X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/d3229c7f727f40436cad66fba5f3345e0b3eede5..98e9073e7ca36edbe8dd0569d67405e2e030f8db:/sdk/cli/bin/arv diff --git a/sdk/cli/bin/arv b/sdk/cli/bin/arv index 533ea39eb7..9783af202f 100755 --- a/sdk/cli/bin/arv +++ b/sdk/cli/bin/arv @@ -1,10 +1,14 @@ #!/usr/bin/env ruby +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 # Arvados cli client # # Ward Vandewege require 'fileutils' +require 'shellwords' if RUBY_VERSION < '1.9.3' then abort <<-EOS @@ -13,23 +17,33 @@ if RUBY_VERSION < '1.9.3' then end begin - require 'curb' - require 'rubygems' - require 'google/api_client' require 'json' + require 'net/http' require 'pp' - require 'trollop' + require 'tempfile' + require 'yaml' +rescue LoadError => error + abort "Error loading libraries: #{error}\n" +end + +begin + require 'rubygems' + # Load the gems with more requirements first, so we respect any version + # constraints they put on gems loaded later. + require 'arvados/google_api_client' + require 'active_support/inflector' require 'andand' + require 'curb' require 'oj' - require 'active_support/inflector' - require 'yaml' - require 'tempfile' -rescue LoadError + require 'trollop' +rescue LoadError => error abort <<-EOS +Error loading gems: #{error} + Please install all required gems: - gem install activesupport andand curb google-api-client json oj trollop yaml + gem install arvados activesupport andand curb json oj trollop EOS end @@ -51,36 +65,6 @@ module Kernel end end -class Google::APIClient - def discovery_document(api, version) - api = api.to_s - 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-#{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 => discovery_uri, - :authenticated => false) - - 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 - - File.open(cached_doc) { |f| JSON.load f } - end - end -end - class ArvadosClient < Google::APIClient def execute(*args) if args.last.is_a? Hash @@ -114,7 +98,15 @@ def init_config end -subcommands = %w(copy create edit keep pipeline run tag ws) +subcommands = %w(copy create edit get keep pipeline run tag ws) + +def exec_bin bin, opts + bin_path = `which #{bin.shellescape}`.strip + if bin_path.empty? + raise "#{bin}: command not found" + end + exec bin_path, *opts +end def check_subcommands client, arvados, subcommand, global_opts, remaining_opts case subcommand @@ -122,28 +114,27 @@ def check_subcommands client, arvados, subcommand, global_opts, remaining_opts arv_create client, arvados, global_opts, remaining_opts when 'edit' arv_edit client, arvados, global_opts, remaining_opts + when 'get' + arv_get client, arvados, global_opts, remaining_opts when 'copy', 'tag', 'ws', 'run' - exec `which arv-#{subcommand}`.strip, *remaining_opts + exec_bin "arv-#{subcommand}", 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 + exec_bin "arv-#{@sub}", remaining_opts elsif @sub == 'docker' - exec `which arv-keepdocker`.strip, *remaining_opts + exec_bin "arv-keepdocker", 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" + puts "Available methods: ls, get, put, docker" end abort when 'pipeline' sub = remaining_opts.shift if sub == 'run' - exec `which arv-run-pipeline-instance`.strip, *remaining_opts + exec_bin "arv-run-pipeline-instance", 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" @@ -153,97 +144,130 @@ def check_subcommands client, arvados, subcommand, global_opts, 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))} + File.executable?(command) || ENV['PATH'].split(':').any? {|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 +def run_editor path + 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? + abort "Could not find any editor to use, please set $VISUAL or $EDITOR to your desired editor." end + exec editor, path + else + Process.wait pid + end + + if $?.exitstatus != 0 + raise "Editor exited with status #{$?.exitstatus}" + end +end + +def edit_and_commit_object initial_obj, tmp_stem, global_opts, &block - if $?.exitstatus == 0 - tmp_file.open - newcontent = tmp_file.read() + content = get_obj_content initial_obj, global_opts - newobj = {} + tmp_file = Tempfile.new([tmp_stem, ".