#!/usr/bin/env ruby # Arvados cli client # # Ward Vandewege require 'fileutils' if RUBY_VERSION < '1.9.3' then abort <<-EOS #{$0.gsub(/^\.\//,'')} requires Ruby version 1.9.3 or higher. EOS end # read authentication data from arvados configuration file if present lineno = 0 config_file = File.expand_path('~/.config/arvados/settings.conf') if File.exist? config_file then File.open(config_file, 'r').each do |line| lineno = lineno + 1 # skip comments if line.match('^\s*#') then next end var, val = line.chomp.split('=', 2) # allow environment settings to override config files. if var and val ENV[var] ||= val else warn "#{config_file}: #{lineno}: could not parse `#{line}'" end end end case ARGV[0] when 'keep' ARGV.shift @sub = ARGV.shift if ['get', 'put', 'ls', 'normalize'].index @sub then # Native Arvados exec `which arv-#{@sub}`.strip, *ARGV elsif ['less', 'check'].index @sub then # wh* shims exec `which wh#{@sub}`.strip, *ARGV else puts "Usage: \n" + "#{$0} keep ls\n" + "#{$0} keep get\n" + "#{$0} keep put\n" + "#{$0} keep less\n" + "#{$0} keep check\n" end abort when 'pipeline' ARGV.shift @sub = ARGV.shift if ['run'].index @sub then exec `which arv-run-pipeline-instance`.strip, *ARGV else puts "Usage: \n" + "#{$0} pipeline run [...]\n" + "(see arv-run-pipeline-instance --help for details)\n" end abort when 'tag' ARGV.shift exec `which arv-tag`.strip, *ARGV end ENV['ARVADOS_API_VERSION'] ||= 'v1' if not ENV.include?('ARVADOS_API_HOST') or not ENV.include?('ARVADOS_API_TOKEN') then abort <<-EOS ARVADOS_API_HOST and ARVADOS_API_TOKEN need to be defined as environment variables. EOS end begin require 'curb' require 'rubygems' require 'google/api_client' require 'json' require 'pp' require 'trollop' require 'andand' require 'oj' require 'active_support/inflector' require 'yaml' rescue LoadError abort <<-EOS Please install all required gems: gem install activesupport andand curb google-api-client json oj trollop EOS end ActiveSupport::Inflector.inflections do |inflect| inflect.irregular 'specimen', 'specimens' inflect.irregular 'human', 'humans' end module Kernel def suppress_warnings original_verbosity = $VERBOSE $VERBOSE = nil result = yield $VERBOSE = original_verbosity return result end end # do this if you're testing with a dev server and you don't care about SSL certificate checks: if ENV['ARVADOS_API_HOST_INSECURE'] suppress_warnings { OpenSSL::SSL::VERIFY_PEER = OpenSSL::SSL::VERIFY_NONE } end class Google::APIClient def discovery_document(api, version) api = api.to_s return @discovery_documents["#{api}:#{version}"] ||= begin # fetch new API discovery doc if stale cached_doc = File.expand_path '~/.cache/arvados/discovery_uri.json' if not File.exist?(cached_doc) or (Time.now - File.mtime(cached_doc)) > 86400 response = self.execute!(:http_method => :get, :uri => self.discovery_uri(api, version), :authenticated => false) FileUtils.makedirs(File.dirname cached_doc) File.open(cached_doc, 'w') do |f| f.puts response.body end end File.open(cached_doc) { |f| JSON.load f } end end end class ArvadosClient < Google::APIClient def execute(*args) if args.last.is_a? Hash args.last[:headers] ||= {} args.last[:headers]['Accept'] ||= 'application/json' end super(*args) end end client = ArvadosClient.new(:host => ENV['ARVADOS_API_HOST'], :application_name => 'arvados-cli', :application_version => '1.0') arvados = client.discovered_api('arvados', ENV['ARVADOS_API_VERSION']) def to_boolean(s) !!(s =~ /^(true|t|yes|y|1)$/i) end def help_methods(discovery_document, resource, method=nil) banner = "\n" banner += "The #{resource} resource type supports the following methods:" banner += "\n\n" discovery_document["resources"][resource.pluralize]["methods"]. each do |k,v| description = '' if v.include? "description" # add only the first line of the discovery doc description description = ' ' + v["description"].split("\n").first.chomp end banner += " #{sprintf("%20s",k)}#{description}\n" end banner += "\n" STDERR.puts banner if not method.nil? and method != '--help' then Trollop::die ("Unknown method #{method.inspect} " + "for resource #{resource.inspect}") end exit 255 end def help_resources(discovery_document, resource) banner = "\n" banner += "This Arvados instance supports the following resource types:" banner += "\n\n" discovery_document["resources"].each do |k,v| description = '' resource_info = discovery_document["schemas"][k.singularize.capitalize] if resource_info and resource_info.include?