+class ArvadosClient < Google::APIClient
+ def execute(*args)
+ if args.last.is_a? Hash
+ args.last[:headers] ||= {}
+ args.last[:headers]['Accept'] ||= 'application/json'
+ end
+ super(*args)
+ 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') 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
+ 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
+end
+
+
+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
+ # Native Arvados
+ exec `which arv-#{@sub}`.strip, *remaining_opts
+ elsif ['less', 'check'].index @sub then
+ # wh* shims
+ exec `which wh#{@sub}`.strip, *remaining_opts
+ elsif @sub == 'docker'
+ exec `which arv-keepdocker`.strip, *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"
+ puts "Available methods: ls, get, put, less, check, docker"
+ end
+ abort
+ when 'pipeline'
+ 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 command_exists?(command)
+ File.executable?(command) || ENV['PATH'].split(':').any? {|folder| File.executable?(File.join(folder, command))}
+end
+
+def run_editor path
+ 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?
+ abort "Could not find any editor to use, please set $VISUAL or $EDITOR to your desired editor."
+ end
+ exec editor, path
+ else
+ Process.wait pid
+ end
+
+ if $?.exitstatus != 0
+ raise "Editor exited with status #{$?.exitstatus}"
+ end
+end
+
+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
+
+ tmp_file = Tempfile.new([tmp_stem, ".#{global_opts[:format]}"])
+ tmp_file.write(content)
+ tmp_file.close
+
+ begin
+ error_text = ''
+ while true
+ begin
+ run_editor tmp_file.path
+
+ tmp_file.open
+ newcontent = tmp_file.read()
+ tmp_file.close
+
+ # Strip lines starting with '#'
+ newcontent = newcontent.lines.select {|l| !l.start_with? '#'}.join
+
+ # Load the new object
+ newobj = case global_opts[:format]
+ when 'json'
+ Oj.load(newcontent)
+ when 'yaml'
+ YAML.load(newcontent)
+ end
+
+ yield newobj
+
+ break
+ rescue => e
+ can_retry = true
+ if e.is_a? Psych::SyntaxError
+ this_error = "YAML error parsing your input: #{e}"
+ elsif e.is_a? JSON::ParserError or e.is_a? Oj::ParseError
+ this_error = "JSON error parsing your input: #{e}"
+ elsif e.is_a? ArvadosAPIError
+ this_error = "API responded with error #{e}"
+ else
+ this_error = "#{e.class}: #{e}"
+ can_retry = false
+ end
+ puts this_error
+
+ tmp_file.open
+ newcontent = tmp_file.read()
+ tmp_file.close
+
+ if newcontent == error_text or not can_retry
+ FileUtils::cp tmp_file.path, tmp_file.path + ".saved"
+ puts "File is unchanged, edit aborted." if can_retry
+ abort "Saved contents to " + tmp_file.path + ".saved"
+ else
+ tmp_file.open
+ tmp_file.truncate 0
+ error_text = this_error.to_s.lines.map {|l| '# ' + l}.join + "\n"
+ error_text += "# Please fix the error and try again.\n"
+ error_text += newcontent.lines.select {|l| !l.start_with? '#'}.join
+ tmp_file.write error_text
+ tmp_file.close
+ end
+ end
+ end
+ ensure
+ tmp_file.close(true)
+ end
+
+ nil
+end
+
+class ArvadosAPIError < RuntimeError
+end
+
+def check_response result
+ begin
+ results = JSON.parse result.body
+ rescue JSON::ParserError, Oj::ParseError => e
+ raise "Failed to parse server response:\n" + e.to_s
+ end
+
+ if result.response.status != 200
+ raise ArvadosAPIError.new("#{result.response.status}: #{
+ ((results['errors'] && results['errors'].join('\n')) ||
+ Net::HTTPResponse::CODE_TO_OBJ[status.to_s].to_s.sub(/^Net::HTTP/, '').titleize)}")
+ end
+
+ results