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               value_info_partitioned = value_info[:value].partition('/') if value_info[:value].andand.class.eql?(String)
  68               value_info_value = value_info_partitioned ? value_info_partitioned[0] : value_info[:value]
  69               value_info_class = resource_class_for_uuid value_info_value
  70               if value_info_class == Link
  71                 # Use the link target, not the link itself, as script
  72                 # parameter; but keep the link info around as well.
  73                 link = Link.find value_info[:value]
  74                 value_info[:value] = link.head_uuid
  75                 value_info[:link_uuid] = link.uuid
  76                 value_info[:link_name] = link.name
  77               else
  78                 # Delete stale link_uuid and link_name data.
  79                 value_info[:link_uuid] = nil
  80                 value_info[:link_name] = nil
  81               end
  82               if value_info_class == Collection
  83                 # to ensure reproducibility, the script_parameter for a
  84                 # collection should be the portable_data_hash
  85                 # keep the collection name and uuid for human-readability
  86                 obj = Collection.find value_info_value
  87                 if value_info_partitioned
  88                   value_info[:value] = obj.portable_data_hash + value_info_partitioned[1] + value_info_partitioned[2]
  89                   value_info[:selection_name] = obj.name ? obj.name + value_info_partitioned[1] + value_info_partitioned[2] : obj.name
  90                 else
  91                   value_info[:value] = obj.portable_data_hash
  92                   value_info[:selection_name] = obj.name
  93                 end
  94                 value_info[:selection_uuid] = obj.uuid
  95               end
  96             end
  97           end
  98         end
  99       end
 100     end
 101     super
 102   end
 103
 104   def graph(pipelines)
 105     return nil, nil if params['tab_pane'] != "Graph"
 106
 107     provenance = {}
 108     pips = {}
 109     n = 1
 110
 111     # When comparing more than one pipeline, "pips" stores bit fields that
 112     # indicates which objects are part of which pipelines.
 113
 114     pipelines.each do |p|
 115       collections = []
 116       hashes = []
 117       jobs = []
 118
 119       p[:components].each do |k, v|
 120         provenance["component_#{p[:uuid]}_#{k}"] = v
 121
 122         collections << v[:output_uuid] if v[:output_uuid]
 123         jobs << v[:job][:uuid] if v[:job]
 124       end
 125
 126       jobs = jobs.compact.uniq
 127       if jobs.any?
 128         Job.where(uuid: jobs).each do |j|
 129           job_uuid = j.uuid
 130
 131           provenance[job_uuid] = j
 132           pips[job_uuid] = 0 unless pips[job_uuid] != nil
 133           pips[job_uuid] |= n
 134
 135           hashes << j[:output] if j[:output]
 136           ProvenanceHelper::find_collections(j) do |hash, uuid|
 137             collections << uuid if uuid
 138             hashes << hash if hash
 139           end
 140
 141           if j[:script_version]
 142             script_uuid = j[:script_version]
 143             provenance[script_uuid] = {:uuid => script_uuid}
 144             pips[script_uuid] = 0 unless pips[script_uuid] != nil
 145             pips[script_uuid] |= n
 146           end
 147         end
 148       end
 149
 150       hashes = hashes.compact.uniq
 151       if hashes.any?
 152         Collection.where(portable_data_hash: hashes).each do |c|
 153           hash_uuid = c.portable_data_hash
 154           provenance[hash_uuid] = c
 155           pips[hash_uuid] = 0 unless pips[hash_uuid] != nil
 156           pips[hash_uuid] |= n
 157         end
 158       end
 159
 160       collections = collections.compact.uniq
 161       if collections.any?
