Module: Export::Coldp::Files::Taxon

Defined in:
lib/export/coldp/files/taxon.rb

Overview

Concepts not mapped:

`namePhrase` - e.g. `sensu lato` this would come from OTU#name

Notes

  • ColDP importer has a normalizing step that recognizes some names no longer point to any OTU

  • CoLDP can not handle assertions that a name that is currently treated as (invalid) was useds as a name (valid) for previously valid concept, i.e. CoL does not track alternative past concept heirarchies

TODO: create map of all possible CoLDP used IRIs and ability to populate project with them automatically

Constant Summary collapse

IRI_MAP = 
{
  extinct: 'https://api.checklistbank.org/datapackage#Taxon.extinct',                         # 1,0
  temporal_range_end: 'https://api.checklistbank.org/datapackage#Taxon.temporal_range_end',   # from https://api.checklistbank.org/vocab/geotime
  temporal_range_start: 'https://api.checklistbank.org/datapackage#Taxon.temporal_range_end', # from https://api.checklistbank.org/vocab/geotime
  lifezone: 'https://api.checklistbank.org/datapackage#Taxon.lifezone',                       # from https://api.checklistbank.org/vocab/lifezone
}
SKIPPED_RANKS = 
%w{
  NomenclaturalRank::Iczn::SpeciesGroup::Superspecies
  NomenclaturalRank::Iczn::SpeciesGroup::Supersuperspecies
}

Class Method Summary collapse

Class Method Details

.according_to_date(otu) ⇒ Object

Potentially reference

Confidence level
   confidence_validated_at (last time this confidence level was deemed OK)



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# File 'lib/export/coldp/files/taxon.rb', line 87

def self.according_to_date(otu)
  # a) Dynamic - !! most recent updated_at stamp for *any* OTU tied data -> this is a big grind: if so add cached_touched_on_date to Otu
  # b) modify Confidence level to include date
  # c) review what SFs does in their model
  nil
end

.according_to_id(otu) ⇒ Object

A reference to the publication of the person who established the taxonomic concept

TW has a plurality of sources that reference this concept, it's a straightforward map
It is somewhat unclear how/whether CoL will use this concept



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# File 'lib/export/coldp/files/taxon.rb', line 80

def self.according_to_id(otu)
  nil
end

.generate(otus, project_members, root_otu_id = nil, reference_csv = nil, prefer_unlabelled_otus = true, skip_name_ids = []) ⇒ Object

.generate(otus, project_members, otu_id, ref_tsv, skip_name_ids)



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# File 'lib/export/coldp/files/taxon.rb', line 115

def self.generate(otus, project_members, root_otu_id = nil, reference_csv = nil, prefer_unlabelled_otus = true, skip_name_ids = [])

  # Until we have RC5 articulations we are simplifying handling the fact
  # that one taxon name can be used for many OTUs. Track to see that
  # an OTU with a given taxon name does not already exist
  #   `taxon_name_id: nil`  - unify via Ruby hash keys
  observed_taxon_name_ids = { }

  # TODO: optional Taxon.alternativeID field allows inclusion of external identifiers: https://github.com/CatalogueOfLife/coldp#alternativeid-1 https://github.com/CatalogueOfLife/coldp#identifiers
  #   e.g., gbif:2704179,col:6W3C4,BOLD:AAJ2287,wikidata:Q157571

  ::CSV.generate(col_sep: "\t") do |csv|

    csv << %w{
      ID
      parentID
      nameID
      namePhrase
      provisional
      accordingToID
      scrutinizer
      scrutinizerID
      scrutinizerDate
      referenceID
      extinct
      temporalRangeStart
      temporalRangeEnd
      environment
      link
      remarks
      modified
      modifiedBy
    }

    root_otu = Otu.find_by(id: root_otu_id) unless root_otu_id.nil?
    taxon_remarks_vocab_id = Predicate.find_by(uri: 'https://github.com/catalogueoflife/coldp#Taxon.remarks',
                                               project_id: otus[0]&.project_id)&.id
    name_phrase_vocab_id = Predicate.find_by(uri: 'https://github.com/catalogueoflife/coldp#Taxon.namePhrase',
                                             project_id: otus[0]&.project_id)&.id
    link_vocab_id = Predicate.find_by(uri: 'https://api.checklistbank.org/vocab/term/col:link',
                                      project_id: otus[0]&.project_id)&.id

    link_base_url = root_otu.data_attributes.where(type: 'InternalAttribute', controlled_vocabulary_term_id: link_vocab_id).first&.value

    otus.each do |o|
      # !! When a name is a synonmy (combination), but that combination has no OTU
      # !! then the parent of the name in the taxon table is nil
      # !! Handle this edge case (probably resolved now)

      # TODO: alter way parent is set to conform to CoLDP status
      #   For OTUs with combinations we might have to change the parenthood?!

      parent_id = nil
      if root_otu_id != o.id
        if pid = o.parent_otu_id(skip_ranks: SKIPPED_RANKS, prefer_unlabelled_otus: prefer_unlabelled_otus)
          parent_id = pid
        else
          puts 'WARNING no parent!!'
          # there is no OTU parent for the hierarchy, at present we just flat skip this OTU
          # Curators can use the create OTUs for valid ids to resolve this data issue
          next
        end
      end

