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     count = {}
 101     provenance = {}
 102     pips = {}
 103     n = 1
 104
 105     pipelines.each do |p|
 106       collections = []
 107
 108       p.components.each do |k, v|
 109         j = v[:job] || next
 110
 111         uuid = j[:uuid].intern
 112         provenance[uuid] = j
 113         pips[uuid] = 0 unless pips[uuid] != nil
 114         pips[uuid] |= n
 115
 116         collections << j[:output]
 117         ProvenanceHelper::find_collections(j[:script_parameters]).each do |k|
 118           collections << k
 119         end
 120
 121         uuid = j[:script_version].intern
 122         provenance[uuid] = {:uuid => uuid}
 123         pips[uuid] = 0 unless pips[uuid] != nil
 124         pips[uuid] |= n
 125       end
 126
 127       Collection.where(uuid: collections.compact).each do |c|
 128         uuid = c.uuid.intern
 129         provenance[uuid] = c
 130         pips[uuid] = 0 unless pips[uuid] != nil
 131         pips[uuid] |= n
 132       end
 133
 134       n = n << 1
 135     end
 136
 137     return provenance, pips
 138   end
 139
 140   def show
 141     @pipelines = [@object]
 142
 143     if params[:compare]
 144       PipelineInstance.where(uuid: params[:compare]).each do |p|
 145         @pipelines << p
 146       end
 147     end
 148
 149     provenance, pips = graph(@pipelines)
 150     if provenance
 151       @prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
 152         :request => request,
 153         :all_script_parameters => true,
 154         :combine_jobs => :script_and_version,
 155         :script_version_nodes => true,
 156         :pips => pips }
 157     end
 158
 159     super
 160   end
 161
 162   def compare
 163     @breadcrumb_page_name = 'compare'
 164
 165     @rows = []          # each is {name: S, components: [...]}
 166
 167     if params['tab_pane'] == "Compare" or params['tab_pane'].nil?
 168       # Build a table: x=pipeline y=component
 169       @objects.each_with_index do |pi, pi_index|
 170         pipeline_jobs(pi).each do |component|
 171           # Find a cell with the same name as this component but no
 172           # entry for this pipeline
 173           target_row = nil
 174           @rows.each_with_index do |row, row_index|
 175             if row[:name] == component[:name] and !row[:components][pi_index]
 176               target_row = row
 177             end
 178           end
 179           if !target_row
 180             target_row = {name: component[:name], components: []}
 181             @rows << target_row
 182           end
 183           target_row[:components][pi_index] = component
 184         end
 185       end
 186
 187       @rows.each do |row|
 188         # Build a "normal" pseudo-component for this row by picking the
 189         # most common value for each attribute. If all values are
 190         # equally common, there is no "normal".
 191         normal = {}              # attr => most common value
 192         highscore = {}           # attr => how common "normal" is
 193         score = {}               # attr => { value => how common }
 194         row[:components].each do |pj|
 195           next if pj.nil?
 196           pj.each do |k,v|
 197             vstr = for_comparison v
 198             score[k] ||= {}
 199             score[k][vstr] = (score[k][vstr] || 0) + 1
 200             highscore[k] ||= 0
 201             if score[k][vstr] == highscore[k]
 202               # tie for first place = no "normal"
 203               normal.delete k
 204             elsif score[k][vstr] == highscore[k] + 1
 205               # more pipelines have v than anything else
 206               highscore[k] = score[k][vstr]
 207               normal[k] = vstr
 208             end
 209           end
 210         end
 211
 212         # Add a hash in component[:is_normal]: { attr => is_the_value_normal? }
 213         row[:components].each do |pj|
 214           next if pj.nil?
 215           pj[:is_normal] = {}
 216           pj.each do |k,v|
 217             pj[:is_normal][k] = (normal.has_key?(k) && normal[k] == for_comparison(v))
 218           end
 219         end
 220       end
 221     end
 222
 223     if params['tab_pane'] == "Graph"
 224       provenance, pips = graph(@objects)
 225
 226       @pipelines = @objects
 227
 228       if provenance
 229         @prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
 230           :request => request,
 231           :all_script_parameters => true,
 232           :combine_jobs => :script_and_version,
 233           :script_version_nodes => true,
 234           :pips => pips }
 235       end
 236     end
 237
 238     @object = @objects.first
 239
 240     show
 241   end
 242
 243   def show_pane_list
 244     panes = %w(Components Log Graph Advanced)
 245     if @object and @object.state.in? ['New', 'Ready']
 246       panes = %w(Inputs) + panes - %w(Log)
 247     end
 248     if not @object.components.values.any? { |x| x[:job] rescue false }
 249       panes -= ['Graph']
 250     end
 251     panes
 252   end
 253
 254   def compare_pane_list
 255     %w(Compare Graph)
 256   end
 257
 258   def index
 259     @limit = 20
 260     super
 261   end
 262
 263   protected
 264   def for_comparison v
 265     if v.is_a? Hash or v.is_a? Array
 266       v.to_json
 267     else
 268       v.to_s
 269     end
 270   end
 271
 272   def find_objects_by_uuid
 273     @objects = model_class.where(uuid: params[:uuids])
 274   end
 275
 276 end