_from_plain_groups ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 100

def generate_from_plain_groups
  genr_arr = []

  combis = @text_groups.reject { |x| x.key?(:bold) }
  combis.each do |combi|
    mids = @alias_info.keys
    rmids = @reaction.all_ids.select do |mid|
      mids.include?(mid) || @mol_map[mid].clone_from
    end
    next if rmids.empty?

    genr = @reaction.clone

    rmids.each do |mid|
      next unless @alias_info.key?(mid)

      mtg = MoleculeTextGroup.new(@mol_map[mid], @alias_info, @scheme)
      mtg.text_groups = [combi]
      gmol = mtg.generate_molecule.first

      genr.replace_molecule(mid, gmol)
    end

    genr_arr.push(genr)
  end

  genr_arr
end

#generate_reaction ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 93

def generate_reaction
  creactions = generate_from_plain_groups
  bg_reactions = generate_from_bold_groups

  creactions.concat(bg_reactions)
end

#inspect ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 211

def inspect
  (
    "#<ReactionTextGroup: id=#{@reaction.arrow_id}, " +
    "alias_groups: #{@alias_groups}, " +
    "plain_groups: #{@plain_groups}, " +
    "bold_groups: #{@bold_groups} >"
  )
end

#interpret ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 42

def interpret
  @bold_groups = []
  @plain_groups = {}

  interpret_reaction_text

  %w[reactant reagent product].each { |g| interpret_molecule_group(g) }

  @plain_groups.select! { |k, _| @alias_groups.include?(k) }
  combis = group_combinations(@plain_groups).map { |g| { group: g } }

  @text_groups = @bold_groups + combis
end

#interpret_molecule_group(group) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 73

def interpret_molecule_group(group)
  group_ids = @reaction.send("#{group}_ids")
  gmols = group_ids.select { |i| @mol_map.key?(i) }
  layout = {}

  gmols.each do |mid|
    mol = @mol_map[mid]
    mtg = MoleculeTextGroup.new(mol, @alias_info, @scheme)
    mtg.interpret

    @bold_groups.concat(mtg.bold_groups)
    @plain_groups.merge!(mtg.plain_groups) { |_, o, n| o.concat(n) }

    layout[mid] = mtg
  end

  @bold_groups.reject! { |bg| bg[:group].empty? }
  instance_variable_set("@#{group}s".to_sym, layout) unless layout.empty?
end

#interpret_reaction_text ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 56

def interpret_reaction_text
  @reaction.text_ids.each do |tid|
    text = @text_map[tid].markdown.gsub(/ *\*\* *\n/, "\n**")
    lines = text.split("\n")

    lines.each do |line|
      groups = reaction_line_bold_groups(line)
      plain, bolds = groups.partition { |x| x[:bold].nil? }

      @bold_groups.concat(bolds)
      plain.each do |nb|
        @plain_groups.merge!(nb) { |_, old, new| old.concat(new) }
      end
    end
  end
end

#max_group_size ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 198

def max_group_size
  max_group_size = 0

  [@reactants, @reagents, @products].each do |group|
    group.each_value do |v|
      gmax = v.bold_groups.count
      max_group_size = gmax if gmax > max_group_size
    end
  end

  max_group_size
end

#reaction_line_bold_groups(line) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 178

def reaction_line_bold_groups(line)
  bold_info, groups = line_bold_groups(line, @alias_groups)

  list_bold = bold_info.reduce([]) do |arr, bold|
    bold.gsub!(":", "")
    norm = normalize_bold(bold)
    barr = norm.empty? ? bold : norm
    arr.push(barr)
  end

  bolds = list_bold.reject(&:empty?)
  return [] if bolds.empty? && groups.empty?

  rgroups = bolds.reduce([]) do |arr, bold|
    arr.concat(normalize_bold_groups(bold, groups))
  end

  bolds.empty? ? [groups] : rgroups
end

#retrieve_alias_groups ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/reaction_text_groups.rb', line 32

def retrieve_alias_groups
  mids = @reaction.all_ids.select { |id| @mol_map.key?(id) }
  @alias_groups = mids.reduce([]) do |arr, mid|
    next arr unless @alias_info.key?(mid)

    alias_groups = @alias_info[mid].map { |i| i[:group] }.compact
    arr.concat(alias_groups.reject(&:empty?))
  end
end