Class: BugGuide::Taxon

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

Overview

Represents a single taxon on BugGuide

One thing to keep in mind is that this will generally be instantiated from search results, so for certain methods, like ‘ancestry`, it will need to perform an additional request to retrieve the relevant data.

Several methods are intended for compatability with the DarwinCore SimpleMultimedia extention (rs.gbif.org/terms/1.0/Multimedia).

Constant Summary collapse

NAME_PATTERN = 
/[\w\s\-\'\.]+/

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(options = {}) ⇒ Taxon

Returns a new instance of Taxon.



16
17
18
19
20
21
 
# File 'lib/bugguide/taxon.rb', line 16

def initialize(options = {})
  options.each do |k,v|
    send("#{k}=", v)
  end
  self.url ||= "http://bugguide.net/node/view/#{id}"
end

Instance Attribute Details

#common_name ⇒ Object Also known as: vernacularName

Returns the value of attribute common_name.



14
15
16
 
# File 'lib/bugguide/taxon.rb', line 14

def common_name
  @common_name
end

#id ⇒ Object Also known as: taxonID

Returns the value of attribute id.



14
15
16
 
# File 'lib/bugguide/taxon.rb', line 14

def id
  @id
end

#name ⇒ Object

Returns the value of attribute name.



14
15
16
 
# File 'lib/bugguide/taxon.rb', line 14

def name
  @name
end

#scientific_name ⇒ Object Also known as: scientificName

Returns the value of attribute scientific_name.



14
15
16
 
# File 'lib/bugguide/taxon.rb', line 14

def scientific_name
  @scientific_name
end

#url ⇒ Object

Returns the value of attribute url.



14
15
16
 
# File 'lib/bugguide/taxon.rb', line 14

def url
  @url
end

Class Method Details

.find(id) ⇒ Object

Find a single BugGuide taxon given its node ID



112
113
114
115
116
117
118
 
# File 'lib/bugguide/taxon.rb', line 112

def self.find(id)
  taxon = BugGuide::Taxon.new(id: id)
  taxon.name = taxon.taxonomy_html.css('.node-title h1').text
  taxon.scientific_name = taxon.taxonomy_html.css('.node-title i').text
  taxon.common_name = taxon.taxonomy_html.css('.node-title').text.split('-').last
  taxon
end

.search(name, options = {}) ⇒ Object

Search for taxa, returns matching BugGuide::Taxon instances



90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
 
# File 'lib/bugguide/taxon.rb', line 90

def self.search(name, options = {})
  # For reference, http://bugguide.net/adv_search/taxon.php?q=Sphecidae returns
  # 117327||Apoid Wasps (Apoidea)- traditional Sphecidae|2302 135|Sphecidae|Thread-waisted Wasps|2700 
  url = "http://bugguide.net/adv_search/taxon.php?q=#{URI.escape(name)}"
  headers = options[:headers] || {}
  f = open(url)
  taxa = []
  open(url, headers) do |f|
    f.read.split("\n").each do |row|
      row = row.split('|').compact.map(&:strip)
      taxa << BugGuide::Taxon.new(
        id: row[0], 
        name: row[1], 
        scientific_name: row[1], 
        common_name: row[2]
      )
    end
  end
  taxa
end

Instance Method Details

#ancestors ⇒ Object

All ancestor taxa of this taxon, or its classification if you prefer that terminology.



57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
 
# File 'lib/bugguide/taxon.rb', line 57

def ancestors
  return @ancestors if @ancestors
  @ancestors = []
  nbsp = Nokogiri::HTML("&nbsp;").text
  @ancestors = taxonomy_html.css('.bgpage-roots a').map do |a|
    next unless a['href'] =~ /node\/view\/\d+\/tree/
    t = BugGuide::Taxon.new(
      id: a['href'].split('/')[-2],
      name: a.text.gsub(nbsp, ' '),
      url: a['href'],
      rank: a['title']
    )
    if name_matches = t.name.match(/(#{NAME_PATTERN})\s+\((#{NAME_PATTERN})\)/)
      t.common_name = name_matches[1]
      t.scientific_name = name_matches[2]
    elsif name_matches = t.name.match(/(#{NAME_PATTERN})\s+\-\s+(#{NAME_PATTERN})/)
      t.common_name = name_matches[2]
      t.scientific_name = name_matches[1]
    end
    next if t.scientific_name == scientific_name
    t
  end.compact
end

#higherClassification ⇒ Object

DarwinCore-compliant taxonomic classification



135
136
137
 
# File 'lib/bugguide/taxon.rb', line 135

def higherClassification
  ancestors.map(&:scientific_name).join(' | ')
end

#rank ⇒ Object Also known as: taxonRank

Taxonomic rank, e.g. kingdom, phylum, order, etc.



51
52
53
54
 
# File 'lib/bugguide/taxon.rb', line 51

def rank
  return @rank if @rank
  @rank = taxonomy_html.css('.bgpage-roots a').last['title'].downcase
end

#rank=(new_rank) ⇒ Object 



45
46
47
48
 
# File 'lib/bugguide/taxon.rb', line 45

def rank=(new_rank)
  @rank = new_rank.downcase
  @rank = nil if @rank == 'no taxon'
end

#taxonomy_html ⇒ Object

HTML source of the taxon’s taxonomy page on BugGuide as a Nokogiri document



82
83
84
85
86
87
 
# File 'lib/bugguide/taxon.rb', line 82

def taxonomy_html
  return @taxonomy_html if @taxonomy_html
  open("http://bugguide.net/node/view/#{id}/tree") do |response|
    @taxonomy_html = Nokogiri::HTML(response.read)
  end
end