apps/workbench/app/controllers/container_requests_controller.rb

   1 class ContainerRequestsController < ApplicationController
   2   skip_around_filter :require_thread_api_token, if: proc { |ctrl|
   3     Rails.configuration.anonymous_user_token and
   4     'show' == ctrl.action_name
   5   }
   6
   7   def generate_provenance(cr)
   8     return if params['tab_pane'] != "Provenance"
   9
  10     nodes = {}
  11     nodes[cr[:uuid]] = cr
  12     @svg = ProvenanceHelper::create_provenance_graph nodes,
  13                                                      "provenance_svg",
  14                                                      {
  15                                                        :request => request,
  16                                                        :direction => :top_down,
  17                                                      }
  18   end
  19
  20   def show_pane_list
  21     panes = %w(Status Log Provenance Advanced)
  22     if @object.andand.state == 'Uncommitted'
  23       panes = %w(Inputs) + panes - %w(Log Provenance)
  24     end
  25     panes
  26   end
  27
  28   def show
  29     generate_provenance(@object)
  30     super
  31   end
  32
  33   def cancel
  34     @object.update_attributes! priority: 0
  35     if params[:return_to]
  36       redirect_to params[:return_to]
  37     else
  38       redirect_to @object
  39     end
  40   end
  41
  42   def update
  43     @updates ||= params[@object.class.to_s.underscore.singularize.to_sym]
  44     input_obj = @updates[:mounts].andand[:"/var/lib/cwl/cwl.input.json"].andand[:content]
  45     if input_obj
  46       workflow = @object.mounts[:"/var/lib/cwl/workflow.json"][:content]
  47       get_cwl_inputs(workflow).each do |input_schema|
  48         if not input_obj.include? cwl_shortname(input_schema[:id])
  49           next
  50         end
  51         required, primary_type, param_id = cwl_input_info(input_schema)
  52         if input_obj[param_id] == ""
  53           input_obj[param_id] = nil
  54         elsif primary_type == "boolean"
  55           input_obj[param_id] = input_obj[param_id] == "true"
  56         elsif ["int", "long"].include? primary_type
  57           input_obj[param_id] = input_obj[param_id].to_i
  58         elsif ["float", "double"].include? primary_type
  59           input_obj[param_id] = input_obj[param_id].to_f
  60         elsif ["File", "Directory"].include? primary_type
  61           re = CollectionsHelper.match_uuid_with_optional_filepath(input_obj[param_id])
  62           if re
  63             c = Collection.find(re[1])
  64             input_obj[param_id] = {"class" => primary_type,
  65                                    "location" => "keep:#{c.portable_data_hash}#{re[4]}",
  66                                    "arv:collection" => input_obj[param_id]}
  67           end
  68         end
  69       end
  70     end
  71     params[:merge] = true
  72     begin
  73       super
  74     rescue => e
  75       flash[:error] = e.to_s
  76       show
  77     end
  78   end
  79
  80   def copy
  81     src = @object
  82
  83     @object = ContainerRequest.new
  84
  85     @object.command = src.command
  86     @object.container_image = src.container_image
  87     @object.cwd = src.cwd
  88     @object.description = src.description
  89     @object.environment = src.environment
  90     @object.mounts = src.mounts
  91     @object.name = src.name
  92     @object.output_path = src.output_path
  93     @object.priority = 1
  94     @object.properties[:template_uuid] = src.properties[:template_uuid]
  95     @object.runtime_constraints = src.runtime_constraints
  96     @object.scheduling_parameters = src.scheduling_parameters
  97     @object.state = 'Uncommitted'
  98     @object.use_existing = false
  99
 100     # set owner_uuid to that of source, provided it is a project and writable by current user
 101     current_project = Group.find(src.owner_uuid) rescue nil
 102     if (current_project && current_project.writable_by.andand.include?(current_user.uuid))
 103       @object.owner_uuid = src.owner_uuid
 104     end
 105
 106     super
 107   end
 108 end