dwca_hunter 0.5.5 → 0.7.0
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- checksums.yaml +4 -4
- data/.byebug_history +37 -0
- data/.gitignore +5 -0
- data/.rubocop.yml +3 -2
- data/.ruby-version +1 -1
- data/Gemfile.lock +50 -77
- data/LICENSE.txt +1 -1
- data/README.md +1 -1
- data/dwca_hunter.gemspec +7 -8
- data/exe/dwcahunter +1 -3
- data/lib/dwca_hunter.rb +31 -0
- data/lib/dwca_hunter/resources/aos-birds.rb +143 -0
- data/lib/dwca_hunter/resources/arctos.rb +93 -91
- data/lib/dwca_hunter/resources/clements.rb +151 -0
- data/lib/dwca_hunter/resources/freebase.rb +51 -49
- data/lib/dwca_hunter/resources/how-moore-birds.rb +168 -0
- data/lib/dwca_hunter/resources/ioc_word_bird.rb +200 -0
- data/lib/dwca_hunter/resources/ipni.rb +3 -2
- data/lib/dwca_hunter/resources/itis.rb +99 -99
- data/lib/dwca_hunter/resources/mammal_divdb.rb +155 -0
- data/lib/dwca_hunter/resources/mammal_species.rb +3 -3
- data/lib/dwca_hunter/resources/mcz.rb +123 -0
- data/lib/dwca_hunter/resources/ncbi.rb +22 -23
- data/lib/dwca_hunter/resources/opentree.rb +5 -5
- data/lib/dwca_hunter/resources/paleobiodb.rb +193 -0
- data/lib/dwca_hunter/resources/paleodb_harvester.rb +140 -0
- data/lib/dwca_hunter/resources/sherborn.rb +91 -0
- data/lib/dwca_hunter/resources/wikispecies.rb +142 -127
- data/lib/dwca_hunter/version.rb +1 -1
- metadata +27 -34
- data/ipni.csv.gz +0 -0
- data/ipniWebName.csv.xz?dl=1 +0 -0
@@ -1,16 +1,16 @@
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#
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# frozen_string_literal: true
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module DwcaHunter
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class ResourceArctos < DwcaHunter::Resource
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def initialize(opts = {})
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@command =
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@title =
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@url =
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@UUID =
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@command = "arctos"
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@title = "Arctos"
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@url = "https://www.dropbox.com/s/3rmny5d8cfm9mmp/arctos.tar.gz?dl=1"
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@UUID = "eea8315d-a244-4625-859a-226675622312"
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@download_path = File.join(Dir.tmpdir,
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"dwca_hunter",
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"arctos",
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"data.zip")
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@synonyms = []
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@names = []
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@vernaculars = []
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@@ -22,7 +22,7 @@ module DwcaHunter
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def download
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puts "Downloading cached verion of the file. Ask Arctos to generate new."
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-
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`curl -s -L #{@url} -o #{@download_path}`
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end
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def unpack
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end
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def make_dwca
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DwcaHunter
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DwcaHunter.logger_write(object_id, "Extracting data")
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get_names
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generate_dwca
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end
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end
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def collect_vernaculars
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file = CSV.open(File.join(@download_dir,
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file = CSV.open(File.join(@download_dir, "common_name.csv"),
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headers: true)
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file.each_with_index do |row, i|
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canonical = row["SCIENTIFIC_NAME"]
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vernacular_name_string = row["COMMON_NAME"]
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canonical
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vernacular_name_string = row['COMMON_NAME']
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if @vernaculars_hash.has_key?(canonical)
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if @vernaculars_hash.key?(canonical)
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@vernaculars_hash[canonical] << vernacular_name_string
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else
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@vernaculars_hash[canonical] = [vernacular_name_string]
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end
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puts "Processed %s vernaculars" % i if i %
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puts "Processed %s vernaculars" % i if i % 10_000 == 0
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end
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end
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def collect_synonyms
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file = CSV.open(File.join(@download_dir,
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file = CSV.open(File.join(@download_dir, "relationships.csv"),
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headers: true)
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file.each_with_index do |row, i|
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canonical = row[
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if @synonyms_hash.
