Class: Step
- Inherits:
-
Object
- Object
- Step
- Defined in:
- lib/rbbt/workflow/step.rb,
lib/rbbt/workflow/accessor.rb,
lib/rbbt/workflow/step/run.rb
Direct Known Subclasses
Constant Summary collapse
- INFO_SERIALIAZER =
Marshal
- STREAM_CACHE =
{}
- STREAM_CACHE_MUTEX =
Mutex.new
Class Attribute Summary collapse
-
.lock_dir ⇒ Object
Returns the value of attribute lock_dir.
-
.log_relay_step ⇒ Object
Returns the value of attribute log_relay_step.
Instance Attribute Summary collapse
-
#bindings ⇒ Object
Returns the value of attribute bindings.
-
#clean_name ⇒ Object
Returns the value of attribute clean_name.
-
#dependencies ⇒ Object
Returns the value of attribute dependencies.
-
#dupped ⇒ Object
readonly
Returns the value of attribute dupped.
-
#exec(no_load = false) ⇒ Object
Returns the value of attribute exec.
-
#inputs ⇒ Object
Returns the value of attribute inputs.
-
#mutex ⇒ Object
Returns the value of attribute mutex.
-
#path ⇒ Object
Returns the value of attribute path.
-
#pid ⇒ Object
Returns the value of attribute pid.
-
#result ⇒ Object
Returns the value of attribute result.
-
#saved_stream ⇒ Object
readonly
Returns the value of attribute saved_stream.
-
#seen ⇒ Object
Returns the value of attribute seen.
-
#stream ⇒ Object
readonly
Returns the value of attribute stream.
-
#task ⇒ Object
Returns the value of attribute task.
Class Method Summary collapse
- .clean(path) ⇒ Object
- .dup_stream(stream) ⇒ Object
- .files_dir(path) ⇒ Object
- .info_file(path) ⇒ Object
- .job_name_for_info_file(info_file, extension = nil) ⇒ Object
- .log(status, message, path, &block) ⇒ Object
- .log_block(status, message, path, &block) ⇒ Object
- .log_progress(status, options = {}, path = nil, &block) ⇒ Object
- .log_string(status, message, path) ⇒ Object
- .purge_stream_cache ⇒ Object
- .started? ⇒ Boolean
- .status_color(status) ⇒ Object
- .step_info(path) ⇒ Object
- .wait_for_jobs(jobs) ⇒ Object
Instance Method Summary collapse
- #_abort ⇒ Object
- #_exec ⇒ Object
- #abort ⇒ Object
- #abort_pid ⇒ Object
- #abort_stream ⇒ Object
- #aborted? ⇒ Boolean
- #checks ⇒ Object
- #child(&block) ⇒ Object
- #clean ⇒ Object
- #dirty? ⇒ Boolean
- #done? ⇒ Boolean
- #dup_inputs ⇒ Object
- #error? ⇒ Boolean
- #exception(ex, msg = nil) ⇒ Object
- #file(name) ⇒ Object
- #files ⇒ Object
-
#files_dir ⇒ Object
{{{ INFO.
- #fork(semaphore = nil) ⇒ Object
- #get_stream ⇒ Object
- #grace ⇒ Object
- #info(check_lock = true) ⇒ Object
-
#info_file ⇒ Object
{{{ INFO.
- #info_lock ⇒ Object
-
#initialize(path, task = nil, inputs = nil, dependencies = nil, bindings = nil, clean_name = nil) ⇒ Step
constructor
A new instance of Step.
- #join ⇒ Object
- #join_stream ⇒ Object
- #kill_children ⇒ Object
- #load ⇒ Object
- #load_file(name, type = nil, options = {}) ⇒ Object
- #log(status, message = nil, &block) ⇒ Object
- #log_progress(status, options = {}, &block) ⇒ Object
- #merge_info(hash) ⇒ Object
- #message(message) ⇒ Object
- #messages ⇒ Object
- #name ⇒ Object
- #prepare_result(value, description = nil, info = {}) ⇒ Object
- #progress_bar(msg, options = {}) ⇒ Object
- #provenance ⇒ Object
- #provenance_paths ⇒ Object
-
#rec_dependencies ⇒ Object
dependencies = self.dependencies ? self.dependencies + new_dependencies : new_dependencies dependencies.flatten! dependencies.uniq! dependencies end.
