apps/workbench/app/controllers/collections_controller.rb

   1 require "arvados/keep"
   2 require "arvados/collection"
   3 require "uri"
   4
   5 class CollectionsController < ApplicationController
   6   include ActionController::Live
   7
   8   skip_around_filter :require_thread_api_token, if: proc { |ctrl|
   9     Rails.configuration.anonymous_user_token and
  10     'show' == ctrl.action_name
  11   }
  12   skip_around_filter(:require_thread_api_token,
  13                      only: [:show_file, :show_file_links])
  14   skip_before_filter(:find_object_by_uuid,
  15                      only: [:provenance, :show_file, :show_file_links])
  16   # We depend on show_file to display the user agreement:
  17   skip_before_filter :check_user_agreements, only: :show_file
  18   skip_before_filter :check_user_profile, only: :show_file
  19
  20   RELATION_LIMIT = 5
  21
  22   def show_pane_list
  23     panes = %w(Files Upload Tags Provenance_graph Used_by Advanced)
  24     panes = panes - %w(Upload) unless (@object.editable? rescue false)
  25     panes
  26   end
  27
  28   def set_persistent
  29     case params[:value]
  30     when 'persistent', 'cache'
  31       persist_links = Link.filter([['owner_uuid', '=', current_user.uuid],
  32                                    ['link_class', '=', 'resources'],
  33                                    ['name', '=', 'wants'],
  34                                    ['tail_uuid', '=', current_user.uuid],
  35                                    ['head_uuid', '=', @object.uuid]])
  36       logger.debug persist_links.inspect
  37     else
  38       return unprocessable "Invalid value #{value.inspect}"
  39     end
  40     if params[:value] == 'persistent'
  41       if not persist_links.any?
  42         Link.create(link_class: 'resources',
  43                     name: 'wants',
  44                     tail_uuid: current_user.uuid,
  45                     head_uuid: @object.uuid)
  46       end
  47     else
  48       persist_links.each do |link|
  49         link.destroy || raise
  50       end
  51     end
  52
  53     respond_to do |f|
  54       f.json { render json: @object }
  55     end
  56   end
  57
  58   def index
  59     # API server index doesn't return manifest_text by default, but our
  60     # callers want it unless otherwise specified.
  61     @select ||= Collection.columns.map(&:name)
  62     base_search = Collection.select(@select)
  63     if params[:search].andand.length.andand > 0
  64       tags = Link.where(any: ['contains', params[:search]])
  65       @objects = (base_search.where(uuid: tags.collect(&:head_uuid)) |
  66                       base_search.where(any: ['contains', params[:search]])).
  67         uniq { |c| c.uuid }
  68     else
  69       if params[:limit]
  70         limit = params[:limit].to_i
  71       else
  72         limit = 100
  73       end
  74
  75       if params[:offset]
  76         offset = params[:offset].to_i
  77       else
  78         offset = 0
  79       end
  80
  81       @objects = base_search.limit(limit).offset(offset)
  82     end
  83     @links = Link.where(head_uuid: @objects.collect(&:uuid))
  84     @collection_info = {}
  85     @objects.each do |c|
  86       @collection_info[c.uuid] = {
  87         tag_links: [],
  88         wanted: false,
  89         wanted_by_me: false,
  90         provenance: [],
  91         links: []
  92       }
  93     end
  94     @links.each do |link|
  95       @collection_info[link.head_uuid] ||= {}
  96       info = @collection_info[link.head_uuid]
  97       case link.link_class
  98       when 'tag'
  99         info[:tag_links] << link
 100       when 'resources'
 101         info[:wanted] = true
 102         info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
 103       when 'provenance'
 104         info[:provenance] << link.name
 105       end
 106       info[:links] << link
 107     end
 108     @request_url = request.url
 109
 110     render_index
 111   end
 112
 113   def show_file_links
 114     Thread.current[:reader_tokens] = [params[:reader_token]]
 115     return if false.equal?(find_object_by_uuid)
 116     render layout: false
 117   end
 118
 119   def show_file
 120     # We pipe from arv-get to send the file to the user.  Before we start it,
 121     # we ask the API server if the file actually exists.  This serves two
 122     # purposes: it lets us return a useful status code for common errors, and
 123     # helps us figure out which token to provide to arv-get.
 124     # The order of searched tokens is important: because the anonymous user
 125     # token is passed along with every API request, we have to check it first.
