require 'rbbt/workflow/step/dependencies' class Step attr_reader :stream, :dupped, :saved_stream def get_stream @mutex.synchronize do Log.low "Getting stream from #{path} #{!@saved_stream} [#{object_id}-#{Misc.fingerprint(@result)}]" begin return nil if @saved_stream if IO === @result @saved_stream = @result else nil end end end end def resolve_input_steps step = false pos = 0 input_options = Workflow === workflow ? workflow.task_info(task_name)[:input_options] : {} new_inputs = inputs.collect do |i| begin if Step === i if i.error? e = i.get_exception if e raise e else raise DependencyError, "Error in dep. #{Log.blue e.path}" end end step = true i.produce unless i.done? || i.error? || i.started? if i.done? if (task.input_options[task.inputs[pos]] || {})[:stream] TSV.get_stream i else if (task.input_options[task.inputs[pos]] || {})[:nofile] i.path else i.load end end elsif i.streaming? and (task.input_options[task.inputs[pos]] || {})[:stream] TSV.get_stream i else i.join if (task.input_options[task.inputs[pos]] || {})[:stream] TSV.get_stream i else if (task.input_options[task.inputs[pos]] || {})[:nofile] i.path else i.load end end end else i end ensure pos += 1 end end @inputs.replace new_inputs if step end def rewind_inputs return if @inputs.nil? Log.debug "Rewinding inputs for #{path}" @inputs.each do |input| next unless input.respond_to? :rewind begin input.rewind Log.debug "Rewinded #{Misc.fingerprint input}" rescue end end end def _exec resolve_input_steps rewind_inputs @exec = true if @exec.nil? begin old = Signal.trap("INT"){ Thread.current.raise Aborted } @task.exec_in((bindings ? bindings : self), *@inputs) ensure Signal.trap("INT", old) end end def exec(no_load=false) dependencies.each{|dependency| dependency.exec(no_load) } @mutex.synchronize do @result = self._exec @result = @result.stream if TSV::Dumper === @result end (no_load or ENV["RBBT_NO_STREAM"]) ? @result : prepare_result(@result, @task.result_description) end def dependency_checks rec_dependencies. select{|dependency| ! (defined? WorkflowRESTClient and WorkflowRESTClient::RemoteStep === dependency) }. select{|dependency| ! Open.remote?(dependency.path) }. select{|dependency| Open.exists?(dependency.info_file) }. select{|dependency| ! dependency.error? } end def input_checks inputs.select{|i| Step === i } end def checks (dependency_checks + input_checks).uniq end def out_of_date checks = self.checks return [] if checks.empty? outdated_time = [] outdated_dep = [] canfail_paths = self.canfail_paths checks.each do |dep| next unless Open.exists?(dep.info_file) begin if dep.done? && self.done? && Open.exists?(dep.path) && Open.exists?(self.path) && (File.mtime(dep.path) > File.mtime(self.path)) outdated_time << dep end rescue end if (! dep.done? && ! canfail_paths.include?(dep.path)) || ! dep.updated? outdated_dep << dep end end Log.high "Some newer files found: #{Misc.fingerprint outdated_time}" if outdated_time.any? Log.high "Some outdated files found: #{Misc.fingerprint outdated_dep}" if outdated_dep.any? outdated_time + outdated_dep end def updated? return true unless (done? || error?) @updated ||= out_of_date.empty? end def kill_children begin children_pids = info[:children_pids] if children_pids and children_pids.any? Log.medium("Killing children: #{ children_pids * ", " }") children_pids.each do |pid| Log.medium("Killing child #{ pid }") begin Process.kill "INT", pid rescue Exception Log.medium("Exception killing child #{ pid }: #{$!.message}") end end end rescue Log.medium("Exception finding children") end end def run(no_load = false) result = nil begin time_elapsed = total_time_elapsed = nil res = @mutex.synchronize do no_load = :stream if no_load Open.write(pid_file, Process.pid.to_s) unless Open.exists?(path) or Open.exists?(pid_file) result = Persist.persist "Job", @task.result_type, :file => path, :check => checks.collect{|dep| dep.path}, :no_load => no_load do if Step === Step.log_relay_step and not self == Step.log_relay_step relay_log(Step.log_relay_step) unless self.respond_to? :relay_step and self.relay_step end Open.write(pid_file, Process.pid.to_s) unless Open.exists? pid_file @exec = false init_info log :setup, "#{Log.color :green, "Setup"} step #{Log.color :yellow, task.name.to_s || ""}" merge_info({ :issued => (issue_time = Time.now), :name => name, :clean_name => clean_name, :workflow => (@workflow || @task.workflow).to_s, :task_name => @task.name, :result_type => @task.result_type, :result_description => @task.result_description, :dependencies => dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]} }) begin run_dependencies rescue Exception FileUtils.rm pid_file if File.exist?