apps/workbench/app/controllers/collections_controller.rb

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