Module: WorkflowRESTHelpers

Included in:
StreamWorkflowTask
Defined in:
lib/rbbt/rest/workflow/jobs.rb,
lib/rbbt/rest/workflow/locate.rb,
lib/rbbt/rest/workflow/render.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#workflow_resources ⇒ Object

Returns the value of attribute workflow_resources.



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# File 'lib/rbbt/rest/workflow/locate.rb', line 2

def workflow_resources
  @workflow_resources
end

Class Method Details

.workflow_resources ⇒ Object 



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# File 'lib/rbbt/rest/workflow/locate.rb', line 4

def self.workflow_resources
  @@workflow_resources ||= [Rbbt.share.views.find(:lib)]
end

Instance Method Details

#abort_job(workflow, job) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 303

def abort_job(workflow, job)
  job.abort
  halt 200, "Aborted #{ job.path }"
end

#clean_job(workflow, job) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 309

def clean_job(workflow, job)
  job.clean

  if format == :jobname
    halt 200, job.name
  elsif ajax or format == :json
    halt 200
  else
    redirect to(File.join("/", workflow.to_s, job.task_name.to_s))
  end
end

#complete_input_set(workflow, task, inputs) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 26

def complete_input_set(workflow, task, inputs)
  given = []
  inputs.each do |key,value|
    next if value.nil?
    given << key.to_s
  end
  given = given.sort

  taken = (workflow.task_info(task.to_sym)[:inputs].collect{|i| i.to_s} + ['jobname']).uniq.sort 

  given === taken 
end

#consume_task_parameters(workflow, task, params = nil) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 6

def consume_task_parameters(workflow, task, params = nil)
  task_inputs = workflow.task_info(task.to_sym)[:inputs]

  task_parameters = {}
  task_inputs.each do |input|

    input_val = consume_parameter(input, params)
    input_val = input_val.strip if String === input_val 
    input_val = [] if input_val == "EMPTY_ARRAY"

    task_parameters[input] = input_val  unless input_val.nil?

    # Param files
    input_val = consume_parameter(input.to_s + '__param_file', params)
    task_parameters[input.to_s + '__param_file'] = input_val unless input_val.nil?
  end

  task_parameters
end

#execution_type(workflow, task) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 53

def execution_type(workflow, task)
  export = type_of_export(workflow, task)
  return cache_type if cache_type
  return :sync if export == :exec and format == :html
  return export if export == :exec 
  return :asynchronous
end

#issue_job(workflow, task, jobname = nil, params = {}) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 216

def issue_job(workflow, task, jobname = nil, params = {})
  execution_type = execution_type(workflow, task)

  inputs = prepare_job_inputs(workflow, task, params)
  job = workflow.job(task, jobname, inputs)

  job.clean if job.aborted?

  clean_job(workflow, job) and clean = true if update.to_s == "clean"
  recursive_clean_job(workflow, job) and clean = true if update.to_s == "recursive_clean"

  case execution_type.to_sym
  when :exec
    show_exec_result job.exec(:stream), workflow, task
  when :stream
    if update == :reload
      job.abort
      job.clean 
    end

    job_url = File.join("/", workflow.to_s, task, job.name)

    stream_job(job, job_url)

  when :synchronous, :sync
    if update == :reload
      job.abort
      job.clean 
    end

    begin
      if not job.started?
        job.run
        job.join
      end

      if format == :jobname
        job.name
      else
        job_url = job.respond_to?(:url)? job.url : File.join("/", workflow.to_s, task, job.name)
        job_url += "?_format=#{@format}" if @format
        redirect to(job_url)
      end
    rescue Exception
      Log.exception $!
      halt 500, $!.message
    end
  when :asynchronous, :async, nil
    if update == :reload
      job.abort
      job.clean 
    end

    begin
      # $rest_cache_semaphore is defined in rbbt-util etc/app.d/semaphores.rb
      job.fork($rest_cache_semaphore) unless job.started?

      if format == :jobname
        job.soft_grace
        content_type :text
        job.name
      else
        job.soft_grace
        job_url = job.respond_to?(:url)? job.url : File.join("/", workflow.to_s, task, job.name)
        job_url += "?_format=#{@format}" if @format
        redirect to(job_url)
      end
    rescue Exception
      Log.exception $!
    end
  else
    raise "Unsupported execution_type: #{ execution_type }"
  end
end

#locate_workflow_template(template, workflow = nil, task = nil) ⇒ Object

Raises:



