Class: RemoteStep
- Inherits:
-
Step
show all
- Defined in:
- lib/rbbt/workflow/remote_workflow/remote_step.rb,
lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb,
lib/rbbt/workflow/remote_workflow/remote_step/rest.rb
Defined Under Namespace
Modules: REST, SSH
Constant Summary
Constants inherited
from Step
Step::INFO_SERIALIZER, Step::MAIN_RSYNC_ARGS, Step::RBBT_DEBUG_CLEAN, Step::STREAM_CACHE, Step::STREAM_CACHE_MUTEX
Instance Attribute Summary collapse
Attributes inherited from Step
#bindings, #dependencies, #dupped, #mutex, #original_task_name, #original_workflow, #overriden, #pid, #real_inputs, #relocated, #result, #saved_stream, #seen, #stream, #workflow
Class Method Summary
collapse
Instance Method Summary
collapse
-
#_restart ⇒ Object
-
#cache_file ⇒ Object
-
#cache_files ⇒ Object
-
#clean_name ⇒ Object
-
#done? ⇒ Boolean
-
#dup_inputs ⇒ Object
-
#exec(noload = false) ⇒ Object
-
#file(file) ⇒ Object
-
#files ⇒ Object
-
#fork(noload = false, semaphore = nil) ⇒ Object
-
#get_stream ⇒ Object
-
#get_streams ⇒ Object
-
#grace ⇒ Object
-
#info(check_lock = false) ⇒ Object
-
#init_info(*args) ⇒ Object
-
#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) ⇒ RemoteStep
constructor
A new instance of RemoteStep.
-
#input_checks ⇒ Object
-
#join ⇒ Object
-
#load_res(res, result_type = nil) ⇒ Object
-
#name ⇒ Object
-
#name=(name) ⇒ Object
-
#nopid? ⇒ Boolean
-
#path ⇒ Object
-
#run(no_load = false) ⇒ Object
-
#running? ⇒ Boolean
-
#short_path ⇒ Object
-
#started? ⇒ Boolean
-
#status ⇒ Object
-
#task_name ⇒ Object
-
#workflow_short_path ⇒ Object
Methods inherited from Step
#_abort, #_clean_finished, #_exec, #abort, #abort_pid, #abort_stream, #aborted?, #access, archive, #archive, #archive_deps, #archived_info, #archived_inputs, #canfail_paths, #checks, #child, clean, #clean, #cmd, #config, #copy_files_dir, #dependency_checks, #dirty?, #dirty_files, dup_stream, #error?, #exception, #execute_and_dup, #execute_dependency, files_dir, #files_dir, #get_exception, info_file, #info_file, #info_lock, #input_dependencies, job_files_for_archive, job_name_for_info_file, #join_stream, #kill_children, #knowledge_base, link_job, #load, #load_dependencies_from_info, #load_file, #load_inputs_from_info, load_serialized_info, #log, log, log_block, #log_dependency_exec, #log_progress, log_progress, log_string, md5_file, #merge_info, #message, #messages, migrate, migrate_source_paths, #missing?, #monitor_stream, #noinfo?, #out_of_date, #overriden?, #overriden_deps, #persist_checks, pid_file, #pid_file, prepare_dependencies, prepare_for_execution, #prepare_result, #produce, #progress_bar, prov_report, prov_report_msg, prov_status_msg, #provenance, #provenance_paths, purge, purge_stream_cache, raise_dependency_error, #rec_access, #rec_dependencies, #recoverable_error?, #recursive_clean, #recursive_inputs, #relay_log, #relocated?, #resolve_input_steps, #resumable?, #rewind_inputs, #run_compute_dependencies, #run_dependencies, #save_file, save_input, save_inputs, save_job_inputs, serialize_info, #set_info, #short_path_real, #soft_grace, #stalled?, #status=, status_color, #status_lock, #step, step_info, #stop_dependencies, #streaming?, #task_signature, #tmp_path, tmp_path, #updatable?, #update, #updated?, wait_for_jobs, #waiting?, #writable?