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canonical = row["scientific_name"]
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if @synonyms_hash.key?(canonical)
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@synonyms_hash[canonical] <<
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{ name_string: row["related_name"], status: row["TAXON_RELATIONSHIP"] }
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else
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@synonyms_hash[canonical] = [
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{ name_string: row["related_name"], status: row["TAXON_RELATIONSHIP"] }
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]
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end
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puts "Processed %s synonyms" % i if i %
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puts "Processed %s synonyms" % i if i % 10_000 == 0
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end
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end
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def collect_names
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@names_index = {}
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file = CSV.open(File.join(@download_dir,
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file = CSV.open(File.join(@download_dir, "classification.csv"),
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headers: true)
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file.each_with_index do |row, i|
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next unless
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next unless row["display_name"]
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name_string = row["display_name"].gsub(%r{</?i>}, "")
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canonical = row["scientific_name"]
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kingdom = row["kingdom"]
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phylum = row["phylum"]
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klass = row["phylclass"]
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subclass = row["subclass"]
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order = row["phylorder"]
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suborder = row["suborder"]
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superfamily = row["superfamily"]
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family = row["family"]
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subfamily = row["subfamily"]
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tribe = row["tribe"]
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genus = row["genus"]
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subgenus = row["subgenus"]
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species = row["species"]
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subspecies = row["subspecies"]
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code = row["nomenclatural_code"]
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taxon_id = "ARCT_#{i + 1}"
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@names << { taxon_id: taxon_id,
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}
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name_string: name_string,
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kingdom: kingdom,
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phylum: phylum,
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klass: klass,
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order: order,
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family: family,
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genus: genus,
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code: code }
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update_vernacular(taxon_id, canonical)
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update_synonym(taxon_id, canonical)
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puts "Processed %s names" % i if i %
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puts "Processed %s names" % i if i % 10_000 == 0
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end
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end
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def update_vernacular(taxon_id, canonical)
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return unless @vernaculars_hash.
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return unless @vernaculars_hash.key?(canonical)
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@vernaculars_hash[canonical].each do |vern|
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@vernaculars << { taxon_id: taxon_id, vern: vern }
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end
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end
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def update_synonym(taxon_id, canonical)
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return unless @synonyms_hash.
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return unless @synonyms_hash.key?(canonical)
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@synonyms_hash[canonical].each do |syn|
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@synonyms << { taxon_id: taxon_id, name_string: syn[:name_string],
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status: syn[:status] }
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end
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end
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def generate_dwca
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DwcaHunter
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@core = [[
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]]
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DwcaHunter.logger_write(object_id,
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"Creating DarwinCore Archive file")
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@core = [["http://rs.tdwg.org/dwc/terms/taxonID",
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"http://rs.tdwg.org/dwc/terms/scientificName",
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"http://rs.tdwg.org/dwc/terms/kingdom",
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"http://rs.tdwg.org/dwc/terms/phylum",
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"http://rs.tdwg.org/dwc/terms/class",
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"http://rs.tdwg.org/dwc/terms/order",
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"http://rs.tdwg.org/dwc/terms/family",
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"http://rs.tdwg.org/dwc/terms/genus",
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"http://rs.tdwg.org/dwc/terms/nomenclaturalCode"]]
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@names.each do |n|
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@core << [n[:taxon_id], n[:name_string],
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n[:kingdom], n[:phylum], n[:klass], n[:order], n[:family],
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n[:genus], n[:code]]
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end
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@extensions << {
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data: [[
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"http://rs.tdwg.org/dwc/terms/taxonID",
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"http://rs.tdwg.org/dwc/terms/vernacularName"
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]],
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file_name: "vernacular_names.txt",
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row_type: "http://rs.gbif.org/terms/1.0/VernacularName"
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}
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@vernaculars.each do |v|
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@extensions[-1][:data] << [v[:taxon_id], v[:vern]]
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@@ -167,12 +169,12 @@ module DwcaHunter
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@extensions << {
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data: [[
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file_name:
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"http://rs.tdwg.org/dwc/terms/taxonID",
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"http://rs.tdwg.org/dwc/terms/scientificName",
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"http://rs.tdwg.org/dwc/terms/taxonomicStatus"
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]],
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file_name: "synonyms.txt"
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}
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@synonyms.each do |s|
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@extensions[-1][:data] << [s[:taxon_id], s[:name_string], s[:status]]
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end
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@@ -180,14 +182,14 @@ module DwcaHunter
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id: @uuid,
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title: @title,
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authors: [
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{email:
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{ email: "dustymc at gmail dot com" }
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],
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metadata_providers: [
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{ first_name:
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last_name:
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email:
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abstract:
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{ first_name: "Dmitry",
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last_name: "Mozzherin",
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email: "dmozzherin@gmail.com" }
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],
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abstract: "Arctos is an ongoing effort to integrate access to specimen data, collection-management tools, and external resources on the internet.",
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url: @url
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}
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super
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@@ -0,0 +1,151 @@
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# frozen_string_literal: true
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module DwcaHunter
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class ResourceClements < DwcaHunter::Resource
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def initialize(opts = {})
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@command = "clements-ebird"
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@title = "The eBird/Clements Checklist of Birds of the World"
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@url = "https://uofi.box.com/shared/static/b4n8zqa99hq9rdga27skkh3870yhujgo.csv"
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@UUID = "577c0b56-4a3c-4314-8724-14b304f601de"
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@download_path = File.join(Dir.tmpdir,
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"dwca_hunter",
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"clements",
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"data.csv")
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@synonyms = []
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@names = []
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@vernaculars = []
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@extensions = []
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@synonyms_hash = {}
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@vernaculars_hash = {}
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super(opts)
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end
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def download
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puts "Downloading cached and modified version of the file."
