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     if cr[:container_uuid]
  13       ContainerRequest.where(requesting_container_uuid: cr[:container_uuid]).each do |child|
  14         nodes[child[:uuid]] = child
  15       end
  16     end
  17     @svg = ProvenanceHelper::create_provenance_graph nodes,
  18                                                      "provenance_svg",
  19                                                      {
  20                                                        :request => request,
  21                                                        :direction => :top_down,
  22                                                      }
  23   end
  24
  25   def show_pane_list
  26     panes = %w(Status Log Provenance Advanced)
  27     if @object.andand.state == 'Uncommitted'
  28       panes = %w(Inputs) + panes - %w(Log Provenance)
  29     end
  30     panes
  31   end
  32
  33   def show
  34     generate_provenance(@object)
  35     super
  36   end
  37
  38   def cancel
  39     @object.update_attributes! priority: 0
  40     if params[:return_to]
  41       redirect_to params[:return_to]
  42     else
  43       redirect_to @object
  44     end
  45   end
  46
  47   def update
  48     @updates ||= params[@object.class.to_s.underscore.singularize.to_sym]
  49     input_obj = @updates[:mounts].andand[:"/var/lib/cwl/cwl.input.json"].andand[:content]
  50     if input_obj
  51       workflow = @object.mounts[:"/var/lib/cwl/workflow.json"][:content]
  52       get_cwl_inputs(workflow).each do |input_schema|
  53         if not input_obj.include? cwl_shortname(input_schema[:id])
  54           next
  55         end
  56         required, primary_type, param_id = cwl_input_info(input_schema)
  57         if input_obj[param_id] == ""
  58           input_obj[param_id] = nil
  59         elsif primary_type == "boolean"
  60           input_obj[param_id] = input_obj[param_id] == "true"
  61         elsif ["int", "long"].include? primary_type
  62           input_obj[param_id] = input_obj[param_id].to_i
  63         elsif ["float", "double"].include? primary_type
  64           input_obj[param_id] = input_obj[param_id].to_f
  65         elsif ["File", "Directory"].include? primary_type
  66           re = CollectionsHelper.match_uuid_with_optional_filepath(input_obj[param_id])
  67           if re
  68             c = Collection.find(re[1])
  69             input_obj[param_id] = {"class" => primary_type,
  70                                    "location" => "keep:#{c.portable_data_hash}#{re[4]}",
  71                                    "arv:collection" => input_obj[param_id]}
  72           end
  73         end
  74       end
  75     end
  76     params[:merge] = true
  77     begin
  78       super
  79     rescue => e
  80       flash[:error] = e.to_s
  81       show
  82     end
  83   end
  84
  85   def copy
  86     src = @object
  87
  88     @object = ContainerRequest.new
  89
  90     @object.command = src.command
  91     @object.container_image = src.container_image
  92     @object.cwd = src.cwd
  93     @object.description = src.description
  94     @object.environment = src.environment
  95     @object.mounts = src.mounts
  96     @object.name = src.name
  97     @object.output_path = src.output_path
  98     @object.priority = 1
  99     @object.properties[:template_uuid] = src.properties[:template_uuid]
 100     @object.runtime_constraints = src.runtime_constraints
 101     @object.scheduling_parameters = src.scheduling_parameters
 102     @object.state = 'Uncommitted'
 103     @object.use_existing = false
 104
 105     # set owner_uuid to that of source, provided it is a project and writable by current user
 106     current_project = Group.find(src.owner_uuid) rescue nil
 107     if (current_project && current_project.writable_by.andand.include?(current_user.uuid))
 108       @object.owner_uuid = src.owner_uuid
 109     end
 110
 111     super
 112   end
 113 end