Constructor Details
#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) ⇒ RemoteStep
Returns a new instance of RemoteStep.
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 7
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
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Instance Attribute Details
#base_name ⇒ Object
Returns the value of attribute base_name.
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5
def base_name
@base_name
end
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#base_url ⇒ Object
Returns the value of attribute base_url.
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5
def base_url
@base_url
end
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Returns the value of attribute input_types.
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5
def input_types
@input_types
end
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Returns the value of attribute inputs.
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5
def inputs
@inputs
end
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#is_exec ⇒ Object
Returns the value of attribute is_exec.
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5
def is_exec
@is_exec
end
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#is_stream ⇒ Object
Returns the value of attribute is_stream.
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5
def is_stream
@is_stream
end
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#result_description ⇒ Object
Returns the value of attribute result_description.
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5
def result_description
@result_description
end
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#result_type ⇒ Object
Returns the value of attribute result_type.
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5
def result_type
@result_type
end
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#started ⇒ Object
Returns the value of attribute started.
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5
def started
@started
end
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Returns the value of attribute stream_input.
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5
def stream_input
@stream_input
end
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#task ⇒ Object
Returns the value of attribute task.
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5
def task
@task
end
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#url ⇒ Object
Returns the value of attribute url.
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5
def url
@url
end
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Class Method Details
.get_streams(inputs, stream_input = nil) ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 70
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?) 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
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Instance Method Details
#_restart ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 332
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
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#cache_file ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 27
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
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#cache_files ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 37
def cache_files
Dir.glob(cache_file + '.*')
end
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#clean_name ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 23
def clean_name
@base_name
end
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#done? ⇒ Boolean
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 179
def done?
return true if cache_files.any?
self.init_job unless @url
@done || status.to_s == 'done' || status.to_s == 'noinfo'
end
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 102
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
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#exec(noload = false) ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 235
def exec(noload = false)
@result ||= begin
if noload == :stream
_run_job(:exec)
else
exec_job
end
ensure
@started = true
end
end
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#file(file) ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 189
def file(file)
@adaptor.get_raw(File.join(url, 'file', file.to_s))
end
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#files ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 185
def files
@adaptor.get_json(File.join(url, 'files'))
end
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#fork(noload = false, semaphore = nil) ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 227
def fork(noload=false, semaphore=nil)
init_job(:asynchronous)
end
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#get_stream ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 193
def get_stream
case @result
when IO
@result
when String
StringIO.new @result
else
nil
end
end
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#get_streams ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 95
def get_streams
return if @inputs_done
@inputs = RemoteStep.get_streams @inputs, @stream_input
@inputs_done = true
@inputs
end
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#grace ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 204
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
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#info(check_lock = false) ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 133
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
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#init_info(*args) ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 349
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
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 328
def input_checks
[]
end
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#join ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 247
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
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#load_res(res, result_type = nil) ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 272
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
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#name ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 113
def name
return nil if @is_exec
return @path if @url.nil?
(Array === @url ? @url.first : @url).split("/").last
end
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#name=(name) ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 119
def name=(name)
@url = [base_url,task, name] * "/"
end
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#nopid? ⇒ Boolean
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 129
def nopid?
false
end
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#path ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 217
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
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#run(no_load = false) ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 41
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
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#running? ⇒ Boolean
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 231
def running?
! %w(done error aborted noinfo).include? status.to_s
end
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#short_path ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 323
def short_path
init_job unless @url
[@task, @name] * "/"
end
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#started? ⇒ Boolean
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 175
def started?
@result != nil || @started || @streaming
end
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#status ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 159
def status
return :done if @done
return nil unless url or started?
begin
status = info[:status]
@done = true if status and status.to_sym == :done
status
rescue
Log.exception $!
nil
ensure
@info = nil
end
end
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#task_name ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 123
def task_name
return task if task
init_job
(Array === @url ? @url.first : @url).split("/")[-2]
end
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#workflow_short_path ⇒ Object
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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 318
def workflow_short_path
init_job unless @url
[@base_url, @task, @name] * "/"
end
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