      # TODO: This was excluding OTUs that were being excluded downstream previously
      # This should never happen now since parent ambiguity is caught above!
      # can be removed in theory
      # TODO: remove once RC5 better modelled
      next if observed_taxon_name_ids[o.taxon_name_id]
      observed_taxon_name_ids[o.taxon_name_id] = nil

      # TODO: Use o.coordinate_otus to summarize accross different instances of the OTU

      sources = o.sources
      source = o.source

      parent_id = (root_otu_id == o.id ? nil : parent_id )

      # some names are skipped (e.g., if they have NOT SPECIFIED names)
      next if skip_name_ids.include?(o.taxon_name_id)

      csv << [
        o.id,                                                                # ID (Taxon)
        parent_id,                                                           # parentID (Taxon)
        o.taxon_name.id,                                                     # nameID (Name)
        name_phrase(o, name_phrase_vocab_id),                                # namePhrase
        provisional(o),                                                      # provisional
        according_to_id(o),                                                  # accordingToID
        scrutinizer(o),                                                      # scrutinizer
        scrutinizer_id(o),                                                   # scrutinizerID
        scrutinizer_date(o),                                                 # scrutizinerDate
        reference_id(sources),                                               # referenceID
        predicate_value(o, :extinct),                                        # extinct
        predicate_value(o, :temporal_range_start),                           # temporalRangeStart
        predicate_value(o, :temporal_range_end),                             # temporalRangeEnd
        predicate_value(o, :lifezone),                                       # environment (formerly named lifezone)
        link(link_base_url, o),                                              # link
        Export::Coldp.sanitize_remarks(remarks(o, taxon_remarks_vocab_id)),  # remarks
        Export::Coldp.modified(o[:updated_at]),                              # modified
        Export::Coldp.modified_by(o[:updated_by_id], project_members)        # modifiedBy
      ]

      Export::Coldp::Files::Reference.add_reference_rows(sources, reference_csv, project_members) if reference_csv
    end
  end
end

.link(link_base_url, otu) ⇒ Object 



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# File 'lib/export/coldp/files/taxon.rb', line 94

def self.link(link_base_url, otu)
  link_base_url&.gsub('{id}', otu.id.to_s) unless link_base_url.nil?
end

.name_phrase(otu, vocab_id) ⇒ Object

Name phrase is for appended phrases like senso stricto and senso lato



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# File 'lib/export/coldp/files/taxon.rb', line 48

def self.name_phrase(otu, vocab_id)
  return nil if vocab_id.nil?
  da = DataAttribute.find_by(type: 'InternalAttribute',
                             controlled_vocabulary_term_id: vocab_id,
                             attribute_subject_id: otu.id)
  da&.value
end

.predicate_value(otu, predicate) ⇒ Object

Parameters:

  • predicate (:symbol) —

    a key from IRI_MAP



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# File 'lib/export/coldp/files/taxon.rb', line 27

def self.predicate_value(otu, predicate)
  return nil unless IRI_MAP[predicate]
  otu.data_attributes.joins(:predicate).where(controlled_vocabulary_terms: {uri: IRI_MAP[predicate]}).first&.value
end

.provisional(otu) ⇒ Object

return [Boolean, nil]

TODO - reason in TW this is provisional name



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# File 'lib/export/coldp/files/taxon.rb', line 34

def self.provisional(otu)
  # nomen dubium
  # incertae sedis
  # unresolved homonym, without replacement
  #
  #
  #
  # * if two OTUs for same name are in OTU set then both have to be provisional
  # * missaplication (?)
  nil
end

.reference_id(sources) ⇒ Object

“supporting the taxonomic concept” Potentially- all other Citations tied to Otu, what exactly supports a concept?



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# File 'lib/export/coldp/files/taxon.rb', line 108

def self.reference_id(sources)
  i = sources.pluck(:id)
  return i.join(',') if i.any?
  nil
end

.remarks(otu, taxon_remarks_vocab_id) ⇒ Object 



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# File 'lib/export/coldp/files/taxon.rb', line 98

def self.remarks(otu, taxon_remarks_vocab_id)
  if !taxon_remarks_vocab_id.nil? && otu.data_attributes.where(controlled_vocabulary_term_id: taxon_remarks_vocab_id).any?
    otu.data_attributes.where(controlled_vocabulary_term_id: taxon_remarks_vocab_id).pluck(:value).join('|')
  else
    nil
  end
end

.scrutinizer(otu) ⇒ Object

The scrutinizer concept is unused at present We’re looking for the canonical implementation of it before we implement/extrapolate from data here.

* crawl attribution for inference on higher/lower
* UI/methods to assign/spam/visualize throught
* project preference (!! should project preferences has reference ids? !!)

according to is the curator responsible for this OTU, comma delimited list of curators We could also look at time-stamp data to detect “staleness” of an OTU concept



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# File 'lib/export/coldp/files/taxon.rb', line 64

def self.scrutinizer(otu)
  nil
end

.scrutinizer_date(otu) ⇒ Object 



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# File 'lib/export/coldp/files/taxon.rb', line 73

def self.scrutinizer_date(otu)
  nil
end

.scrutinizer_id(otu) ⇒ Object

ORCID version of above



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# File 'lib/export/coldp/files/taxon.rb', line 69

def self.scrutinizer_id(otu)
  nil
end