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# File 'lib/rbbt/rest/workflow/locate.rb', line 12

def locate_workflow_template(template, workflow = nil, task = nil)
  resources = workflow_resources
  resources.unshift workflow.libdir.www.views if workflow

  paths = [template]
  paths.unshift [workflow.to_s, template.to_s]*"/" if workflow 
  paths.unshift [workflow.to_s, task.to_s, template.to_s]*"/" if workflow and task

  path = nil
  paths.each do |location|
    path ||= locate_server_file(location, resources, 'haml')
  end

  raise TemplateMissing, "Template not found: [#{ template }, #{workflow}, #{ task }]" if path.nil?

  path
end

#prepare_job_inputs(workflow, task, params) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 61

def prepare_job_inputs(workflow, task, params)
  inputs = workflow.task_info(task)[:inputs]
  input_types = workflow.task_info(task)[:input_types]
  input_options = workflow.task_info(task)[:input_options]

  task_inputs = {}
  inputs.each do |input|
    stream = input_options.include?(input) && input_options[input][:stream]
    value = prepare_input(params, input, input_types[input], stream)
    next if value.nil?
    task_inputs[input] = value
  end
 
  task_inputs
end

#recursive_clean_job(workflow, job) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 291

def recursive_clean_job(workflow, job)
  job.recursive_clean

  if format == :jobname
    halt 200, job.name
  elsif ajax
    halt 200
  else
    redirect to(File.join("/", workflow.to_s, job.task_name.to_s))
  end
end

#show_exec_result(result, workflow, task) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 84

def show_exec_result(result, workflow, task)
  case format.to_sym
  when :html
    show_result_html result, workflow, task, nil
  when :json
    content_type "application/json"
    halt 200, result.to_json
  when :tsv
    content_type "text/tab-separated-values"
    result = result.to_s unless String === result or result.respond_to? :gets
    halt 200, result
  when :literal, :raw
    content_type "text/plain"
    case workflow.task_info(task)[:result_type]
    when :array
      halt 200, result * "\n"
    else
      result = result.to_s unless String === result or result.respond_to? :gets
      halt 200, result
    end
  when :binary
    content_type "application/octet-stream"
    result = result.to_s unless String === result or result.respond_to? :gets
    halt 200, result.to_s
  when :jobname
    halt 200, nil
  else
    raise "Unsupported format: #{ format }"
  end
end

#show_result(job, workflow, task, params = nil) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 115

def show_result(job, workflow, task, params = nil)
  return show_result_html nil, workflow, task, job.name, job, params if @fragment

  case format.to_sym
  when :html
    show_result_html :load, workflow, task, job.name, job, params
  when :table
    halt 200, tsv2html(job.path, :url => "/" << [workflow.to_s, task, job.name] * "/")
  when :entities
    tsv = tsv_process(load_tsv(job.path).first)
    list = tsv.column_values(tsv.fields.first).flatten
    if not AnnotatedArray === list and Annotated === list.first
      list.first.annotate list 
      list.extend AnnotatedArray
    end
    type = list.annotation_types.last
    list_id = "TMP #{type} in #{ [workflow.to_s, task, job.name] * " - " }"
    Entity::List.save_list(type.to_s, list_id, list, user)
    redirect to(Entity::REST.entity_list_url(list_id, type))
  when :map
    tsv = tsv_process(load_tsv(job.path).first)
    type = tsv.keys.annotation_types.last
    column = tsv.fields.first
    map_id = "MAP #{type}-#{column} in #{ [workflow.to_s, task, job.name] * " - " }"
    Entity::Map.save_map(type.to_s, column, map_id, tsv, user)
    redirect to(Entity::REST.entity_map_url(map_id, type, column))
  when :json
    content_type "application/json"
    halt 200, job.load.to_json
  when :tsv
    content_type "text/tab-separated-values"
    job.path ? send_file(job.path, :filename => (params[:filename] || File.basename(job.path))) : halt(200, job.load.to_s)
  when :literal, :raw
    path = job.path
    mime = file_mimetype path
    content_type mime || "text/plain"
    if job.path
      if Open.remote? job.path
        Open.open(job.path, :nocache => true)
      elsif File.exists? job.path
        send_file(job.path, :filename => (params[:filename] || File.basename(job.path)))
      else
        halt 200, job.load
      end
    else
      halt(200, job.load.to_s)
    end
  when :binary
    content_type "application/octet-stream"
    job.path ? send_file(job.path) : halt(200, job.load.to_s)
  when :excel
    require 'rbbt/tsv/excel'
    data = nil
    excel_file = TmpFile.tmp_file
    result = job.load
    result.excel(excel_file, :name => @excel_use_name,:sort_by => @excel_sort_by, :sort_by_cast => @excel_sort_by_cast, :remove_links => true)
    send_file excel_file, :type => 'application/vnd.ms-excel', :filename => job.clean_name + '.xls'
  when :heatmap 
    tsv = job.load
    content_type "text/html"
    data = nil
    png_file = TmpFile.tmp_file
    width = tsv.fields.length * 10 + 500
    height = tsv.size * 10 + 500
    width = 10000 if width > 10000
    height = 10000 if height > 10000
    tsv.R <<-EOF
      rbbt.pheatmap(file='#{png_file}', data, width=#{width}, height=#{height})
    EOF
    send_file png_file, :type => 'image/png', :filename => job.name + ".heatmap.png"
  else
    raise "Unsupported format: #{ format }"
  end
end

