# Arvados cli client
#
-# Ward Vandewege <ward@clinicalfuture.com>
+# Ward Vandewege <ward@curoverse.com>
require 'fileutils'
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
-
-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'
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'
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
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)
!!(s =~ /^(true|t|yes|y|1)$/i)
end
+def head_banner
+ "Arvados command line client\n"
+end
+
def help_methods(discovery_document, resource, method=nil)
- banner = "\n"
- banner += "The #{resource} resource type supports the following methods:"
+ banner = head_banner
+ banner += "Usage: arv #{resource} [method] [--parameters]\n"
+ banner += "Use 'arv #{resource} [method] --help' to get more information about specific methods.\n\n"
+ banner += "The #{resource} resource supports the following methods:"
banner += "\n\n"
discovery_document["resources"][resource.pluralize]["methods"].
each do |k,v|
banner += "\n"
STDERR.puts banner
- if not method.nil? and method != '--help' then
- Trollop::die ("Unknown method #{method.inspect} " +
- "for resource #{resource.inspect}")
+ if not method.nil? and method != '--help' and method != '-h' then
+ abort "Unknown method #{method.inspect} " +
+ "for resource #{resource.inspect}"
end
exit 255
end
-def help_resources(discovery_document, resource)
- banner = "\n"
- banner += "This Arvados instance supports the following resource types:"
- banner += "\n\n"
- discovery_document["resources"].each do |k,v|
- description = ''
- resource_info = discovery_document["schemas"][k.singularize.capitalize]
- if resource_info and resource_info.include?('description')
- # add only the first line of the discovery doc description
- description = ' ' + resource_info["description"].split("\n").first.chomp
- end
- banner += " #{sprintf("%30s",k.singularize)}#{description}\n"
- end
- banner += "\n"
- STDERR.puts banner
-
- if not resource.nil? and resource != '--help' then
- Trollop::die "Unknown resource type #{resource.inspect}"
- end
+def help_resources(option_parser, discovery_document, resource)
+ option_parser.educate
exit 255
end
-def parse_arguments(discovery_document)
+def resource_types discovery_document
resource_types = Array.new()
discovery_document["resources"].each do |k,v|
resource_types << k.singularize
end
+ resource_types
+end
- global_opts = Trollop::options do
+def parse_arguments(discovery_document, subcommands)
+ resources_and_subcommands = resource_types(discovery_document) + subcommands
+
+ option_parser = Trollop::Parser.new do
version __FILE__
- banner "arv: the Arvados CLI tool"
+ banner head_banner
+ banner "Usage: arv [--flags] subcommand|resource [method] [--parameters]"
+ banner ""
+ banner "Available flags:"
+
opt :dry_run, "Don't actually do anything", :short => "-n"
opt :verbose, "Print some things on stderr"
opt :format,
: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."
+ banner ""
+ banner "Available subcommands: #{subcommands.join(', ')}"
+ banner ""
+
+ banner "Available resources: #{discovery_document['resources'].keys.map { |k| k.singularize }.join(', ')}"
+
+ banner ""
+ 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
+ o = option_parser.parse ARGV
end
unless %w(json yaml uuid).include?(global_opts[:format])
end
resource = ARGV.shift
- if global_opts[:resources] or not resource_types.include?(resource)
- help_resources(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
+
+ method = ARGV.shift
+ if not (discovery_document["resources"][resource.pluralize]["methods"].
+ include?(method))
+ help_methods(discovery_document, resource, method)
+ end
- discovered_params = discovery_document\
+ discovered_params = discovery_document\
["resources"][resource.pluralize]\
["methods"][method]["parameters"]
- method_opts = Trollop::options do
- 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
-resource_schema, method, method_opts, global_opts, remaining_opts = parse_arguments(arvados.discovery_document)
+#
+# 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
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']
projects / arvados.git / blobdiff