5 # Ward Vandewege <ward@clinicalfuture.com>
7 if RUBY_VERSION < '1.9.3' then
9 #{$0.gsub(/^\.\//,'')} requires Ruby version 1.9.3 or higher.
17 if ['get', 'put'].index @sub then
19 exec `which arv-#{@sub}`.strip, *ARGV
20 elsif ['ls', 'less', 'check'].index @sub then
22 exec `which wh#{@sub}`.strip, *ARGV
35 if ['run'].index @sub then
36 exec `which arv-run-pipeline-instance`.strip, *ARGV
39 "#{$0} pipeline run [...]\n" +
40 "(see arv-run-pipeline-instance --help for details)\n"
45 ENV['ARVADOS_API_VERSION'] ||= 'v1'
47 if not ENV.include?('ARVADOS_API_HOST') or not ENV.include?('ARVADOS_API_TOKEN') then
49 ARVADOS_API_HOST and ARVADOS_API_TOKEN need to be defined as environment variables.
56 require 'google/api_client'
62 require 'active_support/inflector'
67 Please install all required gems:
69 gem install activesupport andand curb google-api-client json oj trollop
74 ActiveSupport::Inflector.inflections do |inflect|
75 inflect.irregular 'specimen', 'specimens'
76 inflect.irregular 'human', 'humans'
81 original_verbosity = $VERBOSE
84 $VERBOSE = original_verbosity
89 # do this if you're testing with a dev server and you don't care about SSL certificate checks:
90 if ENV['ARVADOS_API_HOST_INSECURE']
91 suppress_warnings { OpenSSL::SSL::VERIFY_PEER = OpenSSL::SSL::VERIFY_NONE }
94 class Google::APIClient
95 def discovery_document(api, version)
97 return @discovery_documents["#{api}:#{version}"] ||= (begin
98 response = self.execute!(
100 :uri => self.discovery_uri(api, version),
101 :authenticated => false
103 response.body.class == String ? JSON.parse(response.body) : response.body
108 class ArvadosClient < Google::APIClient
110 if args.last.is_a? Hash
111 args.last[:headers] ||= {}
112 args.last[:headers]['Accept'] ||= 'application/json'
118 client = ArvadosClient.new(:host => ENV['ARVADOS_API_HOST'], :application_name => 'arvados-cli', :application_version => '1.0')
119 arvados = client.discovered_api('arvados', ENV['ARVADOS_API_VERSION'])
122 !!(s =~ /^(true|t|yes|y|1)$/i)
125 def help_methods(discovery_document, resource, method=nil)
127 banner += "The #{resource} resource type supports the following methods:"
129 discovery_document["resources"][resource.pluralize]["methods"].
132 description = ' ' + v["description"] if v.include?("description")
133 banner += " #{sprintf("%20s",k)}#{description}\n"
138 if not method.nil? and method != '--help' then
139 Trollop::die ("Unknown method #{method.inspect} " +
140 "for resource #{resource.inspect}")
145 def help_resources(discovery_document, resource)
147 banner += "This Arvados instance supports the following resource types:"
149 discovery_document["resources"].each do |k,v|
151 if discovery_document["schemas"].include?(k.singularize.capitalize) and
152 discovery_document["schemas"][k.singularize.capitalize].include?('description') then
153 description = ' ' + discovery_document["schemas"][k.singularize.capitalize]["description"]
155 banner += " #{sprintf("%30s",k.singularize)}#{description}\n"
160 if not resource.nil? and resource != '--help' then
161 Trollop::die "Unknown resource type #{resource.inspect}"
166 def parse_arguments(discovery_document)
167 resource_types = Array.new()
168 resource_types << '--help'
169 discovery_document["resources"].each do |k,v|
170 resource_types << k.singularize
173 global_opts = Trollop::options do
174 banner "arvados cli client"
175 opt :dry_run, "Don't actually do anything", :short => "-n"
176 opt :verbose, "Print some things on stderr", :short => "-v"
177 opt :uuid, "Return the UUIDs of the objects in the response, one per line (default)", :short => nil
178 opt :json, "Return the entire response received from the API server, as a JSON object", :short => "-j"
179 opt :human, "Return the response received from the API server, as a JSON object with whitespace added for human consumption", :short => "-h"
180 opt :pretty, "Synonym of --human", :short => nil
181 opt :yaml, "Return the response received from the API server, in YAML format", :short => "-y"
182 stop_on resource_types
185 resource = ARGV.shift
186 if resource == '--help' or not resource_types.include?(resource)
187 help_resources(discovery_document, resource)
191 if not (discovery_document["resources"][resource.pluralize]["methods"].
