Class: DwcOccurrence

Inherits:
ApplicationRecord show all
Includes:
Housekeeping
Defined in:
app/models/dwc_occurrence.rb

Overview

A Darwin Core Record for the Occurrence core. Field generated from Ruby dwc-meta, which references the same spec that is used in the IPT, and the Dwc Assistant. Each record references a specific CollectionObject, AssertedDistribution, or FieldOccurrence.

Important: This is a cache/index, data here are periodically destroyed and regenerated from multiple tables in TW.

DWC attributes are camelCase to facilitate matching dwcClass is a replacement for the Rails reserved ‘Class’

All DC attributes (attributes not in DwcOccurrence::TW_ATTRIBUTES) in this table are namespaced to dc (“purl.org/dc/terms/”, “rs.tdwg.org/dwc/terms/”)

README:

There is a two part strategy to building the index. 1) An individual record will rebuild on request with `parameter to collection_objects/123/dwc*?build=true`.
2) Wipe, and rebuild on some schedule. It would in theory be possible to track and rebuild when a class of every property was created (or updated), however
this is a lot of overhead to inject/code for a lot of models. It would inject latency at numerous stages that would perhaps impact UI performance.

Several terms are introduced in code:

* ghost - A DwcOccurrence record whose dwc_occurrence object has been destroyed (i.e. an error in cleanup, should ideally never happen)
* stale - an _aproximation_ checking to see that the time of build of related records is _older_ than the current index
* flagged (for rebuild) - a record related to the dwc_occurrence_object(s) has been updated, triggering the need for re-indexing 1 or more records

TODO: The basisOfRecord CVTs are not super informative.

We know collection object is definitely 1:1 with PreservedSpecimen, however
AssertedDistribution could be HumanObservation (if source is person), or ... what? if
its a published record.  Seems we need a 'PublishedAssertation', just like we model the data.

Gotchas.

* updated_at is set by touching the record, not via housekeeping.

Constant Summary collapse

DC_NAMESPACE = 
'http://rs.tdwg.org/dwc/terms/'.freeze
TW_ATTRIBUTES =

Not yet implemented, but likely needed (at an even higher level) ? :id

[
  :id,
  :project_id,
  :created_at,
  :updated_at,
  :created_by_id,
  :updated_by_id,
  :dwc_occurrence_object_type,
  :dwc_occurrence_object_id
].freeze
HEADER_CONVERTERS = 
{
  'dwcClass' => 'class',
}.freeze
NOMENCLATURE_RANKS =

Supported ranks (fields in db)

[
  :kingdom,
  :phylum,
  :dwcClass,
  :order,
  :superfamily,
  :family,
  :subfamily,
  :tribe,
  :subtribe,
  :genus,
  :specificEpithet
].freeze

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#occurrence_identifier ⇒ Object

Returns the value of attribute occurrence_identifier.


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# File 'app/models/dwc_occurrence.rb', line 90

def occurrence_identifier
  @occurrence_identifier
end

Class Method Details

.annotates? ⇒ Boolean

Returns:

  • (Boolean)
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# File 'app/models/dwc_occurrence.rb', line 137

def self.annotates?
  false
end

.by_collection_object_filter(filter_scope: nil, project_id: nil) ⇒ Object

TODO: use filters Return scopes by a collection object filter

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# File 'app/models/dwc_occurrence.rb', line 166

def self.by_collection_object_filter(filter_scope: nil, project_id: nil)
  return DwcOccurrence.none if project_id.nil? || filter_scope.nil?

  c = ::CollectionObject.arel_table
  d = arel_table

  # TODO: hackish
  k = ::CollectionObject.select('coscope.id').from( '(' + filter_scope.to_sql + ') as coscope ' )

  a = self.object_join('CollectionObject')
    .where('dwc_occurrences.project_id = ?', project_id)
    .where(dwc_occurrence_object_id: k)
    .select(::DwcOccurrence.target_columns) # TODO !! Will have to change when AssertedDistribution and other types merge in
  a
end

.computed_columns ⇒ Scope

Returns the columns inferred to have data.

