#
# Ward Vandewege <ward@clinicalfuture.com>
+require 'fileutils'
+
if RUBY_VERSION < '1.9.3' then
abort <<-EOS
#{$0.gsub(/^\.\//,'')} requires Ruby version 1.9.3 or higher.
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'].index @sub then
+ if ['get', 'put', 'ls', 'normalize'].index @sub then
# Native Arvados
exec `which arv-#{@sub}`.strip, *ARGV
- elsif ['ls', 'less', 'check'].index @sub then
+ elsif ['less', 'check'].index @sub then
# wh* shims
exec `which wh#{@sub}`.strip, *ARGV
else
"(see arv-run-pipeline-instance --help for details)\n"
end
abort
+when 'tag'
+ ARGV.shift
+ exec `which arv-tag`.strip, *ARGV
end
ENV['ARVADOS_API_VERSION'] ||= 'v1'
require 'andand'
require 'oj'
require 'active_support/inflector'
+ require 'yaml'
rescue LoadError
abort <<-EOS
-Please install all required gems:
+Please install all required gems:
gem install activesupport andand curb google-api-client json oj trollop
class Google::APIClient
def discovery_document(api, version)
- api = api.to_s
- return @discovery_documents["#{api}:#{version}"] ||= (begin
- response = self.execute!(
- :http_method => :get,
- :uri => self.discovery_uri(api, version),
- :authenticated => false
- )
- response.body.class == String ? JSON.parse(response.body) : response.body
- end)
+ api = api.to_s
+ return @discovery_documents["#{api}:#{version}"] ||=
+ 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
+ response = self.execute!(:http_method => :get,
+ :uri => self.discovery_uri(api, version),
+ :authenticated => false)
+ FileUtils.makedirs(File.dirname cached_doc)
+ File.open(cached_doc, 'w') do |f|
+ f.puts response.body
+ end
+ end
+
+ File.open(cached_doc) { |f| JSON.load f }
+ end
end
end
end
end
-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'])
+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
def to_boolean(s)
!!(s =~ /^(true|t|yes|y|1)$/i)
discovery_document["resources"][resource.pluralize]["methods"].
each do |k,v|
description = ''
- description = ' ' + v["description"] if v.include?("description")
+ if v.include? "description"
+ # add only the first line of the discovery doc description
+ description = ' ' + v["description"].split("\n").first.chomp
+ end
banner += " #{sprintf("%20s",k)}#{description}\n"
end
banner += "\n"
STDERR.puts banner
-
- if not method.nil? and method != '--help' then
+
+ if not method.nil? and method != '--help' then
Trollop::die ("Unknown method #{method.inspect} " +
"for resource #{resource.inspect}")
end
banner += "\n\n"
discovery_document["resources"].each do |k,v|
description = ''
- if discovery_document["schemas"].include?(k.singularize.capitalize) and
- discovery_document["schemas"][k.singularize.capitalize].include?('description') then
- description = ' ' + discovery_document["schemas"][k.singularize.capitalize]["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
+ if not resource.nil? and resource != '--help' then
Trollop::die "Unknown resource type #{resource.inspect}"
end
exit 255
def parse_arguments(discovery_document)
resource_types = Array.new()
- resource_types << '--help'
discovery_document["resources"].each do |k,v|
resource_types << k.singularize
end
global_opts = Trollop::options do
- banner "arvados cli client"
+ version __FILE__
+ banner "arv: the Arvados CLI tool"
opt :dry_run, "Don't actually do anything", :short => "-n"
- opt :verbose, "Print some things on stderr", :short => "-v"
- opt :uuid, "Return the UUIDs of the objects in the response, one per line (default)", :short => nil
- opt :json, "Return the entire response received from the API server, as a JSON object", :short => "-j"
- opt :human, "Return the response received from the API server, as a JSON object with whitespace added for human consumption", :short => "-h"
- opt :pretty, "Synonym of --human", :short => nil
+ opt :verbose, "Print some things on stderr"
+ opt :format,
+ "Set the output format. Must be one of json (default), yaml or uuid.",
+ :type => :string,
+ :default => 'json'
+ opt :short, "Return only UUIDs (equivalent to --format=uuid)"
+ opt :resources, "Display list of resources known to this Arvados instance."
+ conflicts :short, :format
stop_on resource_types
end
-
+
+ unless %w(json yaml uuid).include?(global_opts[:format])
+ $stderr.puts "#{$0}: --format must be one of json, yaml or uuid."
+ $stderr.puts "Use #{$0} --help for more information."
+ abort
+ end
+
+ if global_opts[:short]
+ global_opts[:format] = 'uuid'
+ end
+
resource = ARGV.shift
- if resource == '--help' or not resource_types.include?(resource)
+ if global_opts[:resources] or not resource_types.include?(resource)
help_resources(discovery_document, resource)
end
if body_object["required"] == false
is_required = false
end
- opt resource.to_sym, "#{resource} (request body)", required: is_required, type: :string
+ opt resource.to_sym, "#{resource} (request body)", {
+ required: is_required,
+ type: :string
+ }
end
end
+
discovered_params.each do |k,v|
+ k = k.to_sym
if ['object', 'array'].index(v["type"]) and method_opts.has_key? k
- method_opts[k] = JSON.parse method_opts[k]
+ if method_opts[k].andand.match /^\//
+ method_opts[k] = File.open method_opts[k], 'rb' do |f| f.read end
+ end
end
end
return resource, method, method_opts, global_opts, ARGV
resource_body = request_parameters.delete(resource_schema.to_sym)
if resource_body
request_body = {
- resource_schema => JSON.parse(resource_body)
+ resource_schema => resource_body
}
else
request_body = {}
curl.headers['Accept'] = 'text/plain'
curl.headers['Authorization'] = "OAuth2 #{ENV['ARVADOS_API_TOKEN']}"
if ENV['ARVADOS_API_HOST_INSECURE']
- curl.ssl_verify_peer = false
+ curl.ssl_verify_peer = false
curl.ssl_verify_host = false
end
if global_opts[:verbose]
exit 0
else
request_body[:api_token] = ENV['ARVADOS_API_TOKEN']
+ request_body[:_profile] = true
result = client.execute(:api_method => eval(api_method),
:parameters => request_parameters,
:body => request_body,
abort "Error: #{results["errors"][0]}"
end
-if global_opts[:human] or global_opts[:pretty] then
+case global_opts[:format]
+when 'json'
puts Oj.dump(results, :indent => 1)
-elsif global_opts[:json] then
- puts Oj.dump(results)
-elsif results["items"] and results["kind"].match /list$/i
- results['items'].each do |i| puts i['uuid'] end
-elsif results['uuid'].nil?
- abort("Response did not include a uuid:\n" +
- Oj.dump(results, :indent => 1) +
- "\n")
+when 'yaml'
+ puts results.to_yaml
else
- puts results['uuid']
+ if results["items"] and results["kind"].match /list$/i
+ results['items'].each do |i| puts i['uuid'] end
+ elsif results['uuid'].nil?
+ abort("Response did not include a uuid:\n" +
+ Oj.dump(results, :indent => 1) +
+ "\n")
+ else
+ puts results['uuid']
+ end
end
projects / arvados.git / blobdiff