apps/workbench/app/controllers/collections_controller.rb

   1 class CollectionsController < ApplicationController
   2   include ActionController::Live
   3
   4   skip_around_filter(:require_thread_api_token,
   5                      only: [:show_file, :show_file_links])
   6   skip_before_filter(:find_object_by_uuid,
   7                      only: [:provenance, :show_file, :show_file_links])
   8   # We depend on show_file to display the user agreement:
   9   skip_before_filter :check_user_agreements, only: :show_file
  10   skip_before_filter :check_user_profile, only: :show_file
  11
  12   RELATION_LIMIT = 5
  13
  14   def show_pane_list
  15     %w(Files Provenance_graph Used_by Advanced)
  16   end
  17
  18   def set_persistent
  19     case params[:value]
  20     when 'persistent', 'cache'
  21       persist_links = Link.filter([['owner_uuid', '=', current_user.uuid],
  22                                    ['link_class', '=', 'resources'],
  23                                    ['name', '=', 'wants'],
  24                                    ['tail_uuid', '=', current_user.uuid],
  25                                    ['head_uuid', '=', @object.uuid]])
  26       logger.debug persist_links.inspect
  27     else
  28       return unprocessable "Invalid value #{value.inspect}"
  29     end
  30     if params[:value] == 'persistent'
  31       if not persist_links.any?
  32         Link.create(link_class: 'resources',
  33                     name: 'wants',
  34                     tail_uuid: current_user.uuid,
  35                     head_uuid: @object.uuid)
  36       end
  37     else
  38       persist_links.each do |link|
  39         link.destroy || raise
  40       end
  41     end
  42
  43     respond_to do |f|
  44       f.json { render json: @object }
  45     end
  46   end
  47
  48   def choose
  49     # Find collections using default find_objects logic, then search for name
  50     # links, and preload any other links connected to the collections that are
  51     # found.
  52     # Name links will be obsolete when issue #3036 is merged,
  53     # at which point this entire custom #choose function can probably be
  54     # eliminated.
  55
  56     params[:limit] ||= 40
  57
  58     find_objects_for_index
  59     @collections = @objects
  60
  61     @filters += [['link_class','=','name'],
  62                  ['head_uuid','is_a','arvados#collection']]
  63
  64     @objects = Link
  65     find_objects_for_index
  66
  67     @name_links = @objects
  68
  69     @objects = Collection.
  70       filter([['uuid','in',@name_links.collect(&:head_uuid)]])
  71
  72     preload_links_for_objects (@collections.to_a + @objects.to_a)
  73     super
  74   end
  75
  76   def index
  77     # API server index doesn't return manifest_text by default, but our
  78     # callers want it unless otherwise specified.
  79     @select ||= Collection.columns.map(&:name)
  80     base_search = Collection.select(@select)
  81     if params[:search].andand.length.andand > 0
  82       tags = Link.where(any: ['contains', params[:search]])
  83       @collections = (base_search.where(uuid: tags.collect(&:head_uuid)) |
  84                       base_search.where(any: ['contains', params[:search]])).
  85         uniq { |c| c.uuid }
  86     else
  87       if params[:limit]
  88         limit = params[:limit].to_i
  89       else
  90         limit = 100
  91       end
  92
  93       if params[:offset]
  94         offset = params[:offset].to_i
  95       else
  96         offset = 0
  97       end
  98
  99       @collections = base_search.limit(limit).offset(offset)
 100     end
 101     @links = Link.limit(1000).
 102       where(head_uuid: @collections.collect(&:uuid))
 103     @collection_info = {}
 104     @collections.each do |c|
 105       @collection_info[c.uuid] = {
 106         tag_links: [],
 107         wanted: false,
 108         wanted_by_me: false,
 109         provenance: [],
 110         links: []
 111       }
 112     end
 113     @links.each do |link|
 114       @collection_info[link.head_uuid] ||= {}
 115       info = @collection_info[link.head_uuid]
 116       case link.link_class
 117       when 'tag'
 118         info[:tag_links] << link
 119       when 'resources'
 120         info[:wanted] = true
 121         info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
 122       when 'provenance'
 123         info[:provenance] << link.name
 124       end
 125       info[:links] << link
 126     end
 127     @request_url = request.url
 128
 129     render_index
 130   end
 131
 132   def show_file_links
 133     Thread.current[:reader_tokens] = [params[:reader_token]]
 134     return if false.equal?(find_object_by_uuid)
 135     render layout: false
 136   end
 137
 138   def show_file
 139     # We pipe from arv-get to send the file to the user.  Before we start it,
 140     # we ask the API server if the file actually exists.  This serves two
 141     # purposes: it lets us return a useful status code for common errors, and
 142     # helps us figure out which token to provide to arv-get.
