#
# 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 ~/.config/arvados if present
+# 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
end
end
+subcommands = %w(keep pipeline tag ws)
+
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
+ 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 check\n" +
+ "#{$0} keep docker\n"
end
abort
when 'pipeline'
when 'tag'
ARGV.shift
exec `which arv-tag`.strip, *ARGV
+when 'ws'
+ ARGV.shift
+ exec `which arv-ws`.strip, *ARGV
end
ENV['ARVADOS_API_VERSION'] ||= 'v1'
rescue LoadError
abort <<-EOS
-Please install all required gems:
+Please install all required gems:
gem install activesupport andand curb google-api-client json oj trollop
class Google::APIClient
def discovery_document(api, version)
- api = api.to_s
- return @discovery_documents["#{api}:#{version}"] ||= (begin
- response = self.execute!(
- :http_method => :get,
- :uri => self.discovery_uri(api, version),
- :authenticated => false
- )
- response.body.class == String ? JSON.parse(response.body) : response.body
- end)
+ api = api.to_s
+ return @discovery_documents["#{api}:#{version}"] ||=
+ begin
+ # fetch new API discovery doc if stale
+ cached_doc = File.expand_path '~/.cache/arvados/discovery_uri.json'
+ if not File.exist?(cached_doc) or (Time.now - File.mtime(cached_doc)) > 86400
+ response = self.execute!(:http_method => :get,
+ :uri => self.discovery_uri(api, version),
+ :authenticated => false)
+ FileUtils.makedirs(File.dirname cached_doc)
+ File.open(cached_doc, 'w') do |f|
+ f.puts response.body
+ end
+ end
+
+ File.open(cached_doc) { |f| JSON.load f }
+ end
end
end
end
end
-client = ArvadosClient.new(:host => ENV['ARVADOS_API_HOST'], :application_name => 'arvados-cli', :application_version => '1.0')
-arvados = client.discovered_api('arvados', ENV['ARVADOS_API_VERSION'])
+begin
+ client = ArvadosClient.new(:host => ENV['ARVADOS_API_HOST'], :application_name => 'arvados-cli', :application_version => '1.0')
+ arvados = client.discovered_api('arvados', ENV['ARVADOS_API_VERSION'])
+rescue Exception => e
+ puts "Failed to connect to Arvados API server: #{e}"
+ exit 1
+end
def to_boolean(s)
!!(s =~ /^(true|t|yes|y|1)$/i)
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|
end
banner += "\n"
STDERR.puts banner
-
- if not method.nil? and method != '--help' then
+
+ if not method.nil? and method != '--help' and method != '-h' then
Trollop::die ("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
+def help_resources(option_parser, discovery_document, resource)
+ option_parser.educate
- 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
end
-def parse_arguments(discovery_document)
+def parse_arguments(discovery_document, subcommands)
resource_types = Array.new()
discovery_document["resources"].each do |k,v|
resource_types << k.singularize
end
- global_opts = Trollop::options do
- banner "arv: the Arvados CLI tool"
+ option_parser = Trollop::Parser.new do
+ version __FILE__
+ 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,
: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
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])
$stderr.puts "#{$0}: --format must be one of json, yaml or uuid."
$stderr.puts "Use #{$0} --help for more information."
resource = ARGV.shift
if global_opts[:resources] or not resource_types.include?(resource)
- help_resources(discovery_document, resource)
+ help_resources(option_parser, discovery_document, resource)
end
method = ARGV.shift
["resources"][resource.pluralize]\
["methods"][method]["parameters"]
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")
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
required: is_required,
type: :string
}
- discovered_params[resource.to_sym] = body_object
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)
+# Parse arguments here
+resource_schema, method, method_opts, global_opts, remaining_opts = parse_arguments(arvados.discovery_document, subcommands)
controller = resource_schema.pluralize
api_method = 'arvados.' + controller + '.' + method
exit
end
-request_parameters = {}.merge(method_opts)
+request_parameters = {_profile:true}.merge(method_opts)
resource_body = request_parameters.delete(resource_schema.to_sym)
if resource_body
request_body = {
resource_schema => resource_body
}
else
- request_body = {}
+ request_body = nil
end
case api_method
when
- 'arvados.users.event_stream',
- 'arvados.jobs.log_stream',
'arvados.jobs.log_tail_follow'
# Special case for methods that respond with data streams rather
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]
end
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,
- :authenticated => false)
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
end
begin
puts results['uuid']
end
end
-
-
projects / arvados.git / blobdiff