Module: WorkflowRESTHelpers

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

#clean_job(workflow, job) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 173

def clean_job(workflow, job)
  job.clean

  if ajax
    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 23

def complete_input_set(workflow, task, inputs)
  inputs.keys.sort === workflow.task_info(task.to_sym)[:inputs].sort
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)
    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 41

def execution_type(workflow, task)
  export = type_of_export(workflow, task)
  return export if export == :exec or cache_type.nil?
  return cache_type if cache_type
end

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



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 140

def issue_job(workflow, task, jobname = nil, params = {})
  inputs = prepare_job_inputs(workflow, task, params)
  job = workflow.job(task, jobname, inputs)

  job.clean if update == :clean

  execution_type = execution_type(workflow, task)
  case execution_type
  when :exec
    show_exec_result job.exec, workflow, task
  when :synchronous, :sync
    job.clean if update == :reload
    begin
      job.run(false) unless File.exists? job.info_file
      job_url = to(File.join("/", workflow.to_s, task, job.name)) 
      job_url += "?_format=#{@format}" if @format
      halt 200, job.name if format === :jobname
      redirect job_url
    rescue
      halt 500, $!.message
    end
  when :asynchronous, :async, nil
    job.clean if update == :reload
    job.fork unless File.exists? job.info_file
    job_url = to(File.join("/", workflow.to_s, task, job.name)) 
    job_url += "?_format=#{@format}" if @format
    halt 200, job.name if format === :jobname
    redirect job_url
  else
    raise "Unsupported execution_type: #{ execution_type }"
  end
end

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



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# File 'lib/rbbt/rest/workflow/locate.rb', line 27

def locate_workflow_template(template, workflow = nil, task = nil)

  if workflow
    path = locate_workflow_template_from_resource(workflow.libdir.www.views.find, template, workflow, task)
    return path if path and path.exists?
  end

  workflow_resources.each do |resource|
    path = locate_workflow_template_from_resource(resource, template, workflow, task)
    return path if path and path.exists?
  end

  raise "Template not found: [#{ template }, #{workflow}, #{ task }]"
end

#locate_workflow_template_from_resource(resource, template, workflow = nil, task = nil) ⇒ Object 



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

def locate_workflow_template_from_resource(resource, template, workflow = nil, task = nil)
  template += '.haml' unless template =~ /.+\..+/

  paths = []
  paths << resource[workflow][task][template] if task and workflow
  paths << resource[workflow][template] if workflow
  paths << resource[template]

  paths.each do |path|
    return path.find if path.exists?
  end 

  nil
end

#prepare_job_inputs(workflow, task, params) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 47

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

  task_inputs = {}
  inputs.each do |input|
    value = consume_parameter(input, params)
    param_file = consume_parameter(input.to_s + '__param_file', params)
    next if value.nil? and param_file.nil?
    type = input_types[input]

    fixed_value = fix_input(type, value, param_file)
    task_inputs[input] = fixed_value
  end

  task_inputs
end

#show_exec_result(result, workflow, task) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 71

def show_exec_result(result, workflow, task)
  case format
  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"
    halt 200, result.to_s
  when :literal, :raw
    content_type "text/plain"
    halt 200, result.to_s
  when :binary
    content_type "application/octet-stream"
    halt 200, result.to_s
  else
    raise "Unsupported format: #{ format }"
  end
end

#show_result(job, workflow, task) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 92

def show_result(job, workflow, task)
  case format.to_sym
  when :html
    show_result_html job.load, workflow, task, job.name, job
  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.values.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) : halt(200, job.load.to_s)
  when :literal, :raw
    content_type "text/plain"
    job.path ? send_file(job.path) : halt(200, job.load.to_s)
  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)
    send_file excel_file, :type => 'application/vnd.ms-excel', :filename => job.clean_name + '.xls'
  else
    raise "Unsupported format: #{ format }"
  end
end

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



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 65

def show_result_html(result, workflow, task, jobname = nil, job = nil)
  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)
end

#type_of_export(workflow, task) ⇒ Object 



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# File 'lib/rbbt/rest/workflow/jobs.rb', line 27

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)
    :asynchronous
  else
    raise "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 21

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?

  template_file = locate_workflow_template(template, workflow, task)

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

  layout_file = layout ? locate_template("layout") : nil

  render(template_file, locals, layout_file)
end