- #recursive_clean ⇒ Object
- #relay_log(step) ⇒ Object
- #run(no_load = false) ⇒ Object
- #run_dependencies ⇒ Object
- #running? ⇒ Boolean
- #save_file(name, content) ⇒ Object
- #set_info(key, value) ⇒ Object
- #soft_grace ⇒ Object
- #started? ⇒ Boolean
- #status ⇒ Object
- #status=(status) ⇒ Object
- #step(name) ⇒ Object
- #stop_dependencies ⇒ Object
- #streaming? ⇒ Boolean
- #task_name ⇒ Object
Constructor Details
#initialize(path, task = nil, inputs = nil, dependencies = nil, bindings = nil, clean_name = nil) ⇒ Step
Returns a new instance of Step.
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# File 'lib/rbbt/workflow/step.rb', line 31 def initialize(path, task = nil, inputs = nil, dependencies = nil, bindings = nil, clean_name = nil) path = Path.setup(Misc.sanitize_filename(path)) if String === path path = path.call if Proc === path @path = path @task = task @bindings = bindings @dependencies = case when dependencies.nil? [] when Array === dependencies dependencies else [dependencies] end @mutex = Mutex.new @info_mutex = Mutex.new @inputs = inputs || [] NamedArray.setup @inputs, task.inputs.collect{|s| s.to_s} if task and task.respond_to? :inputs and task.inputs end |
Class Attribute Details
.lock_dir ⇒ Object
Returns the value of attribute lock_dir.
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# File 'lib/rbbt/workflow/step.rb', line 14 def lock_dir @lock_dir end |
.log_relay_step ⇒ Object
Returns the value of attribute log_relay_step.
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# File 'lib/rbbt/workflow/step.rb', line 77 def log_relay_step @log_relay_step end |
Instance Attribute Details
#bindings ⇒ Object
Returns the value of attribute bindings.
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# File 'lib/rbbt/workflow/step.rb', line 8 def bindings @bindings end |
#clean_name ⇒ Object
Returns the value of attribute clean_name.
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# File 'lib/rbbt/workflow/step.rb', line 8 def clean_name @clean_name end |
#dependencies ⇒ Object
Returns the value of attribute dependencies.
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# File 'lib/rbbt/workflow/step.rb', line 8 def dependencies @dependencies end |
#dupped ⇒ Object (readonly)
Returns the value of attribute dupped.
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# File 'lib/rbbt/workflow/step/run.rb', line 3 def dupped @dupped end |
#exec(no_load = false) ⇒ Object
Returns the value of attribute exec.
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# File 'lib/rbbt/workflow/step.rb', line 10 def exec @exec end |
#inputs ⇒ Object
Returns the value of attribute inputs.
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# File 'lib/rbbt/workflow/step.rb', line 8 def inputs @inputs end |
#mutex ⇒ Object
Returns the value of attribute mutex.
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# File 'lib/rbbt/workflow/step.rb', line 11 def mutex @mutex end |
#path ⇒ Object
Returns the value of attribute path.
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# File 'lib/rbbt/workflow/step.rb', line 8 def path @path end |
#pid ⇒ Object
Returns the value of attribute pid.
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# File 'lib/rbbt/workflow/step.rb', line 9 def pid @pid end |
#result ⇒ Object
Returns the value of attribute result.
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# File 'lib/rbbt/workflow/step.rb', line 11 def result @result end |
#saved_stream ⇒ Object (readonly)
Returns the value of attribute saved_stream.