(pid_file) stop_dependencies raise $! end new_inputs = [] @inputs.each_with_index do |input,i| name = @task.inputs[i] type = @task.input_types[name] if type == :directory directory_inputs = file('directory_inputs') input_source = directory_inputs['.source'][name].find input_dir = directory_inputs[name].find case input when Path if input.directory? new_inputs << input else input.open do |io| begin Misc.untar(io, input_source) rescue raise ParameterException, "Error unpackaging tar directory input '#{name}':\n\n#{$!.message}" end end tar_1 = input_source.glob("*") raise ParameterException, "When using tar.gz files for directories, the directory must be the single first level entry" if tar_1.length != 1 FileUtils.ln_s Misc.path_relative_to(directory_inputs, tar_1.first), input_dir new_inputs << input_dir end when File, IO, Tempfile begin Misc.untar(Open.gunzip(input), input_source) rescue raise ParameterException, "Error unpackaging tar directory input '#{name}':\n\n#{$!.message}" end tar_1 = input_source.glob("*") raise ParameterException, "When using tar.gz files for directories, the directory must be the single first level entry" if tar_1.length != 1 FileUtils.ln_s Misc.path_relative_to(directory_inputs, tar_1.first), input_dir new_inputs << input_dir else raise ParameterException, "Format of directory input '#{name}' not understood: #{Misc.fingerprint input}" end else new_inputs << input end end if @inputs @inputs = new_inputs if @inputs if not task.inputs.nil? info_inputs = @inputs.collect do |i| if Path === i i.to_s else i end end set_info :inputs, Misc.remove_long_items(Misc.zip2hash(task.inputs, info_inputs)) end set_info :started, (start_time = Time.now) log :started, "Starting step #{Log.color :yellow, task.name.to_s || ""}" begin result = _exec rescue Aborted, Interrupt log(:aborted, "Aborted") raise $! rescue Exception backtrace = $!.backtrace # HACK: This fixes an strange behaviour in 1.9.3 where some # backtrace strings are coded in ASCII-8BIT backtrace.each{|l| l.force_encoding("UTF-8")} if String.instance_methods.include? :force_encoding set_info :backtrace, backtrace log(:error, "#{$!.class}: #{$!.message}") stop_dependencies raise $! end if not no_load or ENV["RBBT_NO_STREAM"] == "true" result = prepare_result result, @task.description, info if IO === result result = prepare_result result.stream, @task.description, info if TSV::Dumper === result end stream = case result when IO result when TSV::Dumper result.stream end if stream log :streaming, "Streaming step #{Log.color :yellow, task.name.to_s || ""}" callback = Proc.new do if AbortedStream === stream if stream.exception raise stream.exception else raise Aborted end end begin status = self.status if status != :done and status != :error and status != :aborted Misc.insist do merge_info({ :done => (done_time = Time.now), :total_time_elapsed => (total_time_elapsed = done_time - issue_time), :time_elapsed => (time_elapsed = done_time - start_time) }) log :done, "Completed step #{Log.color :yellow, task.name.to_s || ""} in #{time_elapsed.to_i}+#{(total_time_elapsed - time_elapsed).to_i} sec." end end rescue Log.exception $! ensure Step.purge_stream_cache set_info :pid, nil FileUtils.rm pid_file if File.exist?(pid_file) end end abort_callback = Proc.new do |exception| begin if exception self.exception exception else log :aborted, "#{Log.color :red, "Aborted"} step #{Log.color :yellow, task.name.to_s || ""}" if status == :streaming end _clean_finished rescue stop_dependencies set_info :pid, nil FileUtils.rm pid_file if File.exist?(pid_file) end end ConcurrentStream.setup stream, :callback => callback, :abort_callback => abort_callback if AbortedStream === stream exception = stream.exception || Aborted.new("Aborted stream: #{Misc.fingerprint stream}") self.exception exception _clean_finished raise exception end else merge_info({ :done => (done_time = Time.now), :total_time_elapsed => (total_time_elapsed = done_time - issue_time), :time_elapsed => (time_elapsed = done_time - start_time) }) log :ending Step.purge_stream_cache FileUtils.rm pid_file if File.exist?(pid_file) end set_info :dependencies, dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]} if result.nil? && File.exists?(self.tmp_path) && ! File.exists?(self.path) FileUtils.mv self.tmp_path, self.path end result end if no_load @result ||= result self else Step.purge_stream_cache @result = prepare_result result, @task.result_description end end log :done, "Completed step #{Log.color :yellow, task.name.to_s || ""} in #{time_elapsed.to_i}+#{(total_time_elapsed - time_elapsed).to_i} sec." unless stream or time_elapsed.nil? res rescue DependencyError exception $! rescue Aborted, Interrupt abort stop_dependencies raise $! rescue Exception exception $! stop_dependencies raise $! ensure set_info :pid, nil unless no_load end end def produce(force=false, dofork=false) return self if done? and not dirty? if error? or aborted? or stalled? abort if stalled? if force or aborted? or recoverable_error? clean else e = get_exception if e raise e else raise "Error in job: #{self.path}" end end end update if done? if dofork fork(true) unless started? join unless done? else run(true) unless started? join unless done? end self end def fork(no_load = false, semaphore = nil) raise "Can not fork: Step is waiting for proces #{@pid} to finish" if not @pid.nil? and not Process.pid == @pid and Misc.pid_exists?