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