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# File 'lib/rbbt/workflow/step/run.rb', line 3 def saved_stream @saved_stream end |
#seen ⇒ Object
Returns the value of attribute seen.
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# File 'lib/rbbt/workflow/step.rb', line 11 def seen @seen end |
#stream ⇒ Object (readonly)
Returns the value of attribute stream.
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# File 'lib/rbbt/workflow/step/run.rb', line 3 def stream @stream end |
#task ⇒ Object
Returns the value of attribute task.
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# File 'lib/rbbt/workflow/step.rb', line 8 def task @task end |
Class Method Details
.clean(path) ⇒ Object
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# File 'lib/rbbt/workflow/step.rb', line 161 def self.clean(path) info_file = Step.info_file path files_dir = Step.files_dir path if Open.exists?(path) or Open.exists?(info_file) begin self.abort if self.running? rescue Exception end @result = nil @pid = nil Misc.insist do Open.rm info_file if Open.exists? info_file Open.rm info_file + '.lock' if Open.exists? info_file + '.lock' Open.rm path if Open.exists? path Open.rm path + '.lock' if Open.exists? path + '.lock' Open.rm_rf files_dir if Open.exists? files_dir end end end |
.dup_stream(stream) ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 7 def self.dup_stream(stream) case stream when IO, File return stream if stream.closed? STREAM_CACHE_MUTEX.synchronize do case current = STREAM_CACHE[stream] when nil Log.medium "Not duplicating stream #{ Misc.fingerprint(stream) }" STREAM_CACHE[stream] = stream when File if Open.exists? current.path Log.medium "Reopening file #{ Misc.fingerprint(current) }" Open.open(current.path) else Log.medium "Duplicating file #{ Misc.fingerprint(current) } #{current.inspect}" Misc.dup_stream(current) end else Log.medium "Duplicating stream #{ Misc.fingerprint(stream) }" Misc.dup_stream(current) end end when TSV::Dumper#, TSV::Parser stream = stream.stream return stream if stream.closed? STREAM_CACHE_MUTEX.synchronize do if STREAM_CACHE[stream].nil? Log.high "Not duplicating dumper #{ stream.inspect }" STREAM_CACHE[stream] = stream else new = Misc.dup_stream(STREAM_CACHE[stream]) Log.high "Duplicating dumper #{ stream.inspect } into #{new.inspect}" new end end else stream end end |
.files_dir(path) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 37 def self.files_dir(path) path.nil? ? nil : path + '.files' end |
.info_file(path) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 41 def self.info_file(path) path.nil? ? nil : path + '.info' end |
.job_name_for_info_file(info_file, extension = nil) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 56 def self.job_name_for_info_file(info_file, extension = nil) if extension and not extension.empty? info_file.sub(/\.#{extension}\.info$/,'') else info_file.sub(/\.info$/,'') end end |
.log(status, message, path, &block) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 249 def self.log(status, , path, &block) if block if Hash === log_progress(status, , path, &block) else log_block(status, , path, &block) end else log_string(status, , path) end end |
.log_block(status, message, path, &block) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 185 def self.log_block(status, , path, &block) start = Time.now status = status.to_s status_color = self.status_color status Log.info do now = Time.now str = Log.color :reset str << "#{ Log.color status_color, status}" str << ": #{ }" if str << " -- #{Log.color :blue, path.to_s}" if path str << " #{Log.color :yellow, Process.pid}" str end res = yield eend = Time.now Log.info do now = Time.now str = "#{ Log.color :cyan, status.to_s } +#{Log.color :green, "%.2f" % (eend - start)}" str << " -- #{Log.color :blue, path.to_s}" if path str << " #{Log.color :yellow, Process.pid}" str end res end |
.log_progress(status, options = {}, path = nil, &block) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 226 def self.log_progress(status, = {}, path = nil, &block) = Misc.add_defaults , :severity => Log::INFO, :file => path max = Misc. , :max Log::ProgressBar.(max, ) do || begin res = yield raise KeepBar.new res if IO === res res rescue Log.exception $! end end end |
.log_string(status, message, path) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 211 def self.log_string(status, , path) Log.info do status = status.to_s status_color = self.status_color status str = Log.color :reset str << "#{ Log.color status_color, status}" str << ": #{ }" if str << " -- #{Log.color :blue, path.to_s}" if path str << " #{Log.color :yellow, Process.pid}" str end end |
