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
   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       if params[:limit]
  17         limit = params[:limit].to_i
  18       else
  19         limit = 100
  20       end
  21
  22       if params[:offset]
  23         offset = params[:offset].to_i
  24       else
  25         offset = 0
  26       end
  27
  28       @collections = Collection.limit(limit).offset(offset)
  29     end
  30     @links = Link.limit(1000).
  31       where(head_uuid: @collections.collect(&:uuid))
  32     @collection_info = {}
  33     @collections.each do |c|
  34       @collection_info[c.uuid] = {
  35         tag_links: [],
  36         wanted: false,
  37         wanted_by_me: false,
  38         provenance: [],
  39         links: []
  40       }
  41     end
  42     @links.each do |link|
  43       @collection_info[link.head_uuid] ||= {}
  44       info = @collection_info[link.head_uuid]
  45       case link.link_class
  46       when 'tag'
  47         info[:tag_links] << link
  48       when 'resources'
  49         info[:wanted] = true
  50         info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
  51       when 'provenance'
  52         info[:provenance] << link.name
  53       end
  54       info[:links] << link
  55     end
  56     @request_url = request.url
  57   end
  58
  59   def show_file
  60     opts = params.merge(arvados_api_token: Thread.current[:arvados_api_token])
  61     if r = params[:file].match(/(\.\w+)/)
  62       ext = r[1]
  63     end
  64     self.response.headers['Content-Type'] =
  65       Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
  66     self.response.headers['Content-Length'] = params[:size] if params[:size]
  67     self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
  68     self.response_body = FileStreamer.new opts
  69   end
  70
  71
  72   def show
  73     return super if !@object
  74     @provenance = []
  75     @output2job = {}
  76     @output2colorindex = {}
  77     @sourcedata = {params[:uuid] => {uuid: params[:uuid]}}
  78     @protected = {}
  79
  80     colorindex = -1
  81     any_hope_left = true
  82     while any_hope_left
  83       any_hope_left = false
  84       Job.where(output: @sourcedata.keys).sort_by { |a| a.finished_at || a.created_at }.reverse.each do |job|
  85         if !@output2colorindex[job.output]
  86           any_hope_left = true
  87           @output2colorindex[job.output] = (colorindex += 1) % 10
  88           @provenance << {job: job, output: job.output}
  89           @sourcedata.delete job.output
  90           @output2job[job.output] = job
  91           job.dependencies.each do |new_source_data|
  92             unless @output2colorindex[new_source_data]
  93               @sourcedata[new_source_data] = {uuid: new_source_data}
  94             end
  95           end
  96         end
  97       end
  98     end
  99
 100     Link.where(head_uuid: @sourcedata.keys | @output2job.keys).each do |link|
 101       if link.link_class == 'resources' and link.name == 'wants'
 102         @protected[link.head_uuid] = true
 103       end
 104     end
 105     Link.where(tail_uuid: @sourcedata.keys).each do |link|
 106       if link.link_class == 'data_origin'
 107         @sourcedata[link.tail_uuid][:data_origins] ||= []
 108         @sourcedata[link.tail_uuid][:data_origins] << [link.name, link.head_uuid]
 109       end
 110     end
 111     Collection.where(uuid: @sourcedata.keys).each do |collection|
 112       if @sourcedata[collection.uuid]
 113         @sourcedata[collection.uuid][:collection] = collection
 114       end
 115     end
 116
 117     Collection.where(uuid: @object.uuid).each do |u|
 118       puts request
 119       @prov_svg = ProvenanceHelper::create_provenance_graph(u.provenance, "provenance_svg",
 120                                                             {:request => request,
 121                                                               :direction => :bottom_up,
 122                                                               :combine_jobs => :script_only}) rescue nil
 123       @used_by_svg = ProvenanceHelper::create_provenance_graph(u.used_by, "used_by_svg",
 124                                                                {:request => request,
 125                                                                  :direction => :top_down,
 126                                                                  :combine_jobs => :script_only,
 127                                                                  :pdata_only => true}) rescue nil
 128     end
 129   end
 130
 131   protected
 132   class FileStreamer
 133     def initialize(opts={})
 134       @opts = opts
 135     end
 136     def each
 137       return unless @opts[:uuid] && @opts[:file]
 138       env = Hash[ENV].
 139         merge({
 140                 'ARVADOS_API_HOST' =>
 141                 $arvados_api_client.arvados_v1_base.
 142                 sub(/\/arvados\/v1/, '').
 143                 sub(/^https?:\/\//, ''),
 144                 'ARVADOS_API_TOKEN' =>
 145                 @opts[:arvados_api_token],
 146                 'ARVADOS_API_HOST_INSECURE' =>
 147                 Rails.configuration.arvados_insecure_https ? 'true' : 'false'
 148               })
 149       IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
 150                'rb') do |io|
 151         while buf = io.read(2**20)
 152           yield buf
 153         end
 154       end
 155       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
 156     end
 157   end
 158 end