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puts "Go to https://www.birds.cornell.edu/clementschecklist/download/ " \
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"for updates."
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`curl -s -L #{@url} -o #{@download_path}`
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end
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def unpack
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31
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end
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def make_dwca
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34
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DwcaHunter.logger_write(object_id, "Extracting data")
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get_names
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generate_dwca
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end
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private
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40
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+
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def get_names
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Dir.chdir(@download_dir)
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collect_names
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end
|
45
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+
|
46
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def collect_names
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47
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@names_index = {}
|
48
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file = CSV.open(File.join(@download_dir, "data.csv"),
|
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headers: true)
|
50
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file.each_with_index do |row, i|
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51
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name_string = row["scientific name"]
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canonical = name_string
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kingdom = "Animalia"
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phylum = "Chordata"
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klass = "Aves"
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order = row["order"]
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family = row["family"]
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code = "ICZN"
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60
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taxon_id = "gn_#{i + 1}"
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@names << { taxon_id: taxon_id,
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name_string: name_string,
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kingdom: kingdom,
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phylum: phylum,
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klass: klass,
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order: order,
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family: family,
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68
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code: code }
|
69
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+
|
70
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if row["English name"].to_s != ""
|
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@vernaculars << {
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72
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taxon_id: taxon_id,
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vern: row["English name"],
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lang: "end"
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75
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}
|
76
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end
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77
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+
|
78
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+
puts "Processed %s names" % i if i % 10_000 == 0
|
79
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+
end
|
80
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+
end
|
81
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+
|
82
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+
def generate_dwca
|
83
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+
DwcaHunter.logger_write(object_id,
|
84
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+
"Creating DarwinCore Archive file")
|
85
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+
@core = [["http://rs.tdwg.org/dwc/terms/taxonID",
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"http://rs.tdwg.org/dwc/terms/scientificName",
|
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"http://rs.tdwg.org/dwc/terms/kingdom",
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"http://rs.tdwg.org/dwc/terms/phylum",
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"http://rs.tdwg.org/dwc/terms/class",
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"http://rs.tdwg.org/dwc/terms/order",
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"http://rs.tdwg.org/dwc/terms/family",
|
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+
"http://rs.tdwg.org/dwc/terms/nomenclaturalCode"]]
|
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@names.each do |n|
|
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|
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@core << [n[:taxon_id], n[:name_string],
|
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|
+
n[:kingdom], n[:phylum], n[:klass], n[:order], n[:family],
|
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+
n[:code]]
|
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+
end
|
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|
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@extensions << {
|
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data: [[
|
