apps/workbench/app/controllers/collections_controller.rb

   1 class CollectionsController < ApplicationController
   2   skip_around_filter(:require_thread_api_token,
   3                      only: [:show_file, :show_file_links])
   4   skip_before_filter(:find_object_by_uuid,
   5                      only: [:provenance, :show_file, :show_file_links])
   6   # We depend on show_file to display the user agreement:
   7   skip_before_filter :check_user_agreements, only: :show_file
   8   skip_before_filter :check_user_profile, only: :show_file
   9
  10   RELATION_LIMIT = 5
  11
  12   def show_pane_list
  13     %w(Files Provenance_graph Used_by Advanced)
  14   end
  15
  16   def set_persistent
  17     case params[:value]
  18     when 'persistent', 'cache'
  19       persist_links = Link.filter([['owner_uuid', '=', current_user.uuid],
  20                                    ['link_class', '=', 'resources'],
  21                                    ['name', '=', 'wants'],
  22                                    ['tail_uuid', '=', current_user.uuid],
  23                                    ['head_uuid', '=', @object.uuid]])
  24       logger.debug persist_links.inspect
  25     else
  26       return unprocessable "Invalid value #{value.inspect}"
  27     end
  28     if params[:value] == 'persistent'
  29       if not persist_links.any?
  30         Link.create(link_class: 'resources',
  31                     name: 'wants',
  32                     tail_uuid: current_user.uuid,
  33                     head_uuid: @object.uuid)
  34       end
  35     else
  36       persist_links.each do |link|
  37         link.destroy || raise
  38       end
  39     end
  40
  41     respond_to do |f|
  42       f.json { render json: @object }
  43     end
  44   end
  45
  46   def choose
  47     # Find collections using default find_objects logic, then search for name
  48     # links, and preload any other links connected to the collections that are
  49     # found.
  50     # Name links will be obsolete when issue #3036 is merged,
  51     # at which point this entire custom #choose function can probably be
  52     # eliminated.
  53
  54     params[:limit] ||= 40
  55
  56     find_objects_for_index
  57     @collections = @objects
  58
  59     @filters += [['link_class','=','name'],
  60                  ['head_uuid','is_a','arvados#collection']]
  61
  62     @objects = Link
  63     find_objects_for_index
  64
  65     @name_links = @objects
  66
  67     @objects = Collection.
  68       filter([['uuid','in',@name_links.collect(&:head_uuid)]])
  69
  70     preload_links_for_objects (@collections.to_a + @objects.to_a)
  71     super
  72   end
  73
  74   def index
  75     if params[:search].andand.length.andand > 0
  76       tags = Link.where(any: ['contains', params[:search]])
  77       @collections = (Collection.where(uuid: tags.collect(&:head_uuid)) |
  78                       Collection.where(any: ['contains', params[:search]])).
  79         uniq { |c| c.uuid }
  80     else
  81       if params[:limit]
  82         limit = params[:limit].to_i
  83       else
  84         limit = 100
  85       end
  86
  87       if params[:offset]
  88         offset = params[:offset].to_i
  89       else
  90         offset = 0
  91       end
  92
  93       @collections = Collection.limit(limit).offset(offset)
  94     end
  95     @links = Link.limit(1000).
  96       where(head_uuid: @collections.collect(&:uuid))
  97     @collection_info = {}
  98     @collections.each do |c|
  99       @collection_info[c.uuid] = {
 100         tag_links: [],
 101         wanted: false,
 102         wanted_by_me: false,
 103         provenance: [],
 104         links: []
 105       }
 106     end
 107     @links.each do |link|
 108       @collection_info[link.head_uuid] ||= {}
 109       info = @collection_info[link.head_uuid]
 110       case link.link_class
 111       when 'tag'
 112         info[:tag_links] << link
 113       when 'resources'
 114         info[:wanted] = true
 115         info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
 116       when 'provenance'
 117         info[:provenance] << link.name
 118       end
 119       info[:links] << link
 120     end
 121     @request_url = request.url
 122
 123     render_index
 124   end
 125
 126   def show_file_links
 127     Thread.current[:reader_tokens] = [params[:reader_token]]
 128     return if false.equal?(find_object_by_uuid)
 129     render layout: false
 130   end
 131
 132   def show_file
 133     # We pipe from arv-get to send the file to the user.  Before we start it,
 134     # we ask the API server if the file actually exists.  This serves two
 135     # purposes: it lets us return a useful status code for common errors, and
 136     # helps us figure out which token to provide to arv-get.
 137     coll = nil
 138     tokens = [Thread.current[:arvados_api_token], params[:reader_token]].compact
 139     usable_token = find_usable_token(tokens) do
 140       coll = Collection.find(params[:uuid])
 141     end
 142     if usable_token.nil?
 143       return  # Response already rendered.