('description') # add only the first line of the discovery doc description description = ' ' + resource_info["description"].split("\n").first.chomp end banner += " #{sprintf("%30s",k.singularize)}#{description}\n" end banner += "\n" STDERR.puts banner if not resource.nil? and resource != '--help' then Trollop::die "Unknown resource type #{resource.inspect}" end exit 255 end def parse_arguments(discovery_document) resource_types = Array.new() discovery_document["resources"].each do |k,v| resource_types << k.singularize end global_opts = Trollop::options do version __FILE__ banner "arv: the Arvados CLI tool" opt :dry_run, "Don't actually do anything", :short => "-n" opt :verbose, "Print some things on stderr" opt :format, "Set the output format. Must be one of json (default), yaml or uuid.", :type => :string, :default => 'json' opt :short, "Return only UUIDs (equivalent to --format=uuid)" opt :resources, "Display list of resources known to this Arvados instance." conflicts :short, :format stop_on resource_types end unless %w(json yaml uuid).include?(global_opts[:format]) $stderr.puts "#{$0}: --format must be one of json, yaml or uuid." $stderr.puts "Use #{$0} --help for more information." abort end if global_opts[:short] global_opts[:format] = 'uuid' end resource = ARGV.shift if global_opts[:resources] or not resource_types.include?(resource) help_resources(discovery_document, resource) end method = ARGV.shift if not (discovery_document["resources"][resource.pluralize]["methods"]. include?(method)) help_methods(discovery_document, resource, method) end discovered_params = discovery_document\ ["resources"][resource.pluralize]\ ["methods"][method]["parameters"] method_opts = Trollop::options do discovered_params.each do |k,v| opts = Hash.new() opts[:type] = v["type"].to_sym if v.include?("type") if [:datetime, :text, :object, :array].index opts[:type] opts[:type] = :string # else trollop bork end opts[:default] = v["default"] if v.include?("default") opts[:default] = v["default"].to_i if opts[:type] == :integer opts[:default] = to_boolean(v["default"]) if opts[:type] == :boolean opts[:required] = true if v.include?("required") and v["required"] description = '' description = ' ' + v["description"] if v.include?("description") opt k.to_sym, description, opts end body_object = discovery_document["resources"][resource.pluralize]["methods"][method]["request"] if body_object and discovered_params[resource].nil? is_required = true if body_object["required"] == false is_required = false end opt resource.to_sym, "#{resource} (request body)", { required: is_required, type: :string } end end discovered_params.each do |k,v| k = k.to_sym if ['object', 'array'].index(v["type"]) and method_opts.has_key? k if method_opts[k].andand.match /^\// method_opts[k] = File.open method_opts[k], 'rb' do |f| f.read end end end end return resource, method, method_opts, global_opts, ARGV end resource_schema, method, method_opts, global_opts, remaining_opts = parse_arguments(arvados.discovery_document) controller = resource_schema.pluralize api_method = 'arvados.' + controller + '.' + method if global_opts[:dry_run] if global_opts[:verbose] $stderr.puts "#{api_method} #{method_opts.inspect}" end exit end request_parameters = {}.merge(method_opts) resource_body = request_parameters.delete(resource_schema.to_sym) if resource_body request_body = { resource_schema => resource_body } else request_body = {} end case api_method when 'arvados.users.event_stream', 'arvados.jobs.log_stream', 'arvados.jobs.log_tail_follow' # Special case for methods that respond with data streams rather # than JSON (TODO: use the discovery document instead of a static # list of methods) uri_s = eval(api_method).generate_uri(request_parameters) Curl::Easy.perform(uri_s) do |curl| curl.headers['Accept'] = 'text/plain' curl.headers['Authorization'] = "OAuth2 #{ENV['ARVADOS_API_TOKEN']}" if ENV['ARVADOS_API_HOST_INSECURE'] curl.ssl_verify_peer = false curl.ssl_verify_host = false end if global_opts[:verbose] curl.on_header { |data| $stderr.write data } end curl.on_body { |data| $stdout.write data } end exit 0 else request_body[:api_token] = ENV['ARVADOS_API_TOKEN'] request_body[:_profile] = true result = client.execute(:api_method => eval(api_method), :parameters => request_parameters, :body => request_body, :authenticated => false) end begin results = JSON.parse result.body rescue JSON::ParserError => e abort "Failed to parse server response:\n" + e.to_s end if results["errors"] then abort "Error: #{results["errors"][0]}" end case global_opts[:format] when 'json' puts Oj.dump(results, :indent => 1) when 'yaml' puts results.to_yaml else if results["items"] and results["kind"].match /list$/i results['items'].each do |i| puts i['uuid'] end elsif results['uuid'].nil? abort("Response did not include a uuid:\n" + Oj.dump(results, :indent => 1) + "\n") else puts results['uuid'] end end