apps/workbench/app/controllers/collections_controller.rb

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