Class: WorkflowRESTClient::RemoteStep
- Inherits:
-
Step
- Object
- Step
- WorkflowRESTClient::RemoteStep
show all
- Defined in:
- lib/rbbt/rest/client/run.rb,
lib/rbbt/rest/client/step.rb
Constant Summary
Constants inherited
from Step
Step::INFO_SERIALIAZER, Step::STREAM_CACHE, Step::STREAM_CACHE_MUTEX
Instance Attribute Summary collapse
Attributes inherited from Step
#bindings, #dependencies, #dupped, #mutex, #overriden, #pid, #relocated, #result, #saved_stream, #seen, #stream, #workflow
Class Method Summary
collapse
Instance Method Summary
collapse
-
#_clean ⇒ Object
-
#_restart ⇒ Object
-
#_run_job(cache_type = :async) ⇒ Object
-
#abort ⇒ Object
-
#clean ⇒ Object
-
#clean_name ⇒ Object
-
#done? ⇒ Boolean
-
#dup_inputs ⇒ Object
-
#exec(noload = false) ⇒ Object
-
#exec_job ⇒ Object
-
#execute_job(task_url, task_params, cache_type) ⇒ Object
-
#file(file) ⇒ Object
-
#files ⇒ Object
-
#fork(noload = false, semaphore = nil) ⇒ Object
-
#get ⇒ Object
-
#get_stream ⇒ Object
-
#get_streams ⇒ Object
-
#grace ⇒ Object
-
#info(check_lock = false) ⇒ Object
-
#init_job(cache_type = nil, other_params = {}) ⇒ Object
-
#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) ⇒ RemoteStep
constructor
A new instance of RemoteStep.
-
#input_checks ⇒ Object
-
#join ⇒ Object
-
#load ⇒ Object
-
#load_res(res, result_type = nil) ⇒ Object
-
#name ⇒ Object
-
#name=(name) ⇒ Object
-
#nopid? ⇒ Boolean
-
#path ⇒ Object
-
#recursive_clean ⇒ Object
-
#run(no_load = false) ⇒ Object
-
#running? ⇒ Boolean
-
#started? ⇒ Boolean
-
#status ⇒ Object
-
#stream_job(task_url, task_params, stream_input, cache_type = :exec) ⇒ Object
-
#task_name ⇒ Object
Methods inherited from Step
#_abort, #_clean_finished, #_exec, #abort_pid, #abort_stream, #aborted?, #access, #archive, #canfail_paths, #checks, #child, clean, #config, #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, #init_info, #input_dependencies, job_name_for_info_file, #join_stream, #kill_children, #knowledge_base, link_job, #load_file, #load_inputs_from_info, #log, log, log_block, #log_dependency_exec, #log_progress, log_progress, log_string, md5_file, #merge_info, #message, #messages, #missing?, #monitor_stream, #noinfo?, #out_of_date, #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_stream_cache, #rec_access, #rec_dependencies, #recoverable_error?, #recursive_inputs, #relay_log, #relocated?, #resolve_input_steps, #rewind_inputs, #run_compute_dependencies, #run_dependencies, #save_file, save_job_inputs, #set_info, #short_path, #soft_grace, #stalled?, #status=, status_color, #status_lock, #step, step_info, #stop_dependencies, #streaming?, #tmp_path, tmp_path, #updatable?, #update, #updated?, wait_for_jobs, #waiting?, #writable?
Constructor Details
#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) ⇒ RemoteStep
Returns a new instance of RemoteStep.
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# File 'lib/rbbt/rest/client/step.rb', line 23
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
|
Instance Attribute Details
#base_name ⇒ Object
Returns the value of attribute base_name.
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# File 'lib/rbbt/rest/client/step.rb', line 21
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/rest/client/step.rb', line 21
def base_url
@base_url
end
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Returns the value of attribute inputs.
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# File 'lib/rbbt/rest/client/step.rb', line 21
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/rest/client/step.rb', line 21
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/rest/client/step.rb', line 21
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/rest/client/step.rb', line 21
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/rest/client/step.rb', line 21
def result_type
@result_type
end
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Returns the value of attribute stream_input.
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# File 'lib/rbbt/rest/client/step.rb', line 21
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/rest/client/step.rb', line 21
def task
@task
end
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#url ⇒ Object
Returns the value of attribute url.
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# File 'lib/rbbt/rest/client/step.rb', line 21
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/rest/client/step.rb', line 60
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
#_clean ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 375
def _clean
begin
_restart
params = {:_update => :clean}
WorkflowRESTClient.clean_url(url, params) if @url
rescue Exception
Log.exception $!
end
end
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#_restart ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 345
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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#_run_job(cache_type = :async) ⇒ Object
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# File 'lib/rbbt/rest/client/run.rb', line 85
def _run_job(cache_type = :async)
get_streams
task_url = URI.encode(File.join(base_url, task.to_s))
WorkflowRESTClient.__prepare_inputs_for_restclient(inputs)
task_params = inputs.merge(:_cache_type => cache_type, :jobname => base_name, :_format => [:string, :boolean, :tsv, :annotations].include?(result_type) ? :raw : :json)
if cache_type == :stream or cache_type == :exec and stream_input and inputs[stream_input]
io = self.stream_job(task_url, task_params, stream_input, cache_type)
return io
else
execute_job(task_url, task_params, cache_type)
end
end
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#abort ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 92
def abort
return self if status == :done
WorkflowRESTClient.get_json(@url + '?_update=abort') if @url and @name
self
end
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#clean ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 385
def clean
init_job
_clean
self
end
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#clean_name ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 29
def clean_name
@base_name
end
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#done? ⇒ Boolean
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# File 'lib/rbbt/rest/client/step.rb', line 167
def done?