 126     # Otherwise, it's impossible to know whether any other request succeeded
 127     # because of the reader token.
 128     coll = nil
 129     tokens = [(Rails.configuration.anonymous_user_token || nil),
 130               params[:reader_token],
 131               Thread.current[:arvados_api_token]].compact
 132     usable_token = find_usable_token(tokens) do
 133       coll = Collection.find(params[:uuid])
 134     end
 135     if usable_token.nil?
 136       # Response already rendered.
 137       return
 138     end
 139
 140     # If we are configured to use a keep-web server, just redirect to
 141     # the appropriate URL.
 142     if Rails.configuration.keep_web_url or
 143         Rails.configuration.keep_web_download_url
 144       opts = {}
 145       if usable_token == params[:reader_token]
 146         opts[:path_token] = usable_token
 147       elsif usable_token == Rails.configuration.anonymous_user_token
 148         # Don't pass a token at all
 149       else
 150         # We pass the current user's real token only if it's necessary
 151         # to read the collection.
 152         opts[:query_token] = usable_token
 153       end
 154       opts[:disposition] = params[:disposition] if params[:disposition]
 155       return redirect_to keep_web_url(params[:uuid], params[:file], opts)
 156     end
 157
 158     # No keep-web server available. Get the file data with arv-get,
 159     # and serve it through Rails.
 160
 161     file_name = params[:file].andand.sub(/^(\.\/|\/|)/, './')
 162     if file_name.nil? or not coll.manifest.has_file?(file_name)
 163       return render_not_found
 164     end
 165
 166     opts = params.merge(arvados_api_token: usable_token)
 167
 168     # Handle Range requests. Currently we support only 'bytes=0-....'
 169     if request.headers.include? 'HTTP_RANGE'
 170       if m = /^bytes=0-(\d+)/.match(request.headers['HTTP_RANGE'])
 171         opts[:maxbytes] = m[1]
 172         size = params[:size] || '*'
 173         self.response.status = 206
 174         self.response.headers['Content-Range'] = "bytes 0-#{m[1]}/#{size}"
 175       end
 176     end
 177
 178     ext = File.extname(params[:file])
 179     self.response.headers['Content-Type'] =
 180       Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
 181     if params[:size]
 182       size = params[:size].to_i
 183       if opts[:maxbytes]
 184         size = [size, opts[:maxbytes].to_i].min
 185       end
 186       self.response.headers['Content-Length'] = size.to_s
 187     end
 188     self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
 189     begin
 190       file_enumerator(opts).each do |bytes|
 191         response.stream.write bytes
 192       end
 193     ensure
 194       response.stream.close
 195     end
 196   end
 197
 198   def sharing_scopes
 199     ["GET /arvados/v1/collections/#{@object.uuid}", "GET /arvados/v1/collections/#{@object.uuid}/", "GET /arvados/v1/keep_services/accessible"]
 200   end
 201
 202   def search_scopes
 203     begin
 204       ApiClientAuthorization.filter([['scopes', '=', sharing_scopes]]).results
 205     rescue ArvadosApiClient::AccessForbiddenException
 206       nil
 207     end
 208   end
 209
 210   def find_object_by_uuid
 211     if not Keep::Locator.parse params[:id]
 212       super
 213     end
 214   end
 215
 216   def show
 217     return super if !@object
 218
 219     @logs = []
 220
 221     if params["tab_pane"] == "Provenance_graph"
 222       @prov_svg = ProvenanceHelper::create_provenance_graph(@object.provenance, "provenance_svg",
 223                                                             {:request => request,
 224                                                              :direction => :top_down,
 225                                                              :combine_jobs => :script_only}) rescue nil
 226     end
 227
 228     if current_user
 229       if Keep::Locator.parse params["uuid"]
 230         @same_pdh = Collection.filter([["portable_data_hash", "=", @object.portable_data_hash]]).limit(20)
 231         if @same_pdh.results.size == 1
 232           redirect_to collection_path(@same_pdh[0]["uuid"])
 233           return
 234         end
 235         owners = @same_pdh.map(&:owner_uuid).to_a.uniq
 236         preload_objects_for_dataclass Group, owners
 237         preload_objects_for_dataclass User, owners
 238         uuids = @same_pdh.map(&:uuid).to_a.uniq
 239         preload_links_for_objects uuids
 240         render 'hash_matches'
 241         return
 242       else
 243         if Job.api_exists?(:index)
 244           jobs_with = lambda do |conds|
 245             Job.limit(RELATION_LIMIT).where(conds)
