apps/workbench/app/controllers/collections_controller.rb

   1 class CollectionsController < ApplicationController
   2   skip_before_filter :find_object_by_uuid, :only => [:provenance]
   3   skip_before_filter :check_user_agreements, :only => [:show_file]
   4
   5   def show_pane_list
   6     %w(Files Attributes Metadata Provenance_graph Used_by JSON API)
   7   end
   8   def index
   9     if params[:search].andand.length.andand > 0
  10       tags = Link.where(any: ['contains', params[:search]])
  11       @collections = (Collection.where(uuid: tags.collect(&:head_uuid)) |
  12                       Collection.where(any: ['contains', params[:search]])).
  13         uniq { |c| c.uuid }
  14     else
  15       @collections = Collection.limit(100)
  16     end
  17     @links = Link.limit(1000).
  18       where(head_uuid: @collections.collect(&:uuid))
  19     @collection_info = {}
  20     @collections.each do |c|
  21       @collection_info[c.uuid] = {
  22         tag_links: [],
  23         wanted: false,
  24         wanted_by_me: false,
  25         provenance: [],
  26         links: []
  27       }
  28     end
  29     @links.each do |link|
  30       @collection_info[link.head_uuid] ||= {}
  31       info = @collection_info[link.head_uuid]
  32       case link.link_class
  33       when 'tag'
  34         info[:tag_links] << link
  35       when 'resources'
  36         info[:wanted] = true
  37         info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
  38       when 'provenance'
  39         info[:provenance] << link.name
  40       end
  41       info[:links] << link
  42     end
  43     @request_url = request.url
  44   end
  45
  46   def show_file
  47     opts = params.merge(arvados_api_token: Thread.current[:arvados_api_token])
  48     if r = params[:file].match(/(\.\w+)/)
  49       ext = r[1]
  50     end
  51     self.response.headers['Content-Type'] =
  52       Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
  53     self.response.headers['Content-Length'] = params[:size] if params[:size]
  54     self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
  55     self.response_body = FileStreamer.new opts
  56   end
  57
  58
  59   def show
  60     return super if !@object
  61     @provenance = []
  62     @output2job = {}
  63     @output2colorindex = {}
  64     @sourcedata = {params[:uuid] => {uuid: params[:uuid]}}
  65     @protected = {}
  66
  67     colorindex = -1
  68     any_hope_left = true
  69     while any_hope_left
  70       any_hope_left = false
  71       Job.where(output: @sourcedata.keys).sort_by { |a| a.finished_at || a.created_at }.reverse.each do |job|
  72         if !@output2colorindex[job.output]
  73           any_hope_left = true
  74           @output2colorindex[job.output] = (colorindex += 1) % 10
  75           @provenance << {job: job, output: job.output}
  76           @sourcedata.delete job.output
  77           @output2job[job.output] = job
  78           job.dependencies.each do |new_source_data|
  79             unless @output2colorindex[new_source_data]
  80               @sourcedata[new_source_data] = {uuid: new_source_data}
  81             end
  82           end
  83         end
  84       end
  85     end
  86
  87     Link.where(head_uuid: @sourcedata.keys | @output2job.keys).each do |link|
  88       if link.link_class == 'resources' and link.name == 'wants'
  89         @protected[link.head_uuid] = true
  90       end
  91     end
  92     Link.where(tail_uuid: @sourcedata.keys).each do |link|
  93       if link.link_class == 'data_origin'
  94         @sourcedata[link.tail_uuid][:data_origins] ||= []
  95         @sourcedata[link.tail_uuid][:data_origins] << [link.name, link.head_kind, link.head_uuid]
  96       end
  97     end
  98     Collection.where(uuid: @sourcedata.keys).each do |collection|
  99       if @sourcedata[collection.uuid]
 100         @sourcedata[collection.uuid][:collection] = collection
 101       end
 102     end
 103
 104     Collection.where(uuid: @object.uuid).each do |u|
 105       puts request
 106       @prov_svg = ProvenanceHelper::create_provenance_graph(u.provenance, "provenance_svg",
 107                                                             {:request => request,
 108                                                               :direction => :bottom_up,
 109                                                               :combine_jobs => :script_only}) rescue nil
 110       @used_by_svg = ProvenanceHelper::create_provenance_graph(u.used_by, "used_by_svg",
 111                                                                {:request => request,
 112                                                                  :direction => :top_down,
 113                                                                  :combine_jobs => :script_only,
 114                                                                  :pdata_only => true}) rescue nil
 115     end
 116   end
 117
 118   protected
 119   class FileStreamer
 120     def initialize(opts={})
 121       @opts = opts
 122     end
 123     def each
 124       return unless @opts[:uuid] && @opts[:file]
 125       env = Hash[ENV].
 126         merge({
 127                 'ARVADOS_API_HOST' =>
 128                 $arvados_api_client.arvados_v1_base.
 129                 sub(/\/arvados\/v1/, '').
 130                 sub(/^https?:\/\//, ''),
 131                 'ARVADOS_API_TOKEN' =>
 132                 @opts[:arvados_api_token],
 133                 'ARVADOS_API_HOST_INSECURE' =>
 134                 Rails.configuration.arvados_insecure_https ? 'true' : 'false'
 135               })
 136       IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
 137                'rb') do |io|
 138         while buf = io.read(2**20)
 139           yield buf
 140         end
 141       end
 142       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
 143     end
 144   end
 145 end