.purge_stream_cache ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 50 def self.purge_stream_cache return STREAM_CACHE_MUTEX.synchronize do STREAM_CACHE.collect{|k,s| Thread.new do Misc.consume_stream s end } STREAM_CACHE.clear end end |
.started? ⇒ Boolean
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# File 'lib/rbbt/workflow/accessor.rb', line 9 def self.started? info_file.exists? end |
.status_color(status) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 171 def self.status_color(status) status = status.split(">").last case status when "starting" :yellow when "error", "aborted" :red when "done" :green else :cyan end end |
.step_info(path) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 45 def self.step_info(path) begin Open.open(info_file(path)) do |f| INFO_SERIALIAZER.load(f) end rescue Exception Log.exception $! {} end end |
.wait_for_jobs(jobs) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 13 def self.wait_for_jobs(jobs) jobs = [jobs] if Step === jobs begin threads = [] threads = jobs.collect do |j| Thread.new do begin j.join rescue Exception Log.error "Exception waiting for job: #{Log.color :blue, j.path}" raise $! end end end threads.each{|t| t.join } rescue Exception threads.each{|t| t.exit } jobs.each do |j| j.abort end raise $! end end |
Instance Method Details
#_abort ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 381 def _abort return if @aborted @aborted = true return if done? Log.medium{"#{Log.color :red, "Aborting"} #{Log.color :blue, path}"} begin stop_dependencies abort_stream abort_pid rescue Aborted Log.medium{"#{Log.color :red, "Aborting ABORTED RETRY"} #{Log.color :blue, path}"} retry rescue Exception retry ensure if Open.exists? path Log.warn "Aborted job had finished. Removing result -- #{ path }" begin Open.rm path rescue Exception Log.warn "Exception removing result of aborted job: #{$!.}" end end end Log.medium{"#{Log.color :red, "Aborted"} #{Log.color :blue, path}"} end |
#_exec ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 83 def _exec @exec = true if @exec.nil? @task.exec_in((bindings ? bindings : self), *@inputs) end |
#abort ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 408 def abort _abort log(:aborted, "Job aborted") unless aborted? or error? end |
#abort_pid ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 342 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 #{path}: #{ @pid }" begin Process.kill("KILL", @pid) Process.waitpid @pid rescue Exception Log.debug("Aborted job #{@pid} was not killed: #{$!.}") end true end end |
#abort_stream ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 364 def abort_stream stream = get_stream if @result stream ||= @saved_stream @saved_stream = nil if stream and stream.respond_to? :abort and not stream.aborted? begin Log.medium "Aborting job stream #{stream.inspect} -- #{Log.color :blue, path}" stream.abort #stream.close unless stream.closed? rescue Aborted Log.medium "Aborting job stream #{stream.inspect} ABORTED RETRY -- #{Log.color :blue, path}" Log.exception $! retry end end end |
#aborted? ⇒ Boolean
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# File 'lib/rbbt/workflow/accessor.rb', line 305 def aborted? @aborted || status == :aborted end |
#checks ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 98 def checks rec_dependencies.collect{|dependency| dependency.path }.uniq end |
#child(&block) ⇒ Object
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# File 'lib/rbbt/workflow/step.rb', line 140 def child(&block) child_pid = Process.fork &block children_pids = info[:children_pids] if children_pids.nil? children_pids = [child_pid] else children_pids << child_pid end #Process.detach(child_pid) set_info :children_pids, children_pids child_pid end |
#clean ⇒ Object
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# File 'lib/rbbt/workflow/step.rb', line 183 def clean Step.clean(path) self end |
#dirty? ⇒ Boolean
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# File 'lib/rbbt/workflow/step/run.rb', line 102 def dirty? rec_dependencies.collect{|dependency| dependency.path }.uniq.reject{|path| path.exists?}.any? end |
#done? ⇒ Boolean
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# File 'lib/rbbt/workflow/accessor.rb', line 285 def done? path and File.exists? path end |
