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