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"http://rs.tdwg.org/dwc/terms/taxonID",
|
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"http://rs.tdwg.org/dwc/terms/vernacularName",
|
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"http://purl.org/dc/terms/language"
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]],
|
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file_name: "vernacular_names.txt",
|
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|
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row_type: "http://rs.gbif.org/terms/1.0/VernacularName"
|
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|
+
}
|
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+
|
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@vernaculars.each do |v|
|
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@extensions[-1][:data] << [v[:taxon_id], v[:vern], v[:lang]]
|
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+
end
|
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|
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@eml = {
|
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id: @uuid,
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title: @title,
|
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authors: [
|
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{ first_name: "G. F.",
|
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last_name: "Clements"
|
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},
|
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{ first_name: "T. S.",
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last_name: "Schulenberg"
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},
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{ first_name: "M. J.",
|
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last_name: "Iliff"
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},
|
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{ first_name: "S. M.",
|
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last_name: "Billerman"
|
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},
|
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{ first_name: "T. A.",
|
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last_name: "Fredericks"
|
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+
},
|
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{ first_name: "B. L.",
|
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last_name: "Sullivan"
|
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+
},
|
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{ first_name: "C. L.",
|
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+
last_name: "Wood"
|
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+
},
|
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+
],
|
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+
metadata_providers: [
|
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|
+
{ first_name: "Dmitry",
|
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|
+
last_name: "Mozzherin",
|
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|
+
email: "dmozzherin@gmail.com" }
|
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|
+
],
|
143
|
+
abstract: "The eBird/Clements Checklist of Birds of the World" \
|
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|
+
": v2019. Downloaded from " \
|
145
|
+
"https://www.birds.cornell.edu/clementschecklist/download/",
|
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|
+
url: @url
|
147
|
+
}
|
148
|
+
super
|
149
|
+
end
|
150
|
+
end
|
151
|
+
end
|
@@ -1,15 +1,15 @@
|
|
1
|
-
#
|
1
|
+
# frozen_string_literal: true
|
2
2
|
|
3
3
|
module DwcaHunter
|
4
4
|
class ResourceFreebase < DwcaHunter::Resource
|
5
5
|
def initialize(opts = {})
|
6
6
|
@command = "freebase"
|
7
|
-
@title =
|
8
|
-
@uuid =
|
7
|
+
@title = "Freebase"
|
8
|
+
@uuid = "bacd21f0-44e0-43e2-914c-70929916f257"
|
9
9
|
@download_path = File.join(Dir.tmpdir,
|
10
|
-
|
11
|
-
|
12
|
-
|
10
|
+
"dwca_hunter",
|
11
|
+
"freebase",
|
12
|
+
"data.json")
|
13
13
|
@data = []
|
14
14
|
@all_taxa = {}
|
15
15
|
@cleaned_taxa = {}
|
@@ -27,11 +27,11 @@ module DwcaHunter
|
|
27
27
|
end
|
28
28
|
|
29
29
|
def download
|
30
|
-
DwcaHunter
|
31
|
-
|
30
|
+
DwcaHunter.logger_write(object_id,
|
31
|
+
"Querying freebase for species information...")
|
32
32
|
q = {
|
33
33
|
query: [{
|
34
|
-
type:
|
34
|
+
type: "/biology/organism_classification",
|
35
35
|
id: nil,
|
36
36
|
guid: nil,
|
37
37
|
name: nil,
|
@@ -41,16 +41,16 @@ module DwcaHunter
|
|
41
41
|
id: nil,
|
42
42
|
guid: nil,
|
43
43
|
scientific_name: nil,
|
44
|
-
optional: true
|
45
|
-
}
|
44
|
+
optional: true
|
45
|
+
}
|
46
46
|
}],
|
47
|
-
cursor: true
|
47
|
+
cursor: true
|
48
48
|
}
|
49
49
|
|
50
50
|
run_query(q)
|
51
51
|
|
52
52
|
data = JSON.pretty_generate @data
|
53
|
-
f = open(@download_path,
|
53
|
+
f = open(@download_path, "w:utf-8")
|
54
54
|
f.write(data)
|
55
55
|
f.close
|
56
56
|
end
|
@@ -60,31 +60,32 @@ module DwcaHunter
|
|
60
60
|
def run_query(q)
|
61
61
|
count = 0
|
62
62
|
requests_num = 0
|
63
|
-
|
63
|
+
loop do
|
64
64
|
freebase_url = "http://api.freebase.com/api/service/mqlread?query=%s" %
|
65
|
-
|
65
|
+
URI.encode(q.to_json)
|
66
66
|
res = JSON.load RestClient.get(freebase_url)
|
67
67
|
requests_num += 1
|
68
|
-
break if res[
|
68
|
+
break if res["result"].nil? || res["result"].empty?
|
69
|
+
|
69
70
|
if requests_num % 10 == 0
|
70
|
-
DwcaHunter
|
71
|
-
|
71
|
+
DwcaHunter.logger_write(object_id,
|
72
|
+
"Received %s names" % count)
|
72
73
|
end
|
73
|
-
count += res[
|
74
|
-
res[
|
75
|
-
q[:cursor] = res[
|
74
|
+
count += res["result"].size
|
75
|
+
res["result"].each { |d| @data << d }
|
76
|
+
q[:cursor] = res["cursor"]
|
76
77
|
end
|
77
78
|
end
|
78
79
|
|
79
80
|
def organize_data
|
80
|
-
@data = JSON.load(open(@download_path,
|
81
|
+
@data = JSON.load(open(@download_path, "r:utf-8").read)
|
81
82
|
@data.each do |d|
|
82
|
-
scientific_name = d[
|
83
|
+
scientific_name = d["scientific_name"].to_s
|
83
84
|
id = d["id"]
|
84
|
-
parent_id = d[
|
85
|
-
d[
|
85
|
+
parent_id = d["higher_classification"] ?
