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