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