 143     coll = nil
 144     tokens = [Thread.current[:arvados_api_token], params[:reader_token]].compact
 145     usable_token = find_usable_token(tokens) do
 146       coll = Collection.find(params[:uuid])
 147     end
 148
 149     file_name = params[:file]
 150     file_name = ('./' + file_name) if (file_name and file_name.include?('/'))
 151     if usable_token.nil?
 152       return  # Response already rendered.
 153     elsif file_name.nil? or not coll.manifest.has_file?(file_name)
 154       return render_not_found
 155     end
 156
 157     opts = params.merge(arvados_api_token: usable_token)
 158
 159     # Handle Range requests. Currently we support only 'bytes=0-....'
 160     if request.headers.include? 'HTTP_RANGE'
 161       if m = /^bytes=0-(\d+)/.match(request.headers['HTTP_RANGE'])
 162         opts[:maxbytes] = m[1]
 163         size = params[:size] || '*'
 164         self.response.status = 206
 165         self.response.headers['Content-Range'] = "bytes 0-#{m[1]}/#{size}"
 166       end
 167     end
 168
 169     ext = File.extname(params[:file])
 170     self.response.headers['Content-Type'] =
 171       Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
 172     if params[:size]
 173       size = params[:size].to_i
 174       if opts[:maxbytes]
 175         size = [size, opts[:maxbytes].to_i].min
 176       end
 177       self.response.headers['Content-Length'] = size.to_s
 178     end
 179     self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
 180     begin
 181       file_enumerator(opts).each do |bytes|
 182         response.stream.write bytes
 183       end
 184     ensure
 185       response.stream.close
 186     end
 187   end
 188
 189   def sharing_scopes
 190     ["GET /arvados/v1/collections/#{@object.uuid}", "GET /arvados/v1/collections/#{@object.uuid}/", "GET /arvados/v1/keep_services/accessible"]
 191   end
 192
 193   def search_scopes
 194     begin
 195       ApiClientAuthorization.filter([['scopes', '=', sharing_scopes]]).results
 196     rescue ArvadosApiClient::AccessForbiddenException
 197       nil
 198     end
 199   end
 200
 201   def find_object_by_uuid
 202     if not Keep::Locator.parse params[:id]
 203       super
 204     end
 205   end
 206
 207   def show
 208     return super if !@object
 209     if current_user
 210       if Keep::Locator.parse params["uuid"]
 211         @same_pdh = Collection.filter([["portable_data_hash", "=", @object.portable_data_hash]]).limit(1000)
 212         if @same_pdh.results.size == 1
 213           redirect_to collection_path(@same_pdh[0]["uuid"])
 214           return
 215         end
 216         owners = @same_pdh.map(&:owner_uuid).to_a.uniq
 217         preload_objects_for_dataclass Group, owners
 218         preload_objects_for_dataclass User, owners
 219         render 'hash_matches'
 220         return
 221       else
 222         jobs_with = lambda do |conds|
 223           Job.limit(RELATION_LIMIT).where(conds)
 224             .results.sort_by { |j| j.finished_at || j.created_at }
 225         end
 226         @output_of = jobs_with.call(output: @object.portable_data_hash)
 227         @log_of = jobs_with.call(log: @object.portable_data_hash)
 228         @project_links = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 229           .where(head_uuid: @object.uuid, link_class: 'name').results
 230         project_hash = Group.where(uuid: @project_links.map(&:tail_uuid)).to_hash
 231         @projects = project_hash.values
 232
 233         @permissions = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 234           .where(head_uuid: @object.uuid, link_class: 'permission',
 235                  name: 'can_read').results
 236         @logs = Log.limit(RELATION_LIMIT).order("created_at DESC")
 237           .where(object_uuid: @object.uuid).results
 238         @is_persistent = Link.limit(1)
 239           .where(head_uuid: @object.uuid, tail_uuid: current_user.uuid,
 240                  link_class: 'resources', name: 'wants')
 241           .results.any?
