apps/workbench/app/controllers/collections_controller.rb

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