apps/workbench/app/controllers/pipeline_instances_controller.rb

   1 class PipelineInstancesController < ApplicationController
   2   skip_before_filter :find_object_by_uuid, only: :compare
   3   before_filter :find_objects_by_uuid, only: :compare
   4   skip_around_filter :require_thread_api_token, if: proc { |ctrl|
   5     Rails.configuration.anonymous_user_token and
   6     'show' == ctrl.action_name
   7   }
   8
   9   include PipelineInstancesHelper
  10   include PipelineComponentsHelper
  11
  12   def copy
  13     template = PipelineTemplate.find?(@object.pipeline_template_uuid)
  14
  15     source = @object
  16     @object = PipelineInstance.new
  17     @object.pipeline_template_uuid = source.pipeline_template_uuid
  18
  19     if params['components'] == 'use_latest' and template
  20       @object.components = template.components.deep_dup
  21       @object.components.each do |cname, component|
  22         # Go through the script parameters of each component
  23         # that are marked as user input and copy them over.
  24         # Skip any components that are not present in the
  25         # source instance (there's nothing to copy)
  26         if source.components.include? cname
  27           component[:script_parameters].each do |pname, val|
  28             if val.is_a? Hash and val[:dataclass]
  29               # this is user-inputtable, so check the value from the source pipeline
  30               srcvalue = source.components[cname][:script_parameters][pname]
  31               if not srcvalue.nil?
  32                 component[:script_parameters][pname] = srcvalue
  33               end
  34             end
  35           end
  36         end
  37       end
  38     else
  39       @object.components = source.components.deep_dup
  40     end
  41
  42     if params['script'] == 'use_same'
  43       # Go through each component and copy the script_version from each job.
  44       @object.components.each do |cname, component|
  45         if source.components.include? cname and source.components[cname][:job]
  46           component[:script_version] = source.components[cname][:job][:script_version]
  47         end
  48       end
  49     end
  50
  51     @object.components.each do |cname, component|
  52       component.delete :job
  53     end
  54     @object.state = 'New'
  55
  56     # set owner_uuid to that of source, provided it is a project and wriable by current user
  57     current_project = Group.find(source.owner_uuid) rescue nil
  58     if (current_project && current_project.writable_by.andand.include?(current_user.uuid))
  59       @object.owner_uuid = source.owner_uuid
  60     end
  61
  62     super
  63   end
  64
  65   def update
  66     @updates ||= params[@object.class.to_s.underscore.singularize.to_sym]
  67     if (components = @updates[:components])
  68       components.each do |cname, component|
  69         if component[:script_parameters]
  70           component[:script_parameters].each do |param, value_info|
  71             if value_info.is_a? Hash
  72               value_info_partitioned = value_info[:value].partition('/') if value_info[:value].andand.class.eql?(String)
  73               value_info_value = value_info_partitioned ? value_info_partitioned[0] : value_info[:value]
  74               value_info_class = resource_class_for_uuid value_info_value
  75               if value_info_class == Link
  76                 # Use the link target, not the link itself, as script
  77                 # parameter; but keep the link info around as well.
  78                 link = Link.find value_info[:value]
  79                 value_info[:value] = link.head_uuid
  80                 value_info[:link_uuid] = link.uuid
  81                 value_info[:link_name] = link.name
  82               else
  83                 # Delete stale link_uuid and link_name data.
  84                 value_info[:link_uuid] = nil
  85                 value_info[:link_name] = nil
  86               end
  87               if value_info_class == Collection
  88                 # to ensure reproducibility, the script_parameter for a
  89                 # collection should be the portable_data_hash
  90                 # keep the collection name and uuid for human-readability
  91                 obj = Collection.find value_info_value
  92                 if value_info_partitioned
  93                   value_info[:value] = obj.portable_data_hash + value_info_partitioned[1] + value_info_partitioned[2]
  94                   value_info[:selection_name] = obj.name ? obj.name + value_info_partitioned[1] + value_info_partitioned[2] : obj.name
  95                 else
  96                   value_info[:value] = obj.portable_data_hash
  97                   value_info[:selection_name] = obj.name
  98                 end
  99                 value_info[:selection_uuid] = obj.uuid
 100               end
 101             end
 102           end
 103         end
 104       end
 105     end
 106     super
 107   end
 108
 109   def graph(pipelines)
 110     return nil, nil if params['tab_pane'] != "Graph"
 111
 112     provenance = {}
 113     pips = {}
 114     n = 1
 115
 116     # When comparing more than one pipeline, "pips" stores bit fields that
 117     # indicates which objects are part of which pipelines.