 242         @search_sharing = search_scopes
 243
 244         if params["tab_pane"] == "Provenance_graph"
 245           @prov_svg = ProvenanceHelper::create_provenance_graph(@object.provenance, "provenance_svg",
 246                                                                 {:request => request,
 247                                                                   :direction => :bottom_up,
 248                                                                   :combine_jobs => :script_only}) rescue nil
 249         end
 250         if params["tab_pane"] == "Used_by"
 251           @used_by_svg = ProvenanceHelper::create_provenance_graph(@object.used_by, "used_by_svg",
 252                                                                    {:request => request,
 253                                                                      :direction => :top_down,
 254                                                                      :combine_jobs => :script_only,
 255                                                                      :pdata_only => true}) rescue nil
 256         end
 257       end
 258     end
 259     super
 260   end
 261
 262   def sharing_popup
 263     @search_sharing = search_scopes
 264     respond_to do |format|
 265       format.html
 266       format.js
 267     end
 268   end
 269
 270   helper_method :download_link
 271
 272   def download_link
 273     collections_url + "/download/#{@object.uuid}/#{@search_sharing.first.api_token}/"
 274   end
 275
 276   def share
 277     a = ApiClientAuthorization.create(scopes: sharing_scopes)
 278     @search_sharing = search_scopes
 279     render 'sharing_popup'
 280   end
 281
 282   def unshare
 283     @search_sharing = search_scopes
 284     @search_sharing.each do |s|
 285       s.destroy
 286     end
 287     @search_sharing = search_scopes
 288     render 'sharing_popup'
 289   end
 290
 291   protected
 292
 293   def find_usable_token(token_list)
 294     # Iterate over every given token to make it the current token and
 295     # yield the given block.
 296     # If the block succeeds, return the token it used.
 297     # Otherwise, render an error response based on the most specific
 298     # error we encounter, and return nil.
 299     most_specific_error = [401]
 300     token_list.each do |api_token|
 301       begin
 302         using_specific_api_token(api_token) do
 303           yield
 304           return api_token
 305         end
 306       rescue ArvadosApiClient::ApiError => error
 307         if error.api_status >= most_specific_error.first
 308           most_specific_error = [error.api_status, error]
 309         end
 310       end
 311     end
 312     case most_specific_error.shift
 313     when 401, 403
 314       redirect_to_login
 315     when 404
 316       render_not_found(*most_specific_error)
 317     end
 318     return nil
 319   end
 320
 321   def file_enumerator(opts)
 322     FileStreamer.new opts
 323   end
 324
 325   class FileStreamer
 326     include ArvadosApiClientHelper
 327     def initialize(opts={})
 328       @opts = opts
 329     end
 330     def each
 331       return unless @opts[:uuid] && @opts[:file]
 332
 333       env = Hash[ENV].dup
 334
 335       require 'uri'
 336       u = URI.parse(arvados_api_client.arvados_v1_base)
 337       env['ARVADOS_API_HOST'] = "#{u.host}:#{u.port}"
 338       env['ARVADOS_API_TOKEN'] = @opts[:arvados_api_token]
 339       env['ARVADOS_API_HOST_INSECURE'] = "true" if Rails.configuration.arvados_insecure_https
 340
 341       bytesleft = @opts[:maxbytes].andand.to_i || 2**16
 342       io = IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"], 'rb')
 343       while bytesleft > 0 && (buf = io.read([bytesleft, 2**16].min)) != nil
 344         # shrink the bytesleft count, if we were given a maximum byte
 345         # count to read
 346         if @opts.include? :maxbytes
 347           bytesleft = bytesleft - buf.length
 348         end
 349         yield buf
 350       end
 351       io.close
 352       # "If ios is opened by IO.popen, close sets $?."
 353       # http://www.ruby-doc.org/core-2.1.3/IO.html#method-i-close
 354       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
 355     end
 356   end
 357 end