X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/8295ba721133c341fd72350f7ca9438d1a99cdbe..d41563d9a62450f86214c4feac774dd82fc4311c:/sdk/cli/bin/arv diff --git a/sdk/cli/bin/arv b/sdk/cli/bin/arv index 96acd01f8b..185a5b0673 100755 --- a/sdk/cli/bin/arv +++ b/sdk/cli/bin/arv @@ -5,6 +5,7 @@ # Ward Vandewege require 'fileutils' +require 'shellwords' if RUBY_VERSION < '1.9.3' then abort <<-EOS @@ -15,7 +16,7 @@ end begin require 'curb' require 'rubygems' - require 'google/api_client' + require 'arvados/google_api_client' require 'json' require 'pp' require 'trollop' @@ -24,6 +25,7 @@ begin require 'active_support/inflector' require 'yaml' require 'tempfile' + require 'net/http' rescue LoadError abort <<-EOS @@ -51,36 +53,6 @@ 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 +86,15 @@ 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 +102,27 @@ 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" @@ -154,7 +133,7 @@ def check_subcommands client, arvados, subcommand, global_opts, remaining_opts end def command_exists?(command) - File.executable?(command) || ENV['PATH'].split(':').select {|folder| File.executable?(File.join(folder, command))}.any? + File.executable?(command) || ENV['PATH'].split(':').any? {|folder| File.executable?(File.join(folder, command))} end def run_editor path @@ -179,14 +158,7 @@ end def edit_and_commit_object initial_obj, tmp_stem, global_opts, &block - content = case global_opts[:format] - when 'json' - Oj.dump(initial_obj, :indent => 1) - when 'yaml' - initial_obj.to_yaml - else - abort "Unrecognized format #{global_opts[:format]}" - end + content = get_obj_content initial_obj, global_opts tmp_file = Tempfile.new([tmp_stem, ".#{global_opts[:format]}"]) tmp_file.write(content) @@ -211,25 +183,39 @@ def edit_and_commit_object initial_obj, tmp_stem, global_opts, &block Oj.load(newcontent) when 'yaml' YAML.load(newcontent) + else + abort "Unrecognized format #{global_opts[:format]}" end yield newobj break rescue => e - puts "Error: #{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 this_error + tmp_file.open newcontent = tmp_file.read() tmp_file.close - if newcontent == error_text + if newcontent == error_text or not can_retry FileUtils::cp tmp_file.path, tmp_file.path + ".saved" - puts "File is unchanged, edit aborted." + 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 = e.to_s.lines.map {|l| '# ' + l}.join + "\n" + 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 @@ -244,45 +230,32 @@ def edit_and_commit_object initial_obj, tmp_stem, global_opts, &block nil end +class ArvadosAPIError < RuntimeError +end + def check_response result begin results = JSON.parse result.body - rescue JSON::ParserError => e + rescue JSON::ParserError, Oj::ParseError => e raise "Failed to parse server response:\n" + e.to_s end if result.response.status != 200 - raise "#{result.response.status}: " + (results['errors'] && results['errors'].join('\n') || "") + 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 results 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 - +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 "#{uuid} does not appear to be an Arvados uuid" + abort "'#{uuid}' does not appear to be an Arvados uuid" end end @@ -299,6 +272,11 @@ def arv_edit client, arvados, global_opts, remaining_opts abort "Could not determine resource type #{m[2]}" end + return rsc +end + +def fetch_rsc_obj client, arvados, rsc, uuid, remaining_opts + begin result = client.execute(:api_method => eval('arvados.' + rsc + '.get'), :parameters => {"uuid" => uuid}, @@ -306,15 +284,45 @@ def arv_edit client, arvados, global_opts, remaining_opts :headers => { authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN'] }) - oldobj = check_response result + obj = check_response result rescue => e abort "Server error: #{e}" end if remaining_opts.length > 0 - oldobj.select! { |k, v| remaining_opts.include? k } + obj.select! { |k, v| remaining_opts.include? k } end + return obj +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 + +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 + + 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? @@ -325,15 +333,34 @@ def arv_edit client, arvados, global_opts, remaining_opts :headers => { authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN'] }) - check_response result + 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 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