# Ward Vandewege <ward@curoverse.com>
require 'fileutils'
+require 'shellwords'
if RUBY_VERSION < '1.9.3' then
abort <<-EOS
end
-subcommands = %w(copy create edit keep pipeline run tag ws)
+subcommands = %w(copy create edit get keep pipeline run tag ws)
+
+def exec_bin bin, opts
+ bin_path = `which #{bin.shellescape}`.strip
+ if bin_path.empty?
+ raise "#{bin}: command not found"
+ end
+ exec bin_path, *opts
+end
def check_subcommands client, arvados, subcommand, global_opts, remaining_opts
case subcommand
arv_create client, arvados, global_opts, remaining_opts
when 'edit'
arv_edit client, arvados, global_opts, remaining_opts
+ when 'get'
+ arv_get client, arvados, global_opts, remaining_opts
when 'copy', 'tag', 'ws', 'run'
- exec `which arv-#{subcommand}`.strip, *remaining_opts
+ exec_bin "arv-#{subcommand}", 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
+ exec_bin "arv-#{@sub}", remaining_opts
elsif @sub == 'docker'
- exec `which arv-keepdocker`.strip, *remaining_opts
+ exec_bin "arv-keepdocker", 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"
when 'pipeline'
sub = remaining_opts.shift
if sub == 'run'
- exec `which arv-run-pipeline-instance`.strip, *remaining_opts
+ exec_bin "arv-run-pipeline-instance", 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"
def edit_and_commit_object initial_obj, tmp_stem, global_opts, &block
- content = case global_opts[:format]
- when 'json'
- Oj.dump(initial_obj, :indent => 1)
- when 'yaml'
- initial_obj.to_yaml
- else
- abort "Unrecognized format #{global_opts[:format]}"
- end
+ content = get_obj_content initial_obj, global_opts
tmp_file = Tempfile.new([tmp_stem, ".#{global_opts[:format]}"])
tmp_file.write(content)
Oj.load(newcontent)
when 'yaml'
YAML.load(newcontent)
+ else
+ abort "Unrecognized format #{global_opts[:format]}"
end
yield newobj
results
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
-
- # determine controller
-
+def lookup_uuid_rsc arvados, uuid
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 "Could not determine resource type #{m[2]}"
end
+ return rsc
+end
+
+def fetch_rsc_obj client, arvados, rsc, uuid, remaining_opts
+
begin
result = client.execute(:api_method => eval('arvados.' + rsc + '.get'),
:parameters => {"uuid" => uuid},
:headers => {
authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
})
- oldobj = check_response result
+ obj = check_response result
rescue => e
abort "Server error: #{e}"
end
if remaining_opts.length > 0
- oldobj.select! { |k, v| remaining_opts.include? k }
+ obj.select! { |k, v| remaining_opts.include? k }
end
+ return obj
+end
+
+def get_obj_content obj, global_opts
+ content = case global_opts[:format]
+ when 'json'
+ Oj.dump(obj, :indent => 1)
+ when 'yaml'
+ obj.to_yaml
+ else
+ abort "Unrecognized format #{global_opts[:format]}"
+ end
+ return content
+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
+
+ rsc = lookup_uuid_rsc arvados, uuid
+ oldobj = fetch_rsc_obj client, arvados, rsc, uuid, remaining_opts
+
edit_and_commit_object oldobj, uuid, global_opts do |newobj|
newobj.select! {|k| newobj[k] != oldobj[k]}
if !newobj.empty?
exit 0
end
+def arv_get 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 [--format json|yaml] get [uuid] [fields...]\n\n"
+ puts "Fetch the specified Arvados object, select the specified fields,\n"
+ puts "and print a text representation.\n"
+ exit 255
+ end
+
+ rsc = lookup_uuid_rsc arvados, uuid
+ obj = fetch_rsc_obj client, arvados, rsc, uuid, remaining_opts
+ content = get_obj_content obj, global_opts
+
+ puts content
+ exit 0
+end
+
def arv_create client, arvados, global_opts, remaining_opts
types = resource_types(arvados.discovery_document)
create_opts = Trollop::options do
if body_object["required"] == false
is_required = false
end
- opt resource.to_sym, "#{resource} (request body)", {
+ _resource_opt_desc = "Either a string representing #{resource} as JSON or a filename from which to read #{resource} JSON (use '-' to read from stdin)."
+ if is_required
+ _resource_opt_desc += " This option must be specified."
+ end
+ opt resource.to_sym, _resource_opt_desc, {
required: is_required,
type: :string
}
request_parameters = {_profile:true}.merge(method_opts)
resource_body = request_parameters.delete(resource_schema.to_sym)
if resource_body
+ # check if resource_body is valid JSON by attempting to parse it
+ _is_json = true
+ begin
+ # we don't actually need the results of the parsing,
+ # just checking for the JSON::ParserError exception
+ JSON.parse resource_body
+ rescue JSON::ParserError => e
+ _is_json = false
+ end
+ _is_readable_file = false
+ # if resource_body is not valid JSON, it should be a filename (or '-' for stdin)
+ if resource_body == '-'
+ _is_readable_file = true
+ _resource_body_file = $stdin
+ elsif File.readable? resource_body
+ _is_readable_file = true
+ _resource_body_file = File.open(resource_body, 'r')
+ end
+ if _is_json and _is_readable_file
+ abort "Argument '#{resource_body}' specified for option '--#{resource_schema.to_sym}' is both valid JSON and a readable file, cannot continue (suggest renaming the file '#{resource_body}')."
+ elsif !_is_json and !_is_readable_file
+ if File.exists? resource_body
+ # specified file exists but is not readable
+ abort "File '#{resource_body}' specified for option '--#{resource_schema.to_sym}' exists but is not readable."
+ else
+ # specified file does not exist
+ abort "File '#{resource_body}' specified for option '--#{resource_schema.to_sym}' does not exist."
+ end
+ elsif _is_readable_file
+ resource_body = _resource_body_file.read()
+ _resource_body_file.close()
+ end
request_body = {
resource_schema => resource_body
}
projects / arvados.git / blobdiff