Returns:

  • (Scope) —

    the columns inferred to have data

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# File 'app/models/dwc_occurrence.rb', line 218

def self.computed_columns
  select(target_columns)
end

.empty_fields ⇒ Array

Returns of column names as symbols that are blank in ALL projects (not just this one).

Returns:

  • (Array) —

    of column names as symbols that are blank in ALL projects (not just this one)

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# File 'app/models/dwc_occurrence.rb', line 184

def self.empty_fields
  empty_in_all_projects = ActiveRecord::Base.connection.execute("select attname
  from pg_stats
  where tablename = 'dwc_occurrences'
  and most_common_vals is null
  and most_common_freqs is null
  and histogram_bounds is null
  and correlation is null
  and null_frac = 1;").pluck('attname').map(&:to_sym)

  empty_in_all_projects #  - target_columns
end

.excluded_columns ⇒ Array

Returns of symbols.

Returns:

  • (Array) —

    of symbols

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# File 'app/models/dwc_occurrence.rb', line 212

def self.excluded_columns
  ::DwcOccurrence.columns.collect{|c| c.name.to_sym} - (self.target_columns - [:dwc_occurrence_object_id, :dwc_occurrence_object_type])
end

.object_join(target) ⇒ Object

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# File 'app/models/dwc_occurrence.rb', line 141

def self.object_join(target)
  return DwcOccurrence.none unless ['CollectionObject', 'AssertedDistribution', 'FieldOccurrence'].include?(target)
  a = arel_table
  b = target.safe_constantize.arel_table # hmm - :: required
  j = a.join(b).on(a[:dwc_occurrence_object_type].eq(target).and(a[:dwc_occurrence_object_id].eq(b[:id])))
  joins(j.join_sources)
end

.scoped_by_otu(otu) ⇒ Scope

Returns all DwcOccurrences for the Otu

  • Includes synonymy (coordinate OTUs).

Returns:

  • (Scope) —

    all DwcOccurrences for the Otu

    • Includes synonymy (coordinate OTUs).

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# File 'app/models/dwc_occurrence.rb', line 152

def self.scoped_by_otu(otu)
  if otu.taxon_name_id.present?
    ::Queries::DwcOccurrence::Filter.new({
      taxon_name_id: otu.taxon_name_id,
    }).all
  else
    ::Queries::DwcOccurrence::Filter.new({
      otu_id: otu.id,
    }).all
  end
end

.stale(kind = 'CollectionObject') ⇒ Object (protected)

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# File 'app/models/dwc_occurrence.rb', line 368

def self.stale(kind = 'CollectionObject')
  tbl = kind.tableize
  DwcOccurrence.joins("LEFT JOIN #{tbl} tbl on dwc_occurrences.dwc_occurrence_object_id = tbl.id")
    .where('tbl.id IS NULL and dwc_occurrences.dwc_occurrence_object_type = ?', kind )
end

.sweep ⇒ Object (protected)

Delete all DwcOccurrence records where object is missing.

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# File 'app/models/dwc_occurrence.rb', line 361

def self.sweep
  %w{CollectionObject AssertedDistribution FieldOccurrence}.each do |k|
    stale(k).delete_all
  end
  true
end

.target_columns ⇒ Array

!! TODO: When we come to adding AssertedDistributions, FieldOccurrnces, etc. we will have to make this more flexible

Returns:

  • (Array) —

    of symbols

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# File 'app/models/dwc_occurrence.rb', line 201

def self.target_columns
  [:id, # must be in position 0
   :occurrenceID,
   :basisOfRecord,
   :dwc_occurrence_object_id,   # !! We don't want this, but need it in joins, it is removed in trim via `.excluded_columns` below
   :dwc_occurrence_object_type, # !! ^
  ] + CollectionObject::DwcExtensions::DWC_OCCURRENCE_MAP.keys
end

