Class: FishTank::Taxon

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

Direct Known Subclasses

Arm, Fish, Tetrapod

Defined Under Namespace

Classes: Arm, Fish, Tetrapod

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(taxon_id: nil) ⇒ Taxon

Returns a new instance of Taxon.



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# File 'lib/fishtank/taxon.rb', line 9

def initialize(taxon_id: nil)
  @label = taxon_id 
  @stats = {}
  get_metadata
  crunch_stats
end

Instance Attribute Details

#label ⇒ Object

METADATA = {}



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# File 'lib/fishtank/taxon.rb', line 6

def label
  @label
end

#stats ⇒ Object

Returns the value of attribute stats.



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# File 'lib/fishtank/taxon.rb', line 7

def stats
  @stats
end

Instance Method Details

#attributes ⇒ Object 



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# File 'lib/fishtank/taxon.rb', line 81

def attributes
end

#base_for(id) ⇒ Object 



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# File 'lib/fishtank/taxon.rb', line 77

def base_for(id)
  BASE + id
end

#crunch_stats ⇒ Object 



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# File 'lib/fishtank/taxon.rb', line 49

def crunch_stats
  totals = {} 

  stats.keys.each do |entity|
    stats[entity][:raw].each do |k, count|
      totals[k] ||= 0
      totals[k] += count 
    end 
  end

  description.each do |entity, v|
    stats[entity][:crunched] ||= {}
    totals.keys.each do |t|
      v = totals[t] == 0 ? 0.to_f : stats[entity][:raw][t].to_f / totals[t].to_f
      stats[entity][:crunched][t] = v 
    end
  end
  true
end

#get_metadata ⇒ Object 



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# File 'lib/fishtank/taxon.rb', line 32

def get_metadata
  @stats ||= {}
  description.each do |k, v|
    @stats[k] ||= {}
    @stats[k][:raw] ||= {}

    xml = get_nexml(k) 
    o = SimpleNexml.new(doc: xml, taxon: label)
    @stats[k][:raw] = o.stats[:count]

    FishTank::QUALITIES.each do |q|
      @stats[k][:raw][q] = get_phenotype_total(k, q)
    end
  end
  true 
end

#get_nexml(entity) ⇒ XML

Returns:

  • (XML) 


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# File 'lib/fishtank/taxon.rb', line 17

def get_nexml(entity)
  Phenoscape::Ontotrace.ontotrace(taxon: iri_for(label), entity: some_iri(entity), ret: 'noko')
end

#get_phenotype_total(entity, quality) ⇒ Integer

Returns:

  • (Integer) 


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# File 'lib/fishtank/taxon.rb', line 22

def get_phenotype_total(entity, quality)
  Phenoscape::Taxa.annotations(
    in_taxon: base_for(label), 
    entity: base_for(entity), 
    quality: base_for(quality),
    total: true,
    parts: true
  )['total']
end

#iri_for(id) ⇒ Object 



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# File 'lib/fishtank/taxon.rb', line 73

def iri_for(id)
  '<' + base_for(id) + '>'
end

#pic_height ⇒ Integer

Returns:

  • (Integer) 


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# File 'lib/fishtank/taxon.rb', line 94

def pic_height
  100
end

#pic_width ⇒ Integer

Returns:

  • (Integer) 


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# File 'lib/fishtank/taxon.rb', line 89

def pic_width
  60 
end

#some_iri(entity) ⇒ Object 



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# File 'lib/fishtank/taxon.rb', line 69

def some_iri(entity)
  iri_for('BFO_0000050') + ' some ' +  iri_for(entity) 
end

#symmetry ⇒ Object 



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# File 'lib/fishtank/taxon.rb', line 84

def symmetry
  return {}
end