#show_result_html(result, workflow, task, jobname = nil, job = nil, params = nil) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 77

def show_result_html(result, workflow, task, jobname = nil, job = nil, params = nil)
  params ||= {}
  result_type = workflow.task_info(task)[:result_type]
  result_description = workflow.task_info(task)[:result_description]
  workflow_render('job_result', workflow, task, {:result => result, :type => result_type, :description => result_description, :jobname => jobname, :job => job}.merge(params))
end

#stream_job(job, job_url = nil) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 190

def stream_job(job, job_url = nil)
  job.clean if job.recoverable_error?

  unless job.started? or job.done?
    job.fork(:stream) 
    job.soft_grace
  end

  raise "Error in #{job.path}: " + job.messages.last if job.error?

  s = TSV.get_stream job

  sout, sin = Misc.pipe

  Misc.consume_stream(s, true, sin)

  headers "RBBT-STREAMING-JOB-URL" => to(job_url) if job_url

  ConcurrentStream.setup(sout, :pair => s, :autojoin => true) do
    job.abort unless job.done?
  end


  halt 200, sout
end

#type_of_export(workflow, task) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 39

def type_of_export(workflow, task)
  task = task.to_sym
  case
  when workflow.exec_exports.include?(task)
    :exec
  when workflow.synchronous_exports.include?(task)
    :synchronous
  when (workflow.asynchronous_exports.include?(task) or workflow.stream_exports.include?(task))
    :asynchronous
  else
    raise "Access denied: no known export type for #{ workflow }##{ task }."
  end
end

#workflow_partial(template, workflow = nil, task = nil, params = {}) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/render.rb', line 45

def workflow_partial(template, workflow = nil, task = nil, params = {})
  workflow = consume_parameter(:workflow, params) if workflow.nil?
  task     = consume_parameter(:task, params) if workflow.nil?

  template_file = locate_workflow_template(template, workflow, task)

  locals = params.dup
  locals[:workflow] = workflow if workflow
  locals[:task]     = task if task

  render_partial(template_file, locals)
end

#workflow_render(template, workflow = nil, task = nil, params = {}) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/render.rb', line 6

def workflow_render(template, workflow = nil, task = nil, params = {})
  workflow = consume_parameter(:workflow, params) if workflow.nil?
  task     = consume_parameter(:task, params) if workflow.nil?
  job      = consume_parameter(:job, params) if job.nil?

  template_file = locate_workflow_template(template, workflow, task)

  locals = params.dup
  locals[:workflow] = workflow if workflow
  locals[:task]     = task if task

  if layout
    layout_file = workflow.libdir.www.views[workflow.to_s]["layout.haml"] if workflow.libdir
    layout_file = locate_template("layout") unless layout_file and layout_file.exists?
  else
    layout_file = nil
  end

  if job 
    locals[:job] = job 
    @step = job
    @title = [[workflow.to_s,task] * "#", job.clean_name] * " "
    cache_type = execution_type(workflow, task)
    server_key = $app_name
    html_dir = job.file('.html')
    other_params = params.dup
    other_params.delete_if{|k,v| k[0] == "_"}
    other_params.delete :result
    other_params[:template_file] = template_file
    cache_file = html_dir[server_key + "_" << Misc.obj2digest(other_params)]
    cache_type = false if params[:cache] == FalseClass
    render(template_file, locals, layout_file, [task,workflow,job.name] * "-", :cache_type => cache_type, :cache_file => cache_file)
  else
    cache_type = :async
    cache_type = false if params[:cache] == FalseClass
    render(template_file, locals, layout_file, [workflow.to_s, task, template_file.to_s].compact * "-", :cache_type => :async )
  end
end