Instance Method Details

#as_json(options = {}) ⇒ Object

Strip nils when ‘to_json` used

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# File 'app/models/dwc_occurrence.rb', line 93

def as_json(options = {})
  super(options.merge(except: attributes.keys.select{ |key| self[key].nil? }))
end

#asserted_distribution ⇒ Object

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# File 'app/models/dwc_occurrence.rb', line 114

def asserted_distribution
  dwc_occurrence_object_type == 'AssertedDistribution' ? dwc_occurrence_object : nil
end

#basis ⇒ Object

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# File 'app/models/dwc_occurrence.rb', line 222

def basis
  case dwc_occurrence_object_type
  when 'CollectionObject'
    if dwc_occurrence_object.is_fossil?
      return 'FossilSpecimen'
    else
      return 'PreservedSpecimen'
    end
  when 'AssertedDistribution'
    # Used to fork b/b Source::Human and Source::Bibtex:
    case dwc_occurrence_object.source&.type || dwc_occurrence_object.sources.order(cached_nomenclature_date: :DESC).first.type
    when 'Source::Bibtex'
      return 'MaterialCitation'
    when 'Source::Human'
      return 'HumanObservation'
    else # Not recommended at this point
      return 'Occurrence'
    end
  when 'FieldOccurrence'
    if dwc_occurrence_object.machine_output?
      return 'MachineObservation'
    else
      return 'HumanObservation'
    end
  end

  'Undefined'
end

#collecting_event ⇒ Object

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# File 'app/models/dwc_occurrence.rb', line 122

def collecting_event
  collection_object&.collecting_event || field_occurrence&.collecting_event
end

#collection_object ⇒ Object

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# File 'app/models/dwc_occurrence.rb', line 110

def collection_object
  dwc_occurrence_object_type == 'CollectionObject' ? dwc_occurrence_object : nil
end

#create_object_uuid ⇒ Object (protected)

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# File 'app/models/dwc_occurrence.rb', line 347

def create_object_uuid
  @occurrence_identifier = Identifier::Global::Uuid::TaxonworksDwcOccurrence.create!(
    identifier_object: dwc_occurrence_object,
    by: dwc_occurrence_object&.creator, # revisit, why required?
    project_id: dwc_occurrence_object&.project_id, # Current.project_id,  # revisit, why required?
    is_generated: true)
end

#dwc_json ⇒ Object

Returns Hash

  • Legally formatted DwC fields only, with things like ‘dwcClass` translated

  • Only fields with values returned

  • Keys are sorted.

Returns:

  • Hash

    • Legally formatted DwC fields only, with things like ‘dwcClass` translated

    • Only fields with values returned

    • Keys are sorted

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# File 'app/models/dwc_occurrence.rb', line 102

def dwc_json
  a = as_json.reject!{|k,v| TW_ATTRIBUTES.include?(k.to_sym) || v.nil?}
  HEADER_CONVERTERS.keys.each do |k|
    a[ HEADER_CONVERTERS[k] ] = a.delete(k) if a[k]
  end
  a.sort.to_h
end

#field_occurrence ⇒ Object

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# File 'app/models/dwc_occurrence.rb', line 118

def field_occurrence
  dwc_occurrence_object_type == 'FieldOccurrence' ? dwc_occurrence_object : nil
end

#generate_uuid_if_required(force = false) ⇒ Object

TODO: quick check if occurrenceID exists in table?! <-> locking sync !?

Parameters:

  • force (Boolean) (defaults to: false) —

    true - only create identifier if identifier exists false - check if occurrenceID is present, if it is, assume identifier (still) exists

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# File 'app/models/dwc_occurrence.rb', line 263

def generate_uuid_if_required(force = false)
  if force # really make sure there is an object to work with
    create_object_uuid if !occurrence_identifier && !dwc_occurrence_object.nil? # TODO: can be simplified when inverse_of/validation added to identifiers
  else # assume if occurrenceID is not blank identifier is present
    if occurrenceID.blank?
      create_object_uuid if !occurrence_identifier && !dwc_occurrence_object.nil? # TODO: can be simplified when inverse_of/validation added to identifiers
    end
  end
end

#is_stale? ⇒ Boolean

!! This a spot check, it’s not (yet) coded to be comprehensive. !! You should request a full rebuild (rebuild=true) at display time !! to ensure an up-to-date individual record

Returns:

  • (Boolean) —

    By looking at the data, determine if a related record has been updated since this record ws updated at.

