apps/workbench/app/controllers/collections_controller.rb

   1 class CollectionsController < ApplicationController
   2   skip_around_filter :thread_with_mandatory_api_token, only: [:show_file]
   3   skip_before_filter :find_object_by_uuid, only: [:provenance, :show_file]
   4   skip_before_filter :check_user_agreements, only: [:show_file]
   5
   6   def show_pane_list
   7     %w(Files Attributes Metadata Provenance_graph Used_by JSON API)
   8   end
   9
  10   def set_persistent
  11     case params[:value]
  12     when 'persistent', 'cache'
  13       persist_links = Link.filter([['owner_uuid', '=', current_user.uuid],
  14                                    ['link_class', '=', 'resources'],
  15                                    ['name', '=', 'wants'],
  16                                    ['tail_uuid', '=', current_user.uuid],
  17                                    ['head_uuid', '=', @object.uuid]])
  18       logger.debug persist_links.inspect
  19     else
  20       return unprocessable "Invalid value #{value.inspect}"
  21     end
  22     if params[:value] == 'persistent'
  23       if not persist_links.any?
  24         Link.create(link_class: 'resources',
  25                     name: 'wants',
  26                     tail_uuid: current_user.uuid,
  27                     head_uuid: @object.uuid)
  28       end
  29     else
  30       persist_links.each do |link|
  31         link.destroy || raise
  32       end
  33     end
  34
  35     respond_to do |f|
  36       f.json { render json: @object }
  37     end
  38   end
  39
  40   def index
  41     if params[:search].andand.length.andand > 0
  42       tags = Link.where(any: ['contains', params[:search]])
  43       @collections = (Collection.where(uuid: tags.collect(&:head_uuid)) |
  44                       Collection.where(any: ['contains', params[:search]])).
  45         uniq { |c| c.uuid }
  46     else
  47       if params[:limit]
  48         limit = params[:limit].to_i
  49       else
  50         limit = 100
  51       end
  52
  53       if params[:offset]
  54         offset = params[:offset].to_i
  55       else
  56         offset = 0
  57       end
  58
  59       @collections = Collection.limit(limit).offset(offset)
  60     end
  61     @links = Link.limit(1000).
  62       where(head_uuid: @collections.collect(&:uuid))
  63     @collection_info = {}
  64     @collections.each do |c|
  65       @collection_info[c.uuid] = {
  66         tag_links: [],
  67         wanted: false,
  68         wanted_by_me: false,
  69         provenance: [],
  70         links: []
  71       }
  72     end
  73     @links.each do |link|
  74       @collection_info[link.head_uuid] ||= {}
  75       info = @collection_info[link.head_uuid]
  76       case link.link_class
  77       when 'tag'
  78         info[:tag_links] << link
  79       when 'resources'
  80         info[:wanted] = true
  81         info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
  82       when 'provenance'
  83         info[:provenance] << link.name
  84       end
  85       info[:links] << link
  86     end
  87     @request_url = request.url
  88   end
  89
  90   def show_file
  91     # We pipe from arv-get to send the file to the user.  Before we start it,
  92     # we ask the API server if the file actually exists.  This serves two
  93     # purposes: it lets us return a useful status code for common errors, and
  94     # helps us figure out which token to provide to arv-get.
  95     coll = nil
  96     usable_token = find_usable_token do
  97       coll = Collection.find(params[:uuid])
  98     end
  99     if usable_token.nil?
 100       return  # Response already rendered.
