X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/1060cff7480331bcad2b4564e270922b2b3b1f94..fe3f19bb8f0a684de9c5a7d1f7c619943d0daca0:/sdk/cli/bin/arv diff --git a/sdk/cli/bin/arv b/sdk/cli/bin/arv index 36ec037bd8..da65b07bf0 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 @@ -85,7 +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 @@ -93,28 +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" @@ -150,14 +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) @@ -182,6 +183,8 @@ 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 @@ -246,25 +249,7 @@ def check_response result 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 @@ -287,6 +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}, @@ -294,15 +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? @@ -314,15 +334,33 @@ def arv_edit client, arvados, global_opts, remaining_opts authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN'] }) results = check_response result - puts "Updated object #{results['uuid']}" + 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 @@ -521,7 +559,11 @@ 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 } @@ -587,6 +629,38 @@ 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 + _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 + _is_json = false + end + _is_readable_file = false + # if resource_body is not valid JSON, it should be a filename (or '-' for stdin) + if resource_body == '-' + _is_readable_file = true + _resource_body_file = $stdin + elsif File.readable? resource_body + _is_readable_file = true + _resource_body_file = File.open(resource_body, 'r') + end + if _is_json and _is_readable_file + abort "Argument '#{resource_body}' specified for option '--#{resource_schema.to_sym}' is both valid JSON and a readable file, cannot continue (suggest renaming the file '#{resource_body}')." + elsif !_is_json and !_is_readable_file + if File.exists? resource_body + # specified file exists but is not readable + abort "File '#{resource_body}' specified for option '--#{resource_schema.to_sym}' exists but is not readable." + else + # specified file does not exist + abort "File '#{resource_body}' specified for option '--#{resource_schema.to_sym}' does not exist." + end + elsif _is_readable_file + resource_body = _resource_body_file.read() + _resource_body_file.close() + end request_body = { resource_schema => resource_body }