# Arvados cli client
#
-# Ward Vandewege <ward@clinicalfuture.com>
+# Ward Vandewege <ward@curoverse.com>
require 'fileutils'
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(keep pipeline run tag ws edit)
def check_subcommands client, arvados, subcommand, global_opts, remaining_opts
case subcommand
puts "Available methods: run"
end
abort
+ when 'run'
+ exec `which arv-run`.strip, *remaining_opts
when 'tag'
exec `which arv-tag`.strip, *remaining_opts
when 'ws'
end
end
+def arv_edit_save_tmp tmp
+ FileUtils::cp tmp.path, tmp.path + ".saved"
+ puts "Saved contents to " + tmp.path + ".saved"
+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 "Fetch the specified Arvados object, select the specified fields, \n"
# 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
- if /^[a-f0-9]{32}/.match n
+ if /^[a-f0-9]{32}/.match uuid
abort "Arvados collections are not editable."
else
abort "#{n} does not appear to be an Arvados uuid"
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']
require 'tempfile'
- tmp = Tempfile.new([n, "." + global_opts[:format]])
+ tmp = Tempfile.new([uuid, "." + global_opts[:format]])
tmp.write(content)
tmp.close
n += 1
end
puts "\nTry again (y/n)? "
- yn = $stdin.read 1
+ yn = "X"
+ while not ["y", "Y", "n", "N"].include?(yn)
+ yn = $stdin.read 1
+ end
if yn == 'n' or yn == 'N'
- exit 1
+ arv_edit_save_tmp tmp
+ abort
end
end
else
end
end
- tmp.close(true)
-
- if newobj != results
- api_method = 'arvados.' + rsc + '.update'
- dumped = Oj.dump(newobj)
- result = client.execute(:api_method => eval(api_method),
- :parameters => {"uuid" => n, rsc.singularize => dumped},
- :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
+ begin
+ if newobj != results
+ api_method = 'arvados.' + rsc + '.update'
+ dumped = Oj.dump(newobj)
- if result.response.status != 200
- puts "Update failed. Server responded #{result.response.status}: #{results['errors']} "
- puts "Update body was:"
- puts dumped
+ 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
+ abort
+ end
+
+ begin
+ results = JSON.parse result.body
+ rescue JSON::ParserError => e
+ 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
+ abort
+ end
+ else
+ puts "Object is unchanged, did not update."
end
- else
- puts "Object is unchanged, did not update."
+ ensure
+ tmp.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
if not subcommands.include? resource
if not resource_types.include?(resource)
- puts "Resource or subcommand '#{resource}' is not recognized.\n\n"
+ puts "Resource or subcommand '#{resource}' is not recognized.\n\n" if !resource.nil?
help_resources(option_parser, discovery_document, resource)
end
projects / arvados.git / blobdiff