+def init_config
+ # read authentication data from arvados configuration file if present
+ lineno = 0
+ config_file = File.expand_path('~/.config/arvados/settings.conf') rescue nil
+ if not config_file.nil? and 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
+end
+
+subcommands = %w(create edit keep pipeline tag ws)
+
+def check_subcommands client, arvados, subcommand, global_opts, remaining_opts
+ case subcommand
+ when 'create'
+ arv_create client, arvados, global_opts, remaining_opts
+ when 'edit'
+ arv_edit client, arvados, global_opts, remaining_opts
+ when 'keep'
+ @sub = remaining_opts.shift
+ if ['get', 'put', 'ls', 'normalize'].index @sub then
+ # Native Arvados
+ exec `which arv-#{@sub}`.strip, *remaining_opts
+ elsif ['less', 'check'].index @sub then
+ # wh* shims
+ exec `which wh#{@sub}`.strip, *remaining_opts
+ elsif @sub == 'docker'
+ exec `which arv-keepdocker`.strip, *remaining_opts
+ else
+ puts "Usage: arv keep [method] [--parameters]\n"
+ puts "Use 'arv keep [method] --help' to get more information about specific methods.\n\n"
+ puts "Available methods: ls, get, put, less, check, docker"
+ end
+ abort
+ when 'pipeline'
+ sub = remaining_opts.shift
+ if sub == 'run'
+ exec `which arv-run-pipeline-instance`.strip, *remaining_opts
+ else
+ puts "Usage: arv pipeline [method] [--parameters]\n"
+ puts "Use 'arv pipeline [method] --help' to get more information about specific methods.\n\n"
+ puts "Available methods: run"
+ end
+ abort
+ when 'tag'
+ exec `which arv-tag`.strip, *remaining_opts
+ when 'ws'
+ exec `which arv-ws`.strip, *remaining_opts
+ end
+end
+
+def arv_edit_save_tmp tmp
+ FileUtils::cp tmp.path, tmp.path + ".saved"
+ puts "Saved contents to " + tmp.path + ".saved"
+end
+
+def command_exists?(command)
+ ENV['PATH'].split(':').each {|folder| File.executable?(File.join(folder, command))}
+end
+
+def run_editor tmp_file, global_opts
+ need_edit = true
+ while need_edit
+ pid = Process::fork
+ if pid.nil?
+ editor = nil
+ [ENV["VISUAL"], ENV["EDITOR"], "nano", "vi"].each do |e|
+ editor ||= e if e and command_exists? e
+ end
+ if editor.nil?
+ puts "Could not find any editor to use, please set $VISUAL or $EDITOR to your desired editor."
+ exit 1
+ end
+ exec editor, tmp_file.path
+ else
+ Process.wait pid
+ end
+
+ if $?.exitstatus == 0
+ tmp_file.open
+ newcontent = tmp_file.read()
+
+ newobj = {}
+ begin
+ case global_opts[:format]
+ when 'json'
+ newobj = Oj.load(newcontent)
+ when 'yaml'
+ newobj = YAML.load(newcontent)
+ end
+ need_edit = false
+ rescue Exception => e
+ n = 1
+ newcontent.each_line do |line|
+ puts "#{n.to_s.rjust 4} #{line}"
+ n += 1
+ end
+ puts "Parse error! " + e.to_s
+ puts "\nTry again (y/n)? "
+ yn = "X"
+ while not ["y", "Y", "n", "N"].include?(yn)
+ yn = $stdin.read 1
+ end
+ if yn == 'n' or yn == 'N'
+ arv_edit_save_tmp tmp_file
+ abort
+ end
+ end
+ else
+ puts "Editor exited with status #{$?.exitstatus}"
+ exit $?.exitstatus
+ end
+ end
+
+ newobj
+end
+
+def arv_edit client, arvados, global_opts, remaining_opts
+ uuid = remaining_opts.shift
+ if uuid.nil? or uuid == "-h" or uuid == "--help"
+ puts head_banner
+ puts "Usage: arv edit [uuid] [fields...]\n\n"
+ puts "Fetch the specified Arvados object, select the specified fields, \n"
+ puts "open an interactive text editor on a text representation (json or\n"
+ puts "yaml, use --format) and then update the object. Will use 'nano'\n"
+ puts "by default, customize with the EDITOR or VISUAL environment variable.\n"
+ exit 255
+ end
+
+ if not $stdout.tty?
+ puts "Not connected to a TTY, cannot run interactive editor."
+ exit 1
+ end
+
+ # determine controller
+
+ m = /([a-z0-9]{5})-([a-z0-9]{5})-([a-z0-9]{15})/.match uuid
+ if !m
+ if /^[a-f0-9]{32}/.match uuid
+ abort "Arvados collections are not editable."
