Class: PaperCatalog

Inherits:
Catalog::Nomenclature show all
Defined in:
lib/catalog/nomenclature/paper_catalog.rb

Overview

Paper style comprehansive checklist

Instance Attribute Summary collapse

Attributes inherited from Catalog

#catalog_targets, #entries

Instance Method Summary collapse

Methods inherited from Catalog::Nomenclature

#names

Methods inherited from Catalog

all_dates, #build, chronological_item_sort, #citations, #entries_sorted, #entry_sort_valid?, #items, #items_chronologically, #objects_for_source, #reference_object_global_id, #reference_object_valid_taxon_name_global_id, #sources, #sources_to_json, topic_year_metadata, #topics, #topics_to_json, year_hash, year_metadata

Constructor Details

#initialize(classification_scope: nil, project_id: nil, rank_filter: nil, otu_filter: nil, taxon_name_filter: nil, accepted_only: false, type_information: false, distribution: false, otu_contents: false) ⇒ PaperCatalog

Returns a new instance of PaperCatalog.



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 74

def initialize(
  classification_scope: nil,
  project_id: nil,
  rank_filter: nil,
  otu_filter: nil,
  taxon_name_filter: nil,
  accepted_only: false,
  type_information: false,
  distribution: false,
  otu_contents: false)

  @classification_scope = classification_scope
  @project_id = project_id
  @rank_filter = rank_filter.to_s.downcase.split('|')
  @otu_filter = otu_filter
  @taxon_name_filter = taxon_name_filter
  @accepted_only = accepted_only
  @type_information = type_information
  @distribution = distribution
  @otu_contents = otu_contents
  @taxon_name_ids = []
  @otu_id_filter_array = otu_filter_array

  #Main logic
  @results_hash = {names: {}, sources: {}}
  @position = 0

  build_the_list
end

Instance Attribute Details

#accepted_only ⇒ Object

Optional attribute. Restrict output to valid_names “accepted_only=true”



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 35

def accepted_only
  @accepted_only
end

#classification_scope ⇒ Object

Higher level taxon to include all descendants



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 10

def classification_scope
  @classification_scope
end

#distribution ⇒ Object

Optional attribute to add distribution “distribution=true”



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 45

def distribution
  @distribution
end

#otu_contents ⇒ Object

Optional attribute to add otu_contents



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 50

def otu_contents
  @otu_contents
end

#otu_filter ⇒ Object

Optional attribute. Restrict output to particular otus_ids “otu_filter=3|5|15”.



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 25

def otu_filter
  @otu_filter
end

#otu_id_filter_array ⇒ Object

Returns list of otu_ids



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 62

def otu_id_filter_array
  @otu_id_filter_array
end

#project_id ⇒ Object

Required attribute to build the key



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 15

def project_id
  @project_id
end

#rank_filter ⇒ Object

Optional attribute. Restrict output to particular ranks “rank_filter=genus|species|subspecies”. Returns all ranks if values is nil



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 20

def rank_filter
  @rank_filter
end

#results_hash ⇒ Object

Returns taxa sorted hierarchically with all metadata



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 72

def results_hash
  @results_hash
end

#source_hash ⇒ Object

Returns list of sources



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 67

def source_hash
  @source_hash
end

#taxon_name_filter ⇒ Object

Optional attribute. Restrict output to particular taxon_name_ids “taxon_name_filter=3|5|15”.



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 30

def taxon_name_filter
  @taxon_name_filter
end

#taxon_name_ids ⇒ Object

Returns list of taxon_name_ids



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 57

def taxon_name_ids
  @taxon_name_ids
end

#type_information ⇒ Object

Optional attribute. Add type information “type=true”



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 40

def type_information
  @type_information
end

Instance Method Details

#build_the_list ⇒ Object 



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# File 'lib/catalog/nomenclature/paper_catalog.rb', line 104

def build_the_list
  results_hash
  return {} if project_id.nil?
  return {} if classification_scope.blank? && otu_filter.blank? && taxon_name_filter.blank?

  taxon = classification_scope.blank? ? nil : TaxonName.find(classification_scope.to_i)

  if !taxon_name_filter.blank?
    tn_ids = taxon_name_filter.to_s.split('|').map(&:to_i)
    TaxonName.where(id: tn_ids).each do |t|
      add_taxon_to_results(t) if t.id == t.cached_valid_taxon_name_id
    end
  elsif !taxon.nil?
    #   ancestors = get_ancestors(taxon)
    # descendants = get_descendants(taxon)
  end
  if results_hash.names.count > 0 && accepted_only.to_s != 'true'
    # synonyms = get_synonyms
  end
  if taxon_name_ids.count > 0
    # statuses = get_taxon_name_classifications
    # relationships = get_taxon_name_relationships
  end
end