dwca_hunter 0.5.3 → 0.7.2
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- checksums.yaml +4 -4
- data/.byebug_history +37 -0
- data/.gitignore +5 -0
- data/.rubocop.yml +11 -2
- data/.ruby-version +1 -1
- data/Gemfile.lock +90 -84
- data/LICENSE.txt +1 -1
- data/README.md +1 -1
- data/dwca_hunter.gemspec +13 -12
- data/exe/dwcahunter +1 -5
- data/lib/dwca_hunter.rb +33 -0
- data/lib/dwca_hunter/resource.rb +8 -3
- data/lib/dwca_hunter/resources/aos-birds.rb +143 -0
- data/lib/dwca_hunter/resources/arctos.rb +115 -149
- 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/index-fungorum.rb +131 -0
- data/lib/dwca_hunter/resources/ioc_word_bird.rb +200 -0
- data/lib/dwca_hunter/resources/ion.rb +98 -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 +186 -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 +166 -184
- data/lib/dwca_hunter/version.rb +1 -1
- metadata +54 -32
- data/ipni.csv.gz +0 -0
- data/ipniWebName.csv.xz?dl=1 +0 -0
@@ -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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end
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def make_dwca
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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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def get_names
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Dir.chdir(@download_dir)
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collect_names
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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, "data.csv"),
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headers: true)
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file.each_with_index do |row, i|
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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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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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code: code }
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if row["English name"].to_s != ""
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@vernaculars << {
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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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}
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end
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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 generate_dwca
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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/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[: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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"http://purl.org/dc/terms/language"
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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], v[:lang]]
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end
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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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],
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abstract: "The eBird/Clements Checklist of Birds of the World" \
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": v2019. Downloaded from " \
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"https://www.birds.cornell.edu/clementschecklist/download/",
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url: @url
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}
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super
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end
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end
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end
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#
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# frozen_string_literal: true
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module DwcaHunter
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class ResourceFreebase < DwcaHunter::Resource
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def initialize(opts = {})
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@command = "freebase"
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@title =
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@uuid =
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@title = "Freebase"
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@uuid = "bacd21f0-44e0-43e2-914c-70929916f257"
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@download_path = File.join(Dir.tmpdir,
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"dwca_hunter",
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"freebase",
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"data.json")
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@data = []
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@all_taxa = {}
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@cleaned_taxa = {}
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@@ -27,11 +27,11 @@ module DwcaHunter
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end
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def download
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DwcaHunter
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DwcaHunter.logger_write(object_id,
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"Querying freebase for species information...")
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q = {
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query: [{
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type:
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type: "/biology/organism_classification",
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id: nil,
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guid: nil,
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name: nil,
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id: nil,
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guid: nil,
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scientific_name: nil,
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optional: true
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}
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optional: true
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}
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}],
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cursor: true
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cursor: true
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}
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run_query(q)
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data = JSON.pretty_generate @data
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f = open(@download_path,
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f = open(@download_path, "w:utf-8")
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f.write(data)
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f.close
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end
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def run_query(q)
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count = 0
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requests_num = 0
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-
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loop do
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freebase_url = "http://api.freebase.com/api/service/mqlread?query=%s" %
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URI.encode(q.to_json)
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res = JSON.load RestClient.get(freebase_url)
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requests_num += 1
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break if res[
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break if res["result"].nil? || res["result"].empty?
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if requests_num % 10 == 0
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DwcaHunter
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DwcaHunter.logger_write(object_id,
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"Received %s names" % count)
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end
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count += res[
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res[
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q[:cursor] = res[
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count += res["result"].size
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res["result"].each { |d| @data << d }
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q[:cursor] = res["cursor"]
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end
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end
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def organize_data
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@data = JSON.load(open(@download_path,
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@data = JSON.load(open(@download_path, "r:utf-8").read)
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@data.each do |d|
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scientific_name = d[
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scientific_name = d["scientific_name"].to_s
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id = d["id"]
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parent_id = d[
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d[
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parent_id = d["higher_classification"] ?
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d["higher_classification"]["id"] :
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nil
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synonyms = d[
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synonyms = d["synonym_scientific_name"]
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@all_taxa[id] = { id: id,
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parent_id: parent_id,
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scientific_name: scientific_name,
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@all_taxa.each do |k, v|
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next unless v[:scientific_name] && v[:scientific_name].strip != ""
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parent_id = v[:parent_id]
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until (@all_taxa[parent_id] &&
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@all_taxa[parent_id][:scientific_name]) || parent_id.nil?
