Class: NomenclaturalRank

Inherits:
Object
  • Object
show all
Defined in:
app/models/nomenclatural_rank.rb

Overview

A NomenclaturalRank is used to assert the (organizational) position of a taxon name within a nomenclatural hierarchy, according to the governed (or not) levels described in a corresponding nomenclatural code.

See /lib/ranks.rb for related constants and hooks.

Direct Known Subclasses

Icn, Icnp, Icvcn, Iczn

Defined Under Namespace

Classes: Icn, Icnp, Icvcn, Iczn

Class Method Summary collapse

Class Method Details

.abbreviation ⇒ String?

Returns a TW preferred abbreviated name for this rank, e.g. “fam.”.

Returns:

  • (String, nil) —

    a TW preferred abbreviated name for this rank, e.g. “fam.”



78
79
80
 
# File 'app/models/nomenclatural_rank.rb', line 78

def self.abbreviation
  nil
end

.bottom_rank ⇒ NomenclaturalRank (private)

Returns the lowest assignable rank within the nomenclatural group (e.g. ICZN species, genus, family) that this class is part of.

Returns:

  • (NomenclaturalRank) —

    the lowest assignable rank within the nomenclatural group (e.g. ICZN species, genus, family) that this class is part of



158
159
160
161
162
163
 
# File 'app/models/nomenclatural_rank.rb', line 158

def self.bottom_rank
  all = self.descendants
  all.select!{|r| !r.parent_rank.nil?}
  all_parents = all.collect{|i| i.parent_rank}
  all.detect{|r| !all_parents.include?(r)}
end

.collect_descendants_to_s(*classes) ⇒ Object

TODO: move this to lib/application_ennumeration !! The use of this moved into a frozen or || solution likely.



99
100
101
102
103
104
105
 
# File 'app/models/nomenclatural_rank.rb', line 99

def self.collect_descendants_to_s(*classes)
  ans = []
  classes.each do |klass|
    ans += klass.descendants.collect{|k| k.to_s}
  end
  ans
end

.collect_to_s(*args) ⇒ Object

TODO: move this to string method



93
94
95
 
# File 'app/models/nomenclatural_rank.rb', line 93

def self.collect_to_s(*args)
  args.collect{|arg| arg.to_s}
end

.nomenclatural_code ⇒ Symbol?

Returns the name of the nomenclatural code, as a short symbol (:iczn, :icn, etc.), or nil.

Returns:

  • (Symbol, nil) —

    the name of the nomenclatural code, as a short symbol (:iczn, :icn, etc.), or nil



32
33
34
35
36
37
38
39
 
# File 'app/models/nomenclatural_rank.rb', line 32

def self.nomenclatural_code

  return :iczn if self.name.to_s =~ /Iczn/
  return :icnp if self.name.to_s =~ /Icnp/
  return :icvcn if self.name.to_s =~ /Icvcn/
  return :icn if self.name.to_s =~ /Icn/ # order matters
  nil
end

.nomenclatural_code_class ⇒ NomenclaturalRank?

TODO: unused

Returns:



44
45
46
47
48
49
50
51
52
53
54
55
56
57
 
# File 'app/models/nomenclatural_rank.rb', line 44

def self.nomenclatural_code_class
  case self.nomenclatural_code
  when :iczn
    NomenclaturalRank::Iczn
  when :icnp
    NomenclaturalRank::Icnp
  when :icvcn
    NomenclaturalRank::Icvcn
  when :icn
    NomenclaturalRank::Icn
  else
    nil
  end
end

.order_ranks(rank_classes) ⇒ Object

Parameters:

  • ranks —

    Array of rank classes as string ( [ “NomenclaturalRank::Iczn::HigherClassificationGroup::Infraclass”, …] )



109
110
111
 
# File 'app/models/nomenclatural_rank.rb', line 109

def self.order_ranks(rank_classes)
  rank_classes.sort{|a,b| RANKS.index(a) <=> RANKS.index(b)}
end

.ordered_ranks ⇒ ordered Array of NomenclaturalRank (private)

Used to build constants in config/initializers/constants/ranks.rb.

!! Further code should reference those constants rather than call this method.