#dup_inputs ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 75 def dup_inputs return if @dupped or ENV["RBBT_NO_STREAM"] == 'true' @inputs = @inputs.collect do |input| Step.dup_stream input end @dupped = true end |
#error? ⇒ Boolean
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# File 'lib/rbbt/workflow/accessor.rb', line 301 def error? status == :error end |
#exception(ex, msg = nil) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 269 def exception(ex, msg = nil) self._abort ex_class = ex.class.to_s set_info :backtrace, ex.backtrace set_info :exception, {:class => ex_class, :message => ex., :backtrace => ex.backtrace} if msg.nil? log :error, "#{ex_class} -- #{ex.}" else log :error, "#{msg} -- #{ex.}" end end |
#file(name) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 322 def file(name) Path.setup(File.join(files_dir, name.to_s)) end |
#files ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 315 def files files = Dir.glob(File.join(files_dir, '**', '*')).reject{|path| File.directory? path}.collect do |path| Misc.path_relative_to(files_dir, path) end files end |
#files_dir ⇒ Object
{{{ INFO
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# File 'lib/rbbt/workflow/accessor.rb', line 311 def files_dir @files_dir ||= Step.files_dir path end |
#fork(semaphore = nil) ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 285 def fork(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] @pid = Process.fork do Misc.pre_fork begin RbbtSemaphore.wait_semaphore(semaphore) if semaphore FileUtils.mkdir_p File.dirname(path) unless File.exists? File.dirname(path) begin res = run true set_info :forked, true rescue Aborted Log.debug{"Forked process aborted: #{path}"} log :aborted, "Job aborted (#{Process.pid})" raise $! rescue Exception Log.debug("Exception '#{$!.}' caught on forked process: #{path}") raise $! ensure join_stream end begin children_pids = info[:children_pids] if children_pids children_pids.each do |pid| if Misc.pid_exists? pid begin Process.waitpid pid rescue Errno::ECHILD Log.low "Waiting on #{ pid } failed: #{$!.}" end end end set_info :children_done, Time.now end rescue Exception Log.debug("Exception waiting for children: #{$!.}") 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 Process.detach(@pid) self end |
#get_stream ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 62 def get_stream @mutex.synchronize do begin return nil if @saved_stream if IO === @result @saved_stream = @result else nil end end end end |
#grace ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 435 def grace until done? or result or error? or aborted? or streaming? sleep 1 end self end |
#info(check_lock = true) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 86 def info(check_lock = true) return {} if info_file.nil? or not Open.exists? info_file begin Misc.insist do begin return @info_cache if @info_cache and File.ctime(info_file) < @info_cache_time rescue Exception raise $! end begin @info_cache = Misc.insist(3, 1.6, info_file) do Misc.insist(2, 1, info_file) do Misc.insist(3, 0.2, info_file) do raise TryAgain, "Info locked" if check_lock and info_lock.locked? Open.open(info_file) do |file| INFO_SERIALIAZER.load(file) #|| {} end end end end @info_cache_time = Time.now @info_cache end end rescue Exception Log.debug{"Error loading info file: " + info_file} Log.exception $! Open.rm info_file Misc.sensiblewrite(info_file, INFO_SERIALIAZER.dump({:status => :error, :messages => ["Info file lost"]})) raise $! end end |
#info_file ⇒ Object
{{{ INFO
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# File 'lib/rbbt/workflow/accessor.rb', line 74 def info_file @info_file ||= Step.info_file(path) end |
#info_lock ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 78 def info_lock @info_lock = begin path = Persist.persistence_path(info_file + '.lock', {:dir => Step.lock_dir}) Lockfile.new path, :refresh => false, :dont_use_lock_id => true end if @info_lock.nil? @info_lock end |
#join ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 442 def join grace 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 sleep 1 until path.exists? self ensure set_info :joined, true end end |
#join_stream ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 413 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 raise $! end end end |
