Module: DwcOccurrencesHelper

Defined in:
app/helpers/dwc_occurrences_helper.rb

Instance Method Summary collapse

Instance Method Details

#collector_global_id_metadata(dwc_occurrences = nil, project_id = nil) ⇒ Object 



81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
 
# File 'app/helpers/dwc_occurrences_helper.rb', line 81

def collector_global_id_metadata(dwc_occurrences = nil, project_id = nil)
  records = dwc_occurrences
  project_id ||= sessions_current_project_id

  # Anticipate multiple sources of records in future (e.g. AssertedDistribution)
  records ||= ::DwcOccurrence.where(project_id: project_id)

  a = ::Person
    .left_joins(:identifiers)
    .joins(collecting_events: [:collection_objects])
    .joins("JOIN dwc_occurrences dwo on dwo.dwc_occurrence_object_id = collection_objects.id AND dwo.dwc_occurrence_object_type = 'CollectionObject'")
    .where(dwo: {project_id: project_id})
    .order(:cached)

  with_global_id = a.where("identifiers.type ILIKE 'Identifier::Global%'").distinct.pluck(:id, :cached)
  without_global_id =  a.where("(identifiers.id is null) OR identifiers.type not ILIKE 'Identifier::Global%'").distinct.pluck(:id, :cached)

  return {
    without_global_id: without_global_id,
    with_global_id: with_global_id
  }
end

#dwc_column(dwc_occurrence) ⇒ Object 



17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
 
# File 'app/helpers/dwc_occurrences_helper.rb', line 17

def dwc_column(dwc_occurrence)
  return nil if dwc_occurrence.nil?

  r = []
  dwc_occurrence.dwc_occurrence_object.dwc_occurrence_attributes(false).each do |k, v|
    #    CollectionObject::DwcExtensions::DWC_OCCURRENCE_MAP.keys.each do |k|
    next if [:footprintWKT].include?(k)
    if !v.blank?
      r.push tag.tr( (tag.td(k) + tag.td(v)).html_safe )
    end
  end

  r.push tag.tr( (tag.td('basisOfRecord') + tag.td(dwc_occurrence.basisOfRecord)).html_safe )
  tag.table(r.join.html_safe)
end

#dwc_determined_to_rank(otu, project_id) ⇒ Object

!! Rescopes to valid TaxonName

Returns:

  • Hash a rank -> number of determinations to that rank (and not finer) result



122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
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
 
# File 'app/helpers/dwc_occurrences_helper.rb', line 122

def dwc_determined_to_rank(otu, project_id)
  # the target levels
  d = [
    :dwcClass,
    :order,
    :family,
    :genus,
    :specificEpithet
  ]

  return {} if otu.taxon_name.nil?

  tn = otu.taxon_name.valid_taxon_name

  pid = otu.project_id

  # Around a 3x speedup from filter-based derivations
  s = "select sum(\"individualCount\") from dwc_occurrences dwc
         join taxon_determinations td on dwc.dwc_occurrence_object_id = td.taxon_determination_object_id AND td.taxon_determination_object_type = 'CollectionObject' AND td.project_id = #{pid}
         join otus o on td.otu_id = o.id AND o.project_id = #{pid}
         join taxon_names tn on o.taxon_name_id = tn.id AND tn.project_id = #{pid}
         join taxon_name_hierarchies tnh on tnh.descendant_id = tn.id AND tnh.ancestor_id = #{tn.id}
         where dwc.project_id = #{pid}"

  r = tn.rank_name.to_sym
  r = :dwcClass if r == :class

  t = {
    specificEpithet: 0
  }

  # Select counts for only relevant ranks
  i = false
  d.each do |rank|
    if i
      t[rank] = 0
    elsif rank == r
      i = true
      t[rank] = 0
    end
  end

  # So we can use empty_rank facet
  q = ::Queries::DwcOccurrence::Filter.new( project_id: )

  k = t.keys.sort{|a,b| d.index(a) <=> d.index(b)}

  # We must make ranks we don't reference null to, so
  # use this master list
  a = DwcOccurrence::NOMENCLATURE_RANKS

  k.each do |r|
    p = s.dup
    # puts "--- #{r} present"
    p << " AND dwc.\"#{r}\" IS NOT NULL"
    absent = a[a.index(r)+1..a.length] # find all empty ranks below this rank
    # puts absent

    q.empty_rank = absent
    if i = q.empty_rank_facet&.to_sql&.gsub(/dwc_occurrences/, 'dwc')
      p << ' AND ' + i
    end

    t[r] = DwcOccurrence.find_by_sql(p).first.sum
  end

  # Cleanup for human readability
  t[:class] = t[:dwcClass] if t[:dwcClass]
  t[:species] = t[:specificEpithet] # always

  t.delete(:dwcClass)
  t.delete(:specificEpithet)

