Module: Export::Coldp::Files::TypeMaterial

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

Overview

ID nameID citation status referenceID locality country latitude longitude altitude host date collector institutionCode catalogNumber associatedSequences sex link remarks

Class Method Summary collapse

Class Method Details

.date(co) ⇒ Object 



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

def self.date(co)
  co.dwc_event_date&.split('/')[0] unless co.dwc_event_date.nil?
end

.generate(otu, project_members, reference_csv = nil) ⇒ Object 



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# File 'lib/export/coldp/files/type_material.rb', line 45

def self.generate(otu, project_members, reference_csv = nil )

  tm = nil

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

    csv << %w{
      ID
      nameID
      citation
      status
      referenceID
      locality
      country
      latitude
      longitude
      altitude
      host
      date
      collector
      institutionCode
      catalogNumber
      associatedSequences
      sex
      link
      modified
      modifiedBy
      remarks
    }

    tm = type_material(otu)

    tm.each do |r|
      text = csv << [
        nil,                                                            # ID: don't expose TW internal type material ID
        r.protonym_id,                                                  # nameID
        nil,                                                            # citation ?! co.buffered_collecting_event
        r.type_type,                                                    # status
        r.source_id,                                                    # referenceID
        r.locality,                                                     # locality
        r.country,                                                      # country
        r.decimalLatitude,                                              # latitude
        r.decimalLongitude,                                             # longitude
        r.verbatimElevation,                                            # altitude
        nil,                                                            # host
        r.eventDate,                                                    # date
        r.recordedBy,                                                   # collector
        r.institutionCode,                                              # institutionCode
        r.catalogNumber,                                                # catalogNumber
        nil,                                                            # associatedSequences: unclear what is wanted? https://github.com/CatalogueOfLife/coldp#associatedsequences
        r.sex,                                                          # sex
        nil,                                                            # link # maybe to GBIF by occurrenceID
        Export::Coldp.modified(r.updated_at),                           # modified
        Export::Coldp.modified_by(r.updated_by_id, project_members),    # modifiedBy
        nil                                                             # remarks
      ]
    end
  end

  # TODO: Many people likely don't cite TypeMaterial directly, but rather the Protonym, we could
  # use that proxy.
  sources = Source.with(name_scope: tm)
    .joins(:citations)
    .joins("JOIN name_scope ns on ns.id = citations.citation_object_id AND citations.citation_object_type = 'TypeMaterial'")
    .distinct

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

  text
end

.locality(co) ⇒ Object 



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# File 'lib/export/coldp/files/type_material.rb', line 23

def self.locality(co)
  [co.dwc_country, co.dwc_state_province, co.dwc_county, co.dwc_locality].compact.join(', ')
end

.type_material(otu) ⇒ Object

We need to catch types for valid and invalid names.



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# File 'lib/export/coldp/files/type_material.rb', line 32

def self.type_material(otu)
  a = ::Export::Coldp::Files::Name.core_names(otu).unscope(:select).select(:id)
  b = ::Export::Coldp::Files::Name.invalid_core_names(otu).unscope(:select).select(:id)
  c = ::Queries.union(TaxonName, [a,b]).select(:id)

  TypeMaterial.with(name_scope: c)
    .joins(collection_object: [:dwc_occurrence])
    .joins('JOIN name_scope on name_scope.id = type_materials.protonym_id')
    .left_joins(:source) # original only, not subsequent here, probably people are using Protonym as a proxy
    .select('type_materials.*, MAX(sources.id) source_id, country, locality, "decimalLatitude", "decimalLongitude", "verbatimElevation", "eventDate", "recordedBy", "institutionCode", "catalogNumber", sex')
    .group('type_materials.id , country, locality, "decimalLatitude", "decimalLongitude", "verbatimElevation", "eventDate", "recordedBy", "institutionCode", "catalogNumber", sex')
end