#kill_children ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 106 def kill_children begin children_pids = info[:children_pids] if children_pids and children_pids.any? Log.medium("Killing children: #{ children_pids * ", " }") children_pids.each do |pid| Log.medium("Killing child #{ pid }") begin Process.kill "INT", pid rescue Exception Log.medium("Exception killing child #{ pid }: #{$!.}") end end end rescue Log.medium("Exception finding children") end end |
#load ⇒ Object
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# File 'lib/rbbt/workflow/step.rb', line 154 def load return prepare_result @result, @task.result_description if @result and not @path == @result join if not done? return Persist.load_file(@path, @task.result_type) if @path.exists? exec end |
#load_file(name, type = nil, options = {}) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 342 def load_file(name, type = nil, = {}) if type.nil? and name =~ /.*\.(\w+)$/ extension = name.match(/.*\.(\w+)$/)[1] case extension when "tc" type = :tc when "tsv" type = :tsv when "list", "ary", "array" type = :array when "yaml" type = :yaml when "marshal" type = :marshal else type = :other end else type ||= :other end case type.to_sym when :tc Persist.open_tokyocabinet(file(name), false) when :tsv TSV.open Open.open(file(name)), when :array #Open.read(file(name)).split /\n|,\s*/ Open.read(file(name)).split "\n" when :yaml YAML.load(Open.open(file(name))) when :marshal Marshal.load(Open.open(file(name))) else Open.read(file(name)) end end |
#log(status, message = nil, &block) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 261 def log(status, = nil, &block) self.status = status if self. Log.uncolor() end Step.log(status, , path, &block) end |
#log_progress(status, options = {}, &block) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 240 def log_progress(status, = {}, &block) Step.log_progress(status, , file(:progress), &block) end |
#merge_info(hash) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 133 def merge_info(hash) return nil if @exec or info_file.nil? value = Annotated.purge value if defined? Annotated Open.lock(info_file, :lock => info_lock) do i = info(false) i.merge! hash @info_cache = i Misc.sensiblewrite(info_file, INFO_SERIALIAZER.dump(i), :force => true, :lock => false) @info_cache_time = Time.now value end end |
#message(message) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 167 def () set_info(:messages, ( || []) << ) end |
#messages ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 159 def if = info[:messages] else set_info(:messages, []) if self.respond_to?(:set_info) end end |
#name ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 64 def name path.sub(/.*\/#{Regexp.quote task.name.to_s}\/(.*)/, '\1') end |
#prepare_result(value, description = nil, info = {}) ⇒ Object
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# File 'lib/rbbt/workflow/step.rb', line 97 def prepare_result(value, description = nil, info = {}) case when IO === value begin res = case @task.result_type when :array array = [] while line = value.gets array << line.strip end array when :tsv begin TSV.open(value) rescue IOError TSV.setup({}) end else value.read end value.join if value.respond_to? :join res rescue Exception value.abort if value.respond_to? :abort self.abort raise $! end when (not defined? Entity or description.nil? or not Entity.formats.include? description) value when (Annotated === value and info.empty?) value when Annotated === value annotations = value.annotations info.each do |k,v| value.send("#{h}=", v) if annotations.include? k end value else Entity.formats[description].setup(value, info.merge(:format => description)) end end |
#progress_bar(msg, options = {}) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 244 def (msg, = {}) max = [:max] Log::ProgressBar.new max, {:desc => msg, :file => file(:progress)}.merge() end |
#provenance ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 380 def provenance provenance = {} dependencies.each do |dep| next unless dep.path.exists? if File.exists? dep.info_file provenance[dep.path] = dep.provenance if File.exists? dep.path else provenance[dep.path] = nil end end {:inputs => info[:inputs], :provenance => provenance} end |
#provenance_paths ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 393 def provenance_paths provenance = {} dependencies.each do |dep| provenance[dep.path] = dep.provenance_paths if File.exists? dep.path end provenance end |
#rec_dependencies ⇒ Object
dependencies = self.dependencies ? self.dependencies + new_dependencies : new_dependencies
dependencies.flatten!
