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