init_job unless @url
@done || status.to_s == 'done' || status.to_s == 'noinfo'
end
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# File 'lib/rbbt/rest/client/step.rb', line 98
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/rest/client/step.rb', line 240
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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#exec_job ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 340
def exec_job
res = _run_job(:exec)
load_res res, result_type == :array ? :json : result_type
end
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#execute_job(task_url, task_params, cache_type) ⇒ Object
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# File 'lib/rbbt/rest/client/run.rb', line 45
def execute_job(task_url, task_params, cache_type)
WorkflowRESTClient.capture_exception do
task_url = URI.encode(File.join(base_url, task.to_s))
sout, sin = Misc.pipe
post_thread = Thread.new(Thread.current) do |parent|
bl = lambda do |rok|
if Net::HTTPOK === rok
_url = rok["RBBT-STREAMING-JOB-URL"]
@url = File.join(task_url, File.basename(_url)) if _url
rok.read_body do |c,_a, _b|
sin.write c
end
sin.close
else
parent.raise "Error in RestClient: " << rok.message
end
end
Log.debug{ "RestClient execute: #{ url } - #{Misc.fingerprint task_params}" }
RestClient::Request.execute(:method => :post, :url => task_url, :payload => task_params, :block_response => bl)
end
reader = Zlib::GzipReader.new(sout)
res_io = Misc.open_pipe do |sin|
while c = reader.read(Misc::BLOCK_SIZE)
sin.write c
end
sin.close
@done = true
end
ConcurrentStream.setup(res_io, :threads => [post_thread]) do
@done = true
@streaming = false
end
end
end
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#file(file) ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 176
def file(file)
WorkflowRESTClient.get_raw(File.join(url, 'file', file))
end
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#fork(noload = false, semaphore = nil) ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 224
def fork(noload=false, semaphore=nil)
init_job(:asynchronous)
end
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#get ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 274
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
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#get_stream ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 180
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/rest/client/step.rb', line 85
def get_streams
return if @inputs_done
@inputs = WorkflowRESTClient::RemoteStep.get_streams @inputs, @stream_input
@inputs_done = true
@inputs
end
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#grace ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 191
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/rest/client/step.rb', line 129
def info(check_lock=false)
@done = @info && @info[:status] && @info[:status].to_sym == :done
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 = 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
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#init_job(cache_type = nil, other_params = {}) ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 203
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?
@last_info_time = nil
@done = false
get_streams
@name ||= Persist.memory("RemoteSteps", :workflow => self, :task => task, :jobname => @name, :inputs => inputs, :cache_type => cache_type) do
Misc.insist 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
end
if Open.remote? @name
@url = @name
@name = File.basename(@name)
else
@url = File.join(base_url, task.to_s, @name)
end
self
end
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# File 'lib/rbbt/rest/client/step.rb', line 391
def input_checks
[]
end
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#join ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 252
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
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#load ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 333
def load
params = {}
join unless done? or streaming?
raise get_exception if error? or aborted?
load_res get
end
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#load_res(res, result_type = nil) ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 288
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
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#name ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 109
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/rest/client/step.rb', line 115
def name=(name)
@url = [base_url,task, name] * "/"
end
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#nopid? ⇒ Boolean
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# File 'lib/rbbt/rest/client/step.rb', line 125
def nopid?
false
end
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#path ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 232
def path
if @url
Misc.add_GET_param(@url, "_format", "raw")
else
[base_url, task, @base_name + '-' + Misc.fingerprint(inputs)] * "/"
end
end
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#recursive_clean ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 362
def recursive_clean
Log.warn "Not doing recursive cleans"
return
begin
_restart
params = {:_update => :recursive_clean}
WorkflowRESTClient.get_raw(url, params)
rescue Exception
Log.exception $!
end
self
end
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#run(no_load = false) ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 33
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
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#running? ⇒ Boolean
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# File 'lib/rbbt/rest/client/step.rb', line 228
def running?
! %w(done error aborted noinfo).include? status.to_s
end
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#started? ⇒ Boolean
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# File 'lib/rbbt/rest/client/step.rb', line 163
def started?
@result != nil || @started || @streaming
end
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#status ⇒ Object
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# File 'lib/rbbt/rest/client/step.rb', line 148
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
nil
ensure
@info = nil
end
end
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#stream_job(task_url, task_params, stream_input, cache_type = :exec) ⇒ Object
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# File 'lib/rbbt/rest/client/run.rb', line 3
def stream_job(task_url, task_params, stream_input, cache_type = :exec)
require 'rbbt/util/misc/multipart_payload'
WorkflowRESTClient.capture_exception do
@streaming = true
Log.debug{ "RestClient stream #{Process.pid}: #{ task_url } #{stream_input} #{cache_type} - #{Misc.fingerprint task_params}" }
res = RbbtMutiplartPayload.issue task_url, task_params, stream_input, nil, nil, true
type = res.gets
out = case type.strip
when "LOCATION"
@url = res.gets
@url.sub!(/\?.*/,'')
join
WorkflowRESTClient.get_raw(@url)
@done = true
@streaming = false
when /STREAM: (.*)/
@url = $1.strip
res.callback = Proc.new do
Log.medium "Done streaming result from #{@url}"
@done = true
@streaming = false
end
res
when "BULK"
begin
res.read
ensure
@done = true
@streaming = false
end
else
raise "What? " + type
end
ConcurrentStream.setup(out, :filename => @url)
out
end
end
|
#task_name ⇒ Object
119
120
121
122
123
|
# File 'lib/rbbt/rest/client/step.rb', line 119
def task_name
return task if task
init_job
(Array === @url ? @url.first : @url).split("/")[-2]
end
|