Module: BiologicalAssociation::GlobiExtensions

Extended by:
ActiveSupport::Concern
Included in:
BiologicalAssociation
Defined in:
app/models/biological_association/globi_extensions.rb

Instance Method Summary collapse

Instance Method Details

#globi_extension_json ⇒ Object

Don’t use dwc_



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# File 'app/models/biological_association/globi_extensions.rb', line 83

def globi_extension_json
  r = {}
  Export::CSV::Globi::HEADERS.each do |h|
    if m = GLOBI_EXTENSION_MAP[h.to_sym]
      r[h] = send(m)
    end
  end
  r
end

#globi_extension_row ⇒ Object

Don’t use dwc_



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# File 'app/models/biological_association/globi_extensions.rb', line 70

def globi_extension_row
  r = []
  Export::CSV::Globi::HEADERS.each do |h|
    if m = GLOBI_EXTENSION_MAP[h.to_sym]
      r.push send(m)
    else
      r.push nil
    end
  end
  r
end

#globi_interaction_type_id ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 178

def globi_interaction_type_id
  dwc_relationship_of_resource_id
end

#globi_interaction_type_name ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 182

def globi_interaction_type_name
  dwc_relationship_of_resource
end

#globi_source_catalog_number ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 102

def globi_source_catalog_number
  if biological_association_subject_type == 'CollectionObject'
    biological_association_subject.dwc_catalog_number
  end
end

#globi_source_collection_code ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 108

def globi_source_collection_code
  if biological_association_subject_type == 'CollectionObject'
    biological_association_subject.dwc_collection_code
  end
end

#globi_source_institution_code ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 114

def globi_source_institution_code
  if biological_association_subject_type == 'CollectionObject'
    biological_association_subject.dwc_institution_code
  else
  end
end

#globi_source_life_stage_id ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 141

def globi_source_life_stage_id
  if biological_association_subject_type == 'CollectionObject'
    biological_association_subject.biocuration_classes.tagged_with_uri(::DWC_ATTRIBUTE_URIS[:lifeStage])
      .pluck(:uri)&.join(', ').presence
  else
    nil # Maybe some OTU data attribute property list as above
  end
end

#globi_source_life_stage_name ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 150

def globi_source_life_stage_name
  if biological_association_subject_type == 'CollectionObject'
    biological_association_subject.dwc_life_stage
  else
    nil # Maybe some OTU data attribute property list
  end
end

#globi_source_occurrence_id ⇒ Object

TODO: use alias



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# File 'app/models/biological_association/globi_extensions.rb', line 94

def globi_source_occurrence_id
  if biological_association_subject_type == 'CollectionObject'
    biological_association_object.dwc_occurrence_id
  end

  #     dwc_resource_id
end

#globi_source_sex_id ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 158

def globi_source_sex_id
  if biological_association_subject_type == 'CollectionObject'
    biological_association_subject.biocuration_classes.tagged_with_uri(::DWC_ATTRIBUTE_URIS[:sex])
      .pluck(:uri)&.join(', ').presence
  else
    nil # Maybe some OTU data attribute property list as above
  end
end

#globi_source_sex_name ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 167

def globi_source_sex_name
  if biological_association_subject_type == 'CollectionObject'
    biological_association_subject.dwc_sex
  else
    nil # Maybe some OTU data attribute property list
  end
end

#globi_source_taxon_name ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 121

def globi_source_taxon_name
  if biological_association_subject_type == 'CollectionObject'
    biological_association_subject.dwc_scientific_name
  else
    dwc_resource
  end
end

#globi_source_taxon_path ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 137

def globi_source_taxon_path
  ApplicationController.helpers.ancestry_path(biological_association_subject.ancestry)
end

#globi_source_taxon_rank ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 129

def globi_source_taxon_rank
  if biological_association_subject_type == 'CollectionObject'
    biological_association_subject.dwc_taxon_rank
  else
    biological_association_subject.taxon_name&.rank
  end
end

#globi_target_catalog_number ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 196

def globi_target_catalog_number
  if biological_association_object_type == 'CollectionObject'
    biological_association_object.dwc_catalog_number
  end
end

#globi_target_collection_code ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 202

def globi_target_collection_code
  if biological_association_object_type == 'CollectionObject'
    biological_association_object.dwc_collection_code
  end
end

#globi_target_institution_code ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 208

def globi_target_institution_code
  if biological_association_object_type == 'CollectionObject'
    biological_association_object.dwc_institution_code
  else
  end
end

#globi_target_life_stage_id ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 235

def globi_target_life_stage_id
  if biological_association_object_type == 'CollectionObject'
    biological_association_object.biocuration_classes.tagged_with_uri(::DWC_ATTRIBUTE_URIS[:lifeStage])
      .pluck(:uri)&.join(', ').presence
  else
    nil # Maybe some OTU data attribute property list as above
  end
end

#globi_target_life_stage_name ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 244

def globi_target_life_stage_name
  if biological_association_object_type == 'CollectionObject'
    biological_association_object.dwc_life_stage
  else
    nil # Maybe some OTU data attribute property list
  end
end

#globi_target_occurrence_id ⇒ Object

TODO: use alias



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# File 'app/models/biological_association/globi_extensions.rb', line 190

def globi_target_occurrence_id
  if biological_association_object_type == 'CollectionObject'
    biological_association_object.dwc_occurrence_id
  end
end

#globi_target_sex_id ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 252

def globi_target_sex_id
  if biological_association_object_type == 'CollectionObject'
    biological_association_object.biocuration_classes.tagged_with_uri(::DWC_ATTRIBUTE_URIS[:sex])
      .pluck(:uri)&.join(', ').presence
  else
    nil # Maybe some OTU data attribute property list as above
  end
end

#globi_target_sex_name ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 261

def globi_target_sex_name
  if biological_association_object_type == 'CollectionObject'
    biological_association_object.dwc_sex
  else
    nil # Maybe some OTU data attribute property list
  end
end

#globi_target_taxon_name ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 215

def globi_target_taxon_name
  if biological_association_object_type == 'CollectionObject'
    biological_association_object.dwc_scientific_name
  else
    dwc_related_resource
  end
end

#globi_target_taxon_path ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 231

def globi_target_taxon_path
  ApplicationController.helpers.ancestry_path(biological_association_object.ancestry)
end

#globi_target_taxon_rank ⇒ Object 



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# File 'app/models/biological_association/globi_extensions.rb', line 223

def globi_target_taxon_rank
  if biological_association_object_type == 'CollectionObject'
    biological_association_object.dwc_taxon_rank
  else
    biological_association_object.taxon_name&.rank
  end
end