Module: OtusHelper

Defined in:
app/helpers/otus_helper.rb

Instance Method Summary collapse

Instance Method Details

Stub a smart link to browse OTUs

Parameters:

  • object (an instance of TaxonName or Otu) —

    if TaxonName is provided JS UI will disambiguate if more options are possible



50
51
52
53
54
 
# File 'app/helpers/otus_helper.rb', line 50

def browse_otu_link(object)
  return nil if object.nil?
  otu = object.metamorphosize
  content_tag(:div, '', 'data-taxon-name' => object_tag(otu), 'data-redirect' => 'true', 'data-id' => otu.id, 'data-klass' => object.class.base_class.name.to_s, 'data-otu-button' => 'true')
end

#label_for_otu(otu) ⇒ Object 



10
11
12
13
14
15
 
# File 'app/helpers/otus_helper.rb', line 10

def label_for_otu(otu)
  return nil if otu.nil?
  [otu.name,
   label_for_taxon_name(otu.taxon_name)
  ].compact.join(': ')
end

#next_otus(otu) ⇒ Array

Returns of OTUs.

Returns:

  • (Array) —

    of OTUs



67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
 
# File 'app/helpers/otus_helper.rb', line 67

def next_otus(otu)
  if otu.taxon_name_id
    o = []
    t = otu.taxon_name.next_sibling
    unless t.nil?
      while o.empty?
        o = t&.otus.to_a
        break if t.nil?
        t = t.next_sibling
      end
    end
    o
  else
    Otu.where(project_id: otu.id).where('id > ?', otu.id).all
  end
end

#otu_autocomplete_selected_tag(otu) ⇒ String

Returns no HTML inside <input>.

Returns:

  • (String) —

    no HTML inside <input>



27
28
29
30
31
32
 
# File 'app/helpers/otus_helper.rb', line 27

def otu_autocomplete_selected_tag(otu)
  return nil if otu.nil? || (otu.new_record? && !otu.changed?)
  [otu.name,
   Utilities::Strings.nil_wrap('[',taxon_name_autocomplete_selected_tag(otu.taxon_name), ']')&.html_safe
  ].compact.join(' ')
end

#otu_distribution(otu, children = true) ⇒ Object

TODO:

* make properties universal
  type: 'Model',
  id: id,
  label: <label>

  • merge origin_otu_id: id to reference coordinate OTUs

target:
  type: Otu
  label:
  id

base:   # one level above target (or one level below shape?!)
  type:
  id:

shape: # Either GeographicArea or Georeference
   type
   id

Returns:

  • Hash A GeoJSON collection of distribution data in x parts

    need a `to_geo_json` for each object

 :asserted_distributions
    with shape
    without shapes
 :collection_objects
      with georeferences
      with GeographicAreas
 :type material
      with georeferences
      with GeographicAreas



158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
 
# File 'app/helpers/otus_helper.rb', line 158

def otu_distribution(otu, children = true)
  return {} if otu.nil?
  otus = if children
           otu.coordinate_otus_with_children
         else
           Otu.coordinate_otus(otu.id)
         end

  t = 40
  if otus.size > t
    return { request_too_large: true,
             message: "The number of children (#{t}) of this OTU is too large to presently return."
    }
  end

  h = {
    'type' => 'FeatureCollection',
    'features' => [],
    'properties' => {
      'target' => { # Top level target
        'id' => otu.id,
        'label' => label_for_otu(otu),
        'type' => 'Otu'
      }
    }
  }

  otus.each do |o|

    # internal target
    t = {
      'id' => o.id,
      'type' => 'Otu',
      'label' => label_for_otu(otu)
    }

    o.current_collection_objects.each do |c|
      if g = collection_object_to_geo_json_feature(c)
        g['properties']['target'] = t
        h['features'].push g
      end
    end

    o.asserted_distributions.each do |a|
      if g = asserted_distribution_to_geo_json_feature(a)
        g['properties']['target'] = t
        h['features'].push g
      end
    end

    o.type_materials.each do |e|
      if g = type_material_to_geo_json_feature(e)
        g['properties']['target'] = t
        h['features'].push g
      end
    end
  end
  h
end