 162         Collection.where(uuid: collections).each do |c|
 163           collection_uuid = c.uuid
 164           provenance[collection_uuid] = c
 165           pips[collection_uuid] = 0 unless pips[collection_uuid] != nil
 166           pips[collection_uuid] |= n
 167         end
 168       end
 169
 170       n = n << 1
 171     end
 172
 173     return provenance, pips
 174   end
 175
 176   def show
 177     # the #show action can also be called by #compare, which does its own work to set up @pipelines
 178     unless defined? @pipelines
 179       @pipelines = [@object]
 180     end
 181
 182     provenance, pips = graph(@pipelines)
 183     if provenance
 184       @prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
 185         :request => request,
 186         :all_script_parameters => true,
 187         :combine_jobs => :script_and_version,
 188         :pips => pips,
 189         :only_components => true,
 190         :no_docker => true,
 191         :no_log => true}
 192     end
 193
 194     super
 195   end
 196
 197   def compare
 198     @breadcrumb_page_name = 'compare'
 199
 200     @rows = []          # each is {name: S, components: [...]}
 201
 202     if params['tab_pane'] == "Compare" or params['tab_pane'].nil?
 203       # Build a table: x=pipeline y=component
 204       @objects.each_with_index do |pi, pi_index|
 205         pipeline_jobs(pi).each do |component|
 206           # Find a cell with the same name as this component but no
 207           # entry for this pipeline
 208           target_row = nil
 209           @rows.each_with_index do |row, row_index|
 210             if row[:name] == component[:name] and !row[:components][pi_index]
 211               target_row = row
 212             end
 213           end
 214           if !target_row
 215             target_row = {name: component[:name], components: []}
 216             @rows << target_row
 217           end
 218           target_row[:components][pi_index] = component
 219         end
 220       end
 221
 222       @rows.each do |row|
 223         # Build a "normal" pseudo-component for this row by picking the
 224         # most common value for each attribute. If all values are
 225         # equally common, there is no "normal".
 226         normal = {}              # attr => most common value
 227         highscore = {}           # attr => how common "normal" is
 228         score = {}               # attr => { value => how common }
 229         row[:components].each do |pj|
 230           next if pj.nil?
 231           pj.each do |k,v|
 232             vstr = for_comparison v
 233             score[k] ||= {}
 234             score[k][vstr] = (score[k][vstr] || 0) + 1
 235             highscore[k] ||= 0
 236             if score[k][vstr] == highscore[k]
 237               # tie for first place = no "normal"
 238               normal.delete k
 239             elsif score[k][vstr] == highscore[k] + 1
 240               # more pipelines have v than anything else
 241               highscore[k] = score[k][vstr]
 242               normal[k] = vstr
 243             end
 244           end
 245         end
 246
 247         # Add a hash in component[:is_normal]: { attr => is_the_value_normal? }
 248         row[:components].each do |pj|
 249           next if pj.nil?
 250           pj[:is_normal] = {}
 251           pj.each do |k,v|
 252             pj[:is_normal][k] = (normal.has_key?(k) && normal[k] == for_comparison(v))
 253           end
 254         end
 255       end
 256     end
 257
 258     if params['tab_pane'] == "Graph"
 259       @pipelines = @objects
 260     end
 261
 262     @object = @objects.first
 263
 264     show
 265   end
 266
 267   def show_pane_list
 268     panes = %w(Components Log Graph Advanced)
 269     if @object and @object.state.in? ['New', 'Ready']
 270       panes = %w(Inputs) + panes - %w(Log)
 271     end
 272     if not @object.components.values.any? { |x| x[:job] rescue false }
 273       panes -= ['Graph']
 274     end
 275     panes
 276   end
 277
 278   def compare_pane_list
 279     %w(Compare Graph)
 280   end
 281
 282   protected
 283   def for_comparison v
 284     if v.is_a? Hash or v.is_a? Array
 285       v.to_json
 286     else
 287       v.to_s
 288     end
 289   end
 290
 291   def load_filters_and_paging_params
 292     params[:limit] = 20
 293     super
 294   end
 295
 296   def find_objects_by_uuid
 297     @objects = model_class.where(uuid: params[:uuids])
 298   end
 299 end