(@pid) and not done? and info[:forked] sout, sin = Misc.pipe if no_load == :stream @pid = Process.fork do sout.close if sout Misc.pre_fork begin RbbtSemaphore.wait_semaphore(semaphore) if semaphore FileUtils.mkdir_p File.dirname(path) unless File.exist? File.dirname(path) begin @forked = true res = run no_load set_info :forked, true if sin io = TSV.get_stream res if io.respond_to? :setup io.setup(sin) sin.pair = io io.pair = sin end begin Misc.consume_stream(io, false, sin) rescue Log.warn "Could not consume stream (#{io.closed? ? 'closed' : 'open'}) into pipe for forked job: #{self.path}" Misc.consume_stream(io) unless io.closed? end end rescue Aborted, Interrupt Log.debug{"Forked process aborted: #{path}"} log :aborted, "Job aborted (#{Process.pid})" raise $! rescue Exception Log.debug("Exception '#{$!.message}' caught on forked process: #{path}") raise $! ensure join_stream end begin children_pids = info[:children_pids] if children_pids children_pids.each do |pid| if Misc.pid_exists? pid begin Process.waitpid pid rescue Errno::ECHILD Log.low "Waiting on #{ pid } failed: #{$!.message}" end end end set_info :children_done, Time.now end rescue Exception Log.debug("Exception waiting for children: #{$!.message}") RbbtSemaphore.post_semaphore(semaphore) if semaphore Kernel.exit! -1 end set_info :pid, nil ensure RbbtSemaphore.post_semaphore(semaphore) if semaphore Kernel.exit! 0 end end sin.close if sin @result = sout if sout Process.detach(@pid) self end def abort_pid @pid ||= info[:pid] case @pid when nil Log.medium "Could not abort #{path}: no pid" false when Process.pid Log.medium "Could not abort #{path}: same process" false else Log.medium "Aborting pid #{path}: #{ @pid }" begin Process.kill("INT", @pid) Process.waitpid @pid rescue Exception Log.debug("Aborted job #{@pid} was not killed: #{$!.message}") end Log.medium "Aborted pid #{path}: #{ @pid }" true end end def abort_stream stream = @result if IO === @result @saved_stream = nil if stream and stream.respond_to? :abort and not stream.aborted? doretry = true begin Log.medium "Aborting job stream #{stream.inspect} -- #{Log.color :blue, path}" stream.abort rescue Aborted, Interrupt Log.medium "Aborting job stream #{stream.inspect} ABORTED RETRY -- #{Log.color :blue, path}" if doretry doretry = false retry end end end end def _clean_finished if Open.exists? path and not status == :done Log.warn "Aborted job had finished. Removing result -- #{ path }" begin Open.rm path rescue Exception Log.warn "Exception removing result of aborted job: #{$!.message}" end end end def _abort return if @aborted @aborted = true Log.medium{"#{Log.color :red, "Aborting"} #{Log.color :blue, path}"} doretry = true begin return if done? abort_pid if running? abort_stream stop_dependencies rescue Aborted, Interrupt Log.medium{"#{Log.color :red, "Aborting ABORTED RETRY"} #{Log.color :blue, path}"} if doretry doretry = false retry end raise $! rescue Exception if doretry doretry = false retry end ensure _clean_finished end end def abort return if done? and (status == :done or status == :noinfo) _abort log(:aborted, "Job aborted") unless aborted? or error? self end def join_stream stream = get_stream if @result @result = nil if stream begin Misc.consume_stream stream stream.join if stream.respond_to? :join rescue Exception stream.abort $! self._abort end end end def soft_grace until done? or File.exist?(info_file) sleep 1 end self end def grace until done? or result or error? or aborted? or streaming? or waiting? sleep 1 end self end def join grace if Open.exists?(info_file) if streaming? join_stream end return self if not Open.exists? info_file return self if info[:joined] pid = @pid Misc.insist [0.1, 0.2, 0.5, 1] do pid ||= info[:pid] end begin if pid.nil? or Process.pid == pid dependencies.each{|dep| dep.join } else begin Log.debug{"Waiting for pid: #{pid}"} Process.waitpid pid rescue Errno::ECHILD Log.debug{"Process #{ pid } already finished: #{ path }"} end if Misc.pid_exists? pid pid = nil dependencies.each{|dep| dep.join } end until (path.exists? && status == :done) or error? or aborted? or waiting? sleep 1 join_stream if streaming? end self ensure begin set_info :joined, true rescue end if File.exists?(info_file) && File.writable?(info_file) @result = nil end end end