+ else
+ abort "#{n} does not appear to be an Arvados uuid"
+ end
+ end
+
+ rsc = nil
+ arvados.discovery_document["resources"].each do |k,v|
+ klass = k.singularize.camelize
+ dig = Digest::MD5.hexdigest(klass).to_i(16).to_s(36)[-5..-1]
+ if dig == m[2]
+ rsc = k
+ end
+ end
+
+ if rsc.nil?
+ abort "Could not determine resource type #{m[2]}"
+ end
+
+ api_method = 'arvados.' + rsc + '.get'
+
+ result = client.execute(:api_method => eval(api_method),
+ :parameters => {"uuid" => uuid},
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
+ begin
+ results = JSON.parse result.body
+ rescue JSON::ParserError => e
+ abort "Failed to parse server response:\n" + e.to_s
+ end
+
+ if remaining_opts.length > 0
+ results.select! { |k, v| remaining_opts.include? k }
+ end
+
+ content = ""
+
+ case global_opts[:format]
+ when 'json'
+ content = Oj.dump(results, :indent => 1)
+ when 'yaml'
+ content = results.to_yaml
+ end
+
+ tmp_file = Tempfile.new([uuid, "." + global_opts[:format]])
+ tmp_file.write(content)
+ tmp_file.close
+
+ newobj = run_editor tmp_file, global_opts
+
+ begin
+ if newobj != results
+ api_method = 'arvados.' + rsc + '.update'
+ dumped = Oj.dump(newobj)
+
+ begin
+ result = client.execute(:api_method => eval(api_method),
+ :parameters => {"uuid" => uuid},
+ :body => { rsc.singularize => dumped },
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
+ rescue Exception => e
+ puts "Error communicating with server, error was #{e}"
+ puts "Update body was:"
+ puts dumped
+ arv_edit_save_tmp tmp_file
+ abort
+ end
+
+ begin
+ results = JSON.parse result.body
+ rescue JSON::ParserError => e
+ arv_edit_save_tmp tmp_file
+ abort "Failed to parse server response:\n" + e.to_s
+ end
+
+ if result.response.status != 200
+ puts "Update failed. Server responded #{result.response.status}: #{results['errors']} "
+ puts "Update body was:"
+ puts dumped
+ arv_edit_save_tmp tmp_file
+ abort
+ end
+ else
+ puts "Object is unchanged, did not update."
+ end
+ ensure
+ tmp_file.close(true)
+ end
+
+ exit 0
+end
+
+def arv_create client, arvados, global_opts, remaining_opts
+ types = resource_types(arvados.discovery_document)
+ create_opts = Trollop::options do
+ opt :project_uuid, "Project uuid in which to create the object", :type => :string
+ stop_on resource_types(arvados.discovery_document)
+ end
+
+ object_type = remaining_opts.shift
+ if object_type.nil?
+ abort "Missing resource type, must be one of #{types.join ', '}"
+ end
+
+ rsc = arvados.discovery_document["resources"].keys.select { |k| object_type == k.singularize }
+ if rsc.empty?
+ abort "Could not determine resource type #{object_type}"
+ end
+ rsc = rsc.first
+
+ discovered_params = arvados.discovery_document["resources"][rsc]["methods"]["create"]["parameters"]
+ method_opts = Trollop::options do
+ banner head_banner
+ banner "Usage: arv create [--project-uuid] #{object_type} [create parameters]"
+ banner ""
+ banner "This method supports the following parameters:"
+ banner ""
+ 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
+ end
+
+
+ newobj = {}
+ if create_opts[:project_uuid]
+ newobj["owner_uuid"] = create_opts[:project_uuid]
+ end
+
+ case global_opts[:format]
+ when 'json'
+ content = Oj.dump(newobj, :indent => 1)
+ when 'yaml'
+ content = newobj.to_yaml
+ end
+
+ tmp_file = Tempfile.new(["", ".#{global_opts[:format]}"])
+ tmp_file.write(content)
+ tmp_file.close
+
+ newobj = run_editor tmp_file, global_opts
+
+ begin
+ api_method = 'arvados.' + rsc + '.create'
+ dumped = Oj.dump(newobj)
+
+ result = client.execute(:api_method => eval(api_method),
+ :parameters => method_opts,
+ :body_object => {object_type => newobj},
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
+
+ begin
+ results = JSON.parse result.body
+ rescue JSON::ParserError => e
+ arv_edit_save_tmp tmp_file
+ abort "Failed to parse server response:\n" + e.to_s
+ end
+
+ if result.response.status != 200
+ puts "Create failed. Server responded #{result.response.status}: #{results['errors']} "
+ puts "Create body was:"
+ puts dumped
+ arv_edit_save_tmp tmp_file
+ abort
+ end
+
+ begin
+ puts "Created object #{results['uuid']}"
+ rescue
+ arv_edit_save_tmp tmp_file
+ abort "Unexpected response:\n#{results}"
+ end
+ ensure
+ tmp_file.close(true)
+ end
+
+ exit 0