 144     elsif params[:file].nil? or not file_in_collection?(coll, params[:file])
 145       return render_not_found
 146     end
 147     opts = params.merge(arvados_api_token: usable_token)
 148     ext = File.extname(params[:file])
 149     self.response.headers['Content-Type'] =
 150       Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
 151     self.response.headers['Content-Length'] = params[:size] if params[:size]
 152     self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
 153     self.response_body = file_enumerator opts
 154   end
 155
 156   def sharing_scopes
 157     ["GET /arvados/v1/collections/#{@object.uuid}", "GET /arvados/v1/collections/#{@object.uuid}/", "GET /arvados/v1/keep_services/accessible"]
 158   end
 159
 160   def search_scopes
 161     begin
 162       ApiClientAuthorization.filter([['scopes', '=', sharing_scopes]]).results
 163     rescue ArvadosApiClient::AccessForbiddenException
 164       nil
 165     end
 166   end
 167
 168   def show
 169     return super if !@object
 170     if current_user
 171       jobs_with = lambda do |conds|
 172         Job.limit(RELATION_LIMIT).where(conds)
 173           .results.sort_by { |j| j.finished_at || j.created_at }
 174       end
 175       @output_of = jobs_with.call(output: @object.portable_data_hash)
 176       @log_of = jobs_with.call(log: @object.portable_data_hash)
 177       @project_links = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 178         .where(head_uuid: @object.uuid, link_class: 'name').results
 179       project_hash = Group.where(uuid: @project_links.map(&:tail_uuid)).to_hash
 180       @projects = project_hash.values
 181
 182       if @object.uuid.match /[0-9a-f]{32}/
 183         @same_pdh = Collection.filter([["portable_data_hash", "=", @object.portable_data_hash]])
 184         owners = @same_pdh.map {|s| s.owner_uuid}.to_a
 185         preload_objects_for_dataclass Group, owners
 186         preload_objects_for_dataclass User, owners
 187       end
 188
 189       @permissions = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 190         .where(head_uuid: @object.uuid, link_class: 'permission',
 191                name: 'can_read').results
 192       @logs = Log.limit(RELATION_LIMIT).order("created_at DESC")
 193         .where(object_uuid: @object.uuid).results
 194       @is_persistent = Link.limit(1)
 195         .where(head_uuid: @object.uuid, tail_uuid: current_user.uuid,
 196                link_class: 'resources', name: 'wants')
 197         .results.any?
 198       @search_sharing = search_scopes
 199     end
 200
 201     if params["tab_pane"] == "Provenance_graph"
 202       @prov_svg = ProvenanceHelper::create_provenance_graph(@object.provenance, "provenance_svg",
 203                                                             {:request => request,
 204                                                               :direction => :bottom_up,
 205                                                               :combine_jobs => :script_only}) rescue nil
 206     end
 207     if params["tab_pane"] == "Used_by"
 208       @used_by_svg = ProvenanceHelper::create_provenance_graph(@object.used_by, "used_by_svg",
 209                                                                {:request => request,
 210                                                                  :direction => :top_down,
 211                                                                  :combine_jobs => :script_only,
 212                                                                  :pdata_only => true}) rescue nil
 213     end
 214     super
 215   end
 216
 217   def sharing_popup
 218     @search_sharing = search_scopes
 219     respond_to do |format|
 220       format.html
 221       format.js
 222     end
 223   end
 224
 225   helper_method :download_link
 226
 227   def download_link
 228     collections_url + "/download/#{@object.uuid}/#{@search_sharing.first.api_token}/"
 229   end
 230
 231   def share
 232     a = ApiClientAuthorization.create(scopes: sharing_scopes)
 233     @search_sharing = search_scopes
 234     render 'sharing_popup'
 235   end
 236
 237   def unshare
 238     @search_sharing = search_scopes
 239     @search_sharing.each do |s|
 240       s.destroy
 241     end
 242     @search_sharing = search_scopes
 243     render 'sharing_popup'
 244   end
 245
 246   protected
 247
 248   def find_usable_token(token_list)
 249     # Iterate over every given token to make it the current token and
 250     # yield the given block.
 251     # If the block succeeds, return the token it used.
 252     # Otherwise, render an error response based on the most specific
 253     # error we encounter, and return nil.
 254     most_specific_error = [401]
 255     token_list.each do |api_token|
 256       begin
 257         using_specific_api_token(api_token) do
 258           yield
 259           return api_token
 260         end
 261       rescue ArvadosApiClient::ApiError => error
 262         if error.api_status >= most_specific_error.first
 263           most_specific_error = [error.api_status, error]
 264         end
 265       end
 266     end
 267     case most_specific_error.shift
 268     when 401, 403
 269       redirect_to_login
 270     when 404
 271       render_not_found(*most_specific_error)
 272     end
 273     return nil
 274   end
 275
 276   def file_in_collection?(collection, filename)
 277     target = CollectionsHelper.file_path(File.split(filename))
 278     collection.files.each do |file_spec|
 279       return true if (CollectionsHelper.file_path(file_spec) == target)
 280     end
 281     false
 282   end
 283
 284   def file_enumerator(opts)
 285     FileStreamer.new opts
 286   end
 287
 288   class FileStreamer
 289     include ArvadosApiClientHelper
 290     def initialize(opts={})
 291       @opts = opts
 292     end
 293     def each
 294       return unless @opts[:uuid] && @opts[:file]
 295
 296       env = Hash[ENV].dup
 297
 298       require 'uri'
 299       u = URI.parse(arvados_api_client.arvados_v1_base)
 300       env['ARVADOS_API_HOST'] = "#{u.host}:#{u.port}"
 301       env['ARVADOS_API_TOKEN'] = @opts[:arvados_api_token]
 302       env['ARVADOS_API_HOST_INSECURE'] = "true" if Rails.configuration.arvados_insecure_https
 303
 304       IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
 305                'rb') do |io|
 306         while buf = io.read(2**16)
 307           yield buf
 308         end
 309       end
 310       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
 311     end
 312   end
 313 end