class WorkflowRESTClient def self.__prepare_inputs_for_restclient(inputs) inputs.each do |k,v| if v.respond_to? :path and not v.respond_to? :original_filename class << v def original_filename File.expand_path(path) end end end if Array === v and v.empty? inputs[k] = "EMPTY_ARRAY" end end end class RemoteStep < Step attr_accessor :url, :base_url, :task, :base_name, :inputs, :result_type, :result_description, :is_exec, :is_stream, :stream_input def initialize(base_url, task = nil, base_name = nil, inputs = nil, result_type = nil, result_description = nil, is_exec = false, is_stream = false, stream_input = nil) @base_url, @task, @base_name, @inputs, @result_type, @result_description, @is_exec, @is_stream, @stream_input = base_url, task, base_name, inputs, result_type, result_description, is_exec, is_stream, stream_input @base_url = "http://" << @base_url unless @base_url =~ /^https?:\/\// @mutex = Mutex.new end def clean_name @base_name end def run(no_load = false) no_load = @is_stream ? :stream : true if no_load @mutex.synchronize do @result ||= begin if @is_exec exec(no_load) elsif no_load == :stream _run_job(:stream) elsif no_load init_job nil else init_job join 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 = WorkflowRESTClient::RemoteStep.get_streams @inputs, @stream_input @inputs_done = true @inputs end def abort return self if status == :done WorkflowRESTClient.get_json(@url + '?_update=abort') if @url and @name self 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) @done = @info && @info[:status] && @info[:status].to_sym == :done @info = Persist.memory("RemoteSteps Info", :url => @url, :persist => true, :update => !@done) do init_job unless @url info = WorkflowRESTClient.get_json(File.join(@url, 'info')) info = WorkflowRESTClient.fix_hash(info) info[:status] = info[:status].to_sym if String === info[:status] info end 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 nil ensure @info = nil end end def started? @result != nil || @started || @streaming end def done? init_job unless @url @done || status.to_s == 'done' end def files WorkflowRESTClient.get_json(File.join(url, 'files')) end def file(file) WorkflowRESTClient.get_raw(File.join(url, 'file', file)) 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 init_job(cache_type = nil, other_params = {}) cache_type = :asynchronous if cache_type.nil? and not @is_exec cache_type = :exec if cache_type.nil? get_streams @name ||= Persist.memory("RemoteSteps", :workflow => self, :task => task, :jobname => @name, :inputs => inputs, :cache_type => cache_type) do WorkflowRESTClient.post_jobname(File.join(base_url, task.to_s), inputs.merge(other_params).merge(:jobname => @name||@base_name, :_cache_type => cache_type)) end if Open.remote? @name @url = @name @name = File.basename(@name) else @url = File.join(base_url, task.to_s, @name) end self end def fork(noload=false, semaphore=nil) init_job(:asynchronous) end def running? ! %w(done error aborted noinfo).include? status.to_s end def path if @url Misc.add_GET_param(@url, "_format", "raw") else [base_url, task, @base_name + '-' + Misc.fingerprint(inputs)] * "/" end end def exec(noload = false) @result ||= begin if noload == :stream _run_job(:exec) else exec_job end ensure @started = true end end def join init_job unless @url Log.debug{ "Joining RestClient: #{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 get params ||= {} params = params.merge(:_format => [:string, :boolean, :tsv, :annotations,:array].include?(result_type.to_sym) ? :raw : :json ) Misc.insist 3, rand(2) + 1 do begin init_job if url.nil? WorkflowRESTClient.get_raw(url, params) rescue Log.exception $! raise $! end end end def load_res(res, result_type = nil) stream = true if res.respond_to? :read join unless stream result_type ||= self.result_type case result_type when :string stream ? res.read : res when :boolean (stream ? res.read : res) == 'true' when :tsv if stream TSV.open(res, :monitor => true) else TSV.open(StringIO.new(res)) end when :annotations if stream Annotated.load_tsv(TSV.open(res)) else Annotated.load_tsv(TSV.open(StringIO.new(res))) end when :array (stream ? res.read : res).split("\n") res.split("\n") else json_text = if IO === res res.read else res end begin JSON.parse json_text rescue case when json_text =~ /^\d+$/ json_text.to_i when json_text =~ /^\d+\.\d/ json_text.to_f else raise $! end end end end def load params = {} join unless done? or streaming? raise get_exception if error? or aborted? load_res get end def exec_job res = _run_job(:exec) load_res res, result_type == :array ? :json : result_type 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 end def recursive_clean return begin params = {:_update => :recursive_clean} init_job(nil, params) WorkflowRESTClient.get_raw(url, params) _restart rescue Exception Log.exception $! end self end def _clean begin params = {:_update => :clean} WorkflowRESTClient.clean_url(url, params) if @url _restart rescue Exception Log.exception $! end end def clean init_job _clean self end def input_checks [] end end end require 'rbbt/rest/client/run'