  t.sort{|a,b| d.index(b) <=> d.index(a) }.to_h
end

#dwc_occurrence_health_tag(dwc_occurrence) ⇒ Object 



3
4
5
6
7
8
9
10
11
12
13
14
15
 
# File 'app/helpers/dwc_occurrences_helper.rb', line 3

def dwc_occurrence_health_tag(dwc_occurrence)
  a = [ ]
  if dwc_occurrence.nil?
    a.push tag.span('Darwin Core Occurrence not built', class: [:feedback, 'feedback-thin', 'feedback-danger'])
  else
    a.push tag.span('Referenced data are younger than this record', class: [:feedback, 'feedback-thin', 'feedback-warning']) if dwc_occurrence.is_stale?
    a.push tag.span('A new version of the DwC builder is available', class: [:feedback, 'feedback-thin', 'feedback-warning']) if DateTime.parse(::Export::Dwca::INDEX_VERSION.last).to_i > dwc_occurrence.updated_at.to_i
  end
  a.push tag.span('Up-to-date', class: [:feedback, 'feedback-info']) if a.empty?

  a.push tag.span('TW DwcOccurrence id (internal index/use only): ' + dwc_occurrence.to_param, class: [:feedback, 'feedback-secondary'])
  a.join(' ').html_safe
end

#dwc_occurrences_metadata(dwc_occurrences = nil, project_id: nil) ⇒ Object 



33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
 
# File 'app/helpers/dwc_occurrences_helper.rb', line 33

def dwc_occurrences_metadata(dwc_occurrences = nil, project_id: nil)
  records = dwc_occurrences
  project_id ||= sessions_current_project_id

  # Anticipate multiple sources of records in future (e.g. AssertedDistribution)
  collection_objects = CollectionObject.where(project_id: project_id)
  records ||= DwcOccurrence.where(project_id: project_id) # .where(dwc_occurrence_object_type: 'CollectionObject').all
  data = collection_objects.joins(:dwc_occurrence)

  a = {
    health: {
      'Kingdom rank present': TaxonName.where(project_id: project_id).with_rank_class_including('Kingdom').any?,
      'DwcOccurrence records without occurrenceID (on collection objects)': records.where(occurrenceID: nil).count,
      'Total collection objects': collection_objects.count,
      'Collection objects without UUids': collection_objects.count - collection_objects.joins(:identifiers).where("identifiers.type ilike 'Identifier::Global::Uuid%'").distinct.count,
      'Collection objects without DwcOccurrence records': collection_objects.where.missing(:dwc_occurrence).count
    },

    # updated_at takes 'updated_at > ?'  to mean "between the time provided for ? and NOW

    collection_objects: {
      record_total: collection_objects.count,
      enumerated_total: collection_objects.sum(:total),
      freshness: {
        never: collection_objects.where.missing(:dwc_occurrence).count,
        one_day: data.where("dwc_occurrences.updated_at >= ?", 1.day.ago).count,
        one_week: data.where("dwc_occurrences.updated_at <= ? and dwc_occurrences.updated_at >= ?", 1.day.ago, 1.week.ago).count,
        one_month: data.where("dwc_occurrences.updated_at <= ? and dwc_occurrences.updated_at >= ?", 1.week.ago, 1.month.ago).count,
        one_year: data.where("dwc_occurrences.updated_at <= ? and dwc_occurrences.updated_at >= ?", 1.month.ago, 1.year.ago).count,
        greater_than_one_year: data.where("dwc_occurrences.updated_at < ?", 1.year.ago).count
      },
    },

    index: { # the dwc_occurrences
      record_total: records.count,
      enumerated_total: records.sum(:individualCount),
      freshness: {
        never: 0,
        one_day: records.where("dwc_occurrences.updated_at >= ?", 1.day.ago).count,
        one_week: records.where("dwc_occurrences.updated_at <= ? and dwc_occurrences.updated_at >= ?", 1.day.ago, 1.week.ago).count,
        one_month: records.where("dwc_occurrences.updated_at <= ? and dwc_occurrences.updated_at >= ?", 1.week.ago, 1.month.ago).count,
        one_year: records.where("dwc_occurrences.updated_at <= ? and dwc_occurrences.updated_at >= ?", 1.month.ago, 1.year.ago).count,
        greater_than_one_year: records.where("dwc_occurrences.updated_at < ?", 1.year.ago).count
      }
    }
  }
end

#is_stale_metadata_tag(dwc_occurrence) ⇒ Object

Returns String html table or empty.

Returns:

  • String html table or empty



105
106
107
108
109
110
111
112
113
114
115
116
117
 
# File 'app/helpers/dwc_occurrences_helper.rb', line 105

def is_stale_metadata_tag(dwc_occurrence)
  d = dwc_occurrence.is_stale_metadata
  u = dwc_occurrence.updated_at
  return '' if d.empty?

  tag.table(
    d.collect{|k,v|
      tag.tr(
        ( tag.td(k.to_s.humanize) + tag.td( (u < v) ? tag.span(v, class: [:feedback, 'feedback-thin', 'feedback-danger']) : distance_of_time_in_words(u, v) ) ).html_safe
      )
    }.join.html_safe
  )
end