Module: WorkflowRESTClient

Defined in:
lib/rbbt/workflow/remote/rest/get.rb,
lib/rbbt/workflow/remote/rest/adaptor.rb

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.execute_job(base_url, task, task_params, cache_type) ⇒ Object 



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# File 'lib/rbbt/workflow/remote/rest/adaptor.rb', line 85

def self.execute_job(base_url, task, task_params, cache_type)
  self.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
          err = StringIO.new
          rok.read_body do |c,_a, _b|
            err.write c
          end
          text = begin
                   reader = Zlib::GzipReader.new(err)
                   reader.read
                 rescue
                   err.rewind
                   err.read
                 end
          ne = @adaptor.parse_exception text
          case ne
          when String
            parent.raise e.class, ne
          when Exception
            parent.raise ne
          else
            parent.raise "Error in RestClient: " << rok.message
          end
        end
      end

      task_params.each do |k,v|
        task_params[k] = v.read if IO === v
      end

      Log.debug{ "RestClient execute: #{ task_url } - #{Misc.fingerprint task_params}" }
      RestClient::Request.execute(:method => :post, :url => task_url, :payload => task_params, :block_response => bl)
    end

    # It seems like now response body are now decoded by Net::HTTP after 2.1
    # https://github.com/rest-client/rest-client/blob/cf3e5a115bcdb8f3344aeac0e45b44d67fac1a42/history.md
    decode = Gem.loaded_specs["rest-client"].version < Gem::Version.create('2.1')
    if decode
      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
    else
      ConcurrentStream.setup(sout, :threads => [post_thread]) do
        @done = true
        @streaming = false
      end
    end

  end
end

Instance Method Details

#_clean ⇒ Object 



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# File 'lib/rbbt/workflow/remote/rest/get.rb', line 231

def _clean
  begin
    _restart
    params = {:_update => :clean}
    @adaptor.clean_url(url, params) if @url
  rescue Exception
    Log.exception $!
  end
end

#_run_job(cache_type = :async) ⇒ Object 



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# File 'lib/rbbt/workflow/remote/rest/get.rb', line 289

def _run_job(cache_type = :async)
  get_streams

  task_url = URI.encode(File.join(base_url, task.to_s))
  @adaptor.__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
    @adaptor.execute_job(base_url, task, task_params, cache_type)
  end

end

#abort ⇒ Object 



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# File 'lib/rbbt/workflow/remote/rest/get.rb', line 192

def abort
  return self if status == :done
  @adaptor.get_json(@url + '?_update=abort') if @url and @name
  self
end

#clean ⇒ Object 



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# File 'lib/rbbt/workflow/remote/rest/get.rb', line 241

def clean
  init_job
  _clean
  self
end

#exec_job ⇒ Object 



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# File 'lib/rbbt/workflow/remote/rest/get.rb', line 187

def exec_job
  res = _run_job(:exec)
  load_res res, result_type == :array ? :json : result_type
end

#get ⇒ Object 



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# File 'lib/rbbt/workflow/remote/rest/get.rb', line 166

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?
      @adaptor.get_raw(url, params)
    rescue
      Log.exception $!
      raise $!
    end
  end
end

#init_job(cache_type = nil, other_params = {}) ⇒ Object 



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# File 'lib/rbbt/workflow/remote/rest/get.rb', line 198

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
      @adaptor.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

#load ⇒ Object 



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# File 'lib/rbbt/workflow/remote/rest/get.rb', line 180

def load
  params = {}
  join unless done? or streaming?
  raise get_exception if error? or aborted?
  load_res get
end

#recursive_clean ⇒ Object 



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# File 'lib/rbbt/workflow/remote/rest/get.rb', line 218

def recursive_clean
  Log.warn "Not doing recursive cleans"
  return
  begin
    _restart
    params = {:_update => :recursive_clean}
    @adaptor.get_raw(url, params)
  rescue Exception
    Log.exception $!
  end
  self
end

#stream_job(task_url, task_params, stream_input, cache_type = :exec) ⇒ Object 



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# File 'lib/rbbt/workflow/remote/rest/get.rb', line 247

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