 101     elsif params[:file].nil? or not file_in_collection?(coll, params[:file])
 102       return render_not_found
 103     end
 104     opts = params.merge(arvados_api_token: usable_token)
 105     ext = File.extname(params[:file])
 106     self.response.headers['Content-Type'] =
 107       Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
 108     self.response.headers['Content-Length'] = params[:size] if params[:size]
 109     self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
 110     self.response_body = file_enumerator opts
 111   end
 112
 113   def show
 114     return super if !@object
 115     @provenance = []
 116     @output2job = {}
 117     @output2colorindex = {}
 118     @sourcedata = {params[:uuid] => {uuid: params[:uuid]}}
 119     @protected = {}
 120
 121     colorindex = -1
 122     any_hope_left = true
 123     while any_hope_left
 124       any_hope_left = false
 125       Job.where(output: @sourcedata.keys).sort_by { |a| a.finished_at || a.created_at }.reverse.each do |job|
 126         if !@output2colorindex[job.output]
 127           any_hope_left = true
 128           @output2colorindex[job.output] = (colorindex += 1) % 10
 129           @provenance << {job: job, output: job.output}
 130           @sourcedata.delete job.output
 131           @output2job[job.output] = job
 132           job.dependencies.each do |new_source_data|
 133             unless @output2colorindex[new_source_data]
 134               @sourcedata[new_source_data] = {uuid: new_source_data}
 135             end
 136           end
 137         end
 138       end
 139     end
 140
 141     Link.where(head_uuid: @sourcedata.keys | @output2job.keys).each do |link|
 142       if link.link_class == 'resources' and link.name == 'wants'
 143         @protected[link.head_uuid] = true
 144         if link.tail_uuid == current_user.uuid
 145           @is_persistent = true
 146         end
 147       end
 148     end
 149     Link.where(tail_uuid: @sourcedata.keys).each do |link|
 150       if link.link_class == 'data_origin'
 151         @sourcedata[link.tail_uuid][:data_origins] ||= []
 152         @sourcedata[link.tail_uuid][:data_origins] << [link.name, link.head_uuid]
 153       end
 154     end
 155     Collection.where(uuid: @sourcedata.keys).each do |collection|
 156       if @sourcedata[collection.uuid]
 157         @sourcedata[collection.uuid][:collection] = collection
 158       end
 159     end
 160
 161     Collection.where(uuid: @object.uuid).each do |u|
 162       @prov_svg = ProvenanceHelper::create_provenance_graph(u.provenance, "provenance_svg",
 163                                                             {:request => request,
 164                                                               :direction => :bottom_up,
 165                                                               :combine_jobs => :script_only}) rescue nil
 166       @used_by_svg = ProvenanceHelper::create_provenance_graph(u.used_by, "used_by_svg",
 167                                                                {:request => request,
 168                                                                  :direction => :top_down,
 169                                                                  :combine_jobs => :script_only,
 170                                                                  :pdata_only => true}) rescue nil
 171     end
 172   end
 173
 174   protected
 175
 176   def find_usable_token
 177     # Iterate over every token available to make it the current token and
 178     # yield the given block.
 179     # If the block succeeds, return the token it used.
 180     # Otherwise, render an error response based on the most specific
 181     # error we encounter, and return nil.
 182     read_tokens = [Thread.current[:arvados_api_token]].compact
 183     if params[:reader_tokens].is_a? Array
 184       read_tokens += params[:reader_tokens]
 185     end
 186     most_specific_error = [401]
 187     read_tokens.each do |api_token|
 188       using_specific_api_token(api_token) do
 189         begin
 190           yield
 191           return api_token
 192         rescue ArvadosApiClient::NotLoggedInException => error
 193           status = 401
 194         rescue => error
 195           status = (error.message =~ /\[API: (\d+)\]$/) ? $1.to_i : nil
 196           raise unless [401, 403, 404].include?(status)
 197         end
 198         if status >= most_specific_error.first
 199           most_specific_error = [status, error]
 200         end
 201       end
 202     end
 203     case most_specific_error.shift
 204     when 401, 403
 205       redirect_to_login
 206     when 404
 207       render_not_found(*most_specific_error)
 208     end
 209     return nil
 210   end
 211
 212   def file_in_collection?(collection, filename)
 213     def normalized_path(part_list)
 214       File.join(part_list).sub(%r{^\./}, '')
 215     end
 216     target = normalized_path([filename])
 217     collection.files.each do |file_spec|
 218       return true if (normalized_path(file_spec[0, 2]) == target)
 219     end
 220     false
 221   end
 222
 223   def file_enumerator(opts)
 224     FileStreamer.new opts
 225   end
 226
 227   class FileStreamer
 228     def initialize(opts={})
 229       @opts = opts
 230     end
 231     def each
 232       return unless @opts[:uuid] && @opts[:file]
 233       env = Hash[ENV].
 234         merge({
 235                 'ARVADOS_API_HOST' =>
 236                 $arvados_api_client.arvados_v1_base.
 237                 sub(/\/arvados\/v1/, '').
 238                 sub(/^https?:\/\//, ''),
 239                 'ARVADOS_API_TOKEN' =>
 240                 @opts[:arvados_api_token],
 241                 'ARVADOS_API_HOST_INSECURE' =>
 242                 Rails.configuration.arvados_insecure_https ? 'true' : 'false'
 243               })
 244       IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
 245                'rb') do |io|
 246         while buf = io.read(2**20)
 247           yield buf
 248         end
 249       end
 250       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
 251     end
 252   end
 253 end