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_class = resource_class_for_uuid(value_info[:value])
  68               if value_info_class == Link
  69                 # Use the link target, not the link itself, as script
  70                 # parameter; but keep the link info around as well.
  71                 link = Link.find value_info[:value]
  72                 value_info[:value] = link.head_uuid
  73                 value_info[:link_uuid] = link.uuid
  74                 value_info[:link_name] = link.name
  75               else
  76                 # Delete stale link_uuid and link_name data.
  77                 value_info[:link_uuid] = nil
  78                 value_info[:link_name] = nil
  79               end
  80               if value_info_class == Collection
  81                 # to ensure reproducibility, the script_parameter for a
  82                 # collection should be the portable_data_hash
  83                 # keep the collection name and uuid for human-readability
  84                 obj = Collection.find value_info[:value]
  85                 value_info[:value] = obj.portable_data_hash
  86                 value_info[:selection_uuid] = obj.uuid
  87                 value_info[:selection_name] = obj.name
  88               end
  89             end
  90           end
  91         end
  92       end
  93     end
  94     super
  95   end
  96
  97   def graph(pipelines)
  98     return nil, nil if params['tab_pane'] != "Graph"
  99
 100     provenance = {}
 101     pips = {}
 102     n = 1
 103
 104     # When comparing more than one pipeline, "pips" stores bit fields that
 105     # indicates which objects are part of which pipelines.
 106
 107     pipelines.each do |p|
 108       collections = []
 109       hashes = []
 110       jobs = []
 111
 112       p[:components].each do |k, v|
 113         provenance["component_#{p[:uuid]}_#{k}"] = v
 114
 115         collections << v[:output_uuid] if v[:output_uuid]
 116         jobs << v[:job][:uuid] if v[:job]
 117       end
 118
 119       jobs = jobs.compact.uniq
 120       if jobs.any?
 121         Job.where(uuid: jobs).each do |j|
 122           job_uuid = j.uuid
 123
 124           provenance[job_uuid] = j
 125           pips[job_uuid] = 0 unless pips[job_uuid] != nil
 126           pips[job_uuid] |= n
 127
 128           hashes << j[:output] if j[:output]
 129           ProvenanceHelper::find_collections(j) do |hash, uuid|
 130             collections << uuid if uuid
 131             hashes << hash if hash
 132           end
 133
 134           if j[:script_version]
 135             script_uuid = j[:script_version]
 136             provenance[script_uuid] = {:uuid => script_uuid}
 137             pips[script_uuid] = 0 unless pips[script_uuid] != nil
 138             pips[script_uuid] |= n
 139           end
 140         end
 141       end
 142
 143       hashes = hashes.compact.uniq
 144       if hashes.any?
 145         Collection.where(portable_data_hash: hashes).each do |c|
 146           hash_uuid = c.portable_data_hash
 147           provenance[hash_uuid] = c
 148           pips[hash_uuid] = 0 unless pips[hash_uuid] != nil
 149           pips[hash_uuid] |= n
 150         end
 151       end
 152
 153       collections = collections.compact.uniq
 154       if collections.any?
 155         Collection.where(uuid: collections).each do |c|
 156           collection_uuid = c.uuid
 157           provenance[collection_uuid] = c
 158           pips[collection_uuid] = 0 unless pips[collection_uuid] != nil
 159           pips[collection_uuid] |= n
 160         end
 161       end
 162
 163       n = n << 1
 164     end
 165
 166     return provenance, pips
 167   end
 168
 169   def show
 170     @pipelines = [@object]
 171
 172     if params[:compare]
 173       PipelineInstance.where(uuid: params[:compare]).each do |p|
 174         @pipelines << p
 175       end
 176     end
 177
 178     provenance, pips = graph(@pipelines)
 179     if provenance
 180       @prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
 181         :request => request,
 182         :all_script_parameters => true,
 183         :combine_jobs => :script_and_version,
 184         :pips => pips,
 185         :only_components => true,
 186         :no_docker => true,
 187         :no_log => true}
 188     end
 189
 190     super
 191   end
 192
 193   def compare
 194     @breadcrumb_page_name = 'compare'
 195
 196     @rows = []          # each is {name: S, components: [...]}
 197
 198     if params['tab_pane'] == "Compare" or params['tab_pane'].nil?
 199       # Build a table: x=pipeline y=component
 200       @objects.each_with_index do |pi, pi_index|
 201         pipeline_jobs(pi).each do |component|
 202           # Find a cell with the same name as this component but no
 203           # entry for this pipeline
 204           target_row = nil
 205           @rows.each_with_index do |row, row_index|
 206             if row[:name] == component[:name] and !row[:components][pi_index]
 207               target_row = row
 208             end
 209           end
 210           if !target_row
 211             target_row = {name: component[:name], components: []}
 212             @rows << target_row
 213           end
 214           target_row[:components][pi_index] = component
 215         end
 216       end
 217
 218       @rows.each do |row|
 219         # Build a "normal" pseudo-component for this row by picking the
 220         # most common value for each attribute. If all values are
 221         # equally common, there is no "normal".
 222         normal = {}              # attr => most common value
 223         highscore = {}           # attr => how common "normal" is
 224         score = {}               # attr => { value => how common }
 225         row[:components].each do |pj|
 226           next if pj.nil?
 227           pj.each do |k,v|
 228             vstr = for_comparison v
 229             score[k] ||= {}
 230             score[k][vstr] = (score[k][vstr] || 0) + 1
 231             highscore[k] ||= 0
 232             if score[k][vstr] == highscore[k]
 233               # tie for first place = no "normal"
 234               normal.delete k
 235             elsif score[k][vstr] == highscore[k] + 1
 236               # more pipelines have v than anything else
 237               highscore[k] = score[k][vstr]
 238               normal[k] = vstr
 239             end
 240           end
 241         end
 242
 243         # Add a hash in component[:is_normal]: { attr => is_the_value_normal? }
 244         row[:components].each do |pj|
 245           next if pj.nil?
 246           pj[:is_normal] = {}
 247           pj.each do |k,v|
 248             pj[:is_normal][k] = (normal.has_key?(k) && normal[k] == for_comparison(v))
 249           end
 250         end
 251       end
 252     end
 253
 254     if params['tab_pane'] == "Graph"
 255       provenance, pips = graph(@objects)
 256
 257       @pipelines = @objects
 258
 259       if provenance
 260         @prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
 261           :request => request,
 262           :all_script_parameters => true,
 263           :combine_jobs => :script_and_version,
 264           :script_version_nodes => true,
 265           :pips => pips }
 266       end
 267     end
 268
 269     @object = @objects.first
 270
 271     show
 272   end
 273
 274   def show_pane_list
 275     panes = %w(Components Log Graph Advanced)
 276     if @object and @object.state.in? ['New', 'Ready']
 277       panes = %w(Inputs) + panes - %w(Log)
 278     end
 279     if not @object.components.values.any? { |x| x[:job] rescue false }
 280       panes -= ['Graph']
 281     end
 282     panes
 283   end
 284
 285   def compare_pane_list
 286     %w(Compare Graph)
 287   end
 288
 289   def index
 290     @limit = 20
 291     super
 292   end
 293
 294   protected
 295   def for_comparison v
 296     if v.is_a? Hash or v.is_a? Array
 297       v.to_json
 298     else
 299       v.to_s
 300     end
 301   end
 302
 303   def find_objects_by_uuid
 304     @objects = model_class.where(uuid: params[:uuids])
 305   end
 306
 307 end