193 help_methods(discovery_document, resource, method)
196 discovered_params = discovery_document\
197 ["resources"][resource.pluralize]\
198 ["methods"][method]["parameters"]
199 method_opts = Trollop::options do
200 discovered_params.each do |k,v|
202 opts[:type] = v["type"].to_sym if v.include?("type")
203 if [:datetime, :text, :object, :array].index opts[:type]
204 opts[:type] = :string # else trollop bork
206 opts[:default] = v["default"] if v.include?("default")
207 opts[:default] = v["default"].to_i if opts[:type] == :integer
208 opts[:default] = to_boolean(v["default"]) if opts[:type] == :boolean
209 opts[:required] = true if v.include?("required") and v["required"]
211 description = ' ' + v["description"] if v.include?("description")
212 opt k.to_sym, description, opts
214 body_object = discovery_document["resources"][resource.pluralize]["methods"][method]["request"]
215 if body_object and discovered_params[resource].nil?
217 if body_object["required"] == false
220 opt resource.to_sym, "#{resource} (request body)", {
221 required: is_required,
224 discovered_params[resource.to_sym] = body_object
228 discovered_params.each do |k,v|
230 if ['object', 'array'].index(v["type"]) and method_opts.has_key? k
231 if method_opts[k].match /^\//
232 method_opts[k] = File.open method_opts[k], 'rb' do |f| f.read end
236 return resource, method, method_opts, global_opts, ARGV
239 resource_schema, method, method_opts, global_opts, remaining_opts = parse_arguments(arvados.discovery_document)
240 controller = resource_schema.pluralize
242 api_method = 'arvados.' + controller + '.' + method
244 if global_opts[:dry_run]
245 if global_opts[:verbose]
246 $stderr.puts "#{api_method} #{method_opts.inspect}"
251 request_parameters = {}.merge(method_opts)
252 resource_body = request_parameters.delete(resource_schema.to_sym)
255 resource_schema => JSON.parse(resource_body)
263 'arvados.users.event_stream',
264 'arvados.jobs.log_stream',
265 'arvados.jobs.log_tail_follow'
267 # Special case for methods that respond with data streams rather
268 # than JSON (TODO: use the discovery document instead of a static
270 uri_s = eval(api_method).generate_uri(request_parameters)
271 Curl::Easy.perform(uri_s) do |curl|
272 curl.headers['Accept'] = 'text/plain'
273 curl.headers['Authorization'] = "OAuth2 #{ENV['ARVADOS_API_TOKEN']}"
274 if ENV['ARVADOS_API_HOST_INSECURE']
275 curl.ssl_verify_peer = false
276 curl.ssl_verify_host = false
278 if global_opts[:verbose]
279 curl.on_header { |data| $stderr.write data }
281 curl.on_body { |data| $stdout.write data }
285 request_body[:api_token] = ENV['ARVADOS_API_TOKEN']
286 request_body[:_profile] = true
287 result = client.execute(:api_method => eval(api_method),
288 :parameters => request_parameters,
289 :body => request_body,
290 :authenticated => false)
294 results = JSON.parse result.body
295 rescue JSON::ParserError => e
296 abort "Failed to parse server response:\n" + e.to_s
299 if results["errors"] then
300 abort "Error: #{results["errors"][0]}"
303 if global_opts[:human] or global_opts[:pretty] then
304 puts Oj.dump(results, :indent => 1)
305 elsif global_opts[:yaml] then
307 elsif global_opts[:json] then
308 puts Oj.dump(results)
309 elsif results["items"] and results["kind"].match /list$/i
310 results['items'].each do |i| puts i['uuid'] end
311 elsif results['uuid'].nil?
312 abort("Response did not include a uuid:\n" +
313 Oj.dump(results, :indent => 1) +