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