#
# Ward Vandewege <ward@clinicalfuture.com>
+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
end
begin
+ require 'curb'
require 'rubygems'
require 'google/api_client'
require 'json'
require 'andand'
require 'oj'
require 'active_support/inflector'
+ require 'yaml'
rescue LoadError
abort <<-EOS
-Please install all required gems:
+Please install all required gems:
- gem install google-api-client json trollop andand oj activesupport
+ gem install activesupport andand curb google-api-client json oj trollop
EOS
end
class Google::APIClient
def discovery_document(api, version)
- api = api.to_s
- return @discovery_documents["#{api}:#{version}"] ||= (begin
- response = self.execute!(
- :http_method => :get,
- :uri => self.discovery_uri(api, version),
- :authenticated => false
- )
- response.body.class == String ? JSON.parse(response.body) : response.body
- end)
+ 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
-client = Google::APIClient.new(:host => ENV['ARVADOS_API_HOST'], :application_name => 'arvados-cli', :application_version => '1.0')
-arvados = client.discovered_api('arvados', ENV['ARVADOS_API_VERSION'])
+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
+
+begin
+ 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'])
+rescue Exception => e
+ puts "Failed to connect to Arvados API server: #{e}"
+ exit 1
+end
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()
- resource_types << '--help'
discovery_document["resources"].each do |k,v|
resource_types << k.singularize
end
global_opts = Trollop::options do
- banner "arvados cli client"
+ 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", :short => "-v"
- opt :uuid, "Return the UUIDs of the objects in the response, one per line (default)", :short => nil
- opt :json, "Return the entire response received from the API server, as a JSON object", :short => "-j"
- opt :human, "Return the response received from the API server, as a JSON object with whitespace added for human consumption", :short => "-h"
- opt :pretty, "Synonym of --human", :short => nil
+ 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
-
- # get the subcommand
- resource_arg = ARGV.shift
- if resource_types.include?(resource_arg) and resource_arg != '--help' then
- # subcommand exists
- # Now see if the method supplied exists
- method = ARGV.shift
- if discovery_document["resources"][resource_arg.pluralize]["methods"].include?(method) then
- # method exists. Collect arguments.
- discovered_params = discovery_document["resources"][resource_arg.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].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
- end
- discovered_params.each do |k,v|
- if v["type"] == "object" and method_opts.has_key? k
- method_opts[k] = JSON.parse method_opts[k]
- end
- end
- else
- banner = "\nThis resource type supports the following methods:\n\n"
- discovery_document["resources"][resource_arg.pluralize]["methods"].each do |k,v|
- description = ''
- description = ' ' + v["description"] if v.include?("description")
- 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.to_s} for command #{resource_arg.to_s}"
- else
- exit 255
- end
- end
-
- else
- banner = "\nThis Arvados instance supports the following resource types:\n\n"
- discovery_document["resources"].each do |k,v|
+ 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 = ''
- if discovery_document["schemas"].include?(k.singularize.capitalize) and
- discovery_document["schemas"][k.singularize.capitalize].include?('description') then
- description = ' ' + discovery_document["schemas"][k.singularize.capitalize]["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
- banner += " #{sprintf("%30s",k.singularize)}#{description}\n"
+ opt resource.to_sym, "#{resource} (request body)", {
+ required: is_required,
+ type: :string
+ }
end
- banner += "\n"
-
- STDERR.puts banner
+ end
- if not resource_arg.nil? and resource_arg != '--help' then
- Trollop::die "Unknown resource type #{resource_arg.inspect}"
- else
- exit 255
+ 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_arg.pluralize, method, method_opts, global_opts, ARGV
+ return resource, method, method_opts, global_opts, ARGV
end
-controller, method, method_opts, global_opts, remaining_opts = parse_arguments(arvados.discovery_document)
+resource_schema, method, method_opts, global_opts, remaining_opts = parse_arguments(arvados.discovery_document)
+controller = resource_schema.pluralize
api_method = 'arvados.' + controller + '.' + method
exit
end
-result = client.execute :api_method => eval(api_method), :parameters => { :api_token => ENV['ARVADOS_API_TOKEN'] }.merge(method_opts), :authenticated => false
-results = JSON.parse result.body
+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| $stdout.write data }
+ end
+ exit 0
+else
+ request_body[:api_token] = ENV['ARVADOS_API_TOKEN']
+ request_body[:_profile] = true
+ result = client.execute(:api_method => eval(api_method),
+ :parameters => request_parameters,
+ :body => request_body,
+ :authenticated => false)
+end
+
+begin
+ results = JSON.parse result.body
+rescue JSON::ParserError => e
+ abort "Failed to parse server response:\n" + e.to_s
+end
if results["errors"] then
abort "Error: #{results["errors"][0]}"
end
-if global_opts[:human] or global_opts[:pretty] then
+case global_opts[:format]
+when 'json'
puts Oj.dump(results, :indent => 1)
-elsif global_opts[:json] then
- puts Oj.dump(results)
-elsif results["items"] and results["kind"].match /list$/i
- results['items'].each do |i| puts i['uuid'] end
+when 'yaml'
+ puts results.to_yaml
else
- puts results['uuid']
+ 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
projects / arvados.git / blobdiff