 118
 119     pipelines.each do |p|
 120       collections = []
 121       hashes = []
 122       jobs = []
 123
 124       p[:components].each do |k, v|
 125         provenance["component_#{p[:uuid]}_#{k}"] = v
 126
 127         collections << v[:output_uuid] if v[:output_uuid]
 128         jobs << v[:job][:uuid] if v[:job]
 129       end
 130
 131       jobs = jobs.compact.uniq
 132       if jobs.any?
 133         Job.where(uuid: jobs).each do |j|
 134           job_uuid = j.uuid
 135
 136           provenance[job_uuid] = j
 137           pips[job_uuid] = 0 unless pips[job_uuid] != nil
 138           pips[job_uuid] |= n
 139
 140           hashes << j[:output] if j[:output]
 141           ProvenanceHelper::find_collections(j) do |hash, uuid|
 142             collections << uuid if uuid
 143             hashes << hash if hash
 144           end
 145
 146           if j[:script_version]
 147             script_uuid = j[:script_version]
 148             provenance[script_uuid] = {:uuid => script_uuid}
 149             pips[script_uuid] = 0 unless pips[script_uuid] != nil
 150             pips[script_uuid] |= n
 151           end
 152         end
 153       end
 154
 155       hashes = hashes.compact.uniq
 156       if hashes.any?
 157         Collection.where(portable_data_hash: hashes).each do |c|
 158           hash_uuid = c.portable_data_hash
 159           provenance[hash_uuid] = c
 160           pips[hash_uuid] = 0 unless pips[hash_uuid] != nil
 161           pips[hash_uuid] |= n
 162         end
 163       end
 164
 165       collections = collections.compact.uniq
 166       if collections.any?
 167         Collection.where(uuid: collections).each do |c|
 168           collection_uuid = c.uuid
 169           provenance[collection_uuid] = c
 170           pips[collection_uuid] = 0 unless pips[collection_uuid] != nil
 171           pips[collection_uuid] |= n
 172         end
 173       end
 174
 175       n = n << 1
 176     end
 177
 178     return provenance, pips
 179   end
 180
 181   def show
 182     # the #show action can also be called by #compare, which does its own work to set up @pipelines
 183     unless defined? @pipelines
 184       @pipelines = [@object]
 185     end
 186
 187     provenance, pips = graph(@pipelines)
 188     if provenance
 189       @prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
 190         :request => request,
 191         :all_script_parameters => true,
 192         :combine_jobs => :script_and_version,
 193         :pips => pips,
 194         :only_components => true,
 195         :no_docker => true,
 196         :no_log => true}
 197     end
 198
 199     super
 200   end
 201
 202   def compare
 203     @breadcrumb_page_name = 'compare'
 204
 205     @rows = []          # each is {name: S, components: [...]}
 206
 207     if params['tab_pane'] == "Compare" or params['tab_pane'].nil?
 208       # Build a table: x=pipeline y=component
 209       @objects.each_with_index do |pi, pi_index|
 210         pipeline_jobs(pi).each do |component|
 211           # Find a cell with the same name as this component but no
 212           # entry for this pipeline
 213           target_row = nil
 214           @rows.each_with_index do |row, row_index|
 215             if row[:name] == component[:name] and !row[:components][pi_index]
 216               target_row = row
 217             end
 218           end
 219           if !target_row
 220             target_row = {name: component[:name], components: []}
 221             @rows << target_row
 222           end
 223           target_row[:components][pi_index] = component
 224         end
 225       end
 226
 227       @rows.each do |row|
 228         # Build a "normal" pseudo-component for this row by picking the
 229         # most common value for each attribute. If all values are
 230         # equally common, there is no "normal".
