# Arvados cli client
#
-# Ward Vandewege <ward@clinicalfuture.com>
+# Ward Vandewege <ward@curoverse.com>
require 'fileutils'
require 'oj'
require 'active_support/inflector'
require 'yaml'
+ require 'tempfile'
rescue LoadError
abort <<-EOS
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
def init_config
# 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
+ 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
end
end
-subcommands = %w(keep pipeline tag ws edit)
+
+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
end
abort
when 'pipeline'
- exec `which arv-run-pipeline-instance`.strip, *remaining_opts
- when 'tag'
- exec `which arv-tag`.strip, *remaining_opts
- when 'ws'
- exec `which arv-ws`.strip, *remaining_opts
- when 'edit'
- arv_edit client, arvados, global_opts, remaining_opts
+ 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
- n = remaining_opts.shift
- if n.nil? or n == "-h" or n == "--help"
+ 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 "Fetchs the specified Arvados object, select the specified fields, and\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 updates the object. Will use 'nano'\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
# determine controller
- m = /([a-z0-9]{5})-([a-z0-9]{5})-([a-z0-9]{15})/.match n
+ m = /([a-z0-9]{5})-([a-z0-9]{5})-([a-z0-9]{15})/.match uuid
if !m
- abort puts "#{n} does not appear to be an arvados uuid"
+ 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
api_method = 'arvados.' + rsc + '.get'
result = client.execute(:api_method => eval(api_method),
- :parameters => {"uuid" => n},
+ :parameters => {"uuid" => uuid},
:authenticated => false,
:headers => {
authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
content = results.to_yaml
end
- require 'tempfile'
-
- tmp = Tempfile.new(n)
- tmp.write(content)
- tmp.close
-
- pid = Process::fork
- if pid.nil?
- editor ||= ENV["VISUAL"]
- editor ||= ENV["EDITOR"]
- editor ||= "nano"
- exec editor, tmp.path
- else
- Process.wait pid
- end
-
- if $?.exitstatus == 0
- tmp.open
- newcontent = tmp.read()
+ tmp_file = Tempfile.new([uuid, "." + global_opts[:format]])
+ tmp_file.write(content)
+ tmp_file.close
- newobj = {}
- case global_opts[:format]
- when 'json'
- newobj = Oj.load(newcontent)
- when 'yaml'
- newobj = YAML.load(newcontent)
- end
- tmp.close
- tmp.unlink
+ newobj = run_editor tmp_file, global_opts
+ begin
if newobj != results
api_method = 'arvados.' + rsc + '.update'
- result = client.execute(:api_method => eval(api_method),
- :parameters => {"uuid" => n, rsc.singularize => Oj.dump(newobj)},
- :authenticated => false,
- :headers => {
- authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
- })
+ 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
def help_resources(option_parser, discovery_document, resource)
option_parser.educate
-
- if not resource.nil? and resource != '--help' then
- Trollop::die "Unknown resource type #{resource.inspect}"
- end
exit 255
end
-def parse_arguments(discovery_document, subcommands)
+def resource_types discovery_document
resource_types = Array.new()
discovery_document["resources"].each do |k,v|
resource_types << k.singularize
end
+ resource_types
+end
- resource_types += subcommands
+def parse_arguments(discovery_document, subcommands)
+ resources_and_subcommands = resource_types(discovery_document) + subcommands
option_parser = Trollop::Parser.new do
version __FILE__
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
resource = ARGV.shift
if not subcommands.include? resource
- if global_opts[:resources] or not resource_types.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
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