 246               .results.sort_by { |j| j.finished_at || j.created_at }
 247           end
 248           @output_of = jobs_with.call(output: @object.portable_data_hash)
 249           @log_of = jobs_with.call(log: @object.portable_data_hash)
 250         end
 251
 252         @project_links = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 253           .where(head_uuid: @object.uuid, link_class: 'name').results
 254         project_hash = Group.where(uuid: @project_links.map(&:tail_uuid)).to_hash
 255         @projects = project_hash.values
 256
 257         @permissions = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 258           .where(head_uuid: @object.uuid, link_class: 'permission',
 259                  name: 'can_read').results
 260         @search_sharing = search_scopes
 261
 262         if params["tab_pane"] == "Used_by"
 263           @used_by_svg = ProvenanceHelper::create_provenance_graph(@object.used_by, "used_by_svg",
 264                                                                    {:request => request,
 265                                                                     :direction => :top_down,
 266                                                                     :combine_jobs => :script_only,
 267                                                                     :pdata_only => true}) rescue nil
 268         end
 269       end
 270     end
 271     super
 272   end
 273
 274   def sharing_popup
 275     @search_sharing = search_scopes
 276     render("sharing_popup.js", content_type: "text/javascript")
 277   end
 278
 279   helper_method :download_link
 280
 281   def download_link
 282     collections_url + "/download/#{@object.uuid}/#{@search_sharing.first.api_token}/"
 283   end
 284
 285   def share
 286     ApiClientAuthorization.create(scopes: sharing_scopes)
 287     sharing_popup
 288   end
 289
 290   def unshare
 291     search_scopes.each do |s|
 292       s.destroy
 293     end
 294     sharing_popup
 295   end
 296
 297   def remove_selected_files
 298     uuids, source_paths = selected_collection_files params
 299
 300     arv_coll = Arv::Collection.new(@object.manifest_text)
 301     source_paths[uuids[0]].each do |p|
 302       arv_coll.rm "."+p
 303     end
 304
 305     if @object.update_attributes manifest_text: arv_coll.manifest_text
 306       show
 307     else
 308       self.render_error status: 422
 309     end
 310   end
 311
 312   def update
 313     updated_attr = params[:collection].each.select {|a| a[0].andand.start_with? 'rename-file-path:'}
 314
 315     if updated_attr.size > 0
 316       # Is it file rename?
 317       file_path = updated_attr[0][0].split('rename-file-path:')[-1]
 318
 319       new_file_path = updated_attr[0][1]
 320       if new_file_path.start_with?('./')
 321         # looks good
 322       elsif new_file_path.start_with?('/')
 323         new_file_path = '.' + new_file_path
 324       else
 325         new_file_path = './' + new_file_path
 326       end
 327
 328       arv_coll = Arv::Collection.new(@object.manifest_text)
 329
 330       if arv_coll.exist?(new_file_path)
 331         @errors = 'Duplicate file path. Please use a different name.'
 332         self.render_error status: 422
 333       else
 334         arv_coll.rename "./"+file_path, new_file_path
 335
 336         if @object.update_attributes manifest_text: arv_coll.manifest_text
 337           show
 338         else
 339           self.render_error status: 422
 340         end
 341       end
 342     else
 343       # Not a file rename; use default
 344       super
 345     end
 346   end
 347
 348   def tags
 349     render
 350   end
 351
 352   def save_tags
 353     tags_param = params['tag_data']
 354     if tags_param
 355       if tags_param.is_a?(String) && tags_param == "empty"
 356         tags = {}
 357       else
 358         tags = tags_param
 359       end
 360     end
 361
 362     if tags
 363       if @object.update_attributes properties: tags
 364         @saved_tags = true
 365         render
 366       else
 367         self.render_error status: 422
 368       end
 369     end
 370   end
 371
 372   protected
 373
 374   def find_usable_token(token_list)
 375     # Iterate over every given token to make it the current token and
 376     # yield the given block.
 377     # If the block succeeds, return the token it used.
 378     # Otherwise, render an error response based on the most specific
 379     # error we encounter, and return nil.
 380     most_specific_error = [401]
 381     token_list.each do |api_token|
 382       begin
 383         # We can't load the corresponding user, because the token may not
 384         # be scoped for that.