 231         normal = {}              # attr => most common value
 232         highscore = {}           # attr => how common "normal" is
 233         score = {}               # attr => { value => how common }
 234         row[:components].each do |pj|
 235           next if pj.nil?
 236           pj.each do |k,v|
 237             vstr = for_comparison v
 238             score[k] ||= {}
 239             score[k][vstr] = (score[k][vstr] || 0) + 1
 240             highscore[k] ||= 0
 241             if score[k][vstr] == highscore[k]
 242               # tie for first place = no "normal"
 243               normal.delete k
 244             elsif score[k][vstr] == highscore[k] + 1
 245               # more pipelines have v than anything else
 246               highscore[k] = score[k][vstr]
 247               normal[k] = vstr
 248             end
 249           end
 250         end
 251
 252         # Add a hash in component[:is_normal]: { attr => is_the_value_normal? }
 253         row[:components].each do |pj|
 254           next if pj.nil?
 255           pj[:is_normal] = {}
 256           pj.each do |k,v|
 257             pj[:is_normal][k] = (normal.has_key?(k) && normal[k] == for_comparison(v))
 258           end
 259         end
 260       end
 261     end
 262
 263     if params['tab_pane'] == "Graph"
 264       @pipelines = @objects
 265     end
 266
 267     @object = @objects.first
 268
 269     show
 270   end
 271
 272   def show_pane_list
 273     panes = %w(Components Log Graph Advanced)
 274     if @object and @object.state.in? ['New', 'Ready']
 275       panes = %w(Inputs) + panes - %w(Log)
 276     end
 277     if not @object.components.values.any? { |x| x[:job] rescue false }
 278       panes -= ['Graph']
 279     end
 280     panes
 281   end
 282
 283   def compare_pane_list
 284     %w(Compare Graph)
 285   end
 286
 287   helper_method :unreadable_inputs_present?
 288   def unreadable_inputs_present?
 289     unless @unreadable_inputs_present.nil?
 290       return @unreadable_inputs_present
 291     end
 292
 293     input_uuids = []
 294     input_pdhs = []
 295     @object.components.each do |k, component|
 296       next if !component
 297       component[:script_parameters].andand.each do |p, tv|
 298         if (tv.is_a? Hash) and ((tv[:dataclass] == "Collection") || (tv[:dataclass] == "File"))
 299           if tv[:value]
 300             value = tv[:value]
 301           elsif tv[:default]
 302             value = tv[:default]
 303           else
 304             value = ''
 305           end
 306           if value.present?
 307             split = value.split '/'
 308             if CollectionsHelper.match(split[0])
 309               input_pdhs << split[0]
 310             else
 311               input_uuids << split[0]
 312             end
 313           end
 314         end
 315       end
 316     end
 317
 318     input_pdhs = input_pdhs.uniq
 319     input_uuids = input_uuids.uniq
 320
 321     preload_collections_for_objects input_uuids if input_uuids.any?
 322     preload_for_pdhs input_pdhs if input_pdhs.any?
 323
 324     @unreadable_inputs_present = false
 325     input_uuids.each do |uuid|
 326       if !collections_for_object(uuid).any?
 327         @unreadable_inputs_present = true
 328         break
 329       end
 330     end
 331     if !@unreadable_inputs_present
 332       input_pdhs.each do |pdh|
 333         if !collection_for_pdh(pdh).any?
 334           @unreadable_inputs_present = true
 335           break
 336         end
 337       end
 338     end
 339
 340     @unreadable_inputs_present
 341   end
 342
 343   protected
 344   def for_comparison v
 345     if v.is_a? Hash or v.is_a? Array
 346       v.to_json
 347     else
 348       v.to_s
 349     end
 350   end
 351
 352   def load_filters_and_paging_params
 353     params[:limit] = 20
 354     super
 355   end
 356
 357   def find_objects_by_uuid
 358     @objects = model_class.where(uuid: params[:uuids])
 359   end
 360 end