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 or AssertedDistribution.

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

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.



93
94
95
 
# File 'app/models/dwc_occurrence.rb', line 93

def occurrence_identifier
  @occurrence_identifier
end

Class Method Details

.annotates? ⇒ Boolean

Returns:

  • (Boolean) 


116
117
118
 
# File 'app/models/dwc_occurrence.rb', line 116

def self.annotates?
  false
end

.asserted_distributions_join ⇒ ActiveRecord::Relation

that matches, consider moving to Shared

Returns:

  • (ActiveRecord::Relation) 


134
135
136
137
138
139
 
# File 'app/models/dwc_occurrence.rb', line 134

def self.asserted_distributions_join
  a = arel_table
  b = ::AssertedDistribution.arel_table
  j = a.join(b).on(a[:dwc_occurrence_object_type].eq('AssertedDistribution').and(a[:dwc_occurrence_object_id].eq(b[:id])))
  joins(j.join_sources)
end

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

TODO: use filters Return scopes by a collection object filter



179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
 
# File 'app/models/dwc_occurrence.rb', line 179

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.collection_objects_join
    .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

.collection_objects_join ⇒ ActiveRecord::Relation

that matches, consider moving to Shared

Returns:

  • (ActiveRecord::Relation) 


125
126
127
128
129
130
 
# File 'app/models/dwc_occurrence.rb', line 125

def self.collection_objects_join
  a = arel_table
  b = ::CollectionObject.arel_table
  j = a.join(b).on(a[:dwc_occurrence_object_type].eq('CollectionObject').and(a[:dwc_occurrence_object_id].eq(b[:id])))
  joins(j.join_sources)
end

.computed_columns ⇒ Scope

Returns the columns inferred to have data.

Returns:

  • (Scope) —

    the columns inferred to have data



231
232
233
 
# File 'app/models/dwc_occurrence.rb', line 231

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)



197
198
199
200
201
202
203
204
205
206
207
208
 
# File 'app/models/dwc_occurrence.rb', line 197

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



225
226
227
 
# File 'app/models/dwc_occurrence.rb', line 225

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

.scoped_by_otu(otu) ⇒ Scope

TODO: Move to DwcOccurrence filter

Returns:

  • (Scope) —

    all DwcOccurrences for the Otu

    • Includes synonymy (coordinate OTUs).



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
 
# File 'app/models/dwc_occurrence.rb', line 147

def self.scoped_by_otu(otu)
  a,b = nil, nil

  if otu.taxon_name_id.present?
    a = ::Queries::DwcOccurrence::Filter.new(
      asserted_distribution_query: {
        taxon_name_query: {
          taxon_name_id: otu.taxon_name_id,
          descendants: false, # include self
          synonymify: true } })

    b = ::Queries::DwcOccurrence::Filter.new(
      collection_object_query: {
        taxon_name_query: {
          taxon_name_id: otu.taxon_name_id,
          descendants: false, # include self
          synonymify: true } })
  else
    a = ::Queries::DwcOccurrence::Filter.new(
      asserted_distribution_query: {
        otu_id: otu.id})

    b = ::Queries::DwcOccurrence::Filter.new(
      collection_object_query: {
        otu_query: { otu_id: otu.id}})
  end

  from("((#{a.all.to_sql}) UNION (#{b.all.to_sql})) as dwc_occurrences")
end

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



374
375
376
377
378
 
# File 'app/models/dwc_occurrence.rb', line 374

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.



367
368
369
370
371
372
 
# File 'app/models/dwc_occurrence.rb', line 367

def self.sweep
  %w{CollectionObject AssertedDistribution}.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



214
215
216
217
218
219
220
221
 
# File 'app/models/dwc_occurrence.rb', line 214

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



66
67
68
 
# File 'app/models/dwc_occurrence.rb', line 66

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

#asserted_distribution ⇒ Object 



99
100
101
 
# File 'app/models/dwc_occurrence.rb', line 99

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

#basis ⇒ Object 



235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
 
# File 'app/models/dwc_occurrence.rb', line 235

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
  end
  'Undefined'
end

#collecting_event ⇒ Object 



103
104
105
 
# File 'app/models/dwc_occurrence.rb', line 103

def collecting_event
  collection_object&.collecting_event
end

#collection_object ⇒ Object 



95
96
97
 
# File 'app/models/dwc_occurrence.rb', line 95

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

#create_object_uuid ⇒ Object (protected) 



353
354
355
356
357
358
359
 
# File 'app/models/dwc_occurrence.rb', line 353

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



75
76
77
78
79
80
81
 
# File 'app/models/dwc_occurrence.rb', line 75

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

#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



269
270
271
272
273
274
275
276
277
 
# File 'app/models/dwc_occurrence.rb', line 269

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.



287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
 
# File 'app/models/dwc_occurrence.rb', line 287

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 



303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
 
# File 'app/models/dwc_occurrence.rb', line 303

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 



107
108
109
110
111
112
113
114
 
# File 'app/models/dwc_occurrence.rb', line 107

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

#set_metadata_attributes ⇒ Object (protected) 



361
362
363
364
 
# File 'app/models/dwc_occurrence.rb', line 361

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 



257
258
259
 
# File 'app/models/dwc_occurrence.rb', line 257

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