apps/workbench/app/controllers/collections_controller.rb

   1 class CollectionsController < ApplicationController
   2   skip_before_filter :find_object_by_uuid, :only => [:graph]
   3
   4   def graph
   5     index
   6   end
   7
   8   def index
   9     @collections = Collection.limit(100).to_hash
  10     @links = Link.eager.limit(100).where(head_kind: 'arvados#collection', link_class: 'resources', name: 'wants') |
  11       Link.eager.limit(100).where(tail_kind: 'arvados#collection', link_class: 'data_origin')
  12     @collections.merge!(Collection.
  13                         limit(100).
  14                         where(uuid: @links.select{|x|x.head_kind=='arvados#collection'}.collect(&:head_uuid) |
  15                               @links.select{|x|x.tail_kind=='arvados#collection'}.collect(&:tail_uuid)).
  16                         to_hash)
  17     @collection_info = {}
  18     @collections.each do |uuid, c|
  19       ci = (@collection_info[uuid] ||= {uuid: uuid})
  20       ci[:created_at] = c.created_at
  21     end
  22     @links.each do |l|
  23       if l.head_kind == 'arvados#collection'
  24         c = (@collection_info[l.head_uuid] ||= {uuid: l.head_uuid})
  25         if l.link_class == 'resources' and l.name == 'wants'
  26           if l.head.respond_to? :created_at
  27             c[:created_at] = l.head.created_at
  28           end
  29           c[:wanted] = true
  30           if l.owner_uuid == current_user.uuid
  31             c[:wanted_by_me] = true
  32           end
  33         end
  34       end
  35       if l.tail_kind == 'arvados#collection'
  36         c = (@collection_info[l.tail_uuid] ||= {uuid: l.tail_uuid})
  37         if l.link_class == 'data_origin'
  38           c[:origin] = l
  39         end
  40       end
  41     end
  42   end
  43
  44   def show_file
  45     opts = params.merge(arvados_api_token: Thread.current[:arvados_api_token])
  46     if r = params[:file].match(/(\.\w+)/)
  47       ext = r[1]
  48     end
  49     self.response.headers['Content-Type'] =
  50       Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
  51     self.response_body = FileStreamer.new opts
  52   end
  53
  54   def show
  55     return super if !@object
  56     @provenance = []
  57     @output2job = {}
  58     @output2colorindex = {}
  59     @sourcedata = {params[:uuid] => {uuid: params[:uuid]}}
  60     @protected = {}
  61
  62     colorindex = -1
  63     any_hope_left = true
  64     while any_hope_left
  65       any_hope_left = false
  66       Job.where(output: @sourcedata.keys).sort_by { |a| a.finished_at || a.created_at }.reverse.each do |job|
  67         if !@output2colorindex[job.output]
  68           any_hope_left = true
  69           @output2colorindex[job.output] = (colorindex += 1) % 10
  70           @provenance << {job: job, output: job.output}
  71           @sourcedata.delete job.output
  72           @output2job[job.output] = job
  73           job.dependencies.each do |new_source_data|
  74             unless @output2colorindex[new_source_data]
  75               @sourcedata[new_source_data] = {uuid: new_source_data}
  76             end
  77           end
  78         end
  79       end
  80     end
  81
  82     Link.where(head_uuid: @sourcedata.keys | @output2job.keys).each do |link|
  83       if link.link_class == 'resources' and link.name == 'wants'
  84         @protected[link.head_uuid] = true
  85       end
  86     end
  87     Link.where(tail_uuid: @sourcedata.keys).each do |link|
  88       if link.link_class == 'data_origin'
  89         @sourcedata[link.tail_uuid][:data_origins] ||= []
  90         @sourcedata[link.tail_uuid][:data_origins] << [link.name, link.head_kind, link.head_uuid]
  91       end
  92     end
  93     Collection.where(uuid: @sourcedata.keys).each do |collection|
  94       if @sourcedata[collection.uuid]
  95         @sourcedata[collection.uuid][:collection] = collection
  96       end
  97     end
  98   end
  99
 100   protected
 101   class FileStreamer
 102     def initialize(opts={})
 103       @opts = opts
 104     end
 105     def each
 106       return unless @opts[:uuid] && @opts[:file]
 107       env = Hash[ENV].
 108         merge({
 109                 'ARVADOS_API_HOST' =>
 110                 $arvados_api_client.arvados_v1_base.
 111                 sub(/\/arvados\/v1/, '').
 112                 sub(/^https?:\/\//, ''),
 113                 'ARVADOS_API_TOKEN' =>
 114                 @opts[:arvados_api_token],
 115                 'ARVADOS_API_HOST_INSECURE' =>
 116                 Rails.configuration.arvados_insecure_https ? 'true' : 'false'
 117               })
 118       IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
 119                'rb') do |io|
 120         while buf = io.read(2**20)
 121           yield buf
 122         end
 123       end
 124       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: $?") if $? != 0
 125     end
 126   end
 127 end