#{global_opts[:format]}"]) + tmp_file.write(content) + tmp_file.close + + begin + error_text = '' + while true 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 + run_editor tmp_file.path + + tmp_file.open + newcontent = tmp_file.read() + tmp_file.close + + # Strip lines starting with '#' + newcontent = newcontent.lines.select {|l| !l.start_with? '#'}.join + + # Load the new object + newobj = case global_opts[:format] + when 'json' + Oj.load(newcontent) + when 'yaml' + YAML.load(newcontent) + else + abort "Unrecognized format #{global_opts[:format]}" + end + + yield newobj + + break + rescue => e + can_retry = true + if e.is_a? Psych::SyntaxError + this_error = "YAML error parsing your input: #{e}" + elsif e.is_a? JSON::ParserError or e.is_a? Oj::ParseError + this_error = "JSON error parsing your input: #{e}" + elsif e.is_a? ArvadosAPIError + this_error = "API responded with error #{e}" + else + this_error = "#{e.class}: #{e}" + can_retry = false end - puts "Parse error! " + e.to_s - puts "\nTry again (y/n)? " - yn = "X" - while not ["y", "Y", "n", "N"].include?(yn) - yn = $stdin.read 1 - end - if yn == 'n' or yn == 'N' - arv_edit_save_tmp tmp_file - abort + puts this_error + + tmp_file.open + newcontent = tmp_file.read() + tmp_file.close + + if newcontent == error_text or not can_retry + FileUtils::cp tmp_file.path, tmp_file.path + ".saved" + puts "File is unchanged, edit aborted." if can_retry + abort "Saved contents to " + tmp_file.path + ".saved" + else + tmp_file.open + tmp_file.truncate 0 + error_text = this_error.to_s.lines.map {|l| '# ' + l}.join + "\n" + error_text += "# Please fix the error and try again.\n" + error_text += newcontent.lines.select {|l| !l.start_with? '#'}.join + tmp_file.write error_text + tmp_file.close end end - else - puts "Editor exited with status #{$?.exitstatus}" - exit $?.exitstatus end + ensure + tmp_file.close(true) end - newobj + nil 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 +class ArvadosAPIError < RuntimeError +end + +def check_response result + begin + results = JSON.parse result.body + rescue JSON::ParserError, Oj::ParseError => e + raise "Failed to parse server response:\n" + e.to_s end - if not $stdout.tty? - puts "Not connected to a TTY, cannot run interactive editor." - exit 1 + if result.response.status != 200 + raise ArvadosAPIError.new("#{result.response.status}: #{ + ((results['errors'] && results['errors'].join('\n')) || + Net::HTTPResponse::CODE_TO_OBJ[status.to_s].to_s.sub(/^Net::HTTP/, '').titleize)}") end - # determine controller + results +end +def lookup_uuid_rsc arvados, uuid 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" + abort "'#{uuid}' does not appear to be an Arvados uuid" end end @@ -260,84 +284,95 @@ def arv_edit client, arvados, global_opts, remaining_opts abort "Could not determine resource type #{m[2]}" end - api_method = 'arvados.' + rsc + '.get' + return rsc +end + +def fetch_rsc_obj client, arvados, rsc, uuid, remaining_opts - 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 + result = client.execute(:api_method => eval('arvados.' + rsc + '.get'), + :parameters => {"uuid" => uuid}, + :authenticated => false, + :headers => { + authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN'] + }) + obj = check_response result + rescue => e + abort "Server error: #{e}" end if remaining_opts.length > 0 - results.select! { |k, v| remaining_opts.include? k } + obj.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) + return obj +end - 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 +def get_obj_content obj, global_opts + content = case global_opts[:format] + when 'json' + Oj.dump(obj, :indent => 1) + when 'yaml' + obj.to_yaml + else + abort "Unrecognized format #{global_opts[:format]}" + end + return content +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 +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 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 + rsc = lookup_uuid_rsc arvados, uuid + oldobj = fetch_rsc_obj client, arvados, rsc, uuid, remaining_opts + + edit_and_commit_object oldobj, uuid, global_opts do |newobj| + newobj.select! {|k| newobj[k] != oldobj[k]} + if !newobj.empty? + result = client.execute(:api_method => eval('arvados.' + rsc + '.update'), + :parameters => {"uuid" => uuid}, + :body_object => { rsc.singularize => newobj }, + :authenticated => false, + :headers => { + authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN'] + }) + results = check_response result + STDERR.puts "Updated object #{results['uuid']}" else - puts "Object is unchanged, did not update." + STDERR.puts "Object is unchanged, did not update." end - ensure - tmp_file.close(true) end exit 0 end +def arv_get 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 [--format json|yaml] get [uuid] [fields...]