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# File 'app/models/dwc_occurrence.rb', line 281

def is_stale?
  case dwc_occurrence_object_type
  when 'CollectionObject'
    times = is_stale_metadata.values
    n = read_attribute(:updated_at)

    times.each do |v|
      return true if v > n
    end

    return false
  else # AssertedDistribution
    return  dwc_occurrence_object.updated_at > updated_at
  end
end

#is_stale_metadata ⇒ Object

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# File 'app/models/dwc_occurrence.rb', line 297

def is_stale_metadata
  case dwc_occurrence_object_type
  when 'CollectionObject'

    o = CollectionObject.select(:id, :updated_at, :collecting_event_id).find_by(id: dwc_occurrence_object_id)
    ce = CollectingEvent.select(:id, :updated_at).find_by(id: o.collecting_event_id)

    td =  dwc_occurrence_object&.taxon_determinations.order(:position).first

    tdr = if td&.otu&.taxon_name&.cached_name_and_author_year != scientificName
            td.updated_at
          else
            nil
          end

    tc = if fieldNumber != o.dwc_field_number
           collecting_event.identifiers.where(type: 'Identifier::Local::FieldNumber').first.updated_at
         else
           nil
         end

    return {
      collection_object: o.updated_at, # Shouldn't be neccessary since on_save rebuilds, but cheap here
      collecting_event: ce&.updated_at,
      trip_code: tc,
      taxon_determination: dwc_occurrence_object.taxon_determinations.order(:position)&.first&.updated_at,
      taxon_determination_reorder: tdr,
      taxon_determination_roles: dwc_occurrence_object.taxon_determinations.order(:position)&.first&.updated_at,
      biocuration_classification: dwc_occurrence_object.biocuration_classifications.order(:updated_at).first&.updated_at,
      georeferences: dwc_occurrence_object.georeferences.order(:updated_at).first&.updated_at,

      data_attributes: dwc_occurrence_object.data_attributes.order(:updated_at).first&.updated_at,

      collection_object_roles: dwc_occurrence_object.roles.order(:updated_at).first&.updated_at,
      collecting_event_data_attributes: dwc_occurrence_object.collecting_event&.data_attributes&.order(:updated_at)&.first&.updated_at,
      collecting_event_roles: dwc_occurrence_object.collecting_event&.roles&.order(:updated_at)&.first&.updated_at
      # citations?
      # tags?!
    }.select{|k,v| !v.nil?}

  else # AssertedDistribution
    {
      asserted_distribution: dwc_occurrence_object.updated_at,
      # TODO: Citations
    }
  end
end

#otu ⇒ Object

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# File 'app/models/dwc_occurrence.rb', line 126

def otu
  case dwc_occurrence_object_type
  when 'AssertedDistribution'
    dwc_occurrence_object.otu
  when 'CollectionObject'
    collection_object.otu
  when 'FieldOccurrence'
    field_occurrence.otu
  end
end

#set_metadata_attributes ⇒ Object (protected)

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# File 'app/models/dwc_occurrence.rb', line 355

def set_metadata_attributes
  write_attribute( :basisOfRecord, basis)
  write_attribute( :occurrenceID, occurrence_identifier&.identifier)  # TODO: Slightly janky to touch this here, might not be needed with new hooks
end

#uuid_identifier_scope ⇒ Object

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# File 'app/models/dwc_occurrence.rb', line 251

def uuid_identifier_scope
  dwc_occurrence_object&.identifiers&.where('identifiers.type like ?', 'Identifier::Global::Uuid%')&.order(:position)
end