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