apps/workbench/app/controllers/collections_controller.rb

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