dependencies.uniq!
dependencies
end
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# File 'lib/rbbt/workflow/step.rb', line 209 def rec_dependencies # A step result with no info_file means that it was manually # placed. In that case, do not consider its dependencies return [] if Open.exists?(self.path.to_s) and not Open.exists? self.info_file return [] if dependencies.nil? or dependencies.empty? new_dependencies = [] dependencies.each{|step| new_dependencies.concat step.rec_dependencies new_dependencies << step } new_dependencies.uniq end |
#recursive_clean ⇒ Object
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# File 'lib/rbbt/workflow/step.rb', line 225 def recursive_clean clean rec_dependencies.each do |step| if Open.exists?(step.info_file) step.clean else end end self end |
#relay_log(step) ⇒ Object
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# File 'lib/rbbt/workflow/step.rb', line 80 def relay_log(step) return self unless Task === self.task and not self.task.name.nil? if not self.respond_to? :original_log class << self attr_accessor :relay_step alias original_log log def log(status, = nil) self.status = status Log.uncolor relay_step.log([task.name.to_s, status.to_s] * ">", .nil? ? nil : ) unless (relay_step.done? or relay_step.error? or relay_step.aborted?) end end end @relay_step = step self end |
#run(no_load = false) ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 171 def run(no_load = false) result = nil begin @mutex.synchronize do no_load = no_load ? :stream : false result = Persist.persist "Job", @task.result_type, :file => path, :check => checks, :no_load => no_load do |lockfile| 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 @exec = false Open.rm info_file if Open.exists? info_file log :setup, "#{Log.color :cyan, "Setup"} #{Log.color :yellow, task.name.to_s || ""}" merge_info({ :pid => Process.pid, :issued => Time.now, :name => name, :clean_name => clean_name, :dependencies => dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]}, }) dup_inputs begin run_dependencies rescue Exception stop_dependencies raise $! end set_info :inputs, Misc.remove_long_items(Misc.zip2hash(task.inputs, @inputs)) unless task.inputs.nil? set_info :started, (start_time = Time.now) log :started, "#{Log.color :magenta, "Starting"} #{Log.color :yellow, task.name.to_s || ""}" begin result = _exec rescue Aborted stop_dependencies log(:aborted, "Aborted") raise $! rescue Exception backtrace = $!.backtrace # HACK: This fixes an strange behaviour in 1.9.3 where some # backtrace strings are coded in ASCII-8BIT set_info :backtrace, backtrace log(:error, "#{$!.class}: #{$!.}") backtrace.each{|l| l.force_encoding("UTF-8")} if String.instance_methods.include? :force_encoding 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, "#{Log.color :magenta, "Streaming"} #{Log.color :yellow, task.name.to_s || ""}" ConcurrentStream.setup stream do begin if status != :done Misc.insist do set_info :done, (done_time = Time.now) set_info :time_elapsed, (time_elapsed = done_time - start_time) log :done, "#{Log.color :magenta, "Completed"} #{Log.color :yellow, task.name.to_s || ""} in #{time_elapsed.to_i} sec." end end rescue Log.exception $! ensure join end end stream.abort_callback = Proc.new do begin log :aborted, "#{Log.color :red, "Aborted"} #{Log.color :yellow, task.name.to_s || ""}" if status == :streaming rescue Log.exception $! end end else set_info :done, (done_time = Time.now) set_info :time_elapsed, (time_elapsed = done_time - start_time) log :done, "#{Log.color :magenta, "Completed"} #{Log.color :yellow, task.name.to_s || ""} in #{time_elapsed.to_i} sec." end result end if no_load @result ||= result self else @result = prepare_result result, @task.result_description end end rescue Exception exception $! raise $! end end |