\n\n" + puts "Fetch the specified Arvados object, select the specified fields,\n" + puts "and print a text representation.\n" + exit 255 + end + + rsc = lookup_uuid_rsc arvados, uuid + obj = fetch_rsc_obj client, arvados, rsc, uuid, remaining_opts + content = get_obj_content obj, global_opts + + puts content + exit 0 +end + def arv_create client, arvados, global_opts, remaining_opts types = resource_types(arvados.discovery_document) create_opts = Trollop::options do @@ -379,60 +414,21 @@ def arv_create client, arvados, global_opts, remaining_opts end end - - newobj = {} + initial_obj = {} 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 + initial_obj["owner_uuid"] = create_opts[:project_uuid] 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) + edit_and_commit_object initial_obj, "", global_opts do |newobj| + result = client.execute(:api_method => eval('arvados.' + rsc + '.create'), + :parameters => method_opts, + :body_object => {object_type => newobj}, + :authenticated => false, + :headers => { + authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN'] + }) + results = check_response result + puts "Created object #{results['uuid']}" end exit 0 @@ -575,14 +571,18 @@ def parse_arguments(discovery_document, subcommands) if body_object["required"] == false is_required = false end - opt resource.to_sym, "#{resource} (request body)", { + resource_opt_desc = "Either a string representing #{resource} as JSON or a filename from which to read #{resource} JSON (use '-' to read from stdin)." + if is_required + resource_opt_desc += " This option must be specified." + end + opt resource.to_sym, resource_opt_desc, { required: is_required, type: :string } end end - discovered_params.each do |k,v| + discovered_params.merge({resource => {'type' => 'object'}}).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 /^\// @@ -641,6 +641,45 @@ end request_parameters = {_profile:true}.merge(method_opts) resource_body = request_parameters.delete(resource_schema.to_sym) if resource_body + # check if resource_body is valid JSON by attempting to parse it + resource_body_is_json = true + begin + # we don't actually need the results of the parsing, + # just checking for the JSON::ParserError exception + JSON.parse resource_body + rescue JSON::ParserError => e + resource_body_is_json = false + end + resource_body_is_readable_file = false + # if resource_body is not valid JSON, it should be a filename (or '-' for stdin) + if resource_body == '-' + resource_body_is_readable_file = true + resource_body_file = $stdin + elsif File.readable? resource_body + resource_body_is_readable_file = true + resource_body_file = File.open(resource_body, 'r') + end + if resource_body_is_json and resource_body_is_readable_file + abort "Argument specified for option '--#{resource_schema.to_sym}' is both valid JSON and a readable file. Please consider renaming the file: '#{resource_body}'" + elsif !resource_body_is_json and !resource_body_is_readable_file + if File.exists? resource_body + # specified file exists but is not readable + abort "Argument specified for option '--#{resource_schema.to_sym}' is an existing file but is not readable. Please check permissions on: '#{resource_body}'" + else + # specified file does not exist + abort "Argument specified for option '--#{resource_schema.to_sym}' is neither valid JSON nor an existing file: '#{resource_body}'" + end + elsif resource_body_is_readable_file + resource_body = resource_body_file.read() + begin + # we don't actually need the results of the parsing, + # just checking for the JSON::ParserError exception + JSON.parse resource_body + rescue JSON::ParserError => e + abort "Contents of file '#{resource_body_file.path}' is not valid JSON: #{e}" + end + resource_body_file.close() + end request_body = { resource_schema => resource_body }