Returns:



171
172
173
174
175
176
177
178
179
180
 
# File 'app/models/nomenclatural_rank.rb', line 171

def self.ordered_ranks
  return false if self.name == 'NomenclaturalRank' # || (rank.class.name =~ /NomenclaturalRank/)
  ordered = []
  bottom = bottom_rank
  top = top_rank
  ordered.push(bottom)
  ordered << ordered.last.parent_rank while ordered.last != top
  ordered.reverse!
  return ordered
end

.parent ⇒ Object

Returns class this method calls Module#module_parent.

Returns:

  • class this method calls Module#module_parent



14
15
16
 
# File 'app/models/nomenclatural_rank.rb', line 14

def self.parent
  self.module_parent
end

.parent_rank ⇒ NomenclaturalRank?

All subclasses must override this method. nil returning classes can not be assigned as a NomenclaturalRank to a TaxonName!

Returns:



72
73
74
 
# File 'app/models/nomenclatural_rank.rb', line 72

def self.parent_rank
  nil
end

.rank_expansion_sql(ranks: [], expand: false, scope: nil, nomenclatural_code: nil, gender: true) ⇒ Object

@param: expand

true - include all columns discovered



117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
 
# File 'app/models/nomenclatural_rank.rb', line 117

def self.rank_expansion_sql(ranks: [], expand: false, scope: nil, nomenclatural_code: nil, gender: true)

  # Get the classes for the ranks supplied
  rank_classes = ranks.collect{|a| Ranks.lookup(:iczn, a)}

  # Expand them to the observed ranks within the scope
  rank_classes += scope.select(:rank_class).distinct.pluck(:rank_class) if expand
  rank_classes.uniq!
  ranks = NomenclaturalRank.order_ranks( rank_classes )

  rank_names = ranks.collect{|a| a.safe_constantize.rank_name}.uniq
  rank_names.delete('nomenclatural rank')

  # TODO: EXPAND TO INCLUDE GENDER VALUE HERE { if ranks includes genera }

 s = rank_names.collect{|n|
    "MAX(CASE WHEN parent.rank_class LIKE \'%::#{n.capitalize}\' THEN parent.name END) AS #{n}"
  }.join(",\n")

  if gender
    g = rank_names.select{|n| n =~ /[Gg]enus/}.collect{|m|
      "MAX(CASE WHEN parent.rank_class LIKE \'%::#{m.capitalize}\' THEN parent.cached_gender END) AS #{m}_gender"
    }.join(",\n")
  end

  s = s + ', ' + g if !g.blank?
  s
end

.rank_name ⇒ String

Returns the “common” name for this rank.

Returns:

  • (String) —

    the “common” name for this rank



20
21
22
23
24
25
26
27
28
 
# File 'app/models/nomenclatural_rank.rb', line 20

def self.rank_name
  n = self.name.demodulize.underscore.humanize.downcase
  if n == 'potentially_validating rank'
    n = 'root'
  elsif n == 'class rank'
    n = 'class'
  end
  n
end

.top_rank ⇒ NomenclaturalRank (private)

Returns the “top” rank for the nomenclatural group (e.g. ICZN species, genus, family) that this rank belongs to.

Returns:

  • (NomenclaturalRank) —

    the “top” rank for the nomenclatural group (e.g. ICZN species, genus, family) that this rank belongs to.



150
151
152
153
154
 
# File 'app/models/nomenclatural_rank.rb', line 150

def self.top_rank
  all = self.descendants
  all.select!{|r| !r.parent_rank.nil?}
  all.detect{|r| !all.include?(r.parent_rank)} # returns the first value found
end

.typical_use ⇒ Boolean

Returns should the rank be displayed in “typical” use?.

Returns:

  • (Boolean) —

    should the rank be displayed in “typical” use?



63
64
65
 
# File 'app/models/nomenclatural_rank.rb', line 63

def self.typical_use
  true
end

.valid_name_ending ⇒ Object 



88
89
90
 
# File 'app/models/nomenclatural_rank.rb', line 88

def self.valid_name_ending
  ''
end

.valid_parents ⇒ Array of NomenclaturalRank

Returns the TaxonName assignable NomenclaturalRanks that this rank descend from.

Returns:



84
85
86
 
# File 'app/models/nomenclatural_rank.rb', line 84

def self.valid_parents
  []
end