 385         using_specific_api_token(api_token, load_user: false) do
 386           yield
 387           return api_token
 388         end
 389       rescue ArvadosApiClient::ApiError => error
 390         if error.api_status >= most_specific_error.first
 391           most_specific_error = [error.api_status, error]
 392         end
 393       end
 394     end
 395     case most_specific_error.shift
 396     when 401, 403
 397       redirect_to_login
 398     when 404
 399       render_not_found(*most_specific_error)
 400     end
 401     return nil
 402   end
 403
 404   def keep_web_url(uuid_or_pdh, file, opts)
 405     munged_id = uuid_or_pdh.sub('+', '-')
 406     fmt = {uuid_or_pdh: munged_id}
 407
 408     tmpl = Rails.configuration.keep_web_url
 409     if Rails.configuration.keep_web_download_url and
 410         (!tmpl or opts[:disposition] == 'attachment')
 411       # Prefer the attachment-only-host when we want an attachment
 412       # (and when there is no preview link configured)
 413       tmpl = Rails.configuration.keep_web_download_url
 414     elsif not Rails.configuration.trust_all_content
 415       check_uri = URI.parse(tmpl % fmt)
 416       if opts[:query_token] and
 417           not check_uri.host.start_with?(munged_id + "--") and
 418           not check_uri.host.start_with?(munged_id + ".")
 419         # We're about to pass a token in the query string, but
 420         # keep-web can't accept that safely at a single-origin URL
 421         # template (unless it's -attachment-only-host).
 422         tmpl = Rails.configuration.keep_web_download_url
 423         if not tmpl
 424           raise ArgumentError, "Download precluded by site configuration"
 425         end
 426         logger.warn("Using download link, even though inline content " \
 427                     "was requested: #{check_uri.to_s}")
 428       end
 429     end
 430
 431     if tmpl == Rails.configuration.keep_web_download_url
 432       # This takes us to keep-web's -attachment-only-host so there is
 433       # no need to add ?disposition=attachment.
 434       opts.delete :disposition
 435     end
 436
 437     uri = URI.parse(tmpl % fmt)
 438     uri.path += '/' unless uri.path.end_with? '/'
 439     if opts[:path_token]
 440       uri.path += 't=' + opts[:path_token] + '/'
 441     end
 442     uri.path += '_/'
 443     uri.path += URI.escape(file)
 444
 445     query = Hash[URI.decode_www_form(uri.query || '')]
 446     { query_token: 'api_token',
 447       disposition: 'disposition' }.each do |opt, param|
 448       if opts.include? opt
 449         query[param] = opts[opt]
 450       end
 451     end
 452     unless query.empty?
 453       uri.query = URI.encode_www_form(query)
 454     end
 455
 456     uri.to_s
 457   end
 458
 459   # Note: several controller and integration tests rely on stubbing
 460   # file_enumerator to return fake file content.
 461   def file_enumerator opts
 462     FileStreamer.new opts
 463   end
 464
 465   class FileStreamer
 466     include ArvadosApiClientHelper
 467     def initialize(opts={})
 468       @opts = opts
 469     end
 470     def each
 471       return unless @opts[:uuid] && @opts[:file]
 472
 473       env = Hash[ENV].dup
 474
 475       require 'uri'
 476       u = URI.parse(arvados_api_client.arvados_v1_base)
 477       env['ARVADOS_API_HOST'] = "#{u.host}:#{u.port}"
 478       env['ARVADOS_API_TOKEN'] = @opts[:arvados_api_token]
 479       env['ARVADOS_API_HOST_INSECURE'] = "true" if Rails.configuration.arvados_insecure_https
 480
 481       bytesleft = @opts[:maxbytes].andand.to_i || 2**16
 482       io = IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"], 'rb')
 483       while bytesleft > 0 && (buf = io.read([bytesleft, 2**16].min)) != nil
 484         # shrink the bytesleft count, if we were given a maximum byte
 485         # count to read
 486         if @opts.include? :maxbytes
 487           bytesleft = bytesleft - buf.length
 488         end
 489         yield buf
 490       end
 491       io.close
 492       # "If ios is opened by IO.popen, close sets $?."
 493       # http://www.ruby-doc.org/core-2.1.3/IO.html#method-i-close
 494       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
 495     end
 496   end
 497 end