Module: Otus::CatalogHelper

Defined in:
app/helpers/otus/catalog_helper.rb

Instance Method Summary collapse

Instance Method Details

#history_otu(otu, r, c, target = nil) ⇒ Object



22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
# File 'app/helpers/otus/catalog_helper.rb', line 22

def history_otu(otu, r, c, target = nil)
  name = otu_tag(otu)
  body = nil
  css = nil
  soft_validation = nil

  if target
    body = link_to(name, browse_taxa_task_path(otu_id: otu.id) )
  else
    body = name
  end

  if otu == r
    css = 'history__reference_otu'
  else
    css = 'history__related_otu'
    soft_validation = soft_validation_alert_tag(otu)
  end

  (:span, body + soft_validation.to_s, class: [css, original_citation_css(otu, c), :history__otu ])
end

#otu_catalog_entry_item_tag(catalog_entry_item) ⇒ Object



3
4
5
# File 'app/helpers/otus/catalog_helper.rb', line 3

def otu_catalog_entry_item_tag(catalog_entry_item)
  otu_catalog_line_tag(catalog_entry_item, catalog_entry_item.base_object) # base object might be wrong!! (reference_otu from entry instead)
end

#otu_catalog_line_tag(otu_catalog_entry_item, reference_otu) ⇒ Object

target = :browse_nomenclature_task_path



7
8
9
10
11
12
13
14
15
16
17
18
19
20
# File 'app/helpers/otus/catalog_helper.rb', line 7

def otu_catalog_line_tag(otu_catalog_entry_item, reference_otu) # target = :browse_nomenclature_task_path
  i = otu_catalog_entry_item
  t = i.base_object
  c = i.citation
  r = reference_otu

  [ history_otu(t, r, c),        # the subject, or protonym
    history_in(c&.source),       # citation for related name
    history_pages(c),           # pages for citation of related name
    history_citation_notes(c), # Notes on the citation
    history_topics(c)           # Topics on the citation
  ].compact.join.html_safe

end

#otu_descendants_and_synonyms(otu = self, data: {}, similar_otus: [], common_names: false, language_alpha2: nil, max_descendants_depth: Float::INFINITY) ⇒ Object

}

Starting from an OTU, recurse via TaxonName and build a descendants heirarchy. Arbitrarily picks one OTU as the basis for the next if there are > 1 per Taxon Name

Parameters:

  • otu (an Otu) (defaults to: self)
  • data (Hash) (defaults to: {})

    the data to return

  • similar_otus (Array) (defaults to: [])

    of otu_ids, the ids of OTUs to skip when assigning nodes (e.g. clones, or similar otus)

  • max_descendants_depth (Numeric) (defaults to: Float::INFINITY)

    the maximum depth of the descendants tree. Default is unbounded

Returns:

  • Hash { otu_id: 123,

    label: label_for_otu(),
    otu_clones: [otu1.id, otu2.id],                   # OTUs with the same taxon name AND `name`
    similar_otus: { otu.id => label_for_otu(), ...},  # OTUs with the same taxon name, but different `name`
    nomenclatural_synonyms: [ full_original_taxon_name_label*, ...},
    descendants: [{ ... as above ...}]
    leaf_node: boolean                                # Signals whether bottom of the tree was reached. Useful max_descendants_depth is set
    


62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
# File 'app/helpers/otus/catalog_helper.rb', line 62

def otu_descendants_and_synonyms(
  otu = self,
  data: {},
  similar_otus: [],
  common_names: false,
  language_alpha2: nil,
  max_descendants_depth: Float::INFINITY
)
  s = Otu.where(taxon_name_id: otu.taxon_name_id).where.not(id: otu.id).where.not(name: (otu.name.presence)).to_a

  similar_otus += s.collect { |p| p.id }

  synonyms = otu.taxon_name&.synonyms.where(type: 'Protonym').where.not(id: otu.taxon_name_id)&.order(:cached, :cached_author_year)

  data = { otu_id: otu.id,
           name: a = full_taxon_name_tag(otu.taxon_name),
           otu_clones: Otu.where(name: otu.name, taxon_name_id: otu.taxon_name_id).where.not(id: otu.id).pluck(:id),
           similar_otus: s.inject({}){|hsh, n| hsh[n.id] = label_for_otu(n) ; hsh },
           nomenclatural_synonyms: ( (synonyms&.collect{|l| full_original_taxon_name_tag(l) || full_taxon_name_tag(l) } || []) - [a]).uniq, # This is labels, combinations can duplicate
           common_names: (common_names ? otu_inventory_common_names(otu, language_alpha2) : []),
           descendants: []}

  if otu.taxon_name
    descendants = otu.taxon_name.descendants.where(parent: otu.taxon_name).that_is_valid
    if max_descendants_depth >= 1
      descendants.order(:cached, :cached_author_year).each do |d|
        if o = d.otus.order(name: 'DESC', id: 'ASC').first # arbitrary pick an OTU, prefer those without `name`. t since we summarize across identical OTUs, this is not an issue
          data[:descendants].push otu_descendants_and_synonyms(
            o,
            data:,
            similar_otus:,
            max_descendants_depth: max_descendants_depth - 1
          ) unless similar_otus.include?(o.id)
        end
      end
      data[:leaf_node] = data[:descendants].empty?
    else
      data[:leaf_node] = descendants.where.not(id: similar_otus).none?
    end
  end
  data
end

#otu_inventory_common_names(otu, language_alpha_2) ⇒ Object



105
106
107
108
109
110
# File 'app/helpers/otus/catalog_helper.rb', line 105

def otu_inventory_common_names(otu, language_alpha_2)
  return nil if otu.nil?
  o = CommonName.where(project_id: sessions_current_project_id, otu:)
  o = o.where(language: Language.where(alpha_2: language_alpha_2.downcase)) if language_alpha_2.present?
  return o.collect{|a| {name: a.name, language: a&.language&.english_name } }
end