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 = {cr[:uuid] => cr}
  11     child_crs = []
  12     col_uuids = []
  13     col_pdhs = []
  14     col_uuids << cr[:output_uuid] if cr[:output_uuid]
  15     col_pdhs += ProvenanceHelper::cr_input_pdhs(cr)
  16
  17     # Search for child CRs
  18     if cr[:container_uuid]
  19       child_crs = ContainerRequest.where(requesting_container_uuid: cr[:container_uuid])
  20
  21       child_crs.each do |child|
  22         nodes[child[:uuid]] = child
  23         col_uuids << child[:output_uuid] if child[:output_uuid]
  24         col_pdhs += ProvenanceHelper::cr_input_pdhs(child)
  25       end
  26     end
  27
  28     output_cols = {} # Indexed by UUID
  29     input_cols = {} # Indexed by PDH
  30     output_pdhs = []
  31
  32     # Batch requests to get all related collections
  33     # First fetch output collections by UUID.
  34     Collection.filter([['uuid', 'in', col_uuids.uniq]]).each do |c|
  35       output_cols[c[:uuid]] = c
  36       output_pdhs << c[:portable_data_hash]
  37     end
  38     # Then, get only input collections by PDH. There could be more than one collection
  39     # per PDH: the number of collections is used on the collection node label.
  40     Collection.filter(
  41       [['portable_data_hash', 'in', col_pdhs - output_pdhs]]).each do |c|
  42       if input_cols[c[:portable_data_hash]]
  43         input_cols[c[:portable_data_hash]] << c
  44       else
  45         input_cols[c[:portable_data_hash]] = [c]
  46       end
  47     end
  48
  49     @svg = ProvenanceHelper::create_provenance_graph(
  50       nodes, "provenance_svg",
  51       {
  52         :request => request,
  53         :direction => :top_down,
  54         :output_collections => output_cols,
  55         :input_collections => input_cols,
  56         :cr_children_of => {
  57           cr[:uuid] => child_crs.select{|child| child[:uuid]},
  58         },
  59       })
  60   end
  61
  62   def show_pane_list
  63     panes = %w(Status Log Provenance Advanced)
  64     if @object.andand.state == 'Uncommitted'
  65       panes = %w(Inputs) + panes - %w(Log Provenance)
  66     end
  67     panes
  68   end
  69
  70   def show
  71     generate_provenance(@object)
  72     super
  73   end
  74
  75   def cancel
  76     @object.update_attributes! priority: 0
  77     if params[:return_to]
  78       redirect_to params[:return_to]
  79     else
  80       redirect_to @object
  81     end
  82   end
  83
  84   def update
  85     @updates ||= params[@object.class.to_s.underscore.singularize.to_sym]
  86     input_obj = @updates[:mounts].andand[:"/var/lib/cwl/cwl.input.json"].andand[:content]
  87     if input_obj
  88       workflow = @object.mounts[:"/var/lib/cwl/workflow.json"][:content]
  89       get_cwl_inputs(workflow).each do |input_schema|
  90         if not input_obj.include? cwl_shortname(input_schema[:id])
  91           next
  92         end
  93         required, primary_type, param_id = cwl_input_info(input_schema)
  94         if input_obj[param_id] == ""
  95           input_obj[param_id] = nil
  96         elsif primary_type == "boolean"
  97           input_obj[param_id] = input_obj[param_id] == "true"
  98         elsif ["int", "long"].include? primary_type
  99           input_obj[param_id] = input_obj[param_id].to_i
 100         elsif ["float", "double"].include? primary_type
 101           input_obj[param_id] = input_obj[param_id].to_f
 102         elsif ["File", "Directory"].include? primary_type
 103           re = CollectionsHelper.match_uuid_with_optional_filepath(input_obj[param_id])
 104           if re
 105             c = Collection.find(re[1])
 106             input_obj[param_id] = {"class" => primary_type,
 107                                    "location" => "keep:#{c.portable_data_hash}#{re[4]}",
 108                                    "arv:collection" => input_obj[param_id]}
 109           end
 110         end
 111       end
 112     end
 113     params[:merge] = true
 114     begin
 115       super
 116     rescue => e
 117       flash[:error] = e.to_s
 118       show
 119     end
 120   end
 121
 122   def copy
 123     src = @object
 124
 125     @object = ContainerRequest.new
 126
 127     # By default the copied CR won't be reusing containers, unless use_existing=true
 128     # param is passed.
 129     command = src.command
 130     if params[:use_existing]
 131       @object.use_existing = true
 132       # Pass the correct argument to arvados-cwl-runner command.
 133       if src.command[0] == 'arvados-cwl-runner'
 134         command = src.command - ['--disable-reuse']
 135         command.insert(1, '--enable-reuse')
 136       end
 137     else
 138       @object.use_existing = false
 139       # Pass the correct argument to arvados-cwl-runner command.
 140       if src.command[0] == 'arvados-cwl-runner'
 141         command = src.command - ['--enable-reuse']
 142         command.insert(1, '--disable-reuse')
 143       end
 144     end
 145
 146     @object.command = command
 147     @object.container_image = src.container_image
 148     @object.cwd = src.cwd
 149     @object.description = src.description
 150     @object.environment = src.environment
 151     @object.mounts = src.mounts
 152     @object.name = src.name
 153     @object.output_path = src.output_path
 154     @object.priority = 1
 155     @object.properties[:template_uuid] = src.properties[:template_uuid]
 156     @object.runtime_constraints = src.runtime_constraints
 157     @object.scheduling_parameters = src.scheduling_parameters
 158     @object.state = 'Uncommitted'
 159
 160     # set owner_uuid to that of source, provided it is a project and writable by current user
 161     current_project = Group.find(src.owner_uuid) rescue nil
 162     if (current_project && current_project.writable_by.andand.include?(current_user.uuid))
 163       @object.owner_uuid = src.owner_uuid
 164     end
 165
 166     super
 167   end
 168 end