#!/usr/bin/env ruby
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
# Arvados cli client
#
-# Ward Vandewege <ward@curoverse.com>
+# Ward Vandewege <ward@curii.com>
require 'fileutils'
+require 'shellwords'
if RUBY_VERSION < '1.9.3' then
abort <<-EOS
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 'optimist'
+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 optimist
EOS
end
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
- args.last[:headers] ||= {}
- args.last[:headers]['Accept'] ||= 'application/json'
- end
- super(*args)
- end
-end
-
def init_config
# read authentication data from arvados configuration file if present
lineno = 0
end
end
-subcommands = %w(create edit keep pipeline tag ws)
+
+subcommands = %w(copy create edit get keep 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
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'
+ 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"
- 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"
+ puts "Available methods: ls, get, put, docker"
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))}
+ 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
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 => { 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
+ create_opts = Optimist::options do
opt :project_uuid, "Project uuid in which to create the object", :type => :string
stop_on resource_types(arvados.discovery_document)
end
rsc = rsc.first
discovered_params = arvados.discovery_document["resources"][rsc]["methods"]["create"]["parameters"]
- method_opts = Trollop::options do
+ method_opts = Optimist::options do
banner head_banner
banner "Usage: arv create [--project-uuid] #{object_type} [create parameters]"
banner ""
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
+ opts[:type] = :string # else optimist bork
end
opts[:default] = v["default"] if v.include?("default")
opts[:default] = v["default"].to_i if opts[:type] == :integer
end
end
-
- newobj = {}
+ initial_obj = {}
if create_opts[:project_uuid]
- newobj["owner_uuid"] = create_opts[:project_uuid]
+ initial_obj["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)
+ 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
def parse_arguments(discovery_document, subcommands)
resources_and_subcommands = resource_types(discovery_document) + subcommands
- option_parser = Trollop::Parser.new do
+ option_parser = Optimist::Parser.new do
version __FILE__
banner head_banner
banner "Usage: arv [--flags] subcommand|resource [method] [--parameters]"
stop_on resources_and_subcommands
end
- global_opts = Trollop::with_standard_exception_handling option_parser do
+ global_opts = Optimist::with_standard_exception_handling option_parser do
o = option_parser.parse ARGV
end
discovered_params = discovery_document\
["resources"][resource.pluralize]\
["methods"][method]["parameters"]
- method_opts = Trollop::options do
+ method_opts = Optimist::options do
banner head_banner
banner "Usage: arv #{resource} #{method} [--parameters]"
banner ""
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
+ opts[:type] = :string # else optimist bork
end
opts[:default] = v["default"] if v.include?("default")
opts[:default] = v["default"].to_i if opts[:type] == :integer
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 /^\//
end
begin
- client = ArvadosClient.new(:host => ENV['ARVADOS_API_HOST'], :application_name => 'arvados-cli', :application_version => '1.0')
+ client = Google::APIClient.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}"
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
}
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']
})
end
+request_id = result.headers[:x_request_id]
begin
results = JSON.parse result.body
rescue JSON::ParserError => e
- abort "Failed to parse server response:\n" + e.to_s
+ err_msg = "Failed to parse server response:\n" + e.to_s
+ if request_id
+ err_msg += "\nRequest ID: #{request_id or client.request_id}"
+ end
+ abort err_msg
end
if results["errors"] then
- abort "Error: #{results["errors"][0]}"
+ err_message = results["errors"][0]
+ if request_id and !err_message.match(/.*req-[0-9a-zA-Z]{20}.*/)
+ err_message += " (#{request_id})"
+ end
+ abort "Error: #{err_message}"
end
case global_opts[:format]
projects / arvados.git / blobdiff