Module: Export::Coldp

Defined in:
lib/export/coldp.rb

Overview

Exports to the Catalog of Life in the new “coldp” format. api.col.plus/datapackage

  • write tests to check for coverage (missing methods)

  • Update all files formats to use tabs

  • Pending handling of both BibTeX and Verbatim

Constant Summary collapse

FILETYPES =
%w{Description Name Synonym VernacularName}.freeze

Class Method Summary collapse

Class Method Details

.basionym_id(taxon_name) ⇒ Object

Parameters:

  • taxon_name (a valid Protonym or a Combination)

    see also exclusion of OTUs/Names based on Ranks not handled



112
113
114
115
116
117
118
119
120
# File 'lib/export/coldp.rb', line 112

def self.basionym_id(taxon_name)
  if taxon_name.type == 'Protonym'
    taxon_name.reified_id
  elsif taxon_name.type == 'Combination'
    taxon_name.protonyms.last.reified_id
  else
    nil
  end
end

.download(otu, request = nil, prefer_unlabelled_otus: true) ⇒ Object



69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
# File 'lib/export/coldp.rb', line 69

def self.download(otu, request = nil, prefer_unlabelled_otus: true)
  file_path = ::Export::Coldp.export(
    otu.id,
    prefer_unlabelled_otus: prefer_unlabelled_otus
  )
  name = "coldp_otu_id_#{otu.id}_#{DateTime.now}.zip"

  ::Download::Coldp.create!(
    name: "ColDP Download for #{otu.otu_name} on #{Time.now}.",
    description: 'A zip file containing CoLDP formatted data.',
    filename: filename(otu),
    source_file_path: file_path,
    request: request,
    expires: 2.days.from_now
  )
end

.download_async(otu, request = nil, prefer_unlabelled_otus: true) ⇒ Object



86
87
88
89
90
91
92
93
94
95
96
97
98
# File 'lib/export/coldp.rb', line 86

def self.download_async(otu, request = nil, prefer_unlabelled_otus: true)
  download = ::Download::Coldp.create!(
    name: "ColDP Download for #{otu.otu_name} on #{Time.now}.",
    description: 'A zip file containing CoLDP formatted data.',
    filename: filename(otu),
    request: request,
    expires: 2.days.from_now
  )

  ColdpCreateDownloadJob.perform_later(otu, download, prefer_unlabelled_otus: prefer_unlabelled_otus)

  download
end

.export(otu_id, prefer_unlabelled_otus: true) ⇒ Object



29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
# File 'lib/export/coldp.rb', line 29

def self.export(otu_id, prefer_unlabelled_otus: true)
  otus = otus(otu_id)

  # source_id: [csv_array]
  ref_csv = {}

  # TODO: This will likely have to change, it is renamed on serving the file.
  zip_file_path = "/tmp/_#{SecureRandom.hex(8)}_coldp.zip"

  Zip::File.open(zip_file_path, Zip::File::CREATE) do |zipfile|
    (FILETYPES - ['Name']).each do |ft|
      m = "Export::Coldp::Files::#{ft}".safe_constantize
      zipfile.get_output_stream("#{ft}.csv") { |f| f.write m.generate(otus, ref_csv) }
    end

    zipfile.get_output_stream('Name.csv') { |f| f.write Export::Coldp::Files::Name.generate(Otu.find(otu_id), ref_csv) }
    zipfile.get_output_stream('Taxon.csv') do |f|
      f.write Export::Coldp::Files::Taxon.generate(otus, otu_id, ref_csv, prefer_unlabelled_otus: prefer_unlabelled_otus)
    end

    # Sort the refs by full citation string
    sorted_refs = ref_csv.values.sort{|a,b| a[1] <=> b[1]}

    d = CSV.generate(col_sep: "\t") do |csv|
      csv << %w{ID citation	doi} # author year source details
      sorted_refs.each do |r|
        csv << r
      end
    end

    zipfile.get_output_stream('References.csv') { |f| f.write d }
  end

  zip_file_path
end

.filename(otu) ⇒ Object



65
66
67
# File 'lib/export/coldp.rb', line 65

def self.filename(otu)
  Zaru::sanitize!("#{Project.find(Current.project_id).name}_coldp_otu_id_#{otu.id}_#{DateTime.now}.zip").gsub(' ', '_').downcase
end

.original_field(taxon_name) ⇒ Boolean

Returns `true` if no parens in `cached_author_year` `false` if parens in `cached_author_year`.

Returns:

  • (Boolean)

    `true` if no parens in `cached_author_year` `false` if parens in `cached_author_year`



106
107
108
# File 'lib/export/coldp.rb', line 106

def self.original_field(taxon_name)
  (taxon_name.type == 'Protonym') && taxon_name.is_original_name?
end

.otus(otu_id) ⇒ Scope

Returns A full set of valid only Otus (= Taxa in CoLDP) that are to be sent. !! At present no OTU with a `name` is sent. In the future this may !! need to change.

Returns:

  • (Scope)

    A full set of valid only Otus (= Taxa in CoLDP) that are to be sent. !! At present no OTU with a `name` is sent. In the future this may !! need to change.



19
20
21
22
23
24
25
26
27
# File 'lib/export/coldp.rb', line 19

def self.otus(otu_id)
  o = ::Otu.find(otu_id)
  return ::Otu.none if o.taxon_name_id.nil?

  Otu.joins(taxon_name: [:ancestor_hierarchies])
    .where('taxon_name_hierarchies.ancestor_id = ?', o.taxon_name_id)
    .where(taxon_name_id: TaxonName.that_is_valid)
    .where('(otus.name IS NULL) OR (otus.name = taxon_names.cached)')
end

.reified_id(taxon_name_id, cached, cached_original_combination) ⇒ Object

Replicate TaxonName.refified_id without having to use AR



123
124
125
126
127
128
129
130
# File 'lib/export/coldp.rb', line 123

def self.reified_id(taxon_name_id, cached, cached_original_combination)
  # Protonym#has_alternate_original?
  if cached_original_combination && (cached != cached_original_combination)
    taxon_name_id.to_s + '-' + Digest::MD5.hexdigest(cached_original_combination)
  else
    taxon_name_id
  end
end