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@@ -103,29 +105,28 @@ module DwcaHunter
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v[:parent_id] = parent_id
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@cleaned_taxa[k] = v
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end
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-
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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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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/parentNameUsageID"]]
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@extensions << { data: [[
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-
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-
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]], file_name:
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DwcaHunter
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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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]], file_name: "synonyms.txt" }
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DwcaHunter.logger_write(object_id,
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"Creating synonyms extension for DarwinCore Archive file")
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count = 0
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@cleaned_taxa.each do |
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@cleaned_taxa.each do |_key, taxon|
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count += 1
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@core << [taxon[:id], taxon[:scientific_name], taxon[:parent_id]]
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if count % BATCH_SIZE == 0
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-
DwcaHunter
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-
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DwcaHunter.logger_write(object_id,
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"Traversing %s extension data record" % count)
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end
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taxon[:synonyms].each do |name|
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@extensions[-1][:data] << [taxon[:id], name]
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@@ -134,19 +135,20 @@ module DwcaHunter
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@eml = {
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id: @uuid,
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title: @title,
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license:
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license: "http://creativecommons.org/licenses/by-sa/3.0/",
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authors: [
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{ url:
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{ url: "http://www.freebase.com/home" }
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],
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abstract: "An entity graph of people, places and things, " \
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"built by a community that loves open data.",
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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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{ first_name: "Dmitry",
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last_name: "Mozzherin",
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email: "dmozzherin@mbl.edu" }
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],
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url: "http://www.freebase.com/home"
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}
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super
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end
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-
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end
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end
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@@ -0,0 +1,168 @@
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# frozen_string_literal: true
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module DwcaHunter
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class ResourceHowardMoore < DwcaHunter::Resource
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def initialize(opts = {})
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@command = "how-moore-birds"
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@title = "Howard and Moore Complete Checklist of the Birds of the World"
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@url = "https://uofi.box.com/shared/static/m71m541dr5unc41xzg4y51d92b7wiy2k.csv"
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@UUID = "85023fe5-bf2a-486b-bdae-3e61cefd41fd"
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@download_path = File.join(Dir.tmpdir,
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"dwca_hunter",
