apps/workbench/app/controllers/collections_controller.rb

   1 class CollectionsController < ApplicationController
   2   skip_before_filter :find_object_by_uuid, :only => [:graph]
   3   skip_before_filter :check_user_agreements, :only => [:show_file]
   4
   5   def graph
   6     index
   7   end
   8
   9   def index
  10     if params[:search].andand.length.andand > 0
  11       tags = Link.where(any: ['contains', params[:search]])
  12       @collections = (Collection.where(uuid: tags.collect(&:head_uuid)) |
  13                       Collection.where(any: ['contains', params[:search]])).
  14         uniq { |c| c.uuid }
  15     else
  16       @collections = Collection.limit(100)
  17     end
  18     @links = Link.limit(1000).
  19       where(head_uuid: @collections.collect(&:uuid))
  20     @collection_info = {}
  21     @collections.each do |c|
  22       @collection_info[c.uuid] = {
  23         tags: [],
  24         wanted: false,
  25         wanted_by_me: false,
  26         provenance: [],
  27         links: []
  28       }
  29     end
  30     @links.each do |link|
  31       @collection_info[link.head_uuid] ||= {}
  32       info = @collection_info[link.head_uuid]
  33       case link.link_class
  34       when 'tag'
  35         info[:tags] << link.name
  36       when 'resources'
  37         info[:wanted] = true
  38         info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
  39       when 'provenance'
  40         info[:provenance] << link.name
  41       end
  42       info[:links] << link
  43     end
  44     @request_url = request.url
  45   end
  46
  47   def show_file
  48     opts = params.merge(arvados_api_token: Thread.current[:arvados_api_token])
  49     if r = params[:file].match(/(\.\w+)/)
  50       ext = r[1]
  51     end
  52     self.response.headers['Content-Type'] =
  53       Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
  54     self.response.headers['Content-Length'] = params[:size] if params[:size]
  55     self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
  56     self.response_body = FileStreamer.new opts
  57   end
  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   end
 104
 105   protected
 106   class FileStreamer
 107     def initialize(opts={})
 108       @opts = opts
 109     end
 110     def each
 111       return unless @opts[:uuid] && @opts[:file]
 112       env = Hash[ENV].
 113         merge({
 114                 'ARVADOS_API_HOST' =>
 115                 $arvados_api_client.arvados_v1_base.
 116                 sub(/\/arvados\/v1/, '').
 117                 sub(/^https?:\/\//, ''),
 118                 'ARVADOS_API_TOKEN' =>
 119                 @opts[:arvados_api_token],
 120                 'ARVADOS_API_HOST_INSECURE' =>
 121                 Rails.configuration.arvados_insecure_https ? 'true' : 'false'
 122               })
 123       IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
 124                'rb') do |io|
 125         while buf = io.read(2**20)
 126           yield buf
 127         end
 128       end
 129       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
 130     end
 131   end
 132 end