#otu_link(otu) ⇒ Object 



34
35
36
37
 
# File 'app/helpers/otus_helper.rb', line 34

def otu_link(otu)
  return nil if otu.nil?
  link_to(otu_tag_elements(otu).join(' ').html_safe, otu)
end

#otu_tag(otu) ⇒ Object 



3
4
5
6
7
8
 
# File 'app/helpers/otus_helper.rb', line 3

def otu_tag(otu)
  return nil if otu.nil?
  a = otu_tag_elements(otu)
  a.push taxon_name_type_short_tag(otu.taxon_name)
  content_tag(:span, a.compact.join(' ').html_safe, class: :otu_tag)
end

#otu_tag_elements(otu) ⇒ Object 



17
18
19
20
21
22
23
 
# File 'app/helpers/otus_helper.rb', line 17

def otu_tag_elements(otu)
  return nil if otu.nil?
  [
    ( otu.name ? content_tag(:span, otu.name, class: :otu_tag_otu_name, title: otu.id) : nil ),
    ( otu.taxon_name ? content_tag(:span, full_taxon_name_tag(otu.taxon_name).html_safe, class: :otu_tag_taxon_name, title: otu.taxon_name.id) : nil)
  ].compact
end

#otus_link_list_tag(otus) ⇒ Object 



43
44
45
 
# File 'app/helpers/otus_helper.rb', line 43

def otus_link_list_tag(otus)
  otus.collect { |o| link_to(o.name, o) }.join(',')
end

#otus_radial(object) ⇒ Object 



61
62
63
 
# File 'app/helpers/otus_helper.rb', line 61

def otus_radial(object)
  content_tag(:div, '', 'data-global-id' => object.to_global_id.to_s, 'data-otu-radial' => 'true')
end

#otus_radial_disambiguate(object) ⇒ Object 



56
57
58
59
 
# File 'app/helpers/otus_helper.rb', line 56

def otus_radial_disambiguate(object)
  otu = object.metamorphosize
  content_tag(:div, '', 'data-taxon-name' => object_tag(otu), 'data-redirect' => 'false', 'data-id' => otu.id, 'data-klass' => object.class.base_class.name.to_s, 'data-otu-button' => 'true')
end

#otus_search_form ⇒ Object 



39
40
41
 
# File 'app/helpers/otus_helper.rb', line 39

def otus_search_form
  render('/otus/quick_search_form')
end

#parent_otus(otu) ⇒ Object 



105
106
107
 
# File 'app/helpers/otus_helper.rb', line 105

def parent_otus(otu)
  otu.taxon_name&.parent&.otus&.all || []
end

#parents_by_nomenclature(otu) ⇒ Object

See also otus#ancestor_otu_ids ?



110
111
112
113
114
115
116
117
118
119
120
121
122
 
# File 'app/helpers/otus_helper.rb', line 110

def parents_by_nomenclature(otu)
  above = [ ]
  if otu.taxon_name_id
    TaxonName.ancestors_of(otu.taxon_name)
      .select('taxon_names.*, taxon_name_hierarchies.generations')
      .that_is_valid.joins(:otus)
      .distinct
      .reorder('taxon_name_hierarchies.generations DESC, taxon_names.cached_valid_taxon_name_id').each do |t|
        above.push [t.cached, t.otus.to_a] # TODO: to_a vs. pluck
      end
  end
  above
end

#previous_otus(otu) ⇒ Array

Some OTUs don't have TaxonName, skip along until we hit one.

Returns:

  • (Array) —

    of OTUs



88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
 
# File 'app/helpers/otus_helper.rb', line 88

def previous_otus(otu)
  if otu.taxon_name_id
    o = []
    t = otu.taxon_name.previous_sibling
    unless t.nil?
      while o.empty?
        o = t&.otus.to_a
        break if t.nil?
        t = t.previous_sibling
      end
    end
    o
  else
    Otu.where(project_id: otu.id).where('id < ?', otu.id).all
  end
end