#run_dependencies ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 125 def run_dependencies @seen ||= [] seen_paths ||= Set.new dependencies.uniq.each do |dependency| dependency_path = dependency.path next if seen_paths.include? dependency_path @seen.concat dependency.rec_dependencies seen_paths.union(dependency.rec_dependencies.collect{|d| d.path}) @seen << dependency seen_paths << dependency_path end @seen.uniq! @seen.delete self return if @seen.empty? log :dependencies, "#{Log.color :magenta, "Dependencies"} #{Log.color :yellow, task.name.to_s || ""}" dupping = [] @seen.each do |dependency| next if (dependency.done? and not dependency.dirty?) or (dependency.streaming? and dependency.running?) dependency.clean dupping << dependency unless dependencies.include? dependency end dupping.each{|dep| dep.dup_inputs} @seen.each do |dependency| next unless dependencies.include? dependency Log.info "#{Log.color :cyan, "dependency"} #{Log.color :yellow, task.name.to_s || ""} => #{Log.color :yellow, dependency.task_name.to_s || ""} -- #{Log.color :blue, dependency.path}" begin dependency.run(true) unless dependency.done? or dependency.started? rescue Aborted Log.error "Aborted dep. #{Log.color :red, dependency.task.name.to_s}" raise $! rescue Interrupt Log.error "Interrupted while in dep. #{Log.color :red, dependency.task.name.to_s}" raise $! rescue Exception Log.error "Exception in dep. #{ Log.color :red, dependency.task.name.to_s }" raise $! end end end |
#running? ⇒ Boolean
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# File 'lib/rbbt/workflow/accessor.rb', line 293 def running? return nil if not Open.exists? info_file return nil if info[:pid].nil? pid = @pid || info[:pid] return Misc.pid_exists?(pid) end |
#save_file(name, content) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 326 def save_file(name, content) content = case when String === content content when Array === content content * "\n" when TSV === content content.to_s when Hash === content content.collect{|*p| p * "\t"} * "\n" else content.to_s end Open.write(file(name), content) end |
#set_info(key, value) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 120 def set_info(key, value) return nil if @exec or info_file.nil? value = Annotated.purge value if defined? Annotated Open.lock(info_file, :lock => info_lock) do i = info(false) i[key] = value @info_cache = i Misc.sensiblewrite(info_file, INFO_SERIALIAZER.dump(i), :force => true, :lock => false) @info_cache_time = Time.now value end end |
#soft_grace ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 428 def soft_grace until Open.exists? info_file sleep 1 end self end |
#started? ⇒ Boolean
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# File 'lib/rbbt/workflow/accessor.rb', line 281 def started? Open.exists? info_file or Open.exists? path end |
#status ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 146 def status begin info[:status] rescue Exception Log.error "Exception reading status: #{$!.}" :error end end |
#status=(status) ⇒ Object
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# File 'lib/rbbt/workflow/accessor.rb', line 155 def status=(status) set_info(:status, status) end |
#step(name) ⇒ Object
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# File 'lib/rbbt/workflow/step.rb', line 236 def step(name) @steps ||= {} @steps[name] ||= begin deps = rec_dependencies.select{|step| step.task_name.to_sym == name.to_sym } deps.first end end |
#stop_dependencies ⇒ Object
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# File 'lib/rbbt/workflow/step/run.rb', line 335 def stop_dependencies dependencies.each do |dep| dep.abort end kill_children end |
#streaming? ⇒ Boolean
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# File 'lib/rbbt/workflow/accessor.rb', line 289 def streaming? IO === @result or @saved_stream or status == :streaming end |
#task_name ⇒ Object
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# File 'lib/rbbt/workflow/step.rb', line 64 def task_name @task.name end |