require 'rbbt/workflow' class RemoteStep < Step attr_accessor :url, :base_url, :task, :base_name, :inputs, :input_types, :result_type, :result_description, :is_exec, :is_stream, :stream_input, :started def initialize(base_url, task = nil, base_name = nil, inputs = nil, input_types = nil, result_type = nil, result_description = nil, is_exec = false, is_stream = false, stream_input = nil) @base_url, @task, @base_name, @inputs, @input_types, @result_type, @result_description, @is_exec, @is_stream, @stream_input = base_url, task, base_name, inputs, input_types, result_type, result_description, is_exec, is_stream, stream_input @base_url = "http://" << @base_url unless @base_url =~ /^[a-z]+:\/\// @mutex = Mutex.new rest = base_url.include?('ssh:') ? false : true if rest @adaptor = RemoteWorkflow::REST self.extend RemoteStep::REST else @adaptor = RemoteWorkflow::SSH self.extend RemoteStep::SSH end end def clean_name @base_name end def cache_file begin digest = Misc.obj2digest([base_url, task.to_s, base_name, inputs]) Rbbt.var.cache.REST[task.to_s][[clean_name, digest].compact * "."].find rescue Log.exception $! raise $! end end def cache_files Dir.glob(cache_file + '.*') end def run(no_load = false) no_load = @is_stream ? :stream : true if no_load @result ||= @mutex.synchronize do begin if @is_exec exec(no_load) elsif no_load == :stream _run_job(:stream) elsif no_load init_job nil else if ! done? init_job produce join end self.load end ensure @started = true end end return @result if no_load == :stream no_load ? Misc.add_GET_param(path, "_format", "raw") : @result end def self.get_streams(inputs, stream_input = nil) new_inputs = {} inputs.each do |k,v| stream = stream_input.to_s == k.to_s if Step === v unless (v.done? or v.streaming?) # or RestClient::Step === v) v.run(true) and v.grace end begin if stream new_inputs[k] = TSV.get_stream(v) else new_inputs[k] = v.load end rescue Exception raise $! end else new_inputs[k] = v end end new_inputs end def get_streams return if @inputs_done @inputs = RemoteStep.get_streams @inputs, @stream_input @inputs_done = true @inputs end def dup_inputs return if @dupped or ENV["RBBT_NO_STREAM"] == 'true' Log.low "Dupping inputs for #{path}" dupped_inputs = {} @inputs.collect do |k,input| dupped_inputs[k] = Step.dup_stream input end @inputs = dupped_inputs @dupped = true end def name return nil if @is_exec return @path if @url.nil? (Array === @url ? @url.first : @url).split("/").last end def name=(name) @url = [base_url,task, name] * "/" end def task_name return task if task init_job (Array === @url ? @url.first : @url).split("/")[-2] end def nopid? false end def info(check_lock=false) return {:status => :waiting } unless started? @done = @info && @info[:status] && (@info[:status].to_sym == :done || @info[:status].to_sym == :error) if !@done && (@last_info_time.nil? || (Time.now - @last_info_time) > 0.5) update = true else update = false end @info = Persist.memory("RemoteSteps Info", :url => @url, :persist => true, :update => update) do @last_info_time = Time.now init_job unless @url info = begin @adaptor.get_json(File.join(@url, 'info')) rescue {:status => :noinfo} end info = RemoteWorkflow.fix_hash(info) info[:status] = info[:status].to_sym if String === info[:status] info end @info end def status return :done if @done return nil unless url or started? #return :streaming if @streaming begin status = info[:status] @done = true if status and status.to_sym == :done status rescue Log.exception $! nil ensure @info = nil end end def started? @result != nil || @started || @streaming end def done? return true if cache_files.any? self.init_job unless @url @done || status.to_s == 'done' || status.to_s == 'noinfo' end def files @adaptor.get_json(File.join(url, 'files')) end def file(file) @adaptor.get_raw(File.join(url, 'file', file.to_s)) end def get_stream case @result when IO @result when String StringIO.new @result else nil end end def grace produce unless @started sleep 0.1 unless started? sleep 0.5 unless started? sleep 1 unless started? while not (done? or started?) sleep 1 end end #{{{ MANAGEMENT def path if @url Misc.add_GET_param(@url, "_format", "raw") elsif @base_name [base_url, task, @base_name + '-' + Misc.fingerprint(inputs)] * "/" else nil end end def fork(noload=false, semaphore=nil) init_job(:asynchronous) end def running? ! %w(done error aborted noinfo).include? status.to_s end def exec(noload = false) @result ||= begin if noload == :stream _run_job(:exec) else exec_job end ensure @started = true end end def join return true if cache_files.any? init_job unless @url produce unless @started Log.debug{ "Joining RemoteStep: #{path}" } if IO === @result res = @result @result = nil Misc.consume_stream(res, true) end if not (self.done? || self.aborted? || self.error?) self.info return self if self.done? || self.aborted? || self.error? sleep 0.2 unless self.done? || self.aborted? || self.error? sleep 1 unless self.done? || self.aborted? || self.error? while not (self.done? || self.aborted? || self.error?) sleep 3 end end self end def load_res(res, result_type = nil) stream = true if res.respond_to? :read join unless stream result_type ||= self.result_type case result_type.to_sym when :string stream ? res.read : res when :boolean (stream ? res.read : res) == 'true' when :tsv if stream TSV.open(res, :monitor => true) else TSV.open(StringIO.new(res)) end when :annotations if stream Annotated.load_tsv(TSV.open(res)) else Annotated.load_tsv(TSV.open(StringIO.new(res))) end when :array (stream ? res.read : res).split("\n") else json_text = if IO === res res.read else res end begin JSON.parse json_text rescue case when json_text =~ /^\d+$/ json_text.to_i when json_text =~ /^\d+\.\d/ json_text.to_f else raise $! end end end end def short_path init_job unless @url [@task, @name] * "/" end def input_checks [] end def _restart @done = nil @name = nil @started = nil @aborted = nil new_inputs = {} inputs.each do |k,i| if File === i new_inputs[k] = File.open(i.path) else new_inputs[k] = i end end @inputs = new_inputs @info = nil end def init_info(*args) i = {:status => :waiting, :pid => Process.pid, :path => path} i[:dependencies] = dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]} if dependencies end end require 'rbbt/workflow/remote_workflow/remote_step/rest' require 'rbbt/workflow/remote_workflow/remote_step/ssh'