Module: DwcOccurrencesHelper

Defined in:
app/helpers/dwc_occurrences_helper.rb

Constant Summary collapse

DWC_OCCURRENCE_DISPLAY_FORMATTERS = 
{
  'footprintWKT' => :display_footprint_wkt
}.freeze

Instance Method Summary collapse

Instance Method Details

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



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# File 'app/helpers/dwc_occurrences_helper.rb', line 107

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

#display_footprint_wkt(value, max_length: 100) ⇒ Object 



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# File 'app/helpers/dwc_occurrences_helper.rb', line 6

def display_footprint_wkt(value, max_length: 100)
  return value if value.blank?

  wkt = value.to_s

  return wkt if wkt.lstrip.start_with?('POINT') || wkt.length <= max_length

  "#{wkt[0, max_length]}..."
end

#dwc_column(dwc_occurrence) ⇒ Object 



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# File 'app/helpers/dwc_occurrences_helper.rb', line 43

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|
    formatter = DWC_OCCURRENCE_DISPLAY_FORMATTERS[k.to_s]
    value = formatter ? public_send(formatter, v) : v
    if !v.blank?
      r.push tag.tr( (tag.td(k) + tag.td(value)).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



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# File 'app/helpers/dwc_occurrences_helper.rb', line 148

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 



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# File 'app/helpers/dwc_occurrences_helper.rb', line 29

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 



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# File 'app/helpers/dwc_occurrences_helper.rb', line 59

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

#format_dwc_occurrence_attributes_for_ui(attributes) ⇒ Object 



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# File 'app/helpers/dwc_occurrences_helper.rb', line 16

def format_dwc_occurrence_attributes_for_ui(attributes)
  attributes = attributes.dup

  attributes.each_key do |key|
    formatter = DWC_OCCURRENCE_DISPLAY_FORMATTERS[key.to_s]
    next if formatter.nil?

    attributes[key] = public_send(formatter, attributes[key])
  end

  attributes
end

#is_stale_metadata_tag(dwc_occurrence) ⇒ Object

Returns String html table or empty.

Returns:

  • String html table or empty



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# File 'app/helpers/dwc_occurrences_helper.rb', line 131

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