X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/9f3ea8afe4b2fe8274cafabef31645ba18e04239..7b5729d984a9c516920270250f050bf72f1896d1:/sdk/cli/bin/arv diff --git a/sdk/cli/bin/arv b/sdk/cli/bin/arv index 13a0d9de3c..533ea39eb7 100755 --- a/sdk/cli/bin/arv +++ b/sdk/cli/bin/arv @@ -2,7 +2,7 @@ # Arvados cli client # -# Ward Vandewege +# Ward Vandewege require 'fileutils' @@ -12,77 +12,6 @@ if RUBY_VERSION < '1.9.3' then 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 - -subcommands = %w(keep pipeline tag ws) - -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 - elsif @sub == 'docker' - exec `which arv-keepdocker`.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" + - "#{$0} keep docker\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 -when 'ws' - ARGV.shift - exec `which arv-ws`.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' @@ -94,16 +23,19 @@ begin require 'oj' require 'active_support/inflector' require 'yaml' + require 'tempfile' rescue LoadError abort <<-EOS Please install all required gems: - gem install activesupport andand curb google-api-client json oj trollop + gem install activesupport andand curb google-api-client json oj trollop yaml EOS end +# Search for 'ENTRY POINT' to see where things get going + ActiveSupport::Inflector.inflections do |inflect| inflect.irregular 'specimen', 'specimens' inflect.irregular 'human', 'humans' @@ -119,25 +51,28 @@ module Kernel 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}"] ||= + discovery_uri = self.discovery_uri(api, version) + discovery_uri_hash = Digest::MD5.hexdigest(discovery_uri) + return @discovery_documents[discovery_uri_hash] ||= 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 + cached_doc = File.expand_path "~/.cache/arvados/discovery-#{discovery_uri_hash}.json" rescue nil + + if cached_doc.nil? or 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), + :uri => discovery_uri, :authenticated => false) - FileUtils.makedirs(File.dirname cached_doc) - File.open(cached_doc, 'w') do |f| - f.puts response.body + + begin + FileUtils.makedirs(File.dirname cached_doc) + File.open(cached_doc, 'w') do |f| + f.puts response.body + end + rescue + return JSON.load response.body end end @@ -156,12 +91,351 @@ class ArvadosClient < Google::APIClient 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 +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(copy create edit keep pipeline run 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 'copy', 'tag', 'ws', 'run' + exec `which arv-#{subcommand}`.strip, *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 + 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_object => { 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 end def to_boolean(s) @@ -191,26 +465,27 @@ def help_methods(discovery_document, resource, method=nil) STDERR.puts banner if not method.nil? and method != '--help' and method != '-h' then - Trollop::die ("Unknown method #{method.inspect} " + - "for resource #{resource.inspect}") + abort "Unknown method #{method.inspect} " + + "for resource #{resource.inspect}" end exit 255 end def help_resources(option_parser, discovery_document, resource) option_parser.educate - - if not resource.nil? and resource != '--help' then - Trollop::die "Unknown resource type #{resource.inspect}" - end exit 255 end -def parse_arguments(discovery_document, subcommands) +def resource_types discovery_document resource_types = Array.new() discovery_document["resources"].each do |k,v| resource_types << k.singularize end + resource_types +end + +def parse_arguments(discovery_document, subcommands) + resources_and_subcommands = resource_types(discovery_document) + subcommands option_parser = Trollop::Parser.new do version __FILE__ @@ -226,7 +501,6 @@ def parse_arguments(discovery_document, subcommands) :type => :string, :default => 'json' opt :short, "Return only UUIDs (equivalent to --format=uuid)" - opt :resources, "Display list of resources known to this Arvados instance." banner "" banner "Use 'arv subcommand|resource --help' to get more information about a particular command or resource." @@ -240,7 +514,7 @@ def parse_arguments(discovery_document, subcommands) banner "Additional options:" conflicts :short, :format - stop_on resource_types + stop_on resources_and_subcommands end global_opts = Trollop::with_standard_exception_handling option_parser do @@ -258,66 +532,101 @@ def parse_arguments(discovery_document, subcommands) end resource = ARGV.shift - if global_opts[:resources] or not resource_types.include?(resource) - help_resources(option_parser, discovery_document, resource) - end - method = ARGV.shift - if not (discovery_document["resources"][resource.pluralize]["methods"]. - include?(method)) - help_methods(discovery_document, resource, method) - end + if not subcommands.include? resource + if not resources_and_subcommands.include?(resource) + puts "Resource or subcommand '#{resource}' is not recognized.\n\n" if !resource.nil? + help_resources(option_parser, discovery_document, resource) + end - discovered_params = discovery_document\ + 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 - banner head_banner - banner "Usage: arv #{resource} #{method} [--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 + method_opts = Trollop::options do + banner head_banner + banner "Usage: arv #{resource} #{method} [--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 - 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 + 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 - 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 + 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 end + return resource, method, method_opts, global_opts, ARGV end +# +# ENTRY POINT +# + +init_config + +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 + +# 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 + +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 + # Parse arguments here resource_schema, method, method_opts, global_opts, remaining_opts = parse_arguments(arvados.discovery_document, subcommands) + +check_subcommands client, arvados, resource_schema, global_opts, remaining_opts + controller = resource_schema.pluralize api_method = 'arvados.' + controller + '.' + method @@ -363,7 +672,7 @@ when else result = client.execute(:api_method => eval(api_method), :parameters => request_parameters, - :body => request_body, + :body_object => request_body, :authenticated => false, :headers => { authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']