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