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"how-moore-birds",
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"data.csv")
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@synonyms = []
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@names = []
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@vernaculars = []
|
17
|
+
@extensions = []
|
18
|
+
@synonyms_hash = {}
|
19
|
+
@vernaculars_hash = {}
|
20
|
+
super(opts)
|
21
|
+
end
|
22
|
+
|
23
|
+
def download
|
24
|
+
puts "Downloading cached verion of the file."
|
25
|
+
puts "Check https://www.howardandmoore.org/howard-and-moore-database/"
|
26
|
+
puts "If there is a more recent edition"
|
27
|
+
`curl -s -L #{@url} -o #{@download_path}`
|
28
|
+
end
|
29
|
+
|
30
|
+
def unpack; end
|
31
|
+
|
32
|
+
def make_dwca
|
33
|
+
DwcaHunter.logger_write(object_id, "Extracting data")
|
34
|
+
get_names
|
35
|
+
generate_dwca
|
36
|
+
end
|
37
|
+
|
38
|
+
private
|
39
|
+
|
40
|
+
def get_names
|
41
|
+
Dir.chdir(@download_dir)
|
42
|
+
collect_names
|
43
|
+
end
|
44
|
+
|
45
|
+
def collect_names
|
46
|
+
file = CSV.open(File.join(@download_dir, "data.csv"),
|
47
|
+
headers: true)
|
48
|
+
file.each_with_index do |row, i|
|
49
|
+
kingdom = "Animalia"
|
50
|
+
phylum = "Chordata"
|
51
|
+
klass = "Aves"
|
52
|
+
family = row["FAMILY_NAME"].capitalize
|
53
|
+
genus = row["GENERA_NAME"].capitalize
|
54
|
+
species = row["SPECIES_NAME"]
|
55
|
+
species_au =
|
56
|
+
"#{row['species_author']} #{row['species_rec_year']}".strip
|
57
|
+
subspecies = row["SUB_SPECIES_NAME"]
|
58
|
+
subspecies_au =
|
59
|
+
"#{row['subspecies_author']} #{row['subspecies_rec_year']}".strip
|
60
|
+
code = "ICZN"
|
61
|
+
|
62
|
+
taxon_id = "gn_#{i + 1}"
|
63
|
+
name_string = species
|
64
|
+
name_string = if subspecies.to_s == "" ||
|
65
|
+
name_string.include?(subspecies)
|
66
|
+
"#{name_string} #{species_au}".strip
|
67
|
+
else
|
68
|
+
"#{name_string} #{subspecies} #{subspecies_au}".strip
|
69
|
+
end
|
70
|
+
|
71
|
+
@names << { taxon_id: taxon_id,
|
72
|
+
name_string: name_string,
|
73
|
+
kingdom: kingdom,
|
74
|
+
phylum: phylum,
|
75
|
+
klass: klass,
|
76
|
+
family: family,
|
77
|
+
genus: genus,
|
78
|
+
code: code }
|
79
|
+
|
80
|
+
if row["species_english_name"].to_s != ""
|
81
|
+
@vernaculars << {
|
82
|
+
taxon_id: taxon_id,
|
83
|
+
vern: row["species_english_name"],
|
84
|
+
lang: "en"
|
85
|
+
}
|
86
|
+
end
|
87
|
+
if row["species_english_name2"].to_s != ""
|
88
|
+
@vernaculars << {
|
89
|
+
taxon_id: taxon_id,
|
90
|
+
vern: row["species_english_name2"],
|
91
|
+
lang: "en"
|
92
|
+
}
|
93
|
+
end
|
94
|
+
|
95
|
+
puts "Processed %s names" % i if i % 10_000 == 0
|
96
|
+
end
|
97
|
+
end
|
98
|
+
|
99
|
+
def update_vernacular(taxon_id, canonical)
|
100
|
+
return unless @vernaculars_hash.key?(canonical)
|
101
|
+
|
102
|
+
@vernaculars_hash[canonical].each do |vern|
|
103
|
+
@vernaculars << { taxon_id: taxon_id, vern: vern }
|
104
|
+
end
|
105
|
+
end
|
106
|
+
|
107
|
+
def update_synonym(taxon_id, canonical)
|
108
|
+
return unless @synonyms_hash.key?(canonical)
|
109
|
+
|
110
|
+
@synonyms_hash[canonical].each do |syn|
|
111
|
+
@synonyms << { taxon_id: taxon_id, name_string: syn[:name_string],
|
112
|
+
status: syn[:status] }
|
113
|
+
end
|
114
|
+
end
|
115
|
+
|
116
|
+
def generate_dwca
|
117
|
+
DwcaHunter.logger_write(object_id,
|
118
|
+
"Creating DarwinCore Archive file")
|
119
|
+
@core = [["http://rs.tdwg.org/dwc/terms/taxonID",
|
120
|
+
"http://rs.tdwg.org/dwc/terms/scientificName",
|
121
|
+
"http://rs.tdwg.org/dwc/terms/kingdom",
|
122
|
+
"http://rs.tdwg.org/dwc/terms/phylum",
|
123
|
+
"http://rs.tdwg.org/dwc/terms/class",
|
124
|
+
"http://rs.tdwg.org/dwc/terms/family",
|
125
|
+
"http://rs.tdwg.org/dwc/terms/genus",
|
126
|
+
"http://rs.tdwg.org/dwc/terms/nomenclaturalCode"]]
|
127
|
+
@names.each do |n|
|
128
|
+
@core << [n[:taxon_id], n[:name_string],
|
129
|
+
n[:kingdom], n[:phylum], n[:klass], n[:family],
|
130
|
+
n[:genus], n[:code]]
|
131
|
+
end
|
132
|
+
@extensions << {
|
133
|
+
data: [[
|
134
|
+
"http://rs.tdwg.org/dwc/terms/taxonID",
|
135
|
+
"http://rs.tdwg.org/dwc/terms/vernacularName",
|
136
|
+
"http://purl.org/dc/terms/language"
|
137
|
+
]],
|
138
|
+
file_name: "vernacular_names.txt",
|
139
|
+
row_type: "http://rs.gbif.org/terms/1.0/VernacularName"
|
140
|
+
}
|
141
|
+
|
142
|
+
@vernaculars.each do |v|
|
143
|
+
@extensions[-1][:data] << [v[:taxon_id], v[:vern], v[:lang]]
|
144
|
+
end
|
145
|
+
|
146
|
+
@eml = {
|
147
|
+
id: @uuid,
|
148
|
+
title: @title,
|
149
|
+
authors: [
|
150
|
+
{
|
151
|
+
last_name: "Christidis"
|
152
|
+
}
|
153
|
+
],
|
154
|
+
metadata_providers: [
|
155
|
+
{ first_name: "Dmitry",
|
156
|
+
last_name: "Mozzherin",
|
157
|
+
email: "dmozzherin@gmail.com" }
|
158
|
+
],
|
159
|
+
abstract: "Christidis et al. 2018. The Howard and Moore Complete " \
|
160
|
+
"Checklist of the Birds of the World, version 4.1 " \
|
161
|
+
"(Downloadable checklist). " \
|
162
|
+
"Accessed from https://www.howardandmoore.org.",
|
163
|
+
url: @url
|
164
|
+
}
|
165
|
+
super
|
166
|
+
end
|
167
|
+
end
|
168
|
+
end
|