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