get taxonomic lineage from ENA for a species name

get_lineage_from_species.cr

#!/usr/bin/env crystal
require "http/client"
require "json"

species = ARGV[0]

species = species.gsub(/\s/, "%20")

r = HTTP::Client.get("https://www.ebi.ac.uk/ena/taxonomy/rest/scientific-name/#{species}", headers: HTTP::Headers{"Accept" => "application/json"})
raise "cannot get the taxonomy" unless r.success?

json = JSON.parse(r.body)

if json.as_a.size < 1
  r = HTTP::Client.get("https://www.ebi.ac.uk/ena/taxonomy/rest/any-name/#{species}", headers: HTTP::Headers{"Accept" => "application/json"})
  raise "cannot get the taxonomy" unless r.success?

  json = JSON.parse(r.body)
end

raise "cannot get the taxonomy" if json.as_a.size < 1

puts "#{json[0]["lineage"]}#{ARGV[0]}"

get_lineage_from_species.rb

#!/nfs/users/nfs_m/mh6/.linuxbrew/homebrew/bin/ruby
require "net/http"
require "uri"
require "json"
require "cgi"

species = ARGV[0]

species = CGI.escapeURIComponent(species)

uri = URI("https://www.ebi.ac.uk/ena/taxonomy/rest/scientific-name/#{species}")
r = Net::HTTP.get_response(uri, {"Accept" => "application/json"})
raise "cannot get the taxonomy" unless r.is_a?(Net::HTTPSuccess)

json = JSON.parse(r.body)

if json.size < 1
  uri =URI("https://www.ebi.ac.uk/ena/taxonomy/rest/any-name/#{species}") 
  r = Net::HTTP.get_response(uri,{"Accept" => "application/json"})
  raise "cannot get the taxonomy" unless r.is_a?(Net::HTTPSuccess)

  json = JSON.parse(r.body)
end

raise "cannot get the taxonomy" if json.size < 1

print "#{json[0]["lineage"]}#{ARGV[0]}"