|
86
|
+
d["higher_classification"]["id"] :
|
86
87
|
nil
|
87
|
-
synonyms = d[
|
88
|
+
synonyms = d["synonym_scientific_name"]
|
88
89
|
@all_taxa[id] = { id: id,
|
89
90
|
parent_id: parent_id,
|
90
91
|
scientific_name: scientific_name,
|
@@ -93,6 +94,7 @@ module DwcaHunter
|
|
93
94
|
|
94
95
|
@all_taxa.each do |k, v|
|
95
96
|
next unless v[:scientific_name] && v[:scientific_name].strip != ""
|
97
|
+
|
96
98
|
parent_id = v[:parent_id]
|
97
99
|
until (@all_taxa[parent_id] &&
|
98
100
|
@all_taxa[parent_id][:scientific_name]) || parent_id.nil?
|
@@ -103,29 +105,28 @@ module DwcaHunter
|
|
103
105
|
v[:parent_id] = parent_id
|
104
106
|
@cleaned_taxa[k] = v
|
105
107
|
end
|
106
|
-
|
107
108
|
end
|
108
109
|
|
109
110
|
def generate_dwca
|
110
|
-
DwcaHunter
|
111
|
-
|
112
|
-
@core = [[
|
113
|
-
|
114
|
-
|
111
|
+
DwcaHunter.logger_write(object_id,
|
112
|
+
"Creating DarwinCore Archive file")
|
113
|
+
@core = [["http://rs.tdwg.org/dwc/terms/taxonID",
|
114
|
+
"http://rs.tdwg.org/dwc/terms/scientificName",
|
115
|
+
"http://rs.tdwg.org/dwc/terms/parentNameUsageID"]]
|
115
116
|
|
116
117
|
@extensions << { data: [[
|
117
|
-
|
118
|
-
|
119
|
-
]], file_name:
|
120
|
-
DwcaHunter
|
121
|
-
|
118
|
+
"http://rs.tdwg.org/dwc/terms/TaxonID",
|
119
|
+
"http://rs.tdwg.org/dwc/terms/scientificName"
|
120
|
+
]], file_name: "synonyms.txt" }
|
121
|
+
DwcaHunter.logger_write(object_id,
|
122
|
+
"Creating synonyms extension for DarwinCore Archive file")
|
122
123
|
count = 0
|
123
|
-
@cleaned_taxa.each do |
|
124
|
+
@cleaned_taxa.each do |_key, taxon|
|
124
125
|
count += 1
|
125
126
|
@core << [taxon[:id], taxon[:scientific_name], taxon[:parent_id]]
|
126
127
|
if count % BATCH_SIZE == 0
|
127
|
-
DwcaHunter
|
128
|
-
|
128
|
+
DwcaHunter.logger_write(object_id,
|
129
|
+
"Traversing %s extension data record" % count)
|
129
130
|
end
|
130
131
|
taxon[:synonyms].each do |name|
|
131
132
|
@extensions[-1][:data] << [taxon[:id], name]
|
@@ -134,19 +135,20 @@ module DwcaHunter
|
|
134
135
|
@eml = {
|
135
136
|
id: @uuid,
|
136
137
|
title: @title,
|
137
|
-
license:
|
138
|
+
license: "http://creativecommons.org/licenses/by-sa/3.0/",
|
138
139
|
authors: [
|
139
|
-
{ url:
|
140
|
-
|
141
|
-
|
140
|
+
{ url: "http://www.freebase.com/home" }
|
141
|
+
],
|
142
|
+
abstract: "An entity graph of people, places and things, " \
|
143
|
+
"built by a community that loves open data.",
|
142
144
|
metadata_providers: [
|
143
|
-
{ first_name:
|
144
|
-
last_name:
|
145
|
-
email:
|
146
|
-
|
145
|
+
{ first_name: "Dmitry",
|
146
|
+
last_name: "Mozzherin",
|
147
|
+
email: "dmozzherin@mbl.edu" }
|
148
|
+
],
|
149
|
+
url: "http://www.freebase.com/home"
|
147
150
|
}
|
148
151
|
super
|
149
152
|